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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 219,747 papers from 869,518 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.

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

1: Histone-organized chromatin in bacteria
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Posted 26 Jan 2023

Histone-organized chromatin in bacteria
141 tweets bioRxiv molecular biology

Antoine Hocher, Shawn Laursen, Paul Radford, Jess Tyson, Carey Lambert, Kathryn Mary Stevens, Mathieu Picardeau, R Elizabeth Sockett, Karolin Luger, Tobias Warnecke

Histones are the principal constituents of chromatin in eukaryotes and most archaea, while bacteria generally rely on an orthogonal set of proteins to organize their chromosomes. However, several bacterial genomes encode proteins with putative histone fold domains. Whether these proteins are structurally and functionally equivalent to archaeal and eukaryotic histones is unknown. Here, we demonstrate that histones are essential and are major components of chromatin in the bacteria Bdellovibrio bacteriovorus and Leptospira interrogans. Patterns of sequence evolution suggest important roles in several additional bacterial clades. Structural analysis of the B. bacteriovorus histone (Bd0055) dimer shows that histone fold topology is conserved between bacteria, archaea, and eukaryotes. Yet, unexpectedly, Bd0055 binds DNA end-on and forms a sheath of tightly packed histone dimers to encase straight DNA. This binding mode is in stark contrast to that employed by archaeal, eukaryotic, and viral histones, which invariably bend and wrap DNA around their outer surface. Our results demonstrate that histones are integral chromatin components across the tree of life and highlight organizational innovation in the domain Bacteria.

2: Axial regionalization in Tiktaalik roseae and the origin of quadrupedal locomotion
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Posted 13 Jan 2023

Axial regionalization in Tiktaalik roseae and the origin of quadrupedal locomotion
135 tweets bioRxiv paleontology

Thomas A Stewart, Justin B Lemberg, Emily Hillan, Isaac Magallanes, Edward B Daeschler, Neil H Shubin

The origin of quadrupedal locomotion in tetrapods entailed the evolution of a regionalized axial skeleton with sacral ribs. These ribs provide linkage between the pelvis and vertebral column and contribute to body support and propulsion by the hind limb. The closest relatives of limbed vertebrates are not known to possess such a connection and, therefore, have typically been described as primarily supporting their bodies against the substrate with pectoral fins. However, data on the axial skeletons of stem tetrapods are sparce, with key features of specimens potentially covered by matrix. Here we provide micro-computed tomography data of the axial skeleton of Tiktaalik roseae and show that its vertebrae and ribs are regionalized along the craniocaudal axis, including expanded and ventrally curved ribs in the sacral region. The sacral ribs would have contacted the expanded iliac blade of the pelvis in a soft tissue connection. No atlas-axis complex is observed, however the basioccipital-exoccipital complex is deconsolidated from the rest of the neurocranium, suggesting increased mobility at occipital-vertebral junction. Thus, axial regionalization that allowed for innovations in head mobility, body support and buttressing the pelvic fin evolved prior to the origin of limbs.

3: A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments
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Posted 26 Jan 2023

A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments
35 tweets bioRxiv cancer biology

Christopher Chidley, Alicia Marie Darnell, Benjamin Louis Gaudio, Evan C Lien, Anna M Barbeau, Matthew G Vander Heiden, Peter Karl Sorger

Blocking the import of nutrients essential for cancer cell proliferation represents a therapeutic opportunity, but it is unclear which transporters to target. Here, we report a CRISPRi/a screening platform to systematically interrogate the contribution of specific nutrient transporters to support cancer cell proliferation in environments ranging from standard culture media to tumor models. We applied this platform to identify the transporters of amino acids in leukemia cells and found that amino acid transport is characterized by high bidirectional flux that is dependent on the composition of the microenvironment. While investigating the role of transporters in cystine starved cells, we uncovered a novel role for serotonin uptake in preventing ferroptosis. Finally, we identified transporters essential for cell proliferation in subcutaneous tumors and found that levels of glucose and amino acids can restrain proliferation in that environment. This study provides a framework for the systematic identification of critical cellular nutrient transporters, characterizing the function of such transporters, and studying how the tumor microenvironment impacts cancer metabolism.

4: Identification of a molnupiravir-associated mutational signature in SARS-CoV-2 sequencing databases
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Posted 27 Jan 2023

Identification of a molnupiravir-associated mutational signature in SARS-CoV-2 sequencing databases
23 tweets medRxiv infectious diseases

Theo Sanderson, Ryan Hisner, I'ah Donovan-Banfield, Thomas Peacock, Christopher Ruis

Molnupiravir, an antiviral medication that has been widely used against SARS-CoV-2, acts by inducing mutations in the virus genome during replication. Most random mutations are likely to be deleterious to the virus, and many will be lethal. Molnupiravir-induced elevated mutation rates have been shown to decrease viral load in animal models. However, it is possible that some patients treated with molnupiravir might not fully clear SARS-CoV-2 infections, with the potential for onward transmission of molnupiravir-mutated viruses. We set out to systematically investigate global sequencing databases for a signature of molnupiravir mutagenesis. We find that a specific class of long phylogenetic branches appear almost exclusively in sequences from 2022, after the introduction of molnupiravir treatment, and in countries and age-groups with widespread usage of the drug. We calculate a mutational spectrum from the AGILE placebo-controlled clinical trial of molnupiravir and show that its signature, with elevated G-to-A and C-to-T rates, largely corresponds to the mutational spectrum seen in these long branches. Our data suggest a signature of molnupiravir mutagenesis can be seen in global sequencing databases, in some cases with onwards transmission.

5: Induction of SARS-CoV-2 N-specific CD8+ T cell immunity in lungs by engineered extracellular vesicles associates with strongly impaired viral replication
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Posted 20 Jan 2023

Induction of SARS-CoV-2 N-specific CD8+ T cell immunity in lungs by engineered extracellular vesicles associates with strongly impaired viral replication
19 tweets bioRxiv immunology

Francesco Manfredi, Chiara Chiozzini, Flavia Ferrantelli, Patrizia Leone, katherina Pugliese, Massimo Spada, Antonio Di Virgilio, Andrea Giovannelli, Mauro Valeri, Andrea Cara, Zuleika Michelini, Mauro Andreotti, Maurizio Federico

Induction of effective immunity in lungs should be a pre-requisite for any vaccine designed to control the severe pathogenic effects generated by respiratory infectious agents. In the case of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 infection, vaccination is expected to associate with significant inhibition of viral replication in lungs. We recently provided evidence that the generation of endogenous extracellular vesicles (EVs) engineered for the incorporation of SARS-CoV-2 Nucleocapsid (N) protein can protect K18-hACE2 transgenic mice from the lethal intranasal infection with the ancestral Wuhan isolate. Actually, it was widely demonstrated that these transgenic mice succumb to SARS-CoV-2 intranasal infection mainly as a consequence of the viral invasiveness of central nervous system, a pathogenetic mechanism almost absent in humans. On the other hand, K18-hACE2 transgenic mice support viral replication in lungs, an event strictly mirroring the major pathogenic signature linked to the severe disease in humans. However, nothing is known about the ability of N-specific CD8+ T cell immunity induced by engineered EVs in controlling viral replication in lungs. To fill the gap, we investigated the immunity generated in lungs by N-engineered EVs in terms of induction of N-specific effectors and resident memory CD8+ T lymphocytes before and after virus challenge carried out three weeks and three months after boosting. At the same time points, viral replication extents in lungs were evaluated. We found that three weeks after second immunization, virus replication was reduced in mice best responding to vaccination by more than 3-logs compared to control group. The impaired viral replication matched with a reduced induction of Spike-specific CD8+ T lymphocytes. The antiviral effect appeared similarly strong when the viral challenge was carried out 3 months after boosting. This inhibitory effect associated with the persistence of a N-specific CD8+ T-resident memory lymphocytes in lungs of N-immunized mice. In view of the quite conserved sequence of the N protein among SARS-CoV-2 variants, these results support the idea that a vaccine strategy focused on the induction of anti-N CD8+ T cell immunity in lungs has the potential to control the replication of emerging variants.

6: Effectiveness of Vaccination and Previous Infection Against Omicron Infection and Severe Outcomes in Children Under 12 Years of Age
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Posted 19 Jan 2023

Effectiveness of Vaccination and Previous Infection Against Omicron Infection and Severe Outcomes in Children Under 12 Years of Age
17 tweets medRxiv infectious diseases

Danyu Lin, Yangjianchen Xu, Yu Gu, Donglin Zeng, Bradford Wheeler, Hayley Young, Zack Moore, Shadia Sunny

Background: Data on the protection conferred by vaccination and previous infection against omicron infection and severe outcomes in children can inform prevention strategies. Methods: We obtained vaccination records and clinical outcomes for 1,368,721 North Carolina residents 11 years of age or younger from October 29, 2021 to January 6, 2023. We used Cox regression to estimate the time varying effects of primary and booster vaccination and previous infection on the risks of omicron infection, hospitalization, and death. Results: For children 5 to 11 years of age, the effectiveness of primary vaccination against infection was 59.9% (95% confidence interval [CI], 58.5 to 61.2), 33.7% (95% CI, 32.6 to 34.8), and 14.9% (95% CI, 12.3 to 17.5) at 1, 4 and 10 months after the first dose; the effectiveness of a monovalent or bivalent booster dose after 1 month was 24.4% (95% CI, 14.4 to 33.2) or 76.7% (95% CI, 45.7 to 90.0); and the effectiveness of omicron infection against reinfection was 79.9% (95% CI, 78.8 to 80.9) and 53.9% (95% CI, 52.3 to 55.5) after 3 and 6 months, respectively. For children 0 4 years of age, the effectiveness of primary vaccination against infection was 63.8% (95% CI, 57.0 to 69.5) and 58.1% (95% CI, 48.3 to 66.1) at 2 and 5 months after the first dose, and the effectiveness of omicron infection against reinfection was 77.3% (95% CI, 75.9 to 78.6) and 64.7% (95% CI, 63.3 to 66.1) after 3 and 6 months, respectively. For both age groups, vaccination and previous infection had better effectiveness against hospitalization and death than against infection. Conclusions: Vaccination was effective against omicron infection and severe outcomes in children under the age of 12 years, although the effectiveness decreased over time. Bivalent boosters were more effective than monovalent boosters. Immunity acquired via omicron infection was very high and waned gradually over time.

7: SPEAR: a Sparse Supervised Bayesian Factor Model for Multi-omic Integration
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Posted 26 Jan 2023

SPEAR: a Sparse Supervised Bayesian Factor Model for Multi-omic Integration
16 tweets bioRxiv bioinformatics

Jeremy P. Gygi, Anna Konstorum, Shrikant Pawar, Steven H. Kleinstein, Leying Guan

Motivation: Unsupervised factor modeling, which preserves the primary sources of data variation through low-dimensional factors, is commonly applied to integrate high-dimensional multi-omics data. However, the resulting factors are suboptimal for prediction tasks due to the separation between factor construction and prediction model learning. A supervised factor model that effectively utilizes the responses while accounting for structural heterogeneity across omics is needed. Results: We present SPEAR, a supervised variational Bayesian framework that decomposes multi-omics data into latent factors with predictive power. The method adaptively determines factor rank, emphasis on factor structure, data relevance and feature sparsity. SPEAR improves reconstruction of underlying factors in synthetic examples and prediction accuracy of COVID-19 severity and breast cancer tumor subtypes. Availability: SPEAR is a publicly available R-package hosted at https://bitbucket.org/kleinstein/SPEAR.

8: Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2.
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Posted 27 Sep 2022

Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2.
14 tweets bioRxiv microbiology

Sarah Sattar, Juraj Kabat, Kailey Jerome, Friederike Feldmann, Kristina Bailey, Masfique Mehedi

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than SARS-CoV or MERS-CoV. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) "PRRARSV", which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. To our surprise, S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel pathogenic feature of SARS-CoV-2.

9: Structural preferences shape the entropic force of disordered protein ensembles
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Posted 21 Jan 2023

Structural preferences shape the entropic force of disordered protein ensembles
9 tweets bioRxiv biophysics

Feng Yu, Shahar Sukenik

Intrinsically disordered protein regions (IDRs) make up over 30% of the human proteome and instead of a native, well-folded structure exist in a dynamic conformational ensemble. Tethering IDRs to a surface (for example, the surface of a well-folded region of the same protein) can reduce the number of accessible conformations in IDR ensembles. This reduces the ensemble's conformational entropy, generating an effective entropic force that pulls away from the point of tethering. Recent experimental work has shown that this entropic force causes measurable, physiologically relevant changes to protein function, but how the magnitude of this force depends on the IDR sequence remains unexplored. Here we use all-atom simulations to analyze how structural preferences encoded in dozens of IDR ensembles contribute to the entropic force they exert upon tethering. We show that sequence-encoded structural preferences play an important role in determining the magnitude of this force and that compact, spherical ensembles generate an entropic force that can be several times higher than more extended ensembles. We further show that changes in the surrounding solution's chemistry can modulate IDR entropic force strength. We propose that the entropic force is a sequence-dependent, environmentally tunable property of terminal IDR sequences.

10: Antiviral treatments lead to the rapid accrual of hundreds of SARS-CoV-2 mutations in immunocompromised patients
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Posted 22 Dec 2022

Antiviral treatments lead to the rapid accrual of hundreds of SARS-CoV-2 mutations in immunocompromised patients
7 tweets medRxiv infectious diseases

Nicholas M Fountain-Jones, Robert Vanhaeften, Jan Williamson, Janelle Maskell, I-Ly Chua, Michael Charleston, Louise Cooley

The antiviral Molnupiravir (Lageviro) is widely used across the world to treat SARS-CoV-2 infection. Molnupiravir reduces viral replication by inducing mutations throughout the genome, yet in patients that do not clear the infection, the longer-term impact of the drug on virus evolution is unclear. Here, we used a case-control approach to monitor SARS-CoV-2 genomes through time in nine immunocompromised -patients with five treated with Molnupiravir. Within days of treatment, we detected a large number of low-frequency mutations in patients and that these new mutations could persist and, in some cases, were fixed in the virus population. All patients treated with the drug accrued new mutations in the spike protein of the virus, including non-synonymous mutations that altered the amino acid sequence. Our study demonstrates that this commonly used antiviral can supercharge viral evolution in immunocompromised patients, potentially generating new variants and prolonging the pandemic.

11: Effectiveness of the Coronavirus Disease 2019 (COVID-19) Bivalent Vaccine
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Posted 19 Dec 2022

Effectiveness of the Coronavirus Disease 2019 (COVID-19) Bivalent Vaccine
7 tweets medRxiv infectious diseases

Nabin K. Shrestha, Patrick C. Burke, Amy S. Nowacki, James F Simon, Amanda Hagen, Steven M. Gordon

Background. The purpose of this study was to evaluate whether a bivalent COVID-19 vaccine protects against COVID-19. Methods. Employees of Cleveland Clinic in employment on the day the bivalent COVID-19 vaccine first became available to employees, were included. The cumulative incidence of COVID-19 was examined over the following weeks. Protection provided by vaccination (analyzed as a time-dependent covariate) was evaluated using Cox proportional hazards regression. The analysis was adjusted for the pandemic phase when the last prior COVID-19 episode occurred, and the number of prior vaccine doses received. Results. Among 51011 employees, 20689 (41%) had had a previous documented episode of COVID-19, and 42064 (83%) had received at least two doses of a COVID-19 vaccine. COVID-19 occurred in 2452 (5%) during the study. Risk of COVID-19 increased with time since the most recent prior COVID-19 episode and with the number of vaccine doses previously received. In multivariable analysis, the bivalent vaccinated state was independently associated with lower risk of COVID-19 (HR, .70; 95% C.I., .61-.80), leading to an estimated vaccine effectiveness (VE) of 30% (95% CI, 20-39%). Compared to last exposure to SARS-CoV-2 within 90 days, last exposure 6-9 months previously was associated with twice the risk of COVID-19, and last exposure 9-12 months previously with 3.5 times the risk. Conclusions. The bivalent COVID-19 vaccine given to working-aged adults afforded modest protection overall against COVID-19, while the virus strains dominant in the community were those represented in the vaccine.

12: Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
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Posted 25 Jan 2023

Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts
7 tweets bioRxiv synthetic biology

Katherine Ilia, Nika Shakiba, Trevor Bingham, Ross D Jones, Michael M Kaminski, Eliezer Aravera, Simone Bruno, Sebastian Palacios, Ron Weiss, James J. Collins, Domitilla Del Vecchio, Thorsten M Schlaeger

Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. Here, we identify the successful reprogramming trajectories of the core pluripotency TF, OCT4, and design a genetic controller that enforces such trajectories with high precision. By combining a genetic circuit that generates a wide range of OCT4 trajectories with live-cell imaging, we track OCT4 trajectories with clonal resolution and find that a distinct constant OCT4 trajectory is required for colony formation. We then develop a synthetic genetic circuit that yields a tight OCT4 distribution around the identified trajectory and outperforms in terms of reprogramming efficiency other circuits that less accurately regulate OCT4. Our synthetic biology approach is generalizable for identifying and enforcing TF dynamics for cell fate programming applications.

13: Biochemical Properties of Naturally Occurring Human Bloom Helicase Variants
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Posted 26 Jan 2023

Biochemical Properties of Naturally Occurring Human Bloom Helicase Variants
6 tweets bioRxiv biochemistry

Rachel R Cueny, Sameer Varma, Kristina H. Schmidt, James L. Keck

Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human BLM cause Bloom syndrome (BS), an autosomal recessive disorder that leads to myriad negative health impacts including a predisposition to cancer. BS-causing mutations in BLM often negatively impact BLM ATPase and helicase activity. While BLM mutations that cause BS have been well characterized both in vitro and in vivo, there are other less studied BLM mutations that exist in the human population that do not lead to BS. Two of these non-BS mutations, encoding BLM P868L and BLM G1120R, when homozygous, increase sister chromatid exchanges in human cells. To characterize these naturally occurring BLM mutant proteins in vitro, we purified the BLM catalytic core (BLMcore, residues 636-1298) with either the P868L or G1120R substitution. We also purified a BLMcore K869A K870A mutant protein, which alters a lysine-rich loop proximal to the P868 residue. We found that BLMcore P868L and G1120R proteins were both able to hydrolyze ATP, bind diverse DNA substrates, and unwind G-quadruplex and duplex DNA structures. Molecular dynamics simulations suggest that the P868L substitution weakens the DNA interaction with the winged-helix domain of BLM and alters the orientation of one lobe of the ATPase domain. Because BLMcore P868L and G1120R retain helicase function in vitro, it is likely that the increased genome instability is caused by specific impacts of the mutant proteins in vivo. Interestingly, we found that BLMcore K869A K870A has diminished ATPase activity, weakened binding to duplex DNA structures, and less robust helicase activity compared to wild-type BLMcore. Thus, the lysine-rich loop may have an important role in ATPase activity and specific binding and DNA unwinding functions in BLM.

14: Medication-related adverse events in patients with cancer and discrepancies in cystatin C- versus creatinine-based eGFR
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Posted 18 Jan 2023

Medication-related adverse events in patients with cancer and discrepancies in cystatin C- versus creatinine-based eGFR
6 tweets medRxiv oncology

Meghan E Sise

Background: Creatinine-based estimated glomerular filtration rate (eGFRCRE) may overestimate kidney function in patients with cancer. Cystatin C-based eGFR (eGFRCYS) is an alternative marker of kidney function. We investigated whether patients with an eGFR discrepancy, defined as eGFRCYS >30% lower than the concurrent eGFRCRE, had an increased risk of adverse events resulting from renally-cleared medications. Patients and Methods: We conducted a cohort study of adult patients with cancer who had serum creatinine and cystatin C measured on the same day between May 2010 and January 2022 at two academic cancer centers in Boston, MA. The primary outcome was the incidence of each of the following medication-related adverse events: 1) supratherapeutic vancomycin levels (>30ug/mL); 2) trimethoprim-sulfamethoxazole-related hyperkalemia (>5.5mEq/L); 3) baclofen-induced neurotoxicity; and 4) supratherapeutic digoxin levels (>2.0ng/mL). Results: 1988 patients with cancer had simultaneous eGFRCYS and eGFRCRE. The mean age was 66 years (SD +/- 14), 965 (49%) were female, and 1555 (78%) were non-Hispanic white. eGFR discrepancy occurred in 579 patients (29%). Patients with eGFR discrepancy were more likely to experience medication-related adverse events compared to those without eGFR discrepancy: vancomycin levels >30ug/mL (24% vs. 10%, p=0.004), trimethoprim- sulfamethoxazole-related hyperkalemia (24% vs. 12%, p=0.013), baclofen-induced neurotoxicity (25% vs. 0%, p=0.13), and supratherapeutic digoxin levels (38% vs. 0%, p=0.03). The adjusted OR for vancomycin levels >30ug/mL was 2.30 (95% CI 1.05 - 5.51, p = 0.047). Conclusion: Among patients with cancer with simultaneous assessment of eGFRCYS and eGFRCRE, medication-related adverse events occur more commonly in those with eGFR discrepancy. These findings underscore the importance of accurate assessment of kidney function and appropriate dosing of renally-cleared medications in patients with cancer.

15: The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
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Posted 15 Jan 2023

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
6 tweets bioRxiv genomics

Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza Revilla, Nicolas Lopez Carranza, Adam Henryk Grywaczewski, Francesco Oteri, Christian Dallago, Evan Trop, Hassan Sirelkhatim, Guillaume Richard, Marcin Skwark, Karim Beguir, Marie Lopez, Thomas Pierrot

Closing the gap between measurable genetic information and observable traits is a longstanding challenge in genomics. Yet, the prediction of molecular phenotypes from DNA sequences alone remains limited and inaccurate, often driven by the scarcity of annotated data and the inability to transfer learnings between prediction tasks. Here, we present an extensive study of foundation models pre-trained on DNA sequences, named the Nucleotide Transformer, integrating information from 3,202 diverse human genomes, as well as 850 genomes from a wide range of species, including model and non-model organisms. These transformer models yield transferable, context-specific representations of nucleotide sequences, which allow for accurate molecular phenotype prediction even in low-data settings. We show that the representations alone match or outperform specialized methods on 11 of 18 prediction tasks, and up to 15 after fine-tuning. Despite no supervision, the transformer models learnt to focus attention on key genomic elements, including those that regulate gene expression, such as enhancers. Lastly, we demonstrate that utilizing model representations alone can improve the prioritization of functional genetic variants. The training and application of foundational models in genomics explored in this study provide a widely applicable stepping stone to bridge the gap of accurate molecular phenotype prediction from DNA sequence alone.

16: Contrasting drivers of abundant phage and prokaryotic communities in tropical, coastal ecosystems across the Isthmus of Panama
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Posted 26 Jan 2023

Contrasting drivers of abundant phage and prokaryotic communities in tropical, coastal ecosystems across the Isthmus of Panama
5 tweets bioRxiv microbiology

Alaina R Weinheimer, Frank O Aylward, Matthieu Leray, Jarrod J Scott

Phages, or viruses that infect bacteria and archaea, are ubiquitous and abundant members of Earth's ecosystems that impact the flow of nutrients, evolution of microbes, and food web dynamics by selectively infecting and killing their prokaryotic hosts. Because phages can only replicate through their hosts, they are inherently linked to processes impacting their hosts' distribution and susceptibility to infection. Despite these links, phages can also be affected by environmental parameters independent of their hosts, such as pH or salinity which impact cell adsorption or virion degradation. To understand these complex links, in this study, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (TEP) and Tropical Western Atlantic (TWA) provinces and compare factors that shape active marine phage and prokaryotic communities. Metagenomic sequencing of seawater from mangroves and reefs of both the TEP and TWA coasts of Panama suggest that pronounced environmental gradients, such as along the TEP mangrove rivers, result in common dispersal and physicochemical parameters shaping both prokaryotic and phage community composition and diversity. Conversely, we find that when environmental conditions are relatively similar across adjacent habitats, such as between the mangroves and reefs in the TWA, prokaryotic communities are more influenced by local abiotic conditions while phage communities are shaped more by dispersal. Collectively, this work provides a framework for addressing the co-variability between viruses and their hosts in marine systems and for identifying the different factors that drive consistent versus disparate trends in community shifts, which is essential to inform models of these interactions in biogeochemical cycling.

17: miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner
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Posted 26 Jan 2023

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner
4 tweets bioRxiv molecular biology

Cledi Alicia Cerda-Jara, Seung Joon Kim, Gwendolin Thomas, Zohreh Farsi, Grygoriy Zolotarov, Elisabeth Georgii, Andrew Woehler, Monika Piwecka, Nikolaus Rajewsky

The circular RNA (circRNA) Cdr1as is conserved across mammals and highly expressed in neurons, where it directly interacts with microRNA miR-7. However, the biological function of this interaction is unknown. Here, using primary forebrain murine neurons, we demonstrate that stimulating neurons by sustained depolarization rapidly induced two-fold transcriptional up-regulation of Cdr1as and strong post-transcriptional stabilization of miR-7. Cdr1as loss caused doubling of glutamate release from stimulated synapses and increased frequency and duration of local neuronal bursts. Moreover, periodicity of neuronal networks was increased and synchronicity was impaired. Strikingly, these effects were reverted by sustained expression of miR-7 which also cleared Cdr1as molecules from neuronal projections. Consistently, without Cdr1as, transcriptomic changes caused by miR-7 overexpression were stronger (including miR-7-targets down-regulation) and enriched in secretion/synaptic plasticity pathways. Altogether, our results suggest that in forebrain neurons Cdr1as buffers miR-7 activity to control glutamatergic excitatory transmission and neuronal connectivity important for long-lasting synaptic adaptations.

18: The Evolution of Local Energetic Frustration in Protein Families
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Posted 25 Jan 2023

The Evolution of Local Energetic Frustration in Protein Families
4 tweets bioRxiv bioinformatics

Maria I. Freiberger, Victoria I. Ruiz-Serra, Camila Pontes, Miguel Romero-Durana, Pablo Galaz-Davison, Cesar Ramirez-Sarmiento, Claudio D. Schuster, Marcelo A. Marti, Peter G Wolynes, Diego U. Ferreiro, R. Gonzalo Parra, Alfonso Valencia

Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present a methodology to analyze local frustration patterns within protein families that allows us to uncover constraints related to stability and function, and identify differential frustration patterns in families with a common ancestry. We have analyzed these signals in very well studied cases such as PDZ, SH3, alpha and beta globins and RAS families. Recent advances in protein structure prediction make it possible to analyze a vast majority of the protein space. An automatic and unsupervised proteome-wide analysis on the SARS-CoV-2 virus demonstrates the potential of our approach to enhance our understanding of the natural phenotypic diversity of protein families beyond single protein instances. We have applied our method to modify biophysical properties of natural proteins based on their family properties, as well as perform unsupervised analysis of large datasets to shed light on the physicochemical signatures of poorly characterized proteins such as emergent pathogens.

19: Evaluation of microbiome association models under realistic and confounded conditions
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Posted 10 May 2022

Evaluation of microbiome association models under realistic and confounded conditions
4 tweets bioRxiv bioinformatics

Jakob Wirbel, Morgan Essex, Sofia K. Forslund, Georg Zeller

Testing for differential abundance is a crucial task in metagenome-wide association studies, complicated by technical or biological confounding and a lack of consensus regarding statistical methodology. Here, we developed a framework for benchmarking differential abundance testing methods based on implanting signals into real data. This strategy yields a ground truth for benchmarking while retaining the statistical characteristics of real metagenomic data, which we quantitatively validated in comparison to previous approaches. Our benchmark revealed dramatic issues with elevated false discovery rates or limited sensitivity for the majority of methods with the exception of limma, linear models and the Wilcoxon test. When additionally modeling confounders, we observed these issues to be exacerbated, but also that linear mixed-effect models or the blocked Wilcoxon test effectively address them. Exploratory analysis of cardiometabolic disease cohorts illustrates the confounding potential of medications and the need to consider confounders to prevent spurious associations in real-world applications.

20: Implicit motor adaptation and perceived hand position without proprioception: A kinesthetic error may be derived from efferent signals
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Posted 20 Jan 2023

Implicit motor adaptation and perceived hand position without proprioception: A kinesthetic error may be derived from efferent signals
4 tweets bioRxiv neuroscience

Jonathan S Tsay, Anisha M Chandy, Romeo Chua, R. Chris Miall, Jonathan Cole, Alessandro Farnè, Richard Ivry, Fabrice R Sarlegna

Our ability to produce successful goal-directed actions involves multiple learning processes. Among these, implicit adaptation is of utmost importance, keeping our sensorimotor system well-calibrated in response to changes in the body and environment. Implicit adaptation is assumed to be driven by a sensory prediction error, the difference between the predicted and actual sensory consequences of a movement. Whereas most models of implicit adaptation have focused on how visual information defines the sensory prediction error, we have recently proposed that this error signal is kinesthetic, the difference between the desired and perceived hand position, with adaptation serving to align these two signals and restore optimal motor performance (Tsay et al., 2022). Here, we examined implicit adaptation and kinesthetic perception in rare individuals who lack proprioceptive signals from the upper limbs. We used a visuomotor rotation task designed to isolate implicit adaptation while simultaneously probing the participants' perceived hand position. Consistent with prior work, control participants exhibited robust implicit adaptation and the signature of kinesthetic re-alignment, an initial bias in perceived hand position towards the visual cursor and a gradual shift back to the movement goal. Strikingly, the time course of both implicit adaptation and kinesthetic re-alignment was preserved in the deafferented group, suggesting that proprioceptive afferents are not necessary for implicit adaptation and kinesthetic re-alignment. We propose that a kinesthetic prediction error derived from efferent motor signals is sufficient to drive implicit adaptation and to re-algin a biased percept of hand position with the movement goal.

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