Abstract This is a review of Białas et al. bioRxiv doi: https://doi.org/10.1101/2021.01.26.428286 posted on January 27, 2021. In this paper, the authors study the HMA domain from two NLR immune receptors. The authors identify a common ancestral version for these domains and highlight a convergent evolution that allows the interaction with a common effector. Summary HMA domains are integrated in some NLRs where they confer novel recognition specificities. The rice Pik-1 receptors, are such a...

Dear authors, thank you for sharing this preprint with everyone. I recently decided to support research in chemical biology by providing feedback and thoughts on preprints in this field. Your preprint caught my eye, and I hope you will find the comments below useful (I hesitate to call this peer review, but if you would like to share what I wrote with a journal please feel free). Kind regards, Milka Comments to authors: In this...

Here, the authors seek to better understand the mechanism of Human Immunodeficiency Virus 1 (HIV-1) viral Integrase (IN). They hypothesize that four major sites on the C-terminal domain (CTD) are responsible for directing the viral integration site. They accomplish this by generating IN mutants at each of the four sites and generated different viruses carrying these mutations to assay for changes in viral transduction, proviral transcription, and viral integration sites. They found that viruses carrying...

Main Claim & Relevance: Extracellular vimentin might be critical to SARS-CoV-2 cell entry. These researchers demonstrated direct binding between vimentin and SARS-CoV-2 virus-like particles (VLPs) coated with SARS-CoV-2 spike protein. They also showed that antibodies against vimentin block in vitro SARS-CoV-2 pseudovirus infection by up to 80% in ACE2 expressing cell lines. Are the findings strong, reliable, potentially informative, not informative, or misleading? Why?: The findings are potentially informative. Immunostaining of human...

Prostate cancer can be assessed using clinicopathological information which takes into account factors such as patient age, PSA levels and also Gleason score. This enables clinicians to determine the severity and progress of the tumour, as well as to determine the most efficient therapeutic agents to treat the disease. Whilst most patients can be treated successfully to reduce tumour burden and to prevent tumour spread, some patients may progress to a more advanced disease state...

We, the students of MICI5029/5049, a Graduate Level Molecular Pathogenesis Journal Club at Dalhousie University in Halifax, NS, Canada, hereby submit a review of the following BioRxiv preprint: Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations. Shane Miersch, Zhijie Li, Reza Saberianfar, Mart Ustav, James Brett Case, Levi Blazer, Chao Chen, Wei Ye, Alevtina Pavlenco, Maryna Gorelik, Julia Garcia Perez, Suryasree Subramania, Serena Singh, Lynda Ploder, Safder Ganaie, Rita E. Chen,...

We, the students of MICI5029/5049, a Graduate Level Molecular Pathogenesis Journal Club at Dalhousie University in Halifax, NS, Canada, hereby submit a review of the following BioRxiv preprint: Horizontal and vertical transmission of transgenerational memories via the Cer1 transposon. Rebecca S. Moore, Rachel Kaletsky, Chen Lesnik, Vanessa Cota, Edith Blackman, Lance R. Parsons, Zemer Gitai, Coleen T. Murphy. bioRxiv 2020.12.28.424563; doi: https://doi.org/10.1101/2020.12.28.424563 We will adhere to the Universal Principled (UP) Review guidelines proposed in: Universal...

COMMENTS ON THE PREPRINT BY Dölle, Adhikari et al. Targeted protein degradation is a very active field at the moment. Many efforts in this area are focusing on transforming known ligands (binders, inhibitors) of proteins with a clear disease relevance into bifunctional (PROTAC-based) degrader molecules. Unlike the traditional antagonist/inhibitor based compounds in preclinical and clinical use that diminish (inhibit) activity of the target, these degrader molecules induce selective degradation of the target. Thus, they remove...

GENERAL COMMENTS ON PREPRINT BY Frost, Rocha and Ciulli In this preprint, Frost, Rocha and Ciulli report results of how cells respond to compounds previously described as inhibitors of von Hippel–Lindau (VHL) protein as measured by quantitative mass spectrometry (MS)-based proteomics. VHL is a well-studied protein that serves as a substrate recruiting/recognition subunit of Cullin RING E3 ligase CRL2VHL. The best characterized substrate of VHL is HIF1a, a hypoxia-inducible transcription factor that is under strict...

Summary Pettman et al. present a commendable approach to a pressing enigma in T cell immunology: how does a T cell receptor (TCR) differentiate between its target and off-targets? The authors developed an SPR method to measure TCR affinity for off-target peptide-MHC complexes that interact with lower affinity than was previously detectable by existing SPR-based approaches . They paired SPR measurements with substantial in vitro work to correlate biophysical affinity with human T cell agonism....

By Yash S. Huilgol[1] UC Berkeley-UCSF Joint Medical Program, Berkeley, CA, USA[2] Editorial Office, Rapid Reviews: COVID-19 Main Claim & Relevance: In this preprint by Ramakrishnan et al [1], inhaled budesonide, a corticosteroid used for long-term COPD and asthma treatment, reducing the likelihood of urgent care, ED visit, or hospitalization among patients with early COVID-19 illness. This amounted to a relative risk reduction of 90%, or a difference in proportions of 13.1% between the budesonide...

bioRxiv preprint doi: https://doi.org/10.1101/2021.10.06.463330; Zhang et al applied a previous developed method (Zhang and Arrenberg 2019) to identify and characterize the receptive fields of many motion-sensitive neurons in zebrafish. They found that some of these neurons behave as "matched filters" (detecting a single motion) and robustly encode translation-induced optic flows. The anatomical arrangement of these neurons in the brain seemed to correlate with their motion sensitivity. The authors also conducted behavior experiments to show that...

bioRxiv preprint doi: https://doi.org/10.1101/2021.10.06.463330; Zhang et al applied a previous developed method (Zhang and Arrenberg 2019) to identify and characterize the receptive fields of many motion-sensitive neurons in zebrafish. They found that some of these neurons behave as "matched filters" (detecting a single motion) and robustly encode translation-induced optic flows. The anatomical arrangement of these neurons in the brain seemed to correlate with their motion sensitivity. The authors also conducted behavior experiments to show that...

In this manuscript, Ting et al. describe three gene clusters - named antagonism resistance clusters (arc1-3) - that are upregulated by the Gac/Rsm danger sensing system and proposed to work as an innate immunity system against antibacterial attacks. This work builds on their previous studies (LeRoux et al., 2015 eLife; LeRoux et al., 2015 J Mol Biol) in which the authors have identified a danger sensing mechanism that bacteria use to sense lysis of neighboring...

We, the students of MICI5029/5049, a Graduate Level Molecular Pathogenesis Journal Club at Dalhousie University in Halifax, NS, Canada, hereby submit a review of the following BioRxiv preprint: Poly(rC)-binding protein 1 limits hepatitis C virus assembly and egress. Sophie E. Cousineau, Selena M. Sagan. bioRxiv 2021.02.28.433252; doi: https://doi.org/10.1101/2021.02.28.433252 We will adhere to the Universal Principled (UP) Review guidelines proposed in: Universal Principled Review: A Community-Driven Method to Improve Peer Review. Krummel M, Blish C,...

We, the students of MICI5029/5049, a Graduate Level Molecular Pathogenesis Journal Club at Dalhousie University in Halifax, NS, Canada, hereby submit a review of the following BioRxiv preprint: Rachel Eguia, Katharine H. D. Crawford, Terry Stevens-Ayers, Laurel Kelnhofer-Millevolte, Alexander L. Greninger, Janet A. Englund, Michael J. Boeckh, Jesse D. Bloom. A human coronavirus evolves antigenically to escape antibody immunity. bioRxiv 2020.12.17.423313; doi:https://doi.org/10.1101/2020.12.17.423313 We will adhere to the Universal Principled (UP) Review guidelines proposed in: Universal...

The major goal of this manuscript is to create a procedure to model the ensemble of conformations present in a cryoEM particle stack. This goal is accomplished by using a variational autoencoder with special attention paid to the ensemble nature of proteins and the low signal-to-noise in cryoEM images by drawing multiple samples from the posterior and summing their corresponding likelihoods in training. Using "simulated" data where the conformations are derived from MD simulation snapshots...

This review is the result of a virtual, live-streamed preprint journal club organized and hosted by PREreview and OHSU's BioData Club. The discussion was joined by 9 people, including OHSU researchers and the event organizing team. Wylezinski et al. investigated the impact of clinical and social determinants of health (SDOH) risk factors on the COVID-19 case growth in Tennessee. To that aim, they used a variety of publicly available data to train machine learning (ML)...

In this article, the authors convincingly demonstrate that the ubiquitin E3 ligase HOIL-1 can ubiquitylate in vitro oligosaccharides, only the second example ever reported of a non-proteinaceous ubiquitylation substrate. They also observe that mice harbouring a catalytic dead version of HOIL-1 cannot efficiently clear polyglucosan from relevant tissues, thereby hypothesising that this aberrant phenotype may arise due to such inclusions not being removed in a HOIL-1 dependent manner. The presented in vitro data are robust,...

Cell wall damage impairs root hair cell patterning and tissue morphogenesis mediated by the Arabidopsis receptor kinase STRUBBELIG Rajneesh Singhal and Deepak D. Bhandari Department of Plant Biology, Michigan State University, East Lansing, USA. This study by Chaudhary and colleagues show that the reduction of cellulose in the cell wall is accompanied by the downregulation of the atypical receptor kinase STRUBBELIG (SUB). Using a combination of genetic mutants, chemical treatments, and microscopy the...

Rapid Review of "Transmission of SARS-CoV-2 Considering Shared Chairs in Outpatient Dialysis: A Real-World Case-Control Study" By Margarita Orlova Student Reviewer, Rapid Reviews: COVID-19 Main Claim & Relevance: Evaluated the rate of SARS-CoV-2 transmission among 170,234 hemodialysis patients focusing on patient-to-patient transmission through shared chairs. Data between February 1st and June 8th, 2020 was used to match 2,379 SARS-CoV-2 positive cases to 2,379 non-SARS-CoV-2 controls through a 14 day traceback. The study concluded that...

GENERAL COMMENTS ON PREPRINT BY Frost, Rocha and Ciulli In this preprint, Frost, Rocha and Ciulli report results of how cells respond to compounds previously described as inhibitors of von Hippel–Lindau (VHL) protein as measured by quantitative mass spectrometry (MS)-based proteomics. VHL is a well-studied protein that serves as a substrate recruiting/recognition subunit of Cullin RING E3 ligase CRL2VHL. The best characterized substrate of VHL is HIF1a, a hypoxia-inducible transcription factor that is under strict...

We, the students of MICI5029/5049, a Graduate Level Molecular Pathogenesis Journal Club at Dalhousie University in Halifax, NS, Canada, hereby submit a review of the following BioRxiv preprint: Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations. Shane Miersch, Zhijie Li, Reza Saberianfar, Mart Ustav, James Brett Case, Levi Blazer, Chao Chen, Wei Ye, Alevtina Pavlenco, Maryna Gorelik, Julia Garcia Perez, Suryasree Subramania, Serena Singh, Lynda Ploder, Safder Ganaie, Rita E. Chen,...

Dear authors, thank you for sharing this preprint with everyone. I recently decided to support research in chemical biology by providing feedback and thoughts on preprints in this field. Your preprint caught my eye, and I hope you will find the comments below useful (I hesitate to call this peer review, but if you would like to share what I wrote with a journal please feel free). Kind regards, Milka Comments to authors: In this...

In this preprint, Singh et al. identify two novel small RNA transcripts produced during SARS-COV-2 infection. The authors go on to demonstrate Dicer-mediated miR-7a production, gene-specific targeting of interferon stimulated genes (ISGs) during the course of infection, and use bioinformatic analyses from clinical isolates to demonstrate these miR transcripts are not a cell culture artifact. Methodology is well-described and conclusions are well justified. The manuscript's one limitation is a loss of function study in which...