eLife

Latest preprint reviews

1. Apoptosis recognition receptors regulate skin tissue repair in mice

   This article has 14 authors:

   1. Olivia Justynski
   2. Kate Bridges
   3. Will Krause
   4. Maria Fernanda Forni
   5. Quan M Phan
   6. Teresa Sandoval-Schaefer
   7. Kristyn Carter
   8. Diane E King
   9. Henry C Hsia
   10. Michael I Gazes
   11. Steven D Vyce
   12. Ryan R Driskell
   13. Kathryn Miller-Jensen
   14. Valerie Horsley

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The authors studied the mechanisms by which dead cells are removed from the wounded skin in a process called efferocytosis. By analyzing different cell populations in the skin, the authors find that proteins involved in mediating the cell death and marking the cells as undergoing this process are elevated during distinct times in the wound healing program. Interestingly, these same proteins are elevated even higher in diabetic wounds. Finally the authors demonstrate that blocking the process of efferocytosis alters the wound healing program, thus illustrating its importance in effective wound repair.

   Reviewed by eLife

2. Regulation of nuclear transcription by mitochondrial RNA in endothelial cells

   This article has 19 authors:

   1. Kiran Sriram
   2. Zhijie Qi
   3. Dongqiang Yuan
   4. Naseeb Kaur Malhi
   5. Xuejing Liu
   6. Riccardo Calandrelli
   7. Yingjun Luo
   8. Alonso Tapia
   9. Shengyan Jin
   10. Ji Shi
   11. Martha Salas
   12. Runrui Dang
   13. Brian Armstrong
   14. Saul J Priceman
   15. Ping H Wang
   16. Jiayu Liao
   17. Rama Natarajan
   18. Sheng Zhong
   19. Zhen Bouman Chen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This work is fundamental in providing compelling evidence of mitochondria-encoded RNAs playing a role in controlling nuclear gene expression. How mitochondria and the nucleus communicates is an important but yet not well-appreciated area of biology. Using the iMARI (in situ mapping of RNA-Genome Interactions) technology developed by this team, the authors found that mitochondria-encoded RNAs play an unexpected role in regulating nuclear gene expressions in endothelial cells and intriguingly, depletion or overexpression of a specific mt-caRNA altered stress-induced transcription of nuclear genes encoding for innate inflammation and endothelial activation. Overall, these findings are interesting and supported by experimental confirmation, bulk-RNA-seq, and snRNA and scRNA-seq data and will be of interest to the field studying RNA regulation, gene expression and cell biology.

   Reviewed by eLife

3. Cell type-specific connectome predicts distributed working memory activity in the mouse brain

   This article has 5 authors:

   1. Xingyu Ding
   2. Sean Froudist-Walsh
   3. Jorge Jaramillo
   4. Junjie Jiang
   5. Xiao-Jing Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This paper presents valuable findings from whole-brain modeling of persistent activity states (underlying working memory) in the mouse brain. The most novel finding is that a spatial gradient of the density of inhibitory neurons supports a corresponding spatial gradient of propensity to support persistent activity. However, the evidence for this finding appears to be incomplete.

   Reviewed by eLife

4. Catalytic activity and autoprocessing of murine caspase-11 mediate noncanonical inflammasome assembly in response to cytosolic LPS

   This article has 10 authors:

   1. Daniel C Akuma
   2. Kimberly A Wodzanowski
   3. Ronit Schwartz Wertman
   4. Patrick M Exconde
   5. Víctor R Vázquez Marrero
   6. Chukwuma E Odunze
   7. Daniel Grubaugh
   8. Sunny Shin
   9. Cornelius Taabazuing
   10. Igor E Brodsky

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Brodsky and colleagues report here an unexpected cis-activation mechanism of caspase-11. The authors use cellular imaging methods and cleavage site mutants to show that the LPS-induced speck formation by caspase-11 depends on the autoprocessing between two subdomains. This new finding opens multiple doors for further investigating how this non-canonical inflammasome is regulated and activated at the molecular level.

   Reviewed by eLife

5. O-GlcNAc signaling increases neuron regeneration through one-carbon metabolism in Caenorhabditis elegans

   This article has 5 authors:

   1. Dilip Kumar Yadav
   2. Andrew C Chang
   3. Noa WF Grooms
   4. Samuel H Chung
   5. Christopher V Gabel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important work reveals that increased flux towards one carbon metabolism improves neuronal regeneration after injury in C. elegans. The presented data are solid and provide compelling support for this conclusion. The manuscript can still be improved in order to strengthen some of the specific conclusions made and to increase the clarity of the presentation.

   Reviewed by eLife

6. Cross-movie prediction of individualized functional topography

   This article has 5 authors:

   1. Guo Jiahui
   2. Ma Feilong
   3. Samuel A Nastase
   4. James V Haxby
   5. M Ida Gobbini

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study presents a tool for hyperaligning functional brain topography between individuals, which is based on fMRI connectivity data gathered when participants watched different movies. The tool is validated through strong correlations between functional topographic maps generated from a participant's own localizer data and those derived from other participants' data based on this hyperalignment, even when the training and target participants were drawn from different datasets. The study will potentially be of interest to researchers working with a wide range of fMRI datasets.

   Reviewed by eLife

7. BrainPy, a flexible, integrative, efficient, and extensible framework for general-purpose brain dynamics programming

   This article has 6 authors:

   1. Chaoming Wang
   2. Tianqiu Zhang
   3. Xiaoyu Chen
   4. Sichao He
   5. Shangyang Li
   6. Si Wu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The paper introduces a new, important framework for neural modelling that promises to offer efficient simulation and analysis tools for a wide range of biologically-realistic neural networks. The paper's examples provide solid support for the ease of use and flexibility of the framework, but the comparison to existing solutions (in particular in terms of accuracy and performance) is incomplete. With a more careful evaluation of the tool's strengths and limitations, the work would be of interest to a wide range of computational neuroscientists and researchers working on biologically inspired machine learning applications.

   Reviewed by eLife

8. Loss of finger control complexity and intrusion of flexor biases are dissociable in finger individuation impairment after stroke

   This article has 8 authors:

   1. Jing Xu
   2. Timothy Ma
   3. Sapna Kumar
   4. Kevin Olds
   5. Jeremy Brown
   6. Jacob Carducci
   7. Alex Forrence
   8. John Krakauer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study presents a new apparatus and experimental paradigm to examine deficits in finger control in stroke patients, with the goal of understanding their potential (biomechanical and neural) underpinnings. The paper presents solid experimental design and quantitative analyses to characterise these deficits and infer their origin, but a few technical aspects related to data analysis and statistics could be improved, and alternative interpretations of the results considered. In addition to the scientific results, this novel methodology can be used as a starting point for further research on hand function impairments in stroke, which is of significance for theoretical studies in neuroscience and applied research in rehabilitation.

   Reviewed by eLife

9. Distinct transcriptomic profile of satellite cells contributes to preservation of neuromuscular junctions in extraocular muscles of ALS mice

   This article has 7 authors:

   1. Ang Li
   2. Jianxun Yi
   3. Xuejun Li
   4. Li Dong
   5. Lyle W Ostrow
   6. Jianjie Ma
   7. Jingsong Zhou

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The manuscript by Jingsong Zhou and colleagues uncovers why the extraocular muscles (EOMs) are preserved while other muscles undergo degenerative changes in amyotrophic lateral sclerosis (ALS). In this work, the authors have used a mouse model of familial ALS that carries a G93A mutation in the Sod1 gene to demonstrate that NaBu treatment partially restores the integrity of NMJ in the limb and diaphragm muscles of G93A mice. The findings of the study offer important information that EOMs are spared in ALS because they produce protective factors for the NMJ and, more specifically, factors secreted by EOM-derived satellite cells. While most of the experimental approaches are convincing, the use of sodium butyrate (NaBu) in this study needs further investigation, as NaBu might have a variety of biological effects. Overall, this work may help develop future therapeutic interventions for patients with ALS.

   Reviewed by eLife

10. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

    This article has 6 authors:

    1. Nicholas James Ose
    2. Paul Campitelli
    3. Tushar Modi
    4. I Can Kazan
    5. Sudhir Kumar
    6. Sefika Banu Ozkan

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This important study investigates various variants of the SARS-COV-2 spike protein using established computational methods, complemented by experimental validation efforts. The evidence, bolstered by an evolutionary approach and protein dynamics, is solid. Placing this research in the broader context of the field could further enrich the manuscript. It will interest biophysicists focused on allostery and protein evolution.

    Reviewed by eLife