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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 1,153 records · Page 64Linked to original sources

bioRxiv2018

Identifying stationary phases in multivariate time-series for highlighting behavioural modes and home range settlements

O_LIRecent advances in bio-logging open promising perspectives in the study animal movements at numerous scales. It is now possible to record time-series of animal locations and ancillary data (e.g. activity level derived from on-board accelerometers) over extended areas and long durations with a high spatial and temporal resolution. Such time-series are often piecewise stationary, as the animal may alternate between different stationary phases (i.e. characterised by a specific mean and variance of some key parameter for limited periods). Identifying when these phases start and end is a critical first step to understand the dynamics of the underlying movement processes.\nC_LIO_LIWe introduce a new segmentation-clustering method we called segclust2d. It can segment bi-(or more generally multi-) variate time-series and possibly cluster the various segments obtained, corresponding to phases assumed to be stationary. It is easy to use, as it only requires specifying the minimum length of a segment (to prevent over-segmentation) based on biological considerations.\nC_LIO_LIAlthough this method can be applied to time-series of any nature, we focus here on two-dimensional piecewise time-series whose phases correspond at small scale to the expressions of different behavioural modes such as transit, feeding and resting, as characterised by two joint metrics such as speed and turning angles or, at larger scale, to temporary home ranges, characterised by stationary distributions of bivariate coordinates.\nC_LIO_LIUsing computer simulations, we show that segcust2d can rival and even outperform previous, more complex methods, which were specifically developed to highlight changes in movement modes or home range shifts (based on Hidden Markov or Ornstein-Uhlenbeck modelling, respectively), which, contrary to our method, require truly informative initial guesses to be efficient. Furthermore we demonstrate it on actual examples involving a zebras small scale movements and an elephants large scale movements, to illustrate the identification of various movement modes and of home range shifts, respectively.\nC_LI

ecology↗

bioRxiv2018

Haplotype assignment of virus NGS data using co-variation of variant frequencies

Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We test this method with synthetic data sets of mixed cytomegalovirus and norovirus genomes, demonstrating high accuracy when longitudinal samples are available.

genomics↗

bioRxiv2018

Fast two-photon volumetric imaging of an improved voltage indicator reveals electrical activity in deeply located neurons in the awake brain

Imaging of transmembrane voltage deep in brain tissue with cellular resolution has the potential to reveal information processing by neuronal circuits in living animals with minimal perturbation. Multi-photon voltage imaging in vivo, however, is currently limited by speed and sensitivity of both indicators and imaging methods. Here, we report the engineering of an improved genetically encoded voltage indicator, ASAP3, which exhibits up to 51% fluorescence responses in the physiological voltage range, sub-millisecond activation kinetics, and full responsivity under two-photon illumination. We also introduce an ultrafast local volume excitation (ULOVE) two-photon scanning method to sample ASAP3 signals in awake mice at kilohertz rates with increased stability and sensitivity. ASAP3 and ULOVE allowed continuous single-trial tracking of spikes and subthreshold events for minutes in deep locations, with subcellular resolution, and with repeated sampling over multiple days. By imaging voltage in visual cortex neurons, we found evidence for cell type-dependent subthreshold modulation by locomotion. Thus, ASAP3 and ULOVE enable continuous high-speed high-resolution imaging of electrical activity in deeply located genetically defined neurons during awake behavior.

neuroscience↗

bioRxiv2018

Hypoxia-induced epigenetic silencing of polo-like kinase 2 promotes fibrosis in atrial fibrillation

Fibrosis and inflammation promote atrial fibrillation (AF) and worsen its clinical outcome. The underlying molecular mechanisms, that are relevant for effective antifibrotic drug development, are still under debate. This study deciphers a novel mechanistic interplay between polo-like kinase 2 (PLK2) and the pro-inflammatory cytokine osteopontin (OPN) in the pathogenesis of atrial fibrosis. Compared to sinus rhythm (SR) controls, right atrial appendages and isolated right atrial fibroblasts from AF patients showed downregulation of PLK2 mRNA and protein levels, which were accompanied by remarkable hypoxia-sensitive DNA-methylation of the PLK2 promotor. In an experimental setting, both, genetic deletion and pharmacological inhibition of PLK2 induced myofibroblast differentiation and reduced fibroblast proliferation. Notably, proteomics from PLK2-deleted fibroblasts revealed de novo secretion of OPN. Accordingly, we observed higher OPN plasma levels in AF patients with atrial fibrosis compared to non-fibrosis AF patients. Hence, we provide evidence for PLK2 reactivation and/or OPN inhibition as potential novel targets to prevent fibrosis progression in AF.

pharmacology and toxicology↗

bioRxiv2018

DNA methylation patterns of replicative senescence are strand-specific and reflect changes in chromatin conformation

Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes at specific sites in the genome. These changes might be due to an directly regulated epigenetic process, or to gradual deregulation of the epigenetic state, which is often referred to as "epigenetic drift". We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated in the course of culture expansion of mesenchymal stem cells (MSCs) and other cell types. During reprogramming into induced pluripotent stem cells (iPSCs) particularly the culture-associated hypomethylation is reversed simultaneously with age-associated and pluripotency-associated DNAm changes. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that upon passaging the DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpolulations of MSCs at later passages. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no preferential interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results indicate that DNAm changes during culture-expansion resembles epigenetic drift, which seems to occur in relation to chromatin conformation.

genomics↗

bioRxiv2018

The GBAF chromatin remodeling complex binds H3K27ac and mediates enhancer transcription

H3K27ac is associated with regulatory active enhancers, but its exact role in enhancer function remains elusive. Using mass spectrometry-based interaction proteomics, we identified the Super Elongation Complex (SEC) and GBAF, a non-canonical GLTSCR1L- and BRD9-containing SWI/SNF chromatin remodeling complex, to be major interactors of H3K27ac. We systematically characterized the composition of GBAF and the conserved GLTSCR1/1L GiBAF-domain, which we found to be responsible for GBAF complex formation and GLTSCR1L nuclear localization. Inhibition of the bromodomain of BRD9 revealed interaction between GLTSCR1L and H3K27ac to be BRD9-dependent and led to GLTSCR1L dislocation from its preferred binding sites at H3K27ac-associated enhancers. GLTSCR1L disassociation from chromatin resulted in genome-wide downregulation of enhancer transcription while leaving most mRNA expression levels unchanged, except for reduced mRNA levels from loci topologically linked to affected enhancers. Our results indicate that GBAF is an enhancer-associated chromatin remodeler important for transcriptional and regulatory activity of enhancers.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=142 HEIGHT=200 SRC=\"FIGDIR/small/445148_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@10c54dborg.highwire.dtl.DTLVardef@9730dforg.highwire.dtl.DTLVardef@9985eorg.highwire.dtl.DTLVardef@1f26844_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2018

OSCA: a tool for omic-data-based complex trait analysis

The rapid increase of omic data in the past decades has greatly facilitated the investigation of associations between omic profiles such as DNA methylation (DNAm) and complex traits in large cohorts. Here, we proposed a mixed-linear-model-based method (called MOMENT) that tests for association between a DNAm probe and trait with all other distal probes fitted in multiple random-effect components to account for the effects of unobserved confounders as well as the correlations between distal probes induced by the confounders. We demonstrated by simulations that MOMENT showed a lower false positive rate and more robustness than existing methods. MOMENT has been implemented in a versatile software package (called OSCA) together with a number of other implementations for omic-data-based analysis including the estimation of variance in a trait captured by all measures of multiple omic profiles, omic-data-based quantitative trait locus (xQTL) analysis, and meta-analysis of xQTL data.

bioinformatics↗

bioRxiv2018

Hydrogenotrophic methanogens of the mammalian gut: functionally similar, thermodynamically different. A modelling approach

Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that, in vitro growth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namely Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with concordance correlation coefficients of 0.94 for CO2, 0.99 for H2 and 0.97 for CH4. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we tested in silico the interactions between these methanogens under an in vivo simulation scenario using a theoretical modelling exercise. In silico simulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.

microbiology↗

bioRxiv2018

Nanoscale organization of rotavirus replication machineries

Rotavirus genome replication and assembly take place in cytoplasmic electron dense inclusions termed viro-plasms (VPs). Previous conventional optical microscopy studies observing the intracellular distribution of rotavirus proteins and their organization in VPs have lacked molecular-scale spatial resolution, due to inherent spatial resolution constraints. In this work we employed super-resolution microscopy to reveal the nanometric-scale organization of VPs formed during rotavirus infection, and quantitatively describe the structural organization of seven viral proteins and viral dsRNA within and around the VPs. The observed viral components are spatially organized as 6 concentric layers, in which NSP5 localizes at the center of the VPs, surrounded by a layer of NSP2 and NSP4 proteins, followed by an intermediate zone comprised of the VP1, VP2, VP6 proteins and the dsRNA. In the outermost zone, we observed a ring of VP4 and finally a layer of VP7. These findings show that rotavirus VPs are highly organized organelles.

microbiology↗

bioRxiv2018

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

Genome mining has become a key technology to explore and exploit natural product diversity through the identification and analysis of biosynthetic gene clusters (BGCs). Initially, this was performed on a single-genome basis; currently, the process is being scaled up to large-scale mining of pan-genomes of entire genera, complete strain collections and metagenomic datasets from which thousands of bacterial genomes can be extracted at once. However, no bioinformatic framework is currently available for the effective analysis of datasets of this size and complexity. Here, we provide a streamlined computational workflow, tightly integrated with antiSMASH and MIBiG, that consists of two new software tools, BiG-SCAPE and CORASON. BiG-SCAPE facilitates rapid calculation and interactive visual exploration of BGC sequence similarity networks, grouping gene clusters at multiple hierarchical levels, and includes a glocal alignment mode that accurately groups both complete and fragmented BGCs. CORASON employs a phylogenomic approach to elucidate the detailed evolutionary relationships between gene clusters by computing high-resolution multi-locus phylogenies of all BGCs within and across gene cluster families (GCFs), and allows researchers to comprehensively identify all genomic contexts in which particular biosynthetic gene cassettes are found. We validate BiG-SCAPE by correlating its GCF output to metabolomic data across 403 actinobacterial strains. Furthermore, we demonstrate the discovery potential of the platform by using CORASON to comprehensively map the phylogenetic diversity of the large detoxin/rimosamide gene cluster clan, prioritizing three new detoxin families for subsequent characterization of six new analogs using isotopic labeling and analysis of tandem mass spectrometric data.

bioinformatics↗

bioRxiv2018

Mitochondria form cholesterol-rich contact sites with the nucleus during retrograde response

Mitochondria drive cellular adaptation to stress by retro-communicating with the nucleus. This process is known as Mitochondrial Retrograde Response (MRR) and is induced by mitochondrial dysfunctions which perturb cell signalling. MRR results in the nuclear stabilization and activation of pro-survival transcription factors such as the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB). Here we demonstrate that MRR is facilitated by the formation of contact sites between mitochondria and the nucleus which establish microdomains of communication between the two organelles. The 18kD Translocator Protein (TSPO), which de-ubiquitylates and stabilizes the mitochondrial network preventing its mitophagy-mediated segregation, is required for this interaction. The tethering TSPO enacts is mediated by the complex formed with the Protein Kinase A via the A-kinase anchoring protein Acyl-CoA Binding Domain Containing 3 (ACBD3) and allows the redistribution of cholesterol which sustains the pro-survival response by blocking NF-kB de-acetylation. This work proposes a new paradigm in the mitochondrial retro-communication by revealing the existence of contact sites between mitochondrial and the nucleus and a signalling role for cholesterol.

cell biology↗

bioRxiv2018

Diversification and collapse of a telomere elongation mechanism

In virtually all eukaryotes, telomerase counteracts chromosome erosion by adding repetitive sequence to terminal ends. Drosophila melanogaster instead relies on specialized retrotransposons that insert preferentially at telomeres. This exchange of goods between host and mobile element--wherein the mobile element provides an essential genome service and the host provides a hospitable niche for mobile element propagation--has been called a genomic symbiosis. However, these telomere-specialized, jockey family elements may actually evolve to selfishly over-replicate in the genomes that they ostensibly serve. Under this intra-genomic conflict model, we expect rapid diversification of telomere-specialized retrotransposon lineages and possibly, the breakdown of this tenuous relationship. Here we report data consistent with both predictions. Searching the raw reads of the 15-million-year-old melanogaster species group, we generated de novo jockey retrotransposon consensus sequences and used phylogenetic tree-building to delineate four distinct telomere-associated lineages. Recurrent gains, losses, and replacements account for this striking retrotransposon lineage diversity. Moreover, an ancestrally telomere-specialized element has escaped, residing now throughout the genome of D. rhopaloa. In D. biarmipes, telomere-specialized elements have disappeared completely. De novo assembly of long-reads and cytogenetics confirmed this species-specific collapse of retrotransposon-dependent telomere elongation. Instead, telomere-restricted satellite DNA and DNA transposon fragments occupy its terminal ends. We infer that D. biarmipes relies instead on a recombination-based mechanism conserved from yeast to flies to humans. Combined with previous reports of adaptive evolution at host proteins that regulate telomere length, telomere-associated retrotransposon diversification and disappearance offer compelling evidence that intra-genomic conflict shapes Drosophila telomere evolution.

evolutionary biology↗

bioRxiv2018

Multifunction control and evaluation of a 3D printed hand prosthesis with the Myo armband by hand amputees

Upper limb amputations are highly impairing injuries that can substantially limit the quality of life of a person. The most advanced dexterous prosthetic hands have remarkable mechanical features. However, in most cases, the control systems are a simple extension of basic control protocols, making the use of the prosthesis not intuitive and sometimes complex. Furthermore, the cost of dexterous prosthetic hands is often prohibitive, especially for the pediatric population and developing countries. 3D printed hand prostheses can represent an opportunity for the future. Open 3D models are increasingly being released, even for dexterous prostheses that are capable of moving each finger individually and actively rotating the thumb. However, the usage and test of such devices by hand amputees (using electromyography and classification methods) is not well explored. The aim of this article is to investigate the usage of a cost-effective system composed of a 3D printed hand prosthesis and a low-cost myoelectric armband. Two subjects with transradial amputation were asked to wear a custom-made socket supporting the HANDi Hand and the Thalmic Labs Myo armband. Afterwards, the subjects were asked to control and use the prosthetic hand to grasp several objects by attempting to perform a set of different hand gestures. Both the HANDi Hand and the Myo armband performed well during the test, which is encouraging considering that the HANDi Hand was developed as a research platform. The results are promising and show the feasibility of the multifunction control of dexterous 3D printed hand prostheses based on low-cost setups. Factors as the level of the amputation, neuromuscular fatigue and mechanical limitations of the 3D printed hand prosthesis can influence the performance of the setup. Practical aspects such as usability and robustness will need to be addressed for successful application in daily life. A video of the tests can be found at the following link: https://youtu.be/iPSCAbd17Qw

bioengineering↗

bioRxiv2018

methyl-ATAC-seq measures DNA methylation at accessible chromatin

Chromatin features are characterized by genome-wide assays for nucleosome location, protein binding sites, 3-dimensional interactions, and modifications to histones and DNA. For example, Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed separately in populations of cells, it is impossible to determine, with certainty, where the features are coincident in the genome by simply overlaying datasets. Here we describe methyl-ATAC-seq (mATAC-seq), which implements modifications to ATAC-seq, including subjecting the output to BS-seq. Merging these assays into a single protocol identifies the locations of open chromatin, and reveals, unambiguously, the DNA methylation state of the underlying DNA. Such combinatorial methods eliminate the need to perform assays independently and infer where features are coincident.

genomics↗

bioRxiv2018

Targeting microbial arsenic resistance genes: a new bioinformatic toolkit informs arsenic ecology and evolution in soil genomes and metagenomes

Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity. We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry. Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

microbiology↗

bioRxiv2018

Dopaminergic medication reduces striatal sensitivity to negative outcomes in Parkinson’s disease

Reduced levels of dopamine in Parkinsons disease (PD) contribute to changes in learning, resulting from the loss of midbrain dopamine neurons that transmit a teaching signal to the striatum. Dopamine medication used by PD patients has previously been linked to either behavioral changes during learning itself or adjustments in approach and avoidance behavior after learning. To date, however, very little is known about the specific relationship between dopaminergic medication-driven differences during learning and subsequent changes in approach/avoidance tendencies in individual patients. We assessed 24 PD patients on and off dopaminergic medication and 24 healthy controls (HC) performing a probabilistic reinforcement learning task, while undergoing functional magnetic resonance imaging. During learning, medication in PD reduced an overemphasis on negative outcomes. When patients were on medication, learning rates were lower for negative (but not positive) outcomes and concurrent striatal BOLD responses showed reduced prediction error sensitivity. Medication-induced shifts in negative learning rates were predictive of changes in approach/avoidance choice patterns after learning, and these changes were accompanied by striatal BOLD response alterations. These findings highlight dopamine-driven learning differences in PD and provide new insight into how changes in learning impact the transfer of learned value to approach/avoidance responses in novel contexts.

neuroscience↗

bioRxiv2018

The G protein-biased PZM21 and TRV130 act as partial agonists of μ-opioid receptors signaling to ion channel targets

Opioids exert many of their acute effects through modulating ion channels via G{beta}{gamma} subunits. Some of their side effects are attributed to {beta}-arrestin recruitment, and several biased agonists that do not activate this pathway have been developed recently. Here we tested the effects of TRV130, PZM21 and herkinorin, three G-protein biased agonists of -opioid receptors (OR), on ion channel targets. Compared to the full OR agonist DAMGO, all three biased agonists induced smaller activation of G protein-coupled inwardly rectifying potassium channels (GIRK2), and smaller inhibition of Transient Receptor Potential Melastatin (TRPM3) channels. Furthermore, co-application of TRV130 or PZM21, but not herkinorin reduced the effects of DAMGO on both ion channels. CaV2.2 was also inhibited less by PZM21 and TRV130 than by DAMGO. TRV130, PZM21 and herkinorin were also less effective than DAMGO in inducing dissociation of the Gi /G{beta}{gamma} complex. We conclude that TRV130, PZM21 are partial agonists of OR.

pharmacology and toxicology↗

bioRxiv2018

The Landscape of Parkin Variants Reveals Pathogenic Mechanisms and Therapeutic Targets in PD

Mutations in Parkin (PARK2) are the most common genetic cause of early-onset Parkinsons disease (PD). Parkin encodes an E3 ubiquitin ligase implicated in the turnover of damaged mitochondria. Hundreds of Parkin missense variants have been reported in public databases, yet the role of most of them in PD remains unclear. We analyzed Parkin variants using clinical, experimental, and structural modeling approaches. For most variants, clinical evidence alone was insufficient to determine pathogenicity. Utilizing a cell model that allows measurement of Parkin-mediated mitophagy and Parkin stability, 51 variants were classified into five groups based on their effect on Parkin function. Most variants were like wildtype but, unexpectedly, several enhanced mitophagy. A minority destabilized Parkin or severely disrupted Parkin-mediated mitophagy, most of which were also determined as pathogenic based on clinical evidence alone. Structural simulation predicted discrete mechanisms explaining both increases and decreases in Parkin function. Interestingly, impaired mitophagy in several of the most common pathogenic Parkin variants could be rescued both by naturally-occurring (p.V224A) and structure-guided designer (p.W403A; p.F146A) hyperactive Parkin variants. These findings provide a coherent framework to classify Parkin variants based on pathogenicity and suggest that several pathogenic Parkin variants represent promising targets for genotype-specific drug design.

neuroscience↗