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Currently indexing 73,081 bioRxiv papers from 318,277 authors.

Most tweeted bioRxiv papers, last 7 days

Results 1 through 20 out of 732


1: Severe acute respiratory syndrome-related coronavirus – The species and its viruses, a statement of the Coronavirus Study Group

Alexander E. Gorbalenya

177 tweets (posted 11 Feb 2020) microbiology

The present outbreak of lower respiratory tract infections, including respiratory distress syndrome, is the third spillover, in only two decades, of an animal coronavirus to humans resulting in a major epidemic. Here, the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the official classification of viruses and taxa naming (taxonomy) of the Coronaviridae family, assessed the novelty of the human pathogen tentatively named 2019-nCoV. Based on phylogeny, taxonomy and established practice, the CSG formally recognizes this virus as a sister to severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus and designates it as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To facilitate communication, the CSG further proposes to use the following naming convention for individual isolates: SARS-CoV-2/Isolate/Host/Date/Location. The spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined. The independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying the entire (virus) species to complement research focused on individual pathogenic viruses of immediate significance. This research will improve our understanding of virus-host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.


2: iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone

Aspyn Palatnick, Bin Zhou et al.

149 tweets (posted 12 Feb 2020) bioinformatics

Following the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is following a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the near horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in remote stations around the world. However, despite the simplicity of the sequen...


3: Macrophages transfer mitochondria to neurons to resolve inflammatory pain

Ramin Raoof, Michiel van der Vlist et al.

115 tweets (posted 13 Feb 2020) neuroscience

The current paradigm states that inflammatory pain passively resolves following the cessation of the inflammatory insult. Yet, in a substantial proportion of patients with inflammatory diseases, such as rheumatoid arthritis and inflammatory bowel disease, spontaneous or treatment-induced resolution of inflammation is not sufficient to resolve pain, resulting in chronic pain. Mechanistic insight as how inflammatory pain is resolved is lacking. Here we show that macrophages actively control resolution of inflammatory pain...


4: Rapid and Efficient Co-Transcriptional Splicing Enhances Mammalian Gene Expression

Kirsten A. Reimer, Claudia Mimoso et al.

88 tweets (posted 12 Feb 2020) molecular biology

Pre-mRNA splicing is tightly coordinated with transcription in yeasts, and introns can be removed soon after they emerge from RNA polymerase II (Pol II). To determine if splicing is similarly rapid and efficient in mammalian cells, we performed long read sequencing of nascent RNA during mouse erythropoiesis. Remarkably, 50% of splicing occurred while Pol II was within 150 nucleotides of 3' splice sites. PRO-seq revealed that Pol II does not pause around splice sites, confirming that mammalian and yeast spliceosomes can ...


5: Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov

Yu Zhao, Zixian Zhao et al.

82 tweets (posted 26 Jan 2020) bioinformatics

A novel coronavirus (2019-nCov) was identified in Wuhan, Hubei Province, China in December of 2019. This new coronavirus has resulted in thousands of cases of lethal disease in China, with additional patients being identified in a rapidly growing number internationally. 2019-nCov was reported to share the same receptor, Angiotensin-converting enzyme 2 (ACE2), with SARS-Cov. Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 RNA expression profile in the normal ...


6: UMAP does not preserve global structure any better than t-SNE when using the same initialization

Dmitry Kobak, George C. Linderman

80 tweets (posted 19 Dec 2019) bioinformatics

One of the most ubiquitous analysis tools employed in single-cell transcriptomics and cytometry is t-distributed stochastic neighbor embedding (t-SNE), used to visualize individual cells as points on a 2D scatter plot such that similar cells are positioned close together. Recently, a related algorithm, called uniform manifold approximation and projection (UMAP) has attracted substantial attention in the single-cell community. In Nature Biotechnology, Becht et al. argued that UMAP is preferable to t-SNE because it better...


7: Climate and urbanization drive mosquito preference for humans

Noah H. Rose, Massamba Sylla et al.

75 tweets (posted 13 Feb 2020) evolutionary biology

The majority of mosquito-borne illness is spread by a few mosquito species that have evolved to specialize in biting humans, yet the precise causes of this behavioral shift are poorly understood. We address this gap in the arboviral vector Aedes aegypti . We first characterize the behaviour of mosquitoes from 27 sites scattered across the species' ancestral range in sub-Saharan Africa, revealing previously unrecognized diversity in female preference for human versus animal odor. We then use modelling to show that this d...


8: Predicting brain function from anatomy using geometric deep learning

Fernanda Lenita Ribeiro, Steffen Bollmann et al.

69 tweets (posted 12 Feb 2020) neuroscience

Whether it be in a single neuron or a more complex biological system like the human brain, form and function are often directly related. The functional organization of human visual cortex, for instance, is tightly coupled with the underlying anatomy. This is seen in properties such as cortical magnification (i.e., there is more cortex dedicated to processing foveal vs. peripheral information) as well as in the presence, placement, and connectivity of multiple visual areas - which is critical for the hierarchical process...


9: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag

Prashant Pradhan, Ashutosh Kumar Pandey et al.

60 tweets (posted 31 Jan 2020) evolutionary biology

This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author.


10: Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

Coline Arnould, Vincent Rocher et al.

56 tweets (posted 13 Feb 2020) molecular biology

DNA Double-Strand Breaks (DSBs) repair is essential to safeguard genome integrity. Upon DSBs, the ATM PI3K kinase rapidly triggers the establishment of megabase-sized, γH2AX-decorated chromatin domains which further act as seeds for the formation of DNA Damage Response (DDR) foci. How these foci are rapidly assembled in order to establish a "repair-prone" environment within the nucleus is yet unclear. Topologically Associating Domains (TADs) are a key feature of 3D genome organization that regulate transcription and rep...


11: Stress fibers are embedded in a contractile cortical network.

Timothee Vignaud, Calina Copos et al.

56 tweets (posted 12 Feb 2020) cell biology

Contractile actomyosin networks generate intracellular forces essential for the regulation of cell shape, migration, and cell-fate decisions, ultimately leading to the remodeling and patterning of tissues. Although actin filaments aligned in bundles represent the main source of traction-force production in adherent cells, there is increasing evidence that these bundles form interconnected and interconvertible structures with the rest of the intracellular actin network. In this study, we explored how these bundles are co...


12: Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019

Matthew C Wong, Sara J Javornik Cregeen et al.

53 tweets (posted 13 Feb 2020) microbiology

A novel coronavirus (nCoV-2019) was the cause of an outbreak of respiratory illness detected in Wuhan, Hubei Province, China in December of 2019. Genomic analyses of nCoV-2019 determined a 96% resemblance with a coronavirus isolated from a bat in 2013 (RaTG13); however, the receptor binding motif (RBM) of these two genomes share low sequence similarity. This divergence suggests a possible alternative source for the RBM coding sequence in nCoV-2019. We identified high sequence similarity in the RBM between nCoV-2019 and ...


13: Single mosquito metatranscriptomics recovers mosquito species, blood meal sources, and microbial cargo, including viral dark matter

Joshua Batson, Amy Kistler et al.

53 tweets (posted 13 Feb 2020) microbiology

Mosquitoes are a disease vector with a complex ecology involving interactions between transmissible pathogens, endogenous microbiota, and human and animal blood meal sources. Unbiased metatranscriptomic sequencing of individual mosquitoes offers a straightforward and rapid way to characterize these dynamics. Here, we profile 148 diverse wild-caught mosquitoes collected in California, detecting sequences from eukaryotes, prokaryotes, and over 70 known and novel viral species. Because we sequenced singletons, it was possi...


14: Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem

Ya-Jou Chen, Pok Man Leung et al.

48 tweets (posted 13 Feb 2020) microbiology

Ecological theory suggests that habitat disturbance differentially influences distributions of generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and other conditions. Microbial community composition and function was profiled in intertidal and subtidal sediments using 16S amplicon sequencing and metagenom...


15: How many bird and mammal extinctions has recent conservation action prevented?

Friederike C Bolam, Louise Mair et al.

47 tweets (posted 12 Feb 2020) ecology

Aichi Target 12 of the Convention on Biological Diversity (CBD) aims to 'prevent extinctions of known threatened species'. To measure its success, we used a Delphi expert elicitation method to estimate the number of bird and mammal species whose extinctions were prevented by conservation action in 1993 - 2020 (the lifetime of the CBD) and 2010 - 2020 (the timing of Aichi Target 12). We found that conservation prevented 21-32 bird and 7-16 mammal extinctions since 1993, and 9-18 bird and 2-7 mammal extinctions since 2010...


16: Genome-enabled insights into the biology of thrips as crop pests

Dorith Rotenberg, Aaron A. Baumann et al.

47 tweets (posted 13 Feb 2020) genomics

Background : The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber and ornamental crops. While there are numerous studies centered on thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance, the underlying genetic mechanisms of the processes governing these areas of research are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Result...


17: The Landscape of Mutational Mosaicism in Autistic and Normal Human Cerebral Cortex

Rachel E Rodin, Yanmei Dou et al.

47 tweets (posted 12 Feb 2020) neuroscience

Although somatic mutations have well-established roles in cancer and certain focal epilepsies, the extent to which mutational mosaicism shapes the developing human brain is poorly understood. Here we characterize the landscape of somatic mutations in the human brain using ultra-deep (~250x) whole-genome sequencing of brains from 59 autism spectrum disorder (ASD) cases and 15 controls. We observe a mean of 26 (±10, range 10-60) somatic single nucleotide variants (sSNVs) per brain present in ≥4% of cells, with enrichment ...


18: Viral integration transforms chromatin to drive oncogenesis

Mehran Karimzadeh, Christopher Arlidge et al.

45 tweets (posted 13 Feb 2020) cancer biology

Human papilloma virus (HPV) drives almost all cervical cancers and up to ~70 of head and neck cancers. Frequent integration into the host genome occurs only for tumourigenic strains of HPV. We hypothesized that changes in the epigenome and transcriptome contribute to the tumourigenicity of HPV. We found that viral integration events often occurred along with changes in chromatin state and expression of genes near the integration site. We investigated whether introduction of new transcription factor binding sites due to ...


19: A population-level invasion by transposable elements in a fungal pathogen

Ursula Oggenfuss, Thomas Badet et al.

45 tweets (posted 12 Feb 2020) genomics

Transposable elements (TEs) are key drivers of adaptive evolution within species. Yet, the propagation of TEs across the genome can be highly deleterious and ultimately lead to genome expansions. Hence, TE activity is likely under complex selection regimes within species. To address this, we analyzed a large whole-genome sequencing dataset of the fungal wheat pathogen Zymoseptoria tritici harboring TE-mediated adaptations to overcome host defenses and fungicides. We built a robust map of genome-wide TE insertion and del...


20: Analysis of cardiac magnetic resonance imaging traits in 29,000 individuals reveals shared genetic basis with dilated cardiomyopathy

James Pirruccello, Alexander G Bick et al.

43 tweets (posted 13 Feb 2020) genomics

Dilated cardiomyopathy (DCM) is an important cause of heart failure and the leading indication for heart transplantation. Many rare genetic variants have been associated with DCM, but common variant studies of the disease have yielded few associated loci. As structural changes in the heart are a defining feature of DCM, we conducted a genome-wide association study (GWAS) of cardiac magnetic resonance imaging (MRI)-derived left ventricular measurements in 29,041 UK Biobank participants. 26 novel loci were associated with...