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Currently indexing 52,871 bioRxiv papers from 244,990 authors.

Most tweeted bioRxiv papers, last 24 hours

Results 1 through 20 out of 218


1: High precision coding in mouse visual cortex

Carsen Stringer, Michalis Michaelos et al.

388 tweets (posted 21 Jun 2019) neuroscience

Single neurons in visual cortex provide unreliable measurements of visual features due to their high trial-to-trial variability. It is not known if this "noise" extends its effects over large neural populations to impair the global encoding of sensory stimuli. We recorded simultaneously from ~20,000 neurons in mouse visual cortex and found that the neural population had discrimination thresholds of 0.3 degrees in an orientation decoding task. These thresholds are ~100 times smaller than those reported behaviorally in mice. The discrepancy between neural and behavioral discrimination could not be explained by the types of stimuli we used, by behavioral states or by the sequential nature of trial-by-trial perceptual learning tasks. These results imply that the limits of sensory perception in mice are not set by neural noise in sensory cortex, but by the limitations of downstream decoders.


2: The effect of bioRxiv preprints on citations and altmetrics

Nicholas Fraser, Fakhri Momeni et al.

194 tweets (posted 22 Jun 2019) scientific communication and education

A potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently publis...


3: High genetic diversity can contribute to extinction in small populations

Christopher C. Kyriazis, Robert K Wayne et al.

64 tweets (posted 21 Jun 2019) evolutionary biology

Human-driven habitat fragmentation and loss has led to a proliferation of small and isolated plant and animal populations that may be threatened with extinction by genetic factors. The prevailing approach for managing these populations is to maintain high genetic diversity, which is often equated with fitness. Increasingly, this is being done using genetic rescue, where individuals from populations with high genetic diversity are translocated to small populations with high levels of inbreeding. However, the potentially ...


4: Motility induced fracture reveals a ductile to brittle crossover in the epithelial tissues of a simple animal

Vivek N. Prakash, Matthew Storm Bull et al.

53 tweets (posted 19 Jun 2019) biophysics

Animals are characterized by their movement, and their tissues are continuously subjected to dynamic force loading while they crawl, walk, run or swim [1]. Tissue mechanics fundamentally determine the ecological niches that can be endured by a living organism [2]. While epithelial tissues provide an important barrier function in animals, they are subjected to extreme strains during day to day physiological activities, such as breathing [1], feeding [3], and defense response [4]. However, failure or inability to withstan...


5: A receptor for herbivore-associated molecular patterns mediates plant immunity

Adam D Steinbrenner, Maria Munoz-Amatriain et al.

40 tweets (posted 22 Jun 2019) plant biology

Plant-herbivore interactions are ubiquitous across nature and drive major agricultural losses. Inducible defense responses triggered through immune recognition aid in host plant protection; however, specific ligand-receptor pairs mediating the initial perception of herbivory remain unknown. Plants in the subtribe Phaseolinae detect herbivore-associated peptides in caterpillar oral secretions and the defined ligands are proteolytic fragments of chloroplastic ATP synthase termed inceptins. Using forward genetic mapping of...


6: Super-resolution Imaging Reveals 3D Structure and Organizing Mechanism of Accessible Chromatin

Liangqi Xie, Peng Dong et al.

34 tweets (posted 21 Jun 2019) molecular biology

Access to cis-regulatory elements packaged in chromatin is essential for directing gene expression and cell viability. Here, we report a super-resolution imaging strategy, 3D ATAC-PALM, that enables direct visualization of the entire accessible genome. We found that active chromosomal segments are organized into spatially-segregated accessible chromatin domains (ACDs). Rapid depletion of CTCF or Cohesin (RAD21 subunit) induced enhanced ACD clustering, reduced physical separation between intrachromosomal ACDs, and differ...


7: Brain state stability during working memory is explained by network control theory, modulated by dopamine D1/D2 receptor function, and diminished in schizophrenia

Urs Braun, Anais Harneit et al.

31 tweets (posted 23 Jun 2019) neuroscience

Dynamical brain state transitions are critical for flexible working memory but the network mechanisms are incompletely understood. Here, we show that working memory entails brain-wide switching between activity states. The stability of states relates to dopamine D1 receptor gene expression while state transitions are influenced by D2 receptor expression and pharmacological modulation. Schizophrenia patients show altered network control properties, including a more diverse energy landscape and decreased stability of work...


8: Genetic screens in isogenic mammalian cell lines without single cell cloning

Peter C DeWeirdt, Kendall R Sanson et al.

26 tweets (posted 23 Jun 2019) genetics

Isogenic pairs of cell lines, which differ by a single genetic modification, are powerful tools for understanding gene function. Generating such pairs for mammalian cells, however, is labor-intensive, time-consuming, and impossible in some cell types. Here we present an approach to create isogenic pairs of cells and screen them with genome-wide CRISPR-Cas9 libraries to generate genetic interaction maps. We queried the anti-apoptotic genes BCL2L1 and MCL1, and the DNA damage repair gene PARP1, via 25 genome-wide screens ...


9: There is no single functional atlas even for a single individual: Parcellation of the human brain is state dependent

Mehraveh Salehi, Abigail S. Greene et al.

22 tweets (posted 01 Oct 2018) neuroscience

The goal of human brain mapping has long been to delineate the functional subunits in the brain and elucidate the functional role of each of these brain regions. Recent work has focused on whole-brain parcellation of functional Magnetic Resonance Imaging (fMRI) data to identify these subunits and create a functional atlas. Functional connectivity approaches to understand the brain at the network level require such an atlas to assess connections between parcels and extract network properties. While no single functional a...


10: Enhancer-dependence of gene expression increases with developmental age

Wenqing Cai, Jialiang Huang et al.

22 tweets (posted 21 Jun 2019) molecular biology

How overall principles of gene regulation (the "logic") may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic and topological profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1 and Myb occupancy. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes employ distal enhancers for long-range regulation through ...


11: Aging-Associated Decrease in the Histone Acetyltransferase KAT6B Causes Myeloid-Biased Hematopoietic Stem Cell Differentiation

Eraj Shafiq Khokhar, Sneha Borikar et al.

16 tweets (posted 22 Jun 2019) cell biology

Aged hematopoietic stem cells (HSCs) undergo biased lineage priming and differentiation toward production of myeloid cells. A comprehensive understanding of gene regulatory mechanisms causing HSC aging is needed to devise new strategies to sustainably improve immune function in aged individuals. Here, a focused shRNA screen of epigenetic factors reveals that the histone acetyltransferase Kat6b regulates myeloid cell production from hematopoietic progenitor cells. Within the stem and progenitor cell compartment, Kat6b is...


12: CD49f is a novel marker to purify functional human iPSC-derived astrocytes

Lilianne Barbar, Tanya Jain et al.

16 tweets (posted 21 Jun 2019) neuroscience

Astrocytes play a central role in the central nervous system (CNS), maintaining brain homeostasis, providing metabolic support to neurons, regulating connectivity of neural circuits, and controlling blood flow as an integral part of the blood-brain barrier. They have been increasingly implicated in the mechanisms of neurodegenerative diseases, prompting a greater need for methods that enable their study. The advent of human induced pluripotent stem cell (iPSC) technology has made it possible to generate patient-specific...


13: Reaction mechanisms of Pol IV, RDR2 and DCL3 drive RNA channeling in the siRNA-directed DNA methylation pathway

Jasleen Singh, Vibhor Mishra et al.

15 tweets (posted 22 Jun 2019) biochemistry

In eukaryotes with multiple small RNA pathways the mechanisms that channel RNAs within specific pathways are unclear. Here, we reveal the reactions that account for channeling in the siRNA biogenesis phase of the Arabidopsis RNA-directed DNA methylation pathway. The process begins with template DNA transcription by NUCLEAR RNA POLYMERASE IV (Pol IV) whose atypical termination mechanism, induced by nontemplate DNA basepairing, channels transcripts to the associated RNA-dependent RNA polymerase, RDR2. RDR2 converts Pol IV...


14: The genomic impact of European colonization of the Americas

Linda Ongaro, Marilia O Scliar et al.

13 tweets (posted 21 Jun 2019) genomics

The human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored. Here we compiled a genome-wide dataset of ~12,000 individuals from twelve American countries and ~6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical m...


15: Predicting dysfunctional age-related task activations from resting-state network alterations

Ravi D. Mill, Brian A Gordon et al.

12 tweets (posted 21 Jun 2019) neuroscience

Alzheimer's disease (AD) is linked to changes in fMRI task activations and fMRI resting-state functional connectivity (restFC), which can emerge early in the timecourse of illness. Study of these fMRI correlates of unhealthy aging has been conducted in largely separate subfields. Taking inspiration from neural network simulations, we propose a unifying mechanism wherein restFC network alterations associated with Alzheimer's disease disrupt the ability for activations to flow between brain regions, leading to aberrant ta...


16: The yellow gene influences Drosophila male mating success through sex comb melanization

Jonathan H Massey, Daayun Chung et al.

12 tweets (posted 18 Jun 2019) animal behavior and cognition

Drosophila melanogaster males perform a series of courtship behaviors that, when successful, result in copulation with a female. For over a century, mutations in the yellow gene, named for its effects on pigmentation, have been known to reduce male mating success. Prior work has suggested that yellow influences mating behavior through effects on wing extension, song, and/or courtship vigor. Here, we rule out these explanations, as well as effects on the nervous system more generally, and find instead that the effects of...


17: Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif

Kelsey Jordan Wood, Munir Nur et al.

12 tweets (posted 22 Jun 2019) plant biology

Pathogens infecting plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen, Bremia lactucae, using comparative genomics and bioinformatics to search for the WY domain. This conserved structural elem...


18: Engineering bacteriocin-mediated resistance against plant pathogenic bacteria in plants

William M Rooney, Rhys Grinter et al.

12 tweets (posted 24 May 2019) plant biology

Pseudomonas syringae (Ps) and related plant pathogenic bacteria are responsible for losses in diverse crops such as tomato, kiwifruit, pepper, olive and soybean. Current solutions, involving the use of chemicals and the introduction of resistance genes, have enjoyed only limited success and may have adverse environmental impacts. Consequently, there is a pressing need to develop alternative technologies to address the problem of bacterial disease in crops. An alternative strategy is to utilise the narrow spectrum protei...


19: Cellular and Molecular Probing of Intact Transparent Human Organs

Shan Zhau, Mihail Ivilinov Todorov et al.

12 tweets (posted 21 May 2019) cell biology

Optical tissue transparency permits cellular and molecular investigation of complex tissues in 3D, a fundamental need in biomedical sciences. Adult human organs are particularly challenging for this approach, owing to the accumulation of dense and sturdy molecules in decades-aged human tissues. Here, we introduce SHANEL method utilizing a new tissue permeabilization approach to clear and label stiff human organs. We used SHANEL to generate the first intact transparent adult human brain and kidney, and perform 3D histolo...


20: Assembly-free single-molecule nanopore sequencing recovers complete virus genomes from natural microbial communities

John Beaulaurier, Elaine Luo et al.

10 tweets (posted 26 Apr 2019) microbiology

Viruses are the most abundant biological entities on Earth, and play key roles in host ecology, evolution, and horizontal gene transfer. Despite recent progress in viral metagenomics, the inherent genetic complexity of virus populations still poses technical difficulties for recovering complete virus genomes from natural assemblages. To address these challenges, we developed an assembly-free, single-molecule nanopore sequencing approach enabling direct recovery of high-quality viral genome sequences from environmental s...