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A unique mode of nucleic acid immunity performed by a single multifunctional enzyme The perpetual arms race between bacteria and their viruses (phages) has given rise to diverse immune systems, including restriction-modification and CRISPR-Cas, which sense and degrade phage-derived nucleic acids. These complex systems rely upon production and maintenance of multiple components to achieve anti-phage defense. However, the prevalence and effectiveness of much simpler, single-component systems that cleave DNA remain unknown. Here, we describe a novel mode of nucleic acid immunity performed by a single enzyme with nuclease and helicase activities, herein referred to as Nhi. This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses. Our observations support a model in which Nhi acts as both the sensor and effector to degrade phage-specific replication intermediates.
Importantly, Nhi homologs are distributed in diverse bacteria and exhibit functional conservation, highlighting the versatility of such compact weapons as major players in anti-phage defense.
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microbiology
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Voluntary motor commands are preferentially released during restricted sensorimotor beta rhythm phases Voluntary movement requires motor commands to be released from motor cortex (M1) and transmitted to spinal motoneurons and effector muscles. M1 activity oscillates between brief excitatory and inhibitory states that correlate with single neuron spiking rates. Here, we asked if the motor commands needed to produce voluntary, self-paced finger movements are preferentially released from M1 during restricted phases of this ongoing sensorimotor oscillatory activity. 21 healthy adults performed a self-paced finger movement task while EEG and EMG signals were recorded. For each finger movement, we identified the individual sensorimotor mu (8-12 Hz) and beta (13-35 Hz) oscillatory phase at the estimated time of motor command release from M1 by subtracting individually-defined MEP latencies from EMG-determined movement onset times. We report that motor commands were preferentially released at ~120{degrees} along the beta cycle but were released uniformly across the mu cycle. These results suggest that motor commands are preferentially released from M1 near optimal peak phases of endogenous beta rhythms.
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neuroscience
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Neuronal population dynamics during motor plan cancellation in non-human primates To understand the cortical neuronal dynamics behind movement generation and control most studies focused on tasks where actions were planned and then executed, using different instances of visuomotor transformations. However, to fully understand the dynamics related to movement control one must also study how movements are actively inhibited. Inhibition, indeed, represents the first level of control both when different alternatives are available and only one solution could be adopted, and when it is necessary to maintain the current position.
We recorded neuronal activity from a multielectrode array in the dorsal premotor (PMd) cortex of monkeys performing a countermanding reaching task that requires, in a subset of trials, to cancel a planned movement before its onset. In the analysis of the neuronal state-space of PMd we found a subspace in which activities conveying temporal information were confined during active inhibition and position holding. Movement execution required activities to escape from this subspace toward an orthogonal subspace and, furthermore, surpass a threshold associated with the maturation of the motor plan. These results revealed further details in the neuronal dynamics underlying movement control, extending the hypothesis that neuronal computation confined in an output-null subspace does not produce movements.
Significance StatementA core question in neuroscience is how the brain generates arm movements. Most studies have approached this issue by investigating the neuronal dynamics that accompany movement production, leaving unanswered the question of which aspects of this dynamics are logically necessary to make the movement. Here we explored this topic by characterizing the neuronal correlates of movement decisions between active inhibition and release of movements. We found that active inhibition and stillness require neuronal signals to be confined in a functional sub-space while actions depend on the transit of activities in an orthogonal space. This dynamics is characterized by a threshold mechanism finally allowing the translation of the motor plan into overt action.
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neuroscience
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Robust effects of corticothalamic feedback during naturalistic visual stimulation Neurons in the dorsolateral geniculate nucleus (dLGN) of the thalamus receive a substantial proportion of modulatory inputs from corticothalamic (CT) feedback and brain stem nuclei. Hypothesizing that these modulatory influences might be differentially engaged depending on the visual stimulus and behavioral state, we performed in vivo extracellular recordings from mouse dLGN while optogenetically suppressing CT feedback and monitoring behavioral state by locomotion and pupil dilation. For naturalistic movie clips, we found CT feedback to consistently increase dLGN response gain and promote tonic firing. In contrast, for gratings, CT feedback effects on firing rates were mixed. For both stimulus types, the neural signatures of CT feedback closely resembled those of behavioral state, yet effects of behavioral state on responses to movies persisted even when CT feedback was suppressed. We conclude that CT feedback modulates visual information on its way to cortex in a stimulus-dependent manner, but largely independently of behavioral state.
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neuroscience
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Influencing factors of telephone-cardiopulmonary resuscitation in China: a qualitative exploration based on managerial perspectives BackgroundTelephone-cardiopulmonary resuscitation(T-CPR) has been proven to systematically improve bystander CPR implementation and thus improve the survival rate of out-of-hospital cardiac arrest (OHCA) patients on a large scale. However, China has a lower proportion of cities that provide T-CPR than other countries.This study aimed to explore the factors affecting the providing of T-CPR based on managerial perspectives and promote the implementation of T-CPR in China to Protect human health.
MethodsThis study adopted a descriptive qualitative method.The managers from health bureau and first-aid Center were recruited to participate through purposive sampling. Data were collected using semi-structured interviews and Colaizzi 7-step analysis method was adopted to summarize and conclude the theme.
ResultsA total of 10 managers were interviewed.Five main themes were identified: (a) bystander factors, (b) dispatching factors, (c) legal factors, (d) guiding factors, and (e) financial factors.
ConclusionIt is urgent to promote the implementation of T-CPR in China.We can promote it by strengthening the training of bystanders in CPR knowledge and skills, developing T-CPR guidance process suitable for Chines national conditions, building an intelligent prehospital emergency system, promoting the legislation of first aid exemption, and providing financial support from various channels.
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systems biology
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Nuclear bundle/cable containing actin during yeast meiosis Actin polymerizes to form filaments/cables for motility, transport, and structural framework in a cell. Recent studies show that actin polymers are present not only in cytoplasm, but also in nuclei of vertebrate cells, and their formation is induced in response to stress. Here, by electron microscopic observation with rapid freezing and high-pressure freezing, we found a unique bundled structure containing actin in nuclei of budding yeast cells undergoing meiosis. The nuclear bundle/cable during meiosis consists of multiple filaments with a rectangular lattice arrangement often showing "feather-like" appearance. The bundle is immuno-labeled with anti-actin antibody and sensitive to an actin-depolymerizing drug. Like cytoplasmic bundles, nuclear bundles with actin are rarely seen in pre-meiotic cells and spores, and are induced during meiotic prophase-I. The formation of the nuclear bundles/cables is independent of meiotic DNA double-stranded breaks. We speculate that nuclear bundles/cables containing actin play a role in nuclear events during meiotic prophase I.
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cell biology
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Environmentally sensitive hotspots in the methylome of the early human embryo In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin specific methylation and germline DMRs, supporting a periconceptional environmental influence. Many SoC-sensitive CpGs overlapped enhancers or sites of active transcription in H1 ESCs and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental hotspots providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.
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genomics
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Overcoming coarse coding in visual cortex via multiplexing: neural correlations differ dramatically when stimulus bundles are presented Sensory receptive fields are large enough that they can contain more than one perceptible stimulus. How, then, can the brain encode information about each of the stimuli that may be present at a given moment? We recently showed that when more than one stimulus is present, single neurons can fluctuate between coding one vs. the other(s) across some time period, suggesting a form of neural multiplexing of different stimuli (Caruso et al., 2018). Here we investigate (a) whether such coding fluctuations occur in early visual cortical areas; (b) how coding fluctuations are coordinated across the neural population; and (c) how coordinated coding fluctuations depend on the parsing of stimuli into separate vs. fused objects. We found coding fluctuations do occur in V1 but only when the two stimuli form separate objects. Such separate objects evoked a novel pattern of V1 spike count ("noise") correlations involving distinct distributions of positive and negative values. This bimodal correlation pattern was most pronounced among pairs of neurons showing the strongest evidence for coding fluctuations or multiplexing. Whether a given pair of neurons exhibited positive or negative correlations depended on whether the two neurons both responded better to the same object or had different object preferences. Distinct distributions of spike count correlations based on stimulus preferences were also seen in V4 for separate objects but not when two stimuli fused to form one object. These findings suggest multiple objects evoke different response dynamics than those evoked by single stimuli, lending support to the multiplexing hypothesis and suggesting a means by which information about multiple objects can be preserved despite the apparent coarseness of sensory coding.
Significance StatementHow the brain separates information about multiple objects despite overlap in the neurons responsive to each item is not well understood. Here we show that some neurons in V1 exhibit coding fluctuations in response to two objects, and that these coding fluctuations are coordinated at the population level in ways that are not observed for single objects. Broadly similar results were obtained in V4. These response dynamics lend support to the hypothesis that information about individual objects may be multiplexed across the neural population, preserving information about each item despite the coarseness of sensory coding.
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neuroscience
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Hackflex: low cost Illumina Nextera Flex sequencing library construction We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower GC content, library construction methods were also tested on P. aeruginosa PAO1 and S. aureus ATCC25923, respectively. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per sample reagent cost for library prep of A$7.22 (USD$5.60), which is 9.87 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial.
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genomics
|
Mechanism of Interaction of BMP and Insulin Signaling in C. elegans Development and Homeostasis A small number of peptide growth factor ligands are used repeatedly in development and homeostasis to drive programs of cell differentiation and function. Cells and tissues must integrate inputs from these diverse signals correctly, while failure to do so leads to pathology, reduced fitness, or death. Previous work using the nematode C. elegans identified an interaction between the bone morphogenetic protein (BMP) and insulin/IGF-1-like signaling (IIS) pathways in the regulation of lipid homeostasis. The molecular components required for this interaction, however, were not known. Here we report that INS-4, one of 40 insulin-like peptides (ILPs), is regulated by BMP signaling to modulate fat accumulation. Furthermore, we find that the IIS transcription factor DAF-16/FoxO, but not SKN-1/Nrf, acts downstream of BMP signaling in lipid homeostasis. Interestingly, BMP activity alters sensitivity of these two transcription factors to IIS-promoted cytoplasmic retention in opposite ways. Finally, we probe the extent of BMP and IIS interactions by testing two additional IIS functions, dauer formation and autophagy induction. Coupled with our previous work and that of other groups, we conclude that BMP and IIS pathways have at least three modes of interaction: independent, epistatic, and antagonistic. The molecular interactions we identify provide new insight into mechanisms of signaling crosstalk and potential therapeutic targets for IIS-related pathologies such as diabetes and metabolic syndrome.
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cell biology
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The lipid kinase PI3Kα is required for the cohesion and survival of cancer cells disseminated in serous cavities. AO_SCPLOWBSTRACTC_SCPLOWBreast, ovarian, digestive and lung adenocarcinomas are often associated with the accumulation of malignant cells in serous cavities. As PI3K is one of the most mutated pathways in cancer, we investigated the importance of oncogenic PI3K in this process. We analyzed tumor cell organization in ascites from carcinomas at diagnosis. In some malignant ascites, tumor cells grew as adhesive coherent masses. Ex-vivo patient-derived cell cultures with the addition of mesenchymal stem cells, as a model of tumoral stroma, favored the compaction of tumorospheres. Ascites-derived ovarian cancer cell lines frequently harbored PIK3CA mutations coexisting with other mutations. PI3K promoted the formation and maintenance of multicellular adhesive PIK3CA-mutant spheroids, promoting cell survival. Cultures in 3D conditions as opposed to cultures in cell monolayers increased chemotherapy resistance, which was overcome by PI3K inhibition. We identified a signaling pathway of interest for the treatment of cancer cells disseminated in serous cavities, limiting cancer progression.
Graphical abstractSchematic representation of PI3K involvement in tumor cell aggregates from ascites. 1) Known involvement of PI3K in primary ovarian tumors. 2) PI3K participates in tumorosphere formation within the peritoneum (treatment with PI3K inhibitors causes a delay in the formation of clusters). 3) PI3K participates in the maintenance of tumorospheres and in resistance to conventional treatment for peritoneal carcinomatosis. PI3K is a target to prevent transcoelomic dissemination and maintenance of tumorospheres in patients with ovarian cancer.
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cancer biology
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HYPK scaffolds the Nedd8 and LC3 proteins to initiate formation of autophagosome around polyneddylated huntingtin exon1 aggregates Selective degradation of protein aggregates by autophagy is an essential homeostatic process of safeguarding cells from the effects of proteotoxicity. Among the ubiquitin-like modifier proteins, Nedd8 conjugation to misfolded proteins is prominent in stress-induced protein aggregates, albeit the function of neddylation in autophagy is unclear. Here, we report that polyneddylation functions as a post-translational modification for autophagic degradation of proteotoxic-stress induced protein aggregates. We also show that HYPK functions as an autophagy receptor in the polyneddylation-dependent aggrephagy. The scaffolding function of HYPK is facilitated by its C-terminal ubiquitin-associated domain and N-terminal tyrosine-type LC3 interacting region which bind to Nedd8 and LC3 respectively. Both Nedd8 and HYPK are positive modulators of basal and induced-autophagy, leading to desensitizing cells from protein aggregates, such as aggregates of mutant huntingtin-exon1. Thus, we propose an additive role of neddylation and HYPK in clearance of protein aggregates by autophagy, resulting in cytoprotective effect during proteotoxic stress.
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cell biology
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KIAA0319 influences cilia length, cell migration and mechanical cell-substrate interaction Following its association with dyslexia in multiple genetic studies, the KIAA0319 gene has been extensively investigated in different animal models but its function in neurodevelopment remains poorly understood.
We developed the first cellular knockout model for KIAA0319 via CRISPR-Cas9n to investigate its role in processes suggested but not confirmed in previous studies, including cilia formation and cell migration. We found that KIAA0319 knockout increased cilia length and accelerated cell migration. Using Elastic Resonator Interference Stress Microscopy (ERISM), we detected an increase in cellular force for the knockout cells that was restored by a rescue experiment. Combining ERISM and immunostaining we show that KIAA0319 depletion reduces the number of podosomes formed by the cells.
Our results suggest an involvement of KIAA0319 in cilia biology and force regulation and show for the first time that podosomes exert highly dynamic, piconewton vertical forces in epithelial cells.
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cell biology
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Hue tuning curves in V4 change with visual context Neurons are often probed by presenting a set of stimuli that vary along one dimension (e.g. color) and quantifying how this stimulus property affect neural activity. An open question, in particular where higher-level areas are involved, is how much tuning measured with one stimulus set reveals about tuning to a new set. Here we ask this question by estimating tuning to hue in macaque V4 from a set of natural scenes and a set of simple color stimuli. We found that hue tuning was strong in each dataset but was not correlated across the datasets, a finding expected if neurons have strong mixed selectivity. We also show how such mixed selectivity may be useful for transmitting information about multiple dimensions of the world. Our finding suggest that tuning in higher visual areas measured with simple stimuli may thus not generalize to naturalistic stimuli.
New & NoteworthyVisual cortex is often investigated by mapping neural tuning to variables selected by the researcher such as color. How much does this approach tell us a neurons general role in vision? Here we show that for strongly hue-tuned neurons in V4, estimating hue tuning from artificial stimuli does not reveal the hue tuning in the context of natural scenes. We show how models of optimal information processing suggest that such mixed selectivity maximizes information transmission.
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neuroscience
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A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences Isogenic cells cultured together show heterogeneity in their proliferation rate. To determine the differences between fast and slow-proliferating cells, we developed a method to sort cells by proliferation rate, and performed RNA-seq on slow and fast proliferating subpopulations of pluripotent mouse embryonic stem cells (mESCs) and mouse fibroblasts. We found that slowly proliferating mESCs have a more naive pluripotent character. We identified an evolutionarily conserved proliferation-correlated transcriptomic signature that is common to all eukaryotes: fast cells have higher expression of genes for protein synthesis and protein degradation. This signature accurately predicted growth rate in yeast and cancer cells, and identified lineage-specific proliferation dynamics during development, using C. elegans scRNA-seq data. In contrast, sorting by mitochondria membrane potential revealed a highly cell-type specific mitochondria-state related transcriptome. mESCs with hyperpolarized mitochondria are fast proliferating, while the opposite is true for fibroblasts. The mitochondrial electron transport chain inhibitor antimycin affected slow and fast subpopulations differently. While a major transcriptional-signature associated with cell-to-cell heterogeneity in proliferation is conserved, the metabolic and energetic dependency of cell proliferation is cell-type specific.
SynopsisBy performing RNA-seq on cells FACS sorted by their proliferation rate, this study identifies a gene expression signature capable of predicting proliferation rates in diverse eukaryotic cell types and species. This signature, applied to scRNAseq data from C.elegans, reveals lineage-specific differences in proliferation during development. In contrast to the universality of the proliferation signature, mitochondria and metabolism related genes show a high degree of cell-type specificity; mouse pluripotent stem cells (mESCs) and differentiated cells (fibroblasts) exhibit opposite relations between mitochondria state and proliferation. Furthermore, we identified a slow proliferating subpopulation of mESCs with higher expression of pluripotency genes. Finally, we show that fast and slow proliferating subpopulations are differentially sensitive to mitochondria inhibitory drugs in different cell types.
HighlightsO_LIA FACS-based method to determine the transcriptomes of fast and slow proliferating subpopulations.
C_LIO_LIA universal proliferation-correlated transcriptional signature indicates high protein synthesis and degradation in fast proliferating cells across cell types and species.
C_LIO_LIApplied to scRNA-seq, the expression signature predicts correctly the global slowdown in proliferation during C. elegans development, with lineage-specific exceptions.
C_LIO_LIMitochondria membrane potential predicts proliferation rate in a cell-type specific manner, with ETC complex III inhibitor having distinct effects on the proliferation of fibroblasts vs mESCs.
C_LI
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systems biology
|
Genetic and epigenetic characteristics associated with. the rapid radiation of Aquilegia species Elucidating the genetic and epigenetic bases underlying species diversification is crucial to understanding the evolution and persistence of biodiversity. As a well-known horticultural plant grown worldwide, the genus Aquilegia (columbine) is also a model system in adaptive radiation research. In this study, we surveyed the genomes and DNA methylomes of ten representative Aquilegia species from the Asian, European and North American lineages. Our inferences of the phylogenies and population structure revealed clearly high genetic and DNA methylomic divergence across the three lineages. By multi-levelled genome-wide scanning, we identified candidate genes exhibiting lineage-specific genetic or epigenetic variation patterns that are signatures of inter-specific divergence. We demonstrated that these species diversification-associated genetic variations and epigenetic variabilities were partially independent but were both functionally related to various biological processes vital to adaptation, including stress tolerance, cell reproduction and DNA repair. Our study provides an exploratory overview of how the established genetic and epigenetic signatures are associated with the rapid radiation of Aquilegia species.
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plant biology
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Gelsolin and dCryAB act downstream of muscle identity genes and contribute to preventing muscle splitting and branching in Drosophila A combinatorial code of identity transcription factors (iTFs) specifies the diversity of muscle types in Drosophila. We previously showed that two iTFs, Lms and Ap, play critical role in the identity of a subset of larval body wall muscles, the lateral transverse (LT) muscles. Intriguingly, a small portion of ap and lms mutants displays an increased number of LT muscles, a phenotype that recalls pathological split muscle fibers in human. However, genes acting downstream of Ap and Lms to prevent these aberrant muscle feature are not known. Here, we applied a cell type specific translational profiling (TRAP) to identify gene expression signatures underlying identity of muscle subsets including the LT muscles. We found that Gelsolin (Gel) and dCryAB, both encoding actin-interacting proteins, displayed LT muscle prevailing expression positively regulated by, the LT iTFs. Loss of dCryAB function resulted in LTs with irregular shape and occasional branched ends also observed in ap and lms mutant contexts. In contrast, enlarged and then split LTs with a greater number of myonuclei formed in Gel mutants while Gel gain of function resulted in unfused myoblasts, collectively indicating that Gel regulates LTs size and prevents splitting by limiting myoblast fusion. Thus, dCryAB and Gel act downstream of Lms and Ap and contribute to preventing LT muscle branching and splitting. Our findings offer first clues to still unknown mechanisms of pathological muscle splitting commonly detected in human dystrophic muscles and causing muscle weakness.
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developmental biology
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Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.
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microbiology
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SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns Human pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins. The splicing activity was assayed with a model HNRNPH1 pre-mRNA containing short 56-nucleotide intron. We identified a known alternative splicing regulator SPF45 (RBM17) as a constitutive splicing factor that is required to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells revealed that SPF45 is essential in the efficient splicing of many short introns. To initiate the spliceosome assembly on a short intron with the truncated poly-pyrimidine tract, the U2AF-homology motif (UHM) of SPF45 competes out that of U2AF65 for binding to the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.
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molecular biology
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X chromosome inactivation in the human placenta is patchy and distinct from adult tissues One of the X chromosomes in genetic females is silenced by a process called X chromosome inactivation (XCI). Variation in XCI across the placenta may contribute to observed sex differences and variability in pregnancy outcomes. However, XCI has predominantly been studied in human adult tissues. Here we sequenced and analyzed DNA and RNA from two locations from 30 full-term pregnancies. Implementing an allele specific approach to examine XCI, we report evidence that XCI in the human placenta is patchy, with large patches of either silenced maternal or paternal X chromosomes. Further, using similar measurements, we show that this is in contrast to adult tissues, which generally exhibit mosaic X-inactivation, where bulk samples exhibit both maternal and paternal X chromosome expression. Further, by comparing skewed samples in placenta and adult tissues, we identify genes that are uniquely silenced or expressed in the placenta compared to adult tissues highlighting the need for tissue-specific maps of XCI.
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genomics
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Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1 Glucose transporter GLUT1 is ubiquitously expressed in the human body from the red cells to the blood-brain barrier to the skeletal muscles. It is physiologically relevant to understand how GLUT1 facilitates diffusion of glucose across the cell membrane. It is also pathologically relevant because GLUT1 deficiency causes neurological disorders and anemia and because GLUT1 overexpression fuels the abnormal growth of cancer cells. This article presents a quantitative investigation of GLUT1 based on all-atom molecular-dynamics (MD) simulations of the transporter embedded in lipid bilayers of asymmetric inner-and-outer-leaflet lipid compositions, subject to asymmetric intra-and-extra-cellular environments. This is in contrast with the current literature of MD studies that have not considered both of the aforementioned asymmetries of the cell membrane. The equilibrium (unbiased) dynamics of GLUT1 shows that it can facilitate glucose diffusion across the cell membrane without undergoing large-scale conformational motions. The Gibbs free-energy profile, which is still lacking in the current literature of GLUT1, quantitatively characterizes the diffusion path of glucose from the periplasm, through an extracellular gate of GLUT1, on to the binding site, and off to the cytoplasm. This transport mechanism is validated by the experimental data that GLUT1 has low water-permeability, uptake-efflux symmetry, and 10 kcal/mol Arrhenius activation barrier around 37{degrees}C.
GRAPHICAL ABSTRACT (or TABLE OF CONTENTS ENTRY)
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biophysics
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Predictive Representations in Hippocampal and Prefrontal Hierarchies As we navigate the world, we use learned representations of relational structures to explore and to reach goals. Studies of how relational knowledge enables inference and planning are typically conducted in controlled small-scale settings. It remains unclear, however, how people use stored knowledge in continuously unfolding navigation, e.g., walking long distances in a city. We hypothesized that multiscale predictive representations guide naturalistic navigation, and these scales are organized along posterior-anterior prefrontal and hippocampal hierarchies. We conducted model-based representational similarity analyses of neuroimaging data measured during navigation of realistically long paths in virtual reality. We tested the pattern similarity of each point-along each path-to a weighted sum of its successor points within predictive horizons of different scales. We found that anterior PFC showed the largest predictive horizons, posterior hippocampus the smallest, with the anterior hippocampus and orbitofrontal regions in between. Our findings offer novel insights into how cognitive maps support hierarchical planning at multiple scales.
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neuroscience
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Oxidation shuts down an auto-inhibitory mechanism of von Willebrand factor The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. In particular, oxidation of methionine residues in specific domains of VWF due to the release of oxidants in inflammatory conditions has been linked to an increased platelet-binding activity. However, the atomistic details how methionine oxidation activates VWF have not been elucidated to date. Yet understanding the activation mechanism of VWF under oxidizing conditions can lead to the development of novel therapeutics that target VWF selectively under inflammatory conditions in order to reduce its thrombotic activity while maintaining its haemostatic function. In this manuscript, we used a combination of a dynamic flow assay and molecular dynamics (MD) simulations to investigate how methionine oxidation removes an auto-inhibitory mechanism of VWF. Results from the dynamic flow assay revealed that oxidation does not directly activate the A1 domain, which is the domain in VWF that contains the binding site to the platelet surface receptor glycoprotein Ib (GpIb), but rather removes the inhibitory function of the neighboring A2 and A3 domains. Furthermore, the MD simulations combined with free energy perturbation calculations suggested that methionine oxidation may destabilize the binding interface between the A1 and A2 domains leading to unmasking of the GpIb-binding site in the A1 domain.
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biophysics
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Evolution and development of male-specific leg brushes in Drosophilidae The origin, diversification, and secondary loss of sexually dimorphic characters are common in animal evolution. In some cases, structurally and functionally similar traits have evolved independently in multiple lineages. Prominent examples of such traits include the male-specific grasping structures that develop on the front legs of many dipteran insects. In this report, we describe the evolution and development of one of these structures, the male-specific "sex brush". The sex brush is composed of densely packed, irregularly arranged modified bristles and is found in several distantly related lineages in the family Drosophilidae. Phylogenetic analysis using 250 genes from over 200 species provides modest support for a single origin of the sex brush followed by many secondary losses; however, independent origins of the sex brush cannot be ruled out completely. We show that sex brushes develop in very similar ways in all brush-bearing lineages. The dense packing of brush hairs is explained by the specification of bristle precursor cells at a near-maximum density permitted by the lateral inhibition mechanism, as well as by the reduced size of the surrounding epithelial cells. In contrast to the female and the ancestral male condition, where bristles are arranged in stereotypical, precisely spaced rows, cell migration does not contribute appreciably to the formation of the sex brush. The complex phylogenetic history of the sex brush can make it a valuable model for investigating coevolution of sex-specific morphology and mating behavior.
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evolutionary biology
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Motor training improves coordination and anxiety in symptomatic Mecp2-null mice despite impaired functional connectivity within the motor circuit Rett Syndrome (RTT) is a severe neurodevelopmental disorder caused by loss of function of the X-linked Methyl-CpG-binding protein 2 (MECP2). Several case studies report that gross motor function can be improved in children with RTT through treadmill walking, but whether the MeCP2-deficient motor circuit can support actual motor learning remains unclear. We used two-photon calcium imaging to simultaneously observe layer (L) 2/3 and L5a excitatory neuronal activity in the motor cortex (M1) while mice adapted to changing speeds on a computerized running wheel. Despite circuit hypoactivity and weakened functional connectivity across L2/3 and L5a, the Mecp2-null circuits firing pattern evolved with improved performance over two weeks. Moreover, trained mice became less anxious and lived 20% longer than untrained mice. Since motor deficits and anxiety are core symptoms of Rett, which is not diagnosed until well after symptom onset, these results underscore the benefit of motor learning.
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neuroscience
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Connectome Constrained Graphical Models of MEG Coherence Structural connectivity by axonal fiber bundles provides the backbone for communication between neural populations. Since axonal transmission occurs on a millisecond time scale, measures of M/EEG functional connectivity sensitive to phase synchronization in a frequency band, such as coherence, are expected to reflect structural connectivity. We develop a complex-valued Gaussian Graphical Model (cGGM) of MEG coherence whose edges are constrained by the structural connectome. The cGGMs edge strengths are summarized by partial coherence, a measure of conditional dependence. We made use of the adaptive graphical lasso (AGL) to fit the cGGMs which allows us to perform inference on the hypothesis that the structural connectome is reflected in MEG coherence in a frequency band. In simulations, we demonstrate that the structural connectivitys influence on the cGGM can be inferred using the AGL. Further, we show that fitting the cGGM is superior to alternative methods at recovering the structural connectome. Graphical modeling of MEG coherence is robust to the source localization estimates required to map MEG from sensors to the cortex. Finally, we show how cG-GMs can be used to explore how distinct parts of the structural connectome contribute to MEG coherence in different frequency bands. We think the cGGM is a useful tool that can improve interpretation of MEG coherence by making a direct link to the structural connectome.
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neuroscience
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Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor The deletion of the third exon of the growth hormone receptor (GHR) is one of the most common genomic structural variants in the human genome. This deletion (GHRd3) has been linked to response to growth hormone, placenta size, birth weight, growth after birth, time of puberty, adult height, and longevity. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. Here, we analyzed thousands of genomes and provide evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals. However, it underwent a paradoxical adaptive reduction in frequency approximately 30 thousand years ago in East Asia that roughly corresponds with the emergence of archaeological evidence for multiple modern human behaviors, dramatic changes in climate, and a concurrent population expansion. Further, we provide evidence that GHRd3 is associated with protection from edematous severe acute malnutrition primarily in males. Using a mouse line engineered to contain the deletion, we found Ghrd3s effect on the liver transcriptome of male mice grown without any calorie restriction mimics response to calorie restriction through regulation of circadian pathways. In contrast, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers. As a likely consequence, the dramatic weight difference between male and female mice disappears among GHRd3 mice under calorie restriction. Our data provide evidence for sex- and environment-dependent effects of GHRd3 and are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.
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evolutionary biology
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Impact of early childhood malnutrition on the adult brain function: an ERP study According to the World Health Organization, 45% of deaths among children under five years of age are caused by malnutrition, which impacts more than 224 million children globally. The Barbados Nutrition Study (BNS) is a 50+ year longitudinal study on a Barbadian cohort with histories of moderate to severe protein-energy malnutrition (PEM) limited to the first year of life and a healthy comparison group. We have previously used quantitative electroencephalography (EEG) to highlight differences in brain function during childhood (lower alpha1 activity and higher theta, alpha2 and beta activity) between participants who suffered from early PEM and controls. In order to determine whether similar differences between the PEM and control groups persisted into adulthood, our current study used recordings obtained during a Go-No-Go task in a subsample of the original BNS cohort (N=53) at ages 45-51 years. We found that previously malnourished adults (n=24) had a higher rate of omission errors on the task relative to controls (n=29). Evoked-Related Potentials (ERP) were significantly different in participants with histories of early PEM, who presented with lower N2 amplitudes (p<0.05). These findings are typically associated with impaired conflict monitoring and/or attention deficits and may therefore be linked to the attentional and executive function deficits that have been previously reported in this cohort in childhood and again in middle-adulthood.
HighlightsO_LIChildhood malnutrition increases risk of brain function alterations.
C_LIO_LIThere is a need to investigate the evolution of those outcomes later in life.
C_LIO_LIAdults who suffered childhood malnutrition undertook a Go-No-Go task during EEG.
C_LIO_LITask performance and N2 amplitude were reduced in malnutrition group (vs control).
C_LIO_LIFirst evidence of adult brain function alteration following childhood malnutrition.
C_LI
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neuroscience
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Cortico-striatal activity driving compulsive reward seeking Addicted individuals compulsively seek drugs. Cortico-striatal projections have been implicated in persevering to seek rewards even when punished. The temporo-spatial determinants of the activity underlying the compulsive reward seeking however remains elusive. Here we trained mice in a seek-take chain, rewarded by optogenetic dopamine neuron self-stimulation (oDASS). Mice that persevered when seeking was punished, exhibited an increased AMPA/NMDA ratio selectively at orbitofrontal cortex (OFC) to dorsal striatum (DS) synapses. In addition, an activity peak of spiny projection neurons (SPNs) in the DS at the moment of signalled reward availability was detected. Chemogenetic inhibition of OFC neurons curbed the activity peak and reduced punished reward seeking, as did optogenetic hyperpolarization of SPNs time locked to the cue predicting reward availability, establishing a causal link. Taken together, we conclude that the strengthening of OFC-DS synapses drives SPNs activity when a reward predictive cue is delivered, thus encouraging reward seeking in subsequent trials.
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neuroscience
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Pulmonary acini exhibit complex changes during postnatal rat lung development Pulmonary acini represent the functional gas-exchanging units of the lung. Due to technical limitations, individual acini cannot be identified on microscopic lung sections. To overcome these limitations, we imaged the right lower lobes of instillation-fixed rat lungs from postnatal days P4, P10, P21, and P60 at the TOMCAT beamline of the Swiss Light Source synchrotron facility at a voxel size of 1.48 m. Individual acini were segmented from the three-dimensional data by closing the airways at the transition from conducting to gas exchanging airways. For a subset of acini (N=268), we followed the acinar development by stereologically assessing their volume and their number of alveoli. We found that the mean volume of the acini increases 23 times during the observed time-frame. The coeffcients of variation dropped from 1.26 to 0.49 and the difference between the mean volumes of the fraction of the 20 % smallest to the 20 % largest acini decreased from a factor of 27.26 (day 4) to a factor of 4.07 (day 60), i.e. shows a smaller dispersion at later time points. The acinar volumes show a very large variation early in lung development and homogenize during maturation of the lung by reducing their size distribution by a factor of 7 until adulthood. The homogenization of the acinar sizes hints at an optimization of the gas-exchange region in the lungs of adult animals and that acini of different size are not evenly distributed in the lungs. This likely leads to more homogeneous ventilation at later stages in lung development.
|
physiology
|
Visualization and Analysis of Whole Depot Adipose Tissue Neural Innervation Little is known about the diversity and function of adipose tissue nerves due, in part, to the inability to effectively visualize the various nerve subtypes residing within these tissues. The tools currently available for researchers to image and quantify adipose tissue innervation are limited and dependent on optical clearing techniques and light sheet microscopy. Here we present a method of tissue processing that uses mechanical force to compress tissue to decrease tissue thickness in the z-axis by expanding it in the x and y-axes whilst leaving cells intact. This has been combined with autofluorescence quenching techniques to permit intact whole tissues to be mounted on slides and imaged on any microscope, with a complementary means to perform whole tissue neurite density quantification. We have included examples of how this technique can be used to further our current knowledge of adipose-nerve communication by characterizing the nerves, nerve-subtypes, and neurovascular interactions within subcutaneous white adipose tissue in mice.
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neuroscience
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Spatially-explicit modeling improves empirical characterization of dispersal Dispersal is a key ecological process, but remains difficult to measure. By recording numbers of dispersed individuals at different distances from the source one can acquire a dispersal gradient. Although dispersal gradients contain information on dispersal, they are influenced by the spatial extent of the source. How can we separate the two contributions to extract knowledge on dispersal?
One could use a small, point-like source for which a dispersal gradient represents a dispersal kernel, which quantifies the probability of an individual dispersal event from a source to a destination point. However, the validity of this approximation cannot be established before conducting measurements.
We formulated a theory that incorporates the spatial extent of sources to estimate dispersal kernels from dispersal gradients. We re-analyzed published dispersal gradients for three major plant pathogens. We also demonstrated using simulations that this approach provides more accurate estimates of dispersal kernels across biologically plausible scenarios. We concluded that the three plant pathogens disperse over substantially shorter distances compared to conventional estimates. Using this method, a significant proportion of published dispersal gradients can be re-analyzed to improve our knowledge about spatial scales of dispersal. Thus, our results can boost progress in characterization of dispersal across taxa.
|
ecology
|
longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth Organs stop growing to achieve a characteristic size and shape in scale with the animals body. Likewise, regenerating organs sense injury extents to instruct appropriate replacement growth. Fish fins exemplify both phenomena through their tremendous diversity of form and remarkably robust regeneration. The classic zebrafish mutant longfint2 develops and regenerates dramatically elongated fins and underlying ray skeleton. We show longfint2 chromosome 2 overexpresses the ether-a-go-go-related voltage-gated potassium channel kcnh2a. Genetic disruption of kcnh2a in cis rescues longfint2, indicating longfint2 is a regulatory kcnh2a allele. We find longfint2 fin overgrowth originates from prolonged outgrowth periods including by showing Kcnh2a chemical inhibition during late stage regeneration fully suppresses overgrowth. Cell transplantations demonstrate longfint2-ectopic kcnh2a acts tissue autonomously within the fin intra-ray mesenchymal lineage. Temporal inhibition of the Ca2+-dependent phosphatase calcineurin indicates it likewise entirely acts late in regeneration to attenuate fin outgrowth. Epistasis experiments suggest longfint2-expressed Kcnh2a inhibits calcineurin output to supersede growth cessation signals. We conclude ion signaling within the growth-determining mesenchyme lineage controls fin size by tuning outgrowth periods rather than altering positional information or cell-level growth potency.
|
developmental biology
|
Ancestral mitochondrial apparatus derived from the bacterial type II secretion system The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion.
|
evolutionary biology
|
Cold exposure drives weight gain and adiposity following chronic suppression of brown adipose tissue Therapeutic activation of thermogenic brown adipose tissue (BAT) may be feasible to prevent, or treat, cardiometabolic disease. However, rodents are commonly housed below thermoneutrality ([~]20{degrees}C) which can modulate their metabolism and physiology including the hyperactivation of brown (BAT) and beige white adipose tissue. We housed animals at thermoneutrality from weaning to chronically supress BAT, mimic human physiology and explore the efficacy of chronic, mild cold-exposure and {beta}3-adrenoreceptor agonism under these conditions. Using metabolic phenotyping and exploratory proteomics we show that transfer from 28{degrees}C to 20{degrees}C drives weight gain and a 125% increase in subcutaneous fat mass, an effect not seen with YM-178 administration thus suggesting a direct effect of a cool ambient temperature in promoting weight gain and further adiposity in obese rats. Following chronic suppression of BAT, uncoupling protein 1 mRNA was undetectable in IWAT in all groups. Using exploratory adipose tissue proteomics, we reveal novel gene ontology terms associated with cold-induced weight gain in BAT and IWAT whilst Reactome pathway analysis highlights the regulation of mitotic (i.e. G2/M transition) and metabolism of amino acids and derivatives pathways. Conversely, YM-178 had minimal metabolic-related effects but modified pathways involved in proteolysis (i.e. eukaryotic translation initiation) and RNA surveillance across both tissues. Taken together these findings are indicative of a novel mechanism whereby animals increase body weight and fat mass following chronic suppression of adaptive thermogenesis from weaning. In addition, treatment with a B3-adrenoreceptor agonist did not improve metabolic health in obese animals raised at thermoneutrality.
|
physiology
|
A parametrized computational framework for description and design of genetic circuits of morphogenesis based on contact-dependent signaling and changes in cell-cell adhesion Synthetic development is a nascent field of research that uses the tools of synthetic biology to design genetic programs directing cellular patterning and morphogenesis in higher eukaryotic cells, such as mammalian cells. One specific example of such synthetic genetic programs was based on cell-cell contact-dependent signaling using synthetic Notch pathways, and was shown to drive formation of multilayered spheroids by modulating cell-cell adhesion via differential expression of cadherin-family proteins. The design method for these genetic programs relied on trial and error, which limited the number of possible circuits and parameter ranges that could be explored. Here we build a parametrized computational framework that, given a cellcell communication network driving changes in cell adhesion and initial conditions as inputs, predicts developmental trajectories. We first built a general computational framework where contact-dependent cell-cell signaling networks and changes in cell-cell adhesion could be designed in a modular fashion. We then use a set of available in vitro results (that we call the "training set" in analogy to similar pipelines in the machine learning field) to parametrize the computational model with values for adhesion and signaling. We then show that this parametrized model can qualitatively predict experimental results from a "testing set" of available in vitro data that varied the genetic network in terms of adhesion combinations, initial number of cells and even changes to the network architecture. Finally, this parametrized model is used to recommend novel network implementation for the formation of a 4-layered structure that has not been reported previously. The framework that we develop here could function as a testing ground to identify the reachable space of morphologies that can be obtained by controlling contact-dependent cell-cell communications and adhesion. Additionally, we discuss how the model could be expanded to include other forms of communication or effectors for the computational design of the next generation of synthetic developmental trajectories.
|
synthetic biology
|
Noncoding RNAs endogenously rule the cancerous regulatory realm while proteins govern the normal All cancers share a commonality in genome activation regulated by a systems endogenous network distinct from normal tissue, but such a network remains elusive. Here, we unearth a systems regulatory network endogenous for all types of cancers and normal human respectively from massive data, including all RNAseq data available from SRA and TCGA, and reveal distinctive systems realm for cancer and normal. In the cancerous realm, noncoding RNAs, especially pseudogenes, dominate endogenous network modules and centrality, and they work as the strongest systems inducers that cis-regulate their targets. However in the normal realm proteins dominate the entire endogenous network centrally controlled by ribosomal proteins and they trans-regulate their targets. Our finding establishes a systems picture of an endogenous mechanism overlooking the cancerous and normal realm, in which noncoding RNAs rule the overall cancer realm while proteins govern the normal one. This fundamentally refreshes the conventional concept of cancerous mechanism.
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genomics
|
Functional single-cell genomics of human cytomegalovirus infection The complex life cycle of herpesviruses is orchestrated by the interplay of host factors and hundreds of viral genes. Understanding how they work together and how perturbations of viral and host factors impact infection represents both a fundamental problem in virology and the basis for designing antiviral interventions. Here, we use CRISPR screening to comprehensively define the functional contribution of each viral and host factor to human cytomegalovirus (HCMV) infection in primary cells. We then record the transcriptomes of tens of thousands of single cells, and monitor how genetic perturbation of critical host and viral factors alters the timing, course, and progression of infection. We find that normally, the large majority of cells follow a stereotypical transcriptional trajectory. Perturbing critical host factors does not change this trajectory per se, but can either stall, delay or accelerate progression along the trajectory, allowing us to pinpoint systematically the stage of infection at which each host factor acts. Conversely, perturbation of viral factors can create distinct, abortive trajectories. Our results reveal a dichotomy between the roles of host and viral factors and more generally provide a road map for functional dissection of host-pathogen interactions.
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systems biology
|
Polygenic adaptation after a sudden change in environment Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Importantly, we describe the two phases of the allele dynamics: a rapid phase in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, which ultimately lead to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, our key results should hold in more general settings, and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.
|
evolutionary biology
|
Minimal DNA Electron Transfer Catalysts Switched by a Chaotropic Ion Here we demonstrate that a DNA nanodevice can perform switchable electron transfer. The nanodevice is comprised of two strands, one of which can be selectively switched between a G-quadruplex and duplex or single-stranded conformations. In the G-quadruplex state, it binds the cofactor hemin, enabling peroxidase activity. This switching ability arises from our discovery that perchlorate, a chaotropic Hofmeister ion, selectively destabilizes duplex over G-quadruplex DNA. By varying perchlorate concentration, we show that the device can be switched between states that do and do not catalyze electron transfer catalysis. State switching can be achieved in three ways: thermally, by dilution, or by concentration. In each case, when operated in the presence of the cofactor hemin, the device catalyzes electron transfer in only the G-quadruplex state.
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synthetic biology
|
Range expansion shifts clonal interference patterns in evolving populations Increasingly, predicting and even controlling evolutionary processes is a sought after goal in fields ranging from agriculture, artificial intelligence, astrobiology, oncology, and infectious diseases. However, our ability to predict evolution and plan such interventions in real populations is limited in part by our understanding of how spatial structure modulates evolutionary dynamics. Among current clinical assays applied to predict drug response in infectious diseases, for instance, many do not explicitly consider spatial structure and its influence on phenotypic heterogeneity, despite it being an inextricable characteristic of real populations. As spatially structured populations are subject to increased interference of beneficial mutants compared to their well-mixed counter-parts, among other effects, this population heterogeneity and structure may non-trivially impact drug response. In spatially-structured populations, the extent of this mutant interference is density dependent and thus varies with relative position within a meta-population in a manner modulated by mutant frequency, selection strength, migration speed, and habitat length, among other factors. In this study, we examine beneficial mutant fixation dynamics along the front of an asexual population expanding its range. We observe that multiple distinct evolutionary regimes of beneficial mutant origin-fixation dynamics are maintained at characteristic length scales along the front of the population expansion. Using an agent-based simulation of range expansion with mutation and selection in one dimension, we measure these length scales across a range of population sizes, selection strengths, and mutation rates. Furthermore, using simple scaling arguments to adapt theory from well-mixed populations, we find that the length scale at the tip of the front within which local mutant fixation occurs in a successive mode decreases with increasing mutation rate, as well as population size in a manner predicted by our derived analytic expression. Finally, we discuss the relevance of our findings to real cellular populations, arguing that this conserved region of successive mutant fixation dynamics at the wave tip can be exploited by emerging evolutionary control strategies.
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evolutionary biology
|
Lytic infection with murine gammaherpesvirus 68 activates host and viral RNA polymerase III-dependent promoters to enhance non-coding RNA expression RNA polymerase III (pol III) transcribes multiple non-coding (nc) RNAs that are essential for cellular function. Pol III-dependent transcription is also engaged during certain viral infections, including the gammaherpesviruses ({gamma}HVs), where pol III-dependent viral ncRNAs promote pathogenesis. Additionally, several host ncRNAs are upregulated during {gamma}HV infection and play integral roles in pathogenesis by facilitating viral establishment and gene expression. Here, we sought to investigate how pol III promoters and transcripts are regulated during gammaherpesvirus infection using the murine gammaherpesvirus 68 ({gamma}HV68) system. To compare the transcription of host and viral pol III-dependent ncRNAs, we analyzed a series of pol III promoters for host and viral ncRNAs using a luciferase reporter optimized to measure pol III activity. We measured promoter activity from the reporter gene at the translation level via luciferase activity and at the transcription level via RT-qPCR. We further measured endogenous ncRNA expression at single cell-resolution by flow cytometry. These studies demonstrated that lytic infection with {gamma}HV68 increased the transcription from multiple host and viral pol III promoters, and further identified the ability of accessory sequences to influence both baseline and inducible promoter activity after infection. RNA flow cytometry revealed the induction of endogenous pol III-derived ncRNAs that tightly correlated with viral gene expression. These studies highlight how lytic gammaherpesvirus infection alters the transcriptional landscape of host cells to increase pol III-derived RNAs, a process that may further modify cellular function and enhance viral gene expression and pathogenesis.
IMPORTANCEGammaherpesviruses are a prime example of how viruses can alter the host transcriptional landscape to establish infection. Despite major insights into how these viruses modify RNA polymerase II-dependent generation of messenger RNAs, how these viruses influence the activity of host RNA polymerase III remains much less clear. Small non-coding RNAs produced by RNA polymerase III are increasingly recognized to play critical regulatory roles in cell biology and virus infection. Studies of RNA polymerase III dependent transcription are complicated by multiple promoter types and diverse RNAs with variable stability and processing requirements. Here, we characterized a reporter system to directly study RNA polymerase III-dependent responses during gammaherpesvirus infection and utilized single-cell flow cytometry-based methods to reveal that gammaherpesvirus lytic replication broadly induces pol III activity to enhance host and viral non-coding RNA expression within the infected cell.
|
microbiology
|
Representation of Task Structure in Human Hippocampus and Orbitofrontal Cortex The hippocampus is thought to support episodic memory, or memory for specific events, but recent work also suggests that it may be involved in extracting structure from the world to guide future decisions and predictions. Recent evidence in rodents suggests that the hippocampus supports decision-making in cooperation with orbitofrontal cortex (OFC), possibly based on representation of task structure. Here, we used functional magnetic resonance imaging (fMRI) to test how the human hippocampus and OFC represents decision-relevant information extracted from previous experiences. Participants performed a task in which they learned values of different foods in grocery store contexts. The task was structured such that we could examine the degree to which neural representations could reflect generalized information about different task structures. Specifically, we manipulated whether a foods desirability varied with store context or not. Some foods were desirable in some store contexts and not in others; some foods were always desirable or undesirable. Participants needed to extract these two task sub-structures (i.e., context-determined vs. context-invariant) from the task structure. We examined hippocampal and OFC activity patterns during a decision-making task after participants were trained with the task structure. Our results showed that both hippocampus and OFC carried task structure information that was relevant to the decision outcomes. Hippocampal and lateral OFC representations differentiated between context-determined (deterministic) and context-invariant (probabilistic) task structures. The degree of this differentiation, an index of task structure representation, was highly correlated between hippocampus and lateral OFC. These results add to a mounting evidence suggesting that the hippocampus and OFC support decision-making by representing task relevant information to the decision outcomes after the task structure is learned.
|
neuroscience
|
Replacement of microglia by brain-engrafted macrophages provide protection against concussive injury Brain resident microglia have a distinct origin compared to macrophages in other organs. Under physiological conditions, microglia are maintained by self-renewal from the local pool, independent of hematopoietic progenitors. Pharmacological depletion of microglia during therapeutic whole-brain irradiation prevents synaptic loss and long-term recognition memory deficits but the mechanisms behind these protective effects are unknown. Here we demonstrate that after a combination of therapeutic whole-brain irradiation and microglia depletion, macrophages originating from circulating monocytes engraft into the brain and replace the microglia pool. Comparisons of transcriptomes reveal that brain-engrafted macrophages have an intermediate phenotype that resembles both monocytes and embryonic microglia. Brain-engrafted macrophages display reduced phagocytic activity for synaptic compartments compared to microglia from normal brains in response to a secondary concussive brain injury. In addition to sparing mice from brain radiotherapy-induced long-term cognitive deficits, replacement of microglia by brain-engrafted macrophages can prevent concussive injury-induced memory loss. These results demonstrate the long-term functional role of brain-engrafted macrophages as a possible therapeutic tool against radiation-induced cognitive deficits.
|
neuroscience
|
Context-invariant neural dynamics underlying the encoding of Bayesian uncertainty, but not confidence Classic decision theories, such as reinforcement learning, typically require the presence of explicit outcomes for learning and belief updating. However, ecological environments are often opaque and explicit feedback, such as those based on values, might not be immediately accessible. It remains unclear whether the neural dynamics underlying belief updating in absence of outcomes differ from those responsible for decision-making based on accessible outcomes. Here, we investigated this question in healthy humans (n=28) using Bayesian modeling and two multi-option fMRI tasks, one with and one without immediate outcome. Model-based fMRI analysis revealed two opposing networks encoding belief updating regardless of the presence of immediate outcomes. A "confidence-building" network including the hippocampus, amygdala, and medial prefrontal cortex (mPFC) became more active as beliefs about action-outcome probabilities were confirmed by newly acquired information. Meanwhile, an "uncertainty-building" network including the anterior insular (AIC), dorsal anterior cingulate (dACC), and dorsolateral prefrontal (dlPFC) cortices became more active as new evidence conflicted with action-outcome estimates. Interestingly, dynamic causal modeling revealed that the confidence network was driven either by the hippocampus when outcomes were not available, or by the mPFC and amygdala when value-based outcomes were immediately accessible. Convsersely, the AIC always drove the activities of dACC and dlPFC, under the modulation of increasing uncertainty, independent of outcome availability. These findings reveal similar network compositions but distinct neural dynamics underlying belief updating in changing environments with and without explicit outcomes, highlighting an asymmetric relationship between decision confidence and uncertainty computation across levels of analysis.
HighlightsO_LIWe investigated belief updating in two tasks, with and without explicit feedback.
C_LIO_LIModel-based fMRI analysis revealed similar neural responses across tasks.
C_LIO_LIThe anterior insula drove an uncertainty-encoding network, across tasks.
C_LIO_LIThe anterior hippocampus drove a confidence-encoding network, w/o feedbacks.
C_LIO_LIThe medial PFC and amygdala drove a confidence-encoding network, with feedbacks.
C_LI
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neuroscience
|
Platinum chemotherapy induces lymphangiogenesis in cancerous and healthy tissues that can be prevented with adjuvant anti-VEGFR3 therapy Chemotherapy has been used to inhibit cancer growth for decades, but emerging evidence shows it can affect the tumor stroma unintentionally promoting cancer malignancy. After treatment of primary tumors, remaining drugs drain via lymphatics. Though all drugs interact with the lymphatics, we know little of their impact on them. Here, we show a previously unknown effect of platinums, a widely used class of chemotherapeutics, to directly induce systemic lymphangiogenesis and activation. These changes are dose-dependent, long-lasting, and occur in healthy and cancerous tissue in multiple mouse models of breast cancer. We saw similar effects in human ovarian and breast cancer patients whose treatment regimens included platinums. Carboplatin treatment of healthy mice prior to mammary tumor inoculation increases cancer metastasis as compared to no pre-treatment. These platinum-induced phenomena could be blocked by VEGFR3 inhibition. These findings have implications for cancer patients receiving platinums and may support the inclusion of anti-VEGFR3 therapy into treatment regimens or differential design of treatment regimens to alter these potential effects.
SummaryPlatinum chemotherapy induces VEGFR3-dependent lymphangiogenesis, priming tissues for metastasis of breast cancer. Inhibition of VEGFR3 via antibody blockade can reverse these effects.
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cancer biology
|
Amitosis confers benefits of sex in the absence of sex to Tetrahymena Sex appears to be the most successful reproductive strategy in eukaryotes despite its many costs. While a complete explanation for sexs success remains elusive, several evolutionary benefits of sex have been identified. It is predicted that, by forgoing these benefits, asexual lineages are evolutionary dead-ends. Consistent with this prediction, many asexual lineages show signs of accelerated accumulation of deleterious mutations compared to their sexual relatives. Despite these low expectations, some asexual eukaryotic lineages appear to be successful, including the ciliate Tetrahymena. Here, we show that the mechanism of somatic nuclear division in Tetrahymena, known as amitosis, provides benefits similar to sex, allowing for the long-term success of asexual lineages. We found that, when compared to mitosis, amitosis with chromosome copy number control reduces mutation load deterministically, slows the accumulation of deleterious mutations under genetic drift, and accelerates adaptation. These benefits arise because, like sex, amitosis can generate substantial genetic variation in fitness among (asexual) progeny. Our results indicate that the ability of Tetrahymena to persist in the absence of sex may depend on non-sexual genetic mechanisms conferring benefits typically provided by sex, as has been found in other asexual lineages.
|
evolutionary biology
|
Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- versus trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- versus trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
|
evolutionary biology
|
Reduction of insulin/IGF-1 receptor rejuvenates immunity via positive feedback circuit Immunosenescence is considered an inevitable decline in immune function during aging. Here we show that genetic inhibition of the DAF-2/insulin/IGF-1 receptor drastically delays immunosenescence and rejuvenates immunity in C. elegans. We find that p38 mitogen-activated protein kinase 1 (PMK-1), a key determinant of immunosenescence, is dispensable for this rejuvenated immunity. Instead, we demonstrate that longevity-promoting DAF-16/FOXO and heat-shock transcription factor 1 (HSF-1) increase immunocompetence in old daf-2(-) animals. The upregulation of DAF-16/FOXO and HSF-1 decreases the expression of the zip-10/bZIP transcription factor, which in turn downregulates INS-7, an agonistic insulin-like peptide, resulting in further reduction of insulin/IGF-1 signaling (IIS). Thus, reduced IIS bypasses immunosenescence and rejuvenates immunity via the upregulation of anti-aging transcription factors that modulate an endocrine insulin-like peptide through a positive feedback mechanism. Because many functions of IIS are conserved across phyla, our study may lead to the development of strategies for human immune rejuvenation.
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genetics
|
Structural and Dynamic Insights Into α-Synuclein Dimer Conformations Parkinsons disease is associated with the aggregation of the protein -synuclein. While -synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate -synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers we identify one that is compact, stable, abundant, and exhibits partially exposed {beta}-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in a proximity that can promote dityrosine covalent linkage implicated in amyloidogenesis. We propose that this -synuclein dimer features etiological relevance to Parkinsons disease.
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biophysics
|
A proximity-dependent biotinylation map of a human cell: an interactive web resource Compartmentalization is a defining characteristic of eukaryotic cells, partitioning cellular processes into discrete subcellular locations. High throughput microscopy1 and biochemical fractionation coupled with mass spectrometry2-6 have helped to define the proteomes of a variety of organelles and macromolecular structures. However, many other intracellular compartments have remained refractory to such approaches, due for example to difficulty in purifying non-membrane bound structures. Proximity-dependent biotinylation techniques such as BioID provide an alternative approach for defining the composition of cellular compartments in living cells7-10. Here we present a BioID-based map of a human cell based on 192 markers from 32 different subcellular compartments, comprising 35,902 high confidence proximity interactions, and defining the intracellular locations of 4,145 unique proteins in HEK 293 cells. Our localization predictions meet or exceed previous-approaches, with higher specificity, and enabled the discovery of proteins at the mitochondrial outer membrane-endoplasmic reticulum (ER) interface that are critical for mitochondrial homeostasis. Based on this dataset, we have established humancellmap.org as a community resource that provides online tools for localization analysis of user BioID data, and demonstrate how this resource can be used to better understand BioID datasets.
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molecular biology
|
CDR3 binding chemistry controls TCR V-domain rotational probability and germline CDR2 'scanning' of polymorphic MHC The mechanism which adapts the T-cell antigen receptor (TCR) within a given major histocompatibility complex (MHC/HLA) genotype is essential for protection against pathogens. Historically attributed to relative affinity, genetically vast TCRs are surprisingly focused towards a micromolar affinity for their respective peptide (p) plus MHC (pMHC) ligands. Thus, the somatic diversity of the TCR with respect to MHC-restriction, and (ultimately) to pathogens, remains enigmatic. Here, we derive a triple integral solution (from fixed geometry) for any given V domain in TCR bound to pMHC. Solved complexes involving HLA-DR and HLA-DQ, where genetic linkage to the TCR is most profound, were examined in detail. Certain V domains displayed rare geometry within this panel--specifying a restricted rotational probability/volumetric density (dV). Remarkably, hydrogen (H) bond charge-relays distinguished these structures from the others; suggesting that CDR3 binding chemistry dictates CDR2 contacts on the opposite MHC-II alpha helix. Together, these data suggest that TCR recapitulate dV and specialise target pMHC recognition.
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immunology
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Estrogen Drives Melanocortin Neurons To Increase Spontaneous Activity and Reduce Sedentary Behavior Estrogen depletion in rodents and humans leads to inactivity, unhealthy fat accumulation, and diabetes1,2, underscoring the conserved metabolic benefits of estrogen that inevitably decline with aging. In rodents, the preovulatory surge in 17{beta}-estradiol (E2) temporarily allows energy expenditure to outpace energy intake, thus coordinating increased physical activity with peak sexual receptivity. To investigate how estrogen rebalances energy allocation in females, we examine estrogen receptor alpha (ER) signaling in the ventrolateral ventromedial hypothalamic nucleus (VMHvl)3-7. We uncover a small population of VMHvlER neurons expressing the melanocortin-4 receptor (MC4R) that integrates estrogen and melanocortin signals and projects to arousal centers in the hippocampus and hindbrain, enabling bursts of physical activity. ER recruitment to the Mc4r gene promotes upregulation of Mc4r in VMHvl neurons during the preovulatory surge or following E2 treatment. We leveraged three models to stimulate VMHvlMC4R neurons, restore MC4R signaling in the VMHvl of hyperphagic MC4R null females, or increase Mc4r levels in the VMHvl by CRISPR-mediated activation. All models increase spontaneous activity, whereas silencing VMHvlMC4R neurons blunts normal activity. Direct activation of the VMHvlMC4R node overrides the inactivity and hypometabolism following hormone depletion. These data extend the impact of MC4R signaling - the most common cause of monogenic human obesity8 - beyond the regulation of food intake. Our findings also rationalize reported sex differences in melanocortin signaling, including the greater disease severity of MC4R insufficiency in women9. The hormone-dependent node identified here illuminates the power of estrogen in motivating behavior during the female reproductive cycle and for maintaining an active lifestyle.
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neuroscience
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An experimentally-derived measure of inter-replicate variation in reference samples: the same-same permutation methodology The multiple testing problem is a well-known statistical stumbling block in high-throughput data analysis, where large scale repetition of statistical methods introduces unwanted noise into the results. While approaches exist to overcome the multiple testing problem, these methods focus on theoretical statistical clarification rather than incorporating experimentally-derived measures to ensure appropriately tailored analysis parameters. Here, we introduce a method for estimating inter-replicate variability in reference samples for a quantitative proteomics experiment using permutation analysis. This can function as a modulator to multiple testing corrections such as the Benjamini-Hochberg ordered Q value test. We refer to this as a same-same analysis, since this method incorporates the use of six biological replicates of the reference sample and determines, through non-redundant triplet pairwise comparisons, the level of quantitative noise inherent within the system. The method can be used to produce an experiment-specific Q value cut-off that achieves a specified false discovery rate at the quantitation level, such as 1%. The same-same method is applicable to any experimental set that incorporates six replicates of a reference sample. To facilitate access to this approach, we have developed a same-same analysis R module that is freely available and ready to use via the internet.
|
biochemistry
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Sugars dominate the seagrass rhizosphere Seagrasses are one of the most efficient sinks of carbon dioxide on Earth1: They bury carbon 35 times faster than tropical rainforests on a per unit area basis2. While we know that carbon sequestration in terrestrial plants is intimately linked to the microorganisms living in their soils3-6, the interactions of seagrasses with their rhizospheres are poorly understood. We show that three seagrass species from two oceans excrete simple sugars, mainly sucrose, into their rhizosphere that accumulate to over 200 {micro}M. Such high concentrations are at least 80 times higher than previously observed in the ocean, and surprising, as sugars are quickly consumed by microorganisms. In situ analyses and incubation experiments indicated that phenolic compounds from the seagrass inhibited microbial consumption of sucrose. Metagenomic and metatranscriptomic analyses of the microbial communities in the seagrass rhizosphere revealed that many members had the genes for degrading sucrose, but these were only expressed by a few specialists that also expressed genes for degrading phenolics. Our results explain why sucrose accumulates under seagrass meadows, where it comprises as much as 40% of the dissolved organic carbon. Destruction of extant seagrass canopies would allow sediment microorganisms to consume the tremendous deposits of sucrose buried underneath their meadows, thereby releasing large amounts of CO2 into the oceans and atmosphere.
|
microbiology
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Multiphoton imaging of neural structure and activity in Drosophila through the intact cuticle We developed a multiphoton imaging method to capture neural structure and activity in behaving flies through the intact cuticles. Our measurements show that the fly head cuticle has surprisingly high transmission at wavelengths > 900 nm, and the difficulty of through-cuticle imaging is due to the air sacs and/or fat tissue underneath the head cuticle. By compressing the air sacs, we performed deep multiphoton imaging of fly brains through the intact cuticle. Our anatomical and functional imaging results show that 2- and 3-photon imaging are comparable in superficial regions such as the mushroom body, but 3-photon imaging is superior in deeper regions such as the central complex and beyond. We further demonstrated 2-photon through-cuticle functional imaging of odor-evoked calcium responses from the mushroom body {gamma}-lobes in behaving flies short-term and long-term (12 consecutive hours). The through-cuticle imaging method developed here extends the time limits of in vivo imaging in flies, and opens up new ways to capture neural structure and activity from the intact fly brain.
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neuroscience
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A multilayer network model of neuron-astrocyte populations in vitro reveals mGluR5 inhibition is protective following traumatic injury Astrocytes communicate bidirectionally with neurons, enhancing synaptic plasticity and promoting the synchronization of neuronal microcircuits. Despite recent advances in understanding neuron-astrocyte signaling, little is known about astrocytic modulation of neuronal activity at the population level, particularly in disease or following injury. We used high-speed calcium imaging of mixed cortical cultures in vitro to determine how population activity changes after disruption of glutamatergic signaling and mechanical injury. We constructed a multilayer network model of neuron-astrocyte connectivity, which captured distinct topology and response behavior from single cell type networks. mGluR5 inhibition decreased neuronal activity, but did not on its own disrupt functional connectivity or network topology. In contrast, injury increased the strength, clustering, and efficiency of neuronal but not astrocytic networks, an effect that was not observed in networks pre-treated with mGluR5 inhibition. Comparison of spatial and functional connectivity revealed that functional connectivity is largely independent of spatial proximity at the microscale, but mechanical injury increased the spatial-functional correlation. Finally, we found that astrocyte segments of the same cell often belong to separate functional communities based on neuronal connectivity, suggesting that astrocyte segments function as independent entities. Our findings demonstrate the utility of multilayer network models for characterizing the multiscale connectivity of two distinct but functionally dependent cell populations.
AUTHOR SUMMARYAstrocytes communicate bidirectionally with neurons, enhancing synaptic plasticity and promoting the synchronization of neuronal microcircuits. We constructed a multilayer network model of neuron-astrocyte connectivity based on calcium activity in mixed cortical cultures, and used this model to evaluate the effect of glutamatergic inhibition and mechanical injury on network topology. We found that injury increased the strength, clustering, and efficiency of neuronal but not astrocytic networks, an effect that was not observed in injured networks pre-treated with a glutamate receptor antagonist. Our findings demonstrate the utility of multilayer network models for characterizing the multiscale connectivity of two distinct but functionally dependent cell populations.
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neuroscience
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Visual discrimination of optical material properties: a large-scale study Complex visual processing involved in perceiving the object materials can be better elucidated by taking a variety of research approaches. Sharing stimulus and response data is an effective strategy to make the results of different studies directly comparable and can assist researchers with different backgrounds to jump into the field. Here, we constructed a database containing several sets of material images annotated with visual discrimination performance. We created the material images using physically-based computer graphics techniques and conducted psychophysical experiments with them in both laboratory and crowdsourcing settings. The observers task was to discriminate materials on one of six dimensions (gloss contrast, gloss distinctness-of-image, translucent vs. opaque, metal vs. plastic, metal vs. glass, and glossy vs. painted). The illumination consistency and object geometry were also varied. We used a non-verbal procedure (an oddity task) applicable for diverse use-cases such as cross-cultural, cross-species, clinical, or developmental studies. Results showed that the material discrimination depended on the illuminations and geometries and that the ability to discriminate the spatial consistency of specular highlights in glossiness perception showed larger individual differences than in other tasks. In addition, analysis of visual features showed that the parameters of higher-order color texture statistics can partially, but not completely, explain task performance. The results obtained through crowdsourcing were highly correlated with those obtained in the laboratory, suggesting that our database can be used even when the experimental conditions are not strictly controlled in the laboratory. Several projects using our dataset are underway.
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neuroscience
|
High and stable ATP levels prevent aberrant intracellular protein aggregation ATP at millimolar levels has recently been implicated in the solubilization of cellular proteins. However, the significance of this high ATP level under physiological conditions and the mechanisms that maintain ATP remain unclear. We herein demonstrated that AMP-activated protein kinase (AMPK) and adenylate kinase (ADK) cooperated to maintain cellular ATP levels regardless of glucose levels. Single cell imaging of ATP-reduced yeast mutants revealed that ATP levels in these mutants repeatedly underwent stochastic and transient depletion, which induced the cytotoxic aggregation of endogenous proteins and pathogenic proteins, such as huntingtin and -synuclein. Moreover, pharmacological elevations in ATP levels in an ATP-reduced mutant prevented the accumulation of -synuclein aggregates and its cytotoxicity. The removal of cytotoxic aggregates depended on proteasomes, and proteasomal activity cooperated with AMPK or ADK to resist proteotoxic stresses. The present study is the first to demonstrate that cellular ATP homeostasis ensures proteostasis and revealed that suppressing the high volatility of cellular ATP levels prevented cytotoxic protein aggregation, implying that AMPK and ADK are important factors that prevent proteinopathies, such as neurodegenerative diseases.
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cell biology
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High resolution, dynamic imaging of early mouse and human liver bud morphogenesis in three dimensions BackgroundLiver organogenesis has thus far served as a paradigm for solid organ formation. The developing liver bud is a well established model of organogenesis, and murine genetic studies demonstrate key molecules involved in key morphogenetic changes. However, the analysis of the liver bud is typically limited to 2D tissue sections, which precludes extensive visualization, quantitation, and analysis. Further, the lack of human liver bud data has further hindered our understanding of human liver organogenesis. Therefore, new analytical and visualization approaches are needed to elicit further morphogenetic details of liver organogenesis and to elucidate differences between mouse and human liver bud growth.
ResultsTo address this need, we focused on high resolution imaging, visualization, and analysis of early liver growth by using available online databases for both mouse (EMAP, Toronto Phenogenomics center) and human (3D Atlas of Human Embryology), noninvasive multimodality imaging studies of the murine embryo, and mouse/human liver weight data. First, we performed three-dimensional (3D reconstructions) of stacked, digital tissue sections that had been initially segmented for the liver epithelium and the septum transversum mesenchyme (STM). 3D reconstruction of both mouse and human data sets enabled visualization and analysis of the dynamics of liver bud morphogenesis, including hepatic cord formation and remodeling, mechanisms of growth, and liver-epithelial STM interactions. These studies demonstrated potentially under-appreciated mechanisms of growth, including rapid exponential growth that is matched at the earliest stages by STM growth, and unique differences between mouse and human liver bud growth. To gain further insight into the exponential liver bud growth that was observed, we plotted volumetric data from 3D reconstruction together with fetal liver growth data from multimodality (optical projection tomography, magnetic resonance imaging, micro-CT) and liver weight data to compose complete growth curves during mouse (E8.5-E18) and human (day 25-300) liver development. For further analysis, we performed curve fitting and parameter estimation, using Gompertzian models, which enables the comparison between mouse and human liver bud growth, as well as comparisons to processes like liver regeneration. To demonstrate the importance of mesenchyme in rapid liver bud growth and morphogenesis in the human liver bud, we performed functional analysis in which human pluripotent stem cell (hPSC)-derived hepatic organoids were used to model collective migration that occurs in vivo, demonstrating that migration is strongly dependent upon mesenchyme.
DiscussionOur data demonstrates improved visualization with 3D images, under-appreciated and potentially new mechanisms of growth, complete liver growth curves with quantitative analysis through embryonic and fetal stages, and a new functional human stem cell-derived liver organoid assay demonstrating mesenchyme-driven collective migration. These data enhance our understanding of liver organogenesis.
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developmental biology
|
Eliminating accidental deviations to minimize generalization error and maximize replicability: applications in connectomics and genomics Replicability, the ability to replicate scientific findings, is a prerequisite for scientific discovery and clinical utility. Troublingly, we are in the midst of a replicability crisis. A key to replicability is that multiple measurements of the same item (e.g., experimental sample or clinical participant) under fixed experimental constraints are relatively similar to one another. Thus, statistics that quantify the relative contributions of accidental deviations--such as measurement error--as compared to systematic deviations--such as individual differences--are critical. We demonstrate that existing replicability statistics, such as intra-class correlation coefficient and fingerprinting, fail to adequately differentiate between accidental and systematic deviations in very simple settings. We therefore propose a novel statistic, discriminability, which quantifies the degree to which an individuals samples are relatively similar to one another, without restricting the data to be univariate, Gaussian, or even Euclidean. Using this statistic, we introduce the possibility of optimizing experimental design via increasing discriminability and prove that optimizing discriminability improves performance bounds in subsequent inference tasks. In extensive simulated and real datasets (focusing on brain imaging and demonstrating on genomics), only optimizing data discriminability improves performance on all subsequent inference tasks for each dataset. We therefore suggest that designing experiments and analyses to optimize discriminability may be a crucial step in solving the replicability crisis, and more generally, mitigating accidental measurement error.
Author SummaryIn recent decades, the size and complexity of data has grown exponentially. Unfortunately, the increased scale of modern datasets brings many new challenges. At present, we are in the midst of a replicability crisis, in which scientific discoveries fail to replicate to new datasets. Difficulties in the measurement procedure and measurement processing pipelines coupled with the influx of complex high-resolution measurements, we believe, are at the core of the replicability crisis. If measurements themselves are not replicable, what hope can we have that we will be able to use the measurements for replicable scientific findings? We introduce the "discriminability" statistic, which quantifies how discriminable measurements are from one another, without limitations on the structure of the underlying measurements. We prove that discriminable strategies tend to be strategies which provide better accuracy on downstream scientific questions. We demonstrate the utility of discriminability over competing approaches in this context on two disparate datasets from both neuroimaging and genomics. Together, we believe these results suggest the value of designing experimental protocols and analysis procedures which optimize the discriminability.
|
neuroscience
|
Sequential and efficient neural-population coding of complex task information Recent work has highlighted that many types of variables are represented in each neocortical area. How can these many neural representations be organized together without interference, and coherently maintained/updated through time? We recorded from large neural populations in posterior cortices as mice performed a complex, dynamic task involving multiple interrelated variables. The neural encoding implied that correlated task variables were represented by uncorrelated neural-population modes, while pairs of neurons exhibited a variety of signal correlations. This finding relates to principles of efficient coding for task-specific information, with neural-population modes as the encoding unit, and applied across posterior cortical regions and layers 2/3 and 5. Remarkably, this encoding function was multiplexed with sequential neural dynamics as well as reliably followed changes in task-variable correlations through time. We suggest that neural circuits can implement time-dependent encoding in a simple way by using random sequential dynamics as a temporal scaffold.
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neuroscience
|
Effect of number and placement of EEG electrodes onmeasurement of neural tracking of speech Measurement of neural tracking of natural running speech from the electroencephalogram (EEG) is an increasingly popular method in auditory neuroscience and has applications in audiology. The method involves decoding the envelope of the speech signal from the EEG signal, and calculating the correlation with the envelope of the audio stream that was presented to the subject. Typically EEG systems with 64 or more electrodes are used. However, in practical applications, set-ups with fewer electrodes are required. Here, we determine the optimal number of electrodes, and the best position to place a limited number of electrodes on the scalp. We propose a channel selection strategy based on an utility metric, which allows a quick quantitative assessment of the influence of a channel (or a group of channels) on the reconstruction error. We consider two use cases: a subject-specific case, where the optimal number and position of the electrodes is determined for each subject individually, and a subject-independent case, where the electrodes are placed at the same positions (in the 10-20 system) for all the subjects. We evaluated our approach using 64-channel EEG data from 90 subjects. In the subject-specific case we found that the correlation between actual and reconstructed envelope first increased with decreasing number of electrodes, with an optimum at around 20 electrodes, yielding 29% higher correlations using the optimal number of electrodes compared to all electrodes. This means that our strategy of removing electrodes can be used to improve the correlation metric in high-density EEG recordings. In the subject-independent case, we obtained a stable decoding performance when decreasing from 64 to 22 channels. When the number of channels was further decreased, the correlation decreased. For a maximal decrease in correlation of 10%, 32 well-placed electrodes were sufficient in 91% of the subjects.
|
neuroscience
|
Cell cycle-dependent active stress drives epithelia remodeling Epithelia have distinct cellular architectures, which are established in development, re-established after wounding, and maintained during tissue homeostasis despite cell turnover and mechanical perturbations. In turn, cell shape also controls tissue function as a regulator of cell differentiation, proliferation, and motility. Here we investigate cell shape changes in a model epithelial monolayer. After the onset of confluence, cells continue to proliferate and change shape over time, eventually leading to a final architecture characterized by arrested motion and more regular cell shapes. Such monolayer remodeling is robust, with qualitatively similar evolution in cell shape and dynamics observed across disparate perturbations. Here we quantify differences in monolayer remodeling guided by the active vertex model to identify underlying order parameters controlling epithelial architecture. When monolayers are formed atop extracellular matrix with varied stiffness, we find the cell density at which motion arrests varies significantly but the cell shape remains constant, consistent with the onset of tissue rigidity. In contrast, pharmacological perturbations can significantly alter the cell shape at which tissue dynamics is arrested, consistent with varied amounts of active stress within the tissue. Across all experimental conditions the final cell shape is well correlated to the cell proliferation rate, and cell cycle inhibition immediately arrests cell motility. Finally, we demonstrate cell-cycle variation in junctional tension as a source of active stress within the monolayer. Thus, the architecture and mechanics of epithelial tissue can arise from an interplay between cell mechanics and stresses arising from cell cycle dynamics.
SIGNIFICANCE STATEMENTThe morphology of biological tissue is determined by the shape and density of constituent cells. Here we measure the dynamics of cells in model epithelial tissues to study the evolution of their shape and density over time. Guided by a mathematical model, we find that cell shape is controlled by rigidity and active stresses within the tissue. We then show that cell cycle dynamics are the source of active stress that drives epithelial remodeling.
|
biophysics
|
Telemetry reveals rapid duel-driven song plasticity in a naturalistic social environment Singing by songbirds is a complex motor skill learnt during juvenile development or, in open-ended learners, before the onset of the breeding season. Outside of these specific periods, it is believed that birdsong does not change. Challenging this, here we demonstrate that in a seasonal songbird, social interactions during the breeding season induce a novel form of singing plasticity in naturalistic social environments. Using custom-made telemetric backpack technology to monitor song-based communication from freely-behaving canaries, we show that males temporally overlap their songs during aggressive duels. Singing duels induce an unexpected fast plasticity in song length, thereby enhancing singing performance and flexibility of a sexually-selected behavior. Remarkably, dueling canaries sing acoustically-similar songs, suggesting that competition within a specific song acoustic space drives dueling behavior. Overall, our findings reveal a previously unrecognized type of song plasticity different from the well-studied slow song plasticity as an imitation process for display purposes.
|
animal behavior and cognition
|
Mutational signatures of replication timing and epigenetic modification persist through the global divergence of mutation spectra across the great ape phylogeny Great ape clades exhibit variation in the relative mutation rates of different three-base-pair genomic motifs, with closely related species having more similar mutation spectra than distantly related species. This pattern cannot be explained by classical demographic or selective forces, but imply that DNA replication fidelity has been perturbed in different ways on each branch of the great ape phylogeny. Here, we use whole-genome variation from 88 great apes to investigate whether these species mutation spectra are broadly differentiated across the entire genome, or whether mutation spectrum differences are driven by DNA compartments that have particular functional features or chromatin states. We perform principal component analysis and mutational signature deconvolution on mutation spectra ascertained from compartments defined by features including replication timing and ancient repeat content, finding evidence for consistent species-specific mutational signatures that do not depend on which functional compartments the spectra are ascertained from. At the same time, we find that many compartments have their own characteristic mutational signatures that appear stable across the great ape phylogeny. For example, in a mutation spectrum PCA compartmentalized by replication timing, the second PC explaining 21.2% of variation separates all species late-replicating regions from their early-replicating regions. Our results suggest that great ape mutation spectrum evolution is not driven by epigenetic changes that modify mutation rates in specific genomic regions, but instead by trans-acting mutational modifiers that affect mutagenesis across the whole genome fairly uniformly.
SIGNIFICANCE STATEMENTAll heritable variation begins with damage or copying mistakes affecting the DNA of sperm, eggs, or embryos. Different DNA motifs can have different mutation rates, and these rates can evolve over time: the spectrum of mutability of three-base-pair motifs has evolved rapidly during great ape diversification. Here, we show that even as ape mutation spectra diverged from each other, ape genomes preserved a landscape of spatial mutation spectrum variation. We can thus deconvolute the mutational process into a mixture of fast-evolving signatures with uniform spatial distributions and conserved signatures that target specific regions. Our findings may ultimately help determine the factors, either genetic or environmental, that contribute to temporal and spatial variation in germline mutagenesis.
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genomics
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Reconstructing the history of variation in effective population size along phylogenies. AO_SCPLOWBSTRACTC_SCPLOWThe nearly-neutral theory predicts specific relations between effective population size (Ne) and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward, owing to the difficulty in estimating Ne. Here, we introduce an integrative framework allowing for an explicit reconstruction of the phylogenetic history of Ne, thus leading to a quantitative test of the nearly-neutral theory and an estimation of the allometric scaling of the ratios of non-synonymous over synonymous polymorphism ({pi}N /{pi}S) and divergence (dN/dS) with respect to Ne. As an illustration, we applied our method to primates, for which the nearly-neutral predictions were mostly verified. Under a purely nearly-neutral model with a constant DFE across species, we find that the variation in{pi} N /{pi}S and dN/dS as a function of Ne is too large to be compatible with current estimates of the DFE based on site frequency spectra. The reconstructed history of Ne shows a ten-fold variation across primates. The mutation rate per generation u, also reconstructed over the tree by the method, varies over a three-fold range and is negatively correlated with Ne. As a result of these opposing trends for Ne and u, variation in{pi} S is intermediate, primarily driven by Ne but substantially influenced by u. Altogether, our integrative framework provides a quantitative assessment of the role of Ne and u in modulating patterns of genetic variation, while giving a synthetic picture of their history over the clade.
SO_SCPLOWIGNIFICANCEC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSTATEMENTC_SCPLOWNatural selection tends to increase the frequency of mutants of higher fitness and to eliminate less fit genetic variants. However, chance events over the life of the individuals in the population are susceptible to introduce deviations from these trends, which are expected to have a stronger impact in smaller populations. In the long-term, these fluctuations, called random drift, can lead to the accumulation of mildly deleterious mutations in the genomes of living species, and for that reason, the effective population size (usually denoted Ne, and which captures the relative strength of drift, relative to selection) has been proposed as a major determinant of the evolution of genome architecture and content. A proper quantitative test of this hypothesis, however, is hampered by the fact that Ne is difficult to estimate in practice. Here, we propose a Bayesian integrative approach for reconstructing the broad-scale variation in Ne across an entire phylogeny, which in turns allows for quantifying how Ne correlates with life history traits and with various measures of genetic diversity and selection strength, between and within species. We apply this approach to the phylogeny of primates, and observe that selection is indeed less efficient in primates characterized by smaller effective population sizes.
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evolutionary biology
|
Dynamic interactions and intracellular fate of label-free GO within mammalian cells: role of lateral sheet size Graphene oxide (GO) holds great potential for biomedical applications, however fundamental understanding of the way it interacts with biological systems is still lacking even though it is essential for successful clinical translation. In this study, we exploit intrinsic fluorescent properties of thin GO sheets to establish the relationship between lateral dimensions of the material, its cellular uptake mechanisms and intracellular fate over time. Label-free GO with distinct lateral dimensions, small (s-GO) and ultra-small (us-GO) were thoroughly characterised both in water and in biologically relevant cell culture medium. Interactions of the material with a range of non-phagocytic mammalian cell lines (BEAS-2B, NIH/3T3, HaCaT, 293T) were studied using a combination of complementary analytical techniques (confocal microscopy, flow cytometry and TEM). The uptake mechanism was initially interrogated using a range of pharmaceutical inhibitors and validated using polystyrene beads of different diameters (0.1 and 1 m). Subsequently, RNA-Seq was used to follow the changes in the uptake mechanism used to internalize s-GO flakes over time. Regardless of lateral dimensions, both types of GO were found to interact with the plasma membrane and to be internalized by a panel of cell lines studied. However, s-GO was internalized mainly via macropinocytosis while us-GO was mainly internalized via clathrin- and caveolae-mediated endocytosis. Importantly, we report the shift from macropinocytosis to clathrin-dependent endocytosis in the uptake of s-GO at 24 h, mediated by upregulation of mTORC1/2 pathway. Finally, we show that both s-GO and us-GO terminate in lysosomal compartments for up to 48 h. Our results offer an insight into the mechanism of interaction of GO with non-phagocytic cell lines over time that can be exploited for the design of biomedically-applicable 2D transport systems.
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cell biology
|
Efficient and robust coding in heterogeneous recurrent networks Cortical networks show a large heterogeneity of neuronal properties. However, traditional coding models have focused on homogeneous populations of excitatory and inhibitory neurons. Here, we analytically derive a class of recurrent networks of spiking neurons that close to optimally track a continuously varying input online, based on two assumptions: 1) every spike is decoded linearly and 2) the network aims to reduce the mean-squared error between the input and the estimate. From this we derive a class of predictive coding networks, that unifies encoding and decoding and in which we can investigate the difference between homogeneous networks and heterogeneous networks, in which each neurons represents different features and has different spike-generating properties. We find that in this framework, type 1 and type 2 neurons arise naturally and networks consisting of a heterogeneous population of different neuron types are both more efficient and more robust against correlated noise. We make two experimental predictions: 1) we predict that integrators show strong correlations with other integrators and resonators are correlated with resonators, whereas the correlations are much weaker between neurons with different coding properties and 2) that type 2 neurons are more coherent with the overall network activity than type 1 neurons.
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neuroscience
|
A Neural Circuit Model of Proprioceptive Feedback from Muscles Recruited during an Isometric Knee Extension The influence of proprioceptive feedback on muscle activity during isometric tasks is the subject of conflicting studies. To better understand the relationship, we performed an isometric knee extension task experiment at four pre-set angles of the knee, recording from five muscles, and for two different hip positions. We applied muscle synergy analysis using NMF on the sEMG recordings to identify structure in the data which changed with internal knee angle, suggesting a link between proprioception and muscle activity. We hypothesised that such patterns in the data arise from the way proprioceptive and cortical signals are integrated in neural circuits of the spinal cord. Using the MIIND neural simulation platform, we developed a computational model based on current understanding of spinal circuits with an adjustable proprioceptive input. The model produces the same synergy patterns as observed in the experimental data indicating that such synergies are indeed encoded in the neural connectivity of the spinal cord and modulated by the proprioceptive input. When matching the proprioceptive input to the knee angles of the experiment, the model predicts the need for three distinct inputs: two to control the normal reciprocity between the agonist and antagonist muscles, and an additional to match the non-linear trend towards the limit of extension. Finally, we discuss the risks of using NMF for synergy analysis and demonstrate how to increase confidence in its results. Future modelling of human motor outputs should include interneuronal spinal circuits such as this to distinguish the modulatory role of supraspinal and peripheral afferent inputs to the spinal cord, during both passive and dynamic tasks.
Significance statementSensory feedback from muscles has a significant role in motor control, but its role in tasks where limbs are held in a fixed position is disputed, because the effect is reduced when muscles are not stretched. Here, we first identified patterns of muscle activity during such tasks which changed with different leg positions. We developed a computational spinal motor circuit model with adjustable muscle stretch input, which reproduced the same patterns of activity as observed experimentally. The model predicts three distinct muscle stretch signals required to produce the activity patterns for all leg positions. Because the connections in the model are based on well known spinal circuits, it is likely the observed activity patterns are generated in the spinal cord.
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neuroscience
|
Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed, however proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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cell biology
|
Parallel Factor Analysis for multidimensional decomposition of fNIRS data SignificanceCurrent techniques for data analysis in functional near-infrared spectroscopy (fNIRS), such as artifact correction, do not allow to integrate the information originating from both wavelengths, considering only temporal and spatial dimensions of the signals structure. Parallel factor analysis (PARAFAC) has previously been validated as a multidimensional decomposition technique in other neuroimaging fields.
AimWe aimed to introduce and validate the use of PARAFAC for the analysis of fNIRS data, which is inherently multidimensional (time, space, wavelength).
ApproachWe used data acquired in 17 healthy adults during a verbal fluency task to compare the efficacy of PARAFAC for motion artifact correction to traditional 2D decomposition techniques, i.e. target principal (tPCA) and independent component analysis (ICA). Correction performance was further evaluated under controlled conditions with simulated artifacts and hemodynamic response functions.
ResultsPARAFAC achieved significantly higher improvement in data quality as compared to tPCA and ICA. Correction in several simulated signals further validated its use and promoted it as a robust method independent of the artifacts characteristics.
ConclusionsThis study describes the first implementation of PARAFAC in fNIRS and provides validation for its use to correct artifacts. PARAFAC is a promising data-driven alternative for multidimensional data analyses in fNIRS and this study paves the way for further applications.
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neuroscience
|
Lymphoid follicle formation and human vaccination responses recapitulated in an organ-on-a-chip Lymphoid follicles (LFs) are responsible for generation of adaptive immune responses in secondary lymphoid organs and form ectopically during chronic inflammation. A human model of LF formation would provide a tool to understand LF development and an alternative to non-human primate models for preclinical evaluation of vaccines. Here, we show that primary human blood B- and T-lymphocytes autonomously assemble into ectopic LFs when cultured in a three-dimensional (3D) extracellular matrix gel within an organ-on-a-chip microfluidic device. Dynamic fluid flow is required for LF formation and prevention of lymphocyte autoactivation. These germinal center-like LFs contain B cells expressing Activation-Induced Cytidine Deaminase and exhibit plasma cell (PC) differentiation upon activation. To explore their utility for vaccine testing, autologous monocyte-derived dendritic cells were integrated into LF Chips. The human LF chips demonstrated improved antibody responses to split virion influenza vaccination compared to 2D cultures, which were enhanced by addition of a squalene-in-water emulsion adjuvant, and this was accompanied by increases in LF size and number. When inoculated with commercial influenza vaccine, PC formation and production of anti-hemagglutinin IgG were observed, as well as secretion of cytokines similar to those observed in vaccinated humans over clinically relevant timescales.
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immunology
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The Role of State Uncertainty in the Dynamics of Dopamine Reinforcement learning models of the basal ganglia map the phasic dopamine signal to reward prediction errors (RPEs). Conventional models assert that, when a stimulus predicts a reward with fixed delay, dopamine activity during the delay should converge to baseline through learning. However, recent studies have found that dopamine ramps up before reward in certain conditions even after learning, thus challenging the conventional models. In this work, we show that sensory feedback causes an unbiased learner to produce RPE ramps. Our model predicts that, when feedback gradually decreases during a trial, dopamine activity should resemble a bump, whose ramp-up phase should furthermore be greater than that of conditions where the feedback stays high. We trained mice on a virtual navigation task with varying brightness, and both predictions were empirically observed. In sum, our theoretical and experimental results reconcile the seemingly conflicting data on dopamine behaviors under the RPE hypothesis.
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neuroscience
|
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learn ing (DL) models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained DL models (BioImage Model Zoo). Hence, non-experts can easily perform common image processing tasks in life-science research with DL-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state-of-the-art solutions and it is equipped with utility tools for developers to include new models. Very recently, several train ing frameworks have adopted the deepImageJ format to deploy their work in one of the most used software in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of DL models in life-sciences applications and bioimage informatics.
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bioengineering
|
Reference transcriptome data in silkworm, Bombyx mori BackgroundThe silkworm Bombyx mori is a lepidopteran model insect with biological and industrial importance. Its high-quality genome sequence has recently become available and the utilization of this information in combination with extensive transcriptomic analyses is expected to provide an elaborate gene model. It will also be possible to clarify gene expression in detail using this approach.
ResultsWe herein performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. Sequences were mapped onto the reference genome assembly and reference transcriptome data was successfully constructed. The reference data provided a nearly complete sequence for sericin-1, a major silk gene with a complex structure. We also markedly improved the gene model for other genes. Transcriptomic expression was investigated in each tissue and a number of transcripts were identified that were exclusively expressed in tissues such as the testis. Transcripts strongly expressed in the midgut formed tight genomic clusters, suggesting that they originated from tandem gene duplication. Transcriptional factor genes expressed in specific tissues or the silk gland subparts were also identified.
ConclusionsWe successfully constructed reference transcriptome data in the silkworm and found that a number of transcripts showed unique expression profiles. These results will facilitate basic studies on the silkworm and accelerate its applications, which will contribute to further advances in lepidopteran and entomological research and the practical use of these insects.
|
genomics
|
A functional corona around extracellular vesicles enhancesangiogenesis during skin regeneration and signals in immune cells Nanoparticles can acquire a protein corona defining their biological identity. Corona functions were not yet considered for cell-derived extracellular vesicles (EVs). Here we demonstrate that nanosized EVs from therapy-grade human placental-expanded (PLX) stromal cells are surrounded by an imageable and functional protein corona when enriched with permissive technology. Scalable EV separation from cell-secreted soluble factors via tangential flow-filtration and subtractive tandem mass-tag proteomics revealed significant enrichment of predominantly immunomodulatory and proangiogenic proteins. Western blot, calcein-based flow cytometry, super-resolution and electron microscopy verified EV identity. PLX-EVs protected corona proteins from protease digestion. EVs significantly ameliorated human skin regeneration and angiogenesis in vivo, induced differential signaling in immune cells, and dose-dependently inhibited T cell proliferation in vitro. Corona removal by size-exclusion or ultracentrifugation abrogated angiogenesis. Re-establishing an artificial corona by cloaking EVs with defined proangiogenic proteins served as a proof-of-concept. Understanding EV corona formation will improve rational EV-inspired nanotherapy design.
|
cell biology
|
Integrating multi-omics data through deep learning for accurate cancer prognosis prediction BackgroundGenomic information is nowadays widely used for precise cancer treatments. Since the individual type of omics data only represents a single view that suffers from data noise and bias, multiple types of omics data are required for accurate cancer prognosis prediction. However, it is challenging to effectively integrate multi-omics data due to the large number of redundant variables but relatively small sample size. With the recent progress in deep learning techniques, Autoencoder was used to integrate multi-omics data for extracting representative features. Nevertheless, the generated model is fragile from data noises. Additionally, previous studies usually focused on individual cancer types without making comprehensive tests on pan-cancer. Here, we employed the denoising Autoencoder to get a robust representation of the multi-omics data, and then used the learned representative features to estimate patients risks.
ResultsBy applying to 15 cancers from The Cancer Genome Atlas (TCGA), our method was shown to improve the C-index values over previous methods by 6.5% on average. Considering the difficulty to obtain multi-omics data in practice, we further used only mRNA data to fit the estimated risks by training XGboost models, and found the models could achieve an average C-index value of 0.627. As a case study, the breast cancer prognosis prediction model was independently tested on three datasets from the Gene Expression Omnibus (GEO), and shown able to significantly separate high-risk patients from low-risk ones (C-index>0.6, p-values<0.05). Based on the risk subgroups divided by our method, we identified nine prognostic markers highly associated with breast cancer, among which seven genes have been proved by literature review.
ConclusionOur comprehensive tests indicated that we have constructed an accurate and robust framework to integrate multi-omics data for cancer prognosis prediction. Moreover, it is an effective way to discover cancer prognosis-related genes.
|
bioinformatics
|
Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity 1Triple-drug therapies have transformed HIV from a fatal condition to a chronic one. These therapies should prevent HIV drug resistance evolution, because one or more drugs suppress any partially-resistant viruses. In practice, such therapies drastically reduced, but did not eliminate, resistance evolution. In this article, we reanalyze published data from an evolutionary perspective and demonstrate several intriguing patterns about HIV resistance evolution - resistance evolves (1) even after years on successful therapy, (2) sequentially, often via one mutation at a time and (3) in a partially predictable order. We describe how these observations might emerge under two models of HIV drugs varying in space or time. Despite decades of work in this area, much opportunity remains to create models with realistic parameters for three drugs, and to match model outcomes to resistance rates and genetic patterns from patients on triple-drug therapy. Further, lessons from HIV may inform other systems.
|
evolutionary biology
|
Evolutionary impact of size-selective harvesting on shoaling behavior: Individual-level mechanisms and possible consequences for natural and fishing mortality Intensive and size-selective harvesting is an evolutionary driver of life-history as well as individual behavioral traits. Yet, whether and to what degree harvesting modifies the collective behavior of exploited species is largely unknown. We present a multi-generation harvest selection experiment with zebrafish (Danio rerio) as a model species to understand the effects of size-selective harvesting on shoaling behavior. The experimental system is based on a large-harvested (typical of most wild capture fisheries targeting larger size classes) and small-harvested (typical of specialized fisheries and gape-limited predators targeting smaller size classes) selection lines. By combining high resolution tracking of fish behavior with computational agent-based modeling we show that shoal cohesion changed in the direction expected by a trade-off between vigilance and the use of social cues. In particular, we document a decrease of vigilance in the small-harvested line, which was linked to an increase in the attention to social cues, favoring more cohesive shoals. Opposing outcomes were found for the large-harvested line, which formed less cohesive shoals. Using the agent-based model we outline possible consequences of changes is shoaling behavior for both fishing and natural mortality. The changes in shoaling induced by large size-selective harvesting may decrease fishing mortality, but increase mortality by natural predators. Our work suggests an insofar overlooked evolutionary mechanism by which size-selective harvesting can affect mortality and in turn population dynamics of exploited fish.
|
ecology
|
Fine human genetic map based on UK10K data set Recombination is a major force that shapes genetic diversity. Determination of recombination rate is important and can theoretically be improved by increasing the sample size. However, it is challenging to estimate recombination rates when the sample size is extraordinarily large because of computational burden. In this study, we used a refined artificial intelligence approach to estimate the recombination rate of the human genome using the UK10K human genomic dataset with 7,562 genomic sequences and its three subsets with 200, 400 and 2,000 genomic sequences under the Out-of-Africa demography model. We not only obtained an accurate human genetic map, but also found that the fluctuation of estimated recombination rate is reduced along the human genome when the sample size is increased. UK10K recombination activity is less concentrated than its subsets. Our results demonstrate how the sample size affects the estimated recombination rate, and analyses of a larger number of genomes result in a more precise estimation of recombination rate.
|
evolutionary biology
|
Gene Ontology Meta Annotator for Plants (GOMAP) Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipelines availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on Fmax) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/. A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/.
|
bioinformatics
|
AMR - An R Package for Working with Antimicrobial Resistance Data Antimicrobial resistance is an increasing threat to global health. Evidence for this trend is generated in microbiological laboratories through testing microorganisms for resistance against antimicrobial agents. International standards and guidelines are in place for this process as well as for reporting data on (inter-)national levels. However, there is a gap in the availability of standardized and reproducible tools for working with laboratory data to produce the required reports. It is known that extensive efforts in data cleaning and validation are required when working with data from laboratory information systems. Furthermore, the global spread and relevance of antimicrobial resistance demands to incorporate international reference data in the analysis process.
In this paper, we introduce the AMR package for R that aims at closing this gap by providing tools to simplify antimicrobial resistance data cleaning and analysis, while incorporating international guidelines and scientifically reliable reference data. The AMR package enables standardized and reproducible antimicrobial resistance analyses, including the application of evidence-based rules, determination of first isolates, translation of various codes for microorganisms and antimicrobial agents, determination of (multi-drug) resistant microorganisms, and calculation of antimicrobial resistance, prevalence and future trends. The AMR package works independently of any laboratory information system and provides several functions to integrate into international workflows (e.g., WHONET software provided by the World Health Organization).
|
microbiology
|
Caveat in Fisher's theorem reveals fitness can change without mutations The fitness of microbial genotypes is linked to their reproduction rate: Mutants reproducing faster than their wild-type counterparts are favoured by selection, but otherwise the mutation is lost. Here I show that relative differences in fitness between two mutants can change over time without invoking new mutations, contravening textbook population genetics theory. Widespread fitness measurements assume the ratio between Malthusian reproduction rates of competing genotypes is constant. But they are not. Here I competed two constructs of Escherichia coli, one harbouring the non-transmissible plasmid pGW155B. The plasmid protects the bacterium against tetracycline, and yet, it was maintained without using the antibiotic. pGW155B imposes a slower reproduction rate due to carriage costs but it also prompts a known trade-off between reproduction and survival, so the construct harbouring pGW155B attains higher densities at the equilibrium. Consequently, if selection favours survival the bacterium could maintain the plasmid, despite its slower reproduction, without using tetracycline. Exclusive reliance on reproduction rates may therefore yield inaccurate fitness measurements, altering our intuition about how natural selection operates, unless competing genotypes reach their equilibrium. This means that selection for plasmid carriage could be stronger than previously thought.
|
evolutionary biology
|
Effective mechanical potential of cell-cell interaction explains basic structural units of three-dimensional morphogenesis Mechanical forces of cell-cell interactions have been suggested to be critical for the emergence of diverse three-dimensional morphologies of multicellular organisms. The direct evaluation of the forces in living systems has been difficult due to technical limitations. Here, we developed a framework for inferring and modeling mechanical forces of cell-cell interactions. First, by analogy to coarse-grained models in molecular and colloidal sciences, cells were assumed to be spherical particles, where the mean forces (i.e. effective forces) of pairwise cell-cell interactions were considered. Then, the forces were statistically inferred from live imaging data, and subsequently, we successfully detected effective mechanical potentials of cell-cell interactions as a function of the cell-cell distances in Madin-Darby canine kidney (MDCK) cells, C.elegans early embryos, and mouse pre-implantation embryos. The qualitative and quantitative differences in the inferred potentials can be a control parameter for morphological transition during the mouse compaction process, and can also reproduce various three-dimensional morphologies including aggregates, cavities, tubes, cups, and two-dimensional sheets, which constitute basic structures observed during morphogenesis. We propose that effective potentials of cell-cell interactions are measurable, and their qualitative and quantitative features are critical for the emergence of diverse three-dimensional morphogenesis.
Significance statementEmergence of diverse morphologies of multicellular organisms is one of the most intriguing phenomena in nature. Mechanical forces generated by cells play central roles in morphogenesis, however, their measurement is technically limited. Furthermore, due to the complex situations in living systems, a model for describing the emergent properties of multicellular systems has not been established. Here, we developed a method for inferring mechanical potential energy of cell-cell interactions, and showed that the quantitative differences in the potential is alone sufficient to describe basic three-dimensional morphologies observed during embryogenesis and organogenesis. This framework sheds light on the emergent properties of multicellular systems.
|
biophysics
|
Network dynamics underlying OFF responses in the auditory cortex Across sensory systems, complex spatio-temporal patterns of neural activity arise following the onset (ON) and offset (OFF) of stimuli. While ON responses have been widely studied, the mechanisms generating OFF responses in cortical areas have so far not been fully elucidated. We examine here the hypothesis that OFF responses are single-cell signatures of recurrent interactions at the network level. To test this hypothesis, we performed population analyses of two-photon calcium recordings in the auditory cortex of awake mice listening to auditory stimuli, and compared linear single-cell and network models. While the single-cell model explained some prominent features of the data, it could not capture the structure across stimuli and trials. In contrast, the network model accounted for the low-dimensional organisation of population responses and their global structure across stimuli, where distinct stimuli activated mostly orthogonal dimensions in the neural state-space.
|
neuroscience
|
Low-dimensional learned feature spaces quantify individual and group differences in vocal repertoires Increases in the scale and complexity of behavioral data pose an increasing challenge for data analysis. A common strategy involves replacing entire behaviors with small numbers of handpicked, domain-specific features, but this approach suffers from several crucial limitations. For example, handpicked features may miss important dimensions of variability, and correlations among them complicate statistical testing. Here, by contrast, we apply the variational autoencoder (VAE), an unsupervised learning method, to learn features directly from data and quantify the vocal behavior of two model species: the laboratory mouse and the zebra finch. The VAE converges on a parsimonious representation that outperforms handpicked features on a variety of common analysis tasks, enables the measurement of moment-by-moment vocal variability on the timescale of tens of milliseconds in the zebra finch, provides strong evidence that mouse ultrasonic vocalizations do not cluster as is commonly believed, and captures the similarity of tutor and pupil birdsong with qualitatively higher fidelity than previous approaches. In all, we demonstrate the utility of modern unsupervised learning approaches to the quantification of complex and high-dimensional vocal behavior.
|
animal behavior and cognition
|
Population coding of strategic variables during foraging in freely-moving macaques To optimize their foraging strategy, animals must continuously make decisions about where to look for food and when to move between locations of possible food sources. Until now it was difficult to examine the neural bases of foraging in naturalistic environments because previous approaches have relied on restrained animals performing trial-based foraging tasks. Here, we allowed unrestrained monkeys to freely interact with concurrent reward options while we wirelessly recorded population activity in dorsolateral prefrontal cortex (dlPFC). Although the relevant reward dynamics were hidden from the animals, they were nonetheless encoded in the population activity and helped predict foraging choices. Surprisingly, the decoded reward dynamics were represented in a subspace of the high-dimensional population activity, and predicted animals subsequent choice better than either the true experimental variables or the raw neural responses. Our results indicate that monkeys foraging strategy is based on a cortical model of reward dynamics as animals freely explore their environment.
|
neuroscience
|
Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data Single-cell transcriptomics enables systematic charting of cellular composition of complex tissues. Identification of cell populations often relies on unsupervised clustering of cells based on the similarity of their scRNA-seq profiles, followed by manual annotation of cell clusters using established marker genes. However, manual selection of marker genes is a time-consuming process that may lead to sub-optimal annotation results as the selected markers must be informative of both the individual cell clusters and various cell types present in the complex samples. Here, we developed a computational platform, termed ScType, which enables data-driven, fully-automated and ultra-fast cell-type identification based solely on given scRNA-seq data, combined with our comprehensive cell marker database as background information. Using a compendium of six scRNA-seq datasets from various human and mouse tissues, we show how ScType provides an unbiased and accurate cell-type annotation by guaranteeing the specificity of positive and negative marker genes both across cell clusters and cell types. We also demonstrate how ScType enables distinguishing between healthy and malignant cell populations, based on single-cell calling of single-nucleotide variants, making it a versatile tool for exploration and use of single-cell transcriptomic data for anticancer applications. The widely-applicable method is deployed both as an interactive web-tool (https://sctype.app), and as an open-source R-package, connected with a comprehensive ScType database of specific markers.
|
systems biology
|
Hybridization disrupts growth-defense strategies and reveals trade-offs masked in unadmixed populations of a perennial plant Organisms are constantly challenged by pathogens and pests which can drive the evolution of growth-defense strategies. Plant stomata are essential for gas-exchange during photosynthesis and conceptually lie at the intersection of the physiological demands of growth and exposure to foliar fungal. Generations of natural selection for locally adapted growth-defense strategies can eliminate variation between traits, potentially masking trade-offs and selection conflicts that may have existed in the past. Hybrid populations offer a unique opportunity to reset the clock on selection and to study potentially maladaptive trait variation before selection removes it. We study the interactions of growth, stomatal, ecopysiological, and disease resistance traits in Poplars (Populus) after infection by the leaf rust Melampsora medusae. Phenotypes were measured in a common garden and genotyped at 227K SNPs. We isolate the effects of hybridization on trait variance, discover correlations between stomatal, ecophysiology and disease resistance, examine trade-offs and selection conflicts, and explore the evolution of growth-defense strategies potentially mediated by selection for stomatal traits on the upper leaf surface. These results suggest an important role for stomata in determining growth-defense strategies in organisms susceptible to foliar pathogens, and reinforces the contribution of hybridization studies towards our understanding of trait evolution.
|
evolutionary biology
|
Information Enhanced Model Selection for Gaussian Graphical Model with Application to Metabolomic Data In light of the low signal-to-noise nature of many large biological data sets, we propose a novel method to learn the structure of association networks using Gaussian graphical models combined with prior knowledge. Our strategy includes two parts. In the first part, we propose a model selection criterion called structural Bayesian information criterion (SBIC), in which the prior structure is modeled and incorporated into Bayesian information criterion (BIC). It is shown that the popular extended BIC (EBIC) is a special case of SBIC. In the second part, we propose a two-step algorithm to construct the candidate model pool. The algorithm is data-driven and the prior structure is embedded into the candidate model automatically. Theoretical investigation shows that under some mild conditions SBIC is a consistent model selection criterion for high-dimensional Gaussian graphical model. Simulation studies validate the superiority of the proposed algorithm over the existing ones and show the robustness to the model misspecification. Application to relative concentration data from infant feces collected from subjects enrolled in a large molecular epidemiological cohort study validates that metabolic pathway involvement is a statistically significant factor for the conditional dependence between metabolites. Furthermore, new relationships among metabolites are discovered which can not be identified by the conventional methods of pathway analysis. Some of them have been widely recognized in biological literature.
|
bioinformatics
|
Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic diversity in the lion (Panthera leo) BackgroundPrevious phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting.
ResultsIn this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail.
ConclusionsThe results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.
|
evolutionary biology
|
Learning Your Heart Actions From Pulse: ECG Waveform Reconstruction From PPG This paper studies the relation between electrocardiogram (ECG) and photoplethysmogram (PPG) and infers the waveform of ECG via the PPG signals that can be obtained from affordable wearable Internet-of-Things (IoT) devices for mobile health. In order to address this inverse problem, a transform is proposed to map the discrete cosine transform (DCT) coefficients of each PPG cycle to those of the corresponding ECG cycle based on our proposed cardiovascular signal model. The proposed method is evaluated with different morphologies of the PPG and ECG signals on three benchmark datasets with a variety of combinations of age, weight, and health conditions using different training setups. Experimental results show that the proposed method can achieve a high prediction accuracy greater than 0.92 in averaged correlation for each dataset when the model is trained subject-wise. With a signal processing and learning system that is designed synergistically, we are able to reconstruct ECG signals by exploiting the relation of these two types of cardiovascular measurement. The reconstruction capability of the proposed method can enable low-cost ECG screening from affordable wearable IoT devices for continuous and long-term monitoring. This work may open up a new research direction to transfer the understanding of the clinical ECG knowledge base to build a knowledge base for PPG and data from wearable devices.
|
bioinformatics
|
Interictal Signatures of Human Periventricular Nodular Heterotopia Periventricular nodular heterotopia (PNH) is a malformation of cortical development that frequently causes drug-resistant epilepsy. The epileptogenicity of ectopic neurons in PNH as well as their role in generating interictal and ictal activity is still a matter of debate. We report the first in vivo microelectrode recording of heterotopic neurons in humans. Highly consistent interictal patterns (IPs) were identified within the nodules: 1) Periodic Discharges PLUS Fast activity (PD+F), Sporadic discharges PLUS Fast activity (SD+F), and 3) epileptic spikes (ES). Neuronal firing rates were significantly modulated during all IPs, suggesting that multiple IPs were generated by the same local neuronal populations. Furthermore, firing rates closely followed IP morphologies. Among the different IPs, SD+FA pattern was found only in the three nodules that were actively involved in seizure generation, but was never observed in the nodule that did not take part in ictal discharges. On the contrary, PD+F and ES were identified in all nodules. Units that were modulated during the IPs were also found to participate in seizures, increasing their firing rate at seizure onset and maintaining an elevated rate during the seizures. Together, nodules in PNH are highly epileptogenic, and show several IPs that provide promising pathognomonic signatures of PNH. Furthermore, our results show that PNH nodules may well initiate seizures.
HighlightsO_LIFirst in vivo microelectrode description of local epileptic activities in human PNH
C_LIO_LIRecordings revealed multiple microscopic epileptic interictal patterns
C_LIO_LIFiring rates of all detected units were significantly modulated during all interictal patterns
C_LIO_LISeizures recruited the same units that are involved in interictal activity
C_LI
|
pathology
|
A CTP-dependent gating mechanism enables ParB spreading on DNA in Caulobacter crescentus Proper chromosome segregation is essential in all living organisms. The ParA-ParB-parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS and spread by sliding to the neighboring DNA 1. Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products are likely associated with re-opening of the gates to release DNA and to recycle ParB. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation, spreading, and recycling.
|
microbiology
|
A Francisella tularensis L,D-carboxypeptidase plays important roles in cell morphology, envelope integrity, and virulence. Francisella tularensis is a Gram-negative, intracellular bacterium that causes the zoonotic disease tularemia. Intracellular pathogens, including F. tularensis, have evolved mechanisms to survive in the harsh environment of macrophages and neutrophils, where they are exposed to cell envelope-damaging molecules. The bacterial cell wall, primarily composed of peptidoglycan (PG), maintains cell morphology, structure, and membrane integrity. Intracellular Gram-negative bacteria protect themselves from macrophage and neutrophil killing by recycling and repairing damaged PG - a process that involves over 50 different PG synthesis and recycling enzymes. Here, we identified a PG recycling enzyme, L,D-carboxypeptidase A (LdcA), of F. tularensis that is responsible for converting PG tetrapeptide stems to tripeptide stems. Unlike E. coli LdcA and most other orthologs, F. tularensis LdcA does not localize to the cytoplasm and also exhibits L,D-endopeptidase activity, converting PG pentapeptide stems to tripeptide stems. Loss of F. tularensis LdcA led to altered cell morphology and membrane integrity, as well as attenuation in a mouse pulmonary infection model and in primary and immortalized macrophages. Finally, an F. tularensis ldcA mutant protected mice against virulent Type A F. tularensis SchuS4 pulmonary challenge.
|
microbiology
|
Learning to learn persistently modifies an entorhinal-hippocampal excitatory-inhibitory subcircuit Cognitive control, the judicious use of relevant information while ignoring distractions, is a feature of everyday cognitive experience, but its neurobiology is understudied. We investigated whether cognitive control training (CCT) changes hippocampal neural circuit function in mice, beyond the changes caused by place learning and memory formation. Mice learned and remembered a conditioned place avoidance during CCT that required ignoring irrelevant locations of shock. They were compared to controls that learned the same place avoidance under lower cognitive control demands. Weeks after CCT, mice learn new tasks in novel environments faster than controls; they learned to learn. We investigated entorhinal cortex-to-dentate gyrus neural circuit changes and report that CCT rapidly changes synaptic circuit function, resulting in an excitatory-inhibitory subcircuit change that persists for months. CCT increases inhibition that attenuates the dentate response to medial entorhinal cortical input, and through disinhibition, potentiates the response to strong inputs, pointing to overall signal-to-noise enhancement. These neurobiological findings support a neuroplasticity hypothesis that, beyond storing item/event associations, CCT persistently optimizes neural circuit information processing.
|
neuroscience
|
Male genital lobe morphology affects the chance to copulate in Drosophila pachea IntroductionMale genitalia are thought to ensure transfer of sperm through direct physical contact with female during copulation. However, little attention has been given to their pre-copulatory role with respect to sexual selection and sexual conflict. Males of the fruitfly Drosophila pachea have a pair of asymmetric external genital lobes, which are primary sexual structures and stabilize the copulatory complex of female and male genitalia. We wondered if genital lobes in D. pachea may have a role before or at the onset of copulation, before genitalia contacts are made.
ResultsWe tested this hypothesis with a D. pachea stock where males have variable lobe lengths. In 92 mate competition trials with a single female and two males, females preferentially engaged into a first copulation with males that had a longer left lobe and that displayed increased courtship vigor. In 53 additional trials with both males having partially amputated left lobes of different lengths, we observed a weaker and non-significant effect of left lobe length on copulation success. Courtship durations significantly increased with female age and when two males courted the female simultaneously, compared to trials with only one courting male. In addition, lobe length did not affect sperm transfer once copulation was established.
ConclusionLeft lobe length affects the chance of a male to engage into copulation. The morphology of this primary sexual trait may affect reproductive success by mediating courtship signals or by facilitating the establishment of genital contacts at the onset of copulation.
|
evolutionary biology
|
A memory-based theory of emotional disorders Learning and memory play a central role in emotional disorders, particularly in depression and posttraumatic stress disorder. We present a new, transdiagnostic theory of how memory and mood interact in emotional disorders. Drawing upon retrieved-context models of episodic memory, we propose that memories form associations with the contexts in which they are encoded, including emotional valence and arousal. Later, encountering contextual cues retrieves their associated memories, which in turn reactivate the context that was present during encoding. We first show how our retrieved-context model accounts for findings regarding the organization of emotional memories in list-learning experiments. We then show how this model predicts clinical phenomena, including persistent negative mood after chronic stressors, intrusive memories of painful events, and the efficacy of cognitive-behavioral therapies.
|
neuroscience
|
A conserved enzyme found in diverse human gut bacteria interferes with anticancer drug efficacy Pharmaceuticals are the top predictor of inter-individual variations in gut microbial community structure1, consistent with in vitro evidence that host-targeted drugs inhibit gut bacterial growth2 and are extensively metabolized by the gut microbiome3,4. In oncology, bacterial metabolism has been implicated in both drug efficacy5,6 and toxicity7,8; however, the degree to which bacterial drug sensitivity and metabolism can be driven by conserved pathways also found in mammalian cells remains poorly understood. Here, we show that anticancer fluoropyrimidine drugs inhibit the growth of diverse gut bacterial strains by disrupting pyrimidine metabolism, as in mammalian cells. Select bacteria metabolized 5-fluorouracil (5-FU) to its inactive metabolite dihydrofluorouracil (DHFU), mimicking the major host pathway for drug clearance. The preTA operon was necessary and sufficient for 5-FU inactivation in Escherichia coli, exhibited high catalytic efficiency for the reductive reaction, decreased the bioavailability and efficacy of oral fluoropyrimidine treatment in mice, and was prevalent in the gut microbiomes of colorectal cancer patients prior to and during treatment. The observed conservation of both the targets and pathways for metabolism of therapeutics across domains highlights the need to distinguish the relative contributions of human and microbial cells to drug disposition9, efficacy, and side effect profiles.
|
microbiology
|
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