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Description: "A modern classic. Dewey's lectures have lost none of their vigor...The historical approach, which underlay the central argument, is beautifully exemplified in his treatments of the origin of philosophy."--Philosophy and Phenomenological Research "It was with this book that Dewey fully launched his campaign for experimental philosophy."--The New Republic Written by an eminent philosopher shortly after the shattering effects of World War I, this volume offers an insightful introduction to the concept of pragmatic humanism. Dewey presents persuasive arguments against traditional philosophical constructs, suggesting their basis in self-justification. He proposes, instead, an examination of core values in terms of their ultimate effects on the self and others. This experimental philosophy was received with both outrage and acclaim for daring to mingle ethics and science. Delivered in 1919 as a series of lectures, Dewey's landmark work appears here in an enlarged edition that features an informative introduction by the author, written more than 25 years after the book's initial publication.
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List price: $11.95Copyright year: 2004Publisher: Dover Publications, IncorporatedPublication date: 6/11/2004Binding: PaperbackPages: 176Size: 5.25" wide x 8.25" long x 0.50" tall Weight: 0.550Language: English
John Dewey was born in 1859 in Burlington, Vermont. He founded the Laboratory School at the University of Chicago in 1896 to apply his original theories of learning based on pragmatism and "directed living." This combination of learning with concrete activities and practical experience helped earn him the title, "father of progressive education." After leaving Chicago he went to Columbia University as a professor of philosophy from 1904 to 1930, bringing his educational philosophy to the Teachers College there. Dewey was known and consulted internationally for his opinions on a wide variety of social, educational and political issues. His many books on these topics began with Psychology (1887), and include The School and Society (1899), Experience and Nature (1925), and Freedom and Culture (1939).Dewey died of pneumonia in 1952.
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In the last few days, Brighton has started get a right old nip in the air. Gone is that long lazy summer only to be replaced with a windy and wet Autumn, that's been blowing cold air right up the back of my jumper. This calls for one thing and one thing only…soup. 'Oh boring, not another bloody soup' I hear you groan, but wait just a minute. This one is good one. It's the kind of soup everyone should have in their recipe bank.
Whilst I'd like to claim the origins of this soup are from my great granny, who got it from her great granny, but it's not. It's sort of from the Leon Cookbook, but with
large lumps of butter removed just a few tweaks here and there. It's the perfect soup for those days just between Winter and Summer…oh and it's gluten and diary free. Bingo!
Pancetta & French Lentil Soup (serves 4)
130g cubed and smoked pancetta
4 tablespoons olive oil
2 medium carrots, chopped
2 sticks celery, chopped
1 large red onion, chopped
3 cloves garlic, sliced
3 bay leaves
1 teaspoon dried oregano
1 tablespoon tomato puree
1 tablespoon balsamic vinegar
200g french lentils
1 litre chicken stock
Heat a large solid pan and add the oil. Once hot cook the pancetta until crisp and brown. Add all the veg and cook gently for about 15 minutes, or until the onions start to pick up a bit of colour. Stir in the bay leaves, oregano and cook for another couple of minutes.
Now add the tomato puree, vinegar and mix well. Tip in the lentils and stir them around to pick up all the flavour. Pour in your chicken stock. Bring to boil, then simmer for 30 minutes until the lentils are very soft.
Take a couple of ladles of soup out of the pot and blitz in your blender. It will be a bit paste like. Mix back into the soup. Season to taste.

subset: commoncrawl


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Nightmare Thief
Nightmare Thief
By Meg Gardiner
Blue Door, Paperback, 9780007337675
Publication Date: October 1, 2011
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Forensic psychiatrist Jo Beckett and her partner, Gabe Quintata, return in a fourth taut, groundbreaking thriller from Edgar Award-winner Gardiner. Available in a tall Premium Edition.
About the Author
Meg Gardiner previously practiced law and taught at the University of California, Santa Barbara. Originally from Southern California, she now lives with her family in London. "The Dirty Secrets Club" is her first novel published in the U.S. She will be promoting "The Dirty Secrets Club" on a national tour this summer.


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Computational analysis of alternative spliced genes on maize chromosome 1
- Grant Reynolds
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1 BioTechnologia vol. 93(1) C pp C 2012 Journal of Biotechnology, Computational Biology and Bionanotechnology RESEARCH PAPER Computational analysis of alternative spliced genes on maize chromosome 1 JOANNA GRACZ 1 *, ALEKSANDRA ŚWIERCZ 1, 2, TOMASZ TWARDOWSKI 1 1 Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland 2 Institute of Computing Science, Poznan University of Technology, Poznań, Poland * Corresponding author: Abstract Alternative splicing is an important part of mrna processing which results in protein diversity in all eukaryotes. In plants, this process is still poorly understood, however recent computational analysis has shown that alternative splicing is far more prevalent than previously thought. For better characterization of alternative splicing in maize, one of the most important crop species, we used AUGUSTUS (web-application deployed on local or remote host) to predict multiple transcripts and alternative splicing events from maize chromosome 1 sequence. From over 300 million bp of chromosome 1, AUGUSTUS software predicted ab initio genes and 20% of the estimated genes have at least two transcripts. For 412 genes with three transcripts we performed additional analysis including EST's alignment, protein identification and comparative evaluation with genes predicted using F genesh and Gramene software. In consequence we have identified alternative splicing events for 42 genes from maize chromosome 1. Key words: Zea mays, alternative splicing, AUGUSTUS, expressed sequence tags Introduction In 1978, a year after the discovery that the gene structure consists of coding regions (exons) interrupted by noncoding sequences (introns), it was proposed that in RNA transcribed from a single gene different exons could be joined together to produce various mrna transcripts (Reddy, 2007). This particular process, called alternative splicing (AS), was initially described for individual genes as isolated events (in 1994, the level of alternative spliced genes in human genome was estimated at less than 5% (Sharp, 1994)). Recent studies indicate that 95% of human genes and around 20-30% of plant genes undergo AS (Severing et al., 2009). This mechanism generates transcriptome diversity and partially explains the discrepancy between an estimated number of genes compared to the number of proteins encoded by the same genome. Most of AS events occur within exons, which affects the binding properties, intercellular localization, stability and activity of translated proteins. Furthermore, some splice isoforms contain premature termination codons (PTC) which are targeted for nonsense-mediated mrna decay (NMD) (Maquat, 2004). This pathway is one of the post-transcriptional mechanisms for regulating gene expression. Although most of AS studies have been performed on humans and other vertebrates, so far several thousand plant genes are known to produce multiple transcripts (Reddy, 2007; Wang and Brendel, 2006). Genes that show AS in plants are often part of fundamental processes such as photosynthesis, flowering or defense responses. One of the first AS events studied in Arabidopsis and spinach was ribulosebisphosphate carboxylase/oxygenase (rubisco) activase nuclear-encoded chloroplast enzyme required for rapid formation of the carbamate on the active site of rubisco (Werneke et al., 1989). Other well-characterized examples of alternative spliced genes in plants include: RNA polymerase II (Dietrich et al., 1990), chorismate synthase (Gorlach et al., 1995), FCA gene which encodes a nuclear ABA receptor (Macknight et al. 2002; Quesada et al., 2003) or splicing factors like serine/arginine-rich (SR) proteins (Lazar and Goodman, 2000; Reddy, 2004). SR proteins are highly conserved non-small nuclear ribonucleoprotein (non-snrnp) that play an important role in regular and alternative splicing.
2 42 J. Gracz, A. Świercz, T. Twardowski The majority of studies on AS or SR proteins in plants were performed on Arabidopsis, however it has been established that SR proteins produce multiple transcripts and utilize non-canonical splice sites in maize as well (Gupta et al., 2005). A few other studies were conducted on maize and revealed, for instance, AS of maize regulatory MuDR transposable element (Hershberger et al., 1995), glutathione S-transferase (bronze2 ) (Marrset al., 1997), waxy (Mareillonnet et al., 1997) or Knox7 (Morere-Le et al., 2007) genes. Despite these reports, the abundance of alternatively spliced genes is still underestimated in maize and other less-characterized plants. Most of AS events in plants are estimated on the basis of ESTs or cdna data, which are generally biased and have diverse quality. Moreover, EST collections represent only a small part of different environmental conditions, whereas plant responses to distinct stresses differ a lot and might affect AS efficiency or splicing patterns. It is likely that better EST coverage in less-studied plants will increase the number of AS events discoveries (Barbazuk et al., 2008). Progress in understanding the process of AS still requires answers to many questions, such as differences of AS patterns between plants and animals, monocots and dicots and between different plant species. To achieve this goal, first of all one has to elucidate constitutive and regulated splicing in specific plant species. An analysis of important bioenergetic and crop plants such as Zea mays will be very helpful in further comparative genomic research, studies on domestication and trait selection for breeding programs. In this paper we have described AS events on maize largest chromosome using ab initio gene prediction and aligning results with EST collection. This approach allows us to identify novel AS genes,determinethe significance of AS phenomenon and can be used to analyze the entire genomes as well. Material and methods As the object of our research we selected maize for its high economic value and in correlation with the studies on this plant previously conducted in our laboratory (Twardowski et al., 2010; Korbin et al., 2011). For ab initio gene prediction, we used AUGUSTUS program available at WWW server (http://augustus. gobics.de) and maize chromosome 1 sequence from GenBank database (accession number GK ). We decided to choose AUGUSTUS program, because it is one of the first gene finder programs that can predict the formation of multiple transcripts for predicted genes. It is also freely available from the web server and has pre-calculated sets of parameters for Zea mays (and also for 48 other species). This software is based on generalized hidden Markov model (GHMM) complex probabilistic model which combines information from a variety of different sources -- signal and sequence content. Exons, introns, the sequence around a splice site etc., correspond to states in the model and each state is connected to a DNA sequence with certain pre-defined emission probabilities. AUGUSTUS, like any other HMM-based gene prediction software, finds an optimal parse, that is the segmentation of the input DNA sequence which is consistent with all the given constrains (Stenke and Morgenstern, 2005; Stenke et al., 2005). For input at AUGUSTUS server, a user can upload sequences of maximum total length of 3 mln bp, therefore it was decided to divide maize chromosome 1 (total length bp) into one hundred fragments of 3 mln bp each and one of bp. To avoid omitting genes that can be located near the ends of those fragments, we created one hundred of bp long sequences which overlapped at neighboring fragments. AUGUSTUS web server has four different options for the number of reported alternative transcripts depending primarily on posterior probability of exons and introns. To perform the scheduled analysis, we chose options with few reported transcripts. The output data in General Feature Format (GFF), consisting of a coding sequence and an amino acids sequence of predicted gene, were converted for further analysis to FASTA file format. In the next step, we selected 412 genes with 3 or more transcripts predicted by AUGUSTUS and searched NCBI EST database with MEGABLAST algorithm. Amino acid sequences translated from selected genes were used to search UniProtKB Database with BLASTP algorithm. The search was performed with Geneious Basic software (Drummond et al., 2010), which is a single desktop application to store, visualize and analyze complex biological data (free version for non-commercial use is available at We also compared the selected genes with predictions obtained from other platforms Gramene and F genesh using the maize genome browser (http://maizesequence.org) and BLASTN algorithm. Gramene is a comparative genome mapping database specializing in
3 Computational analysis of alternative spliced genes on maize chromosome 1 43 Table 1. List of proteins 1 identified from BLASTP alignment to UniProtKB with obtained parameters and UniProtKB accession Gene no. E-value % of identities Identified protein Accession (UniProtKB) e % DNA (cytosine-5)-methyltransferase DRM1 from Arabidopsis thaliana 9LXE e % DNA (cytosine-5)-methyltransferase DRM2 from Arabidopsis thaliana Q9M e % Protein FIZZY-RELATED 2 from Arabidopsis thaliana Q8L3Z e % Probable serine/threonine-protein kinase from Arabidopsis thaliana Q3EDL % e % Phytoene dehydrogenase, chloroplastic/chromoplastic from Solanum lycopersicum 26S proteasome non-atpase regulatory subunit 4 from Arabidopsis thaliana P28554 P e % Asparagine synthetase [glutamine-hydrolyzing] from Sandersonia urantiaca O e % Myb-related protein P from Zea mays P e % Homocysteine S-methyltransferase 2 from Zea mays Q9FUM % Glutamate decarboxylase 2 from Arabidopsis thaliana Q e % Probable 125 kdakinesin-related protein from Arabidopsis thaliana P e % 12-oxophytodienoate reductase 3 from Arabidopsis thaliana Q9FUP % Alpha-galactosidase from Oryza sativa subsp. japonica Q9FXT % Seed lipoxygenase-3 from Glycine max P % Lipoxygenase 2 from Oryza sativa subsp. japonica P e % 65-kDa microtubule-associated protein 6 from Arabidopsis thaliana Q9SIS e % Ferredoxin-NADPreductase, root isozyme, chloroplastic from Oryza sativa subsp. japonica P e % Glutamate dehydrogenase Zea mays Q Amino acid sequences from predicted by AUGUSTUS genes and exon coordinates of respective genes are available in Supplementary materials 1 Table 2 monocots. It brings together ESTs collections, genetic maps, map relations, genes, proteins and publications providing connection between different sources of information (Ware et al., 2002;Youens-Clark et al., 2011). F genesh (Find GENES using HMM); on the other hand, is based on a statistical approach and uses HMM trained on monocots, but does not consider alternative splicing (Solovyev et al., 2006). It was previously used for gene prediction in maize and in comparison with four other programs (GeneMark.hmm, GENESCAN, GlimmerR and Grail) it yielded the most accurate genes predictions (Yao et al., 2005). For the selected gene pool we performed additional search at NCBI Reference RNA Sequences (refseq_rna) database using BLASTN algorithm. The obtained results for mrna and ESTs have been presented in a graphical form using Integrative Genomic Viewer (free available at Results and discussion In the first step of the analysis from AUGUSTUS ab initio prediction based on the information in the genome sequence, we located genes on a maize chromosome 1. This result suggests the existence of a high number of false-positive predictions, because the estimated number of genes in the whole maize genome is about (Schnable et al., 2009). One fifth (9410) of the genes predicted by AUGUSTUS have more than one transcript and 412 genes out of them have three or more. For the following evaluation, we chose these 412 genes with the highest number of predicted transcripts. We assumed that it is more likely that they match real transcripts
4 44 J. Gracz, A. Świercz, T. Twardowski Fig. 1. Outline of AS analysis performed on maize chromosome 1. Flow of data analysis and gene pool restriction with exact number of considered genes. For EST s collection searching we used MEGABLAST algorithm, for F genesh and Gramene BLASTN and for UniProtKB BLASTP expressed in plants (ESTs) or at least one of them does. For aligning transcripts with EST collection using MEGABLAST algorithm, we established E-value threshold on 1e-100 and the level of percentage of identities at 85% for meaningful result. After aligning transcripts (over 1200 sequences) to EST collection for 272 out of 412 (66%) we confirmed the existence of: C all three transcripts for 113 genes (27.4%), C two transcripts for 129 genes (31.3%), C only one transcript for 30 genes (7.3%). In the next step, we compared the results obtained from AUGUSTUS with predictions from Gramene and F genesh. We confirmed AS events for 254 and 156 genes, respectively (for meaningful results we used the same parameters as for MEGABLAST analysis). From Gramene predictions only 23 genes had more than one transcripts, which points towards high sensitivity of AUGUSTUS program. Forty two gens from the pool of 113 genes with three transcripts confirmed by alignment with ESTs were also validated by Gramene and F genesh predictions (Supplementary materials 1 Table 1). Thus we considered these 42 genes as the most probable AS events (see Figure 1). An example of AUGUSTUS outcome (for gene 1) is presented in Figure 2 and in GFF format for every gene in Supplementary material 2. The distribution and location of those 42 genes pool on chromosome 1 is presented in Figure 3. To better depict the relative position of the predicted transcripts, for those 42 gene pool and its confirming data (ESTs and mrnas), we used Integrative Genomics Viewer to present them in correlation with chromosome 1 sequence (Supplementary materials 1 Figure 1). For 16 genes, we found a very accurate exon coordinate prediction made by AUGUSTUS in comparison to the corresponding mrna sequence (genes number: 1, 2, 3, 4, 5, 8, 18, 20, 23, 24, 27, 29, 31, 34, 38 and 41). For the remaining transcripts, there was only a rather small coverage of mrna sequence, which can be partially explained by incomplete collection of the reference maize mrna sequence. Parallel to query ESTs collection, an analysis at the protein level was also performed. It included alignment of amino acids sequences (translated from AU- GUSTUS-predicted genes) to UniProtKB using BLASTP algorithm. We set up E-value threshold at 1e-100 and the percent of identities at least 40%. In this way we identified 18 proteins most of them were from A. thaliana and 3 were from maize (Table 1). For one of the proteins identified from Zea mays, Myb-related protein P, alternative splicing had been confirmed earlier (Grotewold et al., 1991). Similarly, other 3 proteins ( probable serine/ threonine-protein kinase (Yamada et al., 2003), glutamate decarboxylase 2 (Zik et al., 1998) and 65-kDa microtubule associated (Iida et al., 2009) from A. thaliana, have two isoforms arising from alternatively spliced genes. The growing availability of genome sequences has produced enormous amount of data which requires appropriate interpretation to obtain useful information. Therefore, there is still a great need for bioinformatics
5 Computational analysis of alternative spliced genes on maize chromosome 1 45 Fig. 2. Scheme of intron and exon organization of 3 transcript (1.1, 1.2, 1.3) from gene 1 predicted by AUGUSTUS. Each of presented transcripts match different ESTs and mrna. Longest transcript (1.3) consist of 10 exons and one very large intron 6782 nt (between exon 8 and 9), transcript 1.2 consist of only 2 exons and raise from alternative 3N splice site acceptor of exon 9. In transcript 1.1 there is an additional exon, which is located in intron 6 of transcript 1.3 Fig. 3. Distribution and localization of restricted pool of genes predicted by AUGUSTUS tools for gene prediction and specialized applications e.g. searching for mirna, AS events or specific sequences motifs. The purpose of this study was the identification of AS events in transcripts arising from genes located on the maize s largest chromosome. The results of our analysis allowed us to verify the significance of AS, helped us diminish the total number of chromosome 1 genes to those undergoing AS and thus focus on specific ones. Within this in silico experiment we had a chance to evaluate the accuracy of AUGUSTUS predictions, compare it to the other currently available programs and to build a simple pipeline to restrict the pool of candidate genes for further experiments (Fig. 1). AUGUSTUS is one of the few programs that have a training set for maize sequences and setup options to control predicted splice variants per gene. This allows users to choose between sensitivity or specificity of the program output. Despite the fact that we have chosen almost the most stringent options with few predicted transcripts, we have obtained many false positive predictions. One reason for this may be an insufficient training set, because the quality of predictions directly depends on the quality of training sets. Compared with A. thaliana or human genome, maize genome as well as maize s ESTs collections are still insufficiently studied. Another reason may be the high specificity of the maize genome it has a lot of repetitive elements, many of which are transposons and retrotransposons, thus genes occupy only a small fraction of about 10-15% of the genomic sequence. The total proportion of genes undergoing AS events (that is 20%) was consistent with the previously estimated number (Barbazuk et al., 2008). When considering genes with only three or more predicted transcripts, AUGUSTUS makes 66% of correct predictions. Moreover, 58.4% of these genes may undergo AS, which was confirmed by aligning the predicted transcripts with different ESTs. More than half (42) of genes with few predicted transcripts were also validated by other pro-
6 46 J. Gracz, A. Świercz, T. Twardowski grams (Gramene or F genesh). Those 42 genes with 3 alternative transcripts were recognized as novel, previously undescribed, splicing events. Sixteen genes from that pool showed high similarity to mrna deposited in Refseq_rna database. An analysis of the translated amino acid sequences indicated four documented cases of AS events (from 18 identified proteins). These results confirm that AUGUSTUS is a well-constructed program and may serve as an efficient tool for AS searching, although it will still be necessary to improve its abilities. The proposed scheme of in silico analysis can be used for effective reduction of gene pools, which is important especially when expensive biochemical experiments are going to be carried out in the subsequent step of analysis. In further studies on AS in maize, we plan to use 42 genes which were identified at every level of presented analysis. Conclusions genes (including false-positive predictions) were found by AUGUSTUS program in maize chromosome 1. This gene pool was reduced to genes with possible AS events. We further reduced that number to 412 genes with three or more transcripts and have identified 42 genes by aligning their sequences with different ESTs and compared them with predictions obtained using two other gene finder programs (Gramene and F-genesh). We also identified 18 proteins from which 4 were previously demonstrated to have different isoforms that arise from AS events. We recognized AS as a novel event for 42 genes and 14 proteins identified by the described procedure. The foregoing results indicated importance of AS events in maize genome and have demonstrated usefulness of the applied procedure. References Barbazuk W.B., Fu Y., McGinnis K.M. (2008) Genome-wide analyses of alternative splicing in plants: Opportunities and challenges. Genome Res. 18: Dietrich M.A., Prenger J.P., GuilfoyleT.J. (1990) Analysis of the genes encoding the largest subunit of RNA polymerase II in Arabidopsis and soybean. Plant Mol. Biol. 15: Drummond A.J., Ashton B., Cheung M., Heled J., Kearse M., Moir R., Stones-Havas S., Thierer T., Wilson A. (2010) Geneious v5.0 Gorlach J., RaeseckeH.R., Abel G., Wehrli R., Amerhein N., Schmid J. (1995) Organ-specific differences in the ratio of alternatively spliced chorismate synthase (LeCS2) transcripts in tomato. Plant J. 8: Grotewold E., Athma P., Peterson T. (1991) Alternatively spliced products of the maize P gene encode proteins with homology to the DNA-binding domain of myb-like transcription factors. Proc. Natl. Acad. Sci. USA 88: Gupta S., Wang B.B., Stryker G.A., Zanetti M.E., Lal S.K. (2005) Two novel arginine/serine (SR) proteins in maize are differentially spliced and utilize non-canonical splite site. Biochim. Biophys. Acta 1728: Hershberger R.J., Benito M.I., Hardeman K.J., Warren C., Chandler V.L., Walbot V. (1995) Characterization of the major transcripts encoded bu the regulatory MuDR transposable element of maize. Genetics 140: Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K. (2009) Analysis of multiple occurences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-lenghtcdnas. DNA Res. 16: Korbin M., Kuras A., Keller-Przybyłkowicz S., Adamczyk J., Twardowski T., Kietrys A.M., Szopa A., Adamczewski K. (2011) Method to precisely differentiate maize genotypes, simplified molecular test and specific identity biomarker. In Polish Patent Office P Lazar G., Goodman H.M. (2000) The Arabidopsis splicing factor SR1 is regulated by alternative splicing. Plant Mol. Biol. 42: Macknight R., Duroux M., Laurie R., Dijkwel P., Simpson G., Dean C. (2002) Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA. Plant Cell 14: Marrillonnet S., Wessler S.R. (1997) Retrotransposon insertion into maize waxy genes results in tissue-specific RNA processing. Plant Cell 9: Marrs K.A., Walbot V. (1997) Expression and RNA splicing of the maize glutathione S-transferase Bronze2 gene is regulated by cadmium and other stresses. Plant Physiol.113: Maquat L.E. (2004) Nonsense-mediated mrna decay: Splicing, translation and mrnp dynamics. Nat. Rev. Mol. Cell Biol. 5: Morere-Le Paven M.C., Anzala F., Recton A., Limami A.M. (2007) Differential transcription initiation and alternative RNA splicing of Konox7 a class 2 homeobox gene of maize. Gene 401: Quesada V., Macknight R., Dean C., Simpson G.G. (2003) Autoregulation of FCA pre-mrna processing controls Arabidopsis flowering time. EMBO J. 22: ReddyA.S.N.(2004)Plant serine/arginine-richproteins and their role in pre-mrna splicing. Trends Plant Sci. 9: Reddy A.S.N. (2007) Alternative Splicing of Pre-Messenger RNAs in Plants in the Genomic Era. Annu. Rev. Plant Biol. 58: Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S. et al. (2009) The B73 maize genome: complexity, diversity and dynamics. Science 326:
7 Computational analysis of alternative spliced genes on maize chromosome 1 47 Severing E.I., Van Dijk A.D.J., Stiekema W.J., Van Ham R.C.H.J. (2009) Comperative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome. BMC Genomics 10: 154. Sharp P.A. (1994) Split genes and RNA splicing. Cell 77: Solovyev V., Kosarev P., Seledsov I., Vorobyev D. (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 7: S Stanke M., Morgenstern B. (2005) AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constrains. Nucl. Acid Res. 33: Stanke M., Keller O., Gunduz I., Hayes A., Waack S., Morgenstern B. (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucl. Acids Res. 34: Twardowski T., Kietrys A.M., Szopa A., Adamczewski K., Adamczyk J., Korbin M., Kuchta P. (2010) Method to determine the herbicide stress resistance of maize varietes, a diagnostics kit to determine the resistance of maize lines to herbicide stress and use of RNA aptamers to detect resistant and sensitive maize lines. In: Polish Patent Office, P Wang B.B., Brendel V. (2006) Genomewidecomperative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. USA 103: Ware D.H., Jaiswal P., Junjian N., Yap I.V., Pan X., Clark K.Y. at al. (2002) Gramene, a tool for grass genomics. Plant Physiol. 130: Werneke J.M., Chatfield J.M., Ogren W.L. (1989) Alternative mrna splicing generates the two ribulosebisphosphate carboxylase/oxygenaseactivase polypeptides in spinach and Arabidopsis. Plant Cell 1: Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J. et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: Yao H., Guo L., Fu Y., Borsuk L.A., Tsui-Jung W., Skibbe D.S. et al. (2005) Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol. Biol. 57: Youens-Clark K., Buckler E., Casstevens T., Chen C., De- Clerck G., Derwent P. et al. (2011) Gramene database in 2010: updates and extensions. Nucl. Acids Res. 39: D Zik M., Arazi T., Snedden W.A., Fromm H. (1998) Two isoforms of glutamate decarboxylase in Arabidopsis are regulated by calcium/calmodulin and differ in organ distribution. Plant Mol. Biol. 37:
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Anatomy of the smallest coleoptera, featherwing beetles of the tribe nanosellini (Coleoptera, Ptiliidae), and limits of insect miniaturization
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The internal structure of Nanosella sp., Primorskella sp., and Porophila sp. was described from serial sections and total preparations using light and transmission electron microscopy. The most important structural features related to miniaturization are the absence of midgut muscles, abortion of two Malpighian tubes, a decrease in the number of abdominal spiracles, strong reduction of the tracheal system, the absence of the heart, reduction of the circulatory system and its substitution by the fat body, strong oligomerization and concentration of the nervous system, a decrease in the size and number of neurons, and reduction of the left testis and left ovary. The internal structure of featherwing beetles was analyzed for the first time using 3D computer models, which allowed us to demonstrate changes in the relative volume of organs accompanying the body diminution. The excretory and digestive systems change isometrically, while others change allometrically. The relative volume of the musculature decreases, and that of the nervous and reproductive systems increases. The skeleton mass also increases. The possible factors limiting further diminution in Ptiliidae (egg size, the volume of the reproductive and nervous systems, and the skeleton mass) are discussed.
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text: It been discussed a couple of times before but there's never been a definite solution. I'm hosted on LiquidWeb and they use an over-aggressive rule set of mod_security. Unfortunately, and although I have while listed many triggered rules, XenForo still doesn't play well with it. So my question is simple, does anyone have a proper solution or a proper set of rules to be white listed in order for mod_security to work well with XenForo? Or if you have disabled mod_security on your community via htaccess, what security alternate do you use?


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Fergie sets out transfer plans
By Adam Marshall
Last Updated: 01/01/70 1:00am
Sir Alex Ferguson will hang onto Eric Djemba-Djemba and Kieran Richardson.
Sir Alex Ferguson looks like hanging onto Eric Djemba-Djemba and Kieran Richardson, but he is willing to loan out David Jones.
Manchester United have been active in the transfer market this week, farming Chris Eagles out to Watford, while Norwich City boss Nigel Worthington has admitted an interest in taking Richardson on loan.
Cameroon international Djemba-Djemba was tentatively linked with a move to Birmingham City after Blues boss Steve Bruce was spotted at Exeter City's St James Park in midweek.
However, Bruce has rejected the reports and Ferguson stressed the former Nantes man is staying put.
"There have been a few enquiries about Eric over the last few weeks," Ferguson told United's official website. "But we're not in a position to make a decision about that.
"We've loaned Chris Eagles out to Watford. That's one thing that has happened.
"David Jones may also be farmed out depending on how things go in the next two or three days.
"After that, I've got quite a few players out on loan at the moment so I don't anticipate there being any more."
Norwich had been keen to recruit winger Richardson on a temporary basis to help their bid to stave off relegation.
|Man United 2/7 Draw 7/2 Aston Villa 8/1 -
Click here for full odds with Sky Bet


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Princess Doll Hat Crochet Pattern
By Lori Stade
Published by Lori Stade at Smashwords
Copyright 2012 Lori Stade
This epattern is licensed for your personal enjoyment only. This epattern may not be re-sold or given away to other people. If you would like to share this pattern with another person, please purchase an additional copy for each recipient. If you're reading this pattern and did not purchase it, or it was not purchased for your use only, then please return to Smashwords.com and purchase your own copy. Thank you for respecting the hard work of this author.
This is a cute little hat for a child 1 year to 3 years old. It is crocheted from any type of worsted weight yarn. Choose your favorite combination of colors. This is an excellent project for using up your scrap stash. Make a Dolly hat with the same hair color and features as your little one!
Crochet Hooks
Size J/10 6.0 mm 4 UK/Canada


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Spiriva Mist Inhaler Tied to Early Death in New StudyJun 15, 2011 | Parker Waichman LLP
A new study has found that a mist formulation of Spiriva (Tiotropium) may be putting patients with chronic obstructive pulmonary disease (COPD) at risk for premature death. The study, which examined Spiriva delivered via the Respimat inhaler, is published in the British Medical Journal.
Spiriva is available in the U.S. as a powder delivered via a device called the Handihaler. According to a Bloomberg report, the Spiriva Respimat inhaler is available in 55 countries including the U.K., but has not yet been approved for use in the U.S. The U.S. Food & Drug Administration has so far declined to approve Spiriva Respimat due to safety concerns, and is requiring that the mist version to undergo a clinical trial involving 17,000 patients.
The new Spiriva study was conducted by researchers in the U.S. and U.K. The analysis included five clinical trials involving more than 6,500 patients. According to one of the authors of the study, the risk of early death in patients using the Spiriva inhaler appeared to be 52 per cent higher versus those treated with placebo.
"We estimate that there will be one additional death for every 124 patients treated for a year with Tiotropium Respimat. Some of this risk appears to stem from patients dying of heart trouble, especially for those with existing heart problems that may be worsened because of a potential adverse effect of tiotropium on the heart rhythm," Dr Yoon Loke of Norwich Medical School at the University of East Anglia, said in statement.
"There are alternative inhalers that can help patients with COPD. Patients currently using Tiotropium Respimat should not suddenly stop taking their medication, but I would advise them to make an appointment with their doctor to discuss the possibility of switching to a different drug," Dr. Yoon continued. "As Tiotropium Respimat can have an adverse effect on the heart rhythm, patients with a history of palpitations or irregular heartbeat (fast or slow) should mention such problems to their doctor."
COPD is a chronic lung disease that causes breathing difficulty. The disorder affects as many as 24 million Americans, according to the National Heart, Lung and Blood Institute. COPD is estimated to kill as many as 120,000 Americans every year.


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Neverhood Village is the Main Hub World in the Neverhood Series. It is where all the Chaos live and was very peaceful until Dr. Kogg turned almost the whole village into monsters with his Mutation Formula. Later, Kogg kidnapeed all the Small Chaos to use them as batteries for his Kogbot Army.
- Klaymen
- Rico
- Charles
- Fank
- Frank
- Grace
- Claude
- Yoko
- Nora
- Gadz
- Doris
- Lilly
- Esmerelda
- Lolo
- Lala
- Queen Mamuta
Battle For The Neverhood
After Dr. Kogg mutated all the Small Chaos into ferocous monsters, they all run amuk all over the island and the Village is now stranded with only a group of Chaos determined to save everyone.
The Village has no chaos at first but the more monsters you defeat, the more chaos return to the Village.
Fight 2 The End!!
When Kogg stole all the Small Chaos to power up his Kogbot Army, the entire Chao Group go out and destroy as many Kogbots as possible.
Like the first game, at first there are no small chaos


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This film was recorded at the International Crystallography Conference, 1965, Melbourne, Australia, by the CSIRO Film Unit in collaboration with the Australian Academy of Science. If you are at all interested in the history of crystallography, and of science in general, I think you will find this video to be 15 well spent minutes.
This film was made possible with support from UNESCO, the International Council of Scientific Unions, the Australian Academy of Science, the International Union of Crystallography, the International Union of Pure and Applied Physics, the International Atomic Energy Agency and the University of Melbourne.
Are you looking to apply your skills in Integrative Structural Biology to the development of new approaches to explore organization of functional bacterial chromosome? The SIBYLS Group at Lawrence Berkeley National Laboratory is seeking a Postdoctoral Fellow in the field of Integrative Structural Biology. For more details on the position, please see the pdf document below….
SIBYLS has installed new robotics that halve the time it takes to collect a full 96-well plate, from approximately 5 hours to 2.5 hours per plate (with the potential to collect a plate in 10 minutes over the coming year). We believe this will be a game changer for many reasons. We will be able to accommodate more users per week, enable new screening methods, and have more time to offer SEC-coupled SAXS and time resolved SAXS. In addition to the new robotics, we have improved instruments for higher data quality. Our new monitor of transmitted beam intensity should greatly reduce buffer subtraction errors. We have also replaced the windows for lower background. In completing these upgrades, the stage is now set for increased sample to detector distance providing access to lower q (an upgrade that will occur sometime during the summer).
Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. The authors of this paper created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots that measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. These methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.
Yen-Ting Lai1, Greg L. Hura, Kevin N. Dyer, Henry Y. H. Tang, John A. Tainer and Todd O. Yeates Designing and defining dynamic protein cage nanoassemblies in solution 14 Dec 2016:Vol. 2, no. 12
Formation of repressive complex in the mammalian circadian clock is demoted by the secondary pocket of CRY1
In this paper, the authors show that CRY1, a protein coding gene that activates circadian gene expression and metabolic states and circadian oscillators, binds directly to the PAS domain core of CLOCK:BMAL1. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24 hr periodicity of gene expression. Integrative modeling and solution X-ray scattering studies (conducted at the SIBYLS beamline 12.3.1) irrefutably position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. This study is significant for understanding the clock mechanism as fundamental for the development and application of therapies for circadian-related disorders.
SAXS profile of CRY1:CLOCK:BMAL1 repressive complex.
(A) Scattering traces of CRY1:CLOCK:BMAL1 ternary complex (CCB) at different con- centrations are shown. These scattering plots were merged to generate the dataset as the input for FoXSDock. (B) Guinier analysis of CCB shows little or no aggregation of sample. SAXS-calculated molecular weight of the ternary complex is 113 kDa. (C) Kratky plot shows the CCB complex indicates a folded mass with an elongated shape. (D) PDB of FoXSDock HADDOCK driven model that is among the top 20 nearly degenerate docking structures, χ = 2.74.
Michael AK, Fribourgh L, Chelliah Y, Sandate C, Hura GL, Schneidman-Duhovny, Tripathi SM, Takahashi JS, Partch CL "Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1" PNAS 2017 Jan 31, doi:10.1073/pnas.1615310114
Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. In this paper the authors define molecular pathways linking AIF's active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF's central β-strand to modulate a hydrophobic border at the dimerization interface, and (2) an interaction network links AIF's FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. This knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.
Tip link filaments convey force and gate inner-ear hair-cell transduction channels to mediate perception of sound and head movements. Cadherin-23 and protocadherin-15 form tip links through a calcium-dependent interaction of their extracellular domains made of multiple extracellular cadherin (EC) repeats. These repeats are structurally similar, but not identical in sequence, often featuring linkers with conserved calcium-binding sites that confer mechanical strength to them. In a paper recently published in Nature Communications the Sotomayor lab reports the X-ray crystal structures of human protocadherin-15 EC8-EC10 and mouse EC9-EC10, which show an EC8-9 canonical-like calcium-binding linker, and an EC9-10 calcium-free linker that alters the linear arrangement of EC repeats. Molecular dynamics simulations and small-angle X-ray scattering experiments support this non-linear conformation. Simulations also suggest that unbending of EC9-10 confers some elasticity to otherwise rigid tip links. The new structure provides a first view of protocadherin-15's non- canonical EC linkers and suggests how they may function in inner-ear mechanotransduction, with implications for other cadherins.


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Your views on Dallas Eakins so far
View Single Post
Registered User
Join Date: Sep 2010
Posts: 391
vCash: 500
I never thought I'd say this after just 14 games, but I blame Eakins for this mess. The line-matching last night on home ice was mind-boggling. Seriously, its not a sign of weakness to put a checking line up against the other teams top line...
He thinks he is so smart that he is going to do everything counter to 50 years of coaching logic. Sure he likes to keep in shape, is a good talker and has a hot wife but he may also be just stubborn and frankly he might be an idiot. I liked Kruger, all he needed was a better support staff. Instead we got this know-it-all.
To early to fire him, I think we have to ride out the year, and hope by the end of the year he will deserve another, but he has a long ways to go before he gets back in my good books.
He also needs to take Yakupov off the top line, no chemisty with Ebs, its plain to see... Top line should be Nuge, Ebs and Perron. Alright I'm now going to try and take a week off from this mess... scerenity now...
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San Diego, California – (The Hosting News) – September 25, 2007 – Green powered Internet services firm, and web hosting design firm, Greenest Host, has appointed author and international environmental business entrepreneur, Paul Hannam, as Chairman of the Board.
Mr. Hannam is co-founder and Chairman at Bright Green Talent, a venture with the mission to recruit the brightest and the best talent in the world to work for organizations that are committed to sustainability and corporate social responsibility. Previously, he founded a computer recruitment and executive search business in England that topped $50 million in annual revenue. Between 2001 and 2005 he was an Associate Fellow at the Oxford University Environmental Change Institute.
Mr. Hannam explained, "There are lots of synergies between Bright Green Talent and Greenest Host. It is funny how life works. Over seven years ago, I came to the United States to find a growing Internet company in whom I could invest and it changed my life completely. I didn't find that company, but, instead, I ended up joining the green movement. Now, seven years later, I returned to find a thriving green venture in which to invest and I ended up joining an Internet company. Greenest Host is definitely best positioned to provide full service web and marketing outsourcing for green businesses."
The company plans to expand its existing network of green business partners as well as add marketing and technology support to round out their platform of green web services.
Mike Corrales, CEO of Greenest Host added, "We will continue to make it easy for small to midsize businesses to turn their IT infrastructures into zero emissions showcases. However, adding Paul's strategic vision and fantastic connections with the world's green leaders to our record of executing cutting-edge Internet solutions for customers could not be a better fit."
An August 2007 study by the U.S. EPA concluded that U.S. Data Centers consumed 61 billion kilowatt-hours (kWh) of electricity. That is more than all of the nation's televisions and similar to the amount of electricity consumed by approximately 5.8 million average U.S. households. Greenest Host is helping a rapidly growing list of companies reduce their carbon footprint through a 100% solar powered data center operation and web consulting services. The company only offers solutions powered by 100% renewable energy so that there is no need for carbon offsetting.
Greenest Host made its 100% solar powered web hosting plans available in August, including the traditional web hosting solutions such as domain registration, email account hosting, and custom website building. Greenest Host's services, operate through its green technology data center, which operates 100% of the time on clean solar energy. The company has combined cutting edge green power technology with custom, easy-to-use account management software, point-and-click website development tools, and world-class ecommerce software. For the first time, consumers and small businesses have the freedom to sign up for a green technology web hosting account, build a web presence, and know that with every web visitor's click they are reducing carbon emissions. And for every new account created through the end of 2007, Greenest Host will donate $5 to the Environmental Defense Fund – up to $500,000.
Greenest Host also sponsored the Green Power Inside "Million Green Powered Website" campaign, where the goal was to convert one million websites to clean power, resulting in pollution reductions equivalent to:
- 2,000 passenger cars not driven for one year
- 1,070,000 gallons of gasoline not burned
- 21,900 barrels of oil not burned
- 1,200 households not using electricity for a year
- 240,000 tree seedlings grown for 10 years
- 7,900 acres of pine or fir forests storing carbon for one year
- 77 acres of forest preserved from deforestation
- 48 railcars of coal not burned
- 3,200 tons of waste recycled instead of landfilled
Greenest Host provides web hosting, strategic web development, and web marketing, to green and ethical businesses. The company's mandate is to effect change, by offering zero emissions web services from web hosting to full outsourcing of corporate web strategies. The company powers its servers and data center cooling with 100% clean solar power 100% of the time. The service was first launched in August 2007. Greenest Host is a privately held company headquartered in San Diego, California.
To learn more about Greenest Host, please visit: www.greenesthost.com.


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|Reviews for Troubles Melt Like Lemon Drops
| Camerine chapter 1 . 4/12/2007
That was great! *Grins* I wonder if anything like this really would happen if Rodney ate a lemon. Probably not, but one can always wish. XD
Awesome job!
| Llanea chapter 1 . 3/18/2007
lol that was awesome
| Desert Blossom-by-the-Sea chapter 1 . 2/11/2007
Lovely. Almost dying can bring out the honest emotions in people.
I remember, with great fear, my brother almost dying more than once due to asthma. Feeling helpless in a situation like that is probably the worst emotion in the world. Kissing helps! (Although, I sure wouldn't kiss my brother like that! Yuck!)
| NoLongerActiveUser chapter 1 . 2/8/2007
Wow! I can't believe I've missed this one :) *quickly clicks C2 button* What a sweet tale. TPTB have always hinted that Liz & Rodney had history and you fleshed it out nicely. And your anaphylactic bits were very realistic! Poor Rodders... Thank you for posting!
| PurpleYin chapter 1 . 10/3/2006
Why are there not more review for this excellent story? I just adored all of it. The snark set against the caring made it so wonderfully in character while being shippy. The ending was great as well. It was the most wonderful story to read the other day, really cheered me up on a bad day and it's still really good on a reread.
| Fanwoman chapter 1 . 10/2/2006
Darling, darling, yummy, yummy goodness! The combination of humor and drama was lovely, and the ending was sublime. Thank you for this completely delightful story with all of its implications of caring, both of the friendly and romantic varities. I hope you sign up for the ficathon next year, too!
| dwparsnip chapter 1 . 10/2/2006
Very sweet.
Funny and romantic with a dash of drama.
Well done.
| dahan chapter 1 . 9/30/2006
Hehe, lovely ending. _
Seeing Elizabeth so defensive to the competition was certainly smile worthy and it's certainly nice the way the humor goes in the end. Fun fic!
| szhismine chapter 1 . 9/29/2006
great fic!
| the-Bookworm-Princess chapter 1 . 9/28/2006
*is speechless* I heart McWeird! ;) Ach, dahlink, vat can I say? It vas wunderbaar. Or however you spell that. I so heart the ending, with the implied making-out-ness. :D Teehee, this time around I noticed that the line about "noises from the bathroom" or whatever gave me other connotations than that he was showering. *gigglesnort* ANYWAYS. Loved it, loved it, loved it! You must write mcweird again. Oh, lookit! I'm the first reviewer? *sque*


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Packers Ex-boyfriend Sign
December 27, 2011 by staff
Packers Ex-boyfriend Sign, Breaking up is never easy and can be especially hard during the holidays. How do you explain to family and friends at every holiday gathering what happened? And what do you do with any gifts that you bought for you ex? If you're this jilted gal then you use that present for a very public type of revenge.
Just before halftime of the Packer's win over the Bears on Sunday night at Lambeau Field, the NBC cameras captured a female fan in the stands holding up a sign that read, "My cheating ex-boyfriend is watching from couch instead." As she watched her Packers roll 35-21, we can only imagine the cheater watching from his couch, looking down in shame.
Please feel free to send if you have any questions regarding this post , you can contact on
Disclaimer: The views expressed on this site are that of the authors and not necessarily that of U.S.S.POST.


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