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Currently indexing 60,239 bioRxiv papers from 267,831 authors.

Most tweeted bioRxiv papers, last 24 hours

Results 1 through 20 out of 166


1: A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

Alexandre Almeida, Stephen Nayfach et al.

71 tweets (posted 19 Sep 2019) microbiology

Comprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to individual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.


2: Modular and efficient pre-processing of single-cell RNA-seq

Páll Melsted, A. Sina Booeshaghi et al.

29 tweets (posted 17 Jun 2019) bioinformatics

Analysis of single-cell RNA-seq data begins with pre-processing of sequencing reads to generate count matrices. We investigate algorithm choices for the challenges of pre-processing, and describe a workflow that balances efficiency and accuracy. Our workflow is based on the kallisto (<https://pachterlab.github.io/kallisto/>) and bustools (<https://bustools.github.io/>) programs, and is near-optimal in speed and memory. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velo...


3: Bird Song Learning is Mutually Beneficial for Tutee and Tutor

Michael D. Beecher, Çağlar Akçay et al.

25 tweets (posted 20 Sep 2019) animal behavior and cognition

Song learning is generally assumed to be beneficial for a young songbird, but merely incidental, without costs or benefits, for the older song tutors. In the present study we contrast two mutually exclusive hypotheses about the tutor/tutee relationship: (1) that it is cooperative, or at least mutually tolerant, with tutor and tutee mutually benefiting from their relationship, vs. (2) that it is competitive, with tutor and tutee competing over territory, so that one or the other suffers negative fitness consequences of t...


4: A unique mode of nucleic acid immunity performed by a single multifunctional enzyme

S. M. Nayeemul Bari, Lucy Chou-Zheng et al.

19 tweets (posted 19 Sep 2019) microbiology

Organisms spanning all domains of life protect against pathogens using diverse mechanisms of nucleic acid immunity which detect and eliminate foreign genetic material. The perpetual arms race between bacteria and their viruses (phages) has given rise to both innate and adaptive nucleic acid immunity mechanisms, including restriction-modification and CRISPR-Cas, respectively. These sophisticated systems encode multiple components that sense and degrade phage-derived genetic material while leaving the host genome unharmed...


5: Similar somatotopy for active and passive digit representation in primary somatosensory cortex

Zeena-britt Sanders, Daan B Wesselink et al.

16 tweets (posted 05 Sep 2019) neuroscience

Scientists traditionally use passive stimulation to examine organisational properties of the primary somatosensory cortex (SI). Recent research has, however, emphasised the close and bidirectional relationship between somatosensory and motor systems. This suggests active contributions (e.g., direct inputs from the motor system to SI) should also be considered when studying SI representations. Under such a framework, discrepant results are possible when different tasks are used to study the same underlying somatosensory ...


6: Adiponectin and related C1q/TNF-related proteins bind selectively to anionic phospholipids and sphingolipids

Jessica Jane Ye, Xin Bian et al.

16 tweets (posted 20 Sep 2019) biochemistry

Adiponectin (also known as Acrp30) is a well-known adipokine associated with protection from cardiovascular disease, insulin resistance, and inflammation. Though multiple studies have investigated the mechanism of action of adiponectin and its relationship with tissue ceramide levels, several aspects of adiponectin biology remain unexplained, including its high circulating levels, tendency to oligomerize, and marked structural similarity to the opsonin C1q. Given the connection between adiponectin and ceramide metabolis...


7: Coupling chromatin structure and dynamics by live super-resolution imaging

Roman Barth, Kerstin Bystricky et al.

13 tweets (posted 20 Sep 2019) biophysics

Chromatin conformation regulates gene expression and thus constant remodeling of chromatin structure is essential to guarantee proper cell function. To gain insight into the spatio-temporal organization of the genome, we employ high-density photo-activated localization microscopy and deep learning to obtain temporally resolved super-resolution images of chromatin in vivo. In combination with high-resolution dense motion reconstruction, we confirm the existence of elongated ~ 45 to 90 nm wide chromatin blobs, which appea...


8: Antibody against envelope protein from human endogenous retrovirus activates neutrophils in systemic lupus erythematosus

Maria Tokuyama, Bronwyn M Gunn et al.

13 tweets (posted 20 Sep 2019) immunology

Neutrophil activation and the formation of neutrophil extracellular trap (NET) are hallmarks of innate immune activation in systemic lupus erythematosus (SLE) and contribute to the systemic interferon signature. Here we report that the expression of an endogenous retrovirus (ERV) locus ERV-K102, encoding an envelope protein, was significantly elevated in SLE patient blood and was correlated with higher interferon status. Induction of ERV-K102 expression most strongly correlated with reduced transcript levels of epigenet...


9: Intraflagellar transport complex B proteins regulate the Hippo effector Yap1 during cardiogenesis

Marina Peralta, Katerina Jerabkova et al.

11 tweets (posted 20 Sep 2019) developmental biology

Cilia and the intraflagellar transport (IFT) proteins involved in ciliogenesis are associated with congenital heart diseases (CHD). However, the molecular links between cilia, IFT proteins and cardiogenesis are yet to be established. Using a combination of biochemistry, genetics, and live imaging methods, we show that IFT complex B proteins (Ift88, Ift54 and Ift20) modulate the Hippo pathway effector YAP1 in zebrafish and mouse. We demonstrate that this interaction is key to restrict the formation of the proepicardium a...


10: Seeing β-arrestin in action: The role of β-arrestins in Histamine 1 Receptor signaling

Anna Pietraszewska-Bogiel, Joachim Goedhart

10 tweets (posted 19 Sep 2019) molecular biology

Beta-arrestins regulate G protein-coupled receptor functions by influencing their signaling activity and intracellular location. Histamine is a major chemical mediator of allergic reactions, and its action is mainly mediated by the Gq/11- and Gi-coupled H1R. Contrary to accumulating insights into G protein-mediated signaling downstream of H1R, very little is known about the function of Beta-arrestins in H1R signaling. Here, we describe dynamic, live cell measurements of Beta-arrestin recruitment upon H1R activation in H...


11: Not so dry after all – DRY mutants of the AT1A receptor and H1 receptor can induce G protein-dependent signaling

A Pietraszewska-Bogiel, L Joosen et al.

10 tweets (posted 18 Sep 2019) molecular biology

GPCRs are seven transmembrane spanning receptors that regulate a wide array of intracellular signaling cascades in response to various stimuli. To do so, they couple to different heterotrimeric G proteins and adaptor proteins, including arrestins. Importantly, arrestins were shown to regulate GPCR signaling through G proteins, as well as promote G protein-independent signaling events. Several research groups have reported successful isolation of exclusively G protein-dependent and arrestin-dependent signaling downstream...


12: Seeing cells smell: Dynamic optical measurements of Ca2+ and cAMP signaling from Olfactory Receptors transiently expressed in HEK293TN cells

Anna Pietraszewska-Bogiel, Laura van Weeren et al.

10 tweets (posted 16 Sep 2019) molecular biology

Olfactory receptors (ORs) constitute the largest family of G-protein coupled receptors. They are responsible for the perception of odor (olfaction) and also play important roles in other biological processes, including regulation of cell proliferation. Their increasing diagnostic and therapeutic potential, especially for cancer research, requests the ongoing development of methodologies that would allow their robust functional expression in non-olfactory cells, and dynamic analysis of their signaling pathways. To enable...


13: Green, orange, red, and far-red optogenetic tools derived from cyanobacteriochromes

Jaewan Jang, Sherin McDonald et al.

9 tweets (posted 14 Sep 2019) synthetic biology

Existing optogenetic tools for controlling protein-protein interactions are available in a limited number of wavelengths thereby limiting opportunities for multiplexing. The cyanobacteriochrome (CBCR) family of photoreceptors responds to an extraordinary range of colors, but light-dependent binding partners for CBCR domains are not currently known. We used a phage-display based approach to develop small (~50-residue) monomeric binders selective for the green absorbing state (Pg), or for the red absorbing state (Pr) of t...


14: Sema3A Facilitates a Retrograde Death Signal via CRMP4-Dynein Complex Formation in ALS Motor Axons

Roy Maimon, Lior Ankol et al.

9 tweets (posted 19 Sep 2019) neuroscience

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease with selective dysfunction; it causes the death of motor neurons (MNs). In spite of some progress, currently no effective treatment is available for ALS. Before such treatment can be developed, a more thorough understanding of ALS pathogenesis is required. Recently, we demonstrated that ALS-mutated muscles contribute to ALS pathology via secretion of destabilizing factors such as Sema3A; these factors trigger axon degeneration and Neuromuscular Jun...


15: Gene capture by transposable elements leads to epigenetic conflict

Aline Muyle, Danelle K. Seymour et al.

9 tweets (posted 20 Sep 2019) genomics

Plant transposable elements (TEs) regularly capture fragments of host genes. When the host employs siRNAs to silence these TEs, siRNAs homologous to the captured regions may target both the TEs and the genes, potentially leading to their silencing. This epigenetic cross-talk establishes an intragenomic conflict: silencing the TEs comes with the potential cost of silencing the genes. If the genes are important, however, natural selection will act to maintain function by moderating the silencing response. Such moderation ...


16: Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities

Maria A. Nieves-Colón, William J. Pestle et al.

8 tweets (posted 12 Sep 2019) genomics

Indigenous peoples have occupied the island of Puerto Rico since at least 3000 B.C. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of pre-contact Indigenous communities from Puerto Rico. Bone, tooth and dental calculus samples were collected from 124 individuals from three pre-contact archaeological sites: Tib...


17: Neural representation of current and intended task sets during sequential judgements on human faces

Paloma Díaz-Gutiérrez, Sam Gilbert et al.

7 tweets (posted 02 Sep 2019) neuroscience

Engaging in a demanding activity while holding in mind another task to be performed in the near future requires the maintenance of information about both the currently-active task set and the intended one. However, little is known about how the human brain implements such action plans. While some previous studies have examined the neural representation of current task sets and others have investigated delayed intentions, to date none has examined the representation of current and intended task sets within a single exper...


18: A simple, versatile and robust centrifugation-based filtration protocol for the isolation and quantification of α-synuclein monomers, oligomers and fibrils: towards improving experimental reproducibility in α-synuclein research

Senthil T. Kumar, Sonia Donzelli et al.

7 tweets (posted 21 Sep 2019)

Increasing evidence suggests that the process of alpha-synuclein (aSyn) aggregation from monomers into amyloid fibrils via oligomeric intermediates plays an essential role in the pathogenesis of different synucleinopathies, including Parkinsons disease (PD), multiple system atrophy and dementia with Lewy bodies. However, the nature of the toxic species and the mechanisms by which they contribute to neurotoxicity and disease progression remain elusive. Over the past two decades, significant efforts and resources have bee...


19: Three-dimensional characterisation of osteocyte volumes at multiple scales, and its relationship with bone biology and genome evolution in ray-finned fishes

Donald Davesne, Armin D. Schmitt et al.

7 tweets (posted 19 Sep 2019) zoology

Osteocytes, cells embedded within the bone mineral matrix, inform on key aspects of vertebrate biology. In particular, a relationship between volumes of the osteocytes and bone growth and/or genome size has been proposed for several tetrapod lineages. However, the variation in osteocyte volume across different scales is poorly characterised, and mostly relies on incomplete, two-dimensional information. In this study, we propose to characterise the variation of osteocyte volumes in ray-finned fishes (Actinopterygii), a c...


20: The Imposition of Value on Odor: Transient and Persistent Representations of Odor Value in Prefrontal Cortex

Peter Y Wang, Cristian Boboila et al.

6 tweets (posted 30 Aug 2019) neuroscience

The representation of odor in olfactory cortex (piriform) is distributive and unstructured and can only be afforded behavioral significance upon learning. We performed 2-photon imaging to examine the representation of odors in piriform and in two downstream stations, the orbitofrontal cortex (OFC) and medial prefrontal cortex (mPFC), as mice learned olfactory associations. In piriform we observed minor changes in neural activity unrelated to learning. In OFC, 30% of the neurons acquired robust responses to conditioned s...