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Close Window State Cancer Profiles Quick Reference Guides ? Quick Reference Guides Index Interactive Maps Send to Printer Text description of this image. Site Home Policies Accessibility Viewing Files FOIA Contact Us U.S. Department of Health and Human
Skip to Content The National Cancer Institute www.cancer.gov The National Institutes of Health Home About BBRB Mission and Goals BBRB Staff Biorepository Coordinating Committee (BCC) Interactive Timeline Related Initiatives International Initiatives Funding
Mapping of Protein–Protein Interaction Sites by the 'Absence of Interference' Approach
Dhayalan, Arunkumar; Jurkowski, Tomasz P.; Laser, Heike; Reinhardt, Richard; Jia, Da; Cheng, Xiaodong; Jeltsch, Albert
Protein–protein interactions are critical to most biological processes, and locating protein–protein interfaces on protein structures is an important task in molecular biology. We developed a new experimental strategy called the 'absence of interference' approach to determine surface residues involved in protein–protein interaction of established yeast two-hybrid pairs of interacting proteins. One of the proteins is subjected to high-level randomization by error-prone PCR. The resulting library is selected by yeast two-hybrid system for interacting clones that are isolated and sequenced. The interaction region can be identified by an absence or depletion of mutations. For data analysis and presentation, we developed a Web interface that analyzes the mutational spectrum and displays the mutational frequency on the surface of the structure (or a structural model) of the randomized protein†. Additionally, this interface might be of use for the display of mutational distributions determined by other types of random mutagenesis experiments. We applied the approach to map the interface of the catalytic domain of the DNA methyltransferase Dnmt3a with its regulatory factor Dnmt3L. Dnmt3a was randomized with high mutational load. A total of 76 interacting clones were isolated and sequenced, and 648 mutations were identified. The mutational pattern allowed to identify a unique interaction region on the surface of Dnmt3a, which comprises about 500?600 Ĺ2. The results were confirmed by site-directed mutagenesis and structural analysis. The absence-of-interference approach will allow high-throughput mapping of protein interaction sites suitable for functional studies and protein docking. PMID:18191145
Provide maps of demographics, screening and risk factors, incidence and mortality statistics for use in assessing the burden and risk for a major cancer site for the US overall or for a selected state and its counties or parishes. The Healthy People 2020 objective for the US is provided in the legend when appropriate in order to give perspective on how favorably or unfavorably a location compares to this overall goal.
NSDL National Science Digital Library
Lawrence Hall of Science
In this outdoor activity, learners use a mapping technique to become oriented to the major features of an outdoor site. Learners become aware of both physical and biological features including trees, rocks, water, signs of human activity. After completing this activity, learners can try the OBIS Terrestrial Hi-Lo Hunt and add more detail to their map.
Humanin binds MPP8: mapping interaction sites of the peptide and protein.
Maximov, Vadim V; Martynenko, Alina V; Arman, Inga P; Tarantul, Vyacheslav Z
Humanin (HN), a 24-amino acid peptide encoded by the mitochondrial 16S rRNA gene, was discovered by screening a cDNA library from the occipital cortex of a patient with Alzheimer's disease (AD) for a protection factor against AD-relevant insults. Earlier, using the yeast two-hybrid system, we have identified the M-phase phosphoprotein 8 (MPP8) as a binding partner for HN. In the present work, we further confirmed interaction of HN with MPP8 in co-immunoprecipitation experiments and localized an MPP8-binding site in the region between 5 and 12 aa. of HN. We have also shown that an MPP8 fragment (residues 431-560) is sufficient to bind HN. Further studies on functional consequences of the interaction between the potential oncopetide and the oncoprotein may elucidate some aspects of the molecular mechanisms of carcinogenesis. PMID:23532874
[Mapping the interaction site of Rpb2 and Rpb3 subunit of fission yeast RNA polymerase II].
Qu, Z; Zheng, S; Gu, H; Shi, B
To map the interacting site of subunit Rpb2 to subunit Rpb3 of RNA polymerase II in fission yeast Schizosaccharomyces pombe, the yeast two-hybrid system was employed in this paper to screen the interacting clones between Rpb2 and Rpb3.4 fragments of Rpb2 cDNA were cloned into the Ga14 BD vector pAS2. The 4 clones were named as pAS2 Rpb2-1, 2-2, 2-3 and 2-4, respectively. The complete cDNA of Rpb3 was cloned into the Gal 4 AD vector pGADGH. The clone was named as pGADGH Rpb3. The two-hybrid plasmids pGADGH Rpb3 and pAS2Rpb2-1, 2-2, 2-3 or 2-4 respectively were cotransformed into host cell yeast Y190. The interaction positive cotransformants were identified by beta-gal activity assay. The beta-gal positive cotransformants were selected from pGADGH Rpb3 and pAS2Rpb2-4 two-hybrid system. DNA sequencing and alignment results showed that the interacting site of Rpb2 to Rpb3 located within the fragment from base 2701 to 2966 of Rpb2 cDNA, or within the C-termini polypeptide from amino acid 902 to 989 of Rpb2 protein. PMID:12552808
Jérôme Maillot; Hussein Yahia; Anne Verroust
This paper describes a new approach to texture mapping. A global method to lower the distortion of the mapped image is presented; by considering a general optimization function we view the map- ping as an energy-minimization process. We have constructed an interactive texture tool, which is fast and easy to use, to manip- ulate atlases in texture space. We present
An expanded, unified substrate recognition site map for mammalian cytochrome P450s: analysis of molecular interactions between 15 mammalian CYP450 isoforms and 868 substrates.
Zawaira, Alexander; Ching, Lim Yen; Coulson, Lauren; Blackburn, Jonathan; Wei, Yap Chun
The original map of mammalian cytochrome P450 (CYP450) residues involved in substrate recognition was prepared for the CYP2 family by Gotoh in 1992 by manual alignment of mammalian CYP450 residues with substrate recognition site (SRS) residues manually delimited from a bacterial cytochrome P450-substrate complex. Using modern structural bioinformatics tools, we have identified CYP450-ligand interactions in mammalian complexes to create a "X-ray structures" SRS map. In a parallel approach, we have built a "docking" SRS map by successful docking of 868 known substrates of 10 mammalian CYP450 isoforms and analysis of contacts made in docking solutions. We subsequently combined these maps to create a unified description of SRSs. The new map largely agrees with the original map by Gotoh with the six original SRS regions appearing in similar locations along the CYP450 sequence as in Gotoh's map. However, important differences also occur: Two new SRS regions appear before SRS1 and we have assigned them as SRS1'a and SRS1'b; SRS1 is much bigger in our map than in Gotoh's (49 aligned positions versus 28); & SRS2 and SRS3 are co-joined in our map to give a single large SRS region (60 aligned positions) we have designated as SRS(2,3), in contrast to the 9 and 10 aligned positions individually covered by SRS2 and SRS3 respectively in Gotoh's original map. These differences result in the SRS zone covering 33 % of the mammalian CYP450 sequence in our map as opposed to 16 % in Gotoh's map. PMID:21740382
NASA Technical Reports Server (NTRS)
Old aircraft considered not restorable are melted down in on-site furnaces to reclaim the aluminum in their airframes. The process produces aluminum ingots and leaves a residue known as "dross." Because dross contains contaminants like lead silver cadmium and copper, Pima County, the dross dumping site, wanted to locate areas where dross had been dumped. Dr. Larry Lepley and Sandra L. Perry used the Landsat Thematic Mapper to screen for dross. A special two-step procedure was developed to separate the dross dumps (typically no larger than 50 meters across) from the desert background. The project has opened the door for similar applications.
Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites.
Erwin, Graham S; Bhimsaria, Devesh; Eguchi, Asuka; Ansari, Aseem Z
Targeting the genome with sequence-specific synthetic molecules is a major goal at the interface of chemistry, biology, and personalized medicine. Pyrrole/imidazole-based polyamides can be rationally designed to target specific DNA sequences with exquisite precision in?vitro; yet, the biological outcomes are often difficult to interpret using current models of binding energetics. To directly identify the binding sites of polyamides across the genome, we designed, synthesized, and tested polyamide derivatives that enabled covalent crosslinking and localization of polyamide-DNA interaction sites in live human cells. Bioinformatic analysis of the data reveals that clustered binding sites, spanning a broad range of affinities, best predict occupancy in cells. In contrast to the prevailing paradigm of targeting single high-affinity sites, our results point to a new design principle to deploy polyamides and perhaps other synthetic molecules to effectively target desired genomic sites in?vivo. PMID:25066383
Interactive Cardiovascular System Map
NSDL National Science Digital Library
The cardiovascular portion of the InnerBody website is a road map to the human cardiovascular system. It displays all of the main veins and arteries of the human body allowing the user to click on various parts of body and dozens of links to the many different systems appear. Users can hover over the links to discover what each part is named, or click on the link to be brought to a thorough definition and description of the selected system. Users may also �zoom in� on certain parts to view more detail. In addition to the interactive �map,� InnerBody also has images and descriptions about common issues that arise within the cardiovascular system.
mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases
Mitchell, Leslie; Huard, Sylvain; Cotrut, Michael; Pourhanifeh-Lemeri, Roghayeh; Steunou, Anne-Lise; Hamza, Akil; Lambert, Jean-Philippe; Zhou, Hu; Ning, Zhibin; Basu, Amrita; Côté, Jacques; Figeys, Daniel A.; Baetz, Kristin
Recent global proteomic and genomic studies have determined that lysine acetylation is a highly abundant posttranslational modification. The next challenge is connecting lysine acetyltransferases (KATs) to their cellular targets. We hypothesize that proteins that physically interact with KATs may not only predict the cellular function of the KATs but may be acetylation targets. We have developed a mass spectrometry-based method that generates a KAT protein interaction network from which we simultaneously identify both in vivo acetylation sites and in vitro acetylation sites. This modified chromatin-immunopurification coupled to an in vitro KAT assay with mass spectrometry (mChIP-KAT-MS) was applied to the Saccharomyces cerevisiae KAT nucleosome acetyltransferase of histone H4 (NuA4). Using mChIP-KAT-MS, we define the NuA4 interactome and in vitro-enriched acetylome, identifying over 70 previously undescribed physical interaction partners for the complex and over 150 acetyl lysine residues, of which 108 are NuA4-specific in vitro sites. Through this method we determine NuA4 acetylation of its own subunit Epl1 is a means of self-regulation and identify a unique link between NuA4 and the spindle pole body. Our work demonstrates that this methodology may serve as a valuable tool in connecting KATs with their cellular targets. PMID:23572591
Mapping of the CD23 Binding Site on Immunoglobulin E (IgE) and Allosteric Control of the IgE-Fc?RI Interaction*
Borthakur, Susmita; Hibbert, Richard G.; Pang, Marie O. Y.; Yahya, Norhakim; Bax, Heather J.; Kao, Michael W.; Cooper, Alison M.; Beavil, Andrew J.; Sutton, Brian J.; Gould, Hannah J.; McDonnell, James M.
IgE, the antibody that mediates allergic responses, acts as part of a self-regulating protein network. Its unique effector functions are controlled through interactions of its Fc region with two cellular receptors, Fc?RI on mast cells and basophils and CD23 on B cells. IgE cross-linked by allergen triggers mast cell activation via Fc?RI, whereas IgE-CD23 interactions control IgE expression levels. We have determined the CD23 binding site on IgE, using a combination of NMR chemical shift mapping and site-directed mutagenesis. We show that the CD23 and Fc?RI interaction sites are at opposite ends of the C?3 domain of IgE, but that receptor binding is mutually inhibitory, mediated by an allosteric mechanism. This prevents CD23-mediated cross-linking of IgE bound to Fc?RI on mast cells and resulting antigen-independent anaphylaxis. The mutually inhibitory nature of receptor binding provides a degree of autonomy for the individual activities mediated by IgE-Fc?RI and IgE-CD23 interactions. PMID:22815482
statement of significance, location map, site plan, landscape plan, site ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
statement of significance, location map, site plan, landscape plan, site sections, evolution of cemetery landscape. - San Francisco National Cemetery, 1 Lincoln Boulevard, San Francisco, San Francisco County, CA
Mapping of Protein-Protein Interaction Sites in the Plant-Type [2Fe2S] Ferredoxin
Haruka Kameda; Kei Hirabayashi; Kei Wada; Keiichi Fukuyama
Knowing the manner of protein-protein interactions is vital for understanding biological events. The plant-type [2Fe-2S] ferredoxin (Fd), a well-known small iron-sulfur protein with low redox potential, partitions electrons to a variety of Fd-dependent enzymes via specific protein-protein interactions. Here we have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I) at
Mapping the Major Interaction Between Binding Protein and Ig Light Chains to Sites Within the Variable Domain1
David P. Davis; Ritu Khurana; Stephen Meredith; Fred J. Stevens; Yair Argon
Newly synthesized Ig chains are known to interact in vivo with the binding protein (BiP), a major peptide-binding chaperone in the endoplasmic reticulum. The predominant interactions between the light chain and BiP are observed early in the folding pathway, when the light chain is either completely reduced, or has only one disulfide bond. In this study, we describe the in
Yellowstone National Park Interactive Map
NSDL National Science Digital Library
NPS Source: CENSUS
This Yellowstone National Park Map is a handy way to quickly find locations and buildings located in the park. It is currently the most detailed map of Yellowstone national park that can be viewed online. The pull down menu has Yellowstone features such as geyser basins, campgrounds, trails, mountains, and historical points and park structures. Popular geysers, and park locations such as Norris geyser basin, Yellowstone visitor centers, park housing, lodging, and park dining can be easily found. All Yellowstone National Park named structures are indexed so you can easily find the sites that you want to locate.
Sense of Place Evoked by Interactive Maps
Go, Hanyoung
, spatial cognition, and virtual reality literature, this study constructed a conceptual framework to measure how different interactivity levels of a digital map interface affect potential tourists' experience when exploring maps. In addition, the study...
23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 updated to 1931. - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT
24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT
Mapping glycans onto specific N-linked glycosylation sites of Pyrus communis PGIP redefines the interface for EPG-PGIP interactions.
Lim, Jae-Min; Aoki, Kazuhiro; Angel, Peggi; Garrison, Derek; King, Daniel; Tiemeyer, Michael; Bergmann, Carl; Wells, Lance
Polygalacturonase inhibiting proteins (PGIPs) are members of the leucine rich repeat family of proteins, involved in plant defense against fungal pathogens. PGIPs exhibit a remarkable degree of specificity in terms of their ability to bind and inhibit their target molecules, the endopolygalacturonases (EPGs). This specificity has been attributed for certain EPG/PGIP combinations to differences in primary sequence, but this explanation is unable to account for the full range of binding and inhibitory activities observed. In this paper, we have fully characterized the glycosylation on the PGIP derived from Pyrus communis and demonstrated, using a combination of PNGaseF and PNGaseA in (18)O-water, that the Pyrus communis PGIP utilizes all seven potential sites of N-linked glycosylation. Further, we demonstrate that certain sites appear to be modified only by glycans bearing alpha3-linked core fucosylation, while others are occupied by a mixture of fucosylated and nonfucosylated glycans. Modeling of the carbohydrates onto a homologous structure of PGIP indicates potential roles for glycosylation in mediating the interactions of PGIPs with EPGs. PMID:19072240
CEREAS: an interactive computer-mapping system for environmental assessments
J. B. Levenson; M. A. Snider
CEREAS (Categorical Exclusion Review\\/Environmental Assessment System) provides the environmental scientist with the tools needed to quickly process an application for permit to drill (APD). It provides an interactive referencing system for producing maps of potential constraint areas surrounding oil and gas activity sites. The design of the system makes it highly flexible. CEREAS was specifically developed to support the CER
GIS Surface Effects Map Archive, Nevada Test Site, Nevada
Grasso, Dennis N.
The GIS Surface Effects Map Archive contains a comprehensive collection of maps showing the surface effects produced by underground nuclear testing at the Nevada Test Site. From 1951 to 1992, scientists with the U.S. Geological Survey and agencies of the U.S. Department of Energy used field and aerial-photo mapping techniques to painstakingly map such surface effects as collapse sinks, craters, cracks, fractures, faults, and pressure ridges. Shortly after each test, a complex surface effects map was produced. Of the more than 920 underground detonations conducted at the Nevada Test Site, 688 were mapped for surface effects. This archive preserves these original maps in digital format. A Geographic Information System (GIS) was used to digitally reproduce each original, hand-drawn surface effects map and to assemble these maps into the digital data sets of this archive. The archive was designed to allow easy access to the maps, while preserving the original maps for perpetuity. Users can query the detonation sites database; prepare, view, and print individual or composite maps; and perform various types of scientific analysis and management tasks. Spatial analyses and queries can be performed on detonation sites and related surface effects in conjunction with other chronological, geographical, geological, or hydrological information via links to external maps and databases. This browser interface provides information about the archive, the history of surface effects mapping at the Nevada Test Site, the methods used to produce the digital surface effects maps, and links to published reports, data tables, and maps. Location maps show testing areas, operational areas, and detonation sites. Demonstration maps illustrate the methods used to produce the digital surface effects maps and exhibit some of the characteristics and uses for these data. Use the links below to view and print individual surface effects maps, retrieve information about the detonations and types of surface effects produced, and to learn about the organization and intended use of the map data contained in the archive.
Interactive Maps for Community in Online Learning
ERIC Educational Resources Information Center
Cavanaugh, Terence W.; Cavanaugh, Cathy
The online courses studied here used the visual medium of the interactive geographic map as a form of dialogue to reduce students' sense of transactional distance during the course, build their skills with Web 2.0 media, and increase their motivation. Using the dynamic map and the related online spreadsheet, the course participants created digital…
Mapping Letters through Interaction Design
Teresa Iturrioz; Jorge Cano; Monica Wachowicz
Many kinds of text documents (e.g. newspapers, reports and letters) provide a potential source of geo-referenced information that is often underutilized. In interaction design, the use of dynamic icons and animation plays an important role in creating a sense of interactivity and feedback with virtual worlds. This paper shall focus on developing an interaction design approach for improving information retrieval
Topographic Map of Pathfinder Landing Site
NASA Technical Reports Server (NTRS)
Topographic map of the landing site, to a distance of 60 meters from the lander in the LSC coordinate system. The lander is shown schematically in the center; 2.5 meter radius circle (black) centered on the camera was not mapped. Gentle relief [root mean square (rms) elevation variation 0.5 m; rms a directional slope 4O] and organization of topography into northwest and northeast-trending ridges about 20 meters apart are apparent. Roughly 30% of the illustrated area is hidden from the camera behind these ridges. Contours (0.2 m interval) and color coding of elevations were generated from a digital terrain model, which was interpolated by kriging from approximately 700 measured points. Angular and parallax point coordinates were measured manually on a large (5 m length) anaglyphic uncontrolled mosaic and used to calculate Cartesian (LSC) coordinates. Errors in azimuth on the order of 10 are therefore likely; elevation errors were minimized by referencing elevations to the local horizon. The uncertainty in range measurements increases quadratically with range. Given a measurement error of 1/2 pixel, the expected precision in range is 0.3 meter at 10 meter range, and 10 meters at 60 meter range. Repeated measurements were made, compared, and edited for consistency to improve the range precision. Systematic errors undoubtedly remain and will be corrected in future maps compiled digitally from geometrically controlled images. Cartographic processing by U.S. Geological Survey.NOTE: original caption as published in Science MagazineMars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is a division of the California Institute of Technology (Caltech).
The public Human Genome Project: mapping the genome, sequencing, and reassembly, 3D animationSite: DNA Interactive (www.dnai.org)
NSDL National Science Digital Library
DNAi location: Genome>The Project>putting it together>Animations>Hierarchical shotgun (public) Mapping the genome AND Sequencing and assembly This animation shows how the human genome was sequenced using the 'hierarchical shotgun' method of the public Human Genome Project. All the base pairs in our DNA are represented as letters on pieces of paper.
Data visualization in interactive maps and time series
NASA Astrophysics Data System (ADS)
Maigne, Vanessa; Evano, Pascal; Brockmann, Patrick; Peylin, Philippe; Ciais, Philippe
State-of-the-art data visualization has nothing to do with plots and maps we used few years ago. Many opensource tools are now available to provide access to scientific data and implement accessible, interactive, and flexible web applications. Here we will present a web site opened November 2013 to create custom global and regional maps and time series from research models and datasets. For maps, we explore and get access to data sources from a THREDDS Data Server (TDS) with the OGC WMS protocol (using the ncWMS implementation) then create interactive maps with the OpenLayers javascript library and extra information layers from a GeoServer. Maps become dynamic, zoomable, synchroneaously connected to each other, and exportable to Google Earth. For time series, we extract data from a TDS with the Netcdf Subset Service (NCSS) then display interactive graphs with a custom library based on the Data Driven Documents javascript library (D3.js). This time series application provides dynamic functionalities such as interpolation, interactive zoom on different axes, display of point values, and export to different formats. These tools were implemented for the Global Carbon Atlas (http://www.globalcarbonatlas.org): a web portal to explore, visualize, and interpret global and regional carbon fluxes from various model simulations arising from both human activities and natural processes, a work led by the Global Carbon Project.
47 CFR 73.4108 - FM transmitter site map submissions.
Code of Federal Regulations, 2012 CFR
...2012-10-01 2012-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...
47 CFR 73.4108 - FM transmitter site map submissions.
Code of Federal Regulations, 2013 CFR
...2013-10-01 2013-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...
47 CFR 73.4108 - FM transmitter site map submissions.
Code of Federal Regulations, 2011 CFR
...2011-10-01 2011-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...
47 CFR 73.4108 - FM transmitter site map submissions.
Code of Federal Regulations, 2014 CFR
...2014-10-01 2014-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...
47 CFR 73.4108 - FM transmitter site map submissions.
Code of Federal Regulations, 2010 CFR
...2010-10-01 2010-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication...to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and...
Wetlands proximity mapping of 86 waste sites on the Savannah River Plant
Jensen, J.R. (South Carolina Univ., Columbia, SC (USA). Dept. of Geography)
This project developed wetlands proximity maps and provided wetlands information by means of a Geographic Environmental Data Base (GEDB) for each of 11 interaction zones identified in DPST-84-684. It includes an analysis of 86 hazardous waste sites at the Savannah River Plant (SRP). The map of each interaction zone is intended to indicate major wetland and land cover types, with emphasis on locations of hazardous waste sites with wetland areas identified within a 1000 meter radius. Statistics of aerial extent for wetland and land cover for each interaction zone are provided. 80 figs., 93 tabs.
eSales Interactive Mapping -Viewing and Printing Introduction
eSales Interactive Mapping - Viewing and Printing Introduction Our eSales system includes an integrated interactive map facility. This allows you to view and print maps for all lots on offer. Various in the opposite direction, e.g. move mouse to right for westerly direction. Printing of Maps Printing of maps can
Surface-material maps of Viking landing sites on Mars
NASA Technical Reports Server (NTRS)
Moore, H. J.; Keller, J. M.
Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.
GATA-1 binding sites mapped in the -globin locus by using mammalian chIp-chip analysis
Gerstein, Mark
GATA-1 binding sites mapped in the -globin locus by using mammalian chIp-chip analysis Christine E-restricted transcription factors. The hemapoietic lineage-specific transcription factor GATA-1 is important for erythroid identified previously as a putative site of GATA-1 interaction by in vivo footprinting studies. We mapped
Groundwater maps of the Hanford Site, June 1993
Kasza, G.L.; Hartman, M.J.; Jordan, W.A.; Weekes, D.C.
The Groundwater Maps of the Hanford Site, June 1993 is an update of the series of reports that document the configuration of the uppermost unconfined aquifer beneath the Hanford Site. This report series presents the semiannual water level measurements taken at site groundwater monitoring wells each June and December and the groundwater maps derived from these measurements. These reports document the changes in the groundwater level at Hanford as the site has transitioned from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site. Groundwater Maps of the Hanford Site are prepared for the US Department of Energy, Office of Environmental Restoration and Waste Management, by the Hanford Site Operations and Engineering Contractor, Westinghouse Hanford Company (WHC). This document fulfills reporting requirements specified in WHC (1993), Section 8.0 {open_quotes}Water Quality{close_quotes} and also described in the Environmental Monitoring Plan for the Hanford Site (DOE-RL 1991). Maps depicting the water table beneath the Hanford Site south of the Columbia River are presented in this report. Appendix A lists the well identification number, depth to water, casing elevating and the water level elevation for each well measured during June 1993. A summary discussion of the data is included with a well index map, the depth to water map and the contoured map of the water table surface for the Hanford Site and each of the three operational areas (the 100, 200, and 300-1100 Areas).
Optimizing landfill site selection by using land classification maps.
Eskandari, M; Homaee, M; Mahmoodi, S; Pazira, E; Van Genuchten, M Th
Municipal solid waste disposal is a major environmental concern throughout the world. Proper landfill siting involves many environmental, economic, technical, and sociocultural challenges. In this study, a new quantitative method for landfill siting that reduces the number of evaluation criteria, simplifies siting procedures, and enhances the utility of available land evaluation maps was proposed. The method is demonstrated by selecting a suitable landfill site near the city of Marvdasht in Iran. The approach involves two separate stages. First, necessary criteria for preliminary landfill siting using four constraints and eight factors were obtained from a land classification map initially prepared for irrigation purposes. Thereafter, the criteria were standardized using a rating approach and then weighted to obtain a suitability map for landfill siting, with ratings in a 0-1 domain and divided into five suitability classes. Results were almost identical to those obtained with a more traditional environmental landfill siting approach. Because of far fewer evaluation criteria, the proposed weighting method was much easier to implement while producing a more convincing database for landfill siting. The classification map also considered land productivity. In the second stage, the six best alternative sites were evaluated for final landfill siting using four additional criteria. Sensitivity analyses were furthermore conducted to assess the stability of the obtained ranking. Results indicate that the method provides a precise siting procedure that should convince all pertinent stakeholders. PMID:25666474
Interactive map of movable cultural heritage
NASA Astrophysics Data System (ADS)
Moscicka, A.; Marzec, M.
The paper presents the results of a research project connected with using Geographic Information System (GIS) - as a technology and as a tool - to integrate different digital archival collections, present their content in one space and provide on-line access to them from one common level - from an on-line map. Digital archives contain a lot of movable heritage which content has no simple relation to geographic space: manuscripts or old prints can be created in one place, they can describe other places and now they can be stored still in another place. Moreover, each archival object could have been stored in many different places in the past. Presented paper propose the method of creating movable heritage map, based on all geographical places connected with digital collections. The starting point of the study was the international standards for describing digital collections. They provide metadata which are the source of spatial information about archival objects and about spatial, temporal, typological and semantic relations between them. All these aspects were integrated in the GIS and presented as the prototype of an on-line interactive map. Proposed solutions as well as practical applications of the map are presented in the paper.
Soil Liquefaction Susceptibility and Site Class Maps of Washington State
NSDL National Science Digital Library
In response to the Nisqually earthquake of 2001, the Washington State Division of Geology and Earth Resources (DGER) developed two types of earthquake hazard maps for every county in the state: liquefaction susceptibility maps, which outline areas where water-saturated sandy soil loses strength during earthquake shaking, and National Earthquake Hazards Reduction Program (NEHRP) site class maps, which outline areas where soils amplify ground shaking. The maps will be used by state and local governments in Washington to update existing hazard mitigation plans and to delineate geologically hazardous areas for emergency planning and response, planning of local zoning ordinances, and building code enforcement. A link is provided to an ftp site where the maps are stored in folders.
Interactive State of Metropolitan America Indicator Map
NSDL National Science Digital Library
How quickly have the suburbs in the American southeast grown over the past decade? This question, and many others, are answered in fine visual form on this website, created by staff members at The Brookings Institution. Visitors can use the interactive maps to look over population, ethnicity, age, and educational attainment distributions across the United States. Each map contains a zoom feature, and visitors can use the subject indicators to look at different variables. Also, visitors can toggle through different geographic scales of focus, including metro areas, center cities, suburbs, and states. Finally, visitors can also download and read "The State of Metropolitan America" report which provides additional perspective on some of these recent demographic trends.
Antibody Recognition of Cancer-Related Gangliosides and Their Mimics Investigated Using in silico Site Mapping
Mark Agostino; Elizabeth Yuriev; Paul A. Ramsland
Modified gangliosides may be overexpressed in certain types of cancer, thus, they are considered a valuable target in cancer immunotherapy. Structural knowledge of their interaction with antibodies is currently limited, due to the large size and high flexibility of these ligands. In this study, we apply our previously developed site mapping technique to investigate the recognition of cancer-related gangliosides by
REMA: A computer-based mapping tool for analysis of restriction sites in multiple DNA sequences
Jan Szubert; Caroline Reiff; Andrew Thorburn; Brajesh K. Singh
REMA is an interactive web-based program which predicts endonuclease cut sites in DNA sequences. It analyses multiple sequences simultaneously and predicts the number and size of fragments as well as provides restriction maps. The users can select single or paired combinations of all commercially available enzymes. Additionally, REMA permits prediction of multiple sequence terminal fragment sizes and suggests suitable restriction
Techniques for Creating Ecological Site Extent Maps
in ArcCatalog Ecological site data is stored in the coecoclass table . #12;Soil survey polygons Tabular Data Relationships The mapunit table can be joined or related the spatial data. #12;Relationship;Using the Identify tool, data from related tables can be viewed for polygons. #12;Steve Campbell Soil
Direct optical mapping of transcription factor binding sites on field-stretched ?-DNA in nanofluidic devices
Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu
Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage ?-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (? 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422
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Sóbester, András
framework, a student-centered curriculum, and a three-day teaching experiment for seventy-two earth scienceHindawi Publishing Corporation Advances in Human-Computer Interaction Volume 2008, Article ID 874563, 19 pages doi:10.1155/2008/874563 Research Article Embodiment, Multimodality, and Composition
24 CFR 3285.103 - Site suitability with design zone maps.
Code of Federal Regulations, 2011 CFR
...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...
24 CFR 3285.103 - Site suitability with design zone maps.
Code of Federal Regulations, 2013 CFR
...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...
24 CFR 3285.103 - Site suitability with design zone maps.
Code of Federal Regulations, 2014 CFR
...false Site suitability with design zone maps. 3285.103 Section 3285.103 ...103 Site suitability with design zone maps. Prior to the initial installation...home, as indicated on the design zone maps provided with the home, are...
Finding Sites Meeting Compactness and On and Off-site Suitability Criteria in Raster Maps
Pablo Vanegas; Dirk Cattrysse; Anja Wijffels; Jos Van Orshoven
This paper presents an evaluation of the Heuristic for Locating Cells (HLC) for identifying optimal sites in raster maps. The optimal sites are the result of a trade-off between the on-site suitability of individual cells, their spatial configuration, and their off-site impact at the watershed outlet. The evaluation is targeted to a case of reforestation in two sub-basins within the
Comprehensive interaction map of the Arabidopsis MADS box transcription factors
Stefan de Folter; Richard G. H. Immink; Martin Kieffer; L. Parenicová; Stefan R. Henz; Detlef Weigel; Marco Busscher; K. Kooiker; Lucia Colombo; Martin M. Kater; B. Davis; G. C. Angenent
Interactions between proteins are essential for their functioning and the biological processes they control. The elucidation of interaction maps based on yeast studies is a first step toward the understanding of molecular networks and provides a framework of proteins that possess the capacity and specificity to interact. Here, we present a comprehensive plant protein–protein interactome map of nearly all members
13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test ...
Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey
13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test Area 1-125. Specifications No. ENG (NASA)-04-35363-1; Drawing No. 60-09-34; sheet 11. Ref. No. C-l. D.O. SERIES 1597/1. Approved for siting on 24 April 1962. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Leuhman Ridge near Highways 58 & 395, Boron, Kern County, CA
Hanford site Computer Automated Mapping Information System (CAMIS)
Rush, S.F. [ICF Kaiser Hanford Co., Richland, WA (United States)
The Computer Automated Mapping Information System (CAMIS) provides sitewide, networked access to CAD based geographically referenced data. CAMIS allows multiple organizations to maintain and share their data. Information collected and managed according to site-wide standards, enables each organization to focus their limited resources on data issues tied to their own discipline without having to collect or manage reference data outside their respective domains. Sharing information also minimizes redundant data and helps improve the overall quality of the sites` data resources.
Mapping chromatin interactions with 5C technology
Ferraiuolo, Maria A.; Sanyal, Amartya; Naumova, Natalia; Dekker, Job; Dostie, Josée
In eukaryotes, genome organization can be observed on many levels and at different scales. This organization is important not only to reduce chromosome length but also for the proper execution of various biological processes. High-resolution mapping of spatial chromatin structure was made possible by the development of the chromosome conformation capture (3C) technique. 3C uses chemical cross-linking followed by proximity-based ligation of fragmented DNA to capture frequently interacting chromatin segments in cell populations. Several 3C-related methods capable of higher chromosome conformation mapping throughput were reported afterwards. These techniques include the 3C-carbon copy (5C) approach, which offers the advantage of being highly quantitative and reproducible. We provide here a reference protocol for the production of 5C libraries analyzed by next-generation sequencing or onto microarrays. A procedure used to verify that 3C library templates bear the high quality required to produce superior 5C libraries is also described. We believe that this comprehensive detailed protocol will help guide researchers in probing spatial genome organization and its role in various biological processes. PMID:23137922
Systematics of Cetaceans Using Restriction Site Mapping of Mitochondrial DNA
Derek Paul Ohland; Eric H. Harley; Peter B. Best
Phylogenetic analysis of 14 cetacean species, including members from two baleen whale families and three toothed whale families, was undertaken using restriction site mapping of mitochondrial DNA and using cladistic and distance measures to infer phylogenies. The amount of between-taxa sequence divergence inferred from the data was lower than expected from the standard interpretation of the fossil record, but more
Goldberg, Jeffrey L.; Miller, Thomas C.
Computer generation and placement of map type has been refined into a production mode at Mid-Continent Mapping Center (MCMC) for USGS 1:24,000- and 1:25,000-scale Provisional maps. The map collar program is written in FORTRAN using batch processing that allows the program to work in the background.
To be published in the Proceedings of the International Cartographic Conference, Moscow, August 2007. USABILITY PROBLEMS OF WEB MAP SITES
Williamson, John
To be published in the Proceedings of the International Cartographic Conference, Moscow, August of the evaluations were carried out with expert evaluations, during which usability engineers and cartographers and techniques for interface and interaction design of web map sites. Consequently, many people use these sites
Design Issues for Pen-Centric Interactive Maps
Louis Vuurpijl; Don Willems; Ralph Niels; Marcel van Gerven
\\u000a Recent advances in interactive pen-aware systems, pattern recognition technologies, and human–computer interaction have provided\\u000a new opportunities for pen-based communication between human users and intelligent computer systems. Using interactive maps,\\u000a users can annotate pictorial or cartographic information by means of pen gestures and handwriting. Interactive maps may provide\\u000a an efficient means of communication, in particular in the envisaged contexts of crisis
Intelligent Icon Positioning for Interactive Map-based Information Systems
Georg Fuchs; Heidrun Schumann
The combination of map displays with icon techniques is well-suited for visualizing geo- spatial dependent multivariate data. The requirements for icon placement on the map, although not trivial, are not properly attended by most interactive visualization systems. In cartography, a number of methods for automatic text label placement and map generalization has been developed. These are focused on high-quality results,
Andreas Neumann; Andréas M. Winter
Needless to say that there is a high demand for maps on the internet. Several papers had dealt with issues on internet map use and the exploding numbers of hits on busy cartographic websites (7). However, most of the presented maps are of low (carto)-graphical quality and none or little degree of interactivity. This fact is due to a lack
Global Land Survey Impervious Mapping Project Web Site
NASA Technical Reports Server (NTRS)
DeColstoun, Eric Brown; Phillips, Jacqueline
The Global Land Survey Impervious Mapping Project (GLS-IMP) aims to produce the first global maps of impervious cover at the 30m spatial resolution of Landsat. The project uses Global Land Survey (GLS) Landsat data as its base but incorporates training data generated from very high resolution commercial satellite data and using a Hierarchical segmentation program called Hseg. The web site contains general project information, a high level description of the science, examples of input and output data, as well as links to other relevant projects.
Understanding Human-Computer Interactions in Map Revision
Zhou, Jun
Understanding Human-Computer Interactions in Map Revision Jun Zhou, Walter F. Bischof, and Terry a stream of events related to human actions in a real-time cartographic map revision system. The recorded, Human - Com- puter Interaction, and Cognitive Psychology. Surprisingly, very few research re- sults have
Understanding Human-Computer Interactions in Map Revision
Alberta, University of
Understanding Human-Computer Interactions in Map Revision Jun Zhou, Walter F. Bischof, and Terry related to human actions in a real-time map (cartographic) revision sys- tem. The recorded events, Human - Com- puter Interaction, and Cognitive Psychology. Surprisingly, very few research re- sults have
Global Mapping of the Yeast Genetic Interaction Network
Amy Hin Yan Tong; Guillaume Lesage; Gary D. Bader; Huiming Ding; Hong Xu; Xiaofeng Xin; James Young; Gabriel F. Berriz; Renee L. Brost; Michael Chang; YiQun Chen; Xin Cheng; Gordon Chua; Helena Friesen; Debra S. Goldberg; Jennifer Haynes; Christine Humphries; Grace He; Shamiza Hussein; Lizhu Ke; Nevan Krogan; Zhijian Li; Joshua N. Levinson; Hong Lu; Patrice Ménard; Christella Munyana; Ainslie B. Parsons; Owen Ryan; Raffi Tonikian; Tania Roberts; Anne-Marie Sdicu; Jesse Shapiro; Bilal Sheikh; Bernhard Suter; Sharyl L. Wong; Lan V. Zhang; Hongwei Zhu; Christopher G. Burd; Sean Munro; Chris Sander; Jasper Rine; Jack Greenblatt; Matthias Peter; Anthony Bretscher; Graham Bell; Frederick P. Roth; Grant W. Brown; Brenda Andrews; Howard Bussey; Charles Boone
A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to
Ron Li; Kaichang Di; Fengliang Xu
This paper presents techniques for automatic mapping of Mars landing sites using surface-based images, i.e., those taken by Mar s landers and\\/or rovers. An innovative method for automatic tie point selection is presented that includes five steps: interest p oint extraction, interest point matching, parallax verification, gra ph consistency verification and final tie point selection with g ridding. In matching
Insertion site mapping for repeated elements in Mycobacterium tuberculosis.
Moganeradj, Kartyk; Abubakar, Ibrahim; McHugh, Timothy D; Sonnenberg, Pam; Arnold, Catherine
Insertion elements not only act as genetic markers for differentiation of bacteria but their movement in bacterial genomes likely plays an essential role in changing the physical and biochemical traits of the organisms when adapting to new environments. Genomic Insertion Site mapping of transposable elements could shed light on the putative altered function of adjacent genes. In the era of whole genome sequencing where repeat elements are difficult to sequence with short read technologies and in the absence of high throughput technologies especially in poorer resource settings, an alternative approach to their characterisation is needed. A rapid and simple method of insertion site mapping that uses Insertion Sequence 6110 (IS6110) fluorescent amplified fragment length polymorphism (FAFLP) PCR as a foundation and then uses additional selective bases to reduce the number of fragments generated was developed. This was applied to Mycobacterium tuberculosis H37Rv sequenced strain to compare the experimental data with the in silico results. This was successfully achieved for all but two of the sixteen fragments generated by FAFLP and demonstrated that, by using this technique, insertion sites can be mapped onto the genomes of M. tuberculosis. PMID:23262032
An in-depth map of polyadenylation sites in cancer
Lin, Yuefeng; Li, Zhihua; Ozsolak, Fatih; Kim, Sang Woo; Arango-Argoty, Gustavo; Liu, Teresa T.; Tenenbaum, Scott A.; Bailey, Timothy; Monaghan, A. Paula; Milos, Patrice M.; John, Bino
We present a comprehensive map of over 1 million polyadenylation sites and quantify their usage in major cancers and tumor cell lines using direct RNA sequencing. We built the Expression and Polyadenylation Database to enable the visualization of the polyadenylation maps in various cancers and to facilitate the discovery of novel genes and gene isoforms that are potentially important to tumorigenesis. Analyses of polyadenylation sites indicate that a large fraction (?30%) of mRNAs contain alternative polyadenylation sites in their 3? untranslated regions, independent of the cell type. The shortest 3? untranslated region isoforms are preferentially upregulated in cancer tissues, genome-wide. Candidate targets of alternative polyadenylation-mediated upregulation of short isoforms include POLR2K, and signaling cascades of cell–cell and cell–extracellular matrix contact, particularly involving regulators of Rho GTPases. Polyadenylation maps also helped to improve 3? untranslated region annotations and identify candidate regulatory marks such as sequence motifs, H3K36Me3 and Pabpc1 that are isoform dependent and occur in a position-specific manner. In summary, these results highlight the need to go beyond monitoring only the cumulative transcript levels for a gene, to separately analysing the expression of its RNA isoforms. PMID:22753024
An interactive method for digitizing zone maps
NASA Technical Reports Server (NTRS)
Giddings, L. E.; Thompson, E. J.
A method is presented for digitizing maps that consist of zones, such as contour or climatic zone maps. A color-coded map is prepared by any convenient process. The map is then read into memory of an Image 100 computer by means of its table scanner, using colored filters. Zones are separated and stored in themes, using standard classification procedures. Thematic data are written on magnetic tape and these data, appropriately coded, are combined to make a digitized image on tape. Step-by-step procedures are given for digitization of crop moisture index maps with this procedure. In addition, a complete example of the digitization of a climatic zone map is given.
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Help Shopping Cart Contact Site Map Member Login Logout Mission History Membership Annual Report Members Only Member Login Shopping Cart Contact Site Map Home ©2002 American Forest & Paper Association
Quantitative Genetic Interaction Mapping Using the E-MAP Approach
Collins, Sean R.; Roguev, Assen; Krogan, Nevan J.
Genetic interactions represent the degree to which the presence of one mutation modulates the phenotype of a second mutation. In recent years, approaches for measuring genetic interactions systematically and quantitatively have proven to be effective tools for unbiased characterization of gene function and have provided valuable data for analyses of evolution. Here, we present protocols for systematic measurement of genetic interactions with respect to organismal growth rate for two yeast species. PMID:20946812
Cartographic Mapping of Mars Landing Sites: A Historical Perspective
NASA Technical Reports Server (NTRS)
Duxbury, Thomas C.
Initial mapping of Mars began with the early Mariner 4, 6 and 7 flybys in the 1960's. Mariner 9 obtained the first global coverage of Mars in 1971. Viking Orbiters 1 and 2 added new and higher resolution global coverage. The US Geological Survey produced the first digital global cartographic map products in black and white and in color, the mosaicked digital image models (MDIMs). In 1989, the Phobos 88 mission added imaging as well as multispectral mapping of Mars in the equatorial region. The Mars Global Surveyor (MGS) added to the black and white and color global coverage. The most important development for Mars cartography occurred on MGS with its global coverage of Mars using the Mars Observer Laser Altimeter (MOL A) producing precision ground control in latitude, longitude and radius. The next version of the MDIM was produced at 230 m spatial resolution using MOLA precision cartographic control. The Mars Odyssey mission THEMIS instrument has completed its global infrared mapping of Mars at 100 m spatial resolution. The Mars Express mission is completing its global coverage of Mars in stereo at 100 m spatial resolution or better. MGS, Odyssey and Mars Express continue to provide limited surface coverage at the 1 to 20 m resolution. Currently the new Mars Reconnaissance Orbiter is producing images at the 10's of cm level. All of these datasets provide a rich and historic perspective of Mars covering nearly five decades and allow global cartographic map products to be produced in visual and infrared at the 100 m level with specialized cartographic maps being produced for landing sites at the meter or sub-meter spatial resolution level. This work was produced at the Jet Propulsion Laboratory, California Institute of Technology under contract to the National Aeronautics and Space Administration, NAS 7-7120.5d, within the NASA Mars Data Analysis Program and the MGS, Odyssey, Mars Express and MRO Participating Scientist Programs.
Auto-FACE: An NMR Based Binding Site Mapping Program for Fast Chemical Exchange Protein-Ligand Systems
Krishnamoorthy, Janarthanan; Yu, Victor C. K.; Mok, Yu-Keung
Background Nuclear Magnetic Resonance (NMR) spectroscopy offers a variety of experiments to study protein-ligand interactions at atomic resolution. Among these experiments, N Heteronuclear Single Quantum Correlation (HSQC) experiment is simple, less time consuming and highly informative in mapping the binding site of the ligand. The interpretation of N HSQC becomes ambiguous when the chemical shift perturbations are caused by non-specific interactions like allosteric changes and local structural rearrangement. Under such cases, detailed chemical exchange analysis based on chemical shift perturbation will assist in locating the binding site accurately. Methodology/Principal Findings We have automated the mapping of binding sites for fast chemical exchange systems using information obtained from N HSQC spectra of protein serially titrated with ligand of increasing concentrations. The automated program Auto-FACE (Auto-FAst Chemical Exchange analyzer) determines the parameters, e.g. rate of change of perturbation, binding equilibrium constant and magnitude of chemical shift perturbation to map the binding site residues. Interestingly, the rate of change of perturbation at lower ligand concentration is highly sensitive in differentiating the binding site residues from the non-binding site residues. To validate this program, the interaction between the protein and the ligand BH3I-1 was studied. Residues in the hydrophobic BH3 binding groove of were easily identified to be crucial for interaction with BH3I-1 from other residues that also exhibited perturbation. The geometrically averaged equilibrium constant () calculated for the residues present at the identified binding site is consistent with the values obtained by other techniques like isothermal calorimetry and fluorescence polarization assays (). Adjacent to the primary site, an additional binding site was identified which had an affinity of 3.8 times weaker than the former one. Further NMR based model fitting for individual residues suggest single site model for residues present at these binding sites and two site model for residues present between these sites. This implies that chemical shift perturbation can represent the local binding event much more accurately than the global binding event. Conclusion/Significance Detail NMR chemical shift perturbation analysis enabled binding site residues to be distinguished from non-binding site residues for accurate mapping of interaction site in complex fast exchange system between small molecule and protein. The methodology is automated and implemented in a program called "Auto-FACE", which also allowed quantitative information of each interaction site and elucidation of binding mechanism. PMID:20174626
Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems
Kohn, Kurt W.
Eventually to understand the integrated function of the cell cycle regulatory network, we must organize the known interactions in the form of a diagram, map, and/or database. A diagram convention was designed capable of unambiguous representation of networks containing multiprotein complexes, protein modifications, and enzymes that are substrates of other enzymes. To facilitate linkage to a database, each molecular species is symbolically represented only once in each diagram. Molecular species can be located on the map by means of indexed grid coordinates. Each interaction is referenced to an annotation list where pertinent information and references can be found. Parts of the network are grouped into functional subsystems. The map shows how multiprotein complexes could assemble and function at gene promoter sites and at sites of DNA damage. It also portrays the richness of connections between the p53-Mdm2 subsystem and other parts of the network. PMID:10436023
Towards a Typology of Interactivity Functions for Visual Map Exploration
Donata Persson; Georg Gartner; Manfred Buchroithner
Many interactivity functions exist in explorative map applications. This chapter provides a typology of these functions with\\u000a the aim to contribute towards a standardization of the variety of interactive visualization tools. The typology contains 8\\u000a types and around 70 particular interactivity functions and is based on an evaluation of existing divisions and categorizations\\u000a of interactions. The standardization implies a facilitation
Site and Orbit Repeatabilities using Adaptive Mapping Functions
NASA Astrophysics Data System (ADS)
Desjardins, Camille; Gegout, Pascal; Soudarin, Laurent; Biancale, Richard; Perosanz, Felix
The electromagnetic signals emitted by the satellite positioning systems travel at the speed of light in a straight line in a vacuum but are modified in their propagation through the neutral atmosphere by temporal and spatial changes of density, and composition and refractivity. These waves are slowed down and their trajectories are bent. This presentation summarizes the performances of the modeling of the tropospheric propagation by the ray tracing technique through the assimilations of the European Meteorological Centre (ECMWF) in the framework of realizing the geodetic reference frame. This goal is achieved by modeling the spatial variability of the propagation using the time variable three-dimensional physical parameters of the atmosphere. The tropospheric delays obtained by ray tracing in all directions throughout the meteorological model surrounding the geodetic site, are fitted by Adaptive Mapping Functions (AMF) parameterized by several tens of coefficients. The delays produced by the Horizon software are then experimented, kept unchanged or adjusted, when recovering a reference frame based on hundred sites using the GINS software. Without any adjustments of the tropospheric modeling, the subcentimetric performances of the AMF are demonstrated by the repeatability of sites positions and GPS satellites orbits. When some AMF coefficients are adjusted, the accuracy of orbits recovery in term of quadratic mean is 7 to 8 millimeters. This limit is imposed by the lack or deficiency of other models, such as non-tidal and tidal loading respectively. Hence the repeatability of the vertical position is not enhanced by changing the propagation model. At the contrary, the repeatability of the horizontal position of geodetic sites is greatly enhanced by accounting for the azimuthal variability provided by the realistic 3D shapes of the Atmosphere and the Earth and the rigorous interpolations of atmospheric parameters included in Adaptive Mapping Functions with respect to the standard approach.
A geostatistical approach to mapping site response spectral amplifications
Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Tanaka, Y.; Tanaka, H.
If quantitative estimates of the seismic properties do not exist at a location of interest then the site response spectral amplifications must be estimated from data collected at other locations. Currently, the most common approach employs correlations of site class with maps of surficial geology. Analogously, correlations of site class with topographic slope can be employed where the surficial geology is unknown. Our goal is to identify and validate a method to estimate site response with greater spatial resolution and accuracy for regions where additional effort is warranted. This method consists of three components: region-specific data collection, a spatial model for interpolating seismic properties, and a theoretical method for computing spectral amplifications from the interpolated seismic properties. We consider three spatial interpolation schemes: correlations with surficial geology, termed the geologic trend (GT), ordinary kriging (OK), and kriging with a trend (KT). We estimate the spectral amplifications from seismic properties using the square root of impedance method, thereby linking the frequency-dependent spectral amplifications to the depth-dependent seismic properties. Thus, the range of periods for which this method is applicable is limited by the depth of exploration. A dense survey of near-surface S-wave slowness (Ss) throughout Kobe, Japan shows that the geostatistical methods give more accurate estimates of Ss than the topographic slope and GT methods, and the OK and KT methods perform equally well. We prefer the KT model because it can be seamlessly integrated with geologic maps that cover larger regions. Empirical spectral amplifications show that the region-specific data achieve more accurate estimates of observed median short-period amplifications than the topographic slope method. ?? 2010 Elsevier B.V.
Prediction, assessment and validation of protein interaction maps in bacteria.
Wojcik, Jérôme; Boneca, Ivo G; Legrain, Pierre
High-throughput proteomics technologies, especially the yeast two-hybrid system, produce large volumes of protein-protein interaction data organized in networks. The complete sequencing of many genomes raises questions about the extent to which such networks can be transferred between organisms. We attempted to answer this question using the experimentally derived Helicobacter pylori interaction map and the recently described interacting domain profile pair (IDPP) method to predict a virtual map for Escherichia coli. The extensive literature concerning E.coli was used to assess all predicted interactions and to validate the IDPP method, which clusters protein domains by sequence and connectivity similarities. The IDPP method has a much better heuristic value than methods solely based on protein homology. The IDPP method was further applied to Campylobacter jejuni to generate a virtual interaction map. An in-depth comparison of the chemotaxis pathways predicted in E.coli and C.jejuni led to the proposition of new functional assignments. Finally, the prediction of protein-protein interaction maps across organisms enabled us to validate some of the interactions on the original experimental map. PMID:12419263
Seismic site classification and site period mapping of Chennai City using geophysical and geotechnical data
NASA Astrophysics Data System (ADS)
Maheswari, R. Uma; Boominathan, A.; Dodagoudar, G. R.
Subsurface conditions play a major role in the damage potential of earthquakes and the seismic soil amplification of a site which is a critical factor affecting the level of ground shaking. Shear wave velocity ( Vs) of the soil layer is an important parameter influencing the amplification behaviour of the site. Site characterization in calculating seismic hazards is usually based on the near-surface shear wave velocity values. The average shear wave velocity of the top 30 m of the soil, referred to as ( Vs) 30 is commonly adopted by competent building codes to classify the sites for earthquake resistant design of structures and in general it is widely used in microzonation studies. In the present study, the shear wave velocity of soil layers was measured at 30 locations in Chennai City by Multichannel Analysis of Surface Waves (MASW) test. In addition, nearly 300 borehole data were used to estimate Vs based on the correlations between Vs and SPT-N values for Chennai developed by authors earlier. Merging of MASW test results with borehole data yields sufficient coverage of Vs to develop a new site classification map for Chennai based on the NEHRP standard. It is found that part of the city belong to site D category (stiff soil). The developed site period map reveals that the fundamental site period varies in the range of 0.03 to 0.6 s, thus the soil conditions in Chennai pose a potential threat during earthquakes to low rise buildings (less than 6 storeys) which are densely distributed throughout the city.
The Interaction of Landmarks and Map Alignment in You-Are-Here Maps Grant McKenzie1
Klippel, Alexander
The Interaction of Landmarks and Map Alignment in You-Are-Here Maps Grant McKenzie1 , Alexander of how map alignment and the presence of landmarks in maps interact during wayfinding. For the purpose). In the area of navigation support, this reliance drives an urgency for cartographic methods that seamlessly
A proteome-wide protein interaction map for Campylobacter jejuni
Parrish, Jodi R; Yu, Jingkai; Liu, Guozhen; Hines, Julie A; Chan, Jason E; Mangiola, Bernie A; Zhang, Huamei; Pacifico, Svetlana; Fotouhi, Farshad; DiRita, Victor J; Ideker, Trey; Andrews, Phillip; Finley, Russell L
Background Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level models of biological processes. Despite this value, only a limited amount of interaction data is available for prokaryotes. Here we report the systematic identification of protein interactions for the bacterium Campylobacter jejuni, a food-borne pathogen and a major cause of gastroenteritis worldwide. Results Using high-throughput yeast two-hybrid screens we detected and reproduced 11,687 interactions. The resulting interaction map includes 80% of the predicted C. jejuni NCTC11168 proteins and places a large number of poorly characterized proteins into networks that provide initial clues about their functions. We used the map to identify a number of conserved subnetworks by comparison to protein networks from Escherichia coli and Saccharomyces cerevisiae. We also demonstrate the value of the interactome data for mapping biological pathways by identifying the C. jejuni chemotaxis pathway. Finally, the interaction map also includes a large subnetwork of putative essential genes that may be used to identify potential new antimicrobial drug targets for C. jejuni and related organisms. Conclusion The C. jejuni protein interaction map is one of the most comprehensive yet determined for a free-living organism and nearly doubles the binary interactions available for the prokaryotic kingdom. This high level of coverage facilitates pathway mapping and function prediction for a large number of C. jejuni proteins as well as orthologous proteins from other organisms. The broad coverage also facilitates cross-species comparisons for the identification of evolutionarily conserved subnetworks of protein interactions. PMID:17615063
A Physical and Regulatory Map of Host-Influenza Interactions
A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection During the course of a viral infection, viral proteins interact with an array of host proteins influenza and its human host. A combination of yeast two- hybrid analysis and genome-wide expression pro
Molecular interaction maps as information organizers and simulation guides
NASA Astrophysics Data System (ADS)
Kohn, Kurt W.
A graphical method for mapping bioregulatory networks is presented that is suited for the representation of multimolecular complexes, protein modifications, as well as actions at cell membranes and between protein domains. The symbol conventions defined for these molecular interaction maps are designed to accommodate multiprotein assemblies and protein modifications that can generate combinatorially large numbers of molecular species. Diagrams can either be "heuristic," meaning that detailed knowledge of all possible reaction paths is not required, or "explicit," meaning that the diagrams are totally unambiguous and suitable for simulation. Interaction maps are linked to annotation lists and indexes that provide ready access to pertinent data and references, and that allow any molecular species to be easily located. Illustrative interaction maps are included on the domain interactions of Src, transcription control of E2F-regulated genes, and signaling from receptor tyrosine kinase through phosphoinositides to Akt/PKB. A simple method of going from an explicit interaction diagram to an input file for a simulation program is outlined, in which the differential equations need not be written out. The role of interaction maps in selecting and defining systems for modeling is discussed.
Identification and mapping of natural vegetation on a coastal site using a Worldview-2 satellite image
Boyer, Edmond
1 Identification and mapping of natural vegetation on a coastal site using a Worldview-2 satellite on a coastal site using a Worldview-2 satellite image Identification and mapping of natural vegetation" DOI : 10.1016/j.jenvman.2014.05.027 #12;2 Identification and mapping of natural vegetation
MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumoniae.
Fleurie, Aurore; Lesterlin, Christian; Manuse, Sylvie; Zhao, Chao; Cluzel, Caroline; Lavergne, Jean-Pierre; Franz-Wachtel, Mirita; Macek, Boris; Combet, Christophe; Kuru, Erkin; VanNieuwenhze, Michael S; Brun, Yves V; Sherratt, David; Grangeasse, Christophe
In every living organism, cell division requires accurate identification of the division site and placement of the division machinery. In bacteria, this process is traditionally considered to begin with the polymerization of the highly conserved tubulin-like protein FtsZ into a ring that locates precisely at mid-cell. Over the past decades, several systems have been reported to regulate the spatiotemporal assembly and placement of the FtsZ ring. However, the human pathogen Streptococcus pneumoniae, in common with many other organisms, is devoid of these canonical systems and the mechanisms of positioning the division machinery remain unknown. Here we characterize a novel factor that locates at the division site before FtsZ and guides septum positioning in pneumococcus. Mid-cell-anchored protein Z (MapZ) forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. MapZ then positions the FtsZ ring through direct protein-protein interactions. MapZ-mediated control differs from previously described systems mostly on the basis of negative regulation of FtsZ assembly. Furthermore, MapZ is an endogenous target of the Ser/Thr kinase StkP, which was recently shown to have a central role in cytokinesis and morphogenesis of S. pneumoniae. We show that both phosphorylated and non-phosphorylated forms of MapZ are required for proper Z-ring formation and dynamics. Altogether, this work uncovers a new mechanism for bacterial cell division that is regulated by phosphorylation and illustrates that nature has evolved a diversity of cell division mechanisms adapted to the different bacterial clades. PMID:25470041
MapZ beacons the division sites and positions FtsZ-rings in Streptococcus pneumoniae
Zhao, Chao; Cluzel, Caroline; Lavergne, Jean-Pierre; Franz-Wachtel, Mirita; Macek, Boris; Combet, Christophe; Kuru, Erkin; VanNieuwenhze, Michael S.; Brun, Yves V.; Sherratt, David; Grangeasse, Christophe
In every living organism, cell division requires accurate identification of the division site and placement of the division machinery. In bacteria, this process is traditionally considered to begin with the polymerization of the highly conserved tubulin-like protein FtsZ into a ring that locates precisely at midcell1. Over the last decades, several systems have been reported to regulate the spatiotemporal assembly and placement of the FtsZ-ring2-5. However, the human pathogen Streptococcus pneumoniae, as many other organisms, is devoid of these canonical systems and the mechanisms of positioning of the division machinery remain unknown4,6. Here we characterize a novel factor that locates at the division site before FtsZ and guides septum positioning in the pneumococcus. MapZ (Midcell Anchored Protein Z) forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. MapZ then positions the FtsZ-ring through direct protein-protein interactions. MapZ-mediated control differs from previously described systems mostly based on negative regulation of FtsZ assembly. Further, MapZ is an endogenous target of the ser/thr-kinase StkP, which was recently shown to play a central role in cytokinesis and morphogenesis of the pneumococcus7-9. We show that both phosphorylated and non-phosphorylated forms of MapZ are required for proper Z-ring formation and dynamics. Altogether, this work uncovers a new mechanism for bacterial cell division that is regulated by phosphorylation and illustrates that nature has evolved a diversity of cell division mechanisms adapted to the different bacterial clades. PMID:25470041
Digital geologic map database of the Nevada Test Site area, Nevada
Ronald R. Wahl; David A. Sawyer; Scott A. Minor; Michael D. Carr; James C. Cole; W. C. Swadley; Randell J. Laczniak; Richard G. Warren; Katryn S. Green; Colin M. Engle
Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly
R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping
Broman, Karl W.
Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl's static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data. PMID:25527287
Interactive computer methods for generating mineral-resource maps
Calkins, James Alfred; Crosby, A.S.; Huffman, T.E.; Clark, A.L.; Mason, G.T.; Bascle, R.J.
Inasmuch as maps are a basic tool of geologists, the U.S. Geological Survey's CRIB (Computerized Resources Information Bank) was constructed so that the data it contains can be used to generate mineral-resource maps. However, by the standard methods used-batch processing and off-line plotting-the production of a finished map commonly takes 2-3 weeks. To produce computer-generated maps more rapidly, cheaply, and easily, and also to provide an effective demonstration tool, we have devised two related methods for plotting maps as alternatives to conventional batch methods. These methods are: 1. Quick-Plot, an interactive program whose output appears on a CRT (cathode-ray-tube) device, and 2. The Interactive CAM (Cartographic Automatic Mapping system), which combines batch and interactive runs. The output of the Interactive CAM system is final compilation (not camera-ready) paper copy. Both methods are designed to use data from the CRIB file in conjunction with a map-plotting program. Quick-Plot retrieves a user-selected subset of data from the CRIB file, immediately produces an image of the desired area on a CRT device, and plots data points according to a limited set of user-selected symbols. This method is useful for immediate evaluation of the map and for demonstrating how trial maps can be made quickly. The Interactive CAM system links the output of an interactive CRIB retrieval to a modified version of the CAM program, which runs in the batch mode and stores plotting instructions on a disk, rather than on a tape. The disk can be accessed by a CRT, and, thus, the user can view and evaluate the map output on a CRT immediately after a batch run, without waiting 1-3 days for an off-line plot. The user can, therefore, do most of the layout and design work in a relatively short time by use of the CRT, before generating a plot tape and having the map plotted on an off-line plotter.
Mapping the sevoflurane-binding sites of calmodulin
Brath, Ulrika; Lau, Kelvin; Van Petegem, Filip; Erdélyi, Máté
General anesthetics, with sevoflurane (SF) being the first choice inhalational anesthetic agent, provide reversible, broad depressor effects on the nervous system yet have a narrow margin of safety. As characterization of low-affinity binding interactions of volatile substances is exceptionally challenging with the existing methods, none of the numerous cellular targets proposed as chief protagonists in anesthesia could yet be confirmed. The recognition that most critical functions modulated by volatile anesthetics are under the control of intracellular Ca2+ concentration, which in turn is primarily regulated by calmodulin (CaM), motivated us for characterization of the SF–CaM interaction. Solution NMR (Nuclear Magnetic Resonance) spectroscopy was used to identify SF-binding sites using chemical shift displacement, NOESY and heteronuclear Overhauser enhancement spectroscopy (HOESY) experiments. Binding affinities were measured using ITC (isothermal titration calorimetry). SF binds to both lobes of (Ca2+)4-CaM with low mmol/L affinity whereas no interaction was observed in the absence of Ca2+. SF does not affect the calcium binding of CaM. The structurally closely related SF and isoflurane are shown to bind to the same clefts. The SF-binding clefts overlap with the binding sites of physiologically relevant ion channels and bioactive small molecules, but the binding affinity suggests it could only interfere with very weak CaM targets. PMID:25505574
A sequence-tagged site map of human chromosome 11
Smith, M.W.; Clark, S.P.; Hutchinson, J.S. (Salk Institute for Biological Studies, La Jolla, CA (United States))
The authors report the construction of 370 sequence-tagged sites (STSs) that are detectable by PCR amplification under sets of standardized conditions and that have been regionally mapped to human chromosome 11. DNA sequences were determined by sequencing directly from cosmid templates using primers complementary to T3 and T7 promoters present in the cloning vector. Oligonucleotide PCR primers were predicted by computer and tested using a battery of genomic DNAs. Cosmids were regionally localized on chromosome 11 by using fluorescence in situ hybridization or by analyzing a somatic cell hybrid panel. Additional STSs corresponding to known genes and markers on chromosome 11 were also produced under the same series of standardized conditions. The resulting STSs provide uniform coverage of chromosome 11 with an average spacing of 340 kb. The DNA sequence determined for use in STS production corresponds to about 0.1% (116 kb) of chromosome 11 and has been analyzed for the presence of repetitive sequences, similarities to known genes and motifs, and possible exons. Computer analysis of this sequence has identified and therefore mapped at least eight new genes on chromosome 11. 44 refs., 3 figs, 5 tabs.
Epstein–Barr virus and virus human protein interaction maps
Calderwood, Michael A.; Venkatesan, Kavitha; Xing, Li; Chase, Michael R.; Vazquez, Alexei; Holthaus, Amy M.; Ewence, Alexandra E.; Li, Ning; Hirozane-Kishikawa, Tomoko; Hill, David E.; Vidal, Marc; Kieff, Elliott; Johannsen, Eric
A comprehensive mapping of interactions among Epstein–Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on EBV strategies for replication and persistence. Interactions of EBV proteins with each other and with human proteins were assessed by using a stringent high-throughput yeast two-hybrid system. Overall, 43 interactions between EBV proteins and 173 interactions between EBV and human proteins were identified. EBV–EBV and EBV–human protein interaction, or "interactome" maps provided a framework for hypotheses of protein function. For example, LF2, an EBV protein of unknown function interacted with the EBV immediate early R transactivator (Rta) and was found to inhibit Rta transactivation. From a broader perspective, EBV genes can be divided into two evolutionary classes, "core" genes, which are conserved across all herpesviruses and subfamily specific, or "noncore" genes. Our EBV–EBV interactome map is enriched for interactions among proteins in the same evolutionary class. Furthermore, human proteins targeted by EBV proteins were enriched for highly connected or "hub" proteins and for proteins with relatively short paths to all other proteins in the human interactome network. Targeting of hubs might be an efficient mechanism for EBV reorganization of cellular processes. PMID:17446270
Interaction sites of DivIVA and RodA from Corynebacterium glutamicum
Sieger, Boris; Bramkamp, Marc
Elongation growth in actinobacteria is localized at the cell poles. This is in contrast to many classical model organisms where insertion of new cell wall material is localized around the lateral site. We previously described a role of RodA from Corynebacterium glutamicum in apical cell growth and morphogenesis. Deletion of rodA had drastic effects on morphology and growth, likely a result from misregulation of penicillin-binding proteins and cell wall precursor delivery. We identified the interaction of RodA with the polar scaffold protein DivIVA, thus explaining subcellular localization of RodA to the cell poles. In this study, we describe this interaction in detail and map the interaction sites of DivIVA and RodA. A single amino acid residue in the N-terminal domain of DivIVA was found to be crucial for the interaction with RodA. The interaction site of RodA was mapped to its cytoplasmic, C-terminal domain, in a region encompassing the last 10 amino acids (AAs). Deletion of these 10 AAs significantly decreased the interaction efficiency with DivIVA. Our results corroborate the interaction of DivIVA and RodA, underscoring the important role of DivIVA as a spatial organizer of the elongation machinery in Corynebacterineae. PMID:25709601
Mapping the phase diagram of strongly interacting matter
Skokov, V.; Morita, K.; Friman, B. [GSI Helmholtzzentrum fuer Schwerionenforschung, D-64291 Darmstadt (Germany)
We employ a conformal mapping to explore the thermodynamics of strongly interacting matter at finite values of the baryon chemical potential {mu}. This method allows us to identify the singularity corresponding to the critical point of a second-order phase transition at finite {mu}, given information only at {mu}=0. The scheme is potentially useful for computing thermodynamic properties of strongly interacting hot and dense matter in lattice gauge theory. The technique is illustrated by an application to a chiral effective model.
Interactive Maps from the Great Basin Center for Geothermal Energy
The Great Basin Center for Geothermal Energy, part of the University of Nevada, Reno, conducts research towards the establishment of geothermal energy as an economically viable energy source within the Great Basin. The Center specializes in collecting and synthesizing geologic, geochemical, geodetic, geophysical, and tectonic data, and using Geographic Information System (GIS) technology to view and analyze this data and to produce favorability maps of geothermal potential. The interactive maps are built with layers of spatial data that are also available as direct file downloads (see DDE00299). The maps allow analysis of these many layers, with various data sets turned on or off, for determining potential areas that would be favorable for geothermal drilling or other activity. They provide information on current exploration projects and leases, Bureau of Land Management land status, and map presentation of each type of scientific spatial data: geothermal, geophysical, geologic, geodetic, groundwater, and geochemical.
Interactive Maps of Science and Technology Dr. Katy Brner
Bustamante, Fabián E.
Interactive Maps of Science and Technology Dr. Katy Börner Cyberinfrastructure for Network Science for Network Science Center team and the VIVO Team. 3rd International Workshop on Network Theory: "Web Science meets Network Science" Northwestern University. March 4-5, 2011 http://scimaps.org/flat/meeting/100304
Multimodal Interaction with a Map-Based Simulation System
Kenneth Wauchope
LACE was originally developed for the Symbolics Lisp machine, where it had a graphical interface con- sisting of an interactive Map Display System and two tools, the Hierarchy and Rack Systems, for viewing object hierarchies and monitoring the simulation run. We acquired a Common LISP port of LACE (minus the graphical interface) distributed as a testbed application with the TEXPLAN
Mapping protein binding sites on the biomolecular corona of nanoparticles
NASA Astrophysics Data System (ADS)
Kelly, Philip M.; Ĺberg, Christoffer; Polo, Ester; O'Connell, Ann; Cookman, Jennifer; Fallon, Jonathan; Krpeti?, Željka; Dawson, Kenneth A.
Nanoparticles in a biological milieu are known to form a sufficiently long-lived and well-organized 'corona' of biomolecules to confer a biological identity to the particle. Because this nanoparticle–biomolecule complex interacts with cells and biological barriers, potentially engaging with different biological pathways, it is important to clarify the presentation of functional biomolecular motifs at its interface. Here, we demonstrate that by using antibody-labelled gold nanoparticles, differential centrifugal sedimentation and various imaging techniques it is possible to identify the spatial location of proteins, their functional motifs and their binding sites. We show that for transferrin-coated polystyrene nanoparticles only a minority of adsorbed proteins exhibit functional motifs and the spatial organization appears random, which is consistent, overall, with a stochastic and irreversible adsorption process. Our methods are applicable to a wide array of nanoparticles and can offer a microscopic molecular description of the biological identity of nanoparticles.
LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains.
Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernández-Recio, Juan; Gupta, Rishabh; Bent, Andrew
Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM), a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP) receptors, EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2). In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area), Consurf, and PAML (positive selection) analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains. PMID:21789174
LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains
Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernández-Recio, Juan; Gupta, Rishabh; Bent, Andrew
Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM), a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP) receptors, EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2). In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area), Consurf, and PAML (positive selection) analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains. PMID:21789174
Large Scale Wind Turbine Siting Map Report NJ Department of Environmental Protection
Holberton, Rebecca L.
Large Scale Wind Turbine Siting Map Report NJ Department of Environmental Protection September 8 Jersey Department of Environmental Protection's (NJDEP) "Large Scale Wind Turbine Siting Map Management rules to address the development and permitting of wind turbines in the coastal zone
Bayesian Hidden Markov Models to Identify RNA-Protein Interaction Sites in PAR-CLIP
Yun, Jonghyun; Wang, Tao; Xiao, Guanghua
Summary The photoactivatable ribonucleoside enhanced cross-linking immunoprecipitation (PAR-CLIP) has been increasingly used for the global mapping of RNA-protein interaction sites. There are two key features of the PAR-CLIP experiments: The sequence read tags are likely to form an enriched peak around each RNA-protein interaction site; and the cross-linking procedure is likely to introduce a specific mutation in each sequence read tag at the interaction site. Several ad hoc methods have been developed to identify the RNA-protein interaction sites using either sequence read counts or mutation counts alone; however, rigorous statistical methods for analyzing PAR-CLIP are still lacking. In this study, we propose an integrative model to establish a joint distribution of observed read and mutation counts. To pinpoint the interaction sites at single base-pair resolution, we developed a novel modeling approach that adopts non-homogeneous hidden Markov models to incorporate the nucleotide sequence at each genomic location. Both simulation studies and data application showed that our method outperforms the ad hoc methods, and provides reliable inferences for the RNA-protein binding sites from PAR-CLIP data. PMID:24571656
NSDL National Science Digital Library
United States Department of the Interior
This interactive mapping site allows users to build maps of any portion of the United States including overlays of many different kinds of data. Some of the categories of data available include agriculture, biology, climate, environment, geology, and water. The maps are printable and savable and can be shared with others via email.
NSDL National Science Digital Library
From the California Geological Survey, the Online Maps and Data site contains information focused on natural hazards. Topics include minerals, earthquakes, and landslide and erosion hazards. The site also includes the General Location Guide for Ultramafic Rocks in California. The site also has links to a publications page and a new interactive mapping program called the Seismic Hazards Mapping Web page.
Integrated Mapping and Imaging at a Legacy Test Site (Invited)
NASA Astrophysics Data System (ADS)
Sussman, A. J.; Schultz-Fellenz, E. S.; Kelley, R. E.; Sweeney, J. J.; Vigil, S.; DiBenedetto, J.; Chipman, V.
A team of multi-disciplinary geoscientists was tasked to characterize and evaluate a legacy nuclear detonation site in order to develop research locations with the long-term goal of improving treaty monitoring, verification, and other national security applications. There was a test at the site of interest that was detonated on June 12, 1985 in a vertical emplacement borehole at a depth of 608m below the surface in rhyolites. With announced yield of 20-150 kt, the event did not collapse to the surface and form a crater, but rather experienced a subsurface collapse with more subtle surface expressions of deformation. This result provides the team with an opportunity to evaluate a number of surface and subsurface inspection technologies in a broad context. The team collected ground-based visual observation, ground penetrating radar, electromagnetic, ground-based and airborne LiDAR, ground-based and airborne hyperspectral, gravity and magnetics, dc and induction electrical methods, and active seismic data during field campaigns in the summers of 2012 and 2013. Detection of features was performed using various approaches that were assessed for accuracy, efficiency and diversity of target features. For example, whereas the primary target of the ground-based visual observation survey was to map the surface features, the target of the gravity survey was to attempt the detection of a possible subsurface collapse zone which might be located as little as 200 meters below the surface. The datasets from surveys described above are integrated into a geographical information system (GIS) database for analysis and visualization. Other presentations during this session provide further details as to some of the work conducted. Work by Los Alamos National Laboratory and Lawrence Livermore National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946/NST10-NCNS-PD00. Work by National Security Technologies, LLC, was performed under Contract No. DE AC52 06NA25946 with the U.S. Department of Energy. Sandia National Laboratories, is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Methods for Mapping of Interaction Networks Involving Membrane Proteins
Hooker, Brian S.; Bigelow, Diana J.; Lin, Chiann Tso
Numerous approaches have been taken to study protein interactions, such as tagged protein complex isolation followed by mass spectrometry, yeast two-hybrid methods, fluorescence resonance energy transfer, surface plasmon resonance, site-directed mutagenesis, and crystallography. Membrane protein interactions pose significant challenges due to the need to solubilize membranes without disrupting protein-protein interactions. Traditionally, analysis of isolated protein complexes by high-resolution 2D gel electrophoresis has been the main method used to obtain an overall picture of proteome constituents and interactions. However, this method is time consuming, labor intensive, detects only abundant proteins and is not suitable for the coverage required to elucidate large interaction networks. In this review, we discuss the application of various methods to elucidate interactions involving membrane proteins. These techniques include methods for the direct isolation of single complexes or interactors as well as methods for characterization of entire subcellular and cellular interactomes.
NSDL National Science Digital Library
Christopher Griffith
This collection presents maps of blast and fire damage to Hiroshima and Nagasaki, Japan, and the radioactive fallout levels from the Trinity and BRAVO tests. The collection also includes maps of Manhattan Project Era Sites (Hanford, Washington, Oak Ridge, Tennessee, and Los Alamos, New Mexico).
Prediction of proteinprotein interaction sites in heterocomplexes with neural networks
Pazos, Florencio
Prediction of proteinÂprotein interaction sites in heterocomplexes with neural networks Piero on information about evolutionary con- servation and surface disposition. We implement a neural network based protein sur- face. However neural networks trained with a reduced representation of the interacting patch
Prediction protein--protein interaction sites heterocomplexes with neural networks
Pazos, Florencio
Prediction protein--protein interaction sites heterocomplexes with neural networks Piero Fariselli neural network based system, which a cross validation proce dure and allows correct detection 73 face. However neural networks trained a reduced representation of interacting patch sequence profile su
Developing a map of geologically defined site-condition categories for California
Wills, C.J.; Clahan, K.B.
Consideration of site conditions is a vital step in analyzing and predicting earthquake ground motion. The importance of amplification by soil conditions has long been recognized, but though many seismic-instrument sites have been characterized by their geologic conditions, there has been no consistent, simple classification applied to all sites. As classification of sites by shear-wave velocity has become more common, the need to go back and provide a simple uniform classification for all stations has become apparent. Within the Pacific Earthquake Engineering Research Center's Next Generation Attenuation equation project, developers of attenuation equations recognized the need to consider site conditions and asked that the California Geological Survey provide site conditions information for all stations that have recorded earthquake ground motion in California. To provide these estimates, we sorted the available shear-wave velocity data by geologic unit, generalized the geologic units, and prepared a map so that we could use the extent of the map units to transfer the velocity characteristics from the sites where they were measured to sites on the same or similar materials. This new map is different from the California Geological Survey "preliminary site-conditions map of California" in that 19 geologically defined categories are used, rather than National Earthquake Hazards Reduction Program categories. Although this map does not yet cover all of California, when completed it may provide a basis for more precise consideration of site conditions in ground-motion calculations.
Genome-wide map of regulatory interactions in the human genome
Heidari, Nastaran; Phanstiel, Douglas H.; He, Chao; Grubert, Fabian; Jahanbani, Fereshteh; Kasowski, Maya; Zhang, Michael Q.
Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer–promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus. PMID:25228660
Learning to merge: a new tool for interactive mapping
NASA Astrophysics Data System (ADS)
Porter, Reid B.; Lundquist, Sheng; Ruggiero, Christy
The task of turning raw imagery into semantically meaningful maps and overlays is a key area of remote sensing activity. Image analysts, in applications ranging from environmental monitoring to intelligence, use imagery to generate and update maps of terrain, vegetation, road networks, buildings and other relevant features. Often these tasks can be cast as a pixel labeling problem, and several interactive pixel labeling tools have been developed. These tools exploit training data, which is generated by analysts using simple and intuitive paint-program annotation tools, in order to tailor the labeling algorithm for the particular dataset and task. In other cases, the task is best cast as a pixel segmentation problem. Interactive pixel segmentation tools have also been developed, but these tools typically do not learn from training data like the pixel labeling tools do. In this paper we investigate tools for interactive pixel segmentation that also learn from user input. The input has the form of segment merging (or grouping). Merging examples are 1) easily obtained from analysts using vector annotation tools, and 2) more challenging to exploit than traditional labels. We outline the key issues in developing these interactive merging tools, and describe their application to remote sensing.
Mapping the Vertical Structure of the Lunar Regolith in Volcanic Regions and at Constellation Sites
NASA Astrophysics Data System (ADS)
Carter, L. M.; Ghent, R. R.; Bandfield, J. L.; Campbell, B. A.
The upper ten meters of the lunar regolith contains stratigraphy that provides geologic insight, and these upper layers are also what future in-situ instruments will interact with. We use a combination of remote sensing data from ground-based radar observations (Arecibo and Green Bank Telescope at wavelengths of 12.6 cm and 70 cm) and the Lunar Reconnaissance Orbiter spacecraft (Diviner, Mini-RF) to determine how the regolith structure varies across volcanic terrains and possible future landing sites. Radar can detect buried units and provide a measure of roughness, while thermal infrared data provides complimentary information on the surface and near-surface rock abundance in the upper centimeters. Radar and infrared wavelengths are also sensitive to different sized rocks, which can be used to determine where there are increased numbers centimeter-sized rocks. A comparison of these data sets reveals significant differences in regolith stratigraphy across targets. For example, small rilles on the Aristarchus Plateau to the northeast of the Constellation Aristarchus 2 site are surrounded by rock-poor deposits and are likely a secondary source of pyroclastic materials. Some rilles, such as Rima Birt, are surrounded by pyroclastics that change in depth and/or embedded rock abundance along the length of the rille. We will present results from our data analysis and subsequent mapping, focusing on rilles, pyroclastic deposits, and Constellation Region of Interest targets including the Apollo sites.
Coal Mine Information System Map Viewer The Coal Mine Information System (CMIS) Web site was created to provide online access to maps showing
Polly, David
Coal Mine Information System Map Viewer Purpose The Coal Mine Information System (CMIS) Web site was created to provide online access to maps showing locations of coal mines in Indiana. Funding. The CMIS Web site allows users to create maps showing the locations of surface and underground coal mines
Validation of Innovative Exploration Technologies for Newberry Volcano: Drill Site Location Map 2010
Jaffe, Todd
Newberry project drill site location map 2010. Once the exploration mythology is validated, it can be applied throughout the Cascade Range and elsewhere to locate and develop "blind" geothermal resources.
The Shark-Search Algorithm. An Application: Tailored Web Site Mapping
Michael Herscovici; Michal Jacovi; Yoëlle S. Maarek; Dan Pelleg; Menachem Shtalhaim; Ur Sigalit
This paper introduces the "shark search" algorithm, a refined version of one of the first dynamic Web search algorithms, the "fish search". The shark-search has been embodied into a dynamic Web site mapping that enables users to tailor Web maps to their interests. Preliminary experiments show significant improvements over the original fish-search algorithm.
Is it enough to have one ECa map for the site-specific management delineation?
Technology Transfer Automated Retrieval System (TEKTRAN)
The soil apparent electrical conductivity (ECa) has been used to map soil spatial variability and to relate it to the variability of various soil properties thus delineating zones of site-specific management. Most often, a single ECa survey is done and the generated ECa map is considered to infer t...
Preliminary Correlation Map of Geomorphic Surfaces in North-Central Frenchman Flat, Nevada Test Site
Bechtel Nevada
This correlation map (scale = 1:12,000) presents the results of a mapping initiative that was part of the comprehensive site characterization required to operate the Area 5 Radioactive Waste Management Site, a low-level radioactive waste disposal facility located in northern Frenchman Flat at the Nevada Test Site. Eight primary map units are recognized for Quaternary surfaces: remnants of six alluvial fan or terrace surfaces, one unit that includes colluvial aprons associated with hill slopes, and one unit for anthropogenically disturbed surfaces. This surficial geology map provides fundamental data on natural processes for reconstruction of the Quaternary history of northern Frenchman Flat, which in turn will aid in the understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. The bedrock units identified on this map were derived from previous published mapping efforts and are included for completeness.
Final report for the project "Improving the understanding of surface-atmosphere radiative interactions by mapping surface reflectance over the ARM CART site" (award DE-FG02-02ER63351)
Alexander P. Trishchenko; Yi Luo; Konstantin V. Khlopenkov, William M. Park; Zhanqing Li; Maureen Cribb
Surface spectral reflectance (albedo) is a fundamental variable affecting the transfer of solar radiation and the Earth's climate. It determines the proportion of solar energy absorbed by the surface and reflected back to the atmosphere. The International Panel on Climate Change (IPCC) identified surface albedo among key factors influencing climate radiative forcing. Accurate knowledge of surface reflective properties is important for advancing weather forecasting and climate change impact studies. It is also important for determining radiative impact and acceptable levels of greenhouse gases in the atmosphere, which makes this work strongly linked to major scientific objectives of the Climate Change Research Division (CCRD) and Atmospheric Radiation Measurement (ARM) Program. Most significant accomplishments of eth project are listed below. I) Surface albedo/BRDF datasets from 1995 to the end of 2004 have been produced. They were made available to the ARM community and other interested users through the CCRS public ftp site ftp://ftp.ccrs.nrcan.gc.ca/ad/CCRS_ARM/ and ARM IOP data archive under "PI data Trishchenko". II) Surface albedo properties over the ARM SGP area have been described for 10-year period. Comparison with ECMWF data product showed some deficiencies in the ECMWF surface scheme, such as missing some seasonal variability and no dependence on sky-conditions which biases surface energy budget and has some influence of the diurnal cycle of upward radiation and atmospheric absorption. III) Four surface albedo Intensive Observation Period (IOP) Field Campaigns have been conducted for every season (August, 2002, May 2003, February 2004 and October 2004). Data have been prepared, documented and transferred to ARM IOP archive. Nine peer-reviewed journal papers and 26 conference papers have been published.
A Genetic Mapping System in Caenorhabditis Elegans Based on Polymorphic Sequence-Tagged Sites
Williams, B. D.; Schrank, B.; Huynh, C.; Shownkeen, R.; Waterston, R. H.
We devised an efficient genetic mapping system in the nematode Caenorhabditis elegans which is based upon the differences in number and location of the transposable element Tc1 between the Bristol and Bergerac strains. Using the nearly completed physical map of the C. elegans genome, we selected 40 widely distributed sites which contain a Tc1 element in the Bergerac strain, but not in the Bristol strain. For each site a polymerase chain reaction assay was designed that can distinguish between the Bergerac Tc1-containing site and the Bristol ``empty'' site. By combining appropriate assays in a single reaction, one can score multiple sites within single worms. This permits a mutation to be rapidly mapped, first to a linkage group and then to a chromosomal subregion, through analysis of only a small number of progeny from a single interstrain cross. PMID:1321065
Mapping site-specific endonuclease binding to DNA by direct imaging with AFM
Allison, D.P.; Thundat, T.; Doktycz, M.J.; Kerper, P.S.; Warmack, R.J. [Oak Ridge National Lab., TN (United States). Health Sciences Research Div.; Modrich, P. [Duke Univ. Medical Center, Durham, NC (United States). Dept. of Biochemistry; Isfort, R.J. [Procter and Gamble Co., Cincinnati, OH (United States)
Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10{sup 4}, the authors demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS{sup +}) or two (pMP{sup 32}) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in the preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.
Ecoregions of North Dakota and South Dakota: Interactive Map
NSDL National Science Digital Library
Ecoregions denote areas of general similarity in ecosystems and in the type, quality, and quantity of environmental resources. They are designed to serve as a spatial framework for the research, assessment, management, and monitoring of ecosystems and ecosystem components. This interactive map shows the ecoregions of North and South Dakota in increasing levels of detail (from level III to level IV). Clicking on the legend shows information for each type of ecoregion, including a photo and description, physiography, geology, soils type, climate, natural vegetation types, and land use/land cover. A downloadable version is available.
Landing Site Selection and Surface Traverse Planning using the Lunar Mapping & Modeling Portal
NASA Astrophysics Data System (ADS)
Law, E.; Chang, G.; Bui, B.; Sadaqathullah, S.; Kim, R.; Dodge, K.; Malhotra, S.
Introduction: The Lunar Mapping and Modeling Portal (LMMP), is a web-based Portal and a suite of interactive visualization and analysis tools for users to access mapped lunar data products (including image mosaics, digital elevation models, etc.) from past and current lunar missions (e.g., Lunar Reconnaissance Orbiter, Apollo, etc.), and to perform in-depth analyses to support lunar surface mission planning and system design for future lunar exploration and science missions. It has been widely used by many scientists mission planners, as well as educators and public outreach (e.g., Google Lunar XPRICE teams, RESOLVE project, museums etc.) This year, LMMP was used by the Lunar and Planetary Institute (LPI)'s Lunar Exploration internship program to perform lighting analysis and local hazard assessments, such as, slope, surface roughness and crater/boulder distribution to research landing sites and surface pathfinding and traversal. Our talk will include an overview of LMMP, a demonstration of the tools as well as a summary of the LPI Lunar Exploration summer interns' experience in using those tools.
Fengliang Xu
Our project aims to automate Mars mapping and localization using robotic stereo and descent imagery. Stereo vision is a well- studied domain. However, most efforts aim only at a general scene; little work has been done toward a natural, extraterrestrial environment through consideration of its special geometry and features. Our methodology utilized the properties of piece-wise continuity of natural scene
Web GIS in practice III: creating a simple interactive map of England's Strategic Health Authorities using Google Maps API, Google Earth KML, and MSN Virtual Earth Map Control
Maged N Kamel Boulos
This eye-opener article aims at introducing the health GIS community to the emerging online consumer geoinformatics services from Google and Microsoft (MSN), and their potential utility in creating custom online interactive health maps. Using the programmable interfaces provided by Google and MSN, we created three interactive demonstrator maps of England's Strategic Health Authorities. These can be browsed online at http:\\/\\/www.healthcybermap.org\\/GoogleMapsAPI\\/
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI)1
Coulombe, Benoit; Blanchette, Mathieu; Jeronimo, Célia
Defining human protein interaction networks has become essential to develop an overall, systems-based understanding of the molecular events that sustain cell growth in normal and disease conditions. To characterize protein interaction networks from human cells, we have undertaken the development of a systematic, unbiased technology pipeline that couples experimental and computational approaches. This discovery engine is central to the Human Proteotheque Initiative (HuPI), a multidisciplinary project aimed at building a repertoire of comprehensive maps of human protein interaction networks, the Human Proteotheque. The information contained in the Proteotheque is made publicly available through an interactive web site that can be consulted to visualize some of the fundamental molecular connections formed in human cells and to determine putative functions of previously uncharacterized proteins based on guilt by association. The process governing the evolution of HuPI towards becoming a repository of accurate and complete protein interaction maps is described. PMID:18443628
Orbital-science investigation: Part K: geologic sketch map of the candidate Proclus Apollo landing site
Lucchitta, Baerbel Koesters
A panoramic camera frame (fig. 25-69) was used as the base for a geologic sketch map (fig. 25-70) of an area near Proclus Crater. The map was prepared to investigate the usefulness of the Apollo 15 panoramic camera photography in large-scale geologic mapping and to assess the geologic value of this area as a potential Apollo landing site. The area is being considered as a landing site because of the availability of smooth plains terrain and because of the scientific value of investigating plains materials, dark halo craters, and ancient rocks that may be present in the Proclus ray material.
Constraint-based simulation of biological systems described by Molecular Interaction Maps
Bortolussi, Luca
Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca of biochemical networks de- scribed by the graphical notation of Molecular Interaction Maps. Such maps generating the full list of reactions. 1 Introduction The aim of this work is the simulation of biological
A novel approach in model-based mapping of soil water conditions at forest sites
Kai Schwärzel; Karl-Heinz Feger; Janet Häntzschel; Alexander Menzer; Uwe Spank; Falko Clausnitzer; Barbara Köstner; Christian Bernhofer
Knowledge of site-specific water conditions is important in forestland evaluation and fundamental for a sustainable forest management. In Central Europe, traditional site mapping has followed an integrated ecological approach. The assessment of soil water availability is based on overlaying relief and descriptive soil information. It is a relative system referring to an (hypothetical) equilibrium between relief-dependent soil conditions and the
Digital geologic map database of the Nevada Test Site area, Nevada
Wahl, R.R.; Sawyer, D.A.; Minor, S.A.; Carr, M.D.; Cole, J.C.; Swadley, W.C.; Laczniak, R.J.; Warren, R.G.; Green, K.S.; Engle, C.M.
Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.
Digital geologic map database of the Nevada Test Site area, Nevada
Wahl, Ronald R.; Sawyer, David A.; Minor, Scott A.; Carr, Michael D.; Cole, James C.; Swadley, W.C.; Laczniak, Randell J.; Warren, Richard G.; Green, Katryn S.; Engle, Colin M.
Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients. The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.
Mapping Peptide Hormone–Receptor Interactions Using a Disulfide-Trapping Approach†
Monaghan, Paul; Thomas, Beena E.; Woznica, Iwona; Wittelsberger, Angela; Mierke, Dale F.; Rosenblatt, Michael
Efforts to elucidate the nature of the bimolecular interaction of parathyroid hormone (PTH) with its cognate receptor, the PTH receptor type 1 (PTHR1), have relied heavily on benzoylphenylalanine- (Bpa-) based photoaffinity cross-linking. However, given the flexibility, size, and shape of Bpa, the resolution at the PTH–PTHR1 interface appears to be reaching the limit of this technique. Here we employ a disulfide-trapping approach developed by others primarily for use in screening compound libraries to identify novel ligands. In this method, cysteine substitutions are introduced into a specific site within the ligand and a region in the receptor predicted to interact with each other. Upon ligand binding, if these cysteines are in close proximity, they form a disulfide bond. Since the geometry governing disulfide bond formation is more constrained than Bpa cross-linking, this novel approach can be employed to generate a more refined molecular model of the PTH–PTHR1 complex. Using a PTH analogue containing a cysteine at position 1, we probed 24 sites and identified 4 in PTHR1 to which cross-linking occurred. Importantly, previous photoaffinity cross-linking studies using a PTH analogue with Bpa at position 1 only identified a single interaction site. The new sites identified by the disulfide-trapping procedure were used as constraints in molecular dynamics simulations to generate an updated model of the PTH–PTHR1 complex. Mapping by disulfide trapping extends and complements photoaffinity cross-linking. It is applicable to other peptide–receptor interfaces and should yield insights about yet unknown sites of ligand–receptor interactions, allowing for generation of more refined models. PMID:18459800
Mapping peptide hormone-receptor interactions using a disulfide-trapping approach.
Monaghan, Paul; Thomas, Beena E; Woznica, Iwona; Wittelsberger, Angela; Mierke, Dale F; Rosenblatt, Michael
Efforts to elucidate the nature of the bimolecular interaction of parathyroid hormone (PTH) with its cognate receptor, the PTH receptor type 1 (PTHR1), have relied heavily on benzoylphenylalanine- (Bpa-) based photoaffinity cross-linking. However, given the flexibility, size, and shape of Bpa, the resolution at the PTH-PTHR1 interface appears to be reaching the limit of this technique. Here we employ a disulfide-trapping approach developed by others primarily for use in screening compound libraries to identify novel ligands. In this method, cysteine substitutions are introduced into a specific site within the ligand and a region in the receptor predicted to interact with each other. Upon ligand binding, if these cysteines are in close proximity, they form a disulfide bond. Since the geometry governing disulfide bond formation is more constrained than Bpa cross-linking, this novel approach can be employed to generate a more refined molecular model of the PTH-PTHR1 complex. Using a PTH analogue containing a cysteine at position 1, we probed 24 sites and identified 4 in PTHR1 to which cross-linking occurred. Importantly, previous photoaffinity cross-linking studies using a PTH analogue with Bpa at position 1 only identified a single interaction site. The new sites identified by the disulfide-trapping procedure were used as constraints in molecular dynamics simulations to generate an updated model of the PTH-PTHR1 complex. Mapping by disulfide trapping extends and complements photoaffinity cross-linking. It is applicable to other peptide-receptor interfaces and should yield insights about yet unknown sites of ligand-receptor interactions, allowing for generation of more refined models. PMID:18459800
Soils maps supplement to soil moisture ground truth, Lafayette, Indiana, site St. Charles, Missouri, site
NASA Technical Reports Server (NTRS)
Jones, E. B.; Olt, S. E.
A compilation of soils information obtained as the result of a library search of data on the Lafayette, Indiana, site and St. Charles, Missouri, site is presented. Soils data for the Lafayette, Indiana, site are shown in Plates 1 and 2; and soils data for the St. Charles, Missouri, site are shown in Plates 3 and 4.
Comparison of Kriging and coKriging for soil contamination mapping in abandoned mine sites
NASA Astrophysics Data System (ADS)
Lee, Hyeongyu; Choi, Yosoon
Soil contamination mapping around abandoned mines is an important task for the planning and design of mine reclamation. This study compared the ordinary Kriging and the co-Kriging methods for the soil contamination mapping in abandoned mine sites. Four approaches were conducted as follows: (1) soil contamination mapping using the ordinary Kriging and Inductively Coupled Plasma (ICP) data only; (2) soil contamination mapping using the ordinary Kriging and Portable X-Ray Fluorescence (PXRF) data only; (3) soil contamination mapping using the ordinary Kriging and integrated data from ICP and PXRF; and (4) soil contamination mapping using the co-Kriging and integrated data from ICP and PXRF. Results indicate that the approach 3 provides substantial improvements over other three approaches including a more reasonable spatial pattern of soil contamination and reduction in the error of its estimates.
Delineating the functional map of the interaction between nimotuzumab and the epidermal growth factor receptor.
Tundidor, Yaima; García-Hernández, Claudia Patricia; Pupo, Amaury; Cabrera Infante, Yanelys; Rojas, Gertrudis
Molecular details of epidermal growth factor receptor (EGFR) targeting by nimotuzumab, a therapeutic anti-cancer antibody, have been largely unknown. The current study delineated a functional map of their interface, based on phage display and extensive mutagenesis of both the target antigen and the Fv antibody fragment. Five residues in EGFR domain III (R353, S356, F357, T358, and H359T) and the third hypervariable region of nimotuzumab heavy chain were shown to be major functional contributors to the interaction. Fine specificity differences between nimotuzumab and other anti-EGFR antibodies were revealed. Mapping information guided the generation of a plausible in silico binding model. Knowledge about the epitope/paratope interface opens new avenues for the study of tumor sensitivity/resistance to nimotuzumab and for further engineering of its binding site. The developed mapping platform, also validated with the well-known cetuximab epitope, allows a comprehensive exploration of antigenic regions and could be expanded to map other anti-EGFR antibodies. PMID:24759767
Groundwater vulnerability: Interactions of chemical and site properties
Worrall, F.; Besien, T.; Kolpin, D.W.
This study brings together extensive, multi-annual groundwater monitoring datasets from the UK and Midwestern US to test the relative importance of site (e.g. land use, soil and aquifer type) and chemical factors (e.g. solubility in water) and between and within year variations in controlling groundwater contamination by pesticides. ANOVA (general linear modelling) was used to test the significance and proportion of variation explained by each factor and their interactions. Results from both the UK and US datasets show that: (i) Chemical and site factors both have a statistically significant influence on groundwater pollution; (ii) Site factors on their own explain a greater proportion of data variance than chemical factors on their own; (iii) Interaction between site and chemical factors represents the most important control on the occurrence of pesticides in groundwater; (iv) Variation within the year was slight but still significant while there was no significant difference between data from consecutive years. The combination of factors analysed in this study were sufficient to explain the majority of the variation in the data save for that ascribable to the analytical detection limit. The results provide statistical evidence that it is viable to develop both molecular methods and groundwater vulnerability as tools to understanding pollution, but that a greater emphasis should be placed on their interaction to fully understand pesticide contamination. ?? 2002 Elsevier Science B.V. All rights reserved.
Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites
Goodman, Mark M. (Atlanta, GA); Faraj, Bahjat (Lithonia, GA)
Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.
Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites
Goodman, M.M.; Faraj, B.
Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.
Mapping substance P binding sites on the neurokinin-1 receptor using genetic incorporation of a photoreactive amino acid.
Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas; Grunbeck, Amy; Naganathan, Saranga; Schwartz, Thue W; Sakmar, Thomas P
Substance P (SP) is a neuropeptide that mediates numerous physiological responses, including transmission of pain and inflammation through the neurokinin-1 (NK1) receptor, a G protein-coupled receptor. Previous mutagenesis studies and photoaffinity labeling using ligand analogues suggested that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce the photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact with a fluorescently labeled SP analog. Notably, 10 of the receptor variants with BzF in the Nt tail and 4 of those with BzF in ECLII cross-linked efficiently to SP, indicating that these 14 sites are juxtaposed to SP in the ligand-bound receptor. These results show that two distinct regions of the NK1 receptor possess multiple determinants for SP binding and demonstrate the utility of genetically encoded photocross-linking to map complex multitopic binding sites on G protein-coupled receptors in a cell-based assay format. PMID:24831006
Geologic sketch map of the candidate Proclus Apollo landing site, part K
NASA Technical Reports Server (NTRS)
Lucchitta, B. K.
An Apollo 15 panoramic camera frame was used as a base for a geologic sketch map of an area near Proclus Crater. The map was prepared to investigate the usefulness of the panoramic camera photography in large-scale geologic mapping and to assess the geologic value of the area as a potential Apollo landing site. The photographs, taken under high solar illumination, resulted in good definition of albedo features, and stereoscopic viewing provided extreme clarity of topographic relief with terrain units easily delineated. The geological characteristics of the area as evidenced by the high-resolution photographs is discussed. It is concluded that the panoramic camera photographs reveal a wealth of detail and are eminently suited for geologic mapping purposes. In addition, the Proclus area, as a potential landing site, offers relatively rough plains terrain.
Gilbes, Fernando
HABITAT AND BIODIVERSITY MAPPING, FOR THE DETERMINATION OF ALGAL BIOMASS AQUACULTURE SITES production. Here we analyze and map coastal habitats and biodiversity for the optimum the territorial water of Puerto Rico using several factors: benthic habitats, water depth, critical habitat
Sequestration of Polo kinase to microtubules by phosphopriming-independent binding to Map205 is relieved by phosphorylation at a CDK site in mitosis
Archambault, Vincent; D'Avino, Pier Paolo; Deery, Michael J.; Lilley, Kathryn S.; Glover, David M.
The conserved Polo kinase controls multiple events in mitosis and cytokinesis. Although Polo-like kinases are regulated by phosphorylation and proteolysis, control of subcellular localization plays a major role in coordinating their mitotic functions. This is achieved largely by the Polo-Box Domain, which binds prephosphorylated targets. However, it remains unclear whether and how Polo might interact with partner proteins when priming mitotic kinases are inactive. Here we show that Polo associates with microtubules in interphase and cytokinesis, through a strong interaction with the microtubule-associated protein Map205. Surprisingly, this interaction does not require priming phosphorylation of Map205, and the Polo-Box Domain of Polo is required but not sufficient for this interaction. Moreover, phosphorylation of Map205 at a CDK site relieves this interaction. Map205 can stabilize Polo and inhibit its cellular activity in vivo. In syncytial embryos, the centrosome defects observed in polo hypomorphs are enhanced by overexpression of Map205 and suppressed by its deletion. We propose that Map205-dependent targeting of Polo to microtubules provides a stable reservoir of Polo that can be rapidly mobilized by the activity of Cdk1 at mitotic entry. PMID:18832073
Spatial games with cyclic interactions: the response of empty sites
NASA Astrophysics Data System (ADS)
Brown, Bart; Pleimling, Michel
Predator-prey models of the May-Leonard family employ empty sites in a spatial setting as an intermediate step in the reproduction process. This requirement makes the number and arrangement of empty sites important to the formation of space-time patterns. We study the density of empty sites in a stochastic predator-prey model in which the species compete in a cyclic way in two dimensions. In some cases systems of this type quickly form domains of neutral species after which all predation, and therefore, reproduction occur near the interface of competing domains. Using Monte Carlo simulations we investigate the relationship of this density of empty sites to the time-dependent domain length. We further explore the dynamics by introducing perturbations to the interaction rates of the system after which we measure the perturbed density, i.e. the response of empty sites, as the system relaxes. A dynamical scaling behavior is observed in the response of empty sites. This work is supported by the US National Science Foundation through Grant DMR-1205309.
Interactions among localized corrosion sites investigated through experiments and models
NASA Astrophysics Data System (ADS)
Lunt, Tracy T.
It has often been assumed that pitting events occur randomly in time and space and that there is no effect of one event upon another. However, when a pit begins to form and current flows, the local environment is altered. Changes can occur in the local concentration of aggressive species, the potential field and damage can occur to the passivating oxide film. These three competing effects work on different time scales and can affect electrode areas through different distances. Therefore, pitting events can have some influence on the probability of future nearby events. Current time series data collected on a single working electrode experiencing metastable pitting corrosion was first analyzed. The metastable pitting events were found to have correlation and were not randomly distributed in time. Further investigation was performed on an array of 25 working electrodes in order to obtain information on the spatial interactions among metastable and stable pitting sites. The 5-by-5 array consisted of closely spaced, 0.025 cm diameter 316 stainless steel wires. The flush-mounted wire tips were exposed to 0.05 M NaCl solution at 47°C. To examine the environmental changes created by a stable pitting site, one or more electrodes in the array were held at a 1 V vs. SCE causing the entire electrode to corrode at a high rate simulating a single large pit. Two types of interactions were observed when a pit was created in the center of the array. First, inhibition of pitting on nearby electrodes occurred due to ohmic potential drop near the actively corroding pit site. Second, enhancement of pitting was observed due to alternations in the local solution composition and oxide film created by a deactivated pitting site. The ohmic shielding effect was dominant near the active site, however, it dissipated almost immediately after the pit site was deactivated. The other two interactive effects increased pitting probabilities as they endured for a longer time after the current ceased to flow, with oxide film changing lasting more than 10 minutes. The information obtained about the interactions among corrosion sites were then used to develop a spatial metastable pitting model that simulated the behavior found experimentally.
MODIS snow cover mapping accuracy in small mountain catchment - comparison between open and forest sites
NASA Astrophysics Data System (ADS)
Parajka, J.; Holko, L.; Kostka, Z.; Blöschl, G.
Numerous global and regional validation studies examined MODIS snow mapping accuracy by using measurements at climate stations, which are mainly at grassy sites. MODIS accuracy in alpine and forested regions is, however, still not well understood. The main objective of this study is to evaluate MODIS (MOD10A1 and MYD10A1) snow cover products in a small experimental catchment by using extensive snow course measurements at open and forest sites. The MODIS accuracy is tested in the Jalovecky creek catchment (Northern Slovakia) in the period 2000-2011. The results show that the combined Terra and Aqua images enables snow mapping to an overall accuracy of 91.5%. The accuracy at forested, open and mixed land uses at the ?ervenec sites is 92.7%, 98.3% and 81.8%, respectively. The use of a 2-day temporal filter enables a significant reduction in the number of days with cloud coverage and an increase in overall snow mapping accuracy. In total, the 2-day temporal filter decreases the number of cloudy days from 61% to 26% and increases the snow mapping accuracy to 94%. The results indicate three possible factors leading to misclassification of snow as land: patchy snow cover, limited MODIS geolocation accuracy and mapping algorithm errors. Out of a total of 27 misclassification cases, patchy snow cover, geolocation issues and mapping errors occur in 12, 12 and 3 cases, respectively.
MODIS snow cover mapping accuracy in a small mountain catchment - comparison between open and forest sites
NASA Astrophysics Data System (ADS)
Parajka, J.; Holko, L.; Kostka, Z.; Blöschl, G.
Numerous global and regional validation studies have examined MODIS snow mapping accuracy by using measurements at climate stations, which are mainly at open sites. MODIS accuracy in alpine and forested regions is, however, still not well understood. The main objective of this study is to evaluate MODIS (MOD10A1 and MYD10A1) snow cover products in a small experimental catchment by using extensive snow course measurements at open and forest sites. The MODIS accuracy is tested in the Jalovecky creek catchment (northern Slovakia) in the period 2000-2011. The results show that the combined Terra and Aqua images enable snow mapping at an overall accuracy of 91.5%. The accuracies at forested, open and mixed land uses at the ?ervenec sites are 92.7%, 98.3% and 81.8%, respectively. The use of a 2-day temporal filter enables a significant reduction in the number of days with cloud coverage and an increase in overall snow mapping accuracy. In total, the 2-day temporal filter decreases the number of cloudy days from 61% to 26% and increases the snow mapping accuracy to 94%. The results indicate three possible factors leading to misclassification of snow as land: patchy snow cover, limited MODIS geolocation accuracy and mapping algorithm errors. Out of a total of 27 misclassification cases, patchy snow cover, geolocation issues and mapping errors occur in 12, 12 and 3 cases, respectively.
Geomorphic Surface Maps of Northern Frenchman Flat, Nevada Test Site, Southern Nevada
Bechtel Nevada
Large-scale (1:6000) surficial geology maps of northern Frenchman Flat were developed in 1995 as part of comprehensive site characterization required to operate a low-level radioactive waste disposal facility in that area. Seven surficial geology maps provide fundamental data on natural processes and are the platform needed to reconstruct the Quaternary history of northern Frenchman Flat. Reconstruction of the Quaternary history provides an understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. Seven geomorphic surfaces (Units 1 through 7) are recognized, spanning from the early Quaternary to present time.
FLS2-BAK1 Extracellular Domain Interaction Sites Required for Defense Signaling Activation
Koller, Teresa; Bent, Andrew F
Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function. PMID:25356676
FLS2-BAK1 extracellular domain interaction sites required for defense signaling activation.
Koller, Teresa; Bent, Andrew F
Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function. PMID:25356676
Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites
Summerton, Jean C.; Martin, Gregory M.; Evanseck, Jeffrey D.; Chapman, Michael S.
Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3? of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3? have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3? interactions in phosphagen kinases, mutation of arginine kinase Arg280 decreases kcat, as predicted, with little impact upon KM. PMID:25238155
High Resolution Mapping of Enhancer-Promoter Interactions
Reeder, Christopher; Closser, Michael; Poh, Huay Mei; Sandhu, Kuljeet; Wichterle, Hynek; Gifford, David
RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spatial resolution that is insufficient to accurately identify individual enhancers. We introduce Germ, a computational method that estimates the likelihood that any two narrowly defined genomic locations are jointly occupied by RNA Polymerase II. Germ takes a blind deconvolution approach to simultaneously estimate the likelihood of RNA Polymerase II occupation as well as a model of the arrangement of read alignments relative to locations occupied by RNA Polymerase II. Both types of information are utilized to estimate the likelihood that RNA Polymerase II jointly occupies any two genomic locations. We apply Germ to RNA Polymerase II ChIA-PET data from embryonic stem cells to identify the genomic locations that are jointly occupied along with transcription start sites. We show that these genomic locations align more closely with features of active enhancers measured by ChIP-Seq than the locations identified using the ChIA-PET Tool. We also apply Germ to RNA Polymerase II ChIA-PET data from motor neuron progenitors. Based on the Germ results, we observe that a combination of cell type specific and cell type independent regulatory interactions are utilized by cells to regulate gene expression. PMID:25970635
Mapping the tRNA binding site on the surface of human DNMT2 methyltransferase.
Jurkowski, Tomasz P; Shanmugam, Raghuvaran; Helm, Mark; Jeltsch, Albert
The DNMT2 enzyme methylates tRNA-Asp at position C38. Because there is no tRNA-Dnmt2 cocrystal structure available, we have mapped the tRNA binding site of DNMT2 by systematically mutating surface-exposed lysine and arginine residues to alanine and studying the tRNA methylation activity and binding of the corresponding variants. After mutating 20 lysine and arginine residues, we identified eight of them that caused large (>4-fold) decreases in catalytic activity. These residues cluster within and next to a surface cleft in the protein, which is large enough to accommodate the tRNA anticodon loop and stem. This cleft is located next to the binding pocket for the cofactor S-adenosyl-L-methionine, and the catalytic residues of DNMT2 are positioned at its walls or bottom. Many of the variants with strongly reduced catalytic activity showed only a weak loss of tRNA binding or even bound better to tRNA than wild-type DNMT2, which suggests that the enzyme induces some conformational changes in the tRNA in the transition state of the methyl group transfer reaction. Manual placement of tRNA into the structure suggests that DNMT2 mainly interacts with the anticodon stem and loop. PMID:22591353
Chloroplast DNA restriction site mapping and the phylogeny of Ranunculus ( Ranunculaceae )
Jan Thomas Johansson
A chloroplast DNA restriction site map forRanunculus sceleratus (Ranunculaceae) was constructed using 14 restriction endonucleases. The total size of the chloroplast genome is 152.4kb. No inversions were detected relative to the tobacco chloroplast DNA. Cladistic analyses of chloroplast DNA restriction site polymorphism were employed in order to elucidate the phylogeny among 76 species of the genusRanunculus in a wide sense
Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites
Follows, George A.; Dhami, Pawan; Göttgens, Berthold; Bruce, Alexander W.; Campbell, Peter J.; Dillon, Shane C.; Smith, Aileen M.; Koch, Christoph; Donaldson, Ian J.; Scott, Mike A.; Dunham, Ian; Janes, Mary E.; Vetrie, David; Green, Anthony R.
The identification of cis-regulatory elements is central to understanding gene transcription. Hypersensitivity of cis-regulatory elements to digestion with DNaseI remains the gold-standard approach to locating such elements. Traditional methods used to identify DNaseI hypersensitive sites are cumbersome and can only be applied to short stretches of DNA at defined locations. Here we report the development of a novel genomic array-based approach to DNaseI hypersensitive site mapping (ADHM) that permits precise, large-scale identification of such sites from as few as 5 million cells. Using ADHM we identified all previously recognized hematopoietic regulatory elements across 200 kb of the mouse T-cell acute lymphocytic leukemia-1 (Tal1) locus, and, in addition, identified two novel elements within the locus, which show transcriptional regulatory activity. We further validated the ADHM protocol by mapping the DNaseI hypersensitive sites across 250 kb of the human TAL1 locus in CD34+ primary stem/progenitor cells and K562 cells and by mapping the previously known DNaseI hypersensitive sites across 240 kb of the human ?-globin locus in K562 cells. ADHM provides a powerful approach to identifying DNaseI hypersensitive sites across large genomic regions. PMID:16963707
Map model for nonlinear alpha particle interaction with toroidal Alfven waves
Berk, H.L.; Breizman, B.N.; Ye, H.
A map model has been developed for studying the nonlinear interaction of alpha particles with the toroidal Alfven eigenmodes. The map is constructed by assuming a linear interaction during a single poloidal transit, which allows the study of the nonlinear interaction over many transits. By using this map, analytic expressions are obtained for the particle nonlinear bounce frequency, and the wave amplitude threshold for the onset of particle orbit stochasticity. The map model can also facilitate self-consistent simulations which incorporate the time variation of the waves.
Constraint-based simulation of biological systems described by Molecular Interaction Maps
Bortolussi, Luca
Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca to simulate biochemical networks de- scribed by the graphical notation of Molecular Interaction Maps within The aim of this work is the simulation of biological regulatory networks described by the graphical
EmailMap: Visualizing Event Evolution and Contact Interaction within Email Archives
Ouhyoung, Ming
EmailMap: Visualizing Event Evolution and Contact Interaction within Email Archives Sheng-Jie Luo Han-Wei Shen The Ohio State University Figure 1: An example of EmailMap. The blue color flow depicts the event evolution in email archives of a time period, and the color tracks reveal the interaction between
Human-Computer Interaction in Map Revision Systems Jun Zhou and Walter F. Bischof
Zhou, Jun
Human-Computer Interaction in Map Revision Systems Jun Zhou and Walter F. Bischof email@example.com Abstract Cartographic map revision cannot be automated completely because, for legal reasons, a human, but then proceed with little or no human-computer interaction, leaving final editing to the human (Mckeown
Application of a regional approach for hazard mapping at an avalanche site in northern Italy
D. Bocchiola; R. Rosso
The currently adopted approach to avalanche hazard mapping in northern Italy includes avalanche dynamic modelling, coupled with statistical analysis of snow depth at avalanche start. The 30-years and 300-years return period avalanches at a given site are modelled and their run out zone and pressure are evaluated. The snow depth in the avalanche release zone is assumed to coincide with
Home Contact Us Help Site Map Index Search Combating Illegal Logging in Africa
Home · Contact Us · Help · Site Map · Index · Search Combating Illegal Logging in Africa, and corruption in the forest sector at the Africa Forest Law Enforcement and Governance (AFLEG) conference held in Africa "Forest law enforcement and governance are the foundation upon which all real forest conservation
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
Gregory E. Crawford; Ingeborg E. Holt; James Whittle; Bryn D. Webb; Denise Tai; Sean Davis; Elliott H. Margulies; YiDong Chen; John A. Bernat; David Ginsburg; Daixing Zhou; Shujun Luo; Thomas J. Vasicek; Mark J. Daly; Tyra G. Wolfsberg; Francis S. Collins
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear chromatin is a powerful and well-established method of identifying many different types of regulatory elements, but in the past it has been limited to analysis of single loci. We have recently
Technology Transfer Automated Retrieval System (TEKTRAN)
The success of site-specific nematode management depends on a grower or advisor being able to afford to make a map of an infestation that is accurate enough for management decisions. The spatial dependence of nematode infestations and correlation of soil attributes with nematode density were assess...
SPI, mapping, and site ordering in Lattice QCD code on Mira
Kemner, Ken
SPI, mapping, and site ordering in Lattice QCD code on Mira Heechang Na and James Osborn · Motivation · QCD and lattice QCD · Ising model and lattice QCD · Communications with SPI · Resource structure at the same time -> Better latency -> MU SPI communication · Reducing the surface area and number of hops
Mars Landing Site Selection: An exercise in reading geologic maps and other geologic data sets
NSDL National Science Digital Library
Tracy Gregg
Upon arrival in the lab, students are designated as an engineer, a biologist, or a geologist. Working in these groups, each group uses available Mars data (including, but not limited to, Mars geologic maps, topography, thermal inertia data) to identify their top three landing sites on the basis of provided criteria. In jig-saw fashion, new groups are generated consisting of one geologist, one engineer, and one geologist. These new groups must agree on their top three landing sites. Finally, the entire class must agree on a landing site.
A Method for Mapping Intralocus Interactions Influencing Excessive Alcohol Drinking
Phillips, Tamara J.; Reed, Cheryl; Burkhart-Kasch, Sue; Li, Na; Hitzemann, Robert; Yu, Chia-Hua; Brown, Lauren L.; Helms, Melinda L.; Crabbe, John C.; Belknap, John K.
Excessive alcohol (ethanol) consumption is the hallmark of alcohol use disorders. The F1 hybrid cross between the C57BL/6J (B6) and FVB/NJ (FVB) inbred mouse strains, consumes more ethanol than either progenitor strain. The purpose of this study was to utilize ethanol drinking data and genetic information to map genes that result in over-dominant (or heterotic) ethanol drinking. About 600 B6 × FVB F2 mice, half of each sex, were tested for ethanol intake and preference in a 24-h, two-bottle water versus ethanol choice procedure, with ascending ethanol concentrations. They were then tested for ethanol intake in a drinking in the dark (DID) procedure, first, when there was no water choice and then when ethanol was offered versus water. DNA samples were obtained and genome-wide QTL analyses were performed to search for single QTLs (both additive and dominance effects) and interactions between pairs of QTLs, or epistasis. On average, F2 mice consumed excessive amounts of ethanol in the 24-h choice procedure, consistent with high levels of consumption seen in the F1 cross. Consumption in the DID procedure was similar or higher than amounts reported previously for the B6 progenitor. QTLs resulting in heightened consumption in heterozygous compared to homozygous animals were found on Chr 11, 15 and 16 for 24-h choice 30% ethanol consumption, and on Chr 11 for DID. No evidence was found for epistasis between any pair of significant or suggestive QTLs. This indicates that the hybrid over-dominance is due to intralocus interactions at the level of individual QTL. PMID:20033183
A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis
Nardini, Christine
Background Computational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine - the scientific approach to medicine in tight relation with basic science -, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions that occur between molecules related to Rheumatoid Arthritis (RA). Methodology Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by RA. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. This global network has then been topologically analysed, as a whole and tissue-specifically, in order to translate the experimental molecular connections into topological motifs meaningful in the identification of tissue-specific markers and targets in the diagnosis, and possibly in the therapy, of RA. Significance We find that some nodes in the network that prove to be topologically important, in particular AKT2, IL6, MAPK1 and TP53, are also known to be associated with drugs used for the treatment of RA. Importantly, based on topological consideration, we are also able to suggest CRKL as a novel potentially relevant molecule for the diagnosis or treatment of RA. This type of finding proves the potential of in silico analyses able to produce highly refined hypotheses, based on vast experimental data, to be tested further and more efficiently. As research on RA is ongoing, the present map is in fieri, despite being -at the moment- a reflection of the state of the art. For this reason we make the network freely available in the standardised and easily exportable .xml CellDesigner format at 'www.picb.ac.cn/ClinicalGenomicNTW/temp.html' and 'www.celldesigner.org'. PMID:20419126
An approach to mapping haplotype-specific recombination sites in human MHC class III
Levo, A.; Westman, P.; Partanen, J. [Finnish Red Cross Blood Transfusion Service, Helsinki (Finland)
Studies of the major histocompatibility complex (MHC) in mouse indicate that the recombination sites are not randomly distributed and their occurrence is haplotype-dependent. No data concerning haplotype-specific recombination sites in human are available due to the low number of informative families. To investigate haplotype-specific recombination sites in human MHC, we describe an approach based on identification of recombinant haplotypes derived from one conserved haplotype at the population level. The recombination sites were mapped by comparing polymorphic markers between the recombinant and assumed original haplotypes. We tested this approach on the extended haplotype HLA A3; B47; Bf{sup *}F; C4A{sup *}1; C4B{sup *}Q0; DR7, which is most suitable for this analysis. First, it carries a number of rare markers, and second, the haplotype, albeit rare in the general population, is frequent in patients with 21-hydroxylase (21OH) defect. We observed recombinants derived from this haplotype in patients with 21OH defect. All these haplotypes had the centromeric part (from Bf to DR) identical to the original haplotype, but they differed in HLA A and B. We therefore assumed that they underwent recombinations in the segment that separates the Bf and HLA B genes. Polymorphic markers indicated that all break points mapped to two segments near the TNF locus. This approach makes possible the mapping of preferential recombination sites in different haplotypes. 20 refs., 1 fig., 1 tab.
Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis
Yoon, Y.; Sanchez, J.A.; Brun, C. [Roswell Park Cancer Institute, Buffalo, NY (United States)] [and others
New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods. Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit. 51 refs., 5 figs.
Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase
Dave Jacobs; Danielle Glossip; Heming Xing; Anthony J. Muslin; Kerry Kornfeld
MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, form a modular recognition system, as they can function independently or in combination. FXFP is specific
Operation and research at the Ithaca MAP3S regional precipitation chemistry site: Annual progress report for 1988
Butler, T.J.; Likens, G.E.
Ten complete years of precipitation chemistry data, 1977 to 1986, are summarized for the Ithaca MAP3S site. For comparison purposed selected data from the eight other MAP3S sites are included. Notable findings include the following: 1) Monthly concentrations of H/sup +/, SO/sub 4//sup 2/minus//, NO/sub 3//sup /minus//, and NH/sub 4//sup +/ show a high degree of variability from year to year. 2) The Ithaca Site shows a statistically significant (p = 0.05) decline, from 1977 to 1986, in annual volume-weighed H/sup +/ concentration. 3) A statistically significant (p = 0.05) increase in annual volume-weighted NH/sub 4//sup +/ concentration also occurs for this time period at the Ithaca site. 4) Ohio, from 1979 to 1986, shows a significant (p = 0.05) decline in volume-weighted H/sup +/ and SO/sub 4//sup 2/minus// concentration. 5) While there is not a significant (p = 0.05) linear relationship between emissions of SO/sub 2/ and SO/sub 4//sup /minus// concentrations, and emissions of NO/sub x/ and NO/sub 3//sup /minus// concentrations, there is a significant positive relationship for emissions of SO/sub 2/ plus NO/sub x/ versus H/sup +/ concentrations at Ithaca (p = 0.10) and Ohio (p = 0.05). 6) 15% to 30% of dry-deposited particles at the Ithaca site are anthropogenicly derived. On a mass basis, one third of the calcium species are CaSO/sub 4/, probably derived from the conversion of CaCO/sub 3/ interacting with SO/sub 2/ or acidic sulfate. Experimental results suggest this conversion can occur at rates from 0% to 20% per day in the Ithaca area. 13 refs., 23 figs., 2 tabs.
Shear wave velocity mapping of Hat Yai district, southern Thailand: implication for seismic site classification
NASA Astrophysics Data System (ADS)
Yordkayhun, Sawasdee; Sujitapan, Chedtaporn; Chalermyanont, Tanit
Soil characteristics play an important role in the degree of ground shaking due to local site amplification during an earthquake. The objectives of this work are to study shear wave velocity (Vs) distribution in the near surface, and to develop a seismic site classification map for soil effect characterization and seismic hazard assessment in Hat Yai district, southern Thailand. The Vs determination based on the multichannel analysis of surface waves technique, has been carried out and analyzed at 70 measuring sites throughout the district. On the basis of the weighted-average Vs in the upper 30?m depth (Vs30), a seismic site classification map, based on the National Earthquake Hazards Reduction Program (NEHRP) standard has been developed. It is found that the NEHRP site class in Hat Yai can be classified into four groups in accordance with the value of Vs30 within the range of about 150 to 1160?m?s?1. Most parts of the study area are typically classified as site class C and D. Site class C is mostly found within the colluvial and terrace deposits in the western and eastern part of the area, whereas site class D is concentrated in the alluvial sediment of the middle and northern flood plain areas. A small portion of site class B is observed in the western mountain ranges, where there is a thin overburden on the firm rock. There is a remarkably low Vs30 value at only one site, located near the main stream in the northern part of the study area. The results imply that the soil characteristics in the central and northern Hat Yai district pose a medium to high amplification rate with respect to the other regions. Although Vs data alone are insufficient to verify the potential of the amplification of ground shaking, this study provides an initial attempt to understand seismic hazards in the study area.
Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites
Melamed, Daniel; Young, David L.; Miller, Christina R.; Fields, Stanley
Many protein interactions are conserved among organisms despite changes in the amino acid sequences that comprise their contact sites, a property that has been used to infer the location of these sites from protein homology. In an inter-species complementation experiment, a sequence present in a homologue is substituted into a protein and tested for its ability to support function. Therefore, substitutions that inhibit function can identify interaction sites that changed over evolution. However, most of the sequence differences within a protein family remain unexplored because of the small-scale nature of these complementation approaches. Here we use existing high throughput mutational data on the in vivo function of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein, Pab1, to analyze its sites of interaction. Of 197 single amino acid differences in 52 Pab1 homologues, 17 reduce the function of Pab1 when substituted into the yeast protein. The majority of these deleterious mutations interfere with the binding of the RRM2 domain to eIF4G1 and eIF4G2, isoforms of a translation initiation factor. A large-scale mutational analysis of the RRM2 domain in a two-hybrid assay for eIF4G1 binding supports these findings and identifies peripheral residues that make a smaller contribution to eIF4G1 binding. Three single amino acid substitutions in yeast Pab1 corresponding to residues from the human orthologue are deleterious and eliminate binding to the yeast eIF4G isoforms. We create a triple mutant that carries these substitutions and other humanizing substitutions that collectively support a switch in binding specificity of RRM2 from the yeast eIF4G1 to its human orthologue. Finally, we map other deleterious substitutions in Pab1 to inter-domain (RRM2–RRM1) or protein-RNA (RRM2–poly(A)) interaction sites. Thus, the combined approach of large-scale mutational data and evolutionary conservation can be used to characterize interaction sites at single amino acid resolution. PMID:25671604
Chaotic scattering in solitary wave interactions: a singular iterated-map description.
Goodman, Roy H
We derive a family of singular iterated maps--closely related to Poincare maps--that describe chaotic interactions between colliding solitary waves. The chaotic behavior of such solitary-wave collisions depends on the transfer of energy to a secondary mode of oscillation, often an internal mode of the pulse. This map allows us to go beyond previous analyses and to understand the interactions in the case when this mode is excited prior to the first collision. The map is derived using Melnikov integrals and matched asymptotic expansions and generalizes a "multipulse" Melnikov integral. It allows one to find not only multipulse heteroclinic orbits, but exotic periodic orbits. The maps exhibit singular behavior, including regions of infinite winding. These maps are shown to be singular versions of the conservative Ikeda map from laser physics and connections are made with problems from celestial mechanics and fluid mechanics. PMID:18601480
Repeated mapping of reefs constructed by Sabellaria spinulosa Leuckart 1849 at an offshore wind farm site
NASA Astrophysics Data System (ADS)
Pearce, Bryony; Farińas-Franco, Jose M.; Wilson, Christian; Pitts, Jack; deBurgh, Angela; Somerfield, Paul J.
Sabellaria spinulosa reefs are considered to be sensitive and of high conservation status. This article evaluates the feasibility of using remote sensing technology to delineate S. spinulosa reefs. S. spinulosa reef habitats associated with the Thanet Offshore Windfarm site were mapped using high resolution sidescan sonar (410 kHz) and multibeam echo sounder (<1 m2) data in 2005 (baseline), 2007 (pre-construction baseline) and 2012 (post-construction). The S. spinulosa reefs were identified in the acoustic data as areas of distinct irregular texturing. Maps created using acoustic data were validated using quantitative measures of reef quality, namely tube density (as a proxy for the density of live S. spinulosa), percentage cover of S. spinulosa structures (both living and dead) and associated macrofauna derived from seabed images taken across the development site. Statistically significant differences were observed in all physical measures of S. spinulosa as well the number (S) and diversity (H') of associated species, derived from seabed images classified according to the presence or absence of reef, validating the use of high resolution sidescan sonar to map these important biogenic habitats. High precision mapping in the early stages allowed for the micro-siting of wind turbines in a way that caused minimal damage to S. spinulosa reefs during construction. These habitats have since recovered and expanded in extent. The surveys undertaken at the Thanet Offshore Windfarm site demonstrate the importance of repeat mapping for this emerging industry, allowing habitat enhancement to be attributed to the development whilst preventing background habitat degradation from being wrongly attributed to the development.
Geological mapping of the Oak Ridge K-25 Site, Oak Ridge, Tennessee
Lemiszki, P.J.
The Oak Ridge K-25 Site (formerly known as the Oak Ridge Gaseous Diffusion Plant) is located in the southern Appalachian Valley and Ridge province of east Tennessee and overlies an area of folded and faulted Cambrian through Ordovician sedimentary rocks in the footwall of the Whiteoak Mountain fault. Environmental restoration plans for the area require that the geology of the site be well understood because various aspects of the groundwater system are directly influenced by stratigraphic and structural characteristics of the bedrock. This study involved mapping the bedrock geology of an 18-square mile area in and around the plant site. Field mapping focused on: (1) checking the accuracy of previously mapped stratigraphic and fault contacts, (2) dividing the bedrock into distinct stratigraphic units based on field criteria, (3) determining the geometry of map-scale folds and faults, and (4) documenting various aspects of the local fracture system. Besides accomplishing all of the above tasks, results from this study have led to a number of new hypotheses regarding various aspects of the site geology. First, faulting and folding within carbonates of the Chickamauga Supergroup in the plant area has repeated certain rock units, which requires that there be a thrust fault in the subsurface below them. This thrust fault may project to the surface with the Carters Limestone. Second, thrust slices of the Rome Formation that overlie the Chickamauga carbonates may be extremely thin and have a limited aerial extent. Third, part of the Knox Group on McKinney Ridge is folded into an anticline. Evaluating the above hypotheses will require information about the subsurface that can only be acquired through drilling and surface geophysical surveys. The geologic map produced from this study can be used to evaluate the location of coreholes that will more effectively intersect a combination of stratigraphic, structural, and hydrologic targets.
Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites
Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ?G. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ?G because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ?G arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function.
Prion Nucleation Site Unmasked by Transient Interaction with Phospholipid Cofactor
Zurawel, Ashley A.; Walsh, Daniel J.; Fortier, Sean M.; Chidawanyika, Tamutenda; Sengupta, Suvrajit; Zilm, Kurt; Supattapone, Surachai
Infectious mammalian prions can be formed de novo from purified recombinant prion protein (PrP) substrate through a pathway that requires the sequential addition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) and RNA cofactor molecules. Recent studies show that the initial interaction between PrP and POPG causes widespread and persistent conformational changes to form an insoluble intermediate species, termed PrPInt1. Here, we characterize the mechanism and functional consequences of the interaction between POPG and PrP. Negative-stain electron microscopy of PrPInt1 revealed the presence of amorphous aggregates. Pull-down and photoaffinity label experiments indicate that POPG induces the formation of a PrPC polybasic-domain-binding neoepitope within PrPInt1. The ongoing presence of POPG is not required to maintain PrPInt1 structure, as indicated by the absence of stoichiometric levels of POPG in solid-state NMR measurements of PrPInt1. Together, these results show that a transient interaction with POPG cofactor unmasks a PrPC binding site, leading to PrPInt1 aggregation. PMID:24328062
Matrix model maps and reconstruction of AdS supergravity interactions
Cremonini, Sera; Mello Koch, Robert de; Jevicki, Antal [Michigan Center for Theoretical Physics, Randall Laboratory of Physics, University of Michigan, Ann Arbor, MI 48109 (United States); Department of Physics, University of Witwatersrand, Wits, 2050 (South Africa); Department of Physics, Brown University, Providence, RI 02912 (United States)
We consider the question of reconstructing (cubic) SUGRA interactions in AdS/CFT. The method we introduce is based on the matrix model maps (MMP) which were previously successfully employed at the linearized level. The strategy is to start with the map for 1/2 BPS configurations, which is exactly known (to all orders) in the Hamiltonian framework. We then use the extension of the matrix model map with the corresponding Ward identities to completely specify the interaction. A central point in this construction is the nonvanishing of off-shell interactions (even for highest-weight states)
Mapping Control and Affiliation in Teacher-Student Interaction with State Space Grids
ERIC Educational Resources Information Center
Mainhard, M. Tim; Pennings, Helena J. M.; Wubbels, Theo; Brekelmans, Mieke
This paper explores how State Space Grids (SSG), a dynamic systems research method, can be used to map teacher-student interactions from moment-to-moment and thereby to incorporate temporal aspects of interaction. Interactions in two secondary school classrooms are described in terms of level of interpersonal control and affiliation, and of…
Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway
David Kentner; Victor Sourjik
Protein–protein interactions play key roles in virtually all cellular processes, often forming complex regulatory networks. A powerful tool to study interactions in vivo is fluorescence resonance energy transfer (FRET), which is based on the distance-dependent energy transfer from an excited donor to an acceptor fluorophore. Here, we used FRET to systematically map all protein interactions in the chemotaxis signaling pathway
GEO 499/599 Web Mapping and Human Computer Interaction Spring 2013
Jenny, Bernhard
GEO 499/599 Web Mapping and Human Computer Interaction Spring 2013 Instructor Dr. Helen Jenny Burt access OSU Libraries #12;Haklay, Muki (2010): Interacting with Geospatial Technologies (selected and applications in interactive cartographic visualization and teaches the skills of building customized web
Preliminary geologic map of the region around the candidate Proclus Apollo landing site, part J
NASA Technical Reports Server (NTRS)
Wilhelms, D. E.
The Proclus Crater region was mapped to test the value, for photogeologic mapping purposes, of Apollo 15 metric photographs and to estimate the scientific value of the area as a potential landing site. Adjacent frames of the metric photography were overlapped with the base frame to provide stereographic images. Because of the high quality of the photographs, it was found that the geologic units could be more definitely interpreted and dated than those of earlier maps. The photographs tend to confirm the earlier interpretation of the rugged area as composed of bedrock uplifted when the Crisium basin formed. They also suggest that an earlier predominantly volcanic interpretation of the terra in this area might be replaced by an interpretation in which mass wasting and fracturing play the major roles in producing different terrain types. It was concluded that because of apparent lithologic homogeneity, the terra of the Proclus region is an undesirable objective for an extensive manned lunar landing mission.
Application of a regional approach for hazard mapping at an avalanche site in northern Italy
NASA Astrophysics Data System (ADS)
Bocchiola, D.; Rosso, R.
The currently adopted approach to avalanche hazard mapping in northern Italy includes avalanche dynamic modelling, coupled with statistical analysis of snow depth at avalanche start. The 30-years and 300-years return period avalanches at a given site are modelled and their run out zone and pressure are evaluated. The snow depth in the avalanche release zone is assumed to coincide with the three days snow fall depth H72 featuring a return period of 30 years and 300 years, respectively. In the Italian alps only short series of observed snow depth are available, covering a period of 20 years or so, thus requiring a regional approach, or index value approach for the purpose of high return period quantile estimation. Based of former studies, here we apply the index value approach developed for the Lombardia region, in northern Italy, for hazard mapping in a particular avalanche site. A dynamic avalanche model is tuned using the runout data for two major observed avalanche events. Then, the 30-years and 300-years runout zone and dynamic pressure are calculated. It is then shown that the obtained hazard maps are more accurate than those obtained using the evaluation of H72 as deduced from distribution fitting in a single site.
Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis
NASA Technical Reports Server (NTRS)
Crawford, Lisa; Karr, Laurel; Pusey, Marc
A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk'solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 4(sub 3) axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to greater than 500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 yields PHE or ALA and ASN 113 yields ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 4(sub 3) helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.
Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis
NASA Technical Reports Server (NTRS)
Crawford, Lisa; Karr, Laurel J.; Nadarajah, Arunan; Pusey, Marc
A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.
MUDD mapping: an interactive teaching-learning strategy.
Barrington, Kay; Campbell, Barbara
MUDD, an acronym for my understanding through dialogue and debate, is a teaching-learning strategy that assists learners in understanding a particular topic. MUDD mapping can be used as an independent activity carried out by learners in a study group or by a faculty member to conduct an assessment of how well learners are grasping the subject. The authors describe how MUDD mapping was used and illustrates how faculty can facilitate its application in a teaching-learning activity. PMID:18600156
Constraint-based simulation of biological systems described by Molecular Interaction Maps
Bortolussi, Luca
Constraint-based simulation of biological systems described by Molecular Interaction Maps Luca networks described by the graphical notation of Molecular Inter- action Maps within stochastic Concurrent of this work is the simulation of biological regulatory networks described by the graphical notation
Interactive 2D 3D Digital Maps for the support of emergency teams during rescue operations
Paliouras, George
the environment of the incident. The SHARE system will incorporate an enhanced Tele Atlas 2D-3D digital mapInteractive 2D 3D Digital Maps for the support of emergency teams during rescue operations Linde Vande Velde1* , Symeon Chatzinotas3 , Martha Larson2 , Jobst Löffler2 , Georgios Paliouras3 1 Tele Atlas
Narrative Maps An interactive visualisation interface for the geographic and temporal display of historical data
Johnson, Michael J
Maps is intended to facilitate learning by creating a useful interactive visualisation of a narrative. The current version is available on the University of Edinburgh servers at http://xweb.geos.ed.ac.uk/~s0968681/cgi_bin/NarrativeMaps.pl....
NATCARB Interactive Maps and the National Carbon Explorer: a National Look at Carbon Sequestration
NATCARB is a national look at carbon sequestration. The NATCARB home page, National Carbon Explorer (http://www.natcarb.org/) provides access to information and interactive maps on a national scale about climate change, DOE's carbon sequestration program and its partnerships, CO2 emissions, and sinks. This portal provides access to interactive maps based on the Carbon Sequestration Atlas of the United States and Canada.
Operation and research at the Ithaca MAP3S regional precipitation chemistry site
Butler, T.J.; Likens, G.E.
Annual precipitation chemistry data from network start-up through 1988 is presented for the nine MAP3S sites. Time trends show significant negative linear regressions (P < 0.10) for SO{sub 4}{sup 2-} at 2 sites, H{sup +} at 4 sites, Ca{sup ++} at 1 site, and Na{sup +} at 1 site. Significant positive regressions over time include: NH{sub 4}{sup +} at 2 sites, Ca{sup ++} at 1 site, K{sup +} at 4 sites, and Cl{sup {minus}} at 2 sites. The Ithaca site shows the highest number of significant trends, with positive trends for Cl{sup {minus}}, NH{sub 4}{sup +}, Ca{sup ++}, and K{sup +}, and a negative trend for H{sup +}. Linear regressions of annual SO{sub 4}{sup 2-} concentrations on SO2 emissions show a significant positive relationship for Whiteface, Illinois, and Ohio at p < 0.10, 0.02, and 0.05 respectively. Overall for all MAP3S sites, plus Hubbard Brook a 25% decline in SO2 emissions over the region has been accompanied by a 16.5% decline in annual precipitation concentrations of SO{sub 4}{sup 2-}. For the region as a whole, a 20% decline in combined emissions has been accompanied to a 20% decline in H{sup +} concentrations. Thus a linear relationship exists between combined emissions and precipitation H{sup +} concentrations. No strong relationship exists for NOx emissions and precipitation NO{sub 3}{sup {minus}} concentration at the annual, seasonal or monthly level. Removing the NOx transportation sector, removing high and low precipitation values, or high pH values also does little to improve the NOx -- NO{sub 3}{sup {minus}} concentration relationships. Dry deposition components such a PAN, NO2, gaseous HNO{sub 3}, or aerosol NO{sub 3}{sup {minus}} should be included in the future with precipitation NO{sub 3}{sup {minus}} to relate emissions of NOx to nitrogen deposition. 11 refs., 27 figs.,1 tab.
Interaction between LSD and dopamine D2/3 binding sites in pig brain.
Minuzzi, Luciano; Nomikos, George G; Wade, Mark R; Jensen, Svend B; Olsen, Aage K; Cumming, Paul
The psychoactive properties of the hallucinogen LSD have frequently been attributed to high affinity interactions with serotonin 5HT2 receptors in brain. Possible effects of LSD on dopamine D2/3 receptor availability have not previously been investigated in living brain. Therefore, we used PET to map the binding potential (pB) of [11C]raclopride in brain of three pigs, first in a baseline condition, and again at 1 and 4 h after administration of LSD (2.5 microg/kg, i.v.). There was a progressive treatment effect in striatum, where the pB was significantly reduced by 19% at 4 h after LSD administration. Concomitant maps of cerebral blood flow did not reveal significant changes in perfusion during this interval. Subsequent in vitro studies showed that LSD displaced [3H]raclopride (2 nM) from pig brain cryostat sections with an IC50 of 275 nM according to a one-site model. Fitting of a two-site model to the data suggested the presence of a component of the displacement curves with a subnanomolar IC50, comprising 20% of the total [3H]raclopride binding. In microdialysis experiments, LSD at similar and higher doses did not evoke changes in the interstitial concentration of dopamine or its acidic metabolites in rat striatum. Together, these results are consistent with a direct interaction between LSD and a portion of dopamine D2/3 receptors in pig brain, possibly contributing to the psychopharmacology of LSD. PMID:15803496
Statewide Repository and Interactive Map of Coastal Elevation Profiles for Alaska
NASA Astrophysics Data System (ADS)
Gould, A.; Kinsman, N.; Southerland, L.
Beach elevation profiles are a type of temporal coastal data that can be used to better understand coastal environments, document change and assess hazard vulnerability. The value of these measurements increases when sites are revisited seasonally and/or interannually to capture the dynamic range of coastal landforms. Static measurements of the shoreface have been collected by a number of stakeholders in Alaska since the 1960s, but, have not historically been published or made readily accessible. In cooperation with the Alaska Ocean Observing System, the Alaska Division of Geological & Geophysical Surveys (DGGS) has designed a universal data repository to house these coastal measurements. This new database has an interactive map interface that enables easy access to existing profile locations to encourage repeat observations. Users can explore profile measurements collected by DGGS and others as time-series plots and location-based images of the shoreface environment. The database has been designed to accommodate datasets collected with differing techniques, including differential leveling, survey-grade GPS or extraction from lidar-derived digital elevation models. Non-DGGS profile measurements, including community-led efforts, University of Alaska project datasets, and archived United States Geological Survey coastal profiles have also been incorporated into the database and contributions from other entities are welcomed. In addition to exhibiting the new interactive map capabilities, we also provide a case study example from Yakutat, Alaska illustrating how this tool can be incorporated into broader investigations of coastal dynamics and how these measurements can augment shoreline change assessments. The readily accessible nature of this database also promotes local involvement in community-based coastal monitoring, also demonstrated in the Yakutat example.
Spatially mapping of friendliness for human-robot interaction
Tsuyoshi Tasaki; Kazunori Komatani; Tetsuya Ogata; Hiroshi G. Okuno
It is important that robots interact with multiple people. However, most research has dealt with only interaction between one robot and one person and assumed that the distance between them does not change. This paper focuses on the spatial relationships between a robot and multiple people during interaction. Based on the distance between them, our robot selects appropriate functions to
The Documentation of Historic Maps of World Heritage Site City Suzhou
NASA Astrophysics Data System (ADS)
Guangwei, Z.
Documentation and analysis of historic maps enhance understanding of temporal and spatial interactions between events and the evolution of physical canals upon which they occurred. And the challenge of this work lies on carefully sifting of information through the maps drawn with relative accuracy by traditional cartographical principles before the emergence of scientific survey. This research project focuses on sorting out the evolution of historic city Suzhou in a spatio-temporal view. The investigation was conducted through an in-depth analysis of historic maps. Re-projection of the geographical elements of the city to one single georeference, that is to say a standard map BASE, help acquiring an actual sense of the scale and facilitate the recognition of the city's evolution in clear details. It is an important contribution of this thesis in coordination of variously distorted geographical information contained in nineteen periods span from 1229 to 2013 into a single research resource. Through the work both quantitative and qualitative, a clear vision of the evolution and characteristics of the urban structure of ancient Suzhou is achieved. Meanwhile, in the process of projecting the historical geometrical information onto the topographic map, historical bibliographic and cartographic records is key to the data coordination and readjustment, this inspire as well on the cautious utilization of historical materials from ancient time in the recording, documentation work.
Cave detection and mapping in a construction site in Israel: a case study
NASA Astrophysics Data System (ADS)
Ronen, Amit
The Geophysical Institute of Israel (G.I.I.) carried out a Ground Penetrating Radar -- GPR -- survey at the construction site for the administration building of the I.E.C. (The Israel Electricity Company) in the town of Ariel in the Samaria mountains of Israel. The construction workers at the site found a void in one of the pile boreholes and the GPR crew carried out a survey to detect and map the cave. The GPR data show a very clear 'cave shape' with an area of about 81m2, the roof of the cave was at a depth of 5m - 7m, while the floor of the cave was at a depth of 8m - 11m. The volume estimations of the target were incorrect and the construction workers did not find any indication of the existence of the cave under the pile sites except the one prior to the GPR survey.
Mapping the RNA binding sites for human immunodeficiency virus type-1 gag and NC proteins within the complete HIV-1 and -2 untranslated leader regions.
Damgaard, C K; Dyhr-Mikkelsen, H; Kjems, J
Encapsidation of HIV-1 genomic RNA is mediated by specific interactions between the RNA packaging signal and the Gag protein. During maturation of the virion, the Gag protein is processed into smaller fragments, including the nucleocapsid (NC) domain which remains associated with the viral genomic RNA. We have investigated the binding of glutathione- S -transferase (GST) Gag and NC fusion proteins from HIV-1, to the entire HIV-1 and -2 leader RNAencompassing the packaging signal. We have mapped the binding sites at conditions where only about two complexes are formed and find that GST-Gag and GST-NC fusion proteins bind specifically to discrete sites within the leader. Analysis of the HIV-1 leader indicated that GST-Gag strongly associates with the PSI stem-loop and to a lesser extent with regions near the primer binding site. GST-NC binds the same regions but with reversed preferences. The HIV-1 proteins also interact specifically with the 5'-leader of HIV-2 and the major site of interaction mapped to a stem-loop, with homology to the HIV-1 PSI stem-loop structure. The different specificities of Gag and NC may reflect functionally distinct roles in the viral replication, and suggest that the RNA binding specificity of NC is modulated by its structural context. PMID:9685481
ERIC Educational Resources Information Center
Kinney, Douglas M.; McIntosh, Willard L.
Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)
Geological map of the future: digital, interactive, and 3D
NASA Astrophysics Data System (ADS)
Thorleifson, H.
Geological survey agencies are developing methods for government geological mapping in the post-paper map era. Surficial and bedrock maps are being digitized and reconciled, while multiple generations of legends are being made accessible in a categorized format. Regional 3D geological models that integrate soils and geology, surficial and bedrock geology, as well as onshore and offshore are increasingly in demand as the information, technology, and protocols to build them progress. Applications such as regional groundwater modelling require digitizing, reconciliation, and assembly of a digital elevation model, bathymetry, offshore geology, soils, surficial geology, public domain drillhole and geophysical data, bedrock maps, and existing stratigraphic models typically expressed as structure contours. New stratigraphic modelling, particularly required for surficial unconsolidated deposits in many regions, requires information from cored holes logged by geologists as well as geophysical surveys. These high-quality results are extrapolated laterally using drill hole data, commonly large quantities of water well data of varying resolution and reliability. Much effort is required to adequately georeference the drillhole data, and to parse large numbers of unique lithological descriptions. Stratigraphic modelling methods ideally use all data and an approach that permits judgement in the acceptance or rejection of data, while interpolation and extrapolation are guided by genetic insights. Models are best captured as a grid of predicted stratigraphy profiles that convey expert opinion on interpolation and extrapolation from the data points. Reconciliation of mapping with that of neighbouring jurisdictions is a key step, as is balancing subjective definition of strata with more objective geostatistical approaches to characterizing the heterogeneous physical properties of the strata. Progress is readily achievable in undeformed strata, while deformed strata present far greater challenges. Increasingly, databases of observations and measurements are being retained alongside the interpreted model, and models are being assigned varying confidence levels such that the result is seen not as an end but a means for prioritizing new mapping. Current activity is broadening our reliance not only from paper maps to digital models, but also from plan view maps, to drillhole databases, to 3D models, to dynamic models such as groundwater flow models. Pressing user requirements demand that geological survey work rapidly advance along this progression.
Depth-to-Ice Map of an Arctic Site on Mars
NASA Technical Reports Server (NTRS)
2007-01-01Color coding in this map of a far-northern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies. The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow. The depth to the top of the icy layer estimated from these observations, as little as 5 centimeters (2 inches), matches modeling of where it would be if Mars has an active cycle of water being exchanged by diffusion between atmospheric water vapor and subsurface water ice. This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67.5 degrees north latitude, 132 degrees east longitude, in the Martian arctic plains called Vastitas Borealis. It was formerly a candidate landing site for NASA's Phoenix Mars Lander mission. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice. The Thermal Emission Imaging System observed the site in infrared wavelengths during night time, providing surface-temperature information, once on March 13, 2005, during summer in Mars' northern hemisphere, and again on April 8, 2005, during autumn there. The colors on this map signify relative differences in how much the surface temperature changed between those two observations. Blue indicates the locations with the least change. Red indicates areas with most change. Modeling provides estimates that the range of temperature changes shown in this map corresponds to a range in depth-to-ice of 5 centimeters (2 inches) to more than 18 centimeters (more than 7 inches). The sensitivity of this method for estimating the depth is not good for depths greater than about 20 centimeters (8 inches). The temperature-change data are overlaid on a mosaic of black-and-white, daytime images taken in visible-light wavelengths by the same camera, providing information about shapes in the landscape. The 10-kilometer scale bar is 6.2 miles long. NASA's Jet Propulsion Laboratory manages the Mars Odyssey mission for NASA's Science Mission Directorate, Washington, D.C. The Thermal Emission Imaging System was developed by Arizona State University in collaboration with Raytheon Santa Barbara Remote Sensing. Lockheed Martin Space Systems, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.
Applying nitrogen site-specifically using soil electrical conductivity maps and precision agriculture technology.
Lund, E D; Wolcott, M C; Hanson, G P
Soil texture varies significantly within many agricultural fields. The physical properties of soil, such as soil texture, have a direct effect on water holding capacity, cation exchange capacity, crop yield, production capability, and nitrogen (N) loss variations within a field. In short, mobile nutrients are used, lost, and stored differently as soil textures vary. A uniform application of N to varying soils results in a wide range of N availability to the crop. N applied in excess of crop usage results in a waste of the grower"s input expense, a potential negative effect on the environment, and in some crops a reduction of crop quality, yield, and harvestability. Inadequate N levels represent a lost opportunity for crop yield and profit. The global positioning system (GPS)-referenced mapping of bulk soil electrical conductivity (EC) has been shown to serve as an effective proxy for soil texture and other soil properties. Soils with a high clay content conduct more electricity than coarser textured soils, which results in higher EC values. This paper will describe the EC mapping process and provide case studies of site-specific N applications based on EC maps. Results of these case studies suggest that N can be managed site-specifically using a variety of management practices, including soil sampling, variable yield goals, and cropping history. PMID:12805883
Interactive Computer Programs for Sorting and Mapping Dialect Data.
ERIC Educational Resources Information Center
Herrick, Earl M.
This computer program, a mechanization of the handsorted techniques which geographical dialectology has been using, increases the number of hypotheses that can be explored and the various correlations that can be made. It can draw several of the kinds of maps that dialectologists have used in direct atlases. The hardware, software, and program…
Planar maps: an interaction paradigm for graphic design
Patrick Baudelaire; Michel Gangnet
Compared to traditional media, computer illustration software offers superior editing power at the cost of reduced freedom in the picture construction process. To reduce this discrepancy, we propose an extension to the classical paradigm of 2D layered drawing, the map paradigm, that is conducive to a more natural drawing technique. We present the key concepts on which the new paradigm
New predictive equations and site amplification estimates for the next-generation Swiss ShakeMaps
NASA Astrophysics Data System (ADS)
Cauzzi, Carlo; Edwards, Benjamin; Fäh, Donat; Clinton, John; Wiemer, Stefan; Kästli, Philipp; Cua, Georgia; Giardini, Domenico
We present a comprehensive scientific and technical update of the Swiss customization of United States Geological Survey ShakeMap, in use at the Swiss Seismological Service since 2007. The new Swiss ShakeMaps are based on predictive equations for peak ground-motions and response spectra derived from stochastic simulations tailored to Swiss seismicity. Using synthetics allows overcoming the difficulties posed by: (i) the paucity of strong-motion data recordings in Switzerland; (ii) the regional dependence of shear wave energy attenuation and focal depth distribution in the Swiss Alps and foreland; (iii) the depth dependence of stress parameters suggested by macroseismic and instrumental observations. In the new Swiss ShakeMaps, VS,30 is no longer used as proxy for site amplification at regional scale, and is replaced by macroseismic intensity increments for different soil classes, based on the recently revised earthquake catalogue of Switzerland (ECOS-09). The new implementation converts ground-motion levels into macroseismic intensity by means of ground-motion to intensity conversion equations based on the Italian strong-motion and intensity databanks and is therefore well constrained for intensities larger than VII. The new Swiss ShakeMaps show a satisfactory agreement with the macroseimic fields of both large historical events and recent well-recorded earthquakes of moderate magnitude. The new implementation is now fully consistent with the state-of-the-art in engineering seismology in Switzerland.
Fate mapping of the mouse midbrain-hindbrain constriction using a site-specific recombination system.
Zinyk, D L; Mercer, E H; Harris, E; Anderson, D J; Joyner, A L
The mouse midbrain-hindbrain constriction is centrally involved in patterning of the midbrain and anterior hindbrain (cerebellum), as revealed by recent genetic studies using mice and embryological studies in chick (reviewed in [1,2]). This region can act as an organizer region to induce midbrain and cerebellar development. Genes such as Engrailed-1, Pax-2 and Pax-5, which are expressed in the embryonic cells that will form the midbrain and the cerebellum, are required for development of these regions. Fate-mapping experiments at early somite stages in chick have revealed that the cerebellar primordium is located both anterior and posterior to the midbrain-hindbrain constriction, whereas midbrain precursors lie more anteriorly. Fate mapping in mice has been complicated by the inaccessibility of the postimplantation embryo. Here, we report the use of a new in vivo approach involving the Cre-IoxP site-specific recombination system [3] to map the fate of cells in the mouse midbrain-hindbrain constriction. We show that cells originating in the mouse dorsal midbrain-hindbrain constriction during embryonic days 9-12 contribute significantly to the medial cerebellum and colliculi. Our data demonstrate the feasibility of using a recombinase-based lineage-tracing system for fate mapping in the mouse. PMID:9635195
DIVISION S-8—NUTRIENT MANAGEMENT & SOIL & PLANT ANALYSIS Site-Specific Soil Fertility Management: A Model for Map Quality
T. G. Mueller; N. B. Pusuluri; K. K. Mathias; P. L. Cornelius; R. I. Barnhisel
vs. measured values should always be visually examined to assess prediction quality. If the maps are of high The performance of site-specific fertility management (SSFM) sys- quality, the scatter of data will adhere closely to the 1:1 tems depends on the quality of soil property maps used to develop variable-rate fertilizer recommendations. Map quality assessment, line. Residual (i.e., predicted minus
Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs
Simon Cawley; Stefan Bekiranov; Huck H. Ng; Philipp Kapranov; Edward A. Sekinger; Dione Kampa; Antonio Piccolboni; Victor Sementchenko; Jill Cheng; Alan J. Williams; Raymond Wheeler; Brant Wong; Jorg Drenkow; Mark Yamanaka; Sandeep Patel; Shane Brubaker; Hari Tammana; Gregg Helt; Kevin Struhl; Thomas R Gingeras
Using high-density oligonucleotide arrays representing essentially all nonrepetitive sequences on human chromosomes 21 and 22, we map the binding sites in vivo for three DNA binding transcription factors, Sp1, cMyc, and p53, in an unbiased manner. This mapping reveals an unexpectedly large number of transcription factor binding site (TFBS) regions, with a minimal estimate of 12,000 for Sp1, 25,000 for
Depth-to-Ice Map of a Southern Mars Site Near Melea Planum
NASA Technical Reports Server (NTRS)
2007-01-01Color coding in this map of a far-southern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies. The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow. The depth to the top of the icy layer estimated from these observations suggests that in some areas, but not others, water is being exchanged by diffusion between atmospheric water vapor and subsurface water ice. Differences in what type of material lies above the ice appear to affect the depth to the ice. The area in this image with the greatest seasonal change in surface temperature corresponds to an area of sand dunes. This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67 degrees south latitude, 36.5 degrees east longitude, near a plain named Melea Planum. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers or miles wide. The information from the Thermal Emission Imaging System allows more than 100-fold higher resolution in mapping variations in the depth to ice. The Thermal Emission Imaging System observed the site in infrared wavelengths during night time, providing surface-temperature information. It did so once on Dec. 27, 2005, during late summer in Mars' southern hemisphere, and again on Jan. 22, 2006, the first day of autumn there. The colors on this map signify relative differences in how much the surface temperature changed between those two observations. Blue indicates the locations with the least change. Red indicates areas with most change. Modeling provides estimates that the range of temperature changes shown in this map corresponds to a range in depth-to-ice of less than 1 centimeter (0.4 inch) to more than 19 centimeters (more than 7.5 inches). The sensitivity of this method for estimating the depth is not good for depths greater than about 20 centimeters (8 inches). The temperature-change data are overlaid on a mosaic of black-and-white, daytime images taken in infrared wavelengths by the same camera, providing information about shapes in the landscape. The 20-kilometer scale bar is 12.4 miles long. NASA's Jet Propulsion Laboratory manages the Mars Odyssey mission for NASA's Science Mission Directorate, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University in collaboration with Raytheon Santa Barbara Remote Sensing. Lockheed Martin Space Systems, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.
Health 2.0: how interactive Web sites are changing the healthcare industry.
Lombardi, Glenn; Baum, Neil
Having a Web site is no longer a luxury or perk for your practice and your patients. A Web site is a basic necessity that patients are expecting firom their physicians and their practices. But patients want more than a mere Internet presence. They are expecting an interactive Web site, and they want to be able to communicate with the practice and the physicians. This article will discuss the creation of an interactive Web site and why it is necessary for doctors to enhance their Web site so that patients can interact with the practice. PMID:21506467
Mapping Out Atom-Wall Interaction with Atomic Clocks
Derevianko, A.; Obreshkov, B. [Department of Physics, University of Nevada, Reno, Nevada 89557 (United States); Dzuba, V. A. [Department of Physics, University of Nevada, Reno, Nevada 89557 (United States); School of Physics, University of New South Wales, Sydney, 2052 (Australia)
We explore the feasibility of probing atom-wall interaction with atomic clocks based on atoms trapped in engineered optical lattices. Optical lattice is normal to the wall. By monitoring the wall-induced clock shift at individual wells of the lattice, one would measure the dependence of the atom-wall interaction on the atom-wall separation. We find that the induced clock shifts are large and observable at already experimentally demonstrated levels of accuracy. We show that this scheme may uniquely probe the long-range atom-wall interaction in all three qualitatively distinct regimes of the interaction: van der Waals (image-charge interaction), Casimir-Polder (QED vacuum fluctuations), and Lifshitz (thermal-bath fluctuations) regimes.
Mapping out atom-wall interaction with atomic clocks.
Derevianko, A; Obreshkov, B; Dzuba, V A
We explore the feasibility of probing atom-wall interaction with atomic clocks based on atoms trapped in engineered optical lattices. Optical lattice is normal to the wall. By monitoring the wall-induced clock shift at individual wells of the lattice, one would measure the dependence of the atom-wall interaction on the atom-wall separation. We find that the induced clock shifts are large and observable at already experimentally demonstrated levels of accuracy. We show that this scheme may uniquely probe the long-range atom-wall interaction in all three qualitatively distinct regimes of the interaction: van der Waals (image-charge interaction), Casimir-Polder (QED vacuum fluctuations), and Lifshitz (thermal-bath fluctuations) regimes. PMID:19905511
VS30 mapping and soil classification for seismic site effect evaluation in Dinar region, SW Turkey
NASA Astrophysics Data System (ADS)
Ismet Kanl?, Ali; Tildy, Péter; Prónay, Zsolt; P?nar, Ali; Hermann, László
The Dinar earthquake (MS= 6.1) of 1995 October 1 killed 90 people and destroyed more than 4000 buildings. Despite the moderate size of the earthquake, the level of damage was extremely high, which led to many studies that were carried out in the region. The majority of these studies concluded that the main reasons for the damage were the construction errors and the poor soil conditions. However, at that time no appropriate soil condition map based on extended, high density measurements was available. Shear wave velocity is an important parameter for evaluating the dynamic behaviour of soil in the shallow subsurface. Thus site characterization in calculating seismic hazards is usually based on the near surface shear wave velocity values. The average shear wave velocity for the top 30 m of soil is referred to as VS30. For earthquake engineering design purposes, both the Uniform Building Code (UBC) and Eurocode 8 (EC8) codes use VS30 to classify sites according to the soil type. The Vs30 values calculated by using multichannel analysis of surface waves (MASW) were used to create a new soil classification map of the Dinar region. Surface seismic measurements were carried out at 50 locations mostly in Dinar city and its surroundings. The dispersion data of the recorded Rayleigh waves were inverted using a Genetic Algorithm (GA) method to obtain shear wave velocity profiles of the investigated sites. Thus the derived Vs30 map of the Dinar region was transformed to the UBC and EC8 standards. Soil classification results show that most parts of the region, located in alluvial basin, have low shear wave velocity values. These values are within the range of 160-240 m s-1 and thus fall into the SD and SE categories according to the UBC and the C and D categories according to EC8. Within the region, some parts located on the hill zone and the transition zone have better soil conditions [corresponding to SC (UBC) and B (EC8) categories] and have comparatively high shear wave velocities in the range of 500-740 m s-1 and 350-450 m s-1, respectively. VS30 and soil classification maps were compared with the damage distribution associated with the earthquake. In possession of a detailed shear wave velocity map of Dinar City, in general, the results show that there is a correlation between the VS30 values and the damage distribution of the region. In addition to the low VS30 values, the likely causes of the damage were investigated, and it is observed that one of the major factors for high levels of damage is 3-D variations of geological structures.
Mapping of mosquito breeding sites in malaria endemic areas in Pos Lenjang, Kuala Lipis, Pahang, Malaysia
Background The application of the Geographic Information Systems (GIS) to the study of vector transmitted diseases considerably improves the management of the information obtained from the field survey and facilitates the study of the distribution patterns of the vector species. Methods As part of a study to assess remote sensing data as a tool for vector mapping, geographical features like rivers, small streams, forest, roads and residential area were digitized from the satellite images and overlaid with entomological data. Map of larval breeding habitats distribution and map of malaria transmission risk area were developed using a combination of field data, satellite image analysis and GIS technique. All digital data in the GIS were displayed in the WGS 1984 coordinate system. Six occasions of larval surveillance were also conducted to determine the species of mosquitoes, their characteristics and the abundance of habitats. Results Larval survey studies showed that anopheline and culicine larvae were collected and mapped from 79 and 67 breeding sites respectively. Breeding habitats were located at 100-400 m from human settlement. Map of villages with 400 m buffer zone visualizes that more than 80% of Anopheles maculatus s.s. immature habitats were found within the buffer zone. Conclusions This study amplifies the need for a broadening of the GIS approach which is emphasized with the aim of rejuvenating the dynamic aspect of entomological studies in Malaysia. In fact, the use of such basic GIS platforms promote a more rational basis for strategic planning and management in the control of endemic diseases at the national level. PMID:22166101
High Resolution Mapping of Enhancer-Promoter Interactions
Reeder, Christopher
RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for ...
Shared-Screen Interaction: Engaging Groups in Map-Mediated Nonverbal Communication
Konstantinos Chorianopoulos; Tim Rieniets
\\u000a This chapter describes the design and development of an interactive video installation that allows participants to explore\\u000a a map narrative, and engage in group interactions through a shared screen. For this purpose, several layers of cartographic\\u000a information were employed in a computer application, which was programmed with motion-tracking libraries in the open source\\u000a tool processing. The interactive video installation has
Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes.
Liao, Will; Ouyang, Weiming; Zhang, Michael Q; Li, Ming O
The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T cells have not been well characterized. In this study, we focused on mapping the genome wide Foxo1-binding sites in naďve CD4(+) T cells, CD8(+) T cells, and Foxp3(+) regulatory T (Treg) cells. By using chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq), we identified Foxo1 binding sites that were shared among or specific to the three T cell populations. Here we describe the experiments, quality controls, as well as the deep sequencing data. Part of the data analysis has been published by Ouyang W et al. in Nature 2012[1] and Kim MV et al. in Immunity 2013[2], and the associated data set were uploaded to NCBI Gene Expression Omnibus. PMID:25302145
The protein-protein interaction map of Helicobacter pylori
Jean-Christophe Rain; Luc Selig; Hilde De Reuse; Véronique Battaglia; Céline Reverdy; Stéphane Simon; Gerlinde Lenzen; Fabien Petel; Jérôme Wojcik; Vincent Schächter; Y. Chemama; Agnčs Labigne; Pierre Legrain
With the availability of complete DNA sequences for many prokaryotic and eukaryotic genomes, and soon for the human genome itself, it is important to develop reliable proteome-wide approaches for a better understanding of protein function. As elementary constituents of cellular protein complexes and pathways, protein-protein interactions are key determinants of protein function. Here we have built a large-scale protein-protein interaction
The gross architecture of an antibody-combining site as determined by spin-label mapping
Sutton, Brian J.; Gettins, Peter; Givol, David; Marsh, Derek; Wain-Hobson, Simon; Willan, Keith J.; Dwek, Raymond A.
1. A series of Dnp (dinitrophenyl) nitroxide spin labels was used to map the dimensions of the combining site of the Dnp-binding immunoglobulin A myeloma protein MOPC 315. The method compares the observed e.s.r. (electron-spin-resonance) hyperfine splittings with those calculated on the basis of different postulated motions for the spin label. The analysis is complicated by the sensitivity of the e.s.r. hyperfine splitting to the overall `tumbling' time of the antibody–hapten complex and the polarity of the spin-label's environment. When these effects are considered quantitatively, it is then possible to determine the degree of mobility of each hapten which is allowed by the shape of the combining site. 2. The dinitrophenyl ring is rigidly held, and the depth of the site is 1.1–1.2nm and has lateral dimensions at the entrance to the site ?0.6nm×0.9nm. The analysis of the results for spin-labelled haptens with chiral centres allows these lateral dimensions to be refined to 0.8nm and 1.1nm, and it is shown that the site is asymmetric with respect to the plane of the dinitrophenyl ring. 3. A polarity profile of the combining site was also obtained and a positively charged amino acid residue, possibly arginine-95L (light chain), was located at the entrance to the site. 4. The binding of Gd(III) to the antibody–hapten complexes results in quenching of the e.s.r. signal of the nitroxide. By using La(III) as a control, the paramagnetic contribution to the quenching is measured. 5. Analysis of the differential quenchings of the enantiomers of two five-membered nitroxide ring spin labels gives two possible locations of the metal-binding site. One of these is equidistant (0.7nm) from each of the three dinitrophenyl aromatic protons, and nuclear-magnetic-resonance relaxation studies, at 270MHz, on solutions of dinitrobenzene, Gd(III) and the Fv fragment (variable region of heavy and light chain) from protein MOPC 315 support this location for the metal site. 6. The e.s.r. and metal-binding data were then compared with the results of a model of the combining site constructed on the basis of framework invariance in immunoglobulins [Padlan, Davies, Pecht, Givol & Wright (1976) Cold Spring Harbor Symp. Quant. Biol. 41, in the press]. The overall agreement is very good. Assignments of possible chelating groups for the metal can be made. PMID:200219
Digital mapping of the Mars Pathfinder landing site: Design, acquisition, and derivation of cartographic products for science applications
L. R. Gaddis; R. L. Kirk; J. R. Johnson; L. A. Soderblom; A. W. Ward; J. Barrett; K. Becker; T. Becker; J. Blue; D. Cook; E. Eliason; T. Hare; E. Howington-Kraus; C. Isbell; E. M. Lee; B. Redding; R. Sucharski; T. Sucharski; P. H. Smith; D. T. Britt
The Imager for Mars Pathfinder (IMP) acquired more than 16,000 images and provided panoramic views of the surface of Mars at the Mars Pathfinder landing site in Ares Vallis. This paper describes the stereoscopic, multispectral IMP imaging sequences and focuses on their use for digital mapping of the landing site and for deriving cartographic products to support science applications of
Copyright 2004 by the Genetics Society of America A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites
Wendel, Jonathan F.
of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton H. Paterson*,,1 *Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster
Identification and mapping of natural vegetation on a coastal site using a Worldview-2 satellite image.
Rapinel, Sébastien; Clément, Bernard; Magnanon, Sylvie; Sellin, Vanessa; Hubert-Moy, Laurence
Identification and mapping of natural vegetation are major issues for biodiversity management and conservation. Remotely sensed data with very high spatial resolution are currently used to study vegetation, but most satellite sensors are limited to four spectral bands, which is insufficient to identify some natural vegetation formations. The study objectives are to discriminate natural vegetation and identify natural vegetation formations using a Worldview-2 satellite image. The classification of the Worldview-2 image and ancillary thematic data was performed using a hybrid pixel-based and object-oriented approach. A hierarchical scheme using three levels was implemented, from land cover at a field scale to vegetation formation. This method was applied on a 48 km˛ site located on the French Atlantic coast which includes a classified NATURA 2000 dune and marsh system. The classification accuracy was very high, the Kappa index varying between 0.90 and 0.74 at land cover and vegetation formation levels respectively. These results show that Wordlview-2 images are suitable to identify natural vegetation. Vegetation maps derived from Worldview-2 images are more detailed than existing ones. They provide a useful medium for environmental management of vulnerable areas. The approach used to map natural vegetation is reproducible for a wider application by environmental managers. PMID:24973612
Adjustment of footprint correction for airborne flux mapping over the FIFE site
NASA Technical Reports Server (NTRS)
Schuepp, P. H.; Macpherson, J. I.; Desjardins, R. L.
A meaningful interpretation of airborne flux estimates over nonuniform terrain must consider local advection from nonhomogeneous source distributions (footprint correction). An empirical procedure for footprint correction of airborne flux data obtained in the First ISLSCP Field Experiment (FIFE) 1989 is presented, based on simple analytical solutions of the diffusion equation which have been adjusted to approximate more realistic solutions. Optimized estimates of surface flux 'maps' derived from airborne observations are then constructed for maximum correlation between flux estimates and independently observed surface characteristics. This paper also includes an analysis of resolution for the given procedure, in terms of amplitude recovery of hypothetical square-wave distributions of surface flux density, and discusses its implications for the interpretation of the optimized estimates of FIFE surface flux maps. Results show that corrected spatial sink distributions are obtained by the current empirical procedure at the cost of considerable reduction in amplitude recovery of small-scale variations in surface flux density. The high spatial correlation observed between corrected flux maps and surface characteristics such as greenness or surface temperature excess is ascribed to the approximately correct positioning of the main flux gradients across the site, which can be expected to have been reproduced with amplitude recovery equal to or greater than 60 percent.
A chromatin binding site in the tail domain of nuclear lamins that interacts with core histones
Interaction of chromatin with the nuclear envelope and lamina is thought to help determine higher order chromosome organization in the interphase nucleus. Previous studies have shown that nuclear lamins bind chromatin directly. Here we have localized a chromatin binding site to the carboxyl-terminal tail domains of both A- and B-type mammalian lamins, and have characterized the biochemical properties of this binding in detail. Recombinant glutathione-S-transferase fusion proteins containing the tail domains of mammalian lamins C, B1, and B2 were analyzed for their ability to associate with rat liver chromatin fragments immobilized on microtiter plate wells. We found that all three lamin tails specifically bind to chromatin with apparent KdS of 120-300 nM. By examining a series of deletion mutants, we have mapped the chromatin binding region of the lamin C tail to amino acids 396- 430, a segment immediately adjacent to the rod domain. Furthermore, by analysis of chromatin subfractions, we found that core histones constitute the principal chromatin binding component for the lamin C tail. Through cooperativity, this lamin-histone interaction could be involved in specifying the high avidity attachment of chromatin to the nuclear envelope in vivo. PMID:7559784
Interactive Marine Spatial Planning: Siting Tidal Energy Arrays around the Mull of Kintyre
Alexander, Karen A.; Janssen, Ron; Arciniegas, Gustavo; O'Higgins, Timothy G.; Eikelboom, Tessa; Wilding, Thomas A.
The rapid development of the offshore renewable energy sector has led to an increased requirement for Marine Spatial Planning (MSP) and, increasingly, this is carried out in the context of the 'ecosystem approach' (EA) to management. We demonstrate a novel method to facilitate implementation of the EA. Using a real-time interactive mapping device (touch-table) and stakeholder workshops we gathered data and facilitated negotiation of spatial trade-offs at a potential site for tidal renewable energy off the Mull of Kintyre (Scotland). Conflicts between the interests of tidal energy developers and commercial and recreational users of the area were identified, and use preferences and concerns of stakeholders were highlighted. Social, cultural and spatial issues associated with conversion of common pool to private resource were also revealed. The method identified important gaps in existing spatial data and helped to fill these through interactive user inputs. The workshops developed a degree of consensus between conflicting users on the best areas for potential development suggesting that this approach should be adopted during MSP. PMID:22253865
Acoustic mapping of the regional seafloor geology in and around Hawaiian ocean dredged-material disposal sites
Torresan, Michael E.; Gardner, James V.
During January and February 1998 the U.S. Geological Survey Coastal and Marine Geology Team (USGS) conducted regional high-resolution multibeam mapping surveys of the area surrounding EPA-designated ocean disposal sites located offshore of the Hawaiian Islands of Oahu, Kauai, Maui, and Hawaii. The sites are all located within 5 nautical miles of shore on insular shelves or slopes. Regional maps were required of areas much larger than the disposal sites themselves to assess both the regional seafloor geology and the immediate vicinity of the disposal sites. The purpose of the disposal site surveys was to delimit the extent of disposal material by producing detailed bathymetric and backscatter maps of the seafloor with a ± 1 m spatial accuracy and <1% depth error. The advantage of using multibeam over conventional towed, single-beam sidescan sonar is that the multibeam data are accurately georeferenced for precise location of all imaged features. The multibeam produces a coregistered acoustic-backscatter map that is often required to locate individual disposal deposits. These data were collected by the USGS as part of its regional seafloor mapping and in support of ocean disposal site monitoring studies conducted in cooperation with the US Environmental Protection Agency (EPA) and the US Army Corps of Engineers (COE).
A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data*
Aucher, Willy; Becker, Emmanuelle; Ma, Emilie; Miron, Simona; Martel, Arnaud; Ochsenbein, Françoise; Marsolier-Kergoat, Marie-Claude; Guerois, Raphaël
Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/. PMID:20733106
Interactive Web-based Access and Analysis Tools for the Western Climate Mapping Initiative (WestMap)
NASA Astrophysics Data System (ADS)
Comrie, A. C.; Redmond, K.; Glueck, M. F.; Reinbold, H.
The Western Climate Mapping Consortium (WestMap) has developed a prototype web-based interactive access and resource interface to optimize public dissemination and usage of fine-scale spatial climate time series for the western United States. The western U.S. focus reflects the complex climate interactions and diverse geography that make resource management, policy considerations, and climate research challenging in this region. WestMap was conceived by a consortium comprised of the University of Arizona/CLIMAS, the Western Regional Climate Center (WRCC)/Desert Research Institute, and the PRISM group at Oregon State University, along with collaborators at Scripps Institute of Oceanography/California Applications Project, NOAA Climate Diagnostics Center, and the USDA Natural Resource Conservation Service. WestMap evolved in direct response to a multitude of requests to the WRCC and the RISAs from public and private stakeholder communities for lengthy time series of fine-scale spatial climate aggregated to user-specified domains, and related user-friendly web-based access and analysis tools. The WestMap interface is designed to link three stakeholder-driven components, 1) climate data development and operations (access, maintenance); 2) error assessment, data analysis, diagnostics, and related tools; and (3) data access, visualization, and educational resources. The 100-year PRISM 4km monthly temperature and precipitation series serve as the initial data archive, updating automatically once in operational mode. Operational user components are being designed to allow direct stakeholder access to user-specified data and resources most relevant to current needs in a timely manner. Requested resources currently in development and limited testing stages include clickable maps, regional aggregate capabilities, basic statistical analysis, time series visualization, error assessment, and download/print capability. Phased prototype testing, currently underway internally, will continue with broader stakeholder participation into Spring 2007. Operational release of the prototype interface is planned for late Summer 2007. At this meeting, we will share the latest developmental version of the WestMap interface with participants and invite feedback to help maximize the utility of the interface for the greater interdisciplinary climate community having interests in the western United States.
Carbon Sequestration Atlas and Interactive Maps from the Southwest Regional Partnership on Carbon Sequestration
McPherson, Brian
In November of 2002, DOE announced a global climate change initiative involving joint government-industry partnerships working together to find sensible, low cost solutions for reducing GHG emissions. As a result, seven regional partnerships were formed; the Southwest Regional Partnership on Carbon Sequestration (SWP) is one of those. These groups are utilizing their expertise to assess sequestration technologies to capture carbon emissions, identify and evaluate appropriate storage locations, and engage a variety of stakeholders in order to increase awareness of carbon sequestration. Stakeholders in this project are made up of private industry, NGOs, the general public, and government entities. There are a total of 44 current organizations represented in the partnership including electric utilities, oil and gas companies, state governments, universities, NGOs, and tribal nations. The SWP is coordinated by New Mexico Tech and encompasses New Mexico, Arizona, Colorado, Oklahoma, Utah, and portions of Kansas, Nevada, Texas, and Wyoming. Field test sites for the region are located in New Mexico (San Juan Basin), Utah (Paradox Basin), and Texas (Permian Basin).[Taken from the SWP C02 Sequestration Atlas] The SWP makes available at this website their CO2 Sequestration Atlas and an interactive data map.
User-Centric Secure Cross-Site Interaction Framework for Online Social Networking Services
ERIC Educational Resources Information Center
Ko, Moo Nam
Social networking service is one of major technological phenomena on Web 2.0. Hundreds of millions of users are posting message, photos, and videos on their profiles and interacting with other users, but the sharing and interaction are limited within the same social networking site. Although users can share some content on a social networking site…
Interactive global illumination based on coherent surface shadow maps
Tobias Ritschel; Thorsten Grosch; Jan Kautz; Hans-Peter Seidel
Interactive rendering of global illumination effects is a challenging problem. While precomputed radiance transfer (PRT) is able to render such effects in real time the geometry is generally assumed static. This work proposes to replace the precomputed lighting re- sponse used in PRT by precomputed depth. Precomputing depth has the same cost as precomputing visibility, but allows visibility tests for
Mapping the Energy Surface of Transmembrane Helix-Helix Interactions
Jaume Torres; Andreas Kukol; Isaiah T. Arkin
Transmembrane helices are no longer believed to be just hydrophobic segments that exist solely to anchor proteins to a lipid bilayer, but rather they appear to have the capacity to specify function and structure. Specific interactions take place between hydrophobic segments within the lipid bilayer whereby subtle mutations that normally would be considered innocuous can result in dramatic structural differences.
A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis
Gang Wu; Lisha Zhu; Jennifer E. Dent; Christine Nardini; Frank Beier
BackgroundComputational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine - the scientific approach to medicine in tight relation with basic science -, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions
Testing the Usability of Interactive Maps in CommonGIS
Natalia Andrienko; Gennady Andrienko; Hans Voss; Fatima Bernardo; Joana Hipolito; Ursula Kretchmer
The paper reports on an experimental study aimed at assessing the usability of five different interactive tools for exploratory analysis of geographically referenced data implemented in CommonGIS. Usability was assessed in terms of tool learnability, memorability, and user satisfaction. The study provided valuable data concerning the usability of each individual tool; we also derived some conclusions relevant to geovisualization techniques
Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps
Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and for defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of 'hit' genes are measured in a double-shRNA screen and used to construct a genetic interaction map.
Antiferromagnetic interaction between A'-site Mn spins in A-site-ordered perovskite YMn3Al4O12.
Tohyama, Takenori; Saito, Takashi; Mizumaki, Masaichiro; Agui, Akane; Shimakawa, Yuichi
The A-site-ordered perovskite YMn(3)Al(4)O(12) was prepared by high-pressure synthesis. Structural analysis with synchrotron powder X-ray diffraction data and the Mn L-edges X-ray absorption spectrum revealed that the compound has a chemical composition Y(3+)Mn(3+)(3)Al(3+)(4)O(2-)(12) with magnetic Mn(3+) at the A' site and non-magnetic Al(3+) at the B site. An antiferromagnetic interaction between the A'-site Mn(3+) spins is induced by the nearest neighboring Mn-Mn direct exchange interaction and causes an antiferromagnetic transition at 34.3 K. PMID:20108915
Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
Poh, Huay Mei; Peh, Su Qin; Ong, Chin Thing; Zhang, Jingyao; Ruan, Xiaoan; Ruan, Yijun
Genomes are organized into three-dimensional structures, adopting higher-order conformations inside the micron-sized nuclear spaces 7, 2, 12. Such architectures are not random and involve interactions between gene promoters and regulatory elements 13. The binding of transcription factors to specific regulatory sequences brings about a network of transcription regulation and coordination 1, 14. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) was developed to identify these higher-order chromatin structures 5,6. Cells are fixed and interacting loci are captured by covalent DNA-protein cross-links. To minimize non-specific noise and reduce complexity, as well as to increase the specificity of the chromatin interaction analysis, chromatin immunoprecipitation (ChIP) is used against specific protein factors to enrich chromatin fragments of interest before proximity ligation. Ligation involving half-linkers subsequently forms covalent links between pairs of DNA fragments tethered together within individual chromatin complexes. The flanking MmeI restriction enzyme sites in the half-linkers allow extraction of paired end tag-linker-tag constructs (PETs) upon MmeI digestion. As the half-linkers are biotinylated, these PET constructs are purified using streptavidin-magnetic beads. The purified PETs are ligated with next-generation sequencing adaptors and a catalog of interacting fragments is generated via next-generation sequencers such as the Illumina Genome Analyzer. Mapping and bioinformatics analysis is then performed to identify ChIP-enriched binding sites and ChIP-enriched chromatin interactions 8. We have produced a video to demonstrate critical aspects of the ChIA-PET protocol, especially the preparation of ChIP as the quality of ChIP plays a major role in the outcome of a ChIA-PET library. As the protocols are very long, only the critical steps are shown in the video. PMID:22564980
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.
Thomason, Maureen K; Bischler, Thorsten; Eisenbart, Sara K; Förstner, Konrad U; Zhang, Aixia; Herbig, Alexander; Nieselt, Kay; Sharma, Cynthia M; Storz, Gisela
While the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-type E. coli and from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by the rnc and rne mutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts in E. coli and is easily accessible, together with the cDNA coverage plots, in an online genome browser. PMID:25266388
Jules Verne Voyager, Jr: An Interactive Map Tool for Teaching Plate Tectonics
NASA Astrophysics Data System (ADS)
Hamburger, M. W.; Meertens, C. M.
Research Networks Map | Division of Cancer Prevention
Click the check boxes to show or hide sites by category. Zoom in to view sites that are in close proximity to each other; zoom out to view sites in Hawaii and Puerto Rico. A text equivalent of the interactive map is below the map.
Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map*
There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or emergent dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses.
Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica
Joel A. Malek; Jamey M. Wierzbowski; Wei Tao; Stephanie A. Bosak; David J. Saranga; Lynn Doucette-Stamm; Douglas R. Smith; Paul J. McEwan; Kevin J. McKernan
Protein interaction maps can reveal novel pathways and functional complexes, allowing 'guilt by associ- ation' annotation of uncharacterized proteins. To address the need for large-scale protein interaction analyses, a bacterial two-hybrid system was coupled with a whole genome shotgun sequencing approach for microbial genome analysis. We report the first large-scale proteomics study using this system, integrating de novo genome sequencing
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
Elena Nabieva; Kam Jim; Amit Agarwal; Bernard Chazelle; Mona Singh
Motivation: Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are complemented by an abundance of data about other types of functional relationships
Using Hadoop File System and MapReduce in a small/medium Grid site
NASA Astrophysics Data System (ADS)
Riahi, H.; Donvito, G.; Fanň, L.; Fasi, M.; Marzulli, G.; Spiga, D.; Valentini, A.
Data storage and data access represent the key of CPU-intensive and data-intensive high performance Grid computing. Hadoop is an open-source data processing framework that includes fault-tolerant and scalable distributed data processing model and execution environment, named MapReduce, and distributed File System, named Hadoop distributed File System (HDFS). HDFS was deployed and tested within the Open Science Grid (OSG) middleware stack. Efforts have been taken to integrate HDFS with gLite middleware. We have tested the File System thoroughly in order to understand its scalability and fault-tolerance while dealing with small/medium site environment constraints. To benefit entirely from this File System, we made it working in conjunction with Hadoop Job scheduler to optimize the executions of the local physics analysis workflows. The performance of the analysis jobs which used such architecture seems to be promising, making it useful to follow up in the future.
Molecular epidemiology and restriction site mapping of adenovirus type 3 genome types.
Adrian, T; Best, B; Hierholzer, J C; Wigand, R
One hundred thirty-eight strains of adenovirus type 3 isolated from patients in the United States, West Germany, and other regions between 1961 and 1984 were analyzed with six restriction endonucleases; 18 genome types were found. BglII was the most discriminative enzyme. Mapping of altered restriction sites was also performed for all six enzymes. The genome types D1 (like the prototype) and D3 prevailed among 45 and 47 strains, respectively. All genome types could be divided into two groups related to D1 or D3. Several clusters of infections by strains with the same genome type were observed. Only hints of differences were found in the pathogenicities of individual genome types. D1 strains were present in the United States and in Europe; group D3 prevailed almost exclusively in the United States. Images PMID:2546977
Geologic map of the Mine Mountain area, Nevada Test Site, southern Nevada
Cashman, P.H.; Cole, J.C.
The Mine Mountain area is a small range of hills on the west side of the central Yucca Flat basin on the Nevada Test Site, Nye County, Nevada. This map portrays the very complex relationships among the pre-Tertiary stratigraphic units of the region. Rocks and structures of the Mine Mountain area record the compounded effects of: (1) eastward-directed, foreland-vergent thrusting; (2) younger folds and thrusts formed by hinterland vergence in a general westerly direction; and (3) low-angle normal faulting formed by extension along a northeast-southwest trend. All of these structures are older than the oldest middle Miocene volcanic rocks that were deposited on the flanks of the Mine Mountain terrane. High-angle faults that post-date these volcanic rocks locally show displacements of several hundred meters, but do not strongly affect patterns in the pre-Tertiary rocks.
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
Background Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps. PMID:24099179
Mapping of noise impact provoked by the execution of foundation piles at high rise building sites.
de Araújo, Adolpho Guido; Gusmăo, Alexandre Duarte; Rabbani, Emilia Rahnemay Kohman; Fucale, Stela Paulino
The objective of this work is to map, in a limited area inside and outside of the worksite, the environmental impact generated by sound pollution coming from the driving of foundation piles for high rise buildings, as well as to observe and check if the noise levels produced by the emitting source are tolerable in the urban environment. The methodology of the work includes a survey of technical references about the subject; measurement of noises surrounding the worksite during the foundation phase for four distinct buildings, with different types of piles: prefabricated piles, continuous helical displacement piles , traditional compaction piles and Terra Probe compaction piles. A grid of points was built due to the time of driving and after that the measurements of environmental noises were performed emitted by the execution of each type of pile using a sound level meter. The interpretation of the measurements and their impacts on the neighborhood of the building were performed using the computational tool Suffer for creating noise level contours. The X and Y axes of the grid represent the distances in meters of the area studied and the Z axis represents the noise measured in dB. The contours developed represent the mapping of the noise at the worksites and their surroundings. The mapping of the urban impact of noise, the measurement of its dimensions, and the examination of its propagation around the building are important subsides to adequate individual and collective protection procedures. Seventy one points were measured at four building sites with different types of piles, and the results showed that at only three points was the noise within the limits of the Municipal Law of Recife of 70 dB, which proves the relevance of the research. Finally, the comparative analysis between the four types of piles shows that the continuous helical displacement pile emits the lowest noise level among the four pile types studied. PMID:22317218
Limitation of application of conformal mapping on the interaction of an edge dislocation and a crack
Wang, S.; Hu, C.; Lee, S. [Natl Tsing Hua Univ, Hsinchu, Taiwan (China)
The limitation of application of conformal mapping on the interaction between an edge dislocation and a crack is investigated. The in-plane fracture is usually obtained by the method of the Muskhelishvili complex potential. The equation obtained by the method of Muskhelishvili can be solved by Cauchy integral if it is analytic. Based on this point of view, an exact solution of an edge dislocation near a semi-infinite crack is obtained using conformal mapping. However, the conformal mapping cannot be applied to the problem of a wedge crack because the ratio of mapping function to the conjugate of its derivative is not analytic. Generally, most crack problems encounter the same difficulty as the wedge crack in obtaining the analytic form. 11 refs.
An Interactive Map Viewer for the Urban Geology of Ottawa (Canada): an Example of Web Publishing
D. Giroux; R. Bélanger
Developed by the Terrain Sciences Division (TSD) of the Geological Survey of Canada (GSC), an interactive map viewer, called GEOSERV (www.geoserv.org), is now available on the Internet. The purpose of this viewer is to provide engineers, planners, decision makers, and the general public with the geoscience information required for sound regional planning in densely populated areas, such as Canada's national
A simple contact mapping algorithm for identifying potential peptide mimetics in protein–protein interaction partners
Krall, Alex; Brunn, Jonathan; Kankanala, Spandana; Peters, Michael H
A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, "OpenContact" provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mimetics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data necessary for further detailed analysis and drug development. In addition, we used the static parsing/mapping method to develop a peptide mimetic to the cancer protein target, epidermal growth factor receptor. In this case, secondary, loop structure for the peptide was indicated from the intra-protein mapping, and the peptide was subsequently synthesized and shown to exhibit successful binding to the target protein. The case studies, which all involved experimental peptide drug advancement, illustrate many of the challenges associated with the development of peptide biomimetics, in general. Proteins 2014; 82:2253–2262. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:24756879
Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology
Kurt W. Kohn; Mirit I. Aladjem; John N. Weinstein; Yves Pommier
A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become standard. We have prepared many detailed bioregulatory network diagrams using the Molecular Interaction Map (MIM) notation, and now feel confident that it is suitable as a standard. Here we describe
Three-Dimensional Mapping of Near-Field Interactions via Single-Photon
Gerton, Jordan M.
Three-Dimensional Mapping of Near-Field Interactions via Single-Photon Tomography Benjamin D ABSTRACT We demonstrate a near-field tomography method for investigating the coupling between a nanoscopic such as lightning rods,1,2 optical antennae,3-5 and roughened surfaces.6-8 For example, in surface-enhanced Raman
RE Atlas: The U.S. Atlas of Renewable Resources (Interactive Map, GIS Data)
This interactive data map allows a user to explore the locations across the U.S. of many different basic, renewable energy resources. The many layers can be activated one at a time or in multiple combinations and the GIS display draws from a rich combination of data collections.
Feature Description and Feature Interaction Analysis with Use Case Maps and LOTOS
Daniel Amyot; Leďla Charfi; Nicolas Gorse; Tom Gray; Luigi Logrippo; Jacques Sincennes; Bernard Stepien; Tom Ware
A methodology for feature design, specification, and validation is pre- sented. The methodology is based on Use Case Maps for the description of features and on LOTOS with its tools for animation of the features, for feature validation, and for feature interaction detection. It has been developed as a collaborative project between the University of Ottawa and Mitel Corporation, and
Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems
Kurt W. Kohn
Eventually to understand the integrated function of the cell cycle regulatory network, we must organize the known interactions in the form of a diagram, map, and\\/or database. A diagram convention was designed capable of unambiguous representation of networks containing multi- protein complexes, protein modifications, and enzymes that are substrates of other enzymes. To facilitate linkage to a database, each molecular
Klippel, Alexander
CARTOGRAPHIC ANIMATION AND LEGENDS FOR TEMPORAL MAPS: EXPLORATION AND OR INTERACTION email@example.com & firstname.lastname@example.com Abstract Temporal cartographic animations are increasingly common. For users to understand a temporal animation, they must not only apply an appropriate spatial knowledge schema that allows
Available online at www.sciencedirect.com Charting the genetic interaction map of a cell
Boone, Charlie
to those seeking to understand the wiring diagram of the cell. Genome-scale screens for genetic the mapping of genetic interaction networks in genetically tractable model organ- isms amenable to large-scale Costanzo1 , Anastasia Baryshnikova1 , Chad L Myers2 , Brenda Andrews1 and Charles Boone1 Genome sequencing
Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations
Li, Shanshan; Wang, Jiankang; Zhang, Luyan
Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis. PMID:26161656
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
Background Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL). Results Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. Conclusions We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic maps and association mapping. PMID:21205322
M sub 1 muscarinic antagonists interact with. sigma. recognition sites
Hudkins, R.L. (Virginia Commonwealth Univ., Richmond (United States)); DeHaven-Hudkins, D.L. (Sterling Research Group, Malvern, PA (United States))
The M{sub 1}-selective muscarinic antagonists aprophen, caramiphen, carbetapentane, 2-DAEX, dicyclomine, hexahydrosiladifenidol, iodocaramiphen, nitrocaramiphen, oxybutynin and trihexyphenidyl potently inhibited binding to {sigma} sites in brain. Both basic ester and non-ester structural type compounds which exhibit affinity for the muscarinic receptor also demonstrated affinity for the {sigma} site, while the classical antimuscarinic agents atropine and QNB, and the tricyclic pirenzepine, were ineffective in binding to this site. The authors also observed a significant correlation between the K{sub i} values for {sigma}compounds to inhibit ({sup 3}H)pirenzepine binding and their IC{sub 50} values to inhibit carbachol-stimulated phosphoinositide turnover. These observations may aid in elucidating the relationship of {sigma} binding to inhibition of phosphoinositide turnover stimulated by cholinergic agonists.
Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses
Diancourt, Laure; Caro, Valérie; Thaisomboonsuk, Butsaya; Richardson, Jason H.; Jarman, Richard G.; Ponlawat, Alongkot; Lambrechts, Louis
Specific interactions between host genotypes and pathogen genotypes (G×G interactions) are commonly observed in invertebrate systems. Such specificity challenges our current understanding of invertebrate defenses against pathogens because it contrasts the limited discriminatory power of known invertebrate immune responses. Lack of a mechanistic explanation, however, has questioned the nature of host factors underlying G×G interactions. In this study, we aimed to determine whether G×G interactions observed between dengue viruses and their Aedes aegypti vectors in nature can be mapped to discrete loci in the mosquito genome and to document their genetic architecture. We developed an innovative genetic mapping strategy to survey G×G interactions using outbred mosquito families that were experimentally exposed to genetically distinct isolates of two dengue virus serotypes derived from human patients. Genetic loci associated with vector competence indices were detected in multiple regions of the mosquito genome. Importantly, correlation between genotype and phenotype was virus isolate-specific at several of these loci, indicating G×G interactions. The relatively high percentage of phenotypic variation explained by the markers associated with G×G interactions (ranging from 7.8% to 16.5%) is consistent with large-effect host genetic factors. Our data demonstrate that G×G interactions between dengue viruses and mosquito vectors can be assigned to physical regions of the mosquito genome, some of which have a large effect on the phenotype. This finding establishes the existence of tangible host genetic factors underlying specific interactions between invertebrates and their pathogens in a natural system. Fine mapping of the uncovered genetic loci will elucidate the molecular mechanisms of mosquito-virus specificity. PMID:23935524
Evaluating the Effectiveness of Interactive Map Interface Designs: A Case Study Integrating Usability Metrics with Eye-Movement Analysis
Arzu Çöltekin; Benedikt Heil; Simone Garlandini; Sara Irina Fabrikant
This paper proposes combining traditional usability methods with the analysis of eye movement recordings to evaluate interactive map interfaces, and presents a case study in support of this approach. The case study evaluates two informationally equivalent, but differently designed online interactive map interfaces presented to novice users. In a mixed factorial experiment, thirty participants were asked to solve three typical
Site-specific mapping and quantification of protein S-sulfenylation in cells
Yang, Jing; Gupta, Vinayak; Carroll, Kate S.; Liebler, Daniel C.
Cysteine S-sulfenylation provides redox regulation of protein functions, but the global cellular impact of this transient post-translational modification remains unexplored. We describe a chemoproteomic workflow to map and quantify over 1,000 S-sulfenylation sites on more than 700 proteins in intact cells. Quantitative analysis of human cells stimulated with hydrogen peroxide or epidermal growth factor measured hundreds of site selective redox changes. Different cysteines in the same proteins displayed dramatic differences in susceptibility to S-sulfenylation. Newly discovered S-sulfenylations provided mechanistic support for proposed cysteine redox reactions and suggested novel redox mechanisms, including S-sulfenyl-mediated redox regulation of the transcription factor HIF1A by SIRT6. S-sulfenylation is favored at solvent-exposed protein surfaces and is associated with sequence motifs that are distinct from those for other thiol modifications. S-sulfenylations affect regulators of phosphorylation, acetylation and ubiquitylation, which suggests regulatory crosstalk between redox control and signaling pathways. PMID:25175731
Odorant binding by a pheromone binding protein: active site mapping by photoaffinity labeling.
Du, G; Ng, C S; Prestwich, G D
The bacterially expressed recombinant pheromone binding protein (PBP) of Antheraea polyphemus was photoaffinity labeled with (6E,11Z)-[3H]hexadecadienyl diazoacetate, a photoactivatable analog of the naturally occurring acetate pheromone. Radiolabeled peptides were separated from an endoproteinase Lys-C digestion by HPLC and characterized by Edman degradation. The label was exclusively found in the Asp39-Lys58 fragment. Cleavage of this peptide (DDYVMTDRLAGCAINCLATK) with Arg-C gave a single radiolabeled peptide (DDYVMTDR), which was predicted to be alpha-helical. The adjoining LAGCAINCLATK fragment, which is highly conserved in PBP sequences, was predicted to be a hydrophobic beta-strand and has been proposed to be important in recognition of the alkadienyl chain. Edman degradation confirmed the location of the covalently attached ligand at Thr44 of the smaller hydrophilic peptide. In addition, the synthesis of the newly identified pheromone component (4E,9Z)-tetradecadienyl acetate and its photoaffinity analog, (4E,9Z)-[3H]tetradecadienyl diazoacetate, is also described. Mapping of PBP photoaffinity labeled by (4E,9Z)-[3H]14:Dza revealed that the hydrophobic region Asp21-Lys38 adjacent to the primary binding domain Asp39-Lys58 contained a second modification site. The 14-carbon odorant molecule thus had two binding positions within the recognition site, while only a single binding position was available to the 16-carbon pheromone. PMID:8161541
Geologic map of Paleozoic rocks in the Calico Hills, Nevada Test Site, southern Nevada
Cole, J.C.; Cashman, P.H.
The Calico Hills area in the southwestern part of the Nevada Test Site, Nye County, Nevada, exposes a core of pre-Tertiary rocks surrounded by middle Miocene volcanic strata. This map portrays the very complex relationships among the pre-Tertiary stratigraphic units of the region. The Devonian and Mississippian rocks of the Calico Hills are distinct from age-equivalent carbonate-shelf or submarine-fan strata in other parts of the Nevada Test Site. The Calico Hills strata are interpreted to have been deposited beyond the continental shelf edge from alternating silicic and carbonate clastic sources. Structures of the Calico Hills area record the compounded effects of: (1) eastward-directed, foreland-vergent thrusting; (2) younger folds, kink zones, and thrusts formed by hinterland-vergent deformation toward northwesterly and northerly directions; and (3) low-angle normal faults that displaced blocks of Middle Paleozoic carbonate strata across the contractionally deformed terrane. All of these structures are older than any of the middle Miocene volcanic rocks that were erupted across the Calico Hills.
Mapping of contamination at Savannah River Site FBWU by INEEL trolley
Carpenter, M.V.; Gehrke, R.J.; Helmer, R.G.; Josten, N.
The Ford Building Waste Unit (FBWU) 643-11G is a Resource Conservation and Recovery Act/Comprehensive Environmental Response Compensation and Liability Act (RCRA/CERCLA) designated site at the Savannah River Site (SRS) in Aiken, South Carolina. Pre-Work Plan Characterization at the FBWU in May 1996 indicated that radiological contamination was present in surface and near surface soils and identified cesium-137, {sup 137}Cs, the unit specific contaminant, as being primarily in the top 15 cm of soil. The Idaho National Engineering and Environmental Laboratory (INEEL) sent the dig-face trolley system to SRS where it demonstrated its capability over a 6.1-m (20 ft.) x 9.6-m (30 ft.) area to rapidly map the contamination on-line with its large area plastic scintillation detector. Also, an extended-range (10 keV to 3 MeV) Ge detector was used at selected locations to identify and quantify the {sup 137}Cs contamination. The coordinate locations of each measurement acquired in either the scanning or fixed position mode was obtained with a survey system based on radial encoders. Topography measurements were also made during measurements to permit correction of field of view and activity concentrations for changes in the ground to detector distance.
Research Resource: Genome-Wide Mapping of in Vivo Androgen Receptor Binding Sites in Mouse Epididymis
Hu, Shuanggang; Yao, Guangxin; Guan, Xiaojun; Ni, Zimei; Ma, Wubin; Wilson, Elizabeth M.; French, Frank S.; Liu, Qiang; Zhang, Yonglian
Epididymal function depends on androgen signaling through the androgen receptor (AR), although most of the direct AR target genes in epididymis remain unknown. Here we globally mapped the AR binding regions in mouse caput epididymis in which AR is highly expressed. Chromatin immunoprecipitation sequencing indicated that AR bound selectively to 19,377 DNA regions, the majority of which were intergenic and intronic. Motif analysis showed that 94% of the AR binding regions harbored consensus androgen response elements enriched with multiple binding motifs that included nuclear factor 1 and activator protein 2 sites consistent with combinatorial regulation. Unexpectedly, AR binding regions showed limited conservation across species, regardless of whether the metric for conservation was based on local sequence similarity or the presence of consensus androgen response elements. Further analysis suggested the AR target genes are involved in diverse biological themes that include lipid metabolism and sperm maturation. Potential novel mechanisms of AR regulation were revealed at individual genes such as cysteine-rich secretory protein 1. The composite studies provide new insights into AR regulation under physiological conditions and a global resource of AR binding sites in a normal androgen-responsive tissue. PMID:20943813
Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping.
Gagnon, Keith T; Maxwell, E Stuart
Heavy metal cleavage mapping analysis of both assembling and fully mature ribonucleoprotein (RNP) complexes are informative techniques for assessing the intermolecular base pairing between small non-coding RNAs and their interacting target RNAs. Lead cleavage of the RNA in partially or fully assembled RNPs in the absence or presence of the interacting RNA can determine both the accessibility of the base pairing sequence within the RNP itself as well as its interaction with the target RNA. In this chapter, we detail how this technique was used to map the intermolecular RNA:RNA base pairing of a box C/D RNA with its target RNA within the assembling archaeal RNP complex. PMID:25352141
REVIEW ARTICLE Enabling cross-site interactions in social networks
Shehab, Mohamed
using a secret address of content, appropriate access control mechanisms are still not supported application that shares user's photos between Facebook and MySpace based on the cross-site access control network services, including Facebook, MySpace, Twitter, LinkedIn, Hi5, and Orkut have gained user adoption
Near-surface gas mapping studies of salt geologic features at Weeks Island and other sites
Molecke, M.A. [Sandia National Lab., Albuquerque, NM (United States); Carney, K.R.; Autin, W.J.; Overton, E.B. [Louisiana State Univ., Baton Rouge, LA (United States)
Field sampling and rapid gas analysis techniques were used to survey near-surface soil gases for geotechnical diagnostic purposes at the Weeks Island Strategic Petroleum Reserve (SPR) site and other salt dome locations in southern Louisiana. This report presents the complete data, results and interpretations obtained during 1995. Weeks Island 1994 gas survey results are also briefly summarized; this earlier study did not find a definitive correlation between sinkhole No. 1 and soil gases. During 1995, several hundred soil gas samples were obtained and analyzed in the field by gas chromatography, for profiling low concentrations and gas anomalies at ppm to percent levels. The target gases included hydrogen, methane, ethane and ethylene. To supplement the field data, additional gas samples were collected at various site locations for laboratory analysis of target gases at ppb levels. Gases in the near-surface soil originate predominantly from the oil, from petrogenic sources within the salt, or from surface microbial activity. Surveys were conducted across two Weeks Island sinkholes, several mapped anomalous zones in the salt, and over the SPR repository site and its perimeter. Samples were also taken at other south Louisiana salt dome locations for comparative purposes. Notable results from these studies are that elevated levels of hydrogen and methane (1) were positively associated with anomalous gassy or shear zones in the salt dome(s) and (2) are also associated with suspected salt fracture (dilatant) zones over the edges of the SPR repository. Significantly elevated areas of hydrogen, methane, plus some ethane, were found over anomalous shear zones in the salt, particularly in a location over high pressure gas pockets in the salt, identified in the mine prior to SPR operations. Limited stable isotope ratio analyses, SIRA, were also conducted and determined that methane samples were of petrogenic origin, not biogenic.
Interaction map of the Trypanosoma cruzi ribosomal P protein complex (stalk) and the elongation factor 2.
Smulski, Cristian R; Longhi, Silvia A; Ayub, Maximiliano Juri; Edreira, Martin M; Simonetti, Leandro; Gómez, Karina A; Basile, Joaquín N; Chaloin, Olivier; Hoebeke, Johan; Levin, Mariano J
The large subunit of the eukaryotic ribosome possesses a long and protruding stalk formed by the ribosomal P proteins. This structure is involved in the translation step of protein synthesis through interaction with the elongation factor 2 (EF-2). The Trypanosoma cruzi stalk complex is composed of four proteins of about 11?kDa, TcP1?, TcP1?, TcP2?, TcP2? and a fifth TcP0 of about 34 kDa. In a previous work, a yeast two-hybrid (Y2H) protein-protein interaction map of T. cruzi ribosomal P proteins was generated. In order to gain new insight into the assembly of the stalk, a complete interaction map was generated by surface plasmon resonance (SPR) and the kinetics of each interaction was calculated. All previously detected interactions were confirmed and new interacting pairs were found, such as TcP1?-TcP2? and TcP1?-TcP2?. Moreover P2 but not P1 proteins were able to homo-oligomerize. In addition, the region comprising amino acids 210-270 on TcP0 was identified as the region interacting with P1/P2 proteins, using Y2H and SPR. The interaction domains on TcP2? were also mapped by SPR identifying two distinct regions. The assembly order of the pentameric complex was assessed by SPR showing the existence of a hierarchy in the association of the different P proteins forming the stalk. Finally, the TcEF-2 gene was identified, cloned, expressed and refolded. Using SPR analysis we showed that TcEF-2 bound with similar affinity to the four P1/P2 ribosomal P proteins of T. cruzi but with reduced affinity to TcP0. PMID:21360618
An interactive, online Geographic Information System (GIS) for stakeholder participation in environmental site selection
Adams, Christiaan Scott, 1973-
An interactive, online geographic information system (GIS) was developed to enhance the involvement of stakeholders in the public participation processes of site selection issues in the marine environment. Displaying ...
Multi-level assessment protocol (MAP) for adoption in multi-site clinical trials
Guydish, J.; Manser, S.T.; Jessup, M.; Tajima, B.; Sears, C.; Montini, T.
The National Institute on Drug Abuse (NIDA) Clinical Trials Network (CTN) is intended to test promising drug abuse treatment models in multi-site clinical trials, and to support adoption of new interventions into clinical practice. Using qualitative research methods we asked: How might the technology of multi-site clinical trials be modified to better support adoption of tested interventions? A total of 42 participants, representing 8 organizational levels ranging from clinic staff to clinical trial leaders, were interviewed about their role in the clinical trial, its interactions with clinics, and intervention adoption. Among eight clinics participating in the clinical trial, we found adoption of the tested intervention in one clinic only. In analysis of interview data we identified four conceptual themes which are likely to affect adoption and may be informative in future multi-site clinical trials. We offer the conclusion that planning for adoption in the early stages of protocol development will better serve the aim of integrating new interventions into practice. PMID:20890376
Groundwater vulnerability: interactions of chemical and site properties
Fred Worrall; Tim Besien; Dana W Kolpin
This study brings together extensive, multi-annual groundwater monitoring datasets from the UK and Midwestern US to test the relative importance of site (e.g. land use, soil and aquifer type) and chemical factors (e.g. solubility in water) and between and within year variations in controlling groundwater contamination by pesticides. ANOVA (general linear modelling) was used to test the significance and proportion
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures.
Fukuhara, Naoshi; Kawabata, Takeshi
As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Our server is capable of three services. The first is modeling heterodimers from two query amino acid sequences posted by users. The server performs BLAST searches to identify homologous templates in the latest representative dataset of heterodimer structures generated from the PQS database. Structure validity is evaluated by the combination of sequence similarity and knowledge-based contact potential energy as previously described. The server generates a sequence-replaced model PDB file and a MODELLER script to build full atomic models of complex structures. The second service is modeling homodimers from one query sequence. The third service is identification of potentially interacting proteins for one query sequence. The server searches the dataset of heterodimer structures for a homologous template, outputs the candidate interacting sequences in the Uniprot database homologous for the interacting partner template proteins. These features are useful for wide range of researchers to predict putative interaction sites and interacting proteins. PMID:18442990
Nonprimed and DYRK1A-primed GSK3 beta-phosphorylation sites on MAP1B regulate microtubule dynamics in growing axons.
Scales, Timothy M E; Lin, Shen; Kraus, Michaela; Goold, Robert G; Gordon-Weeks, Phillip R
MAP1B is a developmentally regulated microtubule-associated phosphoprotein that regulates microtubule dynamics in growing axons and growth cones. We used mass spectrometry to map 28 phosphorylation sites on MAP1B, and selected for further study a putative primed GSK3 beta site and compared it with two nonprimed GSK3 beta sites that we had previously characterised. We raised a panel of phosphospecific antibodies to these sites on MAP1B and used it to assess the distribution of phosphorylated MAP1B in the developing nervous system. This showed that the nonprimed sites are restricted to growing axons, whereas the primed sites are also expressed in the neuronal cell body. To identify kinases phosphorylating MAP1B, we added kinase inhibitors to cultured embryonic cortical neurons and monitored MAP1B phosphorylation with our panel of phosphospecific antibodies. These experiments identified dual-specificity tyrosine-phosphorylation-regulated kinase (DYRK1A) as the kinase that primes sites of GSK3 beta phosphorylation in MAP1B, and we confirmed this by knocking down DYRK1A in cultured embryonic cortical neurons by using shRNA. DYRK1A knockdown compromised neuritogenesis and was associated with alterations in microtubule stability. These experiments demonstrate that MAP1B has DYRK1A-primed and nonprimed GSK3 beta sites that are involved in the regulation of microtubule stability in growing axons. PMID:19549690
Spa2p functions as a scaffold-like protein to recruit the Mpk1p MAP kinase module to sites of polarized growth.
van Drogen, Frank; Peter, Matthias
Scaffold proteins play a major role in regulating MAP kinase pathways. In yeast, the Mpk1p-MAP kinase pathway functions to maintain the integrity of the cytoskeleton and the cell wall. In this module, the MEKK Bck1p functions upstream of the MEKs Mkk1p and Mkk2p, which in turn activate the MAP kinase Mpk1p. Mpk1p regulates several nuclear targets, including the transcription factors Rlm1p and SBF, and the two HMG1-like proteins NHP6A and NHP6B. Here we show that Mpk1p constitutively shuttles between the nucleus and the cytoplasm, and both Mpk1p and Mkk1p localize to sites of polarized growth in a Spa2p-dependent manner. Spa2p belongs to a group of proteins that includes Bni1p, Bud6p, and Pea2p, which are involved in the dynamic organization of the actin cytoskeleton during polarized growth. FRAP analysis shows that Spa2p-GFP is stably anchored at bud tips, whereas Mpk1p binds transiently. Spa2p interacts with Mkk1p and Mpk1p, and membrane bound Spa2p is sufficient to recruit Mkk1p and Mpk1p but not other MAP kinases to the cell cortex. Taken together, these results suggest that Spa2p functions as a scaffold-like protein for the cell wall integrity pathway during polarized growth. PMID:12361575
Building a Better Web Site: A Practical Guide to Interactivity for Libraries.
ERIC Educational Resources Information Center
Braun, Linda W.
Describes selected commercial and academic Web sites providing interactive services (Amazon; Jones Library, Amherst, MA; Pine Crest Lower School, Ft. Lauderdale, FL; Barnes & Noble; Cal State's Information Literacy Tutorials; PBS's techknow site; K.I.D.S. Report), and argues that libraries that stop at links and policy statements miss…
Digital photogrammetric analysis of the IMP camera images: Mapping the Mars Pathfinder landing site in three dimensions
R. L. Kirk; E. Howington-Kraus; T. Hare; E. Dorrer; D. Cook; K. Becker; K. Thompson; B. Redding; J. Blue; D. Galuszka; E. M. Lee; L. R. Gaddis; J. R. Johnson; L. A. Soderblom; A. W. Ward; P. H. Smith; D. T. Britt
This paper describes our photogrammetric analysis of the Imager for Mars Pathfinder data, part of a broader program of mapping the Mars Pathfinder landing site in support of geoscience investigations. This analysis, carried out primarily with a commercial digital photogrammetric system, supported by our in-house Integrated Software for Imagers and Spectrometers (ISIS), consists of three steps: (1) geometric control: simultaneous
English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life
Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services - - - - - - - - - China Business World Sci-Edu Culture/Life Sports Photos Most Popular FM Briefings Search About China of the International Thermonuclear Experimental Reactor (ITER), which costs 10 billion euros and gathers researchers
English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life
Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services - - - - - - - - - China Business World Sci-Edu Culture/Life Sports Photos Most Popular FM Briefings Search About China project research results will be significant for the International Thermonuclear Experiment Reactor
English home Forum Photo Gallery Features Newsletter Archive About US Help Site Map languages Culture/Life
Help Site Map languages China World Opinion Business Sci-Edu Culture/Life Sports Photos Services - - - - - - - - - China Business World Sci-Edu Culture/Life Sports Photos Most Popular FM Briefings Search About China in thermonuclear reaction, Chinese scientists have already participated in the International Thermonuclear
Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique.
Follows, George A; Janes, Mary E; Vallier, Ludovic; Green, Anthony R; Gottgens, Berthold
Mapping sites within the genome that are hypersensitive to digestion with DNaseI is an important method for identifying DNA elements that regulate transcription. The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has been to use Southern blotting techniques, although we, and others, have recently published alternative methods using a range of technologies including high-throughput sequencing and genomic array tiling paths. In this article, we describe a novel protocol to use real-time PCR to map DHS. Advantages of the technique reported here include the small cell numbers required for each analysis, rapid, relatively low-cost experiments with minimal need for specialist equipment. Presented examples include comparative DHS mapping of known TAL1/SCL regulatory elements between human embryonic stem cells and K562 cells. PMID:17389645
Mapping of the regions involved in homotypic interactions of Tula hantavirus N protein.
Kaukinen, Pasi; Vaheri, Antti; Plyusnin, Alexander
Hantavirus nucleocapsid (N) protein has been suggested to form homodimers and homotrimers that are further integrated into the nucleocapsid filaments around the viral RNA. Here we report detailed mapping of the regions involved in the homotypic N protein interactions in Tula hantavirus (TULV). Peptide scan screening was used to define the interaction regions, and the mammalian two-hybrid assay was used for the functional analysis of N protein mutants. To study linear regions responsible for N protein interaction(s), we used peptide scanning in which N peptides synthesized on membranes recognize recombinant TULV N protein. The data showed that the N protein bound to membrane-bound peptides comprising amino acids 13 to 30 and 41 to 57 in the N-terminal part and 340 to 379, 391 to 407, and 410 to 419 in the C-terminal part of the molecule. Further mapping of the interaction regions by alanine scanning indicated the importance of basic amino acids along the N protein and especially asparagine-394, histidine-395, and phenyalanine-396 in forming the binding interface. Analysis of truncated mutants in the mammalian two-hybrid assay showed that N-terminal amino acids 1 to 43 are involved in and C-terminal amino acids 393 to 398 (VNHFHL) are absolutely crucial for the homotypic interactions. Furthermore, our data suggested a tail-to-tail and head-to-head binding scheme for the N proteins. PMID:14512541
Mapping of the Regions Involved in Homotypic Interactions of Tula Hantavirus N Protein
Kaukinen, Pasi; Vaheri, Antti; Plyusnin, Alexander
Hantavirus nucleocapsid (N) protein has been suggested to form homodimers and homotrimers that are further integrated into the nucleocapsid filaments around the viral RNA. Here we report detailed mapping of the regions involved in the homotypic N protein interactions in Tula hantavirus (TULV). Peptide scan screening was used to define the interaction regions, and the mammalian two-hybrid assay was used for the functional analysis of N protein mutants. To study linear regions responsible for N protein interaction(s), we used peptide scanning in which N peptides synthesized on membranes recognize recombinant TULV N protein. The data showed that the N protein bound to membrane-bound peptides comprising amino acids 13 to 30 and 41 to 57 in the N-terminal part and 340 to 379, 391 to 407, and 410 to 419 in the C-terminal part of the molecule. Further mapping of the interaction regions by alanine scanning indicated the importance of basic amino acids along the N protein and especially asparagine-394, histidine-395, and phenyalanine-396 in forming the binding interface. Analysis of truncated mutants in the mammalian two-hybrid assay showed that N-terminal amino acids 1 to 43 are involved in and C-terminal amino acids 393 to 398 (VNHFHL) are absolutely crucial for the homotypic interactions. Furthermore, our data suggested a tail-to-tail and head-to-head binding scheme for the N proteins. PMID:14512541
Mapping the complex morphology of cell interactions with nanowire substrates using FIB-SEM.
Wierzbicki, Rafa?; Křbler, Carsten; Jensen, Mikkel R B; Lopaci?ska, Joanna; Schmidt, Michael S; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mřlhave, Kristian
Using high resolution focused ion beam scanning electron microscopy (FIB-SEM) we study the details of cell-nanostructure interactions using serial block face imaging. 3T3 Fibroblast cellular monolayers are cultured on flat glass as a control surface and on two types of nanostructured scaffold substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition and image post-processing were specifically optimised for cellular monolayers cultured on nanostructured substrates. Cells display a wide range of interactions with the nanostructures depending on the surface morphology, but also greatly varying from one cell to another on the same substrate, illustrating a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map. The results demonstrate that detailed nanoscale resolution images are required to begin understanding the wide variety of individual cells' interactions with a structured substrate. The map will provide a framework for light microscopy studies of such interactions indicating what modes of interactions must be considered. PMID:23326412
Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping
Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.
Boulos, Maged N Kamel; Warren, Jeffrey; Gong, Jianya; Yue, Peng
The Internet and Public Participation: State Legislature Web Sites and the Many Definitions of Interactivity
ERIC Educational Resources Information Center
Ferber, Paul; Foltz, Franz; Pugliese, Rudy
The interactive nature of the Internet is seen by some as a technological innovation that might boost participation in politics and civic affairs. That potential, however, is clouded by imprecise definitions of interactivity found among scholars and practitioners alike. Evaluation of state legislature Web sites found them to not be very…
Non-canonical Interactions in a Kissing Loop Complex: The Dimerization Initiation Site of HIV-1
Westhof, Eric
Non-canonical Interactions in a Kissing Loop Complex: The Dimerization Initiation Site of HIV-1. Two RNA monomers form a kissing loop complex via intermolecular interactions of the six nucleotide of the kissing helix and are in- corporated into a three-dimensional model of the kissing loop dimer. In addition
Large, motile epifauna interact strongly with harpacticoid copepods and polychaetes at a bathyal site
David Thistle; James E. Eckman; Gordon L. J. Paterson
Strengths of interactions among groups of animals in deep-sea-sediment communities are poorly known. Large, motile epifauna (LME) such as sea cucumbers, star fishes, and demersal fishes occur in the deep sea and are sources of predation, disturbance, and habitat alteration and thus have the potential to interact strongly with infauna. At a site off the southwestern coast of the United
NSDL National Science Digital Library
Russell Graymer
This web site provides an introduction to geologic maps. Topics covered include what is a geologic map, unique features of geologic maps, letter symbols, faults, and strike and dip. Users may click to view colored geologic maps, the geologic map of the United States and the geologic relief map of the United States.
Mapping the Putative G Protein-coupled Receptor (GPCR) Docking Site on GPCR Kinase 2
Beautrait, Alexandre; Michalski, Kevin R.; Lopez, Thomas S.; Mannix, Katelynn M.; McDonald, Devin J.; Cutter, Amber R.; Medina, Christopher B.; Hebert, Aaron M.; Francis, Charnelle J.; Bouvier, Michel; Tesmer, John J. G.; Sterne-Marr, Rachel
G protein-coupled receptor kinases (GRKs) phosphorylate agonist-occupied receptors initiating the processes of desensitization and ?-arrestin-dependent signaling. Interaction of GRKs with activated receptors serves to stimulate their kinase activity. The extreme N-terminal helix (?N), the kinase small lobe, and the active site tether (AST) of the AGC kinase domain have previously been implicated in mediating the allosteric activation. Expanded mutagenesis of the ?N and AST allowed us to further assess the role of these two regions in kinase activation and receptor phosphorylation in vitro and in intact cells. We also developed a bioluminescence resonance energy transfer-based assay to monitor the recruitment of GRK2 to activated ?2A-adrenergic receptors (?2AARs) in living cells. The bioluminescence resonance energy transfer signal exhibited a biphasic response to norepinephrine concentration, suggesting that GRK2 is recruited to G?? and ?2AAR with EC50 values of 15 nm and 8 ?m, respectively. We show that mutations in ?N (L4A, V7E, L8E, V11A, S12A, Y13A, and M17A) and AST (G475I, V477D, and I485A) regions impair or potentiate receptor phosphorylation and/or recruitment. We suggest that a surface of GRK2, including Leu4, Val7, Leu8, Val11, and Ser12, directly interacts with receptors, whereas residues such as Asp10, Tyr13, Ala16, Met17, Gly475, Val477, and Ile485 are more important for kinase domain closure and activation. Taken together with data on GRK1 and GRK6, our data suggest that all three GRK subfamilies make conserved interactions with G protein-coupled receptors, but there may be unique interactions that influence selectivity. PMID:25049229
Method of predicting Splice Sites based on signal interactions
Churbanov, Alexander; Rogozin, Igor B; Deogun, Jitender S; Ali, Hesham
Background Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. Results According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE) and Intronic (ISE) Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. Conclusion Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. Reviewers This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand. PMID:16584568
Comprehensive Human Transcription Factor Binding Site Map for Combinatory Binding Motifs Discovery
Müller-Molina, Arnoldo J.; Schöler, Hans R.; Araúzo-Bravo, Marcos J.
To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%–20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%—far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters. PMID:23209563
Use of stratigraphic and lithofacies maps in hydrogeologic studies: Examples from the General Separations Area, Savannah River Site, S. C
Thayer, P.A. (Univ. of North Carolina, Wilmington, NC (United States). Dept. of Earth Sciences); Smits, A.D. (Science Applications International Corporation, Augusta, GA (United States)); Harris, M.K. (Westinghouse Savannah River Co., Aiken, SC (United States). Environmental Restoration Dept.)
Stratigraphic and lithofacies maps are effective tools for assessing hydrologic properties of Tertiary aquifer and confining units in the 15mi[sup 2] General Separations Area (GSA) at the Savannah River Site, S.C. Pumping tests and laboratory permeability data indicate that the type, geometry, and spatial distribution of lithofacies are important factors controlling the lateral and vertical variability of hydraulic conductivity in unconsolidated terrigenous and carbonate sediments comprising aquifer and confining units. Lithofacies mapping is useful for predicting lateral permeability heterogeneity, particularly in areas where hydraulic data is sparse. The authors used detailed lithologic data from 186 coreholes to construct stratigraphic and lithofacies maps of aquifer and confining units, including: structure contour; isopach; isolith thickness of mud, sand, and carbonate; sand, mud, and carbonate percentage; number of sand and mud beds; sand-mud ratio; clastic ratio; lithofacies; and entropy lithofacies. Data from the stratigraphic and lithofacies maps are being integrated into a ground-water flow model for the GSA and have proved useful for generation of potentiometric surface maps, head difference maps, and contaminant plume maps.
Excited state potential energy surfaces and their interactions in Fe(IV)=O active sites.
Srnec, Martin; Wong, Shaun D; Solomon, Edward I
The non-heme ferryl active sites are of significant interest for their application in biomedical and green catalysis. These sites have been shown to have an S = 1 or S = 2 ground spin state; the latter is functional in biology. Low-temperature magnetic circular dichroism (LT MCD) spectroscopy probes the nature of the excited states in these species including ligand-field (LF) states that are otherwise difficult to study by other spectroscopies. In particular, the temperature dependences of MCD features enable their unambiguous assignment and thus determination of the low-lying excited states in two prototypical S = 1 and S = 2 NHFe(IV)[double bond, length as m-dash]O complexes. Furthermore, some MCD bands exhibit vibronic structures that allow mapping of excited-state interactions and their effects on the potential energy surfaces (PESs). For the S = 2 species, there is also an unusual spectral feature in both near-infrared absorption and MCD spectra - Fano antiresonance (dip in Abs) and Fano resonance (sharp peak in MCD) that indicates the weak spin-orbit coupling of an S = 1 state with the S = 2 LF state. These experimental data are correlated with quantum-chemical calculations that are further extended to analyze the low-lying electronic states and the evolution of their multiconfigurational characters along the Fe-O PESs. These investigations show that the lowest-energy states develop oxyl Fe(III) character at distances that are relevant to the transition state (TS) for H-atom abstraction and define the frontier molecular orbitals that participate in the reactivity of S = 1 vs. S = 2 non-heme Fe(IV)[double bond, length as m-dash]O active sites. The S = 1 species has only one available channel that requires the C-H bond of a substrate to approach perpendicular to the Fe-oxo bond (the ? channel). In contrast, there are three channels (one ? and two ?) available for the S = 2 non-heme Fe(IV)[double bond, length as m-dash]O system allowing C-H substrate approach both along and perpendicular to the Fe-oxo bond that have important implications for enzymatic selectivity. PMID:24916844
Nicotinic Agonist Binding Site Mapped by Methionine- and Tyrosine-Scanning Coupled with Azidochloropyridinyl Photoaffinity Labeling
Tomizawa, Motohiro; Talley, Todd T.; Park, John F.; Maltby, David; Medzihradszky, Katalin F.; Durkin, Kathleen A.; Cornejo-Bravo, Jose M.; Burlingame, Alma L.; Casida, John E.; Taylor, Palmer
Agonists activating nicotinic acetylcholine receptors (nAChR) include potential therapeutic agents and also toxicants such as epibatidine and neonicotinoid insecticides with a chloropyridinyl substituent. Nicotinic agonist interactions with mollusk (Aplysia californica) acetylcholine binding protein, a soluble surrogate of the nAChR extracellular domain, are precisely defined by scanning with 17 methionine and tyrosine mutants within the binding site by photoaffinity labeling with 5-azido-6-chloropyridin-3-yl probes that have similar affinities to their nonazido counterparts. Methionine and tryrosine are the only residues found derivatized, and their reactivity exquisitely depends on the direction of the azido moiety and its apposition to the reactive amino acid side chains. PMID:19459645
Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast
Jong Park; Michael Lappe; Sarah A. Teichmann
In the postgenomic era, one of the most interesting and important chal- lenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist indepen- dently. To study the large-scale patterns and
Spirit rover localization and topographic mapping at the landing site of Gusev crater, Mars
Li, R.; Archinal, B.A.; Arvidson, R.E.; Bell, J.; Christensen, P.; Crumpler, L.; Des Marais, D.J.; Di, K.; Duxbury, T.; Golombek, M.P.; Grant, J.A.; Greeley, R.; Guinn, J.; Johnson, Aaron H.; Kirk, R.L.; Maimone, M.; Matthies, L.H.; Malin, M.; Parker, T.; Sims, M.; Thompson, S.; Squyres, S.W.; Soderblom, L.A.
By sol 440, the Spirit rover has traversed a distance of 3.76 km (actual distance traveled instead of odometry). Localization of the lander and the rover along the traverse has been successfully performed at the Gusev crater landing site. We localized the lander in the Gusev crater using two-way Doppler radio positioning and cartographic triangulations through landmarks visible in both orbital and ground images. Additional high-resolution orbital images were used to verify the determined lander position. Visual odometry and bundle adjustment technologies were applied to compensate for wheel slippage, azimuthal angle drift, and other navigation errors (which were as large as 10.5% in the Husband Hill area). We generated topographic products, including 72 ortho maps and three-dimensional (3-D) digital terrain models, 11 horizontal and vertical traverse profiles, and one 3-D crater model (up to sol 440). Also discussed in this paper are uses of the data for science operations planning, geological traverse surveys, surveys of wind-related features, and other science applications. Copyright 2006 by the American Geophysical Union.
A terrain-based site characterization map of California with implications for the contiguous United States
Yong, Alan K.; Hough, Susan E.; Iwahashi, Junko; Braverman, Amy
We present an approach based on geomorphometry to predict material properties and characterize site conditions using the VS30 parameter (time?averaged shear?wave velocity to a depth of 30 m). Our framework consists of an automated terrain classification scheme based on taxonomic criteria (slope gradient, local convexity, and surface texture) that systematically identifies 16 terrain types from 1?km spatial resolution (30 arcsec) Shuttle Radar Topography Mission digital elevation models (SRTM DEMs). Using 853 VS30 values from California, we apply a simulation?based statistical method to determine the mean VS30 for each terrain type in California. We then compare the VS30 values with models based on individual proxies, such as mapped surface geology and topographic slope, and show that our systematic terrain?based approach consistently performs better than semiempirical estimates based on individual proxies. To further evaluate our model, we apply our California?based estimates to terrains of the contiguous United States. Comparisons of our estimates with 325 VS30 measurements outside of California, as well as estimates based on the topographic slope model, indicate our method to be statistically robust and more accurate. Our approach thus provides an objective and robust method for extending estimates of VS30 for regions where in situ measurements are sparse or not readily available.
Spirit rover localization and topographic mapping at the landing site of Gusev crater, Mars
NASA Astrophysics Data System (ADS)
Li, Rongxing; Archinal, Brent A.; Arvidson, Raymond E.; Bell, Jim; Christensen, Philip; Crumpler, Larry; Des Marais, David J.; Di, Kaichang; Duxbury, Tom; Golombek, Matt; Grant, John; Greeley, Ronald; Guinn, Joe; Johnson, Andrew; Kirk, Randolph L.; Maimone, Mark; Matthies, Larry H.; Malin, Mike; Parker, Tim; Sims, Mike; Thompson, Shane; Squyres, Steven W.; Soderblom, Larry A.
By sol 440, the Spirit rover has traversed a distance of 3.76 km (actual distance traveled instead of odometry). Localization of the lander and the rover along the traverse has been successfully performed at the Gusev crater landing site. We localized the lander in the Gusev crater using two-way Doppler radio positioning and cartographic triangulations through landmarks visible in both orbital and ground images. Additional high-resolution orbital images were used to verify the determined lander position. Visual odometry and bundle adjustment technologies were applied to compensate for wheel slippage, azimuthal angle drift, and other navigation errors (which were as large as 10.5% in the Husband Hill area). We generated topographic products, including 72 ortho maps and three-dimensional (3-D) digital terrain models, 11 horizontal and vertical traverse profiles, and one 3-D crater model (up to sol 440). Also discussed in this paper are uses of the data for science operations planning, geological traverse surveys, surveys of wind-related features, and other science applications.
Expression patterns of FLAGELLIN SENSING 2 map to bacterial entry sites in plant shoots and roots
Beck, Martina; Wyrsch, Ines; Strutt, James; Wimalasekera, Rinukshi; Webb, Alex; Boller, Thomas; Robatzek, Silke
Pathogens can colonize all plant organs and tissues. To prevent this, each cell must be capable of autonomously triggering defence. Therefore, it is generally assumed that primary sensors of the immune system are constitutively present. One major primary sensor against bacterial infection is the FLAGELLIN SENSING 2 (FLS2) pattern recognition receptor (PRR). To gain insights into its expression pattern, the FLS2 promoter activity in ?-glucuronidase (GUS) reporter lines was monitored. The data show that pFLS2::GUS activity is highest in cells and tissues vulnerable to bacterial entry and colonization, such as stomata, hydathodes, and lateral roots. GUS activity is also high in the vasculature and, by monitoring Ca2+ responses in the vasculature, it was found that this tissue contributes to flg22-induced Ca2+ burst. The FLS2 promoter is also regulated in a tissue- and cell type-specific manner and is responsive to hormones, damage, and biotic stresses. This results in stimulus-dependent expansion of the FLS2 expression domain. In summary, a tissue- and cell type-specific map of FLS2 expression has been created correlating with prominent entry sites and target tissues of plant bacterial pathogens. PMID:25205577
Molecular Interaction Maps--A Diagrammatic Graphical Language for Bioregulatory Networks
NSDL National Science Digital Library
Yves Pommier (National Cancer Institute; Center for Cancer Research REV)
Molecular interaction maps (MIMs) use a clear, accurate, and versatile graphical language to depict complex biological processes. Here, we discuss the main features of the MIM language and its potential uses. MIMs can be used as database resources and simulation guides, and can serve to generate new hypotheses regarding the roles of specific molecules in the bioregulatory networks that control progression through the cell cycle, differentiation, and cell death.
Micron-Scale Mapping of Megagauss Magnetic Fields in Petawatt Laser-Solid Interactions
Chatterjee, Gourab; Robinson, A P L; Booth, N; Culfa, O; Dance, R J; Gizzi, L A; Gray, R J; Green, J S; Koester, P; Kumar, G Ravindra; Labate, L; Lad, Amit D; Lancaster, K L; Pasley, J; Woolsey, N C; Rajeev, P P
We report spatially and temporally resolved measurements of magnetic fields generated by petawatt laser-solid interactions with high spatial resolution, using optical polarimetry. The polarimetric measurements map the megagauss magnetic field profiles generated by the fast electron currents at the target rear. The magnetic fields at the rear of a 50 $\\mu$m thick aluminum target exhibit distinct and unambiguous signatures of electron beam filamentation. These results are corroborated by hybrid simulations.
Mapping of single-site magnetic anisotropy tensors in weakly coupled spin clusters by torque magnetometry.
Rigamonti, Luca; Cornia, Andrea; Nava, Andrea; Perfetti, Mauro; Boulon, Marie-Emmanuelle; Barra, Anne-Laure; Zhong, Xiaoliang; Park, Kyungwha; Sessoli, Roberta
Single-crystal torque magnetometry performed on weakly-coupled polynuclear systems provides access to a complete description of single-site anisotropy tensors. Variable-temperature, variable-field torque magnetometry was used to investigate triiron(III) complex [Fe3La(tea)2(dpm)6] (Fe3La), a lanthanum(III)-centred variant of tetrairon(III) single molecule magnets (Fe4) (H3tea = triethanolamine, Hdpm = dipivaloylmethane). Due to the presence of the diamagnetic lanthanoid, magnetic interactions among iron(III) ions (si = 5/2) are very weak (<0.1 cm(?1)) and the magnetic response of Fe3La is predominantly determined by single-site anisotropies. The local anisotropy tensors were found to have Di > 0 and to be quasi-axial with |Ei/Di| ~ 0.05. Their hard axes form an angle of approximately 70° with the threefold molecular axis, which therefore corresponds to an easy magnetic direction for the molecule. The resulting picture was supported by a High Frequency EPR investigation and by DFT calculations. Our study confirms that the array of peripheral iron(III) centres provides substantially noncollinear anisotropy contributions to the ground state of Fe4 complexes, which are of current interest in molecular magnetism and spintronics. PMID:25014192
Functional genomics platform for pooled screening and mammalian genetic interaction maps
Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.
Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of hit genes are measured in a double-shRNA screen and used to construct a genetic interaction map. Our protocol allows for rapid pooled screening under various conditions without a requirement for robotics, in contrast to arrayed approaches. Each stage of the protocol can be implemented in ~2 weeks, with additional time for analysis and generation of reagents. We discuss considerations for screen design, and present complete experimental procedures as well as a full computational analysis suite for identification of hits in pooled screens and generation of genetic interaction maps. While the protocols outlined here were developed for our original shRNA-based approach, they can be applied more generally, including to CRISPR-based approaches. PMID:24992097
Digital geologic map of the Nevada Test Site and vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California
Slate, J.L.; Berry, M.E.; Rowley, P.D.; Fridrich, C.J.; Morgan, K.S.; Workman, J.B.; Young, O.D.; Dixon, G.L.; Williams, V.S.; McKee, E.H.; Ponce, D.A.; Hildenbrand, T.G.; Swadley, W.C.; Lundstrom, S.C.; Ekren, E.B.; Warren, R.G.; Cole, J.C.; Fleck, R.J.; Lanphere, M.A.; Sawyer, D.A.; Minor, S.A.; Grunwald, D.J.; Laczniak, R.J.; Menges, C.M.; Yount, J.C.; Jayko, A.S.
This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map area covers two 30 {times} 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7 1/2-minute quadrangles on the east side. In addition to the NTS, the map area includes the rest of the southwest Nevada volcanic field, part of the Walker Lane, most of the Amargosa Desert, part of the Funeral and Grapevine Mountains, some of Death Valley, and the northern Spring Mountains. This geologic map improves on previous geologic mapping of the same area by providing new and updated Quaternary and bedrock geology, new geophysical interpretations of faults beneath the basins, and improved GIS coverages. This publication also includes a new isostatic gravity map and a new aeromagnetic map. The primary purpose of the three maps is to provide an updated geologic framework to aid interpretation of ground-water flow through and off the NTS. The NTS is centrally located within the area of the Death Valley regional ground-water flow system of southwestern Nevada and adjacent California. During the last 40 years, DOE and its predecessor agencies have conducted about 900 nuclear tests on the NTS, of which 100 were atmospheric tests and the rest were underground tests. More than 200 of the tests were detonated at or beneath the water table, which commonly is about 500 to 600 m below the surface. Because contaminants introduced by these test may move into water supplies off the NTS, rates and directions of ground-water flow must be determined. Knowledge about the ground water also is needed to properly appraise potential future effects of the possible nuclear waste repository at Yucca Mountain, adjacent to the NTS.
Exploring 3D Interaction in Alternate Control-Display Space Mappings Jeroen Keijser Sheelagh Carpendale* Mark Hancock* Tobias Isenberg*
Exploring 3D Interaction in Alternate Control-Display Space Mappings Jeroen Keijser Sheelagh ABSTRACT The desire to have intuitive, seamless 3D interaction fuels research exploration into new approaches to 3D interaction. However, within these explorations we continue to rely on Brunelleschi
Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum.
Coaker, G L; Francis, D M
Two quantitative trait loci (QTL) from Lycopersicon hirsutum, Rcm 2.0 and Rcm 5.1, control resistance to Clavibacter michiganensis subsp. michiganensis ( Cmm). To precisely map both loci, we applied interval mapping techniques to 1,056 individuals in three populations exhibiting F(2) segregation. Based on a 1-LOD confidence interval, Rcm 2.0 mapped to a 14.9-cM interval on chromosome 2 and accounted for 25.7-34.0% of the phenotypic variation in disease severity. Rcm 5.1 mapped to a 4.3-cM interval on chromosome 5 and accounted for 25.8-27.9% of the phenotypic variation. Progeny testing of recombinant plants narrowed the QTL location for Rcm 2.0 to a 4.4-cM interval between TG537-TG091 and to a 2.2-cM interval between CT202-TG358 for Rcm 5.1. A population of 750 individuals exhibiting F(2) segregation was used to detect epistasis between both loci using ANOVA and orthogonal contrasts ( P=0.027), suggesting that resistance was determined by additive gene action and an additive-by-additive epistatic interaction. A partial diallel mating design was used to confirm epistasis, advance superior genotypes, randomize genetic backgrounds, and create recombination opportunities. This crossing scheme created a more balanced population ( n=112) containing the nine F(2) genotypic classes. Parents in the diallel were selected from the previous population based on resistance, genotype at the Rcm 2.0 and Rcm 5.1 loci, and horticultural traits. A replicated trial using the diallel population confirmed additive-by-additive epistasis ( P<0.0001). These results validate the gene action, intra -locus interaction, and map position of two loci controlling resistance to Cmm. PMID:15067391
Elucidation of mechanisms of interaction of a multifunctional peptide Pa-MAP with lipid membranes.
Nascimento, Jéssica M; Oliveira, Maria D L; Franco, Octávio L; Migliolo, Ludovico; de Melo, Celso P; Andrade, César A S
This work aims to investigate the possible mechanism of action of the homologue peptide Pa-MAP based on the Antarctic fish Pleuronectes americanus, through a study by electrical impedance spectroscopy (EIS) of models of bilayer lipid membranes supported (BLM-s) on solid substrates. For comparison and validation of the data obtained by EIS, we also conducted a study evaluating the human peptide LL-37, whose mechanism of action is well described in the literature: its dielectric response was found to be similar to that of Pa-MAP. The results obtained indicate that Pa-MAP has a good potential for use as a membrane-disrupting peptide and also suggest that the corresponding mechanism of action occurs according to the carpet model followed by a detergent-like effect. The addition of either one of these peptides at different concentrations resulted in a drastic decrease in the membrane's resistance, after just 1min of exposure. Additionally, it was seen that the peptides Pa-MAP and LL-37 may act on membranes with different charges, in an indication of a possible broad spectrum antimicrobial activity. These interactions with different membrane compositions have been attributed to the peptides' structure, mainly due to the presence of many hydrophobic amino acid residues, as observed by in silico studies. Here, we describe the Pa-MAP mechanism of action for the first time. Furthermore, we report the data demonstrating that EIS can be used for studies of peptide-membranes interaction, even when small changes on the surface of the electrode can be detected. PMID:25109938
Metallicity at the explosion sites of interacting transients
Taddia, F; Fremling, C; Pastorello, A; Leloudas, G; Fransson, C; Nyholm, A; Stritzinger, M D; Ergon, M; Roy, R; Migotto, K
Context. Some circumstellar-interacting (CSI) supernovae (SNe) are produced by the explosions of massive stars that have lost mass shortly before the SN explosion. There is evidence that the precursors of some SNe IIn were luminous blue variable (LBV) stars. For a small number of CSI SNe, outbursts have been observed before the SN explosion. Eruptive events of massive stars are named as SN impostors (SN IMs) and whether they herald a forthcoming SN or not is still unclear. The large variety of observational properties of CSI SNe suggests the existence of other progenitors, such as red supergiant (RSG) stars with superwinds. Furthermore, the role of metallicity in the mass loss of CSI SN progenitors is still largely unexplored. Aims. Our goal is to gain insight on the nature of the progenitor stars of CSI SNe by studying their environments, in particular the metallicity at their locations. Methods. We obtain metallicity measurements at the location of 60 transients (including SNe IIn, SNe Ibn, and SN IMs), via...
Index to published geologic maps in the region around the potential Yucca Mountain nuclear waste repository site, southern Nye County, Nevada
Yucca Mountain, located in southern Nye County, Nevada is currently being investigated as a potential site for an underground high-level radioactive waste repository. The series of index maps presented in this report provide an up-to-date reference of published geologic maps covering the Candidate Area. The published maps range in scale from 1:1200 through 1:700,000 and includes maps published by the
Mapping of the plasminogen binding site of streptokinase with short synthetic peptides.
Nihalani, D.; Raghava, G. P.; Sahni, G.
Although several recent studies employing various truncated fragments of streptokinase (SK) have demonstrated that the high-affinity interactions of this protein with human plasminogen (HPG) to form activator complex (SK-HPG) are located in the central region of SK, the exact location and nature of such HPG interacting site(s) is still unclear. In order to locate the "core" HPG binding ability in SK, we focused on the primary structure of a tryptic fragment of SK derived from the central region (SK143-293) that could bind as well as activate HPG, albeit at reduced levels in comparison to the activity of the native, full-length protein. Because this fragment was refractory to further controlled proteolysis, we took recourse to a synthetic peptide approach wherein the HPG interacting properties of 16 overlapping 20-mer peptides derived from this region of SK were examined systematically. Only four peptides from this set, viz., SK234-253, SK254-273, SK274-293, and SK263-282, together representing the contiguous sequence SK234-293, displayed HPG binding ability. This was established by a specific HPG-binding ELISA as well as by dot blot assay using 125I-labeled HPG. These results showed that the minimal sequence with HPG binding function resided between residues 234 and 293. None of the synthetic SK peptides was found to activate HPG, either individually or in combination, but, in competition experiments where each of the peptides was added prior to complex formation between SK and HPG, three of the HPG binding peptides (SK234-253, SK254-273, and SK274-293) inhibited strongly the generation of a functional activator complex by SK and HPG. This indicated that residues 234-293 in SK participate directly in intermolecular contact formation with HPG during the formation of the 1:1 SK-HPG complex. Two of the three peptides (SK234-253 and SK274-293), apart from interfering in SK-HPG complex formation, also showed inhibition of the amidolytic activity of free HPN by increasing the K(m) by approximately fivefold. A similar increase in K(m) for amidolysis by HPN as a result of complexation with SK has been interpreted previously to arise from the steric hinderance at or near the active site due to the binding of SK in this region. Thus, our results suggest that SK234-253 and SK274-293 also, like SK, bound close to the active site of HPN, an event that was reflected in the observed alteration in its substrate accessibility. By contrast, whereas the intervening peptide (SK254-273) could not inhibit amidolysis by free HPN, it showed a marked inhibition of the activation of "substrate" PG (human or bovine plasminogen) by activator complex, indicating that this particular region is intimately involved in interaction of the SK-HPG activator complex with substrate plasminogen during the catalytic cycle. This finding provides a rational explanation for one of the most intriguing aspects of SK action, i.e., the ability of the SK-HPG complex to catalyze selectively the activation of substrate molecules of PG to PN, whereas free HPN alone cannot do so. Taken together, the results presented in this paper strongly support a model of SK action in which the segment 234-293 of SK, by virtue of the epitopes present in residues 234-253 and 274-293, binds close to the active center of HPN (or, a cryptic active site, in the case of HPG) during the intermolecular association of the two proteins to form the equimolar activator complex; the segment SK254-273 present in the center of the core region then imparts an ability to the activator complex to interact selectively with substrate PG molecules during each PG activation cycle. PMID:9194188
Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions.
Schumann, Frank H; Riepl, Hubert; Maurer, Till; Gronwald, Wolfram; Neidig, Klaus-Peter; Kalbitzer, Hans Robert
Protein-protein interactions are often studied by chemical shift mapping using solution NMR spectroscopy. When heteronuclear data are available the interaction interface is usually predicted by combining the chemical shift changes of different nuclei to a single quantity, the combined chemical shift perturbation Deltadelta comb In this paper different procedures (published and non-published) to calculate Deltadelta comb are examined that include a variety of different functional forms and weighting factors for each nucleus. The predictive power of all shift mapping methods depends on the magnitude of the overlap of the chemical shift distributions of interacting and non-interacting residues and the cut-off criterion used. In general, the quality of the prediction on the basis of chemical shift changes alone is rather unsatisfactory but the combination of chemical shift changes on the basis of the Hamming or the Euclidian distance can improve the result. The corrected standard deviation to zero of the combined chemical shift changes can provide a reasonable cut-off criterion. As we show combined chemical shifts can also be applied for a more reliable quantitative evaluation of titration data. PMID:17955183
Systematic analysis of the Hmga2 3? UTR identifies many independent regulatory sequences and a novel interaction between distal sites
Kristjánsdóttir, Katla; Fogarty, Elizabeth A.
The 3? untranslated regions (3? UTRs) of mRNAs regulate transcripts by serving as binding sites for regulatory factors, including microRNAs and RNA binding proteins. Binding of such trans-acting factors can control the rates of mRNA translation, decay, and other aspects of mRNA biology. To better understand the role of 3? UTRs in gene regulation, we performed a detailed analysis of a model mammalian 3? UTR, that of Hmga2, with the principal goals of identifying the complete set of regulatory elements within a single 3? UTR, and determining the extent to which elements interact with and affect one another. Hmga2 is an oncogene whose overexpression in cancers often stems from mutations that remove 3?-UTR regulatory sequences. We used reporter assays in cultured cells to generate maps of cis-regulatory information across the Hmga2 3? UTR at different resolutions, ranging from 50 to 400 nt. We found many previously unidentified regulatory sites, a large number of which were up-regulating. Importantly, the overall location and impact of regulatory sites was conserved between different species (mouse, human, and chicken). By systematically comparing the regulatory impact of 3?-UTR segments of different sizes we were able to determine that the majority of regulatory sequences function independently; only a very small number of segments showed evidence of any interactions. However, we discovered a novel interaction whereby terminal 3?-UTR sequences induced internal up-regulating elements to convert to repressive elements. By fully characterizing one 3? UTR, we hope to better understand the principles of 3?-UTR-mediated gene regulation. PMID:25999317
Systematic analysis of the Hmga2 3' UTR identifies many independent regulatory sequences and a novel interaction between distal sites.
Kristjánsdóttir, Katla; Fogarty, Elizabeth A; Grimson, Andrew
The 3' untranslated regions (3' UTRs) of mRNAs regulate transcripts by serving as binding sites for regulatory factors, including microRNAs and RNA binding proteins. Binding of such trans-acting factors can control the rates of mRNA translation, decay, and other aspects of mRNA biology. To better understand the role of 3' UTRs in gene regulation, we performed a detailed analysis of a model mammalian 3' UTR, that of Hmga2, with the principal goals of identifying the complete set of regulatory elements within a single 3' UTR, and determining the extent to which elements interact with and affect one another. Hmga2 is an oncogene whose overexpression in cancers often stems from mutations that remove 3'-UTR regulatory sequences. We used reporter assays in cultured cells to generate maps of cis-regulatory information across the Hmga2 3' UTR at different resolutions, ranging from 50 to 400 nt. We found many previously unidentified regulatory sites, a large number of which were up-regulating. Importantly, the overall location and impact of regulatory sites was conserved between different species (mouse, human, and chicken). By systematically comparing the regulatory impact of 3'-UTR segments of different sizes we were able to determine that the majority of regulatory sequences function independently; only a very small number of segments showed evidence of any interactions. However, we discovered a novel interaction whereby terminal 3'-UTR sequences induced internal up-regulating elements to convert to repressive elements. By fully characterizing one 3' UTR, we hope to better understand the principles of 3'-UTR-mediated gene regulation. PMID:25999317
Superstable cycles for antiferromagnetic Q-state Potts and three-site interaction Ising models on recursive lattices
N. Ananikian; R. Artuso; L. Chakhmakhchyan
We consider the superstable cycles of the Q-state Potts (QSP) and the three-site interaction antiferromagnetic Ising (TSAI) models on recursive lattices. The rational mappings describing the models' statistical properties are obtained via the recurrence relation technique. We provide analytical solutions for the superstable cycles of the second order for both models. A particular attention is devoted to the period three window. Here we present an exact result for the third order superstable orbit for the QSP and a numerical solution for the TSAI model. Additionally, we point out a non-trivial connection between bifurcations and superstability: in some regions of parameters a superstable cycle is not followed by a doubling bifurcation. Furthermore, we use symbolic dynamics to understand the changes taking place at points of superstability and to distinguish areas between two consecutive superstable orbits.
Concept mapping One-Carbon Metabolism to model future ontologies for nutrient-gene-phenotype interactions.
Joslin, A C; Green, R; German, J B; Lange, M C
Advances in the development of bioinformatic tools continue to improve investigators' ability to interrogate, organize, and derive knowledge from large amounts of heterogeneous information. These tools often require advanced technical skills not possessed by life scientists. User-friendly, low-barrier-to-entry methods of visualizing nutrigenomics information are yet to be developed. We utilized concept mapping software from the Institute for Human and Machine Cognition to create a conceptual model of diet and health-related data that provides a foundation for future nutrigenomics ontologies describing published nutrient-gene/polymorphism-phenotype data. In this model, maps containing phenotype, nutrient, gene product, and genetic polymorphism interactions are visualized as triples of two concepts linked together by a linking phrase. These triples, or "knowledge propositions," contextualize aggregated data and information into easy-to-read knowledge maps. Maps of these triples enable visualization of genes spanning the One-Carbon Metabolism (OCM) pathway, their sequence variants, and multiple literature-mined associations including concepts relevant to nutrition, phenotypes, and health. The concept map development process documents the incongruity of information derived from pathway databases versus literature resources. This conceptual model highlights the importance of incorporating information about genes in upstream pathways that provide substrates, as well as downstream pathways that utilize products of the pathway under investigation, in this case OCM. Other genes and their polymorphisms, such as TCN2 and FUT2, although not directly involved in OCM, potentially alter OCM pathway functionality. These upstream gene products regulate substrates such as B12. Constellations of polymorphisms affecting the functionality of genes along OCM, together with substrate and cofactor availability, may impact resultant phenotypes. These conceptual maps provide a foundational framework for development of nutrient-gene/polymorphism-phenotype ontologies and systems visualization. PMID:25091042
An Online Interactive Map Service for Displaying Ground-Water Conditions in Arizona
Tillman, Fred D.; Leake, Stanley A.; Flynn, Marilyn E.; Cordova, Jeffrey T.; Schonauer, Kurt T.
Monitoring the availability of the nation's ground-water supplies is of critical importance to planners and water managers. The general public also has an interest in understanding the status of ground-water conditions, especially in the semi-arid Southwestern United States where much of the water used by municipalities and agriculture comes from the subsurface. Unlike surface-water indicators such as stage or discharge, ground-water conditions may be more difficult to assess and present. Individual well observations may only represent conditions in a limited area surrounding the well and wells may be screened over single or multiple aquifers, further complicating single-well measurement interpretations. Additionally, changes in ground-water conditions may involve time scales ranging from days to many years, depending on recharge, soil properties and depth to the water table. This lack of an easily identifiable ground-water property indicative of current conditions combined with differing time scales of water-level changes makes the presentation of ground-water conditions a difficult task, particularly on a regional basis. One approach is to spatially present several indicators of ground-water conditions that address different time scales and attributes of the aquifer systems. In this report, we describe a publicly-available online interactive map service that presents several different layers of ground-water-conditions information for the alluvial basins in the Lower Colorado River Basin in Arizona (http://montezuma.wr.usgs.gov/website/azgwconditions/). These data layers include wells experiencing water-level decline, wells experiencing water-level rise, recent trends in ground-water levels, change in water level since predevelopment and change in storage since predevelopment. Recent pumpage totals and projected population numbers are also provided for ground-water basins and counties in the region of the Lower Colorado River in Arizona along with a bibliography of U.S. Geological Survey reports for those seeking further information. The methods used to create these data layers are explained with illustrations of example information available on the Web site.
The Interaction of Integrin ?IIb?3 with Fibrin Occurs through Multiple Binding Sites in the ?IIb ?-Propeller Domain*
Podolnikova, Nataly P.; Yakovlev, Sergiy; Yakubenko, Valentin P.; Wang, Xu; Gorkun, Oleg V.; Ugarova, Tatiana P.
The currently available antithrombotic agents target the interaction of platelet integrin ?IIb?3 (GPIIb-IIIa) with fibrinogen during platelet aggregation. Platelets also bind fibrin formed early during thrombus growth. It was proposed that inhibition of platelet-fibrin interactions may be a necessary and important property of ?IIb?3 antagonists; however, the mechanisms by which ?IIb?3 binds fibrin are uncertain. We have previously identified the ?370–381 sequence (P3) in the ?C domain of fibrinogen as the fibrin-specific binding site for ?IIb?3 involved in platelet adhesion and platelet-mediated fibrin clot retraction. In the present study, we have demonstrated that P3 can bind to several discontinuous segments within the ?IIb ?-propeller domain of ?IIb?3 enriched with negatively charged and aromatic residues. By screening peptide libraries spanning the sequence of the ?IIb ?-propeller, several sequences were identified as candidate contact sites for P3. Synthetic peptides duplicating these segments inhibited platelet adhesion and clot retraction but not platelet aggregation, supporting the role of these regions in fibrin recognition. Mutant ?IIb?3 receptors in which residues identified as critical for P3 binding were substituted for homologous residues in the I-less integrin ?M?2 exhibited reduced cell adhesion and clot retraction. These residues are different from those that are involved in the coordination of the fibrinogen ?404–411 sequence and from auxiliary sites implicated in binding of soluble fibrinogen. These results map the binding of fibrin to multiple sites in the ?IIb ?-propeller and further indicate that recognition specificity of ?IIb?3 for fibrin differs from that for soluble fibrinogen. PMID:24338009
Interactive Maps on War and Peace: A WebGIS Application for Civic Education
NASA Astrophysics Data System (ADS)
Wirkus, Lars; Strunck, Alexander
War and violent conflict are omnipresent-be it war in the Middle East, violent conflicts in failed states or increasing military expenditures and exports/ imports of military goods. To understand certain conflicts or peace processes and their possible interrelation, to conduct a well-founded political discussion and to support or influence decision-making, one matter is of special importance: easily accessible and, in particular, reliable data and information. Against this background, the Bonn International Center for Conversion (BICC) in close cooperation with the German Federal Agency for Civic Education (bpb) has been developing a map-based information portal on war and peace with various thematic modules for the latter's online service (http://sicherheitspolitik.bpb.de). The portal will eventually offer nine of such modules that are intended to give various target groups, such as interested members of the public, teachers and learners, policymakers and representatives of the media access to the required information in form of an interactive and country-based global overview or a comparison of different issues. Five thematic modules have been completed so far: War and conflict, peace and demobilization, military capacities, resources and conflict, conventional weapons. The portal offers a broad spectrum of different data processing and visualization tools. Its central feature is an interactive mapping component based on WebGIS and a relational database. Content and data provided through thematic maps in the form of WebGIS layers are generally supplemented by info graphics, data tables and short articles providing deeper knowledge on the respective issue. All modules and their sub-chapters are introduced by background texts. They put all interactive maps of a module into an appropriate context and help the users to also understand the interrelation between various layers. If a layer is selected, all corresponding texts and graphics are shown automatically below the map. Data tables are offered if the copyright of datasets allows such use. All data of all thematic modules is presented in country profiles in a consolidated manner. The portal has been created with Open Source Software. PostgreSQL and PostGIS, MapServer, OpenLayers, MapProxy and cmsmadesimple are combined to manipulate and transform global data sets into interactive thematic maps. A purpose-programmed layer selection menu enables users to select single layers or to combine up to three matching layers from all possible pre-set layer combinations. This applies both to fields of topics within a module and across various modules. Due to the complexity of the structure and visualization constraints, no more than three layers can be combined. The WebGIS-based information portal on war and peace is an excellent example of how GIS technologies can be used for education and outreach. Not only can they play a crucial role in supporting the educational mandate and mission of certain institutions. They can also directly support various target groups in obtaining the knowledge needed by providing a collection of straight forward designed, ready-to-use data, info graphics and maps.
Elucidation of IP6 and Heparin Interaction Sites and Conformational Changes in Arrestin-1 by Solution NMR†
Zhuang, Tiandi; Vishnivetskiy, Sergey A.; Gurevich, Vsevolod V.; Sanders, Charles R.
Arrestins specifically bind activated and phosphorylated G protein-coupled receptors, and orchestrate both receptor trafficking, and channel signaling to G protein-independent pathways via direct interactions with numerous non-receptor partners. Here we report the first successful use of solution NMR to map the binding sites in arrestin-1 (visual arrestin) for two polyanionic compounds that mimic phosphorylated light-activated rhodopsin: inositol hexaphosphate (IP6) and heparin. This yielded a more complete identification of residues involved in the binding with these ligands than has previously been feasible. IP6 and heparin appear to bind to the same site on arrestin-1, centered on a positively charged region in the N-domain. We present the first direct evidence that both IP6 and heparin induced a complete release of the arrestin C-tail. These observations provide novel insight into the nature of arrestin transition from basal to active state and demonstrate the potential of NMR-based methods in the study of protein-protein interactions involving members of the arrestin family. PMID:21050017
Fine mapping of 28S rRNA sites specifically cleaved in cells undergoing apoptosis.
Houge, G; Robaye, B; Eikhom, T S; Golstein, J; Mellgren, G; Gjertsen, B T; Lanotte, M; Dřskeland, S O
Bona fide apoptosis in rat and human leukemia cells, rat thymocytes, and bovine endothelial cells was accompanied by limited and specific cleavage of polysome-associated and monosome-associated 28S rRNA, with 18S rRNA being spared. Specific 28S rRNA cleavage was observed in all instances of apoptotic death accompanied by internucleosomal DNA fragmentation, with cleavage of 28S rRNA and of DNA being linked temporally. This indicates that 28S rRNA fragmentation may be as general a feature of apoptosis as internucleosomal DNA fragmentation and that concerted specific cleavage of intra- and extranuclear polynucleotides occurs in apoptosis. Apoptosis-associated cleavage sites were mapped to the 28S rRNA divergent domains D2, D6 (endothelial cells), and D8. The D2 cuts occurred in hairpin loop junctions considered to be buried in the intact ribosome, suggesting that this rRNA region becomes a target for RNase attack in apoptotic cells. D8 was cleaved in two exposed UU(U) sequences in bulge loops. Treatment with agents causing necrotic cell death or aging of cell lysates failed to produce any detectable limited D2 cleavage but did produce a more generalized cleavage in the D8 region. Of potential functional interest was the finding that the primary cuts in D2 exactly flanked a 0.3-kb hypervariable subdomain (D2c), allowing excision of the latter. The implication of hypervariable rRNA domains in apoptosis represents the first association of any functional process with these enigmatic parts of the ribosomes. PMID:7891700
Isostatic gravity map of the Nevada Test Site and vicinity, Nevada
Ponce, D.A.; Harris, R.N.; Oliver, H.W.
The isostatic gravity map of the Nevada Test Site (NTS) and vicinity is based on about 16,000 gravity stations. Principal facts of the gravity data were listed by Harris and others (1989) and their report included descriptions of base stations, high-precision and absolute gravity stations, and data accuracy. Observed gravity values were referenced to the International Gravity Standardization Net 1971 gravity datum described by Morelli (1974) and reduced using the Geodetic Reference System 1967 formula for the normal gravity on the ellipsoid (International Union of Geodesy and Geophysics, 1971). Free-air, Bouguer, curvature, and terrain corrections for a standard reduction density of 2.67 g/cm{sup 3} were made to compute complete Bouguer anomalies. Terrain corrections were made to a radial distance of 166.7 km from each station using a digital elevation model and a computer procedure by Plouff (1977) and, in general, include manually estimated inner-zone terrain corrections. Finally, isostatic corrections were made using a procedure by Simpson and others (1983) based on an Airy-Heiskanen model with local compensation (Heiskanen and Moritz, 1967) with an upper-crustal density of 2.67 g/cm{sup 3}, a crustal thickness of 25 km, and a density contrast between the lower-crust and upper-mantle of 0.4 g/cm{sup 3}. Isostatic corrections help remove the effects of long-wavelength anomalies related to topography and their compensating masses and, thus, enhance short- to moderate-wavelength anomalies caused by near surface geologic features. 6 refs.
Mapping of promoter sites utilized by T3 RNA polymerase on T3 DNA.
Bailey, J N; McAllister, W T
Promoter locations for the T3 RNA polymerase on the physical map of T3 DNa have been determined. Through the use of conditions favoring the synthesis of RNA from the class II region, an agarose-formaldehyde gel system which improves the resolution of high molecular weight RNAs, and template DNA that was cut by one of several restriction endonucleases prior to transcription, seventeen promoter locations for the T3 RNA polymerase have been mapped. Ten promoters have been identified in the class II region and one promotor has been identified in the class II region and one promotor has been identified in the early (class I) region. The locations of previously mapped class III promoters and the internal termination signal for the T3 RNA polymerase have been mapped more precisely than in previous reports. The resulting transcription map demonstrates a striking similarity to the transcription map of bacteriophage T7. Images PMID:7443532
Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource
Peters, Brandon; Dirscherl, Sara; Dantzer, Jessica; Nowacki, Jonathan; Cross, Scott; Li, Xiaoman; Cornetta, Kenneth; Dinauer, Mary C.; Mooney, Sean D.
Research in gene therapy involving genome integrating vectors, now often includes analysis of vector integration sites across the genome using methods such as ligation mediated (LM)-PCR or linear amplification-mediated (LAM)-PCR. To help researchers analyze these sites and the functions of nearby genes, we have developed SeqMap (http://seqmap.compbio.iupui.edu/) a secure, web-based comprehensive vector integration site management tool that automatically analyzes and annotates large numbers of vector integration sites derived from LM-PCR experiments in human and model organisms upon a common genome database. We believe use of this resource will enable better reproducibility and understanding of this important data. PMID:18580967
Analyzing Interactions by an IIS-Map-Based Method in Face-to-Face Collaborative Learning: An Empirical Study
ERIC Educational Resources Information Center
Zheng, Lanqin; Yang, Kaicheng; Huang, Ronghuai
This study proposes a new method named the IIS-map-based method for analyzing interactions in face-to-face collaborative learning settings. This analysis method is conducted in three steps: firstly, drawing an initial IIS-map according to collaborative tasks; secondly, coding and segmenting information flows into information items of IIS; thirdly,…
Tentative Mapping of Transcription-Induced Interchromosomal Interaction using Chimeric EST and mRNA Data
Unneberg, Per; Claverie, Jean-Michel
Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes in transcription factories. This spatial proximity of actively transcribing genes could provide a means for RNA interaction at the transcript level. We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal interactions. We suggest that chimeric transcripts may be the result of close encounters of active genes, either as functional products or "noise" in the transcription process, and that they could be used as probes for chromosome interactions. We have found a total of 5,614 chimeric ESTs and 587 chimeric mRNAs that meet our selection criteria. Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology. PMID:17330142
Erste klinische Erfahrungen mit dem neuen Non-Contact Mapping-System EnSite
S. G. Spitzer; L. Károlyi; H.-H. Ebert
Zusammenfassung Das Non-Contact Mapping-System ist ein neues Instrument zur Ablation komplexer Arrhythmien. Das System ermöglicht die 3-dimensionale\\u000a visualisierte Darstellung von fokalen oder Reentryarrhythmien. Durch simultanes Mapping genügt theoretisch ein Schlag der\\u000a Arrthythmie zur Erstellung der endokardialen Aktivierungs-Maps. Zu beachten sind der relativ breite Durchmesser sowie die\\u000a potentielle Thrombogenität des Katheters.
Role of Off-site Interactions in Auger Lineshape Analysis from Closed Bands Systems
NASA Astrophysics Data System (ADS)
Cini, M.; Verdozzi, C.
The Cini-Sawatzky theory Auger CVV line shapes from solids and its extensions are based on single or multi-band Hubbard or Anderson models, retaining only the intra-atomic repulsion terms. In this work, we study the role of off-site interactions in closed bands systems. The local interaction terms are treated exactly, as usual, while off-site correlations are intorduced as a self-energy-like correction, on perturbative grounds. Our main result is that the effect of off-site interactions must be taken into account to obtain simultaneous agreement for the shape and the energy position of the CVV spectra. This conclusion is supported by recent experimental evidence and affects the derivation of U values from line shape analysis.
Using a sentiment map for visualizing credibility of news sites on the web
Yukiko Kawai; Yusuke Fujita; Tadahiko Kumamoto; Jianwei Jianwei; Katsumi Tanaka
We have developed a visualizing news system that shows the trend of the news site on the Web for credibility. If users know the trend of the news site, users can evaluate the credibility of each news topic. This system detects and uses sentiments of each news article to resolve the trend of Web site. The trend of Web sites
Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing
Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-qi; Tan, Cong; Li, Chengdao
Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149
Mapping of subaqueous glacier topography in Greenland with multibeam sonars to document ice-ocean interactions
NASA Astrophysics Data System (ADS)
Rignot, E. J.; Fenty, I. G.; Xu, Y.; Cai, C.; Aykutlug, E.; Dupont, T. K.
Very few attempts have been made to map the submerged calving face of tidewater glaciers in the past. Here, we present results from the August 2012 and 2013 campaigns in West Greenland where we visited several glaciers in Atasund, Torssukataq, Uummannaq and Upernavik Fjords. We employ a low frequency multibeam sonar tilted to the side to image the side walls of the glacial fjords, including the submerged calving faces. The results reveal the true depth of the grounding line of these glaciers, which is typically unknown - or known with enormous uncertainties - from traditional ship soundings or from the mapping of glacier thickness, the general shape and slope of the submerged calving fronts, and the presence and spatial distribution of channels of subglacial water discharge that fuel high rates of ice face melting. By repeating the mapping over time on a few glaciers and compensating the data for ice motion, we are able to calculate calving rates and ice melt rates over periods of a few days and compare the ice melt production results with estimates derived from hydrographic surveys. In most examples, knowledge of the sea floor topography is the principal information retrieved from these surveys because it determines whether subsurface warm waters can access the glacier face, but the spatial imaging of the submerged calving face reveals spatial details about ice-ocean interactions that are fundamental to the process of ice melt and complex. Such mappings should be extended to other glaciers and eventually to all tidewater glaciers in Greenland.
Orbital-science investigation: Part J: preliminary geologic map of the region around the candidate Proclus Apollo landing site
Wilhelms, Don E.
The Proclus Crater region was mapped to test the value, for photogeologic mapping purposes, of Apollo 15 metric photographs and to estimate the scientific value of the area as a potential landing site. A metric photographic frame (fig. 25-67) serves as a base for a map of the region around the Proclus Crater (fig. 25-68), and adjacent frames were overlapped with the base frame to provide stereographic images. The excellent stereocoverage allows easy simultaneous observation of topography and albedo. The large forward overlap and the extensive areal photographic coverage provide the best photogeologic data available to date. Brief study has already refined earlier interpretations of the area (refs. 25-7 and 25-32). Although volcanic units have been shown to be extensive in this region, mass wasting apparently has been more important than volcanism in shaping terra landforms.
From local interactions to population dynamics in site-based models of ecology.
Johansson, A; Sumpter, D J T
A central problem in ecology is relating the interactions of individuals-described in terms of competition, predation, interference, etc.-to the dynamics of the populations of these individuals-in terms of change in numbers of individuals over time. Here, we address this problem for a class of site-based ecological models, where local interactions between individuals take place at a finite number of discrete resource sites over non-overlapping generations and, between generations, individuals move randomly between sites over the entire system. Such site-based models have previously been applied to a wide range of ecological systems: from those involving contest or scramble competition for resources to host-parasite interactions and meta-populations. We show how the population dynamics of site-based models can be accurately approximated by and understood through deterministic and stochastic difference equations. Conversely, we use the inverse of this approximation to show what implicit assumptions are made about individual interactions by modelling of population dynamics in terms of difference equations. To this end, we prove a useful and general theorem: that any model in our class of site-based models has a corresponding stochastic difference equation population model, by which it can be approximated. This theorem allows us to calculate long-term population dynamics, evolutionary stable strategies and, by extending our theory to account for large deviations, extinction probabilities for a wide range of site-based systems. Our methodology is then illustrated to various examples of between species competition, predator-prey interactions and co-operation. PMID:14630485
Digital Aeromagnetic Map of the Nevada Test Site and Vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California
Ponce, David A.
An aeromagnetic map of the Nevada Test Site area was prepared from publicly available aeromagnetic data described by McCafferty and Grauch (1997). Magnetic surveys were processed using standard techniques. Southwest Nevada is characterized by magnetic anomalies that reflect the distribution of thick sequences of volcanic rocks, magnetic sedimentary rocks, and the occurrence of granitic rocks. In addition, aeromagnetic data reveal the presence of linear features that reflect faulting at both regional and local scales.
Coexistence and competition of on-site and intersite Coulomb interactions in Mott-molecular-dimers
NASA Astrophysics Data System (ADS)
Arruda, Alberto; Juliano, Raffael; Werlang, Thiago; Craco, Luis
Recent findings of Mott-Hubbard physics in ultracold atoms trapped in periodic potentials have reinvigorated the search for quantum simulators of fermionic and bosonic Hubbard-like models. With this in mind, we performed a systematic study of a two-site realization of the Hubbard model, i.e, in a regime where this model can exactly treated. Particularly, we reveal the interplay between on-site (U) and intersite (V) Coulomb interactions in the extended two-site Hubbard model. Due to its atomic-like form quantum correlations intrinsic to Mott-molecular-dimers are exactly computed. Our results for physical quantities such as double occupancy and specific heat are consistent with those obtained for the one-band Hubbard model, suggesting that a two-site dimer model is able to capture the essential thermodynamic properties of strongly interacting electron systems. It is shown that intersite Coulomb interactions promotes the formation of doublons, which compete with the spin-singlet state induced by the on-site Coulomb repulsion. Our results are expected to be relevant for understanding electronic and thermodynamical properties of interacting electrons in strongly coupled magnetic atoms.
Off-site interactions in the CVV Auger spectrum of noble metals: A study of silver
NASA Astrophysics Data System (ADS)
Cole, R. J.; Verdozzi, C.; Cini, M.; Weightman, P.
The Cini-Sawatzky theory of CVV Auger transitions does not give simultaneous agreement with the position and line shape of the M45N45N45 Auger spectrum of Ag. In accord with recent results for Au, this failure is attributed to the neglect of off-site interactions between the final-state holes. The magnitude of the discrepancy between theory and experiment for Ag is twice that found for Au and this is understood in terms of the difference in the ratio of off-site interaction to d-band width in the two metals.
USGS - Coastal and Marine Geology Program Internet Map Server
NSDL National Science Digital Library
This site from the USGS features marine geology resources, including the Coastal and Marine Map Server, the Gloria Mapping Program and data, and the Coastal and Marine Geology Program. Each of these resources presents data, maps, and publications. For example, the GLORIA system was developed specifically to map the morphology and texture of seafloor features in the deep ocean, while the Coastal and Marine Geology program features an interactive map server to view and create maps using available CMGP data sets.
The Cancer Mortality Maps & Graph Web Site provides interactive maps, graphs (which are accessible to the blind and visually-impaired), text, tables and figures showing geographic patterns and time trends of cancer death rates for the time period 1950-1994 for more than 40 cancer...
A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites
Jianzhong Wu; Tomoko Maehara; Takanori Shimokawa; Shinichi Yamamoto; Chizuko Harada; Yuka Takazaki; Nozomi Ono; Yoshiyuki Mukai; Kazuhiro Koike; Jyunshi Yazaki; Fumiko Fujii; Ayahiko Shomura; Tsuyu Ando; Izumi Kono; Kazunori Waki; Kimiko Yamamoto; Masahiro Yano; Takashi Matsumoto; Takuji Sasaki
To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe
Geologic structure mapping database Spent Fuel Test - Climax, Nevada Test Site
Yow, J.L. Jr.
Information on over 2500 discontinuities mapped at the SFT-C is contained in the geologic structure mapping database. Over 1800 of these features include complete descriptions of their orientations. This database is now available for use by other researchers. 6 references, 3 figures, 2 tables.
Theoretical investigation on nevirapine and HIV1 reverse transcriptase binding site interaction, based on ONIOM method
Mayuso Kuno; Supa Hannongbua; Keiji Morokuma
The ONIOM method was applied to the interaction of nevirapine with the HIV-1 reverse transcriptase binding site. The isolated complex of pyridine (part of nevirapine) and methyl phenol (part of Tyr181) was found at the MP2\\/6-31+G(d) level to have stacking interaction with 8.8 kcal\\/mol binding energy. Optimization of nevirapine and Tyr181 geometry in the pocket of 16 amino acid residues
Mapping the interaction between GRASP65 and GM130, components of a protein complex involved in the stacking of Golgi cisternae.
Barr, F A; Nakamura, N; Warren, G
The nature of the complex containing GRASP65, a membrane protein involved in establishing the stacked structure of the Golgi apparatus, and GM130, a putative Golgi matrix protein and vesicle docking receptor, was investigated. Gel filtration revealed that GRASP65 and GM130 interact in detergent extracts of Golgi membranes under both interphase and mitotic conditions, and that this complex can bind to the vesicle docking protein p115. Using in vitro translation and site-directed mutagenesis in conjunction with immunoprecipitation, the binding site for GRASP65 on GM130 was mapped to the sequence xxNDxxxIMVI-COOH at the C-terminus of GM130, a region known to be required for its localization to the Golgi apparatus. The same approach was used to show that the binding site for GM130 on GRASP65 maps to amino acids 189-201, a region conserved in the mammalian and yeast proteins and reminiscent of PDZ domains. Using green fluorescent protein (GFP)-tagged reporter constructs, it was shown that one essential function of the interaction between GRASP65 and GM130 is in the correct targeting of the two proteins to the Golgi apparatus. PMID:9628863
Toward a physical map of Drosophila buzzatii. Use of randomly amplified polymorphic dna polymorphisms and sequence-tagged site landmarks.
Laayouni, H; Santos, M; Fontdevila, A
We present a physical map based on RAPD polymorphic fragments and sequence-tagged sites (STSs) for the repleta group species Drosophila buzzatii. One hundred forty-four RAPD markers have been used as probes for in situ hybridization to the polytene chromosomes, and positive results allowing the precise localization of 108 RAPDs were obtained. Of these, 73 behave as effectively unique markers for physical map construction, and in 9 additional cases the probes gave two hybridization signals, each on a different chromosome. Most markers (68%) are located on chromosomes 2 and 4, which partially agree with previous estimates on the distribution of genetic variation over chromosomes. One RAPD maps close to the proximal breakpoint of inversion 2z(3) but is not included within the inverted fragment. However, it was possible to conclude from this RAPD that the distal breakpoint of 2z(3) had previously been wrongly assigned. A total of 39 cytologically mapped RAPDs were converted to STSs and yielded an aggregate sequence of 28,431 bp. Thirty-six RAPDs (25%) did not produce any detectable hybridization signal, and we obtained the DNA sequence from three of them. Further prospects toward obtaining a more developed genetic map than the one currently available for D. buzzatii are discussed. PMID:11102375
Interactions between cochlear implant electrode insertion depth and frequency-place mapping
NASA Astrophysics Data System (ADS)
Ba?kent, Deniz; Shannon, Robert V.
While new electrode designs allow deeper insertion and wider coverage in the cochlea, there is still considerable variation in the insertion depth of the electrode array among cochlear implant users. The present study measures speech recognition as a function of insertion depth, varying from a deep insertion of 10 electrodes at 28.8 mm to a shallow insertion of a single electrode at 7.2 mm, in four Med-El Combi 40+ users. Short insertion depths were simulated by inactivating apical electrodes. Speech recognition increased with deeper insertion, reaching an asymptotic level at 21.6 or 26.4 mm depending on the frequency-place map used. Ba?kent and Shannon [J. Acoust. Soc. Am. 116, 3130-3140 (2004)] showed that speech recognition by implant users was best when the acoustic input frequency was matched onto the cochlear location that normally processes that frequency range, minimizing the spectral distortions in the map. However, if an electrode array is not fully inserted into the cochlea, a matched map will result in the loss of considerable low-frequency information. The results show a strong interaction between the optimal frequency-place mapping and electrode insertion depth. Consistent with previous studies, frequency-place matching produced better speech recognition than compressing the full speech range onto the electrode array for full insertion ranges (20 to 25 mm from the round window). For shallower insertions (16.8 and 19.2 mm) a mild amount of frequency-place compression was better than truncating the frequency range to match the basal cochlear location. These results show that patients with shallow electrode insertions might benefit from a map that assigns a narrower frequency range than patients with full insertions. .
Multi-Modal, Multi-Touch Interaction with Maps in Disaster Management Applications
NASA Astrophysics Data System (ADS)
Paelke, V.; Nebe, K.; Geiger, C.; Klompmaker, F.; Fischer, H.
Multi-touch interaction has become popular in recent years and impressive advances in technology have been demonstrated, with the presentation of digital maps as a common presentation scenario. However, most existing systems are really technology demonstrators and have not been designed with real applications in mind. A critical factor in the management of disaster situations is the access to current and reliable data. New sensors and data acquisition platforms (e.g. satellites, UAVs, mobile sensor networks) have improved the supply of spatial data tremendously. However, in many cases this data is not well integrated into current crisis management systems and the capabilities to analyze and use it lag behind sensor capabilities. Therefore, it is essential to develop techniques that allow the effective organization, use and management of heterogeneous data from a wide variety of data sources. Standard user interfaces are not well suited to provide this information to crisis managers. Especially in dynamic situations conventional cartographic displays and mouse based interaction techniques fail to address the need to review a situation rapidly and act on it as a team. The development of novel interaction techniques like multi-touch and tangible interaction in combination with large displays provides a promising base technology to provide crisis managers with an adequate overview of the situation and to share relevant information with other stakeholders in a collaborative setting. However, design expertise on the use of such techniques in interfaces for real-world applications is still very sparse. In this paper we report on interdisciplinary research with a user and application centric focus to establish real-world requirements, to design new multi-modal mapping interfaces, and to validate them in disaster management applications. Initial results show that tangible and pen-based interaction are well suited to provide an intuitive and visible way to control who is changing data in a multi-user command and control interface.
Predicting target-ligand interactions using protein ligand-binding site and ligand substructures
Background Cell proliferation, differentiation, Gene expression, metabolism, immunization and signal transduction require the participation of ligands and targets. It is a great challenge to identify rules governing molecular recognition between chemical topological substructures of ligands and the binding sites of the targets. Methods We suppose that the ligand-target interactions are determined by ligand substructures as well as the physical-chemical properties of the binding sites. Therefore, we propose a fragment interaction model (FIM) to describe the interactions between ligands and targets, with the purpose of facilitating the chemical interpretation of ligand-target binding. First we extract target-ligand complexes from sc-PDB database, based on which, we get the target binding sites and the ligands. Then we represent each binding site as a fragment vector based on a target fragment dictionary that is composed of 199 clusters (denoted as fragements in this work) obtained by clustering 4200 trimers according to their physical-chemical properties. And then, we represent each ligand as a substructure vector based on a dictionary containing 747 substructures. Finally, we build the FIM by generating the interaction matrix M (representing the fragment interaction network), and the FIM can later be used for predicting unknown ligand-target interactions as well as providing the binding details of the interactions. Results The five-fold cross validation results show that the proposed model can get higher AUC score (92%) than three prevalence algorithms CS-PD (80%), BLM-NII (85%) and RF (85%), demonstrating the remarkable predictive ability of FIM. We also show that the ligand binding sites (local information) overweight the sequence similarities (global information) in ligand-target binding, and introducing too much global information would be harmful to the predictive ability. Moreover, The derived fragment interaction network can provide the chemical insights on the interactions. Conclusions The target and ligand bindings are local events, and the local information dominate the binding ability. Though integrating of the global information can promote the predictive ability, the role is very limited. The fragment interaction network is helpful for understanding the mechanism of the ligand-target interaction. PMID:25707321
Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses
In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation. The use of isogenic cell lines also helped identify synthetic lethal relationships, or tumor gene dependencies.
Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics
In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation. The use of isogenic cell lines also helped identify synthetic lethal relationships, or tumor gene dependencies.
Univiewer utility for fast interactive 3D visualization of CMB maps in HEALPix pixelizaton
NASA Astrophysics Data System (ADS)
Mingaliev, Sh. M.; Stolyarov, V. A.
We describe the Univiewer utility for visualizing the celestialmaps in the HEALPix pixelization scheme, which is widely used in data reduction for various experiments involving observations of the cosmic microwave background radiation (CMB). The utility can be used to view the FITS files containing one or several extensions containing HEALPix maps of temperature, intensities, Stokes parameters, integration time per pixel values, etc. The user can interactively change the visualization parameters, apply a coordinate grid, project sky areas onto a plane for further detailed analyses, and compute power spectra. The utility uses OpenGL and wxWidgets cross-platform libraries.
Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks
Markillie, Lye Meng; Lin, Chiann Tso; Adkins, Joshua N.; Auberry, Deanna L.; Hill, Eric A.; Hooker, Brian S.; Moore, Priscilla A.; Moore, Ronald J.; Shi, Liang; Wiley, H. S.; Kery, Vladimir
Most of the current methods for purification and identification of protein complexes use endogenous expression of affinity tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, gel separation, in-gel digestion and mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pulldown assay with denaturing elution, trypsin digestion in organic solvent and LC ESI MS/MS protein identification using SEQUEST analysis. Our method is simple, easy to scale up and automate thus suitable for high throughput mapping of protein interaction networks and functional proteomics.
Entanglement and quantum teleportation in a three-qubit Heisenberg chain with three-site interactions
NASA Astrophysics Data System (ADS)
Xi, Yu-Xing; Cheng, Wei-Wen; Huang, Yan-Xia
The thermal entanglement of a three-qubit XXZ Heisenberg model with three-site interactions in an external magnetic field, and the quantum teleportation via this model in thermal equilibrium state are investigated. It is found that entanglement and average fidelity depend on temperature, magnetic field, and anisotropy parameter . Only ferromagnetic system is suitable for quantum teleportation. interaction is in favor of entanglement, average fidelity, and critical temperatures, while interaction against all of them. Moreover, we also find entanglement does not fully reflect average fidelity in virtue of study the relation between entanglement and average fidelity.
Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein
NASA Technical Reports Server (NTRS)
Gaucher, Eric A.; Miyamoto, Michael M.; Benner, Steven A.
The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures
Brutlag, Doug
1 WebFEATURE: An interactive web tool for identifying and visualizing functional sites University, Stanford CA 94305 USA Abstract WebFEATURE (http://feature.stanford.edu/webfeature/) is a web and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package
Interactions of anthrax lethal factor with protective antigen defined by site-directed spin labeling
McQuade, D. Tyler
, 2010 (sent for review October 29, 2010) The protective antigen (PA) moiety of anthrax toxin forms oligoInteractions of anthrax lethal factor with protective antigen defined by site-directed spin the PA pore. Anthrax toxin, in addition to its importance in regard to the pathogenesis of Bacillus
Ithaca MAP3S regional precipitation chemistry site. Annual progress report, 1 November 1984-31 October 1985
Butler, T.J.; Likens, G.E.
Samples were collected at the MAP3S Regional Precipitation Chemistry Site located 15 km southwest of Ithaca, New York (Lat. 42/sup 0/ 24', Long. 76/sup 0/ 39') at an elevation of 503 m. The surrounding area is rural in nature and consists of gently rolling terrain, vegetated by deciduous forest, abandoned fields, pasture and some agricultural land. Local point sources of combustion products include a 250 mw coal-fired power plant, 23 km NNE of the site and the Cornell University steam-generating plant 16 km ENE of the site. The latter produces emissions of SO/sub 2/ and particulates comparable to a 50 mw coal-fired power plant. Both of these plants are in a quadrant that is consistently downwind of the sampling station. Other local potential sources of particles are from agricultural activity, road dust, and road salt during the winter. Data are collected September 1984 through September 1985.
Mapping Minerals at a Potential Mars Analog Site on the Tibetan Plateau
NASA Astrophysics Data System (ADS)
Mayer, D. P.; Arvidson, R. E.; Wang, A.; Sobron, P.; Zheng, M. P.
A new mineral facies map of lacustrine deposits from the cold, arid Qaidam Basin, China shows hydrated sulfates, carbonates, chlorides and phyllosilicates. This area may offer insight into the history of evaporite deposits identified on Mars.
Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity
Gohl, Daryl M.; Freifeld, Limor; Silies, Marion; Hwa, Jennifer J.; Horowitz, Mark; Clandinin, Thomas R.
Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools. PMID:24374352
Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila
Adryan, Boris; Woerfel, Gertrud; Birch-Machin, Ian; Gao, Shan; Quick, Marie; Meadows, Lisa; Russell, Steven; White, Robert
Background Insulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified. Results We used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites. Conclusion Taken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture. PMID:17705839
The combination of Forest Site Maps, Site specific Growth Models and Nutrient Balance Models as a Basis for Sustainable Management in the Northern Limestone Alps
NASA Astrophysics Data System (ADS)
Ettmayer, C.; Katzensteiner, K.; Eckmüllner, O.
The demand for biomass from forests is rising continuously. Decision support tools for managers and forest authorities should help to avoid negative consequences of increased biomass extraction on ecosystem processes and the sustainable supply of forest services. Those tools have to be site and stand specific. In Alpine regions shallow soils with high organic matter content are widespread on calcareous bedrock. There is increasing evidence that those soils are particularly vulnerable and intensive harvest leads to rapid humus and nutrient losses and a decline of water storage capacity. Such soils may rely on the existence of a continuous forest cover and/or a minimum input of coarse woody debris. For a test region in Tyrol management scenarios will be modelled to predict management effects on sites with calcareous bedrock. Site specific growth and yield models for biomass fractions are developed based on existing inventory data, site maps and high resolution digital surface and terrain models, complemented by stratified biomass and nutrient inventories, and are used for the calculation of different production scenarios. Nutrient balance models taking into account nutrient extraction via harvest, leaching losses as well as gains via atmospheric deposition, and fertilization are used to calculate the potential sustainable harvest intensity. In addition humus dynamics of the frequently shallow rendzic Leptosols is taken into account. Concepts for long term carbon and nutrient management experiments as a basis for adaptive forest management in the Calacareous Alps are developed.
Multiphase Micro-Drop Interaction in Inkjet Printing of 3d Structures for Tactile Maps
NASA Astrophysics Data System (ADS)
Ahmed, Kafeel; McCallum, Don; Sheldon, Derek F.
Ink-jet technology is a novel method for rapid deposition of accurately measured material with high precision. Consequently it has been used for applications such as, deposition of light emitting polymers and more recently for fabricating 3D objects and micro-mechanical structures. Ink-jet technology is also being applied to produce tactile maps for the visually impaired. The efficiency of the tactile maps, as outlined by psychophysical and cartographic studies of haptics, depends on its 3D features. To comprehend and control these features, detailed understanding of interaction amongst micro-drops, which are typically 50?m in diameter, is imperative. Multiphase interaction takes place between each liquid drop at impact with liquid or solid cured drops (deposited previously) and the solid substrate in an envelop of air. The behavior of micro-drops with regards to surface tension, drop coalescence among liquid and solid drops, drop impact kinetics, wettability, surface energy and drop spread has been analyzed using a computational model.
Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.
Haider, Kamran; Huggins, David J
Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets. PMID:24070451
MAP4 Mechanism that Stabilizes Mitochondrial Permeability Transition in Hypoxia: Microtubule Enhancement and DYNLT1 Interaction with VDAC1
Zhang, Yi-ming; Zhang, Jia-ping; Hu, Jiong-yu; Zhang, Qiong; Dai, Xia; Teng, Miao; Zhang, Dong-xia; Huang, Yue-sheng
Mitochondrial membrane permeability has received considerable attention recently because of its key role in apoptosis and necrosis induced by physiological events such as hypoxia. The manner in which mitochondria interact with other molecules to regulate mitochondrial permeability and cell destiny remains elusive. Previously we verified that hypoxia-induced phosphorylation of microtubule-associated protein 4 (MAP4) could lead to microtubules (MTs) disruption. In this study, we established the hypoxic (1% O2) cell models of rat cardiomyocytes, H9c2 and HeLa cells to further test MAP4 function. We demonstrated that increase in the pool of MAP4 could promote the stabilization of MT networks by increasing the synthesis and polymerization of tubulin in hypoxia. Results showed MAP4 overexpression could enhance cell viability and ATP content under hypoxic conditions. Subsequently we employed a yeast two-hybrid system to tag a protein interacting with mitochondria, dynein light chain Tctex-type 1 (DYNLT1), by hVDAC1 bait. We confirmed that DYNLT1 had protein-protein interactions with voltage-dependent anion channel 1 (VDAC1) using co-immunoprecipitation; and immunofluorescence technique showed that DYNLT1 was closely associated with MTs and VDAC1. Furthermore, DYNLT1 interactions with MAP4 were explored using a knockdown technique. We thus propose two possible mechanisms triggered by MAP4: (1) stabilization of MT networks, (2) DYNLT1 modulation, which is connected with VDAC1, and inhibition of hypoxia-induced mitochondrial permeabilization. PMID:22164227
An Overview of Plume Tracker: Mapping Volcanic Emissions with Interactive Radiative Transfer Modeling
NASA Astrophysics Data System (ADS)
Realmuto, V. J.; Berk, A.; Guiang, C.
Infrared remote sensing is a vital tool for the study of volcanic plumes, and radiative transfer (RT) modeling is required to derive quantitative estimation of the sulfur dioxide (SO2), sulfate aerosol (SO4), and silicate ash (pulverized rock) content of these plumes. In the thermal infrared, we must account for the temperature, emissivity, and elevation of the surface beneath the plume, plume altitude and thickness, and local atmospheric temperature and humidity. Our knowledge of these parameters is never perfect, and interactive mapping allows us to evaluate the impact of these uncertainties on our estimates of plume composition. To enable interactive mapping, the Jet Propulsion Laboratory is collaborating with Spectral Sciences, Inc., (SSI) to develop the Plume Tracker toolkit. This project is funded by a NASA AIST Program Grant (AIST-11-0053) to SSI. Plume Tracker integrates (1) retrieval procedures for surface temperature and emissivity, SO2, NH3, or CH4 column abundance, and scaling factors for H2O vapor and O3 profiles, (2) a RT modeling engine based on MODTRAN, and (3) interactive visualization and analysis utilities under a single graphics user interface. The principal obstacle to interactive mapping is the computational overhead of the RT modeling engine. Under AIST-11-0053 we have achieved a 300-fold increase in the performance of the retrieval procedures through the use of indexed caches of model spectra, optimization of the minimization procedures, and scaling of the effects of surface temperature and emissivity on model radiance spectra. In the final year of AIST-11-0053 we will implement parallel processing to exploit multi-core CPUs and cluster computing, and optimize the RT engine to eliminate redundant calculations when iterating over a range of gas concentrations. These enhancements will result in an additional 8 - 12X increase in performance. In addition to the improvements in performance, we have improved the accuracy of the Plume Tracker retrievals through refinements in the description of surface emissivity and use of vector projection to define the misfit between model and observed spectra. Portions of this research were conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.
Rangaraj, K.; Cooper, P.K.; Trego, K.S.
The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3'–5' DNA-dependent helicase, 3'–5' exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.
Digital mapping of the Mars Pathfinder landing site: Design, acquisition, and derivation of cartographic products for science applications
Gaddis, L.R.; Kirk, R.L.; Johnson, J.R.; Soderblom, L.A.; Ward, A.W.; Barrett, J.; Becker, K.; Decker, T.; Blue, J.; Cook, D.; Eliason, E.; Hare, T.; Howington-Kraus, E.; Isbell, C.; Lee, E.M.; Redding, B.; Sucharski, R.; Sucharski, T.; Smith, P.H.; Britt, D.T.
The Imager for Mars Pathfinder (IMP) acquired more than 16,000 images and provided panoramic views of the surface of Mars at the Mars Pathfinder landing site in Ares Vallis. This paper describes the stereoscopic, multispectral IMP imaging sequences and focuses on their use for digital mapping of the landing site and for deriving cartographic products to support science applications of these data. Two-dimensional cartographic processing of IMP data, as performed via techniques and specialized software developed for ISIS (the U.S.Geological Survey image processing software package), is emphasized. Cartographic processing of IMP data includes ingestion, radiometric correction, establishment of geometric control, coregistration of multiple bands, reprojection, and mosaicking. Photogrammetric processing, an integral part of this cartographic work which utilizes the three-dimensional character of the IMP data, supplements standard processing with geometric control and topographic information [Kirk et al., this issue]. Both cartographic and photogrammetric processing are required for producing seamless image mosaics and for coregistering the multispectral IMP data. Final, controlled IMP cartographic products include spectral cubes, panoramic (360?? azimuthal coverage) and planimetric (top view) maps, and topographic data, to be archived on four CD-ROM volumes. Uncontrolled and semicontrolled versions of these products were used to support geologic characterization of the landing site during the nominal and extended missions. Controlled products have allowed determination of the topography of the landing site and environs out to ???60 m, and these data have been used to unravel the history of large- and small-scale geologic processes which shaped the observed landing site. We conclude by summarizing several lessons learned from cartographic processing of IMP data. Copyright 1999 by the American Geophysical Union.
Geophysical logging and geologic mapping data in the vicinity of the GMH Electronics Superfund site near Roxboro, North Carolina
Chapman, Melinda J.; Clark, Timothy W.; Williams, John H.
Geologic mapping, the collection of borehole geophysical logs and images, and passive diffusion bag sampling were conducted by the U.S. Geological Survey North Carolina Water Science Center in the vicinity of the GMH Electronics Superfund site near Roxboro, North Carolina, during March through October 2011. The study purpose was to assist the U.S. Environmental Protection Agency in the development of a conceptual groundwater model for the assessment of current contaminant distribution and future migration of contaminants. Data compilation efforts included geologic mapping of more than 250 features, including rock type and secondary joints, delineation of more than 1,300 subsurface features (primarily fracture orientations) in 15 open borehole wells, and the collection of passive diffusion-bag samples from 42 fracture zones at various depths in the 15 wells.
BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska
NASA Astrophysics Data System (ADS)
Cody, R. P.; Kassin, A.; Gaylord, A. G.; Tweedie, C. E.
In 2013, the Barrow Area Information Database (BAID, www.baid.utep.edu) project resumed field operations in Barrow, AK. The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 11,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, and save or print maps and query results. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. Highlights for the 2013 season include the addition of more than 2000 additional research sites, providing differential global position system (dGPS) support to visiting scientists, surveying over 80 miles of coastline to document rates of erosion, training of local GIS personal, deployment of a wireless sensor network, and substantial upgrades to the BAID website and web mapping applications.
Interactive Weather Information Network
NSDL National Science Digital Library
Offered by the National Oceanic and Atmospheric Administration (NOAA), the Interactive Weather Information Network (IWIN) is a collection of interactive weather maps and satellite images that is updated every five seconds. Visitors can see cloud cover animation loops, NEXRAD Radar images of precipitation, a map of all current weather fronts, and an interactive national map to see information about any particular state. Other information on the site includes a listing of any active weather warnings, a link for world weather data, and more, making this a must-see site for all those users interested in the most current weather happenings anywhere.
A conserved protein interaction network involving the yeast MAP kinases Fus3 and Kss1
Kusari, Anasua B.; Molina, Douglas M.; Sabbagh, Walid; Lau, Chang S.; Bardwell, Lee
The Saccharomyces cerevisiae mitogen-activated protein kinases (MAPKs) Fus3 and Kss1 bind to multiple regulators and substrates. We show that mutations in a conserved docking site in these MAPKs (the CD/7m region) disrupt binding to an important subset of their binding partners, including the Ste7 MAPK kinase, the Ste5 adaptor/scaffold protein, and the Dig1 and Dig2 transcriptional repressors. Supporting the possibility that Ste5 and Ste7 bind to the same region of the MAPKs, they partially competed for Fus3 binding. In vivo, some of the MAPK mutants displayed reduced Ste7-dependent phosphorylation, and all of them exhibited multiple defects in mating and pheromone response. The Kss1 mutants were also defective in Kss1-imposed repression of Ste12. We conclude that MAPKs contain a structurally and functionally conserved docking site that mediates an overall positively acting network of interactions with cognate docking sites on their regulators and substrates. Key features of this interaction network appear to have been conserved from yeast to humans. PMID:14734536
A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
Ghoorah, Anisah W.; Devignes, Marie-Dominique; Alborzi, Seyed Ziaeddin; Smaďl-Tabbone, Malika; Ritchie, David W.
While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements ("?" for helices, "?" for strands, and "?" for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that ? elements are not highly represented in DFBSs compared to ? and ? elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and ?/? contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein. PMID:25860777
Kaichang Di; Fengliang Xu; Rongxing Li
In Mars exploration missions, high-precision landing-site topographic information is crucial for engineering operations and the achievement of scientific goals. Detailed topographic information of landing sites is usually provided by ground panoramic images acquired by lander or rover stereo cameras. This technology was employed for the 1997 Mars Pathfinder (MPF) mission and will also be used in the current 2003 Mars
Profitability Maps as an Input for Site-Specific Management Decision Making
Technology Transfer Automated Retrieval System (TEKTRAN)
For over a decade, farmers have been collecting site-specific yield data. Many have formed doubts about this investment because of their inability to directly apply this information as feedback for improving management. The objective of this case-study analysis was to investigate how site-specific d...
DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites
Gowthaman, Ragul; Lyskov, Sergey; Karanicolas, John
Over the past decade, protein-protein interactions have emerged as attractive but challenging targets for therapeutic intervention using small molecules. Due to the relatively flat surfaces that typify protein interaction sites, modern virtual screening tools developed for optimal performance against "traditional" protein targets perform less well when applied instead at protein interaction sites. Previously, we described a docking method specifically catered to the shallow binding modes characteristic of small-molecule inhibitors of protein interaction sites. This method, called DARC (Docking Approach using Ray Casting), operates by comparing the topography of the protein surface when "viewed" from a vantage point inside the protein against the topography of a bound ligand when "viewed" from the same vantage point. Here, we present five key enhancements to DARC. First, we use multiple vantage points to more accurately determine protein-ligand surface complementarity. Second, we describe a new scheme for rapidly determining optimal weights in the DARC scoring function. Third, we incorporate sampling of ligand conformers "on-the-fly" during docking. Fourth, we move beyond simple shape complementarity and introduce a term in the scoring function to capture electrostatic complementarity. Finally, we adjust the control flow in our GPU implementation of DARC to achieve greater speedup of these calculations. At each step of this study, we evaluate the performance of DARC in a "pose recapitulation" experiment: predicting the binding mode of 25 inhibitors each solved in complex with its distinct target protein (a protein interaction site). Whereas the previous version of DARC docked only one of these inhibitors to within 2 Ĺ RMSD of its position in the crystal structure, the newer version achieves this level of accuracy for 12 of the 25 complexes, corresponding to a statistically significant performance improvement (p < 0.001). Collectively then, we find that the five enhancements described here – which together make up DARC 2.0 – lead to dramatically improved speed and performance relative to the original DARC method. PMID:26181386
Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin.
Gómez, J; Freire, E
The discovery that the protease from the human immunodeficiency virus (HIV) belongs to the aspartic protease family has generated renewed interest in this class of proteins. In this paper, the interactions of endothiapepsin, an aspartic proteinase from the fungus Endothia parasitica, with the inhibitor pepstatin A have been studied by high-sensitivity calorimetric techniques. These experiments have permitted a complete characterization of the temperature and pH-dependence of the binding energetics. The binding reaction is characterized by negative intrinsic binding enthalpy and negative heat capacity changes. The association constant is maximal at low pH (2 x 10(9) M-1 at pH 3) but decreases upon increasing pH (8.1 x 10(6) M-1 at pH 7). The binding of the inhibitor is coupled to the protonation of one of the aspartic moieties in the Asp dyad of the catalytic site of the protein. This phenomenon is responsible for the decrease in the apparent affinity of the inhibitor for the enzyme upon increasing pH. The experimental results presented here indicate that the binding of the inhibitor is favored both enthalpically and entropically. While the favorable enthalpic contribution is intuitively expected, the favorable entropic contribution is due to the large gain in solvent-related entropy associated with the burial of a large hydrophobic surface, that overcompensates the loss in conformational and translational/rotational degrees of freedom upon complex formation. The characteristics of the molecular recognition process have been evaluated by means of structure-based thermodynamic analysis. Three regions in the protein contribute significantly to the free energy of binding: the residues surrounding the Asp dyad (Asp32 in the N-terminal lobe and Asp215 in the C-terminal domain) and the flap region (Ile73 to Asp77). In addition, the rearrangement of residues that are not in immediate contact with the inhibitor provides close to 40% of the protease contribution to the binding free energy. On the other hand, the two statine residues provide more than half of the inhibitor contributions to the total free energy of binding. It is demonstrated that a previously developed empirical structural parametrization of the thermodynamic parameters that define the Gibbs energy, accurately accounts for the binding energetics and its temperature and pH-dependence. PMID:7563055
Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.
Allawi, H T; Dong, F; Ip, H S; Neri, B P; Lyamichev, V I
A rapid and simple method for determining accessible sites in RNA that is independent of the length of target RNA and does not require RNA labeling is described. In this method, target RNA is allowed to hybridize with sequence-randomized libraries of DNA oligonucleotides linked to a common tag sequence at their 5'-end. Annealed oligonucleotides are extended with reverse transcriptase and the extended products are then amplified by using PCR with a primer corresponding to the tag sequence and a second primer specific to the target RNA sequence. We used the combination of both the lengths of the RT-PCR products and the location of the binding site of the RNA-specific primer to determine which regions of the RNA molecules were RNA extendible sites, that is, sites available for oligonucleotide binding and extension. We then employed this reverse transcription with the random oligonucleotide libraries (RT-ROL) method to determine the accessible sites on four mRNA targets, human activated ras (ha-ras), human intercellular adhesion molecule-1 (ICAM-1), rabbit beta-globin, and human interferon-gamma (IFN-gamma). Our results were concordant with those of other researchers who had used RNase H cleavage or hybridization with arrays of oligonucleotides to identify accessible sites on some of these targets. Further, we found good correlation between sites when we compared the location of extendible sites identified by RT-ROL with hybridization sites of effective antisense oligonucleotides on ICAM-1 mRNA in antisense inhibition studies. Finally, we discuss the relationship between RNA extendible sites and RNA accessibility. PMID:11233988
POLYSITE - An interactive package for the selection and refinement of Landsat image training sites
NASA Technical Reports Server (NTRS)
Mack, Marilyn J. P.
A versatile multifunction package, POLYSITE, developed for Goddard's Land Analysis System, is described which simplifies the process of interactively selecting and correcting the sites used to study Landsat TM and MSS images. Image switching between the zoomed and nonzoomed image, color and shape cursor change and location display, and bit plane erase or color change, are global functions which are active at all times. Local functions possibly include manipulation of intensive study areas, new site definition, mensuration, and new image copying. The program is illustrated with the example of a full TM maser scene of metropolitan Washington, DC.
Mapping precursor-binding site on TatC subunit of twin arginine-specific protein translocase by site-specific photo cross-linking.
Zoufaly, Stefan; Fröbel, Julia; Rose, Patrick; Flecken, Tobias; Maurer, Carlo; Moser, Michael; Müller, Matthias
A number of secreted precursor proteins of bacteria, archaea, and plant chloroplasts stand out by a conserved twin arginine-containing sequence motif in their signal peptides. Many of these precursor proteins are secreted in a completely folded conformation by specific twin arginine translocation (Tat) machineries. Tat machineries are high molecular mass complexes consisting of two types of membrane proteins, a hexahelical TatC protein, and usually one or two single-spanning membrane proteins, called TatA and TatB. TatC has previously been shown to be involved in the recognition of twin arginine signal peptides. We have performed an extensive site-specific cross-linking analysis of the Escherichia coli TatC protein under resting and translocating conditions. This strategy allowed us to map the recognition site for twin arginine signal peptides to the cytosolic N-terminal region and first cytosolic loop of TatC. In addition, discrete contact sites between TatC, TatB, and TatA were revealed. We discuss a tentative model of how a twin arginine signal sequence might be accommodated in the Tat translocase. PMID:22362773
Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing.
Li, Yaoguo; He, Maoxian
The pearl oyster, Pinctada fucata (P. fucata), is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL) for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq). With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM), with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW) test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05). These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS). PMID:25369421
Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing
Li, Yaoguo; He, Maoxian
The pearl oyster, Pinctada fucata (P. fucata), is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL) for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq). With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM), with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW) test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05). These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS). PMID:25369421
The HIV-1 5' LTR poly(A) site is inactivated by U1 snRNP interaction with the downstream major splice donor site.
Ashe, M P; Pearson, L H; Proudfoot, N J
The inactivity of the 5' long terminal repeat (LTR) poly(A) site immediately downstream of the cap site maximizes the production of HIV-1 transcripts. In this paper, we demonstrate that this inactivity is mediated by the interaction of the U1 snRNP with the major splice donor site (MSD). The inhibition of the HIV-1 poly(A) site by U1 snRNP relies on a series of delicately balanced RNA processing signals. These include the poly(A) site, the major splice donor site and the splice acceptor sites. The inherent efficiency of the HIV-1 poly(A) site allows maximal activity where there is no donor site (in the 3' LTR) but full inhibition by the downstream MSD (in the 5' LTR). The MSD must interact efficiently with U1 snRNP to completely inhibit the 5' LTR poly(A) site, whereas the splice acceptor sites are inefficient, allowing full-length genomic RNA production. PMID:9312033
Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway.
McCullagh, Emma; Seshan, Anupama; El-Samad, Hana; Madhani, Hiten D
In the Saccharomyces cerevisiae pheromone-response pathway, the transcription factor Ste12 is inhibited by two mitogen-activated protein (MAP)-kinase-responsive regulators, Dig1 and Dig2. These two related proteins bind to distinct regions of Ste12 but are redundant in their inhibition of Ste12-dependent gene expression. Here we describe three functions for Dig1 that are non-redundant with those of Dig2. First, the removal of Dig1 results in a specific increase in intrinsic and extrinsic noise in the transcriptional outputs of the mating pathway. Second, in dig1? cells, Ste12 relocalizes from the nucleoplasmic distribution seen in wild-type cells into discrete subnuclear foci. Third, genome-wide insertional chromatin immunoprecipitation studies revealed that Ste12-dependent genes have increased interchromosomal interactions in dig1? cells. These findings suggest that the regulation of gene expression through long-range gene interactions, a widely observed phenomenon, comes at the cost of increased noise. Consequently, cells may have evolved mechanisms to suppress noise by controlling these interactions. PMID:20852627
Interactive segmentation of tongue contours in ultrasound video sequences using quality maps
NASA Astrophysics Data System (ADS)
Ghrenassia, Sarah; Ménard, Lucie; Laporte, Catherine
Ultrasound (US) imaging is an effective and non invasive way of studying the tongue motions involved in normal and pathological speech, and the results of US studies are of interest for the development of new strategies in speech therapy. State-of-the-art tongue shape analysis techniques based on US images depend on semi-automated tongue segmentation and tracking techniques. Recent work has mostly focused on improving the accuracy of the tracking techniques themselves. However, occasional errors remain inevitable, regardless of the technique used, and the tongue tracking process must thus be supervised by a speech scientist who will correct these errors manually or semi-automatically. This paper proposes an interactive framework to facilitate this process. In this framework, the user is guided towards potentially problematic portions of the US image sequence by a segmentation quality map that is based on the normalized energy of an active contour model and automatically produced during tracking. When a problematic segmentation is identified, corrections to the segmented contour can be made on one image and propagated both forward and backward in the problematic subsequence, thereby improving the user experience. The interactive tools were tested in combination with two different tracking algorithms. Preliminary results illustrate the potential of the proposed framework, suggesting that the proposed framework generally improves user interaction time, with little change in segmentation repeatability.
(-)-Reboxetine inhibits muscle nicotinic acetylcholine receptors by interacting with luminal and non-luminal sites.
Arias, Hugo R; Ortells, Marcelo O; Feuerbach, Dominik
The interaction of (-)-reboxetine, a non-tricyclic norepinephrine selective reuptake inhibitor, with muscle-type nicotinic acetylcholine receptors (AChRs) in different conformational states was studied by functional and structural approaches. The results established that (-)-reboxetine: (a) inhibits (±)-epibatidine-induced Ca(2+) influx in human (h) muscle embryonic (h?1?1??) and adult (h?1?1??) AChRs in a non-competitive manner and with potencies IC50=3.86±0.49 and 1.92±0.48 ?M, respectively, (b) binds to the [(3)H]TCP site with ~13-fold higher affinity when the Torpedo AChR is in the desensitized state compared to the resting state, (c) enhances [(3)H]cytisine binding to the resting but activatableTorpedo AChR but not to the desensitized AChR, suggesting desensitizing properties, (d) overlaps the PCP luminal site located between rings 6' and 13' in the Torpedo but not human muscle AChRs. In silico mutation results indicate that ring 9' is the minimum structural component for (-)-reboxetine binding, and (e) interacts to non-luminal sites located within the transmembrane segments from the Torpedo AChR ? subunit, and at the ?1/? transmembrane interface from the adult muscle AChR. In conclusion, (-)-reboxetine non-competitively inhibits muscle AChRs by binding to the TCP luminal site and by inducing receptor desensitization (maybe by interacting with non-luminal sites), a mechanism that is shared by tricyclic antidepressants. PMID:23917086
Site and Interaction Dependence of Nuclear Stimulated Desorption from Structured Surfaces
NASA Astrophysics Data System (ADS)
Ashkenazy, Y.; Kelson, I.
Molecular dynamics calculations of low energy Nuclear Stimulated Desorption (NSD) of 107Cd from a palladium substrate are presented. The characteristics of the desorption probability are shown to be related both to the site occupied by the 107Cd and to the adsorbate-substrate interaction. The quantitative implications of the theoretical calculations to a specific experimental scenario are discussed, based on preliminary measurements of 107Cd desorption from palladium.
BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.
Mikula, Shawn; Stone, James M; Jones, Edward G
BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses. PMID:19129928
Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways
Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew
As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496
An interactive program for computer-aided map design, display, and query: EMAPKGS2
Pouch, G.W.
EMAPKGS2 is a user-friendly, PC-based electronic mapping tool for use in hydrogeologic exploration and appraisal. EMAPKGS2 allows the analyst to construct maps interactively from data stored in a relational database, perform point-oriented spatial queries such as locating all wells within a specified radius, perform geographic overlays, and export the data to other programs for further analysis. EMAPKGS2 runs under Microsoft?? Windows??? 3.1 and compatible operating systems. EMAPKGS2 is a public domain program available from the Kansas Geological Survey. EMAPKGS2 is the centerpiece of WHEAT, the Windows-based Hydrogeologic Exploration and Appraisal Toolkit, a suite of user-friendly Microsoft?? Windows??? programs for natural resource exploration and management. The principal goals in development of WHEAT have been ease of use, hardware independence, low cost, and end-user extensibility. WHEAT'S native data format is a Microsoft?? Access?? database. WHEAT stores a feature's geographic coordinates as attributes so they can be accessed easily by the user. The WHEAT programs are designed to be used in conjunction with other Microsoft?? Windows??? software to allow the natural resource scientist to perform work easily and effectively. WHEAT and EMAPKGS have been used at several of Kansas' Groundwater Management Districts and the Kansas Geological Survey on groundwater management operations, groundwater modeling projects, and geologic exploration projects. ?? 1997 Elsevier Science Ltd.
A New Tool to Quantify Receptor Recruitment to Cell Contact Sites during Host-Pathogen Interaction
Wester, Michael J.; Davidson, Lisa B.; Steinberg, Stanly L.; Neumann, Aaron K.
To understand the process of innate immune fungal recognition, we developed computational tools for the rigorous quantification and comparison of receptor recruitment and distribution at cell-cell contact sites. We used these tools to quantify pattern recognition receptor spatiotemporal distributions in contacts between primary human dendritic cells and the fungal pathogens C. albicans, C. parapsilosis and the environmental yeast S. cerevisiae, imaged using 3D multichannel laser scanning confocal microscopy. The detailed quantitative analysis of contact sites shows that, despite considerable biochemical similarity in the composition and structure of these species' cell walls, the receptor spatiotemporal distribution in host-microbe contact sites varies significantly between these yeasts. Our findings suggest a model where innate immune cells discriminate fungal microorganisms based on differential mobilization and coordination of receptor networks. Our analysis methods are also broadly applicable to a range of cell-cell interactions central to many biological problems. PMID:24874253
Calculating the habitable zones of multiple star systems with a new interactive Web site
Müller, Tobias W. A.; Haghighipour, Nader [Institute for Astronomy and Astrophysics, University of Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen (Germany)
We have developed a comprehensive methodology and an interactive Web site for calculating the habitable zone (HZ) of multiple star systems. Using the concept of spectral weight factor, as introduced in our previous studies of the calculations of HZ in and around binary star systems, we calculate the contribution of each star (based on its spectral energy distribution) to the total flux received at the top of the atmosphere of an Earth-like planet, and use the models of the HZ of the Sun to determine the boundaries of the HZ in multiple star systems. Our interactive Web site for carrying out these calculations is publicly available at http://astro.twam.info/hz. We discuss the details of our methodology and present its application to some of the multiple star systems detected by the Kepler space telescope. We also present the instructions for using our interactive Web site, and demonstrate its capabilities by calculating the HZ for two interesting analytical solutions of the three-body problem.
Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps | Office of Cancer Genomics
Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and for defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of 'hit' genes are measured in a double-shRNA screen and used to construct a genetic interaction map.
Effect of Surface Site Interactions on Potentiometric Titration of Hematite (?-Fe2O3) Crystal Faces
Chatman, Shawn ME; Zarzycki, Piotr P.; Preocanin, Tajana; Rosso, Kevin M.
Time dependent potentiometric pH titrations were used to study the effect of atomic scale surface structure on the protonation behavior of the structurally well defined hematite/aqueous electrolyte interfaces. Our recently proposed thermodynamic model [1,23] was applied to measured acidimetric and alkalimetric titration hysteresis loops, collected from highly organized (001), (012), and (113) crystal face terminations using pH equilibration times ranging from 15 to 30 mins. Hysteresis loop areas indicate that (001) faces equilibrate faster than the (012) and (113) faces, consistent with the different expected ensembles of singly, doubly, and triply coordinated surface sites on each face. Strongly non-linear hysteretic pH-potential relationships were found, with slopes exceeding Nernstian, collectively indicating that protonation and deprotonation is much more complex than embodied in present day surface complexation models. The asymmetrical shape of the acidimetric and alkalimetric titration branches were used to illustrate a proposed steric "leaky screen" repulsion/trapping interaction mechanism that stems from high affinity singly-coordinated sites electrostatically and sterically screening lower affinity doubly and triply coordinated sites. Our data indicate that site interaction is the dominant phenomenon defining surface potential accumulation behavior on single crystal faces of metal oxide minerals.
Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability
Background Microarray analysis has been used as the first-tier genetic testing to detect chromosomal imbalances and copy number variants (CNVs) for pediatric patients with intellectual and developmental disabilities (ID/DD). To further investigate the candidate genes and underlying dosage-sensitive mechanisms related to ID, cytogenomic mapping of critical regions and bioinformatic mining of candidate brain-expressed genes (BEGs) and their functional interactions were performed. Critical regions of chromosomal imbalances and pathogenic CNVs were mapped by subtracting known benign CNVs from the Databases of Genomic Variants (DGV) and extracting smallest overlap regions with cases from DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). BEGs from these critical regions were revealed by functional annotation using Database for Annotation, Visualization, and Integrated Discovery (DAVID) and by tissue expression pattern from Uniprot. Cross-region interrelations and functional networks of the BEGs were analyzed using Gene Relationships Across Implicated Loci (GRAIL) and Ingenuity Pathway Analysis (IPA). Results Of the 1,354 patients analyzed by oligonucleotide array comparative genomic hybridization (aCGH), pathogenic abnormalities were detected in 176 patients including genomic disorders in 66 patients (37.5%), subtelomeric rearrangements in 45 patients (25.6%), interstitial imbalances in 33 patients (18.8%), chromosomal structural rearrangements in 17 patients (9.7%) and aneuploidies in 15 patients (8.5%). Subtractive and extractive mapping defined 82 disjointed critical regions from the detected abnormalities. A total of 461 BEGs was generated from 73 disjointed critical regions. Enrichment of central nervous system specific genes in these regions was noted. The number of BEGs increased with the size of the regions. A list of 108 candidate BEGs with significant cross region interrelation was identified by GRAIL and five significant gene networks involving cell cycle, cell-to-cell signaling, cellular assembly, cell morphology, and gene expression regulations were denoted by IPA. Conclusions These results characterized ID related cross-region interrelations and multiple networks of candidate BEGs from the detected genomic imbalances. Further experimental study of these BEGs and their interactions will lead to a better understanding of dosage-sensitive mechanisms and modifying effects of human mental development. PMID:24410907
Deconstructing the DGAT1 Enzyme: Membrane Interactions at Substrate Binding Sites
Lopes, Jose L. S.; Beltramini, Leila M.; Wallace, Bonnie A.; Araujo, Ana P. U.
Diacylglycerol acyltransferase 1 (DGAT1) is a key enzyme in the triacylglyceride synthesis pathway. Bovine DGAT1 is an endoplasmic reticulum membrane-bound protein associated with the regulation of fat content in milk and meat. The aim of this study was to evaluate the interaction of DGAT1 peptides corresponding to putative substrate binding sites with different types of model membranes. Whilst these peptides are predicted to be located in an extramembranous loop of the membrane-bound protein, their hydrophobic substrates are membrane-bound molecules. In this study, peptides corresponding to the binding sites of the two substrates involved in the reaction were examined in the presence of model membranes in order to probe potential interactions between them that might influence the subsequent binding of the substrates. Whilst the conformation of one of the peptides changed upon binding several types of micelles regardless of their surface charge, suggesting binding to hydrophobic domains, the other peptide bound strongly to negatively-charged model membranes. This binding was accompanied by a change in conformation, and produced leakage of the liposome-entrapped dye calcein. The different hydrophobic and electrostatic interactions observed suggest the peptides may be involved in the interactions of the enzyme with membrane surfaces, facilitating access of the catalytic histidine to the triacylglycerol substrates. PMID:25719207
Fragile X syndrome: genetic localisation by linkage mapping of two microsatellite repeats FRAXAC1 and FRAXAC2 which immediately flank the fragile site
R I Richards; K Holman; H Kozman; E Kremer; M Lynch; M Pritchard; S Yu; J Mulley; G R Sutherland
We report the genetic localisation of the fragile site at Xq27.3 associated with fragile X syndrome. The position of the fragile site within the multipoint linkage map was determined using two polymorphic microsatellite AC repeat markers FRAXAC1 and FRAXAC2. These markers were physically located within 10 kilobases and on either side of the p(CCG)n repeat responsible for the fragile site.
Restriction site polymorphism-based candidate gene mapping for seedling drought tolerance in cowpea [Vigna unguiculata (L.) Walp.].
Muchero, Wellington; Ehlers, Jeffrey D; Roberts, Philip A
Quantitative trait loci (QTL) studies provide insight into the complexity of drought tolerance mechanisms. Molecular markers used in these studies also allow for marker-assisted selection (MAS) in breeding programs, enabling transfer of genetic factors between breeding lines without complete knowledge of their exact nature. However, potential for recombination between markers and target genes limit the utility of MAS-based strategies. Candidate gene mapping offers an alternative solution to identify trait determinants underlying QTL of interest. Here, we used restriction site polymorphisms to investigate co-location of candidate genes with QTL for seedling drought stress-induced premature senescence identified previously in cowpea. Genomic DNA isolated from 113 F(2:8) RILs of drought-tolerant IT93K503-1 and drought susceptible CB46 genotypes was digested with combinations of EcoR1 and HpaII, Mse1, or Msp1 restriction enzymes and amplified with primers designed from 13 drought-responsive cDNAs. JoinMap 3.0 and MapQTL 4.0 software were used to incorporate polymorphic markers onto the AFLP map and to analyze their association with the drought response QTL. Seven markers co-located with peaks of previously identified QTL. Isolation, sequencing, and blast analysis of these markers confirmed their significant homology with drought or other abiotic stress-induced expressed sequence tags (EST) from cowpea and other plant systems. Further, homology with coding sequences for a multidrug resistance protein 3 and a photosystem I assembly protein ycf3 was revealed in two of these candidates. These results provide a platform for the identification and characterization of genetic trait determinants underlying seedling drought tolerance in cowpea. PMID:19834655
Fine mapping of antigenic site II of herpes simplex virus glycoprotein D.
Isola, V J; Eisenberg, R J; Siebert, G R; Heilman, C J; Wilcox, W C; Cohen, G H
Glycoprotein D (gD) is a virion envelope component of herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) which plays an important role in viral infection and pathogenesis. Previously, anti-gD monoclonal antibodies (MAbs) were arranged into groups which recognize distinct type-common and type-specific sites on HSV-1 gD (gD-1) and HSV-2 gD (gD-2). Several groups recognize discontinuous epitopes which are dependent on tertiary structure. Three groups, VII, II, and V, recognize continuous epitopes present in both native and denatured gD. Previously, group II consisted of a single MAb, DL6, whose epitope was localized between amino acids 268 and 287. In the study reported here, we extended our analysis of the antigenic structure of gD, concentrating on continuous epitopes. The DL6 epitope was localized with greater precision to residues 272 to 279. Four additional MAbs including BD78 were identified, each of which recognizes an epitope within residues 264 to 275. BD78 and DL6 blocked each other in binding to gD. In addition, a mutant form of gD was constructed in which the proline at 273 was replaced by serine. This change removes a predicted beta turn in gD. Neither antibody reacted with this mutant, indicating that the BD78 and DL6 epitopes overlap and constitute an antigenic site (site II) within residues 264 to 279. A separate antigenic site (site XI) was recognized by MAb BD66 (residues 284 to 301). This site was only six amino acids downstream of site II, but was distinct as demonstrated by blocking studies. Synthetic peptides mimicking these and other regions of gD were screened with polyclonal antisera to native gD-1 or gD-2. The results indicate that sites II, V, VII, and XI, as well as the carboxy terminus, are the major continuous antigenic determinants on gD. In addition, the results show that the region from residues 264 through 369, except the transmembrane anchor, contains a series of continuous epitopes. Images PMID:2467994
Mapping protein-protein interactions by localized oxidation: consequences of the reach of hydroxyl radical.
Cheal, Sarah M; Ng, Mindy; Barrios, Brianda; Miao, Zheng; Kalani, Amir K; Meares, Claude F
Hydroxyl radicals generated from a variety of methods, including not only synchrotron radiation but also Fenton reactions involving chelated iron, have become an accepted macromolecular footprinting tool. Hydroxyl radicals react with proteins via multiple mechanisms that lead to both polypeptide backbone cleavage events and side chain modifications (e.g., hydroxylation and carbonyl formation). The use of site-specifically tethered iron chelates can reveal protein-protein interactions, but the interpretation of such experiments will be strengthened by improving our understanding of how hydroxyl radicals produced at a point on a protein react with other protein sites. We have developed methods for monitoring carbonyl formation on proteins as a function of distance from a hydroxyl generator, iron-(S)-1-[p-(bromoacetamido)benzyl]EDTA (FeBABE), conjugated to an engineered cysteine residue. After activation of the chelated iron with ascorbate and peroxide produces new protein carbonyl groups, their positions can be identified using element-coded affinity tagging (ECAT), with carbonyl-specific tags {e.g., rare earth chelates of (S)-2-[4-(2-aminooxy)acetamidobenzyl]-1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid (AOD)} that allow for affinity purification, identification, and relative quantitation of oxidation sites using mass spectrometry. Intraprotein oxidation of single-cysteine mutants of Escherichia coli sigma(70) by tethered FeBABE was used to calibrate the reach of hydroxyl radical by comparison to the crystal structure; the application to protein-protein interactions was demonstrated using the same sigma(70) FeBABE conjugates in complexes with the RNA polymerase core enzyme. The results provide fundamental information for interpreting protein footprinting experiments in other systems. PMID:19354299
Forest Types in the Lower Suwannee River Floodplain, Florida?-A Report and Interactive Map
Darst, M.R.; Light, H.M.; Lewis, L.J.; Sepulveda, A.A.
A map of forest types in the lower Suwannee River floodplain, Florida, was created during a study conducted from 1996 to 2000 by the U.S. Geological Survey in cooperation with the Suwannee River Water Management District. The map is presented with this report on a compact disc with interactive viewing software. The forest map can be used by scientists for ecological studies in the floodplain based on land cover types and by landowners and management personnel making land use decisions. The study area is the 10-year floodplain of the lower Suwannee River from its confluence with the Santa Fe River to the lower limit of forests near the Gulf of Mexico. The floodplain is divided into three reaches: riverine (non-tidal), upper tidal, and lower tidal, due to changes in hydrology, vegetation, and soils with proximity to the coast. The 10-year floodplain covers about 21,170 hectares; nearly 88 percent of this area (18,580 hectares) is mapped as 14 major forest types. Approximately 29 percent (5,319 hectares) of these forests have been altered by agriculture or development. About 75 percent of the area of major forest types (13,994 hectares) is wetland forests and about 25 percent (4,586 hectares) is upland forests. Tidal wetland forests (8,955 hectares) cover a much greater area than riverine wetland forests (5,039 hectares). Oak/pine upland forests are present in the riverine and upper tidal reaches of the floodplain on elevations that are inundated only briefly during the highest floods. High bottomland hardwoods are present on the higher levees, ridges, and flats of the riverine reach where soils are usually sandy. Low bottomland hardwood forests are present in the riverine reach on swamp margins and low levees and flats that are flooded continuously for several weeks or longer every 1 to 3 years. Riverine swamps are present in the lowest and wettest areas of the non-tidal floodplain that are either inundated or saturated most of the time. Upper tidal bottomland hardwood forests are present on sandy soils on high flats and in transitional areas between upland forests and swamps. Upper tidal mixed forests are found on low levees or between swamps and higher forest types. Upper tidal swamps are present at elevations below median monthly high stage and usually have surface soils that are permanently saturated mucks. Lower tidal hammocks are found on higher elevations that do not receive regular tidal inundation but have a high water table and are briefly inundated by storm surges several times a decade. Lower tidal mixed forests include swamps with numerous small hummocks or less common larger hummocks. Lower tidal swamps are found on deep muck soils that are below the elevation of the median daily or monthly high stage. Seven additional land cover types (2,590 hectares) are mapped. Water in the main channel of the lower Suwannee River (1,767 hectares) was mapped separately from open water in the floodplain (239 hectares). Other land cover types are: seepage slopes (70 hectares), isolated forested wetlands (19 hectares), marshes upstream of the tree line (505 hectares), beds of emergent aquatic vegetation (21 hectares), and floodplain glades (46 hectares)
Bayesian model choice and search strategies for mapping interacting quantitative trait Loci.
Yi, Nengjun; Xu, Shizhong; Allison, David B
Most complex traits of animals, plants, and humans are influenced by multiple genetic and environmental factors. Interactions among multiple genes play fundamental roles in the genetic control and evolution of complex traits. Statistical modeling of interaction effects in quantitative trait loci (QTL) analysis must accommodate a very large number of potential genetic effects, which presents a major challenge to determining the genetic model with respect to the number of QTL, their positions, and their genetic effects. In this study, we use the methodology of Bayesian model and variable selection to develop strategies for identifying multiple QTL with complex epistatic patterns in experimental designs with two segregating genotypes. Specifically, we develop a reversible jump Markov chain Monte Carlo algorithm to determine the number of QTL and to select main and epistatic effects. With the proposed method, we can jointly infer the genetic model of a complex trait and the associated genetic parameters, including the number, positions, and main and epistatic effects of the identified QTL. Our method can map a large number of QTL with any combination of main and epistatic effects. Utility and flexibility of the method are demonstrated using both simulated data and a real data set. Sensitivity of posterior inference to prior specifications of the number and genetic effects of QTL is investigated. PMID:14573494
Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map* | Office of Cancer Genomics
There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or emergent dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses.
Mapping the Agonist Binding Site of the GABAA Receptor: Evidence for a b-Strand
Andrew J. Boileau; Amy R. Evers; Anson F. Davis; Cynthia Czajkowski
GABAA receptors, along with the receptors for acetylcholine, glycine, and serotonin, are members of a ligand-gated ion channel superfamily (Ortells and Lunt, 1995). Because of the paucity of crystallographic information for these ligand-gated channels, little is known about the structure of their binding sites or how agonist binding is transduced into channel gating. We used the substituted cysteine accessibility method
Map Your Future through ASA's New and Transfer Student Web Site.
ERIC Educational Resources Information Center
Shelton, Beverley; Isberner, Fred
This paper describes the College of Applied Science and Arts (ASA) at Southern Illinois University Carbondale (SIUC) Transfer and New Students Info Web site that responds to the need for high school and community college students, guidance counselors, and parents to explore and plan a program of study that provides the opportunity to enter the…
Web navigation and the behavioral effects of constantly visible site maps
David R. Danielson
Knowledge regarding how Web information-seekers behave with respect to the structures and cues they are provided with may shed light on general principles of navigation in electronic spaces, and assist designers in making more informed structural decisions. This study examines user movement through hierarchically structured Web sites and the behavioral effects of a constantly visible, textual contents list for relatively
Interaction of Palmitic Acid with Metoprolol Succinate at the Binding Sites of Bovine Serum Albumin
Rahman, Mashiur; Prianka, Farzana; Shohel, Mohammad; Mazid, Md. Abdul
Purpose: The aim of this study was to characterize the binding profile as well as to notify the interaction of palmitic acid with metoprolol succinate at its binding site on albumin. Methods: The binding of metoprolol succinate to bovine serum albumin (BSA) was studied by equilibrium dialysis method (ED) at 27°C and pH 7.4, in order to have an insight in the binding chemistry of the drug to BSA in presence and absence of palmitic acid. The study was carried out using ranitidine as site-1 and diazepam as site-2 specific probe. Results: Different analysis of binding of metoprolol succinate to bovine serum albumin suggested two sets of association constants: high affinity association constant (k1 = 11.0 x 105 M-1) with low capacity (n1 = 2) and low affinity association (k2 = 4.0×105 M-1) constant with high capacity (n2 = 8) at pH 7.4 and 27°C. During concurrent administration of palmitic acid and metoprolol succinate in presence or absence of ranitidine or diazepam, it was found that palmitic acid displaced metoprolol succinate from its binding site on BSA resulting reduced binding of metoprolol succinate to BSA. The increment in free fraction of metoprolol succinate was from 26.27% to 55.08% upon the addition of increased concentration of palmitic acid at a concentration of 0×10-5 M to 16×10-5 M. In presence of ranitidine and diazepam, palmitic acid further increases the free fraction of metoprolol succinate from 33.05% to 66.95% and 40.68% to 72.88%, respectively. Conclusion: This data provided the evidence of interaction at higher concentration of palmitic acid at the binding sites on BSA, which might change the pharmacokinetic properties of metoprolol succinate. PMID:25436195
Road-map to plan and structure the preliminary site investigation program for a geological repository in Japan
Deguchi, Akira; Tsuchi, Hiroyuki; Kitayama, Kazumi [Nuclear Waste Management Organization of Japan (NUMO), Mita NN Bldg., 1-23, Shiba 4-Chome, Minato-ku, Tokyo 108-0014 (Japan); Chapman, Neil [ITC School of Underground Waste Storage and Disposal, Postfach, 3862 Innertkirchen (Switzerland); Andersson, Johan [JA Streamflow AB, Vinodlargatan 6, 117 59 Stockholm (Sweden); Tanaka, Tatsuya [Obayashi Corporation, SHinagawa InterCity B, 2-15-2, Konan, Minatoku, Tokyo, 108-8502 (Japan)
Available in abstract form only. Full text of publication follows: A stepwise site selection process has been adopted for geological disposal of HLW in Japan. Literature surveys (LS), followed by preliminary investigations (PI) and, finally, detailed investigations (DI) in underground facilities will be carried out in the successive selection stages. In the PI stage, surface-based investigations such as borehole surveys and geophysical prospecting will be implemented with two main objectives. The first is to obtain information relating to legal requirements on siting, such as the occurrence of igneous or fault activity, and to confirm the extremely low likelihood of adverse impacts on the candidate site resulting from such phenomena. The second is to obtain the information required for the design and performance assessment of the engineered barrier system and the repository. In order to implement these preliminary investigations rigorously and efficiently within the constraints of a limited time period, budget and resources, PI planning before commencing investigations and on-site PI management during the investigation phase are very important issues. The planning and management of PI have to be performed by NUMO staff, but not all staff have sufficient experience in the range of disciplines involved. NUMO therefore decided to compile existing knowledge and experience in the planning and management of investigations in the form of manuals to be used to improve and maintain internal expertise. Experts with experience in overseas investigation programs were requested to prepare these manuals. This paper outlines the structure and scope of the upper level manual (road-map) and discusses NUMO's experience in applying it in 'dry-runs' to model sites. (authors)
Opportunity rover localization and topographic mapping at the landing site of Meridiani Planum, Mars
NASA Astrophysics Data System (ADS)
Li, Rongxing; Arvidson, Raymond E.; Di, Kaichang; Golombek, Matt; Guinn, Joe; Johnson, Andrew; Maimone, Mark; Matthies, Larry H.; Malin, Mike; Parker, Tim; Squyres, Steven W.; Watters, Wesley A.
This paper presents the results of Mars topographic mapping and lander and rover localization for the Opportunity rover at Meridiani Planum during the Mars Exploration Rover (MER) 2003 mission. By Sol 458, the Opportunity rover traversed a distance of 5.20 km. We localized the lander using two-way Doppler radio positioning and cartographic triangulation of craters visible in both orbital and ground images. Additional high-resolution orbital images were taken to verify the determined lander position. Visual odometry and bundle adjustment techniques were applied to overcome wheel slippages, azimuthal angle drift, and other navigation errors (as large as 21% within Eagle crater). In addition, orbit-to-ground image-based adjustment was applied to correct rover location errors where bundle adjustment was not applicable. We generated timely topographic products, including orthoimages, digital terrain models (DTMs), three-dimensional (3-D) crater models, and rover traverse maps. In particular, detailed 3-D terrain models of major features, such as Endurance crater, have been generated using multisite panoramic stereo images based on bundle adjustment and wide baseline stereo technique.
Iowa magnetic and gravity maps and data: a web site for distribution of data
Kucks, Robert P.; Hill, Patricia L.
Magnetic anomalies are due to variations in the Earth's magnetic field caused by the uneven distribution of magnetic minerals (primarily magnetite) in the rocks that make up the upper part of the Earth's crust. The features and patterns of the magnetic anomalies can be used to delineate details of subsurface geology, including the locations of buried faults and magnetite-bearing rocks and the depth to the base of sedimentary basins. This information is valuable for mineral exploration, geologic mapping, and environmental studies. The Iowa magnetic map is constructed from grids that combine information collected in nine separate magnetic surveys conducted between 1953 and 1972. The data from these surveys are of varying quality. The design and specifications (terrain clearance, sampling rates, line spacing, and reduction procedures) varied from survey to survey depending on the purpose of the project and the technology of that time. Every attempt was made to acquire the data in digital form. All survey grids have been continued to 305 m (1,000 ft) above ground and merged together to form the State compilation.
IGIS (Interactive Geologic Interpretation System) computer-aided photogeologic mapping with image processing, graphics and CAD/CAM capabilities
McGuffie, B.A.; Johnson, L.F.; Alley, R.E.; Lang, H.R. (California Institute of Technology, Pasadena (USA))
Advances in computer technology are changing the way geologists integrate and use data. Although many geoscience disciplines are absolutely dependent upon computer processing, photogeological and map interpretation computer procedures are just now being developed. Historically, geologists collected data in the field and mapped manually on a topographic map or aerial photographic base. New software called the interactive Geologic Interpretation System (IGIS) is being developed at the Jet Propulsion Laboratory (JPL) within the National Aeronautics and Space Administration (NASA)-funded Multispectral Analysis of Sedimentary Basins Project. To complement conventional geological mapping techniques, Landsat Thematic Mapper (TM) or other digital remote sensing image data and co-registered digital elevation data are combined using computer imaging, graphics, and CAD/CAM techniques to provide tools for photogeologic interpretation, strike/dip determination, cross section construction, stratigraphic section measurement, topographic slope measurement, terrain profile generation, rotatable 3-D block diagram generation, and seismic analysis.
Using Student Interactions to Foster Rule-Diagram Mapping during Problem Solving in an Intelligent Tutoring System
ERIC Educational Resources Information Center
Butcher, Kirsten R.; Aleven, Vincent
In many domains, problem solving involves the application of general domain principles to specific problem representations. In 3 classroom studies with an intelligent tutoring system, we examined the impact of (learner-generated) interactions and (tutor-provided) visual cues designed to facilitate rule-diagram mapping (where students connect…
Mapping Fiber and Yield QTLs with Main, Epistatic, and QTL × Environment Interaction Effects in Recombinant Inbred Lines of Upland Cotton
Xinlian Shen; Tianzhen Zhang; Wangzhen Guo; Xiefei Zhu; Xiaoyang Zhang
Most agronomic traits of cotton (Gossypium hirsutum L.) are quan- titatively inherited and affected by environment. The importance of epistasis as the genetic basis for complex traits has been reported in many crops. In this study, a linkage map was constructed by means of a recombinant inbred line (RIL) population derived from 72353TM-1. Main effects, epistatic effects, and environmental interaction
Interactive Radiative Transfer Modeling Tools to Map Volcanic Emissions with Thermal Infrared Remote Sensing
NASA Astrophysics Data System (ADS)
Realmuto, V. J.
The estimation of plume composition from thermal infrared (TIR) radiance measurements is based in radiative transfer (RT) modeling. To model the observed spectra we must consider the temperature, emissivity, and elevation of the surface beneath the plume, plume altitude and thickness, and the local atmospheric temperature and humidity. Our knowledge of these parameters is never perfect, and interactive RT modeling allows us to evaluate the impact of these uncertainties on our estimates of plume composition. Interactive RT modeling has three main components: retrieval procedures for plume components, an engine for RT calculations, and a graphic user interface (GUI) to input radiance data, modify model parameters, launch retrievals, and visualize the resulting estimates of plume composition. The Jet Propulsion Laboratory (JPL), in collaboration with Spectral Sciences, Inc. (SSI), is developing a new class of tools for interactive RT modeling. We will implement RT modeling on graphics processors (GPU) to achieve a 100-fold increase in processing speed, relative to conventional CPU-based processing, and thus enable fully-interactive estimation and visualization of plume composition. The heritage for our new tools is based on the Plume Tracker toolkit, developed at JPL, and MODTRAN RT model, developed by SSI. Plume Tracker integrates retrieval procedures, interactive visualization tools, and an interface to a modified version of MODTRAN under a single GUI. Our new tools will incorporate refinements from a recent adaptation of MODTRAN to optimize modeling the radiative properties of chemical clouds. This presentation will include a review of the foundations of plume mapping in the TIR and examples of the application of Plume Tracker to ASTER, MODIS, and AIRS data. We will present an overview of our tool development effort and discuss the application of these tools to data from new and future instruments, such as the airborne Hyperspectral Thermal Emission Spectrometer and TIR data from the upcoming Hyperspectral Infrared Imager mission. Portions of this research were conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.
Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains.
Martin, Mathew P; Olesen, Sanne H; Georg, Gunda I; Schönbrunn, Ernst
Bromodomain-containing proteins are considered atypical kinases, but their potential to interact with kinase inhibitors is unknown. Dinaciclib is a potent inhibitor of cyclin-dependent kinases (CDKs), which recently advanced to Phase III clinical trials for the treatment of leukemia. We determined the crystal structure of dinaciclib in complex with CDK2 at 1.7 Ĺ resolution, revealing an elaborate network of binding interactions in the ATP site, which explains the extraordinary potency and selectivity of this inhibitor. Remarkably, dinaciclib also interacted with the acetyl-lysine recognition site of the bromodomain testis-specific protein BRDT, a member of the BET family of bromodomains. The binding mode of dinaciclib to BRDT at 2.0 Ĺ resolution suggests that general kinase inhibitors ("hinge binders") possess a previously unrecognized potential to act as protein-protein inhibitors of bromodomains. The findings may provide a new structural framework for the design of next-generation bromodomain inhibitors using the vast chemical space of kinase inhibitors. PMID:24007471
A solid waste disposal site selection procedure based on groundwater vulnerability mapping
Celalettin Simsek; Cem Kincal; Orhan Gunduz
In this study, a new, GIS-based solid waste site selection tool (DUPIT) is introduced to obtain a systematic and unbiased\\u000a methodology during the evaluation phases of alternative solid waste disposal areas with regards to vulnerability to groundwater\\u000a pollution. The proposed tool is an index technique based on the linear combination of five different hydrogeological parameters\\u000a including Depth to groundwater table,
COREMAP: Graphical user interface for displaying reactor core data in an interactive hexagon map
Muscat, F.L.; Derstine, K.L.
COREMAP is a Graphical User Interface (GUI) designed to assist users read and check reactor core data from multidimensional neutronic simulation models in color and/or as text in an interactive 2D planar grid of hexagonal subassemblies. COREMAP is a complete GEODST/RUNDESC viewing tool which enables the user to access multi data set files (e.g. planes, moments, energy groups ,... ) and display up to two data sets simultaneously, one as color and the other as text. The user (1) controls color scale characteristics such as type (linear or logarithmic) and range limits, (2) controls the text display based upon conditional statements on data spelling, and value. (3) chooses zoom features such as core map size, number of rings and surrounding subassemblies, and (4) specifies the data selection for supplied popup subwindows which display a selection of data currently off-screen for a selected cell, as a list of data and/or as a graph. COREMAP includes a RUNDESC file editing tool which creates ``proposed`` Run-description files by point and click revisions to subassembly assignments in an existing EBRII Run-description file. COREMAP includes a fully automated printing option which creates high quality PostScript color or greyscale images of the core map independent of the monitor used, e.g. color prints can be generated with a session from a color or monochrome monitor. The automated PostScript output is an alternative to the xgrabsc based printing option. COREMAP includes a plotting option which creates graphs related to a selected cell. The user specifies the X and Y coordinates types (planes, moment, group, flux ,... ) and a parameter, P, when displaying several curves for the specified (X, Y) pair COREMAP supports hexagonal geometry reactor core configurations specified by: the GEODST file and binary Standard Interface Files and the RUNDESC ordering.
Mapping the Substrate Binding Site of Phenylacetone Monooxygenase from Thermobifida fusca by Mutational Analysis?†
Dudek, Hanna M.; de Gonzalo, Gonzalo; Torres Pazmińo, Daniel E.; St?pniak, Piotr; Wyrwicz, Lucjan S.; Rychlewski, Leszek; Fraaije, Marco W.
Baeyer-Villiger monooxygenases catalyze oxidations that are of interest for biocatalytic applications. Among these enzymes, phenylacetone monooxygenase (PAMO) from Thermobifida fusca is the only protein showing remarkable stability. While related enzymes often present a broad substrate scope, PAMO accepts only a limited number of substrates. Due to the absence of a substrate in the elucidated crystal structure of PAMO, the substrate binding site of this protein has not yet been defined. In this study, a structural model of cyclopentanone monooxygenase, which acts on a broad range of compounds, has been prepared and compared with the structure of PAMO. This revealed 15 amino acid positions in the active site of PAMO that may account for its relatively narrow substrate specificity. We designed and analyzed 30 single and multiple mutants in order to verify the role of these positions. Extensive substrate screening revealed several mutants that displayed increased activity and altered regio- or enantioselectivity in Baeyer-Villiger reactions and sulfoxidations. Further substrate profiling resulted in the identification of mutants with improved catalytic properties toward synthetically attractive compounds. Moreover, the thermostability of the mutants was not compromised in comparison to that of the wild-type enzyme. Our data demonstrate that the positions identified within the active site of PAMO, namely, V54, I67, Q152, and A435, contribute to the substrate specificity of this enzyme. These findings will aid in more dedicated and effective redesign of PAMO and related monooxygenases toward an expanded substrate scope. PMID:21724896
HindIII and Sst I restriction sites mapped on rabbit poxvirus and vaccinia virus DNA.
Wittek, R; Menna, A; Schümperli, D; Stoffel, S; Müller, H K; Wyler, R
The DNAs of two closely related orthopoxviruses, rabbit poxvirus (RPV) and vaccinia virus (VV), were mapped by overlapping-fragment analysis using restriction endonucleases HindIII and Sst I. The exact arrangement of these fragments was accomplished by total digestion of isolated partial restriction products and by end-fragment determination. RPV and VV DNAs showed identical restriction patterns in an internal region comprising approximately 60% of the genome. The size, by electrophoretical analysis of the RPV DNA, was 118 X 10(6) daltons, some 6 X 10(6) daltons less than VV DNA. The two opposite terminal restriction fragments of RPV DNA cross-hybridized to each other. Images PMID:197263
Interaction of an insect lipoprotein with its binding site at the fat body.
Dantuma, N P; Van Marrewijk, W J; Wynne, H J; Van der Horst, D J
A single type of high density lipoprotein (HDLp) binding sites is present at intact fat body tissue and in fat body membranes of larval and adult locusts. HDLp is bound with high affinity (Kd approximately 10(-7) M). This interaction does not require divalent cations and is heat-labile because heat-treatment of fat body membranes results in a substantial reduction of the maximal binding capacity. In addition to unlabeled HDLp and low density lipophorin (LDLp), human low density lipoprotein also seems to compete with radiolabeled HDLp for this binding site, suggesting a relaxed specificity. Induction of lipid mobilization with adipokinetic hormone did not change the binding characteristics of the fat body. An increase in the binding capacity of intact fat body tissue in the adult stage suggests that the number of cell surface binding sites is upregulated during development. However, the total number of HDLp binding sites appears to be constant, because larval and adult fat body membranes have similar binding capacities. PMID:8808769
BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska
NASA Astrophysics Data System (ADS)
Cody, R. P.; Kassin, A.; Gaylord, A.; Brown, J.; Tweedie, C. E.
The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic. The Barrow Area Information Database (BAID, www.baidims.org) is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 9,600 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, and save or print maps and query results. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. BAID has been used to: Optimize research site choice; Reduce duplication of science effort; Discover complementary and potentially detrimental research activities in an area of scientific interest; Re-establish historical research sites for resampling efforts assessing change in ecosystem structure and function over time; Exchange knowledge across disciplines and generations; Facilitate communication between western science and traditional ecological knowledge; Provide local residents access to science data that facilitates adaptation to arctic change; (and) Educate the next generation of environmental and computer scientists. This poster describes key activities that will be undertaken over the next three years to provide BAID users with novel software tools to interact with a current and diverse selection of information and data about the Barrow area. Key activities include: 1. Collecting data on research activities, generating geospatial data, and providing mapping support. 2. Maintaining, updating and innovating the existing suite of BAID geobrowsers. 3. Maintaining and updating aging server hardware supporting BAID. 4. Adding interoperability with other CI using workflows, controlled vocabularies and web services. 5. Linking BAID to data archives at the National Snow and Ice Data Center (NSIDC). 6. Developing a wireless sensor network that provides web based interaction with near-real time climate and other data. 7. Training next generation of environmental and computer scientists and conducting outreach.
Big Data Storytelling through Interactive Maps Jayant Madhavan, Sreeram Balakrishnan, Kathryn Brisbin, Hector Gonzalez, Nitin Gupta,
Tomkins, Andrew
;Figure 1: Map from Guardian Datablog article titled Wikileaks Iraq war logs: every death mapped [10 the more than 50,000 mortality incidents in Iraq recorded in the documents released by Wikileaks. Through
NSDL National Science Digital Library
US Census Bureau
This resource allows users to create interactive maps with layers using census data for the following topics: agriculture, biology, boundaries, climate, environment, geology, history, map reference, people, transportation, and water.
Reconstructing Genome-Wide Protein–Protein Interaction Networks Using Multiple Strategies with Homologous Mapping
Lo, Yu-Shu; Huang, Sing-Han; Luo, Yong-Chun; Lin, Chun-Yu; Yang, Jinn-Moon
Background One of the crucial steps toward understanding the biological functions of a cellular system is to investigate protein–protein interaction (PPI) networks. As an increasing number of reliable PPIs become available, there is a growing need for discovering PPIs to reconstruct PPI networks of interesting organisms. Some interolog-based methods and homologous PPI families have been proposed for predicting PPIs from the known PPIs of source organisms. Results Here, we propose a multiple-strategy scoring method to identify reliable PPIs for reconstructing the mouse PPI network from two well-known organisms: human and fly. We firstly identified the PPI candidates of target organisms based on homologous PPIs, sharing significant sequence similarities (joint E-value ? 1 × 10?40), from source organisms using generalized interolog mapping. These PPI candidates were evaluated by our multiple-strategy scoring method, combining sequence similarities, normalized ranks, and conservation scores across multiple organisms. According to 106,825 PPI candidates in yeast derived from human and fly, our scoring method can achieve high prediction accuracy and outperform generalized interolog mapping. Experiment results show that our multiple-strategy score can avoid the influence of the protein family size and length to significantly improve PPI prediction accuracy and reflect the biological functions. In addition, the top-ranked and conserved PPIs are often orthologous/essential interactions and share the functional similarity. Based on these reliable predicted PPIs, we reconstructed a comprehensive mouse PPI network, which is a scale-free network and can reflect the biological functions and high connectivity of 292 KEGG modules, including 216 pathways and 76 structural complexes. Conclusions Experimental results show that our scoring method can improve the predicting accuracy based on the normalized rank and evolutionary conservation from multiple organisms. Our predicted PPIs share similar biological processes and cellular components, and the reconstructed genome-wide PPI network can reflect network topology and modularity. We believe that our method is useful for inferring reliable PPIs and reconstructing a comprehensive PPI network of an interesting organism. PMID:25602759
Rhodopsin TM6 Can Interact with Two Separate and Distinct Sites on Arrestin: Evidence for Structural Plasticity and Multiple Docking Modes in Arrestin–Rhodopsin Binding
Various studies have implicated the concave surface of arrestin in the binding of the cytosolic surface of rhodopsin. However, specific sites of contact between the two proteins have not previously been defined in detail. Here, we report that arrestin shares part of the same binding site on rhodopsin as does the transducin G? subunit C-terminal tail, suggesting binding of both proteins to rhodopsin may share some similar underlying mechanisms. We also identify two areas of contact between the proteins near this region. Both sites lie in the arrestin N-domain, one in the so-called "finger" loop (residues 67–79) and the other in the 160 loop (residues 155–165). We mapped these sites using a novel tryptophan-induced quenching method, in which we introduced Trp residues into arrestin and measured their ability to quench the fluorescence of bimane probes attached to cysteine residues on TM6 of rhodopsin (T242C and T243C). The involvement of finger loop binding to rhodopsin was expected, but the evidence of the arrestin 160 loop contacting rhodopsin was not. Remarkably, our data indicate one site on rhodopsin can interact with multiple structurally separate sites on arrestin that are almost 30 Ĺ apart. Although this observation at first seems paradoxical, in fact, it provides strong support for recent hypotheses that structural plasticity and conformational changes are involved in the arrestin–rhodopsin binding interface and that the two proteins may be able to interact through multiple docking modes, with arrestin binding to both monomeric and dimeric rhodopsin. PMID:24724832
A 3347Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium)
Junkang Rong; Colette Abbey; John E. Bowers; Curt L. Brubaker; Charlene Chang; Peng W. Chee; Terrye A. Delmonte; Xiaoling Ding; Juan J. Garza; Barry S. Marler; Chan-hwa Park; Gary J. Pierce; Katy M. Rainey; Vipin K. Rastogi; Stefan R. Schulze; Norma L. Trolinder; Jonathan F. Wendel; Thea A. Wilkins; T. Dawn Williams-Coplin; Rod A. Wing; Robert J. Wright; Xinping Zhao; Linghua Zhu; Andrew H. Paterson
We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM (600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit
Baseline mapping study of the Steed Pond aquifer and vadose zone beneath A/M Area, Savannah River Site, Aiken, South Carolina
Jackson, D.G. Jr.
This report presents the second phase of a baseline mapping project conducted for the Environmental Restoration Department (ERD) at Savannah River Site. The purpose of this second phase is to map the structure and distribution of mud (clay and silt-sized sediment) within the vadose zone beneath A/M Area. The results presented in this report will assist future characterization and remediation activities in the vadose zone and upper aquifer zones in A/M Area.
An Interactive 3-D Geologic Map for Lake County, Illinois, United States of America
Andrew J. Stumpf; Donald E. Luman
Please click here to download the map associated with this article.Geological mapping projects undertaken in the Chicago metropolitan areas of northeastern Illinois are providing critical scientific information requested by government officials and public agencies to direct future land use, groundwater extraction, and environmental mitigation. Specifically, in Lake County, the Illinois State Geological Survey is undertaking a program to map glacial
Air-sea interaction at contrasting sites in the Eastern Tropical Pacific : mesoscale variability and atmospheric convection at 10°N
Farrar, J. Thomas (John Thomas), 1976-
The role of ocean dynamics in driving air-sea interaction is examined at two contrasting sites on 125°W in the eastern tropical Pacific Ocean using data from the Pan American Climate Study (PACS) field program. Analysis ...
Characterization, validation and intercomparison of clumping index maps from POLDER, MODIS, and MISR satellite data over reference sites
NASA Astrophysics Data System (ADS)
Pisek, Jan; He, Liming; Chen, Jing; Govind, Ajit; Sprintsin, Michael; Ryu, Youngryel; Arndt, Stefan; Hocking, Darren; Wardlaw, Timothy; Kuusk, Joel; Oliphant, Andrew; Korhonen, Lauri; Fang, Hongliang; Matteucci, Giorgio; Longdoz, Bernard; Raabe, Kairi
Vegetation foliage clumping significantly alters its radiation environment and therefore affects vegetation growth as well as water and carbon cycles. The clumping index is useful in ecological and meteorological models because it provides new structural information in addition to the effective leaf area index (LAI) retrieved from mono-angle remote sensing and allows accurate separation of sunlit and shaded leaves in the canopy. Not accounting for the foliage clumping in LAI retrieval algorithms leads to substantial underestimation of actual LAI, especially for needleleaf forests. Normalized Difference between Hotspot and Darkspot (NDHD) index has been previously used to retrieve global clumping index maps from POLarization and Directionality of the Earth's Reflectances (POLDER) data at ~6 km resolution, from Moderate Resolution Imaging Spectroradiometer (MODIS) Bidirectional Reflectance Distribution Function (BRDF) product at 500 m resolution. Most recently the algorithm was applied with Multi-angle Imaging SpectroRadiometer (MISR) data at 275 m resolution over selected areas. In this presentation we characterize and intercompare the three products over a set of sites representing diverse biomes and different canopy structures. The products are also directly validated with both in-situ vertical profiles and seasonal trajectories of clumping index. We illustrate that the vertical distribution of foliage and especially the effect of understory needs to be taken into account while validating foliage clumping products from remote sensing products with values measured in the field. Satellite measurements respond to the structural effects near the top of canopies, while ground measurements may be biased by the lower vegetation layers. Additionally, caution should be taken regarding the misclassification in land cover maps as their errors can be propagated into the foliage clumping maps. Our results indicate that MODIS data and MISR data with 275 m in particular can provide good quality clumping index estimates at pertinent scales for modeling local carbon and energy fluxes.
Extended Hubbard Model with off-site interactions: two-particle spectrum and Auger lineshapes
NASA Astrophysics Data System (ADS)
Verdozzi, C.
A method is presented to calculate the Green's function of two particles on a periodic lattice, with arbitrary distance-dependent interactions (Extended Hubbard Model). We develop the exact results together with their dispersionless limit (local approximation) for the sake of comparison. Numerical calculations for a repulsive, Thomas-Fermi-like potential illustrate the effects of including off-site interactions on a Simple Cubic lattice. For strong correlations, the spectrum differs qualitatively from that of the Hubbard model, and may show several resonant states instead of just one. The formalism lends itself to many physical applications: here, we discuss its consequences for the theory of Auger Core-Valence- Valence (CVV) line shapes of solids. *Temporary address: Sandia National Labs., Albuquerque NM 87185-1413
Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors.
Lakkaraju, Sirish Kaushik; Yu, Wenbo; Raman, E Prabhu; Hershfeld, Alena V; Fang, Lei; Deshpande, Deepak A; MacKerell, Alexander D
Occluded ligand-binding pockets (LBP) such as those found in nuclear receptors (NR) and G-protein coupled receptors (GPCR) represent a significant opportunity and challenge for computer-aided drug design. To determine free energies maps of functional groups of these LBPs, a Grand-Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) strategy is combined with the Site Identification by Ligand Competitive Saturation (SILCS) methodology. SILCS-GCMC/MD is shown to map functional group affinity patterns that recapitulate locations of functional groups across diverse classes of ligands in the LBPs of the androgen (AR) and peroxisome proliferator-activated-? (PPAR?) NRs and the metabotropic glutamate (mGluR) and ?2-adreneric (?2AR) GPCRs. Inclusion of protein flexibility identifies regions of the binding pockets not accessible in crystal conformations and allows for better quantitative estimates of relative ligand binding affinities in all the proteins tested. Differences in functional group requirements of the active and inactive states of the ?2AR LBP were used in virtual screening to identify high efficacy agonists targeting ?2AR in Airway Smooth Muscle (ASM) cells. Seven of the 15 selected ligands were found to effect ASM relaxation representing a 46% hit rate. Hence, the method will be of use for the rational design of ligands in the context of chemical biology and the development of therapeutic agents. PMID:25692383
Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors
Occluded ligand-binding pockets (LBP) such as those found in nuclear receptors (NR) and G-protein coupled receptors (GPCR) represent a significant opportunity and challenge for computer-aided drug design. To determine free energies maps of functional groups of these LBPs, a Grand-Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) strategy is combined with the Site Identification by Ligand Competitive Saturation (SILCS) methodology. SILCS-GCMC/MD is shown to map functional group affinity patterns that recapitulate locations of functional groups across diverse classes of ligands in the LBPs of the androgen (AR) and peroxisome proliferator-activated-? (PPAR?) NRs and the metabotropic glutamate (mGluR) and ?2-adreneric (?2AR) GPCRs. Inclusion of protein flexibility identifies regions of the binding pockets not accessible in crystal conformations and allows for better quantitative estimates of relative ligand binding affinities in all the proteins tested. Differences in functional group requirements of the active and inactive states of the ?2AR LBP were used in virtual screening to identify high efficacy agonists targeting ?2AR in Airway Smooth Muscle (ASM) cells. Seven of the 15 selected ligands were found to effect ASM relaxation representing a 46% hit rate. Hence, the method will be of use for the rational design of ligands in the context of chemical biology and the development of therapeutic agents. PMID:25692383
Seth Bates; Tony Smith
\\u000a SharePoint Foundation 2010 provides the core document management, list management, workflow, collaboration, and application\\u000a platform services for a SharePoint environment. SharePoint sites are the foundation on which business solutions based on the\\u000a Office system store and manage information. Sites provide locations where groups of people can work together and share information.\\u000a They can also be used to collect team and
Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.
Cortes, Teresa; Schubert, Olga T; Rose, Graham; Arnvig, Kristine B; Comas, Ińaki; Aebersold, Ruedi; Young, Douglas B
Deciphering physiological changes that mediate transition of Mycobacterium tuberculosis between replicating and nonreplicating states is essential to understanding how the pathogen can persist in an individual host for decades. We have combined RNA sequencing (RNA-seq) of 5' triphosphate-enriched libraries with regular RNA-seq to characterize the architecture and expression of M. tuberculosis promoters. We identified over 4,000 transcriptional start sites (TSSs). Strikingly, for 26% of the genes with a primary TSS, the site of transcriptional initiation overlapped with the annotated start codon, generating leaderless transcripts lacking a 5' UTR and, hence, the Shine-Dalgarno sequence commonly used to initiate ribosomal engagement in eubacteria. Genes encoding proteins with active growth functions were markedly depleted from the leaderless transcriptome, and there was a significant increase in the overall representation of leaderless mRNAs in a starvation model of growth arrest. The high percentage of leaderless genes may have particular importance in the physiology of nonreplicating M. tuberculosis. PMID:24268774
3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.
Ahmed, Mostafa H; Koparde, Vishal N; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E
Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low-resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (?-? stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone-dependent (?, ?) bins, a map similarity metric based on the correlation coefficient was applied to each map-map pair to build matrices suitable for clustering with k-means. The first bin (-200°?????-155°; -205°?????-160°), representing 631 tyrosines, reduced to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single ?1 /?2 rotamer. The last environment has weak or no interactions with the tyrosine ring and its ?1 /?2 rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. Proteins 2015; 83:1118-1136. © 2015 Wiley Periodicals, Inc. PMID:25900573
High Resolution Mapping of an Alleged Chemical Weapons Dump Site in the Santa Cruz Basin, offshore California
NASA Astrophysics Data System (ADS)
Brewer, P. G.; Peltzer, E. T.; Walz, P. M.; Caress, D. W.; Thomas, H. J.
Nautical charts record seven locations off the coast of California labeled as 'Chemical Munitions Dumping Area, Disused' that together cover some 12,000 km2 of sea floor. However only one such chemical munitions site is officially documented and no record exists of any chemical munitions disposed of at other locations, thus creating confusion. We have executed a one day AUV mapping survey of a corner of one such site in the Santa Cruz Basin, south of Port Hueneme, to examine and investigate the debris field. The region is covered with soft sediment and the overlying water is very low in oxygen at ~10 ?mol/kg. The processed 110 kHz sidescan data revealed some 754 targets in 25.6 km2 for an average of 29 targets per km2. This was followed by two ROV dives to investigate the targets identified. We found but one false positives among the over 40 targets visited, and found items ranging from two distinct lines of unmarked or labeled and now empty barrels, two target drones, and much miscellaneous debris including 4-packs of cat food cans and a large ships mast over 30m in length. There was zero evidence of chemical weapons materiel as expected given the lack of official records. Almost all of the targets were covered in dense and colorful assemblages of invertebrates: sponges, anemones, and crabs. Where barrels were sufficiently open for full visual inspection, the interior sea floor appeared to have become fully anoxic and was covered in white and yellow bacterial mat. The area chosen for our survey (centered at 33.76 deg N 119.56 deg W) was across the north western boundary of the marked site, and represents only ~ 10% percent of the designated area. Our expectation, that human nature would drive the disposal activities to the nearest corner of the chosen area rather than the center of the field appears to have been confirmed. Objects were found both within and outside of the boundary of the dump site. We have not surveyed the full marked area but there appears to be the substantial possibility of a gross error in the labeling of charts. Our results show that simple, rapid, and cost effective surveys of these sites can be made, that the found debris field of rusted barrels and other objects appears to have contained more mundane waste material that long ago dissipated or hydrolyzed. It is likely that the majority of disposed material is far from the center of the charted area and thus a re-drawing of the warning zone following additional surveying of the actual extent of the dump site to reflect this would be a significant improvement.
GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.
Zhao, Qi; Xie, Yubin; Zheng, Yueyuan; Jiang, Shuai; Liu, Wenzhong; Mu, Weiping; Liu, Zexian; Zhao, Yong; Xue, Yu; Ren, Jian
Small ubiquitin-like modifiers (SUMOs) regulate a variety of cellular processes through two distinct mechanisms, including covalent sumoylation and non-covalent SUMO interaction. The complexity of SUMO regulations has greatly hampered the large-scale identification of SUMO substrates or interaction partners on a proteome-wide level. In this work, we developed a new tool called GPS-SUMO for the prediction of both sumoylation sites and SUMO-interaction motifs (SIMs) in proteins. To obtain an accurate performance, a new generation group-based prediction system (GPS) algorithm integrated with Particle Swarm Optimization approach was applied. By critical evaluation and comparison, GPS-SUMO was demonstrated to be substantially superior against other existing tools and methods. With the help of GPS-SUMO, it is now possible to further investigate the relationship between sumoylation and SUMO interaction processes. A web service of GPS-SUMO was implemented in PHP+JavaScript and freely available at http://sumosp.biocuckoo.org. PMID:24880689
Varenicline Interactions at the 5-HT3 Receptor Ligand Binding Site are Revealed by 5-HTBP.
Price, Kerry L; Lillestol, Reidun K; Ulens, Chris; Lummis, Sarah C R
Cys-loop receptors are the site of action of many therapeutic drugs. One of these is the smoking cessation agent varenicline, which has its major therapeutic effects at nicotinic acetylcholine (nACh) receptors but also acts at 5-HT3 receptors. Here, we report the X-ray crystal structure of the 5-HT binding protein (5-HTBP) in complex with varenicline, and test the predicted interactions by probing the potency of varenicline in a range of mutant 5-HT3 receptors expressed in HEK293 cells and Xenopus oocytes. The structure reveals a range of interactions between varenicline and 5-HTBP. We identified residues within 5 Ĺ of varenicline and substituted the equivalent residues in the 5-HT3 receptor with Ala or a residue with similar chemical properties. Functional characterization of these mutant 5-HT3 receptors, using a fluorescent membrane potential dye in HEK cells and voltage clamp in oocytes, supports interactions between varenicline and the receptor that are similar to those in 5-HTBP. The structure also revealed C-loop closure that was less than in the 5-HT-bound 5-HTBP, and hydrogen bonding between varenicline and the complementary face of the binding pocket via a water molecule, which are characteristics consistent with partial agonist behavior of varenicline in the 5-HT3 receptor. Together, these data reveal detailed insights into the molecular interaction of varenicline in the 5-HT3 receptor. PMID:25648658
Prestin surface expression and activity are augmented by interaction with MAP1S, a microtubule-associated protein.
Bai, Jun-Ping; Surguchev, Alexei; Ogando, Yudelca; Song, Lei; Bian, Shumin; Santos-Sacchi, Joseph; Navaratnam, Dhasakumar
Prestin is a member of the SLC26 family of anion transporters that is responsible for outer hair cell (OHC) electromotility. Measures of voltage-evoked charge density (Q(sp)) of prestin indicated that the protein is highly expressed in OHCs, with single cells expressing up to 10 million molecules within the lateral membrane. In contrast, charge density measures in transfected cells indicated that they express, at best, only a fifth as many proteins on their surface. We sought to determine whether associations with other OHC-specific proteins could account for this difference. Using a yeast two-hybrid technique, we found microtubule-associated protein 1S (MAP1S) bound to prestin. The interaction was limited to the STAS domain of prestin and the region connecting the heavy and light chain of MAP1S. Using reciprocal immunoprecipitation and Forster resonance energy transfer, we confirmed these interactions. Furthermore, co-expression of prestin with MAP1S resulted in a 2.7-fold increase in Q(sp) in single cells that was paralleled by a 2.8-fold increase in protein surface expression, indicating that the interactions are physiological. Quantitative PCR data showed gradients in the expression of prestin and MAP1S across the tonotopic axis that may partially contribute to a previously observed 6-fold increase in Q(sp) in high frequency hair cells. These data highlight the importance of protein partner effects on prestin. PMID:20418376
Cloud fraction at the ARM SGP site: reducing uncertainty with self-organizing maps
NASA Astrophysics Data System (ADS)
Kennedy, Aaron D.; Dong, Xiquan; Xi, Baike
Instrument downtime leads to uncertainty in the monthly and annual record of cloud fraction (CF), making it difficult to perform time series analyses of cloud properties and perform detailed evaluations of model simulations. As cloud occurrence is partially controlled by the large-scale atmospheric environment, this knowledge is used to reduce uncertainties in the instrument record. Synoptic patterns diagnosed from the North American Regional Reanalysis (NARR) during the period 1997-2010 are classified using a competitive neural network known as the self-organizing map (SOM). The classified synoptic states are then compared to the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) instrument record to determine the expected CF. A number of SOMs are tested to understand how the number of classes and the period of classifications impact the relationship between classified states and CFs. Bootstrapping is utilized to quantify the uncertainty of the instrument record when statistical information from the SOM is included. Although all SOMs significantly reduce the uncertainty of the CF record calculated in Kennedy et al. (Theor Appl Climatol 115:91-105, 2014), SOMs with a large number of classes and separated by month are required to produce the lowest uncertainty and best agreement with the annual cycle of CF. This result may be due to a manifestation of seasonally dependent biases in NARR. With use of the SOMs, the average uncertainty in monthly CF is reduced in half from the values calculated in Kennedy et al. (Theor Appl Climatol 115:91-105, 2014).
Fluid expulsion sites on the Cascadia accretionary prism: mapping diagenetic deposits with processed GLORIA imagery
Carson, Bobb; Seke, Erol; Paskevich, Valerie F.; Holmes, Mark L.
Point-discharge fluid expulsion on accretionary prisms is commonly indicated by diagenetic deposition of calcium carbonate cements and gas hydrates in near-surface (<10 m below seafloor; mbsf) hemipelagic sediment. The contrasting clastic and diagenetic lithologies should be apparent in side scan images. However, sonar also responds to variations in bottom slope, so unprocessed images mix topographic and lithologic information. We have processed GLORIA imagery from the Oregon continental margin to remove topographic effects. A synthetic side scan image was created initially from Sea Beam bathymetric data and then was subtracted iteratively from the original GLORIA data until topographic features disappeared. The residual image contains high-amplitude backscattering that we attribute to diagenetic deposits associated with fluid discharge, based on submersible mapping, Ocean Drilling Program drilling, and collected samples. Diagenetic deposits are concentrated (1) near an out-of-sequence thrust fault on the second ridge landward of the base of the continental slope, (2) along zones characterized by deep-seated strikeslip faults that cut transversely across the margin, and (3) in undeformed Cascadia Basin deposits which overlie incipient thrust faults seaward of the toe of the prism. There is no evidence of diagenetic deposition associated with the frontal thrust that rises from the dčcollement. If the dčcollement is an important aquifer, apparently the fluids are passed either to the strike-slip faults which intersect the dčcollement or to the incipient faults in Cascadia Basin for expulsion. Diagenetic deposits seaward of the prism toe probably consist dominantly of gas hydrates
Genetic interaction and mapping studies on the leaflet development (lld) mutant in Pisum sativum.
Kumar, Sushil; Mishra, Raghvendra Kumar; Kumar, Arvind; Chaudhary, Swati; Sharma, Vishakha; Kumari, Renu
In Pisum sativum, the completely penetrant leaflet development (lld) mutation is known to sporadically abort pinnae suborgans in the unipinnate compound leaf. Here, the frequency and morphology of abortion was studied in each of the leaf suborgans in 36 genotypes and in presence of auxin and gibberellin, and their antagonists. Various lld genotypes were constructed by multifariously recombining lld with a coch homeotic stipule mutation and with af, ins, mare, mfp, tl and uni-tac leaf morphology mutations. It was observed that the suborgans at all levels of pinna subdivisions underwent lld-led abortion events at different stages of development. As in leafblades, lld aborted the pinnae in leaf-like compound coch stipules. The lld mutation interacted with mfp synergistically and with other leaf mutations additively. The rod-shaped and trumpet-shaped aborted pea leaf suborgans mimicked the phenotype of aborted leaves in HD-ZIP-III-deficient Arabidopsis thaliana mutants. Suborganwise aborted morphologies in lld gnotypes were in agreement with basipetal differentiation of leaflets and acropetal differentiation in tendrils. Altogether, the observations suggested that LLD was the master regulator of pinna development. On the basis of molecular markers found linked to lld, its locus was positioned on the linkage group III of the P. sativum genetic map. PMID:23271018
HAZPAC; an interactive map of Pacific Rim natural hazards, population, and infrastructure
Bemis, B.L.; Goss, H.V.; Yurkovich, E.S.; Perron, T.J.; Howell, D.G.
This is an online version of a CD-ROM publication. The text files that describe using this publication make reference to software provided on the disc. For this online version the software can be downloaded for free from Adobe Systems and Environmental Systems Research Institute, Inc. (ESRI). Welcome to HAZPAC! HAZPAC is an interactive map about natural hazard risk in the Pacific Rim region. It is intended to communicate to a broad audience the ideas of 'Crowding the Rim,' which is an international, public-private partnership that fosters collaborative solutions for regional risks. HAZPAC, which stands for 'HAZards of the PACific,' uses Geographic Information System (GIS) technology to help people visualize the socioeconomic connections and shared hazard vulnerabilities among Pacific Rim countries, as well as to explore the general nature of risk. Please refer to the 'INTRODUCTION TO HAZPAC' section of the readme file below to determine which HAZPAC project will be right for you. Once you have decided which HAZPAC project is suitable for you, please refer to the 'GETTING STARTED' sections in the readme file for some basic information that will help you begin using HAZPAC. Also, we highly recommend that you follow the Tutorial exercises in the project-specific HAZPAC User Guides. The User Guides are PDF (Portable Document Format) files that must be read with Adobe Acrobat Reader (a free copy of Acrobat Reader is available using the link near the bottom of this page).
HumanWildlife Interactions 4(1):103111, Spring 2010 Habitat correlates of jaguar kill-sites of
HumanWildlife Interactions 4(1):103111, Spring 2010 Habitat correlates of jaguar kill and economic conflict. We investigated habitat characteristics of kill sites of cattle in Sonora, Mexico, from nonlethal methods to limit predation. Kill-sites were positively associated with oak, semitropical
MARs Tools for Interactive ANalysis (MARTIAN): Google Maps Tools for Visual Exploration of Geophysical Modeling on Mars
NASA Astrophysics Data System (ADS)
Dimitrova, L. L.; Haines, M.; Holt, W. E.; Schultz, R. A.; Richard, G.; Haines, A. J.
Interactive maps of surface-breaking faults and stress models on Mars provide important tools to engage undergraduate students, educators, and scientists with current geological and geophysical research. We have developed a map based on the Google Maps API -- an Internet based tool combining DHTML and AJAX, -- which allows very large maps to be viewed over the World Wide Web. Typically, small portions of the maps are downloaded as needed, rather than the entire image at once. This set-up enables relatively fast access for users with low bandwidth. Furthermore, Google Maps provides an extensible interactive interface making it ideal for visualizing multiple data sets at the user's choice. The Google Maps API works primarily with data referenced to latitudes and longitudes, which is then mapped in Mercator projection only. We have developed utilities for general cylindrical coordinate systems by converting these coordinates into equivalent Mercator projection before including them on the map. The MARTIAN project is available at http://rock.geo.sunysb.edu/~holt/Mars/MARTIAN/. We begin with an introduction to the Martian surface using a topography model. Faults from several datasets are classified by type (extension vs. compression) and by time epoch. Deviatoric stresses due to gravitational potential energy differences, calculated from the topography and crustal thickness, can be overlain. Several quantitative measures for the fit of the stress field to the faults are also included. We provide introductory text and exercises spanning a range of topics: how are faults identified, what stress is and how it relates to faults, what gravitational potential energy is and how variations in it produce stress, how the models are created, and how these models can be evaluated and interpreted. The MARTIAN tool is used at Stony Brook University in GEO 310: Introduction to Geophysics, a class geared towards junior and senior geosciences majors. Although this project is in its early stages, high school and college teachers, as well as researchers have expressed interest in using and extending these tools for visualizing and interacting with data on Earth and other planetary bodies.
Functional Mapping of the Lectin Activity Site on the ?-Prism Domain of Vibrio cholerae Cytolysin
Rai, Anand Kumar; Paul, Karan; Chattopadhyay, Kausik
Vibrio cholerae cytolysin (VCC) is a prominent member in the family of ?-barrel pore-forming toxins. It induces lysis of target eukaryotic cells by forming transmembrane oligomeric ?-barrel channels. VCC also exhibits prominent lectin-like activity in interacting with ?1-galactosyl-terminated glycoconjugates. Apart from the cytolysin domain, VCC harbors two lectin-like domains: the ?-Trefoil and the ?-Prism domains; however, precise contribution of these domains in the lectin property of VCC is not known. Also, role(s) of these lectin-like domains in the mode of action of VCC remain obscure. In the present study, we show that the ?-Prism domain of VCC acts as the structural scaffold to determine the lectin activity of the protein toward ?1-galactosyl-terminated glycoconjugates. Toward exploring the physiological implication of the ?-Prism domain, we demonstrate that the presence of the ?-Prism domain-mediated lectin activity is crucial for an efficient interaction of the toxin toward the target cells. Our results also suggest that such lectin activity may act to regulate the oligomerization ability of the membrane-bound VCC toxin. Based on the data presented here, and also consistent with the existing structural information, we propose a novel mechanism of regulation imposed by the ?-Prism domain's lectin activity, implicated in the process of membrane pore formation by VCC. PMID:23209283
Mapping the natural variation in whole bone stiffness and strength across skeletal sites.
Schlecht, Stephen H; Bigelow, Erin M R; Jepsen, Karl J
Traits of the skeletal system are coordinately adjusted to establish mechanical homeostasis in response to genetic and environmental factors. Prior work demonstrated that this 'complex adaptive' process is not perfect, revealing a two-fold difference in whole bone stiffness of the tibia across a population. Robustness (specifically, total cross-sectional area relative to length) varies widely across skeletal sites and between sexes. However, it is unknown whether the natural variation in whole bone stiffness and strength also varies across skeletal sites and between men and women. We tested the hypotheses that: 1) all major long bones of the appendicular skeleton demonstrate inherent, systemic constraints in the degree to which morphological and compositional traits can be adjusted for a given robustness; and 2) these traits covary in a predictable manner independent of body size and robustness. We assessed the functional relationships among robustness, cortical area (Ct.Ar), cortical tissue mineral density (Ct.TMD), and bone strength index (BSI) across the long bones of the upper and lower limbs of 115 adult men and women. All bones showed a significant (p<0.001) positive regression between BSI and robustness after adjusting for body size, with slender bones being 1.7-2.3 times less stiff and strong in men and 1.3-2.8 times less stiff and strong in women compared to robust bones. Our findings are the first to document the natural inter-individual variation in whole bone stiffness and strength that exist within populations and that is predictable based on skeletal robustness for all major long bones. Documenting and further understanding this natural variation in strength may be critical for differentially diagnosing and treating skeletal fragility. PMID:24999223
Mapping of a cholinergic binding site by means of synthetic peptides, monoclonal antibodies, and. alpha. -bungarotoxin
Conti-Tronconi, B.M.; Tang, Fen; Diethelm, B.M.; Spencer, S.R. (Univ. of Minnesota, St. Paul (USA)); Reinhardt-Maelicke, S.; Maelicke, A. (Max-Planck-Institut fur Ernahrungsphysiologie, Dortmund (West Germany))
Previous studies by several laboratories have identified a narrow sequence region of the nicotinic acetylcholine receptor (AChR) {alpha} subunit, flanking the cysteinyl residues at positions 192 and 193, as containing major elements of, if not all, the binding site for cholinergic ligands. In the present study, the authors used a panel of synthetic peptides as representative structural elements of the AChR to investigate whether additional segments of the AChR sequences are able to bind {alpha}-bungarotoxin ({alpha}-BTX) and several {alpha}-BTX-competitive monoclonal antibodies (mAbs). The mAbs used (WF6, WF5, and W2) were raised against native Torpedo AChR, specifically recognize the {alpha}-subunit, and bind to AChR in a mutually exclusive fashion with {alpha}-BTX. The binding of WF5 and W2 to Torpedo AChR is inhibited by all cholinergic ligands. WF6 competes with agonists, but not with low mol. wt. antagonists, for AChR binding. Peptides {alpha}181-200 and {alpha}55-74 both inhibited binding of {sup 125}I-{alpha}-BTX to native Torpedo AChR. None of the peptides corresponding to sequence segments from other subunits bound {alpha}-BTX or WF6, or interfered with their binding. Therefore, the cholinergic binding site is not a single narrow sequence region, but rather two or more discontinuous sequence segments within the N-terminal extracellular region of the AChR {alpha} subunit, folded together in the native structure of the receptor, contribute to form a cholinergic binding region.
Super-resolution mapping of reactive sites on titania-based nanoparticles with water-soluble fluorogenic probes.
Tachikawa, Takashi; Yonezawa, Tomoyuki; Majima, Tetsuro
Interfacial charge transfer at the heterogeneous surface of semiconductor nanoparticles is a fundamental process that is relevant to many important applications, such as photocatalysis, solar cells, and sensors. In this study, we developed new water-soluble fluorogenic probes for interfacial electron transfer reactions on semiconductor nanoparticles. The synthesized boron-dipyrromethene-based fluorescence dyes have one or two sulfonate groups, which confer solubility in aqueous media, and a dinitrophenyl group as a redox reaction site. These probes produce the corresponding fluorescent products via multiple interfacial electron transfer processes, allowing us to investigate the photoinduced redox reactions over individual pristine and Au-nanoparticle-deposited TiO(2) nanoparticles at the single-particle, single-molecule levels. The minimum probe concentration to detect single-product molecules on a single TiO(2) nanoparticle was found to be in the nanomolar range (<10 nM) in acidic solution. Furthermore, super-resolution mapping of the reaction sites revealed that visible-light-induced reduction reactions preferentially occurred on the TiO(2) surface within a distance of a few tens of nanometers around the deposited Au nanoparticles. This result was qualitatively interpreted on the basis of plasmon-induced electron and/or energy transfer mechanisms. Overall, this study provides a great deal of valuable information related to solar-energy-conversion processes that is impossible or difficult to obtain from ensemble-averaged experiments. PMID:23215155
Proteomic Quantification and Site-Mapping of S-Nitrosylated Proteins Using Isobaric iodoTMT Reagents
S-Nitrosylation is a redox-based protein post-translational modification in response to nitric oxide signaling and is involved in a wide range of biological processes. Detection and quantification of protein S-nitrosylation have been challenging tasks due to instability and low abundance of the modification. Many studies have used mass spectrometry (MS)-based methods with different thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides by anti-TMT resin, and importantly, unambiguous modification site-mapping and multiplex quantification by liquid chromatography–tandem MS. Additionally, we significantly improved anti-TMT peptide enrichment efficiency by competitive elution. Using ISA, we identified a set of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic pathways. ISA proved to be an effective proteomic approach for quantitative analysis of S-nitrosylation in complex samples and will facilitate the elucidation of molecular mechanisms of nitrosative stress in disease. PMID:24926564
Precise mapping of the Goodpasture epitope(s) using phage display, site-directed mutagenesis, and surface plasmon resonance.
Gozalbo-Rovira, Roberto; Rodríguez-Díaz, Jesús; Saus, Juan; Cervera, Javier
Goodpasture disease is an autoimmune disorder mediated by circulating autoantibodies against the noncollagenous-1 (NC1) domain of the ?3 chain of type IV collagen (?3(IV)NC1). The structure of Goodpasture epitope(s) has been previously mapped into two main binding regions (E(A) and E(B)) of the ?3(IV)NC1 domain using a residue mutation approach on the highly related ?1(IV)NC1 domain. Here we combined phage display and surface plasmon resonance technology to more precisely localize the pathogenic binding sites. Peptides mimicking the Goodpasture epitope(s) were used to identify residues involved in autoantibody binding and found involvement of eight residues previously unrecognized within and outside of the E(A) or E(B) regions. Residue involvement in pathogenic reactivity was confirmed by site-directed mutagenesis on a more divergent ?2(IV)NC1 molecule. From a mutant (M1) of the ?2(IV)NC1 molecule, harboring residues previously identified as belonging to the Goodpasture epitope, additional chimeras were generated on the bases of phage display findings. All these mutants were shown to display higher reactivity with circulating Goodpasture autoantibodies than the M1 mutant. Thus, our results more precisely define Goodpasture epitope determinants and open new avenues to delineate comprehensive autoantibody-blocking agents for therapeutics. PMID:23254898
BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska.
NASA Astrophysics Data System (ADS)
Cody, R. P.; Kassin, A.; Kofoed, K. B.; Copenhaver, W.; Laney, C. M.; Gaylord, A. G.; Collins, J. A.; Tweedie, C. E.
The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic and the Barrow Area Information Database (BAID, www.barrowmapped.org) tracks and facilitates a gamut of research, management, and educational activities in the area. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 12,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, save or print maps and query results, and filter or view information by space, time, and/or other tags. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. Recent advances include the addition of more than 2000 new research sites, provision of differential global position system (dGPS) and Unmanned Aerial Vehicle (UAV) support to visiting scientists, surveying over 80 miles of coastline to document rates of erosion, training of local GIS personal to better make use of science in local decision making, deployment and near real time connectivity to a wireless micrometeorological sensor network, links to Barrow area datasets housed at national data archives and substantial upgrades to the BAID website and web mapping applications.
Human platelets express CAR with localization at the sites of intercellular interaction.
Gupalo, Elena; Buriachkovskaia, Liudmila; Othman, Maha
Adenovirus has a wide tissue tropism. The virus attaches to the surface of cells via the fiber protein knob binding to the Coxsackie and Adenovirus receptor known as CAR. Virus entry inside cells is facilitated by integrins ?V?3 and ?V?5. Mice platelets are shown to be the predominant Ad binding blood cell type and the virus is documented inside platelets. CAR was identified on human platelets in one study yet contradicted in another. The presence of CAR appears to be the most reasonable initial step for virus entry into platelets and is a key to the understanding of platelet adenovirus interaction. This study aimed to re investigate the presence of CAR on human platelets. Platelets were tested by indirect immune-fluorescence using rabbit H-300 polyclonal anti-CAR antibody and goat anti-rabbit IgG F(ab')2 Texas Red antibodies, alongside with CAR positive and negative controls. Platelets were found to express CAR on their surface and in contrast to the previous study only 3.5 ± 1.9% of the tested platelets did express CAR. In addition, CAR was seen within intracellular aggregates localized at the sites of cell-cell contacts indicating that CAR expression might be upregulated in response to platelet stimulation. We confirm the presence of CAR on human platelets, we provide explanation to some of the discrepancies in this regards and we add that this receptor is localized at the sites of intercellular interaction. PMID:21962080
Human platelets express CAR with localization at the sites of intercellular interaction
Adenovirus has a wide tissue tropism. The virus attaches to the surface of cells via the fiber protein knob binding to the Coxsackie and Adenovirus receptor known as CAR. Virus entry inside cells is facilitated by integrins ?V?3 and ?V?5. Mice platelets are shown to be the predominant Ad binding blood cell type and the virus is documented inside platelets. CAR was identified on human platelets in one study yet contradicted in another. The presence of CAR appears to be the most reasonable initial step for virus entry into platelets and is a key to the understanding of platelet adenovirus interaction. This study aimed to re investigate the presence of CAR on human platelets. Platelets were tested by indirect immune-fluorescence using rabbit H-300 polyclonal anti-CAR antibody and goat anti-rabbit IgG F(ab')2 Texas Red antibodies, alongside with CAR positive and negative controls. Platelets were found to express CAR on their surface and in contrast to the previous study only 3.5 ± 1.9% of the tested platelets did express CAR. In addition, CAR was seen within intracellular aggregates localized at the sites of cell-cell contacts indicating that CAR expression might be upregulated in response to platelet stimulation. We confirm the presence of CAR on human platelets, we provide explanation to some of the discrepancies in this regards and we add that this receptor is localized at the sites of intercellular interaction. PMID:21962080
Regulation of actin-myosin interaction by conserved periodic sites of tropomyosin
Barua, Bipasha; Winkelmann, Donald A.; White, Howard D.; Hitchcock-DeGregori, Sarah E.
Cooperative activation of actin-myosin interaction by tropomyosin (Tm) is central to regulation of contraction in muscle cells and cellular and intracellular movements in nonmuscle cells. The steric blocking model of muscle regulation proposed 40 y ago has been substantiated at both the kinetic and structural levels. Even with atomic resolution structures of the major players, how Tm binds and is designed for regulatory function has remained a mystery. Here we show that a set of periodically distributed evolutionarily conserved surface residues of Tm is required for cooperative regulation of actomyosin. Based on our results, we propose a model of Tm on a structure of actin-Tm-myosin in the "open" (on) state showing potential electrostatic interactions of the residues with both actin and myosin. The sites alternate with a second set of conserved surface residues that are important for actin binding in the inhibitory state in the absence of myosin. The transition from the closed to open states requires the sites identified here, even when troponin + Ca2+ is present. The evolutionarily conserved residues are important for actomyosin regulation, a universal function of Tm that has a common structural basis and mechanism. PMID:23091026
Interactive Web-Based Map: Applications to Large Data Sets in the Geosciences. Interactive Web-Based Map: Applications to Large Data Sets in the Geosciences
Z. A. Garbow; N. R. Olson; D. A. Yuen; J. M. Boggs
Current advances in computer hardware, information technology and data collection techniques have produced very large data sets, sometimes more than terabytes,in a wide variety of scientific and engineering disciplines. We must harness this opportunity to visualize and extract useful information from geophysical and geological data. We have taken the task of data-mining by using a map-like approach over the web
A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.
Davis, G L; McMullen, M D; Baysdorfer, C; Musket, T; Grant, D; Staebell, M; Xu, G; Polacco, M; Koster, L; Melia-Hancock, S; Houchins, K; Chao, S; Coe, E H
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits. PMID:10388831
Multiple Interacting Sites of Ectopic Spike Electrogenesis in Primary Sensory Neurons
Amir, Ron; Kocsis, Jeffery D.; Devor, Marshall
Ectopic discharge generated in injured afferent axons and cell somata in vivo contributes significantly to chronic neuropathic dysesthesia and pain after nerve trauma. Progress has been made toward understanding the processes responsible for this discharge using a preparation consisting of whole excised dorsal root ganglia (DRGs) with the cut nerve attached. In the in vitro preparation, however, spike activity originates in the DRG cell soma but rarely in the axon. We have now overcome this impediment to understanding the overall electrogenic processes in soma and axon, including the resulting discharge patterns, by modifying the bath medium in which recordings are made. At both sites, bursts can be triggered by subthreshold oscillations, a phasic stimulus, or spikes arising elsewhere in the neuron. In the soma, once triggered, bursts are maintained by depolarizing afterpotentials, whereas in the axon, an additional process also plays a role, delayed depolarizing potentials. This alternative process appears to be involved in "clock-like" bursting, a discharge pattern much more common in axons than somata. Ectopic spikes arise alternatively in the soma, the injured axon end (neuroma), and the region of the axonal T-junction. Discharge sequences, and even individual multiplet bursts, may be a mosaic of action potentials that originate at these alternative electrogenic sites within the neuron. Correspondingly, discharge generated at these alternative sites may interact, explaining the sometimes-complex firing patterns observed in vivo. PMID:15758167
Mutational Analysis of Substrate Interactions with the Active Site of Dialkylglycine Decarboxylase
Fogle, Emily J.; Toney, Michael D.
Pyridoxal phosphate (PLP) dependent enzymes catalyze many different types of reactions at the ?-, ?-, and ?-carbons of amine and amino acid substrates. Dialkylglycine decarboxylase (DGD) is an unusual PLP dependent enzyme that catalyzes two reaction types, decarboxylation and transamination, in the same active site. A structurally-based, functional model has been proposed for the DGD active site, which maintains that R406 is important in determining substrate specificity through interactions with the substrate carboxylate while W138 provides specificity for short-chain alkyl groups. The mechanistic roles of R406 and W138 were investigated using site directed mutagenesis, alternate substrates, and analysis of steady-state and half-reaction kinetics. Experiments on the R406M and R406K mutants confirm the importance of R406 in substrate binding. Surprisingly, this work also shows that the positive charge of R406 facilitates catalysis of decarboxylation. The W138F mutant demonstrates that W138 indeed acts to limit the size of the subsite C binding pocket, determining specificity for 2,2-dialkylglycines with small side chains as predicted by the model. Finally, work with the double mutant W138F/M141R shows that these mutations expand substrate specificity to include L-glutamate and lead to an increase in specificity for L-glutamate over 2-aminoisobutyrate of approximately eight orders of magnitude compared to WT DGD. PMID:20540501
Joan BERTRAN; Antoni MARGALIDA
SUMMARY.—Interactive behaviour between Bearded Vultures Gypaetus barbatus and Comnon Ravens Corvus corax in the nesting sites: predation risk and kleptoparasitism. Aims: Aggressive interactions between the Bearded Vulture Gypaetus barbatus and the Comnon Raven Cor- vus corax are frequent in the Pyrenean nesting sectors shared by both species. The Bearded Vulture's nesting sectors are vulnerable to kleptoparasitism (food is stored in
Effect of Mutations in the A Site of 16 S rRNA on Aminoglycoside Antibiotic-Ribosome Interaction
Dahlquist, Kam D.
is recognized by the ribosome. Decoding occurs on the small (30 S) subunit of the prokaryo- tic ribosomeEffect of Mutations in the A Site of 16 S rRNA on Aminoglycoside Antibiotic-Ribosome Interaction occurs upon interaction of an mRNA codon-tRNA anticodon complex with the small subunit of the ribosome
Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells.
He, Yanghua; Carrillo, Jose A; Luo, Juan; Ding, Yi; Tian, Fei; Davidson, Irit; Song, Jiuzhou
DNase I hypersensitive sites (DHSs) mark diverse classes of cis-regulatory regions, such as promoters and enhancers. MSB-1 derived from chicken Marek's disease (MD) lymphomas is an MDV-transformed CD4+ T-cell line for MD study. Previously, DNase I HS sites were studied mainly in human cell types for mammalian. To capture the regulatory elements specific to MSB1 cells and explore the molecular mechanisms of T-cell transformation caused by MDV in MD, we generated high-quality of DHSs map and gene expression profile for functional analysis in MSB1 cell line. The total of 21,724 significant peaks of DHSs was identified from around 40 million short reads. DHSs distribution varied between chromosomes and they preferred to enrich in the gene-rich chromosomes. More interesting, DHSs enrichments appeared to be scarce on regions abundant in CpG islands. Besides, we integrated DHSs into the gene expression data and found that DHSs tended to enrich on high expressed genes throughout whole gene regions while DHSs did not show significant changes for low and silent expressed genes. Furthermore, the correlation of DHSs with lincRNAs expression was also calculated and it implied that enhancer-associated lincRNAs probably originated from enhancer-like regions of DHSs. Together, our results indicated that DNase I HS sites highly correlate with active genes expression in MSB1 cells, suggesting DHSs can be considered as markers to identify the cis-regulatory elements associated with chicken Marek's disease. PMID:25352859
mMAPS: A Flow-Proteometric Technique to Analyze Protein-Protein Interactions in Individual Signaling Complexes
Chou, Chao-Kai; Lee, Heng-Huan; Tsou, Pei-Hsiang; Chen, Chun-Te; Hsu, Jung-Mao; Yamaguchi, Hirohito; Wang, Ying-Nai; Lee, Hong-Jen; Hsu, Jennifer L.; Lee, Jin-Fong; Kameoka, Jun; Hung, Mien-Chie
Signal transduction is a dynamic process that regulates cellular functions through multiple types of biomolecular interactions, such as the interactions between proteins and between proteins and nucleic acids. However, the techniques currently available for identifying protein-protein or protein–nucleic acid complexes typically provide information about the overall population of signaling complexes in a sample instead of information about the individual signaling complexes therein. We developed a technique called "microchannel for multiparameter analysis of proteins in a single complex" (mMAPS) that simultaneously detected individual target proteins either singly or in a multicomponent complex in cell or tissue lysates. We detected the target proteins labeled with fluorophores by flow proteometry, which provided quantified data in the form of multidimensional fluorescence plots. Using mMAPS, we quantified individual complexes of epidermal growth factor (EGF) with its receptor EGFR, EGFR with signal transducer and activator of transcription 3 (STAT3), and STAT3 with the acetylase p300 and DNA in lysates from cultured cells with and without treatment with EGF, as well as in lysates from tumor xenograft tissue. Consistent with the ability of this method to reveal the dynamics of signaling protein interactions, we observed that cells treated with EGF induced the interaction of EGF with EGFR and the autophosphorylation of EGFR, but this interaction decreased with longer treatment time. Thus, we expect that this technique may reveal new aspects of molecular interaction dynamics. PMID:24595109
Investigation of a Hamiltonian with two sources of anisotropy: The Dzyaloshinskii--Moriya and single-site interactions
Coffey, D. (Center for Materials Science, Los Alamos National Laboratory, Los Alamos, New Mexico (USA))
La{sub 2}CuO{sub 4} is an {ital S}=1/2 system with almost tetragonal symmetry so that there is no single-site interaction term giving rise to anisotropy and the magnetic anisotropy of the system can be explained in terms of the Dzyaloshinskii--Moriya interaction which can lead to weak ferromagnetism even in a system with predominantly antiferromagnetic interactions. However, the closely related compounds, La{sub 2}NiO{sub 4} and La{sub 2}CoO{sub 4}, are {ital S}=1 and {ital S}=3/2 systems, respectively, so that a single-site interaction term is present and it is of interest to see how this interaction changes the magnetic properties of these compounds. Here the classical magnetic ground states are calculated for model Hamiltonians, appropriate to the different low-temperature structural phases of the compounds, containing both interactions.
Association Mapping of Disease Resistance Traits in Rainbow Trout Using Restriction Site Associated DNA Sequencing
Campbell, Nathan R.; LaPatra, Scott E.; Overturf, Ken; Towner, Richard; Narum, Shawn R.
Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site?associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs. PMID:25354781
Single-cell polyadenylation site mapping reveals 3? isoform choice variability
Velten, Lars; Anders, Simon; Pekowska, Aleksandra; Järvelin, Aino I; Huber, Wolfgang; Pelechano, Vicent; Steinmetz, Lars M
Cell-to-cell variability in gene expression is important for many processes in biology, including embryonic development and stem cell homeostasis. While heterogeneity of gene expression levels has been extensively studied, less attention has been paid to mRNA polyadenylation isoform choice. 3? untranslated regions regulate mRNA fate, and their choice is tightly controlled during development, but how 3? isoform usage varies within genetically and developmentally homogeneous cell populations has not been explored. Here, we perform genome-wide quantification of polyadenylation site usage in single mouse embryonic and neural stem cells using a novel single-cell transcriptomic method, BATSeq. By applying BATBayes, a statistical framework for analyzing single-cell isoform data, we find that while the developmental state of the cell globally determines isoform usage, single cells from the same state differ in the choice of isoforms. Notably this variation exceeds random selection with equal preference in all cells, a finding that was confirmed by RNA FISH data. Variability in 3? isoform choice has potential implications on functional cell-to-cell heterogeneity as well as utility in resolving cell populations. PMID:26040288
Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions.
Turner, Leslie M; Harr, Bettina
Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone. PMID:25487987
Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis.
Piya, Sarbottam; Shrestha, Sandesh K; Binder, Brad; Stewart, C Neal; Hewezi, Tarek
The phytohormone auxin regulates nearly all aspects of plant growth and development. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA) proteins repress auxin-inducible genes by inhibiting auxin response transcription factors (ARFs). Experimental evidence suggests that heterodimerization between Aux/IAA and ARF proteins are related to their unique biological functions. The objective of this study was to generate the Aux/IAA-ARF protein-protein interaction map using full length sequences and locate the interacting protein pairs to specific gene co-expression networks in order to define tissue-specific responses of the Aux/IAA-ARF interactome. Pairwise interactions between 19 ARFs and 29 Aux/IAAs resulted in the identification of 213 specific interactions of which 79 interactions were previously unknown. The incorporation of co-expression profiles with protein-protein interaction data revealed a strong correlation of gene co-expression for 70% of the ARF-Aux/IAA interacting pairs in at least one tissue/organ, indicative of the biological significance of these interactions. Importantly, ARF4-8 and 19, which were found to interact with almost all Aux-Aux/IAA showed broad co-expression relationships with Aux/IAA genes, thus, formed the central hubs of the co-expression network. Our analyses provide new insights into the biological significance of ARF-Aux/IAA associations in the morphogenesis and development of various plant tissues and organs. PMID:25566309
Large, motile epifauna interact strongly with harpacticoid copepods and polychaetes at a bathyal site
NASA Astrophysics Data System (ADS)
Thistle, David; Eckman, James E.; Paterson, Gordon L. J.
Strengths of interactions among groups of animals in deep-sea-sediment communities are poorly known. Large, motile epifauna (LME) such as sea cucumbers, star fishes, and demersal fishes occur in the deep sea and are sources of predation, disturbance, and habitat alteration and thus have the potential to interact strongly with infauna. At a site off the southwestern coast of the United States (32°57.3'N, 117°32.2'W, 780 m depth), we excluded the LME from five 75- ×75-cm plots with cages. After 143 d, we sampled these plots and five plots of the same size paired with them as controls. Abundances of harpacticoid copepods and polychaetes were significantly lower in cages than in controls. In several cages, nematodes and kinorhynchs were also dramatically less abundant than in paired controls. Results suggest that LME ordinarily affect the infaunal assemblage in such a way that harpacticoids and polychaetes (and perhaps nematodes and kinorhynchs) can maintain higher abundances than they can in the absence of LME, indicating that strong interactions can influence the organization of deep-sea-sediment communities. In a multivariate analysis of environmental parameters, cage and control samples were intermixed, so if the effect is transmitted by alterations of the environment by the LME, the nature of the alterations must be relatively local and remains to be discovered.
Reference interaction site model and optimized perturbation theories of colloidal dumbbells with increasing anisotropy
NASA Astrophysics Data System (ADS)
Munaň, Gianmarco; Gámez, Francisco; Costa, Dino; Caccamo, Carlo; Sciortino, Francesco; Giacometti, Achille
We investigate thermodynamic properties of anisotropic colloidal dumbbells in the frameworks provided by the Reference Interaction Site Model (RISM) theory and an Optimized Perturbation Theory (OPT), this latter based on a fourth-order high-temperature perturbative expansion of the free energy, recently generalized to molecular fluids. Our model is constituted by two identical tangent hard spheres surrounded by square-well attractions with same widths and progressively different depths. Gas-liquid coexistence curves are obtained by predicting pressures, free energies, and chemical potentials. In comparison with previous simulation results, RISM and OPT agree in reproducing the progressive reduction of the gas-liquid phase separation as the anisotropy of the interaction potential becomes more pronounced; in particular, the RISM theory provides reasonable predictions for all coexistence curves, bar the strong anisotropy regime, whereas OPT performs generally less well. Both theories predict a linear dependence of the critical temperature on the interaction strength, reproducing in this way the mean-field behavior observed in simulations; the critical density—that drastically drops as the anisotropy increases—turns to be less accurate. Our results appear as a robust benchmark for further theoretical studies, in support to the simulation approach, of self-assembly in model colloidal systems.
Analysis of ground response data at Lotung large-scale soil- structure interaction experiment site
Chang, C.Y.; Mok, C.M.; Power, M.S. (Geomatrix Consultants, Inc., San Francisco, CA (United States))
The Electric Power Research Institute (EPRI), in cooperation with the Taiwan Power Company (TPC), constructed two models (1/4-scale and 1/2-scale) of a nuclear plant containment structure at a site in Lotung (Tang, 1987), a seismically active region in northeast Taiwan. The models were constructed to gather data for the evaluation and validation of soil-structure interaction (SSI) analysis methodologies. Extensive instrumentation was deployed to record both structural and ground responses at the site during earthquakes. The experiment is generally referred to as the Lotung Large-Scale Seismic Test (LSST). As part of the LSST, two downhole arrays were installed at the site to record ground motions at depths as well as at the ground surface. Structural response and ground response have been recorded for a number of earthquakes (i.e. a total of 18 earthquakes in the period of October 1985 through November 1986) at the LSST site since the completion of the installation of the downhole instruments in October 1985. These data include those from earthquakes having magnitudes ranging from M{sub L} 4.5 to M{sub L} 7.0 and epicentral distances range from 4.7 km to 77.7 km. Peak ground surface accelerations range from 0.03 g to 0.21 g for the horizontal component and from 0.01 g to 0.20 g for the vertical component. The objectives of the study were: (1) to obtain empirical data on variations of earthquake ground motion with depth; (2) to examine field evidence of nonlinear soil response due to earthquake shaking and to determine the degree of soil nonlinearity; (3) to assess the ability of ground response analysis techniques including techniques to approximate nonlinear soil response to estimate ground motions due to earthquake shaking; and (4) to analyze earth pressures recorded beneath the basemat and on the side wall of the 1/4 scale model structure during selected earthquakes.
Mapping the CD4 binding site for human immunodeficiency virus by alanine-scanning mutagenesis.
Ashkenazi, A; Presta, L G; Marsters, S A; Camerato, T R; Rosenthal, K A; Fendly, B M; Capon, D J
Infection of mononuclear cells by human immunodeficiency virus (HIV) begins with binding of the viral envelope glycoprotein, gp120, to its receptor, CD4. CD4 contains four extracellular immunoglobulin-like domains, the first of which (V1) is sufficient for HIV binding. V1 contains three sequences homologous to the antigen-complementarity-determining regions (CDR1 to -3) of immunoglobulin variable domains. While all three immunoglobulin CDRs are involved in antigen binding, only amino acids within and flanking the CDR2-like region of CD4 have been shown previously to be involved in gp120 binding. To investigate whether other regions in V1 take part in gp120 binding, we substituted alanine for each of 64 amino acids, including all of the hydrophilic residues in this domain. Mutations at four locations outside the CDR2-like sequence (amino acids 29, 59-64, 77-81, and 85) markedly affected gp120 binding, but not the overall structure of V1 as probed with eight conformationally sensitive monoclonal antibodies. Thus, the gp120-binding site of CD4 is not limited to the CDR2-like sequence and consists of several discontinuous segments. Several amino acids were identified that are critical for the conformation of V1; the importance of these residues suggests some differences in the folding of this domain compared to immunoglobulin variable domains. Three amino acid substitutions were found that increase the affinity for gp120 significantly (1.7- to 2-fold individually and 4.2-fold when combined), suggesting that it may be possible to improve the HIV-blocking ability of CD4-based molecules by increasing their gp120 binding affinity. Images PMID:2402498
Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways
Ben Lehner; Catriona Crombie; Julia Tischler; Angelo Fortunato; Andrew G Fraser
Most heritable traits, including disease susceptibility, are affected by interactions between multiple genes. However, we understand little about how genes interact because very few possible genetic interactions have been explored experimentally. We have used RNA interference in Caenorhabditis elegans to systematically test ?65,000 pairs of genes for their ability to interact genetically. We identify ?350 genetic interactions between genes functioning
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Lan V Zhang; Oliver D King; Sharyl L Wong; Debra S Goldberg; Amy HY Tong; Guillaume Lesage; Brenda Andrews; Howard Bussey; Charles Boone; Frederick P Roth
ABSTRACT: BACKGROUND: Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence homology, and expression correlation. Recurring patterns of interconnection, or 'network motifs', have revealed biological insights for networks containing either one or two types of interaction. RESULTS: To study more complex relationships involving multiple biological interaction types, we assembled an
FLOWMAP—An Interactive Graphic Mapping Program for Displaying Patient Origin-Destination Patterns in Space and Time *
Evatt, Bob; Schneider, Jerry; Polissar, Lincoln; Francis, Anita
The design and use of an interactive graphics computer program called FLOWMAP is described. FLOWMAP allows the interactive design of flow maps at a graphics terminal using patient origin-destination data. The user has several options available that allow changes in the maps to be made quickly and easily to aid their comprehensibility. Several results from using the options are illustrated. Instructions for preparing the input data and using the program are also included, as are specific hardware and software requirements. Data representing the origin-destination attributes of 34,000 cancer patients in 13 counties in the western part of the State of Washington over the 1974-1978 time period are used to illustrate the capabilities of FLOWMAP.
Maps: Finding Our Place in the World
NSDL National Science Digital Library
How do we find our way through the world, geographically speaking? Do we all carry around a type of "mental map" in our head, formed through experience and repetition? Some would say yes, some would beg to differ. Maps remain a powerful way to represent the world in all its spatial glory, and this online exhibit from The Field Museum explores the history of maps and their history over the millennia. Designed to complement an ongoing exhibition at the Museum, the site includes a photo gallery, information about the participating institutions, and about researchers at the Museum who use maps and mapping technology in their own work. The interactive feature is definitely worth a look, as visitors can examine two dozen different maps in detail from Chicago to the Marshall Islands. One can imagine that this remarkable site could also be used in classrooms to expose students to the wide variety of maps that have been created by human hands.
Use of Ecological Risk Data in the Development of Visions, Conceptual Site Models and Maps for Department of Energy Lands: Ensuring Sustainability of Protecting Human and Ecological Health
Joanna Burger
Recent interest in understanding the human and ecological health risks of contaminants on lands in the United States has led some managers and public policy makers to use extensive narratives associated with maps and Conceptual Site Models (CSM) in their Vision statements. While narratives are descriptive, CSMs can graphically depict the sources, releases, transport and exposure pathways, and receptors, together
Ontology Mapping: An Information Retrieval and Interactive Activation Network Based Approach
Ming Mao
Ontology mapping is to find semantic correspondences between similar elements of different ontologies. It is cri tical to achieve semantic interoperability in the WWW. This paper proposes a new generic and scalable ontology mapping approach based on propagation theory, information retrieval technique and artificial intelligence model. The ap proach utilizes both linguistic and structural information, measures the similarity of different
The Interaction of Plasminogen Activator Inhibitor 1 With Plasminogen Activators (Tissue-Type and Urokinase-Type) and Fibrin: Localization of Interaction Sites and Physiologic Relevance
Jaap Keijer; Marijke Linders; Anton-Jan van Zonneveld; Hartmut J. Ehrlich; Jan-Paul de Boer; Hans Pannekoek
tory protein of the fibrinolytic system, harbors interaction sitesfor plasminogen activators (tissue-type (t-PA) and uroki- nase-type (u-PA)) and for fibrin. In this study, anti-PAl-1 monocional antibodies (MoAbs) were used to identify interac- tion sites of PAI-1 with these components. The binding sites of 18 different MoAbs were established and are located on five distinct \\
Coupled reference interaction site model/simulation approach for thermochemistry of solvation: theory and prospects.
Freedman, Holly; Truong, Thanh N
We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from a single molecular dynamics or Monte Carlo simulation. Here we describe in detail the coupled RISM/simulation approach, and offer some error analysis. Finally we give the results of its application to a set of small test molecules in aqueous solution. The success shown in some of our results demonstrates that the coupled RISM/simulation approach is worth considering further as a potentially useful tool in studies of solvated systems, such as aqueous molecular biosystems. PMID:15260773
Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing
Dellino, Gaetano Ivan; Cittaro, Davide; Piccioni, Rossana; Luzi, Lucilla; Banfi, Stefania; Segalla, Simona; Cesaroni, Matteo; Mendoza-Maldonado, Ramiro; Giacca, Mauro; Pelicci, Pier Giuseppe
We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (?1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G1 and the probability of firing during S. PMID:23187890
Digital photogrammetric analysis of the IMP camera images: Mapping the Mars Pathfinder landing site in three dimensions
NASA Astrophysics Data System (ADS)
Kirk, R. L.; Howington-Kraus, E.; Hare, T.; Dorrer, E.; Cook, D.; Becker, K.; Thompson, K.; Redding, B.; Blue, J.; Galuszka, D.; Lee, E. M.; Gaddis, L. R.; Johnson, J. R.; Soderblom, L. A.; Ward, A. W.; Smith, P. H.; Britt, D. T.
This paper describes our photogrammetric analysis of the Imager for Mars Pathfinder data, part of a broader program of mapping the Mars Pathfinder landing site in support of geoscience investigations. This analysis, carried out primarily with a commercial digital photogrammetric system, supported by our in-house Integrated Software for Imagers and Spectrometers (ISIS), consists of three steps: (1) geometric control: simultaneous solution for refined estimates of camera positions and pointing plus three-dimensional (3-D) coordinates of ~103 features sitewide, based on the measured image coordinates of those features; (2) topographic modeling: identification of ~3×105 closely spaced points in the images and calculation (based on camera parameters from step 1) of their 3-D coordinates, yielding digital terrain models (DTMs); and (3) geometric manipulation of the data: combination of the DTMs from different stereo pairs into a sitewide model, and reprojection of image data to remove parallax between the different spectral filters in the two cameras and to provide an undistorted planimetric view of the site. These processes are described in detail and example products are shown. Plans for combining the photogrammetrically derived topographic data with spectrophotometry are also described. These include photometric modeling using surface orientations from the DTM to study surface microtextures and improve the accuracy of spectral measurements, and photoclinometry to refine the DTM to single-pixel resolution where photometric properties are sufficiently uniform. Finally, the inclusion of rover images in a joint photogrammetric analysis with IMP images is described. This challenging task will provide coverage of areas hidden to the IMP, but accurate ranging of distant features can be achieved only if the lander is also visible in the rover image used.
Nuclear quadrupole interaction of111Cd on type-1 Cu-sites in blue copper proteins
NASA Astrophysics Data System (ADS)
Tröger, W.; Butz, T.; Danielsen, E.; Bauer, R.; Thoenes, U.; Messerschmidt, A.; Huber, R.; Canters, G. W.; den Blaauwen, T.
The nuclear quadrupole interaction (NQI) of111Cd substituted for Cu(II) on type-1 sites in blue copper proteins is characterized by high values of ?0 in the region of 300 Mrad/s, close to that for the catalytic zinc site in alcohol dehydrogenase. Type-1 Cu has usually two sulfur ligands and two nitrogen ligands and in some cases an oxygen ligand in either a distorted tetrahedral geometry or in a trigonal bipyramidal geometry. The near tetrahedral arrangement together with the ligand sphere containing the same number of sulfur ligands explains the value of ?0 in the blue copper proteins. The present work determined the partial NQI for methionine using the known structure of azurin. This value was then used in the angular overlap model to calculate the NQI for ascorbate oxidase the structure of which is also known and gave good agreement with experiment. NQI data for laccase and stellacyanin the structures of which are unknown, are also given.
The interaction site for tamoxifen aziridine with the bovine estrogen receptor
Ratajczak, T.; Wilkinson, S.P.; Brockway, M.J.; Haehnel, R.M.; Moritz, R.L.; Begg, G.S.; Simpson, R.J. (Univ. of Western Australia, Subiaco)
Calf uterine estrogen receptor was covalently labeled with ({sup 3}H)tamoxifen aziridine during affinity chromatography purification. After carboxymethylation, affinity labeled receptor was digested with trypsin under limit conditions and the labeled peptides were fractionated by reversed-phase high performance liquid chromatography into one major and two minor components. Sequence analysis of the dominant labeled fragment indicated the facile cleavage of label during Edman degradation but identified two peptides, both derived from the extreme carboxyl terminus of the steroid-binding domain. The 17 residues of one peptide were fully conserved in all estrogen receptors. This fragment contained five nucleophilic amino acids and was considered as the more favored interaction site for tamoxifen aziridine. A corresponding region of the glucocorticoid receptor has recently been identified as one of three major contact sites for glucocorticoids. A comparison of amino acid physical characteristics in the hormone-binding domains of human estrogen and glucocorticoid receptors demonstrated an excellent structural correlation between the two regions and delineated elements in the estrogen receptor which may be directly involved in estradiol binding.
Interaction of substrate and effector binding sites in the ArsA ATPase.
Zhou, T; Liu, S; Rosen, B P
The ars operon of plasmid R773 confers resistance to antimonials and arsenicals in Escherichia coli by encoding an ATP-dependent extrusion system for the oxyanions. The catalytic subunit, the ArsA protein, is an ATPase with two nucleotide binding consensus sequences, one in the N-terminal half and one in the C-terminal half of the protein. The ArsA ATPase is allosterically activated by tricoordinate binding of As(3+) or Sb(3+) to three cysteine thiolates. Previous measurements suggested that the intrinsic fluorescence of tryptophans might be useful for examining binding of Mg2+ ATP and antimonite. In the present study an increase in intrinsic tryptophan fluorescence was observed upon addition of Mg2+ ATP. This enhancement was reversed by addition of antimonite. The ArsA protein contains four tryptophan residues: Trp159, Trp253, Trp522, and Trp524. The first two were altered to tyrosine residues by site-directed mutagenesis. Cells expressing both the arsAW159Y and arsAW253Y mutations retained resistance to arsenite, and the purified W159Y and W253Y proteins retained ATPase activity. While the intrinsic tryptophan fluorescence of the W253Y protein responded to addition of Mg2+ ATP, intrinsic tryptophan fluorescence in the purified W159Y protein was no longer enhanced by substrate. These results suggest that Trp159 is conformationally coupled to one or both of the nucleotide binding sites and provides a useful probe for the interaction of effector and substrate binding sites. PMID:7577951
Unexpected Properties of ?-Containing GABAA Receptors in Response to Ligands Interacting with the ?+ ?? Site
Varagic, Zdravko; Scholze, Petra; Wimmer, Laurin; Mihovilovic, Marko M.; Sieghart, Werner
GABAA receptors are the major inhibitory neurotransmitter receptors in the central nervous system and are the targets of many clinically important drugs, which modulate GABA induced chloride flux by interacting with separate and distinct allosteric binding sites. Recently, we described an allosteric modulation occurring upon binding of pyrazoloquinolinones to a novel binding site at the extracellular ?+ ?? interface. Here, we investigated the effect of 4-(8-methoxy-3-oxo-3,5-dihydro-2H-pyrazolo[4,3-c]quinolin-2-yl)benzonitrile (the pyrazoloquinolinone LAU 177) at several ??, ??? and ??? receptor subtypes. LAU 177 enhanced GABA-induced currents at all receptors investigated, and the extent of modulation depended on the type of ? and ? subunits present within the receptors. Whereas the presence of a ?2 subunit within ???2 receptors did not dramatically change LAU 177 induced modulation of GABA currents compared to ?? receptors, we observed an unexpected threefold increase in modulatory efficacy of this compound at ?1?2,3? receptors. Steric hindrance experiments as well as inhibition by the functional ?+ ?? site antagonist LAU 157 indicated that the effects of LAU 177 at all receptors investigated were mediated via the ?+ ?? interface. The stronger enhancement of GABA-induced currents by LAU 177 at ?1?3? receptors was not observed at ?4,6?3? receptors. Other experiments indicated that this enhancement of modulatory efficacy at ?1?3? receptors was not observed with another ?+ ?? modulator, and that the efficacy of modulation by ?+ ?? ligands is influenced by all subunits present in the receptor complex and by structural details of the respective ligand. PMID:24072672
Unexpected Properties of ?-Containing GABAA Receptors in Response to Ligands Interacting with the ?+ ?- Site.
Mirheydari, Pantea; Ramerstorfer, Joachim; Varagic, Zdravko; Scholze, Petra; Wimmer, Laurin; Mihovilovic, Marko M; Sieghart, Werner; Ernst, Margot
GABAA receptors are the major inhibitory neurotransmitter receptors in the central nervous system and are the targets of many clinically important drugs, which modulate GABA induced chloride flux by interacting with separate and distinct allosteric binding sites. Recently, we described an allosteric modulation occurring upon binding of pyrazoloquinolinones to a novel binding site at the extracellular ?+ ?- interface. Here, we investigated the effect of 4-(8-methoxy-3-oxo-3,5-dihydro-2H-pyrazolo[4,3-c]quinolin-2-yl)benzonitrile (the pyrazoloquinolinone LAU 177) at several ??, ??? and ??? receptor subtypes. LAU 177 enhanced GABA-induced currents at all receptors investigated, and the extent of modulation depended on the type of ? and ? subunits present within the receptors. Whereas the presence of a ?2 subunit within ???2 receptors did not dramatically change LAU 177 induced modulation of GABA currents compared to ?? receptors, we observed an unexpected threefold increase in modulatory efficacy of this compound at ?1?2,3? receptors. Steric hindrance experiments as well as inhibition by the functional ?+ ?- site antagonist LAU 157 indicated that the effects of LAU 177 at all receptors investigated were mediated via the ?+ ?- interface. The stronger enhancement of GABA-induced currents by LAU 177 at ?1?3? receptors was not observed at ?4,6?3? receptors. Other experiments indicated that this enhancement of modulatory efficacy at ?1?3? receptors was not observed with another ?+ ?- modulator, and that the efficacy of modulation by ?+ ?- ligands is influenced by all subunits present in the receptor complex and by structural details of the respective ligand. PMID:24072672
Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks
Dubois, Laurence; Bataillé, Laetitia; Painset, Anaďs; Le Gras, Stéphanie; Jost, Bernard; Crozatier, Michčle; Vincent, Alain
Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles. PMID:26204530
Development of a Detailed Stress Map of Oklahoma for Avoidance of Potentially Active Faults When Siting Wastewater Injection Wells
NASA Astrophysics Data System (ADS)
Alt, R. C., II; Zoback, M. D.
We report progress on a project to create a detailed map of in situ stress orientations and relative magnitudes throughout the state of Oklahoma. It is well known that the past 5 years has seen a remarkable increase in seismicity in much of the state, potentially related to waste water injection. The purpose of this project is to attempt to utilize detailed knowledge of the stress field to identify which pre-existing faults could be potentially active in response to injection-related pore pressure increases. Over 50 new stress orientations have been obtained, principally utilizing wellbore image data provided by the oil and gas industry. These data reveal a very uniform ENE direction of maximum compressive stress through much of the state. As earthquake focal plane mechanisms indicate strike-slip faulting, the stress orientation data indicate which pre-existing faults are potentially active. The data are consistent with slip on the near-vertical, NE-trending fault associated with at least one of the M 5+ earthquakes in the Prague, OK sequence in 2011. If successful, it would demonstrate that combining detailed information about pre-existing faults and the current stress field could be used to guide the siting of injection wells so as to decrease the potential for injection-related seismicity.
Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin
Yogesha, S.D.; SHarff, A.; Bricogne, G.; Izard, .T. (Globel Phasing); (Scripps)
The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic {alpha}-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 {angstrom} resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 {alpha}-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle.
Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin
Yogesha, SD; Sharff, A; Bricogne, G; Izard, T
The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic ?-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 Ĺ resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 ?-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle. PMID:21648001
Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin.
Yogesha, S D; Sharff, A; Bricogne, G; Izard, T
The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic ?-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 Ĺ resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 ?-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle. PMID:21648001
The UAH GeoIntegrator: A Web Mapping System for On-site Data Insertion and Viewing
M. He; D. Hardin; T. Sever; D. Irwin
There is a growing need in the scientific community to combine data colleted in the field with maps, imagery and other layered sources. For example, a biologist, who has collected pollination data during a field study, may want to see his data presented on a regional map. There are many commercial web mapping tools available, but they are expensive, and
Modeling Groundwater-Surface Water Interaction and Contaminant Transport of Chlorinated Solvent Contaminated Site
NASA Astrophysics Data System (ADS)
Yimer Ebrahim, Girma; Jonoski, Andreja; van Griensven, Ann; Dujardin, Juliette; Baetelaan, Okke; Bronders, Jan
Chlorinated-solvent form one of the largest groups of environmental chemicals. Their use and misuse in industry have lead to a large entry of these chemicals into the environment, resulting in widespread dissemination and oftentimes environmental contamination. Chlorinated solvent contamination of groundwater resources has been widely reported. For instance, there has been much interest in the assessment of these contaminant levels and their evolutions with time in the groundwater body below the Vilvoorde-Machelen industrial area (Belgium). The long industrial history of the area has lead to complex patterns of pollution from multiple sources and the site has been polluted to the extent that individual plumes are not definable any more. Understanding of groundwater/surface water interaction is a critical component for determining the fate of contaminant both in streams and ground water due to the fact that groundwater and surface water are in continuous dynamic interaction in the hydrologic cycle. The interaction has practical consequences in the quantity and quality of water in either system in the sense that depletion and/or contamination of one of the system will eventually affect the other one. The transition zone between a stream and its adjacent aquifer referred to as the hyporheic zone plays a critical role in governing contaminant exchange and transformation during water exchange between the two water bodies. The hyporheic zone of Zenne River ( the main receptor ) is further complicated due to the fact that the river banks are artificially trained with sheet piles along its reach extending some 12 m below the surface. This study demonstrates the use of MODFLOW, a widely used modular three-dimensional block-centred finite difference, saturated flow model for simulating the flow and direction of movement of groundwater through aquifer and stream-aquifer interaction and the use of transport model RT3D, a three-dimensional multi-species reactive transport model capable of incorporating multiple chemical and biological reactions to model the movement and chemical alteration of chlorinated solvents as they move with groundwater through the subsurface and reach to the surface water of the Zenne River . Keywords: MODFLOW, RT3D, Chlorinated-solvent; groundwater/surface water interaction ACKNOWLEDGEMENT The authors would like to thank the EU/FP7 AQUAREHAB Project for the financial support.
Genotype to Phenotype Maps: Multiple Input Abiotic Signals Combine to Produce Growth Effects via Attenuating Signaling Interactions in Maize
Makumburage, G. Buddhika; Richbourg, H. Lee; LaTorre, Kalindi D.; Capps, Andrew; Chen, Cuixen; Stapleton, Ann E.
The complexity of allele interactions constrains crop improvement and the prediction of disease susceptibility. Additive allele effects are the foundation for selection in animal and plant breeding, and complex genetic and environmental interactions contribute to inefficient detection of desirable loci. Manipulation and modeling of other sources of variation, such as environmental variables, have the potential to improve our prediction of phenotype from genotype. As an example of our approach to analysis of the network linking environmental input to alleles, we mapped the genetic architecture of single and combined abiotic stress responses in two maize mapping populations and compared the observed genetic architecture patterns to simple theoretical predictions. Comparisons of single and combined stress effects on growth and biomass traits exhibit patterns of allele effects that suggest attenuating interactions among physiological signaling steps in drought and ultraviolet radiation stress responses. The presence of attenuating interactions implies that shared QTL found in sets of environments could be used to group environment types and identify underlying environmental similarities, and that patterns of stress-dependent genetic architecture should be studied as a way to prioritize prebreeding populations. A better understanding of whole-plant interactor pathways and genetic architecture of multiple-input environmental signaling has the potential to improve the prediction of genomic value in plant breeding and crop modeling. PMID:24142926
Interaction of Batrachotoxin with the Local Anesthetic Receptor Site in Transmembrane Segment IVS6 of the Voltage-Gated Sodium Channel
Nancy J. Linford; Angela R. Cantrell; Yusheng Qu; Todd Scheuer; William A. Catterall
The voltage-gated sodium channel is the site of action of more than six classes of neurotoxins and drugs that alter its function by interaction with distinct, allosterically coupled receptor sites. Batrachotoxin (BTX) is a steroidal alkaloid that binds to neurotoxin receptor site 2 and causes persistent activation. BTX binding is inhibited allosterically by local anesthetics. We have investigated the interaction
Developing of a VS30 map for addressing site effects for Portugal: evaluation of the effectiveness of using VS30-proxies for stable continental regions.
NASA Astrophysics Data System (ADS)
Vilanova, Susana; Narciso, Joao; Carvalho, Joao; Pinto, Carlos; Lopes, Isabel; Nemser, Eliza; Borges, Jose; Oliveira, Carlos
The need to perform first-order estimates for site amplification in a regional sense has been strongly emphasized in recent years. The use site-amplification maps is of major importance for addressing both land-use planning (seismic-hazard maps) and emergency planning (instrumental intensity maps). Project SCENE, funded by the Portuguese Foundation for Science and Technology (FCT), aimed at gathering and acquiring shear-wave velocity profiles in diverse lithological and geological formations in Portugal, in order to develop a regional site conditions map to be used for including first-order site-effects into seismic hazard assessment maps. Within the scope of project SCENE thirty sites where strong motion stations are installed were characterized using shear-wave seismic refraction. The project SCENE shear-wave database also includes a significant amount of shear-wave refraction data available from FCT project NEFITAG and from previously performed CAPSA and ERSTA campaigns. Few sites characterised by using other methods (multichannel analysis of surface waves and invasive profiles) were also included in the database. The shear-wave database currently includes 85 shear-wave depth sections or profiles from a variety of lithological/geological formations. In addition to the shear-wave profile database we compiled geotechnical and geological profiles in the vicinity of the sites analysed. We performed a careful evaluation of the geological conditions for each site in the database using the largest scale available (usually 1:50 000). A smaller scale map (1:500000) was also used in order to evaluate the bias introduced by the scale-dependent map accuracy. We grouped the sites into six generalized geological units: S1 - igneous and metamorphic rocks; S2 - old sedimentary rocks (Limestones, marly limestones, dolomites, conglomerates and sandstones); S3 - Sand, sandstones, clays and conglomerates of Miocene age; S4 - Sandstones, gravels, sands and clays of Pliocene age; S5 - Sand deposits and clays, terrace deposits of Pleistocene age; and S6 - Alluvium, mud, sands, clay, silt and sand dune of Holocene age. The time-average shear-wave velocity in the upper 30m (Vs30) from the database sites range from 123m/s to 1870m/s. The variance of the distribution of Vs30 values varies significantly with the generalized geological unit, being larger S1 and S2 units. The use of proxies based either on the geological-geographical units developed for California by Wills and Clahan (2006) or on correlations with the topographic slope for stable continental regions (Wald and Allen, 2007) shows relatively unbiased total residual distributions of the logarithm of Vs30, although with a large variance. However, the performance of both methods varies significantly with the generalized geological unit analyzed. Both methods are highly biased towards lower values of Vs30 for unit S1 (hard rock). The topographic-slope method shows inconsistent bias for each generalized unit. These results are not in agreement with those of Lemoine et al. (2012) who concluded that, for stable continental regions, the topographic-slope method performance was best for rock sites (A/B NERPH class). This discrepancy points to the limitations of the database on near-surface site-conditions used in project SHARE in what concerns stable continental regions.