eLife

Latest preprint reviews

1. A network regularized linear model to infer spatial expression pattern for single cell

   This article has 3 authors:

   1. Chaohao Gu
   2. Hu Chen
   3. Zhandong Liu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The development of glmSMA represents a valuable advancement in spatial transcriptomics analysis, offering a mathematically robust regression-based approach that achieves higher-resolution mapping of single-cell RNA sequencing data to spatial locations than existing methods. The evidence is convincing, as the authors demonstrate the method's superiority by formulating it as a convex optimization problem that ensures stable solutions, coupled with successful validation across multiple biological systems. The rigorous mathematical framework and validation across diverse tissues enable precise spatial mapping of cellular heterogeneity at enhanced resolution.

   Reviewed by eLife

2. scRNA+TCR-seq reveals the proportion and characteristics of dual TCR Treg cells in mouse lymphoid and non-lymphoid tissues

   This article has 6 authors:

   1. Yuanyuan Xu
   2. Qi Peng
   3. Xiaoping Lu
   4. Long Ma
   5. Jun Li
   6. Xinsheng Yao

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study reanalyzed previously published scRNA-seq and TCR-seq data to examine the proportion and characteristics of dual-TCR-expressing Treg cells in mice, presenting some useful insights into TCR diversity and immune regulation. However, the evidence is incomplete, particularly with respect to data interpretation, statistical rigor, and the functionality of dual -TCR Treg cells. The study is potentially of interest to immunologists studying T-cell biology.

   Reviewed by eLife

3. Estimation of Rotavirus Vaccine Effectiveness Based on Whole Genome Sequences

   This article has 15 authors:

   1. Jiye Kwon
   2. Jose Jaimes
   3. Mary E Wikswo
   4. Eileen J Klein
   5. Mary Allen Staat
   6. James D Chappell
   7. Geoffrey A Weinberg
   8. Christopher J Harrison
   9. Rangaraj Selvarangan
   10. Coreen Johnson
   11. Daniel M Weinberger
   12. Joshua L Warren
   13. Mathew D Esona
   14. Michael D Bowen
   15. Virginia E Pitzer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Kwon et al. present an important paper using a novel approach to estimating rotavirus vaccine efficacy using data from a passive surveillance network in the US. They provide convincing evidence to support their conclusion that using the whole genome, rather than previous use of two surface proteins, enhances our understanding of strain-specific vaccine efficacy. These findings have implications for this vaccine specifically as well as type-specific vaccine evaluation more generally.

   Reviewed by eLife

4. Cap-independent co-expression of dsRNA-sensing and NF-κB pathway inhibitors enables controllable self-amplifying RNA expression with reduced immunotoxicity

   This article has 7 authors:

   1. Tony KY Lim
   2. Anne Ritoux
   3. Luke W Paine
   4. Larissa Ferguson
   5. Tawab Abdul
   6. Laura J Grundy
   7. Ewan St John Smith

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this manuscript, Lim and collaborators present an important system for developing self-amplifying RNA with convincing evidence that it does not provoke a strong host inflammatory response in cultured cells. This approach could be further strengthened going forward by testing these self-amplying RNAs in an in vivo system.

   Reviewed by eLife

5. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2412.12965

6. Dimerization and dynamics of human angiotensin-I converting enzyme revealed by cryo-EM and MD simulations

   This article has 4 authors:

   1. Jordan M Mancl
   2. Xiaoyang Wu
   3. Minglei Zhao
   4. Wei-Jen Tang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study shows, for the first time, the structure and snapshots of the dynamics of the full-length soluble Angiotensin-I converting enzyme dimer. The combination of structural and computational analyses provides compelling evidence that reveals the conformational dynamics of the complex and key regions mediating the conformational change. This fundamental work illustrates how conformational heterogeneity can be used to gain insights into protein function.

   Reviewed by eLife

7. Zinc is a Key Regulator of the Sperm-Specific K+ Channel (Slo3) Function

   This article has 6 authors:

   1. Rizki Tsari Andriani
   2. Tanadet Pipatpolkai
   3. Haruhiko Miyata
   4. Masahito Ikawa
   5. Yasushi Okamura
   6. Takafumi Kawai

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding on the role of intracellular zinc as a regulator of the sperm-specific potassium channel Slo3, demonstrating that zinc export during capacitation contributes to alkalinization-induced membrane hyperpolarization. The electrophysiological evidence supporting zinc-mediated inhibition of Slo3 is solid, though the mechanistic basis of this inhibition is not complete, as the proposed zinc-binding site involving E169 and E205 has not been directly tested through double-mutant analysis. This work will be of interest to reproductive biologists and ion channel biophysicists studying the molecular mechanisms of sperm capacitation.

   Reviewed by eLife

8. MMP21 behaves as a fluid flow transported morphogen to impart laterality during development

   This article has 11 authors:

   1. Tim Ott
   2. Amelie Brugger
   3. Emmanuelle Szenker-Ravi
   4. Yvonne Kurrle
   5. Olivia Aberle
   6. Matthias Tisler
   7. Martin Blum
   8. Sandra Whalen
   9. Patrice Bouvagnet
   10. Bruno Reversade
   11. Axel Schweickert

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This report explores the role of matrix metalloprotease MMP21 in left-right patterning in Xenopus. Based on a series of compelling experiments, the authors demonstrate that MMP21 can be secreted and acts upstream of dand5 without affecting cilia flow. The experiments are interesting and valuable; however, the claims by the authors lack consideration of other models that could also explain their findings.

   Reviewed by eLife

9. Lifestyles shape genome size and gene content in fungal pathogens

   This article has 4 authors:

   1. Anna Fijarczyk
   2. Pauline Hessenauer
   3. Richard Hamelin
   4. Christian R Landry

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study addresses a topic that is frequently discussed in the literature but is under-assessed, namely correlations among genome size, repeat content, and pathogenicity in fungi. Contrary to previous assertions, the authors found that repeat content is not associated with pathogenicity. Rather, pathogenic lifestyle was found to be better explained by the number of protein-coding genes, with other genomic features associated with insect association status. The results are considered solid, although there remain concerns about potential biases stemming from the underlying data quality of the analyzed genomes.

   Reviewed by eLife

10. Viral-mediated Pou5f1 (Oct4) overexpression and inhibition of Notch signaling synergistically induce neurogenic competence in mammalian Müller glia

    This article has 5 authors:

    1. Nguyet Le
    2. Sherine Awad
    3. Isabella Palazzo
    4. Thanh Hoang
    5. Seth Blackshaw

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This manuscript demonstrates that Oct4 overexpression synergizes with Notch inhibition (Rbpj knockout) to promote the conversion of adult murine Müller glia (MG) into bipolar cells. These findings are important as the authors used rigorous genetic lineage tracing (GLAST-CreER; Sun-GFP) to confirm that neurogenesis indeed originates from MGs, addressing a key issue in the field. The single-cell multiomic analyses are compelling, and while functional studies of MG-derived bipolar cells would strengthen the conclusions, they are beyond the scope of this study.

    Reviewed by eLife