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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,773 bioRxiv papers from 265,845 authors.

Most downloaded bioRxiv papers, since beginning of last month

56,319 results found. For more information, click each entry to expand.

561: Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer's disease
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Posted to bioRxiv 07 Jul 2019

Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer's disease
321 downloads neuroscience

Samuel Morabito, Emily Miyoshi, Neethu Michael, Vivek Swarup

Alzheimer's disease (AD) is a devastating neurological disorder characterized by changes in cell-type proportions and consequently marked alterations of the transcriptome. Here we use a data-driven systems biology approach across multiple cohorts of human AD, encompassing different brain regions, and integrate with multi-scale datasets comprising of DNA methylation, histone acetylation, transcriptome- and genome-wide association studies as well as quantitative trait loci to define the genetic architecture of AD. We perform co-expression network analysis across more than twelve hundred human brain samples, identifying robust AD-associated dysregulation of the transcriptome, unaltered in normal human aging. We further integrate co-expression modules with single-cell transcriptome generated from 27,321 nuclei from postmortem human brain to identify AD-specific transcriptional changes and assess cell-type proportion changes in the human AD brain. We also show that genetic variants of AD are enriched in a glial AD-associated module and identify key transcription factors regulating co-expressed modules. Additionally, we validate our results in multiple published human AD datasets which are easily accessible using our online resource (https://swaruplab.bio.uci.edu/consensusAD) .

562: The Molecular and Structural Asymmetry of the Plasma Membrane
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Posted to bioRxiv 11 Jul 2019

The Molecular and Structural Asymmetry of the Plasma Membrane
321 downloads cell biology

Joseph H Lorent, Lakshmi Ganesan, Gia Longsworth, Erdinc Sezgin, Kandice R Levental, Ed Lyman, Ilya Levental

A fundamental feature of cellular plasma membranes (PM) is the asymmetric distribution of lipids between the bilayer leaflets. This asymmetry is central to cellular physiology, regulating signaling, apoptosis, coagulation, and cell-cell fusion. While the broad transbilayer distributions of some lipid types are well established, the detailed lipidomic asymmetry of the PM has not been characterized and thus the compositions of the individual leaflets remain poorly understood. Further, how these compositional differences contribute to structural asymmetries between PM leaflets in living cells is not defined. Here, we report the distinct lipidomes and biophysical properties of both monolayers in living mammalian PMs. Using mass spectrometry coupled to enzymatic digestion, we report the detailed compositions of PM leaflets of human erythrocytes. We find a dramatic asymmetry in phospholipid unsaturation, with the cytoplasmic leaflet being ~2-fold more unsaturated than the exoplasmic. Atomistic simulations of lipid mixtures compiled from the lipidomic observations suggested significant asymmetries in lipid order, packing, and dynamics between the two PM leaflets. These were probed directly in the PM of living cells by Fluorescence Lifetime Imaging Microscopy (FLIM) of leaflet-selective, environment-sensitive probes. The outer PM leaflet is highly packed and ordered, resembling a liquid ordered phase, whereas the inner leaflet is significantly more disordered. This biophysical asymmetry is maintained in the endocytic system. These observations reveal the detailed compositional and biophysical asymmetry of mammalian plasma membranes, elucidating fundamental design principles of living membranes.

563: Perifornical Area Urocortin-3 Neurons Promote Infant-directed Neglect and Aggression
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Posted to bioRxiv 09 Jul 2019

Perifornical Area Urocortin-3 Neurons Promote Infant-directed Neglect and Aggression
321 downloads neuroscience

Anita E Autry, Zheng Wu, Johannes Kohl, Dhananjay Bambah-Mukku, Nimrod D Rubinstein, Brenda Marin-Rodriguez, Ilaria Carta, Victoria Sedwick, Catherine Dulac

Mammals invest considerable resources in protecting and nurturing young offspring. However, under certain physiological and environmental conditions, animals neglect or attack young conspecifics. Males in some species attack unfamiliar infants to gain reproductive advantage and females kill or neglect their young during stressful circumstances such as food shortage or threat of predation. In humans, stress is a risk factor in both sexes for peripartum disorders and associated impairments in parent-infant interactions. While recent studies have uncovered dedicated neural pathways mediating the positive control of parenting, the regulation of infant-directed neglect and aggression and the relationship between these behaviours and stress are poorly understood. Here we show that urocortin-3 (Ucn3)-expressing neurons in the perifornical area (PeFAUcn3) of the hypothalamus are activated during infant-directed attacks in males and females, but not other forms of aggression. Opto- and chemogenetic manipulations of PeFAUcn3 neurons demonstrate the role of this neuronal population in the negative control of parenting in both males and females. PeFAUcn3 neurons receive input from areas associated with vomeronasal sensing, stress, and parenting, and send major projections to the ventromedial hypothalamus (VMH), ventral lateral septum (LSv) and amygdalohippocampal area (AHi). Optogenetic activation of PeFAUcn3 axon terminals in these regions triggers different aspects of infant-directed agonistic responses, such as neglect and aggression. Thus, PeFAUcn3 neurons emerge as a critical hub for the expression of infant-directed neglect and aggression, providing a new framework to examine the positive and negative regulation of parenting.

564: Benchmarking Tools for Copy Number Aberration Detection from Single-cell DNA Sequencing Data
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Posted to bioRxiv 09 Jul 2019

Benchmarking Tools for Copy Number Aberration Detection from Single-cell DNA Sequencing Data
321 downloads bioinformatics

Xian Fan, Mohammadamin Edrisi, Nicholas Navin, Luay Nakhleh

Accurate detection of copy number aberrations (CNA) can aid in understanding the genetic causes of diseases. Three methods (CopyNumber, Ginkgo, and HMMcopy) have been applied to single-cell DNA sequencing data for CNA detection. In this paper, we benchmarked these three methods on simulated as well as biological datasets. We found that HMMcopy has the best accuracy of the three methods in terms of breakpoint detection but that Ginkgo is better in terms of detecting the actual copy numbers. In terms of computational requirements, HMMcopy consumes the least memory, but is in between the two other methods in terms of running time. While single-cell DNA sequencing is very promising for elucidating and understanding CNAs, even the best existing method does not exceed 80% accuracy. New methods that significantly improve upon the accuracy of these three methods are needed. Furthermore, with the large datasets being generated, the methods must be computationally efficient.

565: Recovering signals of ghost archaic introgression in African populations
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Posted to bioRxiv 21 Mar 2018

Recovering signals of ghost archaic introgression in African populations
320 downloads genomics

Arun Durvasula, Sriram Sankararaman

While introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. Using 405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations that recover about 482 and 502 megabases of archaic sequence, respectively. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day African populations.

566: The role of lipoprotein subfractions in coronary artery disease: A Mendelian randomization study
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Posted to bioRxiv 03 Jul 2019

The role of lipoprotein subfractions in coronary artery disease: A Mendelian randomization study
320 downloads genetics

Qingyuan Zhao, Jingshu Wang, Zhen Miao, Nancy R Zhang, Sean Hennessy, Dylan S Small, Daniel J Rader

Lipoprotein subfractions and particle sizes are increasingly used in observational studies to predict the risk of cardiovascular diseases. However, the causal role of the different subfractions remain largely uncertain because the conventional study designs are subject to unmeasured confounding. We used Mendelian randomization and public GWAS summary data to estimate the effect of 82 lipoprotein subfraction and particle size traits on the occurrence of coronary artery disease and myocardial infarction. We found that, unlike LDL and VLDL subfractions, HDL subfraction traits appear to have heterogeneous effects on coronary artery disease according to particle size. The concentration of medium HDL particles may have a protective effect on coronary artery disease that is independent of traditional lipid factors.

567: A new twist on bacterial motility – Two distinct type IV pili revealed by cryoEM
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Posted to bioRxiv 31 Jul 2019

A new twist on bacterial motility – Two distinct type IV pili revealed by cryoEM
320 downloads biophysics

Alexander Neuhaus, Muniyandi Selvaraj, Ralf Salzer, Julian Langer, Kerstin Kruse, Kelly Sanders, Bertram Daum, Beate Averhoff, Vicki Gold

Many bacteria express flexible protein filaments on their surface that enable a variety of important cellular functions. Type IV pili are examples of such filaments and are comprised of a helical assembly of repeating pilin subunits. Type IV pili are involved in motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). They are therefore powerful structures that enable bacterial proliferation and genetic adaptation, potentially leading to the development of pathogenicity and antibiotic resistance. They are also targets for drug development. By a complement of experimental approaches, we show that the bacterium Thermus thermophilus produces two different forms of type IV pilus. We have determined the structures of both and built atomic models. The structures answer key unresolved questions regarding the molecular architecture of type IV pili and identify a new type of pilin. We also delineate the roles of the two filaments in promoting twitching and natural transformation.

568: CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis
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Posted to bioRxiv 23 Jan 2019

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis
319 downloads genomics

Qian Zhu, Nan Liu, Stuart H Orkin, Guo-cheng Yuan

We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. CUT&RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.

569: Single-cell glycolytic activity regulates membrane tension 1 and HIV-1 fusion
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Posted to bioRxiv 04 Jul 2019

Single-cell glycolytic activity regulates membrane tension 1 and HIV-1 fusion
319 downloads immunology

Charles A Coomer, Irene Carlon-Andres, Maro Iliopoulou, Michael L. Dustin, Ewoud B Compeer, Alex A Compton, Sergi Padilla-Parra

There has been resurgence in determining the role of host metabolism in viral infection yet deciphering how the metabolic state of single cells affects viral entry and fusion remains unknown. Here, we have developed a novel assay multiplexing genetically encoded biosensors with single virus tracking (SVT) to evaluate the influence of global metabolic processes on the success rate of virus entry in single cells. We found that cells with a lower ATP:ADP ratio prior to virus addition were less permissive to virus fusion and infection. These results indicated a relationship between host metabolic state and the likelihood for virus-cell fusion to occur. SVT revealed that HIV-1 viruses were arrested at hemifusion in glycolytically-inactive cells. Interestingly, cells acutely treated with glycolysis inhibitor 2-deoxyglucose (2-DG) become resistant to virus infection and also display less surface membrane cholesterol. Addition of cholesterol in these in glycolytically-inactive cells rescued the virus entry block at hemifusion and enabled completion of HIV-1 fusion. Further investigation with FRET-based membrane tension and membrane-order reporters revealed a link between host cell glycolytic activity and host membrane order and tension. Indeed, cells treated with 2-DG possessed lower plasma membrane lipid order and higher tension values, respectively. Our novel imaging approach that combines lifetime imaging (FLIM) and SVT revealed not only changes in plasma membrane tension at the point of viral fusion, but also that HIV is less likely to enter cells at areas of higher membrane tension. We therefore have identified a connection between host cell glycolytic activity and membrane tension that influences HIV-1 fusion in real-time at the single-virus fusion level in live cells. As glycolytic activity sets membrane tension levels by altering cellular cholesterol surface levels, our results suggest additional previously unknown benefits of cholesterol-lowering medication in HIV-1 patients.

570: Origination of the circadian clock system in stem cells regulates cell differentiation in Arabidopsis thaliana.
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Posted to bioRxiv 22 Jul 2019

Origination of the circadian clock system in stem cells regulates cell differentiation in Arabidopsis thaliana.
319 downloads plant biology

Kotaro Torii, Keisuke Inoue, Keita Bekki, Kazuya Haraguchi, Minoru Kubo, Yuki Kondo, Takamasa Suzuki, Hanako Shimizu, Kyohei Uemoto, Masato Saito, Hiroo Fukuda, Takashi Araki, Motomu Endo

The circadian clock regulates various physiological responses. To achieve this, both animals and plants have distinct circadian clocks in each tissue that are optimized for that tissue's respective functions. However, if and how the tissue-specific circadian clocks are involved in specification of cell types remains unclear. Here, by implementing a single-cell transcriptome with a new analytics pipeline, we have reconstructed an actual time-series of the cell differentiation process at single-cell resolution, and discovered that the Arabidopsis circadian clock is involved in the process of cell differentiation through transcription factor BRI1-EMS SUPPRESSOR 1 (BES1) signaling. In this pathway, direct repression of LATE ELONGATED HYPOCOTYL (LHY) expression by BES1 triggers reconstruction of the circadian clock in stem cells. The reconstructed circadian clock regulates cell differentiation through fine-tuning of key factors for epigenetic modification, cell-fate determination, and the cell cycle. Thus, the establishment of circadian systems precedes cell differentiation and specifies cell types.

571: Resolving heterogeneous high-mass macromolecular machineries by Orbitrap-based single particle charge detection mass spectrometry
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Posted to bioRxiv 28 Jul 2019

Resolving heterogeneous high-mass macromolecular machineries by Orbitrap-based single particle charge detection mass spectrometry
318 downloads biophysics

Albert J.R. Heck, Tobias P. Woerner, Joost Snijder, Antonette D Bennett, Mavis Agbandje-McKenna, Alexander Makarov

Here we show that single particle charge-detection mass spectrometry (CD-MS) can be performed on a ubiquitous Orbitrap mass analyser and applied to the analysis of high-mass (megadalton) heterogeneous biomolecular assemblies. We demonstrate that single particle high-mass ions can survive in the Orbitrap for seconds, whereby their measured signal amplitudes scale linearly with charge state over the entire m/z range. Orbitrap based single particle CD-MS can be used to resolve mixed ion populations, accurately predict charge states, and consequently also the mass of the ions. We successfully applied CD-MS to challenging natural and biotherapeutic protein assemblies, such as IgM oligomers, designed protein nano-cages, ribosome particles and intact, empty- and genome-loaded Adeno-associated virus particles. Single particle CD-MS combined with native MS on existing Orbitrap platforms will greatly expand its application, especially in the mass analysis of megadalton heterogeneous biomolecular assemblies.

572: Machine translation of cortical activity to text with an encoder-decoder framework
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Posted to bioRxiv 22 Jul 2019

Machine translation of cortical activity to text with an encoder-decoder framework
317 downloads neuroscience

Joseph G. Makin, David A. Moses, Edward F Chang

A decade after the first successful attempt to decode speech directly from human brain signals, accuracy and speed remain far below that of natural speech or typing. Here we show how to achieve high accuracy from the electrocorticogram at natural-speech rates, even with few data (on the order of half an hour of spoken speech). Taking a cue from recent advances in machine translation and automatic speech recognition, we train a recurrent neural network to map neural signals directly to word sequences (sentences). In particular, the network first encodes a sentence-length sequence of neural activity into an abstract representation, and then decodes this representation, word by word, into an English sentence. For each participant, training data consist of several spoken repeats of a set of some 30-50 sentences, along with the corresponding neural signals at each of about 250 electrodes distributed over peri-Sylvian speech cortices. Average word error rates across a validation (held-out) sentence set are as low as 7% for some participants, as compared to the previous state of the art of greater than 60%. Finally, we show how to use transfer learning to overcome limitations on data availability: Training certain components of the network under multiple participants' data, while keeping other components (e.g., the first hidden layer) "proprietary," can improve decoding performance--despite very different electrode coverage across participants.

573: CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources
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Posted to bioRxiv 08 Jul 2019

CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources
317 downloads bioinformatics

Kevin Vervier, Hilary P. Browne, Trevor Lawley

The Biolog Phenotype Microarray (PM) and Anaerobic MicroPlates (AN) 96-well plates utilise colorimetric redox reactions to rapidly screen bacteria for the ability to utilise different carbon sources and other metabolites. Measurement of substrate utilisation as bacterial growth curves typically involves extended data normalization, outlier detection, and statistical analysis. The CarboLogR package streamlines this process with a Shiny application, guiding users from raw data generated from Biolog assays to growth profile comparison. We applied chemoinformatics approaches to define clusters of carbon sources, based on molecular similarities, increasing statistical power. Altogether, CarboLogR is a novel integrated tool providing automatic and high-level resolution for bacterial growth patterns and carbon source usage. Availability and Implementation: CarboLogR application can be downloaded and installed from Github repository https://github.com/kevinVervier/CarboLogR. Tutorial, data, and examples can be downloaded at https://github.com/kevinVervier/CarboLogR/vignettes. Contact: kv4@sanger.ac.uk

574: Bright split red fluorescent proteins with enhanced complementation efficiency for the tagging of endogenous proteins and visualization of synapses
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Posted to bioRxiv 25 Oct 2018

Bright split red fluorescent proteins with enhanced complementation efficiency for the tagging of endogenous proteins and visualization of synapses
317 downloads cell biology

Siyu Feng, Aruna Varshney, Doris Coto Villa, Cyrus Modavi, John Kohler, Fatima Farah, Nebat Ali, Joachim D Mueller, Miri VanHoven, Bo Huang

Self-associating split fluorescent proteins (FPs) have been widely used for labeling proteins, scaffolding protein assembly and detecting cell-cell contacts. Newly developed self-associating split FPs, however, have suffered from suboptimal fluorescence signal. Here, by investigating the complementation process, we have demonstrated two approaches to improve split FPs: assistance through SpyTag/SpyCatcher interaction and directed evolution. The latter has yielded two split sfCherry3 variants with substantially enhanced overall brightness, facilitating the tagging of endogenous proteins by gene editing. Based on sfCherry3, we have further developed a new red-colored trans-synaptic marker called Neuroligin-1 sfCherry3 Linker Across Synaptic Partners (NLG-1 CLASP) for multiplexed visualization of neuronal synapses in living animals, demonstrating its broad applications.

575: Ecological causes of uneven diversification and richness in the mammal tree of life
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Posted to bioRxiv 04 Jan 2019

Ecological causes of uneven diversification and richness in the mammal tree of life
317 downloads evolutionary biology

Nathan S. Upham, Jacob A Esselstyn, Walter Jetz

The uneven distribution of species in the tree of life is rooted in unequal speciation and extinction among groups. Yet the causes of differential diversification are little known despite their relevance for sustaining biodiversity into the future. Here we investigate rates of species diversification across extant Mammalia, a compelling system that includes our own closest relatives. We develop a new phylogeny of nearly all ~6000 species using a 31-gene supermatrix and fossil node- and tip-dating approaches to establish a robust evolutionary timescale for mammals. Our findings link the causes of uneven modern species richness with ecologically-driven variation in rates of speciation and/or extinction, including 24 detected shifts in net diversification. Speciation rates are a stronger predictor of among-clade richness than clade age, countering claims of clock-like speciation in large phylogenies. Surprisingly, speciation rate heterogeneity in recent radiations shows limited association with latitude, despite the well-known increase in species richness toward the equator. Instead, we find a deeper-time association where clades of high-latitude species have the highest speciation rates, suggesting that species durations are shorter (turnover is higher) outside than inside the tropics. At shallower timescales (i.e., young clades), diurnality and low vagility are both linked to greater speciation rates and extant richness. We suggest that high turnover among small-ranged allopatric species has erased the signal of vagility in older clades, while diurnality has adaptively promoted lineage persistence. These findings highlight the underappreciated joint roles of ephemeral (turnover-based) and adaptive (persistence-based) processes of diversification, which manifest in recent and more ancient evolutionary radiations of mammals to explain modern diversity.

576: Microglia are necessary for normal functional development of adult-born neurons in the olfactory bulb
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Posted to bioRxiv 25 Jul 2019

Microglia are necessary for normal functional development of adult-born neurons in the olfactory bulb
316 downloads neuroscience

Jenelle L Wallace, Julia Lord, Lasse Dissing-Olesen, Beth Stevens, Venkatesh N Murthy

Microglia play key roles in regulating synapse development and refinement in the developing brain, but it is unknown whether they are similarly involved during adult neurogenesis. By transiently ablating microglia from the healthy adult mouse brain, we show that microglia are necessary for the normal functional development of adult-born granule cells (abGCs) in the olfactory bulb. Microglia ablation reduces the odor responses of developing, but not preexisting GCs in vivo in both awake and anesthetized mice. Microglia preferentially target their motile processes to interact with mushroom spines on abGCs, and when microglia are absent, abGCs develop smaller spines and receive weaker excitatory synaptic inputs. These results suggest that microglia promote the development of excitatory synapses onto developing abGCs, which may impact the function of these cells in the olfactory circuit.

577: Surpassing the physical Nyquist limit to produce super-resolution cryo-EM reconstructions
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Posted to bioRxiv 19 Jun 2019

Surpassing the physical Nyquist limit to produce super-resolution cryo-EM reconstructions
316 downloads biophysics

J. Ryan Feathers, Katherine A. Spoth, J. Christopher Fromme

Recent advances in single-particle cryo-electron microscopy (cryo-EM) methods have led to the determination of hundreds of high-resolution (< 4.0 Å) macromolecular structures. However, access to high-end instrumentation can be scarce and expensive. The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In principle, super-resolution imaging should enable reconstructions to surpass the physical Nyquist limit by increasing sampling frequency, yet there are no reports of reconstructions that do so. Here we report the use of super-resolution imaging with the K3 direct electron detector to produce super-resolution cryo-EM reconstructions significantly surpassing the physical Nyquist limit. We demonstrate that super-resolution imaging can be used to capture high-resolution information at lower magnifications, facilitating the imaging of thousands of particles per micrograph and maximizing the use of limited instrument time. Remarkably, using this approach we produced a 3.7 Å reconstruction of jack bean urease with particles selected from a single micrograph.

578: RNA velocity and protein acceleration from single-cell multiomics experiments
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Posted to bioRxiv 06 Jun 2019

RNA velocity and protein acceleration from single-cell multiomics experiments
316 downloads bioinformatics

Gennady Gorin, Valentine Svensson, Lior Pachter

The simultaneous quantification of protein and RNA makes possible the inference of past, present and future cell states from single experimental snapshots. To enable such temporal analysis from multimodal single-cell experiments, we introduce an extension of the RNA velocity method that leverages estimates of unprocessed transcript and protein abundances to extrapolate cell states. We apply the model to four datasets and demonstrate consistency among landscapes and phase portraits.

579: Estimates of genetic load in small populations suggest extensive purging of deleterious alleles
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Posted to bioRxiv 09 Jul 2019

Estimates of genetic load in small populations suggest extensive purging of deleterious alleles
316 downloads genomics

Tom van der Valk, Marc de Manuel, Tomas Marques-Bonet, Katerina Guschanski

Declining populations are expected to experience negative genetic consequences of inbreeding, which over time can drive them to extinction. Yet, many species have survived in small populations for thousands of generations without apparent fitness effects, possibly due to genetic purging of partially deleterious recessive alleles in inbred populations. We estimate the abundance of deleterious alleles in a range of mammals and find that conversely to current conservation thinking species with historically small population size and low genetic diversity generally have lower genetic load compared to species with large population sizes. Rapid population declines will thus dis-proportionally affect species with high diversity, as they carry many deleterious alleles that can reach fixation before being removed by genetic purging.

580: The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production
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Posted to bioRxiv 24 Jun 2019

The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production
316 downloads microbiology

Stefano Campanaro, Laura Treu, Luis M Rodríguez Rojas, Adam Kovalovszki, Ryan Ziels, Irena Maus, Xinyu Zhu, Panagiotis G Kougias, Arianna Basile, Gang Luo, Andreas Schlüter, Konstantinos T. Konstantinidis, Irini Angelidaki

Background: Microorganisms in biogas reactors are essential for degradation of organic matter and methane production.. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. Results: Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1,635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be >50% complete and nearly half ≥90% complete with ≤5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth rate for microbes involved in different steps of the food chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter. Conclusions: The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.

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