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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 124,478 papers from 534,878 authors.

Most tweeted biology preprints, last 24 hours

*There are gaps in historical Twitter data, most notably in spring 2020. This may result in some preprints appearing with less tweets than they should.

141 results found. For more information, click each entry to expand.

1: SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome
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Posted 13 Dec 2020

SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome
102 tweets bioRxiv genomics

Liguo Zhang, Alexsia Richards, Andrew Khalil, Emile Wogram, Haiting Ma, Richard A. Young, Rudolf Jaenisch

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
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Posted 19 Jun 2019

Motility induced fracture reveals a ductile to brittle crossover in the epithelial tissues of a simple animal
37 tweets bioRxiv biophysics

Vivek N. Prakash, Matthew S. Bull, Manu Prakash

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 withstand to these extreme strains can result in epithelial fractures [5, 6] and associated diseases [7,8]. From a materials science perspective, how properties of living cells and their interactions prescribe larger scale tissue rheology and adaptive response in dynamic force landscapes remains an important frontier [9]. Motivated by pushing tissues to the limits of their integrity, we carry out a multi-modal study of a simple yet highly dynamic organism, the Trichoplax Adhaerens [10,11,12], across four orders of magnitude in length (1um to 10 mm), and six orders in time (0.1 sec to 10 hours). We report the discovery of abrupt, bulk epithelial tissue fractures (10 sec) induced by the organisms own motility. Coupled with rapid healing (10 min), this discovery accounts for dramatic shape change and physiological asexual division in this early divergent metazoan. We generalize our understanding of this phenomena by codifying it in a heuristic model, highlighting the fundamental questions underlying the debonding/bonding criterion in a soft active living material by evoking the concept of an epithelial alloy. Using a suite of quantitative experimental and numerical techniques, we demonstrate a force driven ductile to brittle material transition governing the morphodynamics of tissues pushed to the edge of rupture. This work contributes to an important discussion at the core of developmental biology [13,14,15,16,17], with important applications to an emerging paradigm in materials and tissue engineering [5,18,19,20], wound healing and medicine [8,21,22].

3: Spatial structure impacts adaptive therapy by shaping intra-tumoral competition
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Posted 04 Nov 2020

Spatial structure impacts adaptive therapy by shaping intra-tumoral competition
17 tweets bioRxiv cancer biology

Maximilian A R Strobl, Jill Gallaher, Jeffrey West, Mark Robertson-Tessi, Philip K. Maini, Alexander Anderson

(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 the impact of different microenvironmental factors on the comparison between continuous drug administration and adaptive therapy. (3) Results: We show that the degree of crowding, the initial resistance fraction, the presence of resistance costs, and the rate of tumour cell turnover are key determinants of the benefit of adaptive therapy, and we study in detail how these factors alter competition between cells. We find that intra-specific competition between resistant cells plays an unexpectedly important role in the ability to control resistance. To conclude we show how differences in resistance cost and turnover change the tumour's spatial organisation and may explain differences in cycling speed observed in a cohort of 67 prostate cancer patients undergoing intermittent androgen deprivation therapy; (4) Conclusion: Our work provides insights into how adaptive therapy leverages inter- and intra-specific competition to control resistance, and shows that the tumour's spatial architecture will likely be an important factor in determining the quantitative benefit of adaptive therapy in patients.

4: 3D Mapping of Neurofibrillary Tangle Burden in the Human Medial Temporal Lobe
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Posted 17 Jan 2021

3D Mapping of Neurofibrillary Tangle Burden in the Human Medial Temporal Lobe
16 tweets bioRxiv neuroscience

Paul A Yushkevich, Mónica Muñoz López, Maria Mercedes Iñiguez de Onzoño Martin, Ranjit Ittyerah, Sydney Lim, Sadhana Ravikumar, Madigan L. Bedard, Stephen Pickup, Weixia Liu, Jiancong Wang, Ling Yu Hung, Jade Lasserve, Nicolas Vergnet, Long Xie, Mengjin Dong, Salena Cui, Lauren McCollum, John L Robinson, Theresa Schuck, Robin de Flores, Murray Grossman, M. Dylan Tisdall, Karthik Prabhakaran, Gabor Mizsei, Sandhitsu R. Das, Emilio Artacho-Pérula, María del Mar Arroyo Jiménez, María Pilar Marcos Rabal, Francisco Javier Molina Romero, Sandra Cebada Sánchez, José Carlos Delgado González, Carlos de la Rosa-Prieto, Marta Córcoles Parada, Edward B. Lee, John Q Trojanowski, Daniel T. Ohm, Laura E.M. Wisse, David A. Wolk, David J. Irwin, Ricardo Insausti

Abstract Tau protein neurofibrillary tangles (NFT) are closely linked to neuronal/synaptic loss and cognitive decline in Alzheimer's disease (AD) and related dementias. Our knowledge of the pattern of NFT progression in the human brain, critical to the development of imaging biomarkers and interpretation of in vivo imaging studies in AD, is based on conventional 2D histology studies that only sample the brain sparsely. To address this limitation, ex vivo MRI and dense serial histological imaging in 18 human medial temporal lobe (MTL) specimens were used to construct 3D quantitative maps of NFT burden in the MTL at individual and group levels. These maps reveal significant variation in NFT burden along the anterior-posterior axis. While early NFT pathology is thought to be confined to the transentorhinal region, we find similar levels of NFT burden in this region and other MTL subregions, including amygdala, temporopolar cortex, and subiculum/CA1.

5: Recurrent mutations in SARS-CoV-2 genomes isolated from mink point to rapid host-adaptation
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Posted 16 Nov 2020

Recurrent mutations in SARS-CoV-2 genomes isolated from mink point to rapid host-adaptation
12 tweets bioRxiv genomics

Lucy van Dorp, Cedric CS Tan, Su Datt Lam, Damien Richard, Christopher Owen, Dorothea Berchtold, Christine Orengo, François Balloux

Severe acute respiratory coronavirus 2 (SARS-CoV-2), the agent of the ongoing COVID-19 pandemic, jumped into humans from an unknown animal reservoir in late 2019. In line with other coronaviruses, SARS-CoV-2 has the potential to infect a broad range of hosts. SARS-CoV-2 genomes have now been isolated from cats, dogs, lions, tigers and minks. SARS-CoV-2 seems to transmit particularly well in mink farms with outbreaks reported in Spain, Sweden, the Netherlands, Italy, the USA and Denmark. Genomic data from SARS-CoV-2 isolated from infected minks provides a natural case study of a secondary host jump of the virus, in this case from humans to animals, and occasionally back again. We screened published SARS-CoV-2 genomes isolated from minks for the presence of recurrent mutations common in mink but infrequent in SARS-CoV-2 genomes from human infections. We identify 23 recurrent mutations including three nonsynonymous mutations in the Receptor Binding Domain of the SARS-CoV-2 spike protein that independently emerged at least four times but are only very rarely observed in strains circulating in humans. The repeat emergence of mutations across phylogenetically distinct lineages of the virus isolated from minks points to ongoing adaptation of SARS-CoV-2 to a new host. The rapid acquisition and spread of SARS-CoV-2 mutations in minks suggests that if a similar phenomenon of host adaptation had occurred upon its jump into humans, those human-specific mutations would likely have reached fixation already before the first SARS-CoV-2 genomes were generated. ### Competing Interest Statement The authors have declared no competing interest.

6: Mutation rate variations in the human genome are encoded in DNA shape
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Posted 18 Jan 2021

Mutation rate variations in the human genome are encoded in DNA shape
11 tweets bioRxiv genomics

Zian Liu, Md Abul Hassan Samee

Single nucleotide mutation rates have critical implications for human evolution and genetic diseases. Accurate modeling of these mutation rates has long remained an open problem since the rates vary substantially across the human genome. A recent model, however, explained much of the variation by considering higher order nucleotide interactions in the local (7-mer) sequence context around mutated nucleotides. Despite this model's predictive value, we still lack a clear understanding of the biophysical mechanisms underlying the variations in genome-wide mutation rates. DNA shape features are geometric measurements of DNA structural properties, such as helical twist and tilt, and are known to capture information on interactions between neighboring nucleotides within a local context. Motivated by this characteristic of DNA shape features, we used them to model mutation rates in the human genome. These DNA shape feature based models improved both the accuracy (up to 14%) and the interpretability over the current nucleotide sequence-based models. The models also discovered the specific shape features that capture the most variability in mutation rates, and distinguished between the most and the least mutated sequence contexts, thus characterizing mutation promoting properties of the genomic DNA. To our knowledge, this is the first attempt that demonstrates the structural underpinnings of nucleotide mutations in the human genome and lays the groundwork for future studies to incorporate DNA shape information in modeling genetic variations.

7: Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
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Posted 17 Jan 2021

Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
11 tweets bioRxiv genomics

Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries, Hubert Pausch

Background: Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between the bovine reference genome (ARS-UCD1.2) and a highly continuous Angus-based assembly (UOA Angus 1). Results: Read mapping accuracy did not differ notably between the ARS-UCD1.2 and UOA Angus 1 assemblies. We discovered 22,744,517 and 22,559,675 high-quality variants from ARS-UCD1.2 and UOA Angus 1, respectively. The concordance between sequence- and array-called genotypes was high and the number of variants deviating from Hardy-Weinberg proportions was low at segregating sites for both assemblies. More artefactual INDELs were genotyped from UOA Angus 1 than ARS-UCD1.2 alignments. Using the composite likelihood ratio test, we detected 40 and 33 signatures of selection from ARS-UCD1.2 and UOA Angus 1, respectively, but the overlap between both assemblies was low. Using the 161 sequenced Brown Swiss cattle as a reference panel, we imputed sequence variant genotypes into a mapping cohort of 30,499 cattle that had microarray-derived genotypes. The accuracy of imputation (Beagle R2) was very high (0.87) for both assemblies. Genome-wide association studies between imputed sequence variant genotypes and six dairy traits as well as stature produced almost identical results from both assemblies. Conclusions: The ARS-UCD1.2 and UOA Angus 1 assemblies are suitable for reference-guided genome analyses in Brown Swiss cattle. Although differences in read mapping and genotyping accuracy between both assemblies are negligible, the choice of the reference genome has a large impact on detecting signatures of selection using the composite likelihood ratio test. We developed a workflow that can be adapted and reused to compare the impact of reference genomes on genome analyses in various breeds, populations and species.

8: FiCoS: a fine- and coarse-grained GPU-powered deterministic simulator for biochemical networks
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Posted 17 Jan 2021

FiCoS: a fine- and coarse-grained GPU-powered deterministic simulator for biochemical networks
10 tweets bioRxiv systems biology

Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Giulia Capitoli, Simone Spolaor, Leonardo Rundo, Giancarlo Mauri, Daniela Besozzi

Mathematical models of biochemical networks can largely facilitate the comprehension of the mechanisms at the basis of cellular processes, as well as the formulation of hypotheses that can then be tested with targeted laboratory experiments. However, two issues might hamper the achievement of fruitful outcomes. On the one hand, detailed mechanistic models can involve hundreds or thousands of molecular species and their intermediate complexes, as well as hundreds or thousands of chemical reactions, a situation generally occurring when rule-based models are analysed. On the other hand, the computational analysis of a model typically requires the execution of a large number of simulations for its calibration or to test the effect of perturbations. As a consequence, the computational capabilities of modern Central Processing Units can be easily overtaken, possibly making the modeling of biochemical networks a worthless or ineffective effort. To the aim of overcoming the limitations of the current state-of-the-art simulation approaches, we present in this paper FiCoS, a novel "black- box" deterministic simulator that effectively realizes both a fine- and a coarse-grained parallelization on Graphics Processing Units. In particular, FiCoS exploits two different integration methods, namely the Dormand-Prince and the Radau IIA, to efficiently solve both non-stiff and stiff systems of coupled Ordinary Differential Equations. We tested the performance of FiCoS against different deterministic simulators, by considering models of increasing size and by running analyses with increasing computational demands. FiCoS was able to dramatically speedup the computations up to 855x, showing to be a promising solution for the simulation and analysis of large- scale models of complex biological processes.

9: The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold
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Posted 14 Jul 2020

The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold
8 tweets bioRxiv plant biology

Michaël Moison, Javier Martínez Pacheco, Leandro Lucero, Camille Fonouni-Farde, Johan Rodríguez-Melo, Natanael Mansilla, Aurélie Christ, Jérémie Bazin, Moussa Benhamed, Fernando Ibañez, Martin Crespi, Jose Estevez, Federico Ariel

Plant long noncoding RNAs (lncRNAs) have emerged as important regulators of chromatin dynamics, impacting on transcriptional programs leading to different developmental outputs. The lncRNA AUXIN REGULATED PROMOTER LOOP ( APOLO ) directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation, leading to transcriptional shifts. Here, we show that APOLO recognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and controls RHD6 transcriptional activity leading to cold-enhanced RH elongation. Furthermore, we demonstrate that APOLO interacts with the transcription factor WRKY42 and modulates its binding to the RHD6 promoter. WRKY42 is required for the activation of RHD6 by low temperatures and WRKY42 deregulation impairs cold-induced RH expansion. Collectively, our results indicate that a novel ribonucleoprotein complex involving APOLO and WRKY42 forms a regulatory hub which activates RHD6 by shaping its epigenetic environment and integrates signals governing RH growth and development.

10: Tissue-resident macrophages regulate lymphatic vessel growth and patterning in the developing heart
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Posted 02 Jul 2020

Tissue-resident macrophages regulate lymphatic vessel growth and patterning in the developing heart
8 tweets bioRxiv developmental biology

Thomas J Cahill, Xin Sun, Christophe Ravaud, Cristina Villa del Campo, Konstantinos Klaourakis, Irina-Elena Lupu, Allegra M Lord, Cathy Browne, Sten Eirik W Jacobsen, David R Greaves, David G Jackson, Sally A. Cowley, William James, Robin P Choudhury, Joaquim Miguel Vieira, Paul R. Riley

Macrophages are components of the innate immune system with key roles in tissue inflammation and repair. It is now evident that macrophages also support organogenesis, but few studies have characterized their identity, ontogeny and function during heart development. Here, we show that resident macrophages in the subepicardial compartment of the developing heart coincide with the emergence of new lymphatics and interact closely with the nascent lymphatic capillaries. Consequently, global macrophage-deficiency led to extensive vessel disruption with mutant hearts exhibiting shortened and mis-patterned lymphatics. The origin of cardiac macrophages was linked to the yolk sac and fetal liver. Moreover, Csf1r+ and Cx3cr1+ myeloid sub-lineages were found to play essential functions in the remodeling of the lymphatic endothelium. Mechanistically, macrophage hyaluronan was found to be required for lymphatic sprouting by mediating direct macrophage-lymphatic endothelial cell interactions. Together, these findings reveal insight into the role of macrophages as indispensable mediators of lymphatic growth during the development of the mammalian cardiac vasculature.

11: Anesthetics fragment hippocampal network activity, alter spine dynamics and affect memory consolidation
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Posted 06 Jun 2020

Anesthetics fragment hippocampal network activity, alter spine dynamics and affect memory consolidation
8 tweets bioRxiv neuroscience

Wei Yang, Mattia Chini, Jastyn A Poepplau, Andrey Formozov, Alexander Dieter, Patrick Piechocinski, Cynthia Rais, Fabio Morellini, Olaf Sporns, Ileana L Hanganu-Opatz, J. Simon Wiegert

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) on network activity and structural spine dynamics in the hippocampal CA1 area of adult mice. GAs robustly reduced spiking activity, decorrelated cellular ensembles, albeit with distinct activity signatures, and altered spine dynamics. CA1 network activity under all three anesthetics was different to natural sleep. Iso anesthesia most closely resembled unperturbed activity during wakefulness and sleep, and network alterations recovered more readily than with Keta/Xyl and MMF. Correspondingly, memory consolidation was impaired after exposure to Keta/Xyl and MMF, but not Iso. Thus, different anesthetics distinctly alter hippocampal network dynamics, synaptic connectivity, and memory consolidation, with implications for GA strategy appraisal in animal research and clinical settings.

12: MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
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Posted 07 Oct 2020

MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
7 tweets bioRxiv bioinformatics

Samuel M. Nicholls, Radoslaw Poplawski, Matthew J. Bull, Anthony Underwood, Michael Chapman, Khalil Abu-Dahab, Ben Taylor, Ben Jackson, Sara Rey, Roberto Amato, Rich Livett, Sónia Gonçalves, Ewan M. Harrison, Sharon J Peacock, David Aanensen, Andrew Rambaut, Thomas R. Connor, Nick J Loman, The COVID-19 Genomics UK (COG-UK) Consortium

Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of even large epidemics. With increased availability of sequencing it is possible for agile networks of sequencing facilities to collaborate on the sequencing and analysis of epidemic genomic data. In response to the ongoing SARS-CoV-2 pandemic in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed with the aim of rapidly sequencing SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of Majora, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network. The system was designed and implemented pragmatically to stand up capacity rapidly in a pandemic caused by a novel virus. This approach has underpinned the success of COG-UK, which has rapidly become the leading contributor of SARS-CoV-2 genomes to international databases and has generated over 60,000 sequences to date. ### Competing Interest Statement The authors have declared no competing interest.

13: Formation and Spontaneous Long-Term Repatterning of Headless Planarian Flatworms
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Posted 17 Jan 2021

Formation and Spontaneous Long-Term Repatterning of Headless Planarian Flatworms
7 tweets bioRxiv developmental biology

Johanna Bischof, Jennifer LaPalme, Kelsie Miller, Junji Morokuma, Kate Williams, Chris Fields, Michael Levin

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 prevention of head regeneration happens to a different degree along the anterior-posterior axis, with very anterior wounds regenerating heads even under ERK inhibition. Remarkably, 4 to 18 weeks after injury, the headless animals induced by ERK inhibition remodel to regain single-headed morphology, in the absence of further injury, in a process driven by Wnt/{beta}-catenin signaling. Interestingly, headless animals are likely to exhibit unstable axial polarity, and cutting or fissioning prior to remodeling can result in body-wide reversal of anterior-posterior polarity. Our data reveal new aspects of how ERK signaling regulates regeneration in planaria and show anatomical remodeling on very long timescales.

14: An updated structural model of the A domain of the Pseudomonas putida XylR regulator exposes a distinct interplay with aromatic effectors
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Posted 17 Jan 2021

An updated structural model of the A domain of the Pseudomonas putida XylR regulator exposes a distinct interplay with aromatic effectors
7 tweets bioRxiv microbiology

Pavel Dvorak, Carlos Alvarez-Carreno, Sergio Ciordia, Alberto Paradela, Victor de Lorenzo

A revised model of the aromatic binding A domain of the sigma 54-dependent regulator XylR of Pseudomonas putida mt-2 was produced based on the known 3D structures of homologous regulators PoxR, MopR, and DmpR. The resulting frame was instrumental for mapping the large number of mutations known to alter effector specificity, which were then reinterpreted under a dependable spatial reference. Some of these changes involved the predicted aromatic-binding pocket but others occurred in distant locations, including dimerization interfaces and putative zinc-binding site. The effector pocket was buried within the protein structure and accessible from the outside only through a narrow tunnel. The model was experimentally validated by treating the cells in vivo and the purified protein in vitro with benzyl bromide, which reacts with accessible nucleophilic residues on the protein surface. Proteomic analyses of the thereby tagged peptides confirmed the predicted in/out distribution of residues but also suggested that the fully-folded protein is not accessible by externally added effectors. The data thus suggested that XylR inducers assist the folding and/or the structuring of the A domain in an intramolecular non-repressive form rather than interacting dynamically with the aromatic partner once a fully structured protein is shaped.

15: Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants
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Posted 17 Dec 2020

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants
6 tweets bioRxiv biophysics

Natália Teruel, Olivier Mailhot, Rafael Najmanovich

The SARS-CoV-2 Spike protein needs to be in an open-state conformation to interact with ACE2 as part of the viral entry mechanism. We utilise coarse-grained normal-mode analyses to model the dynamics of Spike and calculate transition probabilities between states for 17081 Spike variants. Our results correctly model an increase in open-state occupancy for the more infectious D614G via an increase in flexibility of the closed-state and decrease of flexibility of the open-state. We predict the same effect for several mutations on Glycine residues (404, 416, 504, 252) as well as residues K417, D467 and N501, including the N501Y mutation, explaining the higher infectivity of the B.1.1.7 and 501.V2 strains. This is, to our knowledge, the first use of normal-mode analysis to model conformational state transitions and the effect of mutations thereon. The specific mutations of Spike identified here may guide future studies to increase our understanding of SARS-CoV-2 infection mechanisms and guide public health in their surveillance efforts.

16: Trait plasticity and covariance along a continuous soil moisture gradient
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Posted 19 Feb 2020

Trait plasticity and covariance along a continuous soil moisture gradient
6 tweets bioRxiv plant biology

J Grey Monroe, Haoran Cai, David L Des Marais

Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because it is primarily informed by experiments considering soil moisture variability at two discrete levels - wet and dry - rather than as a continuously varying environmental gradient. Here we used experimental and statistical methods based on function-valued traits to explore responses to a continuous soil moisture gradient in physiological and morphological traits in two species and five genotypes each of the model grass Brachypodium. We find that most traits exhibit non-linear responses to soil moisture variability. We also observe differences in the shape of these non-linear responses between traits, species, and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. These results point to the importance of considering non-linearity in plant-water relations to understand plastic and evolutionary responses to changing climates.

17: COMPARE, an ultra-fast and robust suite for multiparametric screening, identifies phenotypic drug responses in acute myeloid leukemia
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Posted 09 Jan 2021

COMPARE, an ultra-fast and robust suite for multiparametric screening, identifies phenotypic drug responses in acute myeloid leukemia
5 tweets bioRxiv cancer biology

Morteza Chalabi Hajkarim, Ella Karjalainen, Mikhail Osipovitch, Konstantinos Dimopoulos, Sandra Leigh Gordon, Francesca Ambri, Kasper Dindler Rasmussen, Kirsten Gronbaek, Kristian Helin, Krister Wennerberg, Kyoung Jae Won

Multiparametric phenotypic screening of cells, for example assessing their responses to small molecules or knockdown/knockout of specific genes, is a powerful approach to understanding cellular systems and identifying potential new therapeutic strategies. However, automated tools for analyzing similarities and differences between a large number of tested conditions have not been readily available. Methods designed for clustering cells cannot identify differences between samples effectively. We introduce COMPARE for ultra-fast and robust analysis of multiparametric high-throughput screening. Applying a mass-aware gridding algorithm using hypercubes, COMPARE performs automatic and effective similarity comparison for hundreds to thousands of tests and provides information about the treatment effect. Particularly for screening data, COMPARE is equipped with modules to remove various sources of bias. Benchmarking tests show that COMPARE can circumvent batch effects and perform a similarity analysis substantially faster than conventional analysis tools. Applying COMPARE to high-throughput flow cytometry screening data, we were able to distinguish subtle phenotypic drug responses in a human sample and a genetically engineered mouse model with acute myeloid leukemia (AML). COMPARE revealed groups of drugs with similar responses even though their mechanisms are distinct from each other. In another screening, COMPARE effectively circumvented batch effects and grouped samples from AML and myelodysplastic syndrome (MDS) patients using clinical flow cytometry data.

18: Cognitive boundary signals in the human medial temporal lobe shape episodic memory representation
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Posted 16 Jan 2021

Cognitive boundary signals in the human medial temporal lobe shape episodic memory representation
5 tweets bioRxiv neuroscience

Jie Zheng, Andrea Gomez Palacio Schjetnan, Mar Yebra, Clayton P. Mosher, Suneil Kalia, Taufik A Valiante, Adam Mamelak, Gabriel Kreiman, Ueli Rutishauser

While experience unfolds continuously, memories are organized as a set of discrete events that bind together the "where", "when", and "what" of episodic memory. This segmentation of continuous experience is thought to be facilitated by the detection of salient environmental or cognitive events. However, the underlying neural mechanisms and how such segmentation shapes episodic memory representations remain unclear. We recorded from single neurons in the human medial temporal lobe while subjects watched videos with different types of embedded boundaries and were subsequently evaluated for memories of the video contents. Here we show neurons that signal the presence of cognitive boundaries between subevents from the same episode and neurons that detect the abstract separation between different episodes. The firing rate and spike timing of these boundary-responsive neurons were predictive of later memory retrieval accuracy. At the population level, abrupt neural state changes following boundaries predicted enhanced memory strength but impaired order memory, capturing the behavioral tradeoff subjects exhibited when recalling episodic content versus temporal order. Successful retrieval was associated with reinstatement of the neural state present following boundaries, indicating that boundaries structure memory search. These findings reveal a neuronal substrate for detecting cognitive boundaries and show that cognitive boundary signals facilitate the mnemonic organization of continuous experience as a set of discrete episodic events.

19: How robust are cross-population signatures of polygenic adaptation in humans?
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Posted 13 Jul 2020

How robust are cross-population signatures of polygenic adaptation in humans?
4 tweets bioRxiv genetics

Alba Refoyo-Martínez, Siyang Liu, Anja Moltke Jørgensen, Xin Jin, Anders Albrechtsen, Alicia R Martin, Fernando Racimo

Over the past decade, summary statistics from genome-wide association studies (GWASs) have been used to detect and quantify polygenic adaptation in humans. Several studies have reported signatures of natural selection at sets of SNPs associated with complex traits, like height and body mass index. However, more recent studies suggest that some of these signals may be caused by biases from uncorrected population stratification in the GWAS data with which these tests are performed. Moreover, past studies have predominantly relied on SNP effect size estimates obtained from GWAS panels of European ancestries, which are known to be poor predictors of phenotypes in non-European populations. Here, we collated GWAS data from multiple anthropometric and metabolic traits that have been measured in more than one cohort around the world, including the UK Biobank, FINRISK, Chinese NIPT, Biobank Japan, APCDR and PAGE. We then evaluated how robust signals of polygenic score overdispersion (which have been interpreted as suggesting polygenic adaptation) are to the choice of GWAS cohort used to identify associated variants and their effect size estimates. We did so while using the same panel to obtain population allele frequencies (The 1000 Genomes Project). We observe many discrepancies across tests performed on the same phenotype and find that association studies performed using multiple different cohorts, like meta-analyses and mega-analyses, tend to produce scores with strong overdispersion across populations. This results in apparent signatures of polygenic adaptation which are not observed when using effect size estimates from biobank-based GWASs of homogeneous ancestries. Indeed, we were able to artificially create score overdispersion when taking the UK Biobank cohort and simulating a meta-analysis on multiple subsets of the cohort. Finally, we show that the amount of overdispersion in scores for educational attainment - a trait with strong social implications and high potential for misinterpretation - is also strongly dependent on the specific GWAS used to build them. This suggests that extreme caution should be taken in the execution and interpretation of future tests of polygenic score overdispersion based on population differentiation, especially when using summary statistics from a GWAS that combines multiple cohorts.

20: SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification
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Posted 18 Mar 2017

SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification
4 tweets bioRxiv bioinformatics

Manuel Tardaguila, Lorena de la Fuente, Cristina Marti, Cécile Pereira, Francisco Jose Pardo-Palacios, Hector del Risco, Marc Ferrell, Maravillas Mellado, Marissa Macchietto, Kenneth Verheggen, Mariola Edelmann, Iakes Ezkurdia, Jesus Vazquez, Michael Tress, Ali Mortazavi, Lennart Martens, Susana Rodriguez-Navarro, Victoria Moreno, Ana Conesa

High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in very well annotated organisms as mice and humans. Nonetheless, there is a need for studies and tools that characterize these novel isoforms. Here we present SQANTI, an automated pipeline for the classification of long-read transcripts that computes 47 descriptors that can be used to assess the quality of the data and of the preprocessing pipelines. We applied SQANTI to a neuronal mouse transcriptome using PacBio long reads and illustrate how the tool is effective in readily describing the composition of and characterizing the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach, and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, result more frequently in novel ORFs than novel UTRs and are enriched in both general metabolic and neural specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases we find that alternative isoforms are elusive to proteogenomics detection and are variable in protein changes with respect to the principal isoform of their genes. SQANTI allows the user to maximize the analytical outcome of long read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes. SQANTI is available at https://bitbucket.org/ConesaLab/sqanti.

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