eLife

Latest preprint reviews

1. Fragile nucleosomes are essential for RNA Polymerase II to transcribe in eukaryotes

   This article has 11 authors:

   1. Lingbo Li
   2. Samuel Hunter
   3. Sonia Leach
   4. Yonghua Zhuang
   5. Haolin Liu
   6. Junfeng Gao
   7. Qianqian Zhang
   8. Timothy J. Stasevich
   9. Hiroshi Kimura
   10. Robin Dowell
   11. Gongyi Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study addresses an important problem in gene regulation, namely, which features of chromatin regulate potential RNA Polymerase 2 activity at a locus. The authors provided evidence that specific post-translational modifications of histones within the gene body are correlated with Pol II transcription, that these modifications are dynamic, and that they can be regulated by Pol II activity. The manuscript contributes to the concept of "fragile nucleosomes" as a unifying framework for key epigenetic drivers of transcription; however, the quality of the evidence provided is inadequate in support of the claims made, and further evidence teasing out the mechanistic aspects of the work would strengthen its impact. This work will be of interest to the fields of transcriptional regulation, chromatin structure, and epigenetics.

   Reviewed by eLife

2. Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm’s Canal

   This article has 14 authors:

   1. Revathi Balasubramanian
   2. Nicholas Tolman
   3. Taibo Li
   4. Abdul Hannan
   5. Violet Bupp-Chickering
   6. Karina Polanco
   7. Aakriti Bhandari
   8. Sally Zhou
   9. Marina Simón
   10. John Peregrin
   11. Christa Montgomery
   12. Krishnakumar Kizhatil
   13. Jiang Qian
   14. Simon W.M. John

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important work advances our understanding of the development of the visual system. The data presented is compelling and provides a detailed single-cell atlas of post-natal anterior chamber development in mice, highlighting the trabecular meshwork and Schlemm's canal.

   Reviewed by eLife

3. The livebearers platyfish and swordtails partially regenerate their hearts with persistent scarring

   This article has 6 authors:

   1. Vincent Hisler
   2. Lana Rees
   3. Simon Blanchoud
   4. Heidi E.L. Lischer
   5. Rémy Bruggmann
   6. Anna Jaźwińska

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents important findings on how cardiac regenerative capacity diverges across species by examining heart repair in two species of livebearers, platyfish and swordtails. In contrast to zebrafish, the livebearer species show persistent scarring after cryo-injury, and the work highlights how lineage-specific anatomical and immunological traits may constrain regenerative competence. The study is compelling, the data are convincing, and the results contribute to our understanding of the mechanisms underlying heart regeneration across vertebrates.

   Reviewed by eLife

4. PKD2L1 channels segregated to the apical compartment are the exclusive dual-mode pH sensor in cerebrospinal fluid-contacting neurons

   This article has 5 authors:

   1. Magdalena Vitar
   2. Daniel Prieto
   3. Stavros Malas
   4. Raúl E. Russo
   5. Federico F. Trigo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study on the sensory roles of Cerebrospinal fluid-contacting neurons (CBF-cn) in mammals. The authors identify PKD2L1 as the predominant pH-sensing channel CBF-cn and show how the apical extension is used as an amplifier of chemical changes in the content of the Cerebrospinal fluid. The evidence is solid in experimental design but limited in mechanistic interpretation, as the electrophysiological analyses require re-evaluation.

   Reviewed by eLife

5. Separating selection from mutation in antibody language models

   This article has 9 authors:

   1. Frederick A. Matsen
   2. Will Dumm
   3. Kevin Sung
   4. Mackenzie M. Johnson
   5. David Rich
   6. Tyler Starr
   7. Yun S. Song
   8. Julia Fukuyama
   9. Hugh K. Haddox

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study introduces a new biology-informed strategy for deep learning models aiming to predict mutational effects in antibody sequences. It provides solid evidence that separating selection from the nucleotide-level mutation process improves performance over the objectives of protein language models inspired by natural language processing. This paper should be of interest to computational immunologists, but also to the broader community interested in deep learning for biological sequence data and evolution.

   Reviewed by eLife

6. Direct MRI of Collagen

   This article has 4 authors:

   1. Jason Daniel van Schoor
   2. Markus Weiger
   3. Emily Louise Baadsvik
   4. Klaas Paul Pruessmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental work substantially advances our understanding of a major research question: whether collagen can be directly imaged with MRI. The evidence supporting the conclusion is compelling, with methods, data, and analyses that are more rigorous than those currently considered state-of-the-art. The work will be of high interest to MR physicists and clinicians, as collagen is the most abundant protein in the human body and plays an essential role in health.

   Reviewed by eLife

7. A dual role for PGLYRP1 in host defense and immune regulation during B. pertussis infection

   This article has 6 authors:

   1. David M Rickert
   2. Sasha Cardozo
   3. Nicholas H Carbonetti
   4. William E Goldman
   5. Karen M Scanlon
   6. Ciaran Skerry

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Rickert and colleagues demonstrate that the host peptidoglycan-binding protein PGLYRP1 has both beneficial and detrimental effects on Bordetella pertussis infection in mice. Using a solid array of techniques, the study provides useful insights into how peptidoglycan species may alter host immune responses. The data on the bactericidal effects on B. pertussis are incomplete, and further experiments are needed to draw conclusions on this question.

   Reviewed by eLife

8. Investigating the native functions of [NiFe]-carbon monoxide dehydrogenases through genomic context analysis

   This article has 2 authors:

   1. Maximilian Böhm
   2. Henrik Land

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable analysis of a large dataset of [NiFe]-CODHs, integrating genomic context, operon organization, and clade-specific gene neighborhoods to discern patterns of functional diversification and adaptation. Carefully looking at the CODH genomic context, e.g., CODH-HCP co-occurrence, the authors gain insight into enzymatic activity, biotechnological potential, and differential functional roles. The approach aligns with current standards in genomic enzymology to characterize newly identified enzymes. With solid support, this work provides a broadly informative contribution to the field.

   Reviewed by eLife

9. A conserved Hsp70 phosphorylation regulates cell cycle progression after DNA damage

   This article has 6 authors:

   1. Thomas Moss
   2. Alexandra Wooldredge
   3. Koustav Bhakta
   4. Matthew Cronin
   5. Jason E. Gestwicki
   6. Shaeri Mukherjee

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This potentially valuable manuscript focuses on the phosphorylation of residue T495 as a mechanism to inactivate HSP70 and disrupt cell cycle progression in response to DNA damage. The evidence supporting this model is incomplete and would be strengthened by additional studies defining the extent of T495 phosphorylation induced by DNA damage, identifying the kinase responsible for phosphorylating T495 of HSP70, and further elucidation of the functional implications of T495 phosphorylation in human cells. This work will be of interest to scientists focused on topics including chaperone biology, proteostasis, cell cycle progression, and DNA damage.

   Reviewed by eLife, preLights

10. Dynamic updating of spatial working memory across eye movements: a computational investigation of transsaccadic integration

    This article has 9 authors:

    1. Sijia Zhao
    2. Thomas Parr
    3. Rob Udale
    4. Verena Klar
    5. Gabriel David Jones
    6. Anna Scholcz
    7. Sofia Toniolo
    8. Sanjay G Manohar
    9. Masud Husain

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study makes an important contribution by revealing how saccades selectively disrupt spatial working memory while sparing other object features, and by demonstrating how this mechanism is altered in aging and neurodegeneration. The findings are supported by convincing evidence derived from well-controlled eye-tracking experiments and systematic generative model comparisons. Together, the work provides a computationally grounded framework that is of importance for understanding trans-saccadic memory and its clinical relevance.

    Reviewed by eLife