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Currently indexing 70,543 bioRxiv papers from 307,989 authors.

Most tweeted bioRxiv papers, last 24 hours

Results 1 through 20 out of 512

 

1: A Connectome of the Adult Drosophila Central Brain

C. Shan Xu, Michal Januszewski et al.

393 tweets (posted 21 Jan 2020) neuroscience

The neural circuits responsible for behavior remain largely unknown. Previous efforts have reconstructed the complete circuits of small animals, with hundreds of neurons, and selected circuits for larger animals. Here we (the FlyEM project at Janelia and collaborators at Google) summarize new methods and present the complete circuitry of a large fraction of the brain of a much more complex animal, the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses, and proofread such large data sets; new methods that define cell types based on connectivity in addition to morphology; and new methods to simplify access to a large and evolving data set. From the resulting data we derive a better definition of computational compartments and their connections; an exhaustive atlas of cell examples and types, many of them novel; detailed circuits for most of the central brain; and exploration of the statistics and structure of different brain compartments, and the brain as a whole. We make the data public, with a web site and resources specifically designed to make it easy to explore, for all levels of expertise from the expert to the merely curious. The public availability of these data, and the simplified means to access it, dramatically reduces the effort needed to answer typical circuit questions, such as the identity of upstream and downstream neural partners, the circuitry of brain regions, and to link the neurons defined by our analysis with genetic reagents that can be used to study their functions. Note: In the next few weeks, we will release a series of papers with more involved discussions. One paper will detail the hemibrain reconstruction with more extensive analysis and interpretation made possible by this dense connectome. Another paper will explore the central complex, a brain region involved in navigation, motor control, and sleep. A final paper will present insights from the mushroom body, a center of multimodal associative learning in the fly brain.

https://rxivist.org/papers/71599
https://doi.org/10.1101/2020.01.21.911859

2: Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin

Zheng-Li Shi, Peng Zhou et al.

358 tweets (posted 23 Jan 2020) microbiology

Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laborat...

https://rxivist.org/papers/71702
https://doi.org/10.1101/2020.01.22.914952

3: Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV

Michael C Letko, Vincent Munster

227 tweets (posted 22 Jan 2020) microbiology

Over the past 20 years, several coronaviruses have crossed the species barrier into humans, causing outbreaks of severe, and often fatal, respiratory illness. Since SARS-CoV was first identified in animal markets, global viromics projects have discovered thousands of coronavirus sequences in diverse animals and geographic regions. Unfortunately, there are few tools available to functionally test these novel viruses for their ability to infect humans, which has severely hampered efforts to predict the next zoonotic viral...

https://rxivist.org/papers/71628
https://doi.org/10.1101/2020.01.22.915660

4: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy

Alexander Spark, Alexandre Kitching et al.

71 tweets (posted 21 Jan 2020) biophysics

Super-Resolution (SR) Microscopy based on 3D Single-Molecule Localization Microscopy (SMLM) is now well established and its wide-spread adoption has led to the development of more than 36 software packages, dedicated to quantitative evaluation of the spatial and temporal detection of fluorophore photoswitching. While the initial emphasis in the 3D SMLM field has clearly been on improving resolution and data quality, there is now a marked absence of 3D visualization approaches that enable the straightforward, high-fideli...

https://rxivist.org/papers/71533
https://doi.org/10.1101/2020.01.20.912733

5: High-resolution cryo-EM using beam-image shift at 200 keV

Jennifer N. Cash, Sarah Kearns et al.

67 tweets (posted 21 Jan 2020) biophysics

Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilizes beam-image shift to improve throughput. Despite implementation on well-aligned 300 keV cryo-EM instruments, it remains unknown how well beam-image shift data collection affects data quality on 200 keV instruments and whether any aberrations can be computationally corrected. To test this, we collected and analyzed a cryo-EM dataset of aldolase at 200 keV using beam-image shift. This analysis shows that beam tilt on the instrume...

https://rxivist.org/papers/71601
https://doi.org/10.1101/2020.01.21.914507

6: A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

Jean Claude Semuto Ngabonziza, Chloé Loiseau et al.

49 tweets (posted 21 Jan 2020) microbiology

The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to have clonally expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sis...

https://rxivist.org/papers/71584
https://doi.org/10.1101/2020.01.20.912998

7: A super sensitive auxin-inducible degron system with an engineered auxin-TIR1 pair

Kohei Nishimura, Ryotaro Yamada et al.

46 tweets (posted 20 Jan 2020) bioengineering

Auxin-Inducible Degron (AID) technology enables conditional depletion of targeted proteins. However, the applicability of the AID in vertebrate cells has been limited due to cytotoxicity caused by high auxin concentrations. Here, we establish an improved AID system using an engineered orthogonal auxin-TIR1 pair, which exhibits over 1,000 times stronger binding. With ~1,000-fold less auxin concentration, we achieved to generate the AID-based knockout cells in various human and mouse cell lines in a single transfection.

https://rxivist.org/papers/71495
https://doi.org/10.1101/2020.01.20.912113

8: SparK: A Publication-quality NGS Visualization Tool

Stefan Kurtenbach, J. William Harbour

43 tweets (posted 16 Nov 2019) bioinformatics

While there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATA...

https://rxivist.org/papers/66459
https://doi.org/10.1101/845529

9: Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction

Marco Tognetti, Attila Gabor et al.

40 tweets (posted 21 Jan 2020) systems biology

Although genetic and epigenetic abnormalities in breast cancer have been extensively studied, it remains difficult to identify those patients who will respond to particular therapies. This is due in part to our lack of understanding of how the variability of cellular signaling affects drug sensitivity. Here, we used mass cytometry to characterize the single-cell signaling landscapes of 62 breast cancer cell lines and five lines from healthy tissue. We quantified 34 markers in each cell line upon stimulation by the growt...

https://rxivist.org/papers/71535
https://doi.org/10.1101/2020.01.21.907691

10: Connectomics analysis reveals first, second, and third order thermosensory and hygrosensory neurons in the adult Drosophila brain

Elizabeth C. Marin, Ruairi J.V. Roberts et al.

39 tweets (posted 21 Jan 2020) neuroscience

Animals exhibit innate and learned preferences for temperature and humidity - conditions critical for their survival and reproduction. Here, we leveraged a whole adult brain electron microscopy volume to study the circuitry associated with antennal thermosensory and hygrosensory neurons, which target specific ventroposterior (VP) glomeruli in the Drosophila melanogaster antennal lobe. We have identified two new VP glomeruli, in addition to the five known ones, and the projection neurons (VP PNs) that relay VP informatio...

https://rxivist.org/papers/71531
https://doi.org/10.1101/2020.01.20.912709

11: Genomic and protein structure modelling analysis depicts the origin and infectivity of 2019-nCoV, a new coronavirus which caused a pneumonia outbreak in Wuhan, China

Ning Dong, Xuemei Yang et al.

38 tweets (posted 21 Jan 2020) microbiology

Detailed genomic and structure-based analysis of a new coronavirus, namely 2019-nCoV, showed that the new virus is a new type of bat coronavirus and is genetically fairly distant from the human SARS coronavirus. Structure analysis of the spike (S) protein of this new virus showed that its S protein only binds weakly to the ACE2 receptor on human cells whereas the human SARS coronavirus exhibits strongly affinity to the ACE receptor. These findings suggest that the new virus does not readily transmit between humans and s...

https://rxivist.org/papers/71556
https://doi.org/10.1101/2020.01.20.913368

12: Head Movements Control the Activity of Primary Visual Cortex in a Luminance Dependent Manner

Guy Bouvier, Yuta Senzai et al.

34 tweets (posted 21 Jan 2020) neuroscience

The vestibular system broadcasts head-movement related signals to sensory areas throughout the brain, including visual cortex. These signals are crucial for the brain's ability to assess whether motion of the visual scene results from the animal's head-movements. How head-movements impact visual cortical circuits remains, however, poorly understood. Here, we discover that ambient luminance profoundly transforms how mouse primary visual cortex (V1) processes head-movements. While in darkness, head movements result in an ...

https://rxivist.org/papers/71579
https://doi.org/10.1101/2020.01.20.913160

13: Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity

C. Titus Brown, Dominik Moritz et al.

29 tweets (posted 05 Nov 2018) bioinformatics

Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome. Our software implementa...

https://rxivist.org/papers/35986
https://doi.org/10.1101/462788

14: Binary and analog variation of synapses between cortical pyramidal neurons

Sven Dorkenwald, Nicholas L. Turner et al.

29 tweets (posted 31 Dec 2019) neuroscience

Learning from experience depends at least in part on changes in neuronal connections. We present the largest map of connectivity to date between cortical neurons of a defined type (L2/3 pyramidal cells), which was enabled by automated analysis of serial section electron microscopy images with improved handling of image defects. We used the map to identify constraints on the learning algorithms employed by the cortex. Previous cortical studies modeled a continuum of synapse sizes (Arellano et al., 2007) by a log-normal d...

https://rxivist.org/papers/69942
https://doi.org/10.1101/2019.12.29.890319

15: Translation is required for miRNA-dependent decay of endogenous transcripts.

Adriano Biasini, Stefano de Pretis et al.

28 tweets (posted 21 Jan 2020) genomics

Posttranscriptional repression by microRNA (miRNA) occurs through transcript destabilization or translation inhibition. Whereas RNA degradation explains most miRNA-dependent repression, transcript decay occurs co-translationally, raising questions regarding the requirement of target translation to miRNA-dependent transcript destabilization. To assess the contribution of translation to miRNA-mediated RNA destabilization, we decoupled these two molecular processes by dissecting the impact of miRNA loss of function on cyto...

https://rxivist.org/papers/71553
https://doi.org/10.1101/2020.01.21.913483

16: Smchd1 is a maternal effect gene required for autosomal imprinting

Iromi Wanigasuriya, Quentin Gouil et al.

27 tweets (posted 21 Jan 2020) genomics

Genomic imprinting establishes allele-biased expression of a suite of mammalian genes based on their parent of origin. Imprinted expression is achieved via parent-of-origin specific epigenetic marks under the control of maternal effect proteins supplied in the oocyte. Here we report Structural maintenance of chromosomes hinge domain containing 1 (Smchd1) as a novel maternal effect gene that regulates the imprinting of 16 genes. The majority of these genes only show loss of imprinting post-implantation, indicating matern...

https://rxivist.org/papers/71555
https://doi.org/10.1101/2020.01.20.913376

17: How Sensitive are EEG Results to Preprocessing Methods: A Benchmarking Study

Kay Robbins, Jonathan O. Touryan et al.

27 tweets (posted 21 Jan 2020) neuroscience

EEG preprocessing approaches have not been standardized, and even those studies that follow best practices contain variations in the ways that the recommended methods are applied. An open question for researchers is how sensitive the results of EEG analyses are to preprocessing methods and parameters. To address this issue, we analyze the effect of preprocessing methods on downstream EEG analysis using several simple signal and event-related measures. Signal measures include recording-level channel amplitudes, study-lev...

https://rxivist.org/papers/71550
https://doi.org/10.1101/2020.01.20.913327

18: Human immune system variation during one year

Tadepall Lakshmikanth, Sayyed Auwn Muhammad et al.

26 tweets (posted 23 Jan 2020) immunology

The human immune system varies extensively between individuals, but variation within individuals over time has not been well characterized. Systems-level analyses allow for simultaneous quantification of many interacting immune system components, and the inference of global regulatory principles. Here we present a longitudinal, systems-level analysis in 99 healthy adults, 50 to 65 years of age and sampled every 3rd month during one year. We describe the structure of inter-individual variation and characterize extreme ph...

https://rxivist.org/papers/71723
https://doi.org/10.1101/2020.01.22.915025

19: Complete connectomic reconstruction of olfactory projection neurons in the fly brain

Alexander Shakeel Bates, Philipp Schlegel et al.

24 tweets (posted 20 Jan 2020) neuroscience

Nervous systems contain sensory neurons, local neurons, projection neurons and motor neurons. To understand how these building blocks form whole circuits, we must distil these broad classes into neuronal cell types and describe their network connectivity. Using an electron micrograph dataset for an entire Drosophila melanogaster brain, we reconstruct the first complete inventory of olfactory projections connecting the antennal lobe, the insect analogue of the mammalian olfactory bulb, to higher-order brain regions in an...

https://rxivist.org/papers/71446
https://doi.org/10.1101/2020.01.19.911453

20: Strategies for cellular deconvolution in human brain RNA sequencing data

Olukayode A. Sosina, Matthew N Tran et al.

24 tweets (posted 20 Jan 2020) genomics

Statistical deconvolution strategies have emerged over the past decade to estimate the proportion of various cell populations in homogenate tissue sources like brain using gene expression data. Here we show that several existing deconvolution algorithms which estimate the RNA composition of homogenate tissue, relates to the amount of RNA attributable to each cell type, and not the cellular composition relating to the underlying fraction of cells. Incorporating "cell size" parameters into RNA-based deconvolution algorith...

https://rxivist.org/papers/71453
https://doi.org/10.1101/2020.01.19.910976