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Currently indexing 125,201 papers from 537,614 authors.

Most tweeted biology preprints, last 24 hours

Results 1 through 20 out of 117

 

1: SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome

Liguo Zhang, Alexsia Richards et al.

49 tweets (posted 13 Dec 2020) genomics

Prolonged SARS-CoV-2 RNA shedding and recurrence of PCR-positive tests have been widely reported in patients after recovery, yet these patients most commonly are non-infectious. Here we investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the human genome and that transcription of the integrated sequences might account for PCR-positive tests. In support of this hypothesis, we found chimeric transcripts consisting of viral fused to cellular sequences in published data sets of SARS-CoV-2 infected cultured cells and primary cells of patients, consistent with the transcription of viral sequences integrated into the genome. To experimentally corroborate the possibility of viral retro-integration, we describe evidence that SARS-CoV-2 RNAs can be reverse transcribed in human cells by reverse transcriptase (RT) from LINE-1 elements or by HIV-1 RT, and that these DNA sequences can be integrated into the cell genome and subsequently be transcribed. Human endogenous LINE-1 expression was induced upon SARS-CoV-2 infection or by cytokine exposure in cultured cells, suggesting a molecular mechanism for SARS-CoV-2 retro-integration in patients. This novel feature of SARS-CoV-2 infection may explain why patients can continue to produce viral RNA after recovery and suggests a new aspect of RNA virus replication.

https://rxivist.org/papers/121400
https://doi.org/10.1101/2020.12.12.422516

2: Striatal Direct Pathway Targets Npas1+ Pallidal Neurons

Qiaoling Cui, Xixun Du et al.

20 tweets (posted 02 Sep 2020) neuroscience

The classic basal ganglia circuit model asserts a complete segregation of the two striatal output pathways. Empirical data argue that, in addition to indirect-pathway striatal projection neurons (iSPNs), direct-pathway striatal projection neurons (dSPNs) innervate the external globus pallidus (GPe). However, the functions of the latter were not known. In this study, we interrogated the organization principles of striatopallidal projections and their roles in full-body movement in mice (both males and females). In contra...

https://rxivist.org/papers/100587
https://doi.org/10.1101/2020.09.02.273615

3: An integrative analysis of genomic and exposomic data for complex traits and phenotypic prediction

Xuan Zhou, Sang Hong Lee

16 tweets (posted 10 Nov 2020) genetics

Complementary to the genome, the concept of exposome has been proposed to capture the totality of human environmental exposures. While there has been some recent progress on the construction of the exposome, few tools exist that can integrate the genome and exposome for complex trait analyses. Here we propose a linear mixed model approach to bridge this gap, which jointly models the random effects of the two omics layers on phenotypes of complex traits. We illustrate our approach using traits from the UK Biobank (e.g., ...

https://rxivist.org/papers/103635
https://doi.org/10.1101/2020.11.09.373704

4: Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses

Dylan H. Morris, Kwe Claude Yinda et al.

6 tweets (posted 16 Oct 2020) microbiology

Environmental conditions affect virus inactivation rate and transmission potential. Understanding those effects is critical for anticipating and mitigating epidemic spread. Ambient temperature and humidity strongly affect the inactivation rate of enveloped viruses, but a mechanistic, quantitative theory of those effects has been elusive. We measure the stability of the enveloped respiratory virus SARS-CoV-2 on an inert surface at nine temperature and humidity conditions and develop a mechanistic model to explain and pre...

https://rxivist.org/papers/101131
https://doi.org/10.1101/2020.10.16.341883

5: BoxCar and library-free data-independent acquisition substantially improve the depth, range, and completeness of label-free quantitative proteomics in Arabidopsis

Devang Mehta, Sabine Scandola et al.

6 tweets (posted 08 Nov 2020) plant biology

The last decade has seen significant advances in the application of quantitative mass spectrometry-based proteomics technologies to tackle important questions in plant biology. The current standard for quantitative proteomics in plants is the use of data-dependent acquisition (DDA) analysis with and without the use of chemical labels. However, major limitations of the DDA approach are the preferential measurement higher abundant proteins, and the presence of missing values for proteins measured across replicate and inde...

https://rxivist.org/papers/103380
https://doi.org/10.1101/2020.11.07.372276

6: Spatial structure impacts adaptive therapy by shaping intra-tumoral competition

Maximilian A R Strobl, Jill Gallaher et al.

6 tweets (posted 04 Nov 2020) cancer biology

(1) Background: Adaptive therapy aims to tackle cancer drug resistance by leveraging intra-tumoral competition between drug-sensitive and resistant cells. Motivated by promising results in prostate cancer there is growing interest in extending this approach to other cancers. Here we present a theoretical study of intra-tumoral competition during adaptive therapy, to identify under which circumstances it will be superior to aggressive treatment; (2) Methods: We use a 2-D, on-lattice, agent-based tumour model to examine t...

https://rxivist.org/papers/102985
https://doi.org/10.1101/2020.11.03.365163

7: Cyanobacterial NOS expression improves nitrogen use efficiency, nitrogen-deficiency tolerance and yield in Arabidopsis

Del Castello Fiorella, Foresi Noelia et al.

4 tweets (posted 08 Oct 2020) plant biology

Developing strategies to improve nitrogen (N) use efficiency (NUE) in plants is a challenge to reduce environmental problems linked to over‐fertilization. The nitric oxide synthase (NOS) enzyme from the cyanobacteria Synechococcus PCC 7335 (SyNOS) has been recently identified and characterized. SyNOS catalyzes the conversion of arginine to citrulline and nitric oxide (NO), and then 70% of the produced NO is rapidly oxidized to nitrate by an unusual globin domain in its 5'-terminus. In this study, we assessed whether SyN...

https://rxivist.org/papers/96800
https://doi.org/10.1101/2020.10.08.331702

8: Luminal nutrients activate distinct patterns in submucosal and myenteric neurons in the mouse small intestine

Candice Fung, Marlene M Hao et al.

4 tweets (posted 20 Jan 2021) neuroscience

Nutrient signals sensed by enteroendocrine cells are conveyed to the enteric nervous system (ENS) to initiate intestinal reflexes. We addressed whether there are specific enteric pathways dedicated to detecting different luminal nutrients. Calcium imaging was performed on intact jejunal preparations from Wnt1-cre;R26R-GCaMP3 and Villin-cre;R26R-GCaMP3 mice which express a fluorescent calcium indicator in their ENS or intestinal epithelium, respectively. Glucose, acetate, and L-phenylalanine were perfused onto the mucosa...

https://rxivist.org/papers/125993
https://doi.org/10.1101/2021.01.19.427232

9: SpecSeg: cross spectral power-based segmentation of neurons and neurites in chronic calcium imaging datasets

Leander de Kraker, Koen Seignette et al.

4 tweets (posted 21 Oct 2020) neuroscience

Imaging calcium signals in neurons of awake, behaving animals using single- or multi-photon microscopy facilitates the study of coding in large neural populations. Such experiments produce massive datasets requiring powerful methods to extract responses from hundreds of neurons. We present SpecSeg, a new open-source toolbox for 1) segmentation of regions of interest (ROIs) representing neuronal structures, 2) inspection and manual editing of ROIs, 3) neuropil correction and signal extraction and 4) matching of ROIs in s...

https://rxivist.org/papers/101591
https://doi.org/10.1101/2020.10.20.345371

10: A comparative analysis of quantitative metrics of root architectural phenotypes

Harini Rangarajan, Jonathan Lynch

4 tweets (posted 02 Dec 2020) plant biology

High throughput phenotyping is important to bridge the gap between genotype and phenotype. The methods used to describe the phenotype therefore should be robust to measurement errors, relatively stable over time, and most importantly, provide a reliable estimate of elementary phenotypic components. In this study, we use functional-structural modeling to evaluate quantitative phenotypic metrics used to describe root architecture to determine how they fit these criteria. Our results show that phenes such as root number, r...

https://rxivist.org/papers/119758
https://doi.org/10.1101/2020.12.01.406827

11: SARS-CoV and SARS-CoV-2 are transmitted through the air between ferrets over more than one meter distance

Jasmin S Kutter, Dennis de Meulder et al.

3 tweets (posted 19 Oct 2020) microbiology

SARS-CoV-2 emerged in late 2019 and caused a pandemic, whereas the closely related SARS-CoV was contained rapidly in 2003. Here, a newly developed experimental set-up was used to study transmission of SARS-CoV and SARS-CoV-2 through the air between ferrets over more than a meter distance. Both viruses caused a robust productive respiratory tract infection resulting in transmission of SARS-CoV-2 to two of four indirect recipient ferrets and SARS-CoV to all four. A control pandemic A/H1N1 influenza virus also transmitted ...

https://rxivist.org/papers/101350
https://doi.org/10.1101/2020.10.19.345363

12: Resveratrol And Pterostilbene Potently Inhibit SARS-CoV-2 Infection In Vitro

B.M. Ellen ter, N. Dinesh Kumar et al.

2 tweets (posted 24 Sep 2020) microbiology

The current COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has an enormous impact on human health and economy[1][1]. In search for therapeutic options, researchers have proposed resveratrol, a food supplement with known antiviral, anti-inflammatory and anti-oxidant properties as an advantageous antiviral therapy for SARS-CoV-2 infection[2][2]–[4][3]. Here, we provide evidence that both resveratrol and its metabolically more stable structural analog, pterostilbene, exhibit...

https://rxivist.org/papers/98346
https://doi.org/10.1101/2020.09.24.285940

13: Vimentin intermediate filaments mediate cell shape on visco-elastic substrates

Maxx Swoger, Sarthak Gupta et al.

2 tweets (posted 08 Sep 2020) biophysics

The ability of cells to take and change shape is a fundamental feature underlying development, wound repair, and tissue maintenance. Central to this process is physical and signaling interactions between the three cytoskeletal polymeric networks: F-actin, microtubules, and intermediate filaments (IFs). Vimentin is an IF protein that is essential to the mechanical resilience of cells and regulates cross-talk amongst the cytoskeleton, but its role in how cells sense and respond to the surrounding extracellular matrix is l...

https://rxivist.org/papers/100083
https://doi.org/10.1101/2020.09.07.286237

14: Courtship behaviour reveals temporal regularity is a critical social cue in mouse communication

Catherine Perrodin, Colombine Verzat et al.

2 tweets (posted 28 Jan 2020) neuroscience

While animals navigating the real world face a barrage of sensory input, their brains evolved to perceptually compress multidimensional information by selectively extracting the features relevant for survival. Notably, communication signals supporting social interactions in several mammalian species consist of acoustically complex sequences of vocalizations. However, little is known about what information listeners extract from such time-varying sensory streams. Here, we utilize female mice’s natural behavioural respons...

https://rxivist.org/papers/72240
https://doi.org/10.1101/2020.01.28.922773

15: Morphometric reconstructions atlas shows insult-driven plasticity in cortical VIP/ChAT interneurons

Nadav Yayon, Oren Amsalem et al.

2 tweets (posted 25 Aug 2020) neuroscience

We developed an automatic morphometric reconstruction pipeline, Pop-Rec, and used it to study the morphologies of cortical cholinergic VIP/ChAT interneurons (VChIs). Cholinergic networks control high cognitive functions, but their local modulation and stress-driven plasticity patterns remained elusive. Reconstructing thousands of local VChIs registered to their exact coordinates in multiple cleared murine cortices highlighted distinct populations of bipolar and multipolar VChIs which differed in their dendritic spatial ...

https://rxivist.org/papers/95645
https://doi.org/10.1101/2020.08.25.263178

16: Minimal genome-wide human CRISPR-Cas9 library

Emanuel Gonçalves, Mark Thomas et al.

2 tweets (posted 21 Nov 2019) genomics

CRISPR guide-RNA libraries have been iteratively optimised to provide increasingly efficient reagents, although their large size is a barrier for many applications. We designed an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9), by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other libraries while preserving assay sensitivity and specificity. MinLibCas9 increases the dynamic range of CRISPR-Cas9 loss-of-function screens and...

https://rxivist.org/papers/66844
https://doi.org/10.1101/848895

17: Muscle strength, size and composition following 12 months of gender-affirming treatment in transgender individuals: retained advantage for the transwomen

A Wiik, TR Lundberg et al.

2 tweets (posted 26 Sep 2019) physiology

Objectives: This study explored the effects of gender-affirming treatment, which includes inhibition of endogenous sex hormones and replacement with cross-sex hormones, on muscle function, size and composition in 11 transwomen (TW) and 12 transmen (TM). Methods: Isokinetic knee extensor and flexor muscle strength was assessed at baseline (T00), 4 weeks after gonadal suppression of endogenous hormones but before hormone replacement (T0), and 3 (T3) and 11 (T12) months after hormone replacement. In addition, at T00 and T1...

https://rxivist.org/papers/61827
https://doi.org/10.1101/782557

18: Functional Immune Deficiency Syndrome via Intestinal Infection in COVID-19

Erica T. Prates, Michael R Garvin et al.

2 tweets (posted 10 Apr 2020) systems biology

Using a Systems Biology approach, we integrated genomic, transcriptomic, proteomic, and molecular structure information to provide a holistic understanding of the COVID-19 pandemic. The expression data analysis of the Renin Angiotensin System indicates mild nasal, oral or throat infections are likely and that the gastrointestinal tissues are a common primary target of SARS-CoV-2. Extreme symptoms in the lower respiratory system likely result from a secondary-infection possibly by a comorbidity-driven upregulation of ACE...

https://rxivist.org/papers/79557
https://doi.org/10.1101/2020.04.06.028712

19: A cross-species assessment of behavioral flexibility in compulsive disorders

Nabil Benzina, Karim N’Diaye et al.

2 tweets (posted 06 Feb 2019) neuroscience

Background Compulsive behaviors, one of the core symptoms of Obsessive-Compulsive Disorder (OCD), are defined as repetitive behaviors performed through rigid rituals. The lack of behavioral flexibility has been as being one of the primary causes of compulsions, but studies exploring this dimension have shown inconsistencies in different tasks performed in human and animal models of compulsive behavior. The aim of this study was so to assess the involvement of behavioral flexibility in compulsion, with a similar approach...

https://rxivist.org/papers/43365
https://doi.org/10.1101/542100

20: Open Science Saves Lives: Lessons from the COVID-19 Pandemic

Lonni Besançon, Nathan Peiffer-Smadja et al.

2 tweets (posted 14 Aug 2020) scientific communication and education

In the last decade Open Science principles, such as Open Access, study preregistration, use of preprints, making available data and code, and open peer review, have been successfully advocated for and are being slowly adopted in many different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of some of these Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns a...

https://rxivist.org/papers/94465
https://doi.org/10.1101/2020.08.13.249847