eLife

Latest preprint reviews

1. Perturbations in eIF3 subunit stoichiometry alter expression of ribosomal proteins and key components of the MAPK signaling pathways

   This article has 11 authors:

   1. Anna Herrmannová
   2. Jan Jelínek
   3. Klára Pospíšilová
   4. Farkas Kerényi
   5. Tomáš Vomastek
   6. Kathleen Watt
   7. Jan Brábek
   8. Mahabub Pasha Mohammad
   9. Susan Wagner
   10. Ivan Topisirovic
   11. Leoš Shivaya Valášek

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study demonstrates mRNA-specific regulation of translation by subunits of the eukaryotic initiation factor complex 3 (eIF3) using convincing methods, data, and analyses. The investigations have generated important information that will be of interest to biologists studying translation regulation. However, the physiological significance of the gene expression changes that were observed is not clear.

   Reviewed by eLife

2. Endocytic recycling is central to circadian collagen fibrillogenesis and disrupted in fibrosis

   This article has 20 authors:

   1. Joan Chang
   2. Adam Pickard
   3. Jeremy A Herrera
   4. Sarah O'Keefe
   5. Richa Garva
   6. Matthew Hartshorn
   7. Anna Hoyle
   8. Lewis Dingle
   9. John Knox
   10. Thomas A Jowitt
   11. Madeleine Coy
   12. Jason Wong
   13. Adam Reid
   14. Yinhui Lu
   15. Cédric Zeltz
   16. Rajamiyer V Venkateswaran
   17. Patrick T Caswell
   18. Stephen High
   19. Donald Gullberg
   20. Karl E Kadler

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study describes a novel mechanism for how collagen fibrils are formed. The authors present compelling evidence that collagen-I fibrillogenesis relies on a functional endocytic system for recycling collagen-I, with circadian-regulated VPS33b and integrin-α11 being critical for fibril assembly. This is an important study for the understanding of the pathophysiology of collagen fibrillogenesis.

   Reviewed by eLife

3. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2306.15352v3

4. Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy

   This article has 10 authors:

   1. Lesia Semenova
   2. Yingfan Wang
   3. Shane Falcinelli
   4. Nancie Archin
   5. Alicia D Cooper-Volkheimer
   6. David M Margolis
   7. Nilu Goonetilleke
   8. David M Murdoch
   9. Cynthia D Rudin
   10. Edward P Browne

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Semenova et al. have studied a large cross-sectional cohort of people living with HIV on suppressive antiretroviral therapy and performed high dimensional flow-cytometry for analysis with data science/machine learning approaches to investigate associations of immunological and clinical parameters and intact/total HIV DNA levels (and categorizations). The study is useful in introducing these new methods and large data set and appears mostly solid, though some of the claims were incompletely supported by the modeling results. The authors have revised the text to fairly reflect their results, yet open questions remain about utility, particularly as to the value of categorical classification (vs continuous measurement) of reservoir size.

   Reviewed by eLife

5. Associations of proton pump inhibitors with susceptibility to influenza, pneumonia, and COVID-19: Evidence from a large population-based cohort study

   This article has 13 authors:

   1. Ruijie Zeng
   2. Yuying Ma
   3. Lijun Zhang
   4. Dongling Luo
   5. Rui Jiang
   6. Huihuan Wu
   7. Zewei Zhuo
   8. Qi Yang
   9. Jingwei Li
   10. Felix W Leung
   11. Chongyang Duan
   12. Weihong Sha
   13. Hao Chen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This useful study aimed to quantify associations between regular use of proton-pump inhibitors (PPI) with the occurrence of respiratory infections, such as influenza, pneumonia, COVID-19, and others over a period of several years. PPI use was associated with increased risks of influenza, pneumonia, but not of COVID-19, although severity and mortality of COVID-19 infections were higher in PPI users. There are inevitable weaknesses of the study design used, such as the fact that PPI use was only measured at one time-point whereas infections were assessed over a long time period, but these are appropriately highlighted in the discussion. Weaknesses are highlighted in the discussion and the study presents convincing evidence for the conclusions overall.

   Reviewed by eLife

6. ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis

   This article has 25 authors:

   1. Stephanie Guillet
   2. Tomi Lazarov
   3. Natasha Jordan
   4. Bertrand Boisson
   5. Maria Tello
   6. Barbara Craddock
   7. Ting Zhou
   8. Chihiro Nishi
   9. Rohan Bareja
   10. Hairu Yang
   11. Frederic Rieux-Laucat
   12. Rosa Irene Fregel Lorenzo
   13. Sabrina D Dyall
   14. David Isenberg
   15. David D'Cruz
   16. Nico Lachmann
   17. Olivier Elemento
   18. Agnes Viale
   19. Nicholas D Socci
   20. Laurent Abel
   21. Shigekazu Nagata
   22. Morgan Huse
   23. W Todd Miller
   24. Jean-Laurent Casanova
   25. Frédéric Geissmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     In this important study, the authors found, with the use of statistical methods, that compound heterozygous rare deletion variants affecting the kinase-domain of non-receptor tyrosine kinase TNK2/ACK1 and PTK6/BRK are associated with human systemic lupus erythematosus (SLE). The authors use a convincing mouse experimental model and human-induced pluripotent stem cell (hiPSC)-derived macrophages to clarify cause-effect relationships and the cellular basis of nephritis. With the identification of new SLE-related genes, this manuscript improves our understanding of human SLE pathogenesis.

   Reviewed by eLife

7. OsNF-YB7 inactivates OsGLK1 to inhibit chlorophyll biosynthesis in rice embryo

   This article has 5 authors:

   1. Zongju Yang
   2. Tianqi Bai
   3. Zhiguo E
   4. Baixiao Niu
   5. Chen Chen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This paper provides important insights into the role of rice OsNF-YB7, an ortholog of Arabidopsis LEC1, in chlorophyll biosynthesis, uncovering the genetic and molecular basis for negative regulation of chlorophyll production in the rice embryo. Mutational analysis, gene expression profiles and protein interaction combine for convincing evidence that OsNF-YB7 represses chlorophyll biosynthesis.

   Reviewed by eLife

8. Defining cell type-specific immune responses in a mouse model of allergic contact dermatitis by single-cell transcriptomics

   This article has 14 authors:

   1. Youxi Liu
   2. Meimei Yin
   3. Xiaoting Mao
   4. Shuai Wu
   5. Shuangping Wei
   6. Shujun Heng
   7. Yichun Yang
   8. Jinwen Huang
   9. Zhuolin Guo
   10. Chuan Li
   11. Chao Ji
   12. Liu Hu
   13. Wenjie Liu
   14. Ling-juan Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study uses single-cell RNA-seq to obtain a more granular understanding of cell subsets within allergic contact dermatitis in a model system with DNFB. The convincing data revela unique subpopulations of dermal fibroblasts as key responders to interferon gamma and likely as mediators of dermatitis. This study has many novel aspects and provides a unique resource as well.

   Reviewed by eLife

9. Full-length direct RNA sequencing uncovers stress granule-dependent RNA decay upon cellular stress

   This article has 10 authors:

   1. Showkat Ahmad Dar
   2. Sulochan Malla
   3. Vlastimil Martinek
   4. Matthew John Payea
   5. Christopher Tai-Yi Lee
   6. Jessica Martin
   7. Aditya Jignesh Khandeshi
   8. Jennifer L Martindale
   9. Cedric Belair
   10. Manolis Maragkakis

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study describes mRNA shortening during cellular stress and interestingly observes that this shortening is dependent on localization in stress granules. Surprisingly, this mRNA shortening does not appear to require the shortening of poly A tails. These are novel, paradigm-shifting findings, using cutting-edge technologies and convincing data, that should be of broad interest to the RNA community and beyond.

   Reviewed by eLife, PREreview

10. Disparity in temporal and spatial relationships between resting-state electrophysiological and fMRI signals

    This article has 3 authors:

    1. Wenyu Tu
    2. Samuel R Cramer
    3. Nanyin Zhang

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This important study combines fMRI and electrophysiology in sedated and awake rats to show that LFPs strongly explain spatial correlations in resting-state fMRI but only weakly explain temporal variability. The authors propose that other, electrophysiology-invisible mechanisms contribute to the fMRI signal. The evidence supporting the separation of spatial and temporal correlations is convincing, and the authors consider alternative potential factors that could account for the differences in spatial and temporal correlation that were observed. This work will be of interest to researchers who study the mechanisms behind resting-state fMRI.

    Reviewed by eLife