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Currently indexing 124,632 papers from 535,495 authors.

Most tweeted biology preprints, last 24 hours

Results 1 through 20 out of 157


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

Liguo Zhang, Alexsia Richards et al.

182 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.


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

Vivek N. Prakash, Matthew S. Bull et al.

25 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...


3: One-shot generation of duodecuple (12x) mutant Arabidopsis: Highly efficient routine editing in model species

Karen Barthel, Patrick Martin et al.

22 tweets (posted 01 Apr 2020) plant biology

Genome editing by RNA-guided nucleases in model species is still hampered by low efficiencies, and isolation of transgene-free individuals often requires tedious PCR screening. Here, we present a toolkit that mitigates these drawbacks for Nicotiana benthamiana and Arabidopsis thaliana. The toolkit is based on an intron-optimized SpCas9-coding gene (zCas9i), which conveys dramatically enhanced editing efficiencies. The zCas9i gene is combined with remaining components of the genome editing system in recipient vectors, wh...


4: Polygenic adaptation after a sudden change in environment

Laura Katharine Hayward, Guy Sella

21 tweets (posted 03 Oct 2019) evolutionary biology

Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Importantly, we describe the two phases of the allele dynamics: a rapid phase in which directiona...


5: An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies

Yafei Liu, Wai Tuck Soh et al.

15 tweets (posted 18 Dec 2020) microbiology

SARS-CoV-2 infection causes severe symptoms in a subset of patients, suggesting the presence of certain unknown risk factors. Although antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike have been shown prevent SARS-CoV-2 infection, the effects of antibodies against other spike protein domains are largely unknown. Here, we screened a series of anti-spike monoclonal antibodies from COVID-19 patients, and found that some of antibodies against the N-terminal domain (NTD) dramatically enhanced the b...


6: Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes

Madeline G Andrews, Tanzila Mukhtar et al.

13 tweets (posted 18 Jan 2021) neuroscience

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) readily infects a variety of cell types impacting the function of vital organ systems, with particularly severe impact on respiratory function. It proves fatal for one percent of those infected. Neurological symptoms, which range in severity, accompany a significant proportion of COVID-19 cases, indicating a potential vulnerability of neural cell types. To assess whether human cortical cells can be directly infected by SARS-CoV-2, we utilized primary human...


7: Distributed networks for auditory memory contribute differentially to recall precision

Sung-Joo Lim, Christiane Thiel et al.

13 tweets (posted 18 Jan 2021) neuroscience

The representations held in working memory are inherently noisy, but attention directed to relevant objects can effectively enhance their fidelity. While recent working memory models suggest that memory representations are distributed across sensory and cognitive-control brain regions, it remains unknown how multiple brain networks generate this attentional gain in fidelity. Here, we investigated the contributions of the distinct brain networks in maintaining and enhancing memory representations using psychophysical mod...


8: constclust: Consistent Clusters for scRNA-seq

Isaac Virshup, Jarny Choi et al.

12 tweets (posted 09 Dec 2020) bioinformatics

Unsupervised clustering to identify distinct cell types is a crucial step in the analysis of scRNA-seq data. Current clustering methods are dependent on a number of parameters whose effect on the resulting solution's accuracy and reproducibility are poorly understood. The adjustment of clustering parameters is therefore ad-hoc, with most users deviating minimally from default settings. constclust is a novel meta-clustering method based on the idea that if the data contains distinct populations which a clustering method ...


9: Human induced pluripotent stem cell-derived vessels as dynamic atherosclerosis model on a chip

Anna Mallone, Christoph Gericke et al.

11 tweets (posted 27 Nov 2020) bioengineering

Atherosclerosis is an arterial disease characterized by intravascular plaques. Disease hallmarks are vessel stenosis and hyperplasia, eventually escalating into plaque rupture and acute clinical presentations. Innate immune cells and local variations in hemodynamics are core players in the pathology, but their mutual relationship has never been investigated before due to the lack of modeling systems with adequate degree of complexity. Here, we combined computational fluid dynamics and tissue-engineering to achieve, for ...


10: Millisecond-scale molecular dynamics simulation of spike RBD structure reveals evolutionary adaption of SARS-CoV-2 to stably bind ACE2

Gard Nelson, Oleksandr Buzko et al.

11 tweets (posted 12 Dec 2020) biophysics

The Receptor Binding Domain (RBD) of the SARS-CoV-2 surface spike (S) protein interacts with host angiotensin converting enzyme 2 (ACE2) to gain entry to host cells and initiate infection 1-3. Detailed, accurate understanding of key interactions between S RBD and ACE2 provides critical information that may be leveraged in the development of strategies for the prevention and treatment of COVID-19. Utilizing the published sequences and cryo-EM structures of both the viral S RBD and ACE2 4,5, we performed in silico molecul...


11: cDC1 and interferons promote spontaneous CD4+ and CD8+ T cell protective responses to breast cancer

Raphaël Mattiuz, Carine Brousse et al.

10 tweets (posted 24 Dec 2020) immunology

Here we show that efficient breast cancer immunosurveillance relies on cDC1, conventional CD4+ T cells, CD8+ cytotoxic T lymphocytes (CTL) and later NK/NK T cells. For this process, cDC1 were required constitutively, but especially during the T cell priming phase. In the tumor microenvironment, cDC1 interacted physically and jointly with both CD4+ T cells and tumorspecific CD8+ T cells. We found that interferon (IFN) responses were necessary for the rejection of breast cancer, including cDC1-intrinsic signaling by IFN-{...


12: COVID-19-associated olfactory dysfunction reveals SARS-CoV-2 neuroinvasion and persistence in the olfactory system

Guilherme Dias De Melo, Francoise Lazarini et al.

9 tweets (posted 18 Nov 2020) neuroscience

While recent investigations have revealed viral, inflammatory and vascular factors involved in SARS-CoV-2 lung pathogenesis, the pathophysiology of neurological disorders in COVID-19 remains poorly understood. Yet, olfactory and taste dysfunction are rather common in COVID-19, especially in pauci-symptomatic patients which constitutes the most frequent clinical manifestation of the infection. We conducted a virologic, molecular, and cellular study of the olfactory system from COVID-19 patients presenting acute loss of s...


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

Lonni Besançon, Nathan Peiffer-Smadja et al.

9 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...


14: Anesthetics fragment hippocampal network activity, alter spine dynamics and affect memory consolidation

Wei Yang, Mattia Chini et al.

9 tweets (posted 06 Jun 2020) neuroscience

General anesthesia is characterized by reversible loss of consciousness accompanied by transient amnesia. Yet, long-term memory impairment is an undesirable side-effect. How different types of general anesthetics (GAs) affect the hippocampus, a brain region central to memory formation and consolidation, is poorly understood. Using extracellular recordings, chronic 2-photon imaging and behavioral analysis, we monitor the effects of isoflurane (Iso), medetomidine/midazolam/fentanyl (MMF), and ketamine/xylazine (Keta/Xyl) ...


15: Immunological memory to SARS-CoV-2 assessed for up to eight months after infection

Jennifer M Dan, Jose Mateus et al.

8 tweets (posted 16 Nov 2020) immunology

Understanding immune memory to SARS-CoV-2 is critical for improving diagnostics and vaccines, and for assessing the likely future course of the COVID-19 pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 254 samples from 188 COVID-19 cases, including 43 samples at [≥] 6 months post-infection. IgG to the Spike protein was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month post symptom onset. SARS-CoV-2-specific CD4+ T ce...


16: Context-dependent effects of IL-2 rewire immunity into distinct cellular circuits

Carly E. Whyte, Kailash Singh et al.

8 tweets (posted 20 Dec 2020) immunology

Interleukin 2 (IL-2) is a key homeostatic cytokine, with potential therapeutic applications in both immunogenic and tolerogenic immune modulation. Clinical application has been hampered by pleiotropic functionality and wide-spread receptor expression, with unexpected adverse events during trials. To characterize the IL-2 homeostatic network, we developed a novel mouse strain allowing IL-2 production to be diverted. Rewiring of IL-2 production to diverse leukocyte sources allowed the identification of contextual influenc...


17: A human coronavirus evolves antigenically to escape antibody immunity

Rachel Eguia, Katharine H.D. Crawford et al.

7 tweets (posted 18 Dec 2020) microbiology

There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera...


18: Formation and Spontaneous Long-Term Repatterning of Headless Planarian Flatworms

Johanna Bischof, Jennifer LaPalme et al.

7 tweets (posted 17 Jan 2021) developmental biology

Regeneration requires the production of large numbers of new cells, and thus cell division regulators, particularly ERK signaling, are critical in regulating this process. In the highly regenerative planarian flatworm, questions remain as to whether ERK signaling controls overall regeneration or plays a head-specific role. Here we show that ERK inhibition in the 3 days following amputation delays regeneration, but that all tissues except the head can overcome this inhibition, resulting in headless regenerates. This prev...


19: A crocodylian-style cloaca in a non-avialan dinosaur

Phil R. Bell, Michael Pittman et al.

7 tweets (posted 12 Oct 2020) paleontology

Our knowledge of the reproductive biology of dinosaurs covers a range of aspects, from brooding behaviour to nesting style and the timing of sexual maturity. Yet, the basic anatomy and function of the cloaca in non-avialan dinosaurs remains unknown. Here, we describe the outer morphology of the only known non-avialan dinosaur cloaca, preserved in an exceptional specimen of the early-diverging ceratopsian dinosaur Psittacosaurus . We clarify the position of the cloaca with respect to the ischia and caudal vertebrae and d...


20: Cell surface hydrophobicity determines Pseudomonas aeruginosa aggregate assembly

Sheyda Azimi, Jacob Thomas et al.

7 tweets (posted 14 Jan 2021) microbiology

It is now well established that bacteria live in structured aggregates during chronic infections, where they evolve to adapt to the host environment in order to evade host immune responses and therapeutic interventions. Despite recent developments on how the physical properties of polymers impact on aggregate formation, changes in bacterial properties to overcome this have been overlooked. Here we show that even with physical entropic forces imposed by polymers in a sputum medium environment, lipopolysaccharide (LPS) pl...