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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 667 records · Page 37Linked to original sources

bioRxiv2016

Genome-wide analysis of phased nucleosomal arrays reveals the functional characteristic of the nucleosome remodeler ACF

Regular successions of positioned nucleosomes - phased nucleosome arrays (PNAs) - are predominantly known from transcriptional start sites (TSS). It is unclear whether PNAs occur elsewhere in the genome. To generate a comprehensive inventory of PNAs for Drosophila, we applied spectral analysis to nucleosome maps and identified thousands of PNAs throughout the genome. About half of them are not near TSS and strongly enriched for a novel sequence motif. Through genome-wide reconstitution of physiological chromatin in Drosophila embryo extracts we uncovered the molecular basis of PNA formation. We identified Phaser, an unstudied zinc finger protein that positions nucleosomes flanking the new motif. It also revealed how the global activity of the chromatin remodeler CHRAC/ACF, together with local barrier elements, generates islands of regular phasing throughout the genome. Our work demonstrates the potential of chromatin assembly by embryo extracts as a powerful tool to reconstitute chromatin features on a global scale in vitro.

molecular biology↗

bioRxiv2016

Critical minimum temperature limits xylogenesis and maintains treelines on the Tibetan Plateau

Physiological and ecological mechanisms that define treelines are still debated. It is suggested that the absence of trees above the treeline is caused by the low temperature that limits growth. Thus, we raise the hypothesis that there is a critical minimum temperature (CTmin) preventing xylogenesis at treeline. We tested this hypothesis by examining weekly xylogenesis across three and four growing seasons in two natural Smith fir (Abies georgei var. smithii) treeline sites on the south-eastern Tibetan Plateau. Despite differences in the timing of cell differentiation among years, minimum air temperature was the dominant climatic variable associated with xylem growth; the critical minimum temperature (CTmin) for the onset and end of xylogenesis occurred at 0.7{+/-}0.4 {degrees}C. A process-based-modeled chronology of tree-ring formation using this CTmin was consistent with actual tree-ring data. This extremely low CTmin permits Smith fir growing at treeline to complete annual xylem production and maturation and provides both support and a mechanism for treeline formation.

ecology↗

bioRxiv2016

Incorporating the Rate of Transcriptional Change Improves Construction of Transcription Factor Regulatory Networks

Transcriptional regulatory networks (TRNs) can be developed by computational approaches that infer regulator-target gene interactions from transcriptional assays. Successful algorithms that generate predictive, accurate TRNs enable the identification of regulator-target relationships in conditions where experimentally determining regulatory interactions is a challenge. Improving the ability of TRNs to successfully predict known regulator-target relationships in model species will enhance confidence in applying these approaches to determine regulator-target interactions in non-model species where experimental validation is challenging. Many transcriptional profiling experiments are performed across multiple time points; therefore we sought to improve regulator-target predictions by adjusting how time is incorporated into the network. We created ExRANGES, which incorporates Expression in a Rate-Normalized GEne Specific manner that adjusts how expression data is provided to the network algorithm. We tested this on a two different network construction approaches and found that ExRANGES prioritizes targets differently than traditional expression and improves the ability of these networks to accurately predict known regulator targets. ExRANGES improved the ability to correctly identify targets of transcription factors in large data sets in four different model systems: mouse, human, Arabidopsis, and yeast. Finally, we examined the performance of ExRANGES on a small data set from field-grown Oryza sativa and found that it also improved the ability to identify known targets even with a limited data set.\n\nAuthor SummaryTo understand how organisms can turn a collection of genes into a physiological response, we need to understand how certain genes are turned on and off. In model organisms, the ability to identify direct targets of transcription factors via ChIP-Seq in a high-throughput manner has advanced our understanding of transcriptional regulatory networks and how organisms regulate gene expression. However, for non-model organisms, it remains a challenge to identify TF-target relationships through experimental approaches such as ChIP-Seq. Without this information, the ability to understand regulatory control is limited. Computational approaches to identify regulator-target relationships in silico from easily attainable transcriptional data offer a solution. Several approaches exist for identifying gene regulatory networks, including many that take advantage of time series data. Most of these approaches weigh the relationship between regulators and putative targets at all time points equally. However, many regulators may control a single target in response to different inputs. In our approach, we focus on the association between regulators and targets primarily at times when there is a significant change in expression. ExRANGES essentially weights the expression value of each time point by the slope change after that time point so that relationships between regulators and targets are emphasized at the time points when the transcript levels are changing. This change in input into network identification algorithms improves the ability to predict regulator-target interactions and could be applied to many different algorithms We hope this improvement will increase the ability to identify regulators of interest in non-model species.

bioinformatics↗

bioRxiv2016

Exosomes purified from a single cell type have diverse morphology and composition

Extracellular vesicles (EVs) are produced by all known organisms and have important roles in cell communication and physiology. Exosomes are known in the literature to be small round EVs (40 to 100 nm in diameter) and are commonly purified with a serial ultracentrifugation protocol followed by density gradient floatation. Great morphological diversity has been described before regarding EVs found in body fluids such as blood plasma, breast milk and ejaculate. However, a detailed morphological analysis has never been performed on exosomes purified from a single cell type.\n\nTherefore, the aim of this study was to analyze and quantify via multiple electron microscopy techniques the morphology of exosomes purified from the human mast cell line HMC-1. The results revealed a novel spectrum of diversity in exosomes, which suggests that subpopulations of exosomes with different and specific functions might also exist. Our findings therefore argue that a new and more efficient way of defining exosome subpopulations is necessary. A system was proposed where exosomes were classified into nine different categories according to their size and shape. Three additional morphological features could also be found in exosomes regardless of their classification.\n\nThese findings show that morphological diversity is found among exosomes purified from a single cell line, similarly to what was previously observed for EVs in body fluids. This knowledge can help improving the interpretation of experimental results and widening our general understanding of the biological functions of exosomes.

cell biology↗

bioRxiv2016

Diffusion or advection? Mass transfer and diffusive boundary layer landscapes of the brown alga Fucus vesiculosus

The role of hyaline hairs on the thallus of brown-algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized setup for 2D-and 3D-mapping with O2-microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O2 flux between algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited both increased and decreased DBL thickness as compared to areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was a local increase in the DBL thickness. We also found indications for advective O2 transport driven by pressure gradients or vortex-shedding downstream from dense tufts of hyaline hairs alleviating local mass-transfer resistance imposed by thickened DBL. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant-microbe interactions.

biophysics↗

bioRxiv2016

Accuracy in wrist-worn, sensor-based measurements of heart rate and energy expenditure in a diverse cohort

BackgroundThe ability to measure activity and physiology through wrist-worn devices provides an opportunity for cardiovascular medicine. However, the accuracy of commercial devices is largely unknown.\n\nObjectiveTo assess the accuracy of seven commercially available wrist-worn devices in estimating heart rate (HR) and energy expenditure (EE) and to propose a wearable sensor evaluation framework.\n\nMethodsWe evaluated the Apple Watch, Basis Peak, Fitbit Surge, Microsoft Band, Mio Alpha 2, PulseOn, and Samsung Gear S2. Participants wore devices while being simultaneously assessed with continuous telemetry and indirect calorimetry while sitting, walking, running, and cycling. Sixty volunteers (29 male, 31 female, age 38 {+/-} 11 years) of diverse age, height, weight, skin tone, and fitness level were selected. Error in HR and EE was computed for each subject/device/activity combination.\n\nResultsDevices reported the lowest error for cycling and the highest for walking. Device error was higher for males,greater body mass index, darker skin tone, and walking. Six of the devices achieved a median error for HR below 5% during cycling. No device achieved an error in EE below 20 percent. The Apple Watch achieved the lowest overall error in both HR and EE, while the Samsung Gear S2 reported the highest.\n\nConclusionsMost wrist-worn devices adequately measure HR in laboratory-based activities, but poorly estimate EE, suggesting caution in the use of EE measurements as part of health improvement programs. We propose reference standards for the validation of consumer health devices (http://precision.stanford.edu/).\n\nAbbreviations

bioinformatics↗

bioRxiv2016

Distributed alpha networks underlie individual differences in memory performance

Episodic memory, our ability to remember specific events, varies considerably across individuals. However, little is known about the neural basis of this variability. To address this issue, we investigated the role of distributed networks of oscillatory activity, as measured through electroencephalography (EEG). We observed that individual differences in alpha network structure reliably predict individual memory capacity. Specifically, individuals whose network profiles during encoding were most different from their resting state networks exhibited greatest subsequent memory performance, suggesting that optimal information processing requires substantial shifts in large-scale oscillatory organization. Furthermore, these results were not observed in circumscribed topographical regions or individual connections, indicating that distributed network approaches were more sensitive to functional processes than more conventional methods. These findings uncover a physiological correlate of individual differences in episodic memory and demonstrate the utility of multivariate EEG techniques to uncover brain-behavior correlates.

neuroscience↗

bioRxiv2016

Dynamic compensation, parameter identifiability, and equivariances

A recent paper by Karin, Swisa, Glaser, Dor, and Alon introduced the mathematical notion of dynamical compensation (DC) in biological circuits, arguing that DC helps explain important features of glucose homeostasis as well as other key physiological regulatory mechanisms. The present paper establishes a connection between DC and two well-known notions in systems biology: system equivalence and parameter (un)identifiability. This recasting leads to effective tests for verifying DC in mathematical models.

systems biology↗

bioRxiv2016

The Constancy of Colored After-Images

We undertook psychophysical experiments to determine whether the color of the after-image produced by viewing a colored patch which is part of a complex multi-colored scene depends on the wavelength-energy composition of the light reflected from that patch. Our results show that, just as the color of a patch which is part of a complex scene is independent of the wavelength-energy composition of the light coming from it alone, but depends as well on the wavelength-energy composition of the light coming from its surrounds, so is the color of its after-image. Hence, traditional accounts of after-images as being the result of retinal adaptation or the perceptual result of physiological opponency, are inadequate. We propose instead that the color of after-images is generated after colors themselves are generated in the visual brain.

neuroscience↗

bioRxiv2016

Activity-dependent expression of reporter proteins at dendritic spines for synaptic activity mapping and optogenetic stimulation

Increasing evidence points to the importance of dendritic spines in the formation and allocation of memories, and alterations of spine number and physiology are associated to memory and cognitive disorders. Synaptic connections and pathways constitute the physical substrate that conveys information in the brain, and different combinations of active synaptic connections are believed to be responsible for the encoding of specific memories. In addition, modifications of the activity of such subsets of synapses are believed to be crucial for memory establishment, but a way to directly test this hypothesis, by selectively controlling the activity of potentiated spines, is currently lagging behind. Therefore it would be important to develop methods to tag active synapses for mapping functionally active connections and to selectively stimulate or interfere with active synapses. Here we introduce an approach to express light-sensitive membrane channels at synapses in an activity-dependent way by means of RNA and protein regulatory sequences. This approach is based on the local expression of reporter proteins, including optogenetic probes, at activated synapses and will allow the mapping of previously active synapses and the re-activation of the neuron only at these sites. This will allow extending the investigation of memory processes beyond the current neuron tagging technologies, whose resolution is limited at the cellular scale. Thus, it will be possible to unveil and recall the synaptic engram out of the global set of synapses.

neuroscience↗

bioRxiv2016

The DOE Systems Biology Knowledgebase (KBase)

The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology -- predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling; (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system.

bioinformatics↗

bioRxiv2016

GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

BackgroundGene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.\n\nFindingsA certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we have converted the command line Ensembl Compara GeneTrees pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.\n\nConclusionsGeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxys user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

bioinformatics↗

bioRxiv2016

Assembly of photoactive Orange Carotenoid Protein from its domains unravels a carotenoid shuttle mechanism

The Orange Carotenoid Protein (OCP) is indispensable for cyanobacterial photoprotection by quenching phycobilisome fluorescence upon photoconversion from the orange OCPO to the red OCPR form. Cyanobacterial genomes frequently harbor, besides genes for Orange Carotenoid Proteins (OCPs), several genes encoding homologs of OCPs N- or C-terminal domains (NTD, CTD). Unlike the well-studied NTD homologs, called Red Carotenoid Proteins (RCPs), the role of CTD homologs remains elusive. We show how OCP can be reassembled from its functional domains. Expression of Synechocystis OCP-CTD in carotenoid-producing Escherichia coli yielded violet-colored proteins, which, upon mixing with the RCP-apoprotein, produced an orange-like photoswitchable form that further photoconverted into a species spectroscopically indistinguishable from RCP, thus demonstrating a unique carotenoid shuttle mechanism. The CTD itself is a novel, dimeric carotenoid-binding protein, which effectively quenches singlet oxygen and interacts with the Fluorescence Recovery Protein, assigning physiological roles to CTD homologs and explaining the evolutionary process of OCP formation.\n\nOne Sentence SummaryThe C-domain of cyanobacterial OCP dimerizes, binds a carotenoid, and delivers it to the N-domain forming photoactive OCP.

biophysics↗

bioRxiv2016

Opportune cell culture conditions permit transfer of the neurosphere paradigm to cells of the cerebellar granule cell lineage by being permissive to sonic hedgehog signaling

The in vitro study of neural progenitors is based around the idea that defined culture conditions can emulate an environment which maintains an undifferentiated state and self-renewal capability of explanted progenitor cells, culminating in the growth of neurospheres. Neurosphere culture systems are used to study cells of physiological origin as well as transformed cells. In the case of the cerebellar granule cell lineage, neurosphere cultures have been produced from medulloblastoma tumors, while non-transformed granule progenitors are reported to be transient in vitro. SHH signaling is a key signaling pathway with roles in morphogenesis and cell proliferation in the central nervous system, in particular, involved in mitogenic signaling within the context of postnatal cerebellar granule cell expansion. In this paper, I demonstrate that in addition to commonly used mitogens such as EGF and bFGF, the SHH pathway agonist SAG, as well as genetic activation of SHH signaling by PTCH1 deletion, can lead to the growth of neurospheres from postnatal day 7 (p7) cerebellar explants.\n\nI also show that these neurosphere adhere to the cerebellar GCP lineage.. Strikingly, mSS cells can be maintained indefinitely in culture, as demonstrated by extensive clonogenic capability, assayed over a period of 10 weeks. In the context of self-renewal, I assay gene expression of POU3f2, POU5f1, NANOG, and SOX2, genes associated with neural progenitors, which I find expressed in mSS cells. Importantly, mSS cultures are continuously dependent on SAG for their clonogenic potential and SHH pathway activation, assayed by expression of GLI1, PTCH1 and NMYC. In addition to the aforementioned extensive self-renewal capability, mSS neurosphere cultures also maintain the ability to differentiate. In vitro differentiation leads to formation of cells with typical granule cell morphology and which are positive for beta3-tubulin and express GABRA6.\n\nOverall, my work demonstrates that by applying culture conditions which are tailored towards biological characteristics of specific regions of the central nervous system the paradigm of the neurosphere can be expanded to include lineages not previously studied in this way. In particular, I apply this principle to unmask the property of cells from the GCP lineage as having extensive self-renewal capability in vitro.

cell biology↗

bioRxiv2016

Hnf4a mediates microbial control of intestinal gene expression and inflammation

Microbiota influence diverse aspects of intestinal epithelial physiology and disease in part by controlling tissue-specific transcription of host genes. However, host genomic mechanisms mediating microbial control of host gene expression are poorly understood. Using an unbiased screening strategy, we found that the zebrafish Hepatic nuclear factor 4 alpha (Hnf4a) transcription factor specifically binds and activates a microbiota-suppressed intestinal epithelial transcriptional enhancer. Genetic analysis disclosed that zebrafish hnf4a activates nearly half of the genes that are suppressed by microbiota, suggesting microbiota negatively regulate Hnf4a. In support, analysis of genomic architecture in mouse intestinal epithelial cells revealed that microbiota colonization leads to activation or inactivation of hundreds of enhancers along with drastic genome-wide reduction of Hnf4a and Hnf4g occupancy. Interspecies meta-analysis suggests Hnf4a may mediate microbial contributions to inflammatory bowel disease pathogenesis. These results indicate Hnf4a plays a critical conserved role in maintaining intestinal homeostasis in response to microbiota and inflammation.

genomics↗

bioRxiv2016

In vitro reconstitution of T cell receptor-mediated segregation of the CD45 phosphatase

T cell signaling initiates upon binding of peptide-major histocompatibility complex (pMHC) on an antigen-presenting cell (APC) to the T cell receptor (TCR) on a T cell. TCR phosphorylation in response to pMHC binding is accompanied by segregation of the transmembrane phosphatase CD45 away from TCR-pMHC complexes. The kinetic segregation hypothesis proposes that CD45 exclusion shifts the local kinase-phosphatase balance to favor TCR phosphorylation. Spatial partitioning may arise from the size difference between the large CD45 extracellular domain and the smaller TCR-pMHC complex, although parsing potential contributions of extracellular protein size, actin activity, and lipid domains is difficult in living cells. Here, we reconstitute segregation of CD45 from bound receptor-ligand pairs using purified proteins on model membranes. Using a model receptor-ligand pair (FRB-FKBP), we first test physical and computational predictions for protein organization at membrane interfaces. We then show that the TCR-pMHC interaction causes partial exclusion of CD45. Comparing two developmentally-regulated isoforms of CD45, the larger RABC variant is excluded more rapidly and efficiently (~50%) than the smaller R0 isoform (~20%), suggesting that CD45 isotypes could regulate signaling thresholds in different T cell subtypes. Similar to the sensitivity of T cell signaling, TCR-pMHC interactions with Kds of [≤]15 M were needed to exclude CD45. We further show that the co-receptor PD-1 with its ligand PD-L1, immunotherapy targets that inhibit T cell signaling, also exclude CD45. These results demonstrate that the binding energies of physiological receptor-ligand pairs on the T cell are sufficient to create spatial organization at membrane-membrane interfaces.\n\nSIGNIFICANCE STATEMENTThe interface between a T cell and an antigen-presenting cell (APC) results in the formation of biochemically distinct plasma membrane domains that initiate signaling cascades. Here, using biochemical reconstitution and microscopy, we show that the binding energies of the TCRpMHC and PD-1-PD-L1 complexes are sufficient to create spatial organization at a model membrane-membrane interface. We show that spatial organization depends upon receptor-ligand binding affinity and the relative sizes of the extracellular domains. These biophysical parameters may be used to fine-tune signaling cascades in T cells.

immunology↗

bioRxiv2017

Growth is required for perception of water availability to pattern plant root branches

Water availability is a potent regulator of development in plants and acts as a positional cue to induce root branching through a process termed hydropatterning. The mechanism by which roots perceive the spatial distribution of water to position lateral branches is unknown. Here we reveal that a root's developmental competence for hydropatterning is limited to the root tip, where tissue growth occurs. Mathematical modeling suggests that water uptake during growth creates spatial biases in tissue water potential, and we show that these gradients predict the position of future lateral branches. By altering growth dynamics with exogenous chemical and environmental treatments, we demonstrate that growth is necessary to allow roots to distinguish environments with relatively high or low water availability and pattern branching accordingly. Furthermore, we show that these cues regulate a number of other physiologically important pathways. Our work supports a sense-by-growth mechanism governing lateral root hydropatterning, in which water availability cues are rendered interpretable through growth-sustained water movement.

plant biology↗

bioRxiv2017

Tracking the Subtle Mutations Thriving Host Sensing by the Plant Pathogen Streptomyces scabies

The acquisition of genetic material conferring the arsenal necessary for host virulence is a prerequisite on the path to become a plant pathogen. More subtle mutations are also required for perception of cues witnessing the presence of the target host and optimal conditions for colonization. The decision to activate the pathogenic lifestyle is not taken lightly and involves efficient systems monitoring environmental conditions. But how can a pathogen timely trigger the expression of virulence genes if the main signal inducing its pathogenic behavior originates from cellulose, the most abundant polysaccharide on earth? This situation is encountered by Streptomyces scabies responsible for common scab disease on tuber and root crops. We here propose a series of hypotheses of how S. scabies could optimally distinguish whether cello-oligosaccharides originate from decomposing lignocellulose (nutrient sources) or, instead, emanate from living and expanding plant tissue (virulence signals), and accordingly adapt its physiological response.

microbiology↗