eLife

Latest preprint reviews

1. Identification of a conserved S2 epitope present on spike proteins from all highly pathogenic coronaviruses

   This article has 26 authors:

   1. Rui P Silva
   2. Yimin Huang
   3. Annalee W Nguyen
   4. Ching-Lin Hsieh
   5. Oladimeji S Olaluwoye
   6. Tamer S Kaoud
   7. Rebecca E Wilen
   8. Ahlam N Qerqez
   9. Jun-Gyu Park
   10. Ahmed M Khalil
   11. Laura R Azouz
   12. Kevin C Le
   13. Amanda L Bohanon
   14. Andrea M DiVenere
   15. Yutong Liu
   16. Alison G Lee
   17. Dzifa A Amengor
   18. Sophie R Shoemaker
   19. Shawn M Costello
   20. Eduardo A Padlan
   21. Susan Marqusee
   22. Luis Martinez-Sobrido
   23. Kevin N Dalby
   24. Sheena D'Arcy
   25. Jason S McLellan
   26. Jennifer A Maynard

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Silva and colleagues present useful findings related to the isolation of an anti-S2 antibody that recognizes a previously uncharacterized SARS-CoV2 Spike (S) epitope, adding to the growing repertoire of anti-S antibodies that broadly cross-react against human and zoonotic coronaviruses. The evidence supporting the claims of the authors is solid, although antibody effectiveness as a prophylactic or therapeutic reagent in an animal model would have strengthened the study. The work will be of interest to biologists working to develop pan-coronavirus therapies.

   Reviewed by eLife, ScreenIT

2. Inactivation of Invs/Nphp2 in renal epithelial cells drives infantile nephronophthisis like phenotypes in mouse

   This article has 5 authors:

   1. Yuanyuan Li
   2. Wenyan Xu
   3. Svetlana Makova
   4. Martina Brueckner
   5. Zhaoxia Sun

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Germline inactivation of NPHP2, which encodes a protein that localizes to the transition zone at the base of the primary cilium, results in infantile kidney cysts and fibrosis. In this study, the authors provide solid evidence that increased cell proliferation and fibrosis precede cyst formation in Nphp-2 mouse models, that mutant renal epithelial cells are responsible for the phenotype, and that genetic inhibition of ciliogenesis in this model reduces disease severity. They also show that valproic acid, a drug that affects a number of cellular targets and is used to treat other human conditions, slows disease progression. One limitation of the study is that it provides limited insights into the mechanisms responsible for any of its interesting observations.

   Reviewed by eLife

3. lncRNA read-through regulates the BX-C insulator Fub-1

   This article has 6 authors:

   1. Airat Ibragimov
   2. Xin Yang Bing
   3. Yulii V Shidlovskii
   4. Michael Levine
   5. Pavel Georgiev
   6. Paul Schedl

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This fundamental work substantially advances our understanding of how neighboring genes on a chromosome can be separately controlled in time and space. The evidence supporting the conclusions is compelling, with state-of-the-art genetic perturbations and imaging. The work will be of broad interest to geneticists and cell biologists.

   Reviewed by eLife

4. Phantasus, a web application for visual and interactive gene expression analysis

   This article has 6 authors:

   1. Maksim Kleverov
   2. Daria Zenkova
   3. Vladislav Kamenev
   4. Margarita Sablina
   5. Maxim N Artyomov
   6. Alexey A Sergushichev

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a useful tool called Phantasus, a web application to analyze gene expression data generated by microarray or RNA-seq technologies. The web application will help biologists end users, and non-bioinformatics experts to analyze new data or replicate transcriptomic studies. Local use of the Phantasus through its Bioconductor package reveals an incomplete functionality concerning the current best practices in analyzing bulk RNA-seq data.

   Reviewed by eLife

5. A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity

   This article has 7 authors:

   1. Barbara Bravi
   2. Andrea Di Gioacchino
   3. Jorge Fernandez-de-Cossio-Diaz
   4. Aleksandra M Walczak
   5. Thierry Mora
   6. Simona Cocco
   7. Rémi Monasson

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     In this important work, the authors present a sequence-based approach using transfer learning and Restricted Boltzmann Machines to predict antigen immunogenicity and specificity. The evidence and methodology are compelling. This work should be of interest to immunologists, computational biologists, and biophysicists.

   Reviewed by eLife

6. The CD73 immune checkpoint promotes tumor cell metabolic fitness

   This article has 7 authors:

   1. David Allard
   2. Isabelle Cousineau
   3. Eric H Ma
   4. Bertrand Allard
   5. Yacine Bareche
   6. Hubert Fleury
   7. John Stagg

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study demonstrates a non-canonical, cancer-cell intrinsic role of the ectonucleotidase CD73 in the regulation of cancer cell metabolism. The evidence supporting the claims is solid, although further experimental details and conditions would strengthen the evidence provided.

   Reviewed by eLife

7. Regulation of different phases of AMPA receptor intracellular transport by 4.1N and SAP97

   This article has 5 authors:

   1. Caroline Bonnet
   2. Justine Charpentier
   3. Natacha Retailleau
   4. Daniel Choquet
   5. Françoise Coussen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study by Bonnet et al addresses the question of how AMPA receptor numbers at the synapse are regulated during basal conditions and during chemically induced Long Term Potentiation. Specifically, the study aims to determine the molecular mechanisms that contribute to the intracellular trafficking of AMPA receptors and determine their insertion into the synaptic plasma membrane. Using compelling methodology, the authors dissect the distinct roles of two proteins that bind to the C-terminal domain of the AMPA receptor subunit GluA1: 4.1N and SAP97. The findings will be of interest to anyone trying to understand molecular events contributing to synaptic plasticity in health and disease, and more broadly, the method could be adapted for tracking intracellular movements of a wide range of proteins.

   Reviewed by eLife

8. Selection of HIV-1 for resistance to fifth-generation protease inhibitors reveals two independent pathways to high-level resistance

   This article has 12 authors:

   1. Ean Spielvogel
   2. Sook-Kyung Lee
   3. Shuntai Zhou
   4. Gordon J Lockbaum
   5. Mina Henes
   6. Amy Sondgeroth
   7. Klajdi Kosovrasti
   8. Ellen A Nalivaika
   9. Akbar Ali
   10. Nese Kurt Yilmaz
   11. Celia A Schiffer
   12. Ronald Swanstrom

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript significantly advances our understanding of the development of drug resistance in the HIV-1 protease. The paper addresses the fundamental relationship between resistance mutations and inhibitor structure and will be useful in the design and development of the next generation of inhibitors.

   Reviewed by eLife

9. Study of efficacy and longevity of immune response to third and fourth doses of COVID-19 vaccines in patients with cancer: A single arm clinical trial

   This article has 23 authors:

   1. Astha Thakkar
   2. Kith Pradhan
   3. Benjamin Duva
   4. Juan Manuel Carreno
   5. Srabani Sahu
   6. Victor Thiruthuvanathan
   7. Sean Campbell
   8. Sonia Gallego
   9. Tushar D Bhagat
   10. Johanna Rivera
   11. Gaurav Choudhary
   12. Raul Olea
   13. Maite Sabalza
   14. Lauren C Shapiro
   15. Matthew Lee
   16. Ryann Quinn
   17. Ioannis Mantzaris
   18. Edward Chu
   19. Britta Will
   20. Liise-anne Pirofski
   21. Florian Krammer
   22. Amit Verma
   23. Balazs Halmos

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study evaluates the immunogenicity of 3rd and 4th doses of SARS-CoV2 vaccinations in patients with cancer. Their study is notable in that neutralization of Omicron was absent in all patients after the third dose but increased to 33% after the fourth dose. With the definitions and patient population better described, this paper would be of interest to those studying the effects of repeated COVID boosters on Omicron immunity.

   Reviewed by eLife

10. A model of hippocampal replay driven by experience and environmental structure facilitates spatial learning

    This article has 2 authors:

    1. Nicolas Diekmann
    2. Sen Cheng

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This paper proposes a new computational model for replay that is biologically realistic and accounts for a number of important phenomena in hippocampal replay. This is an important study with implications for multiple subfields. Whilst the majority of claims are convincingly supported by the data, simulation analyses for some crucial aspects of replay literature are currently incomplete.

    Reviewed by eLife