eLife

Latest preprint reviews

1. Distinct prokaryotic gut microbiome and proviral-immune axes of pathophysiology in Sickle Cell Disease

   This article has 11 authors:

   1. Zachary N Flamholz
   2. Jennifer De Los Santos
   3. Karen Ireland
   4. Janine Keenan
   5. Jacob S Kazmi
   6. Aakash Mahant Mahant
   7. Anayeli Correa
   8. Paul S Frenette
   9. Betsy C Herold
   10. Deepa Manwani
   11. Libusha Kelly

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable metagenomic analysis of the gut microbiome in sickle cell disease (SCD) patients, revealing associations between bacteriophage, host immunity, and SCD pathophysiology. While these data are interesting and helpful for hypothesis generation, they are deemed incomplete; additional experiments would be needed to test causality and to provide mechanistic insight. Despite these limitations, this work will be of broad interest to researchers studying SCD, immunology, phage biology, and the microbiome, adding to the small but growing literature suggesting a microbial component to SCD.

   Reviewed by eLife

2. The openretina Project: Collaborative Retina Modelling Across Datasets and Species

   This article has 12 authors:

   1. Federico D’Agostino
   2. Thomas Zenkel
   3. Baptiste Lorenzi
   4. Michaela Vystrčilová
   5. Dominic Gonschorek
   6. Samuel Suhai
   7. Samuele Virgili
   8. Alexander S Ecker
   9. Olivier Marre
   10. Larissa Höfling
   11. Thomas Euler
   12. Matthias Bethge

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript presents openretina, an open-source platform that integrates retinal datasets, model training, benchmarking, and in silico analysis tools within a unified framework. The resource is valuable because it addresses long-standing challenges in reproducibility, accessibility, and cross-study comparison in computational retina research, while providing a foundation for community-driven model development and evaluation. The supporting evidence is solid, with the authors demonstrating a functional and well-documented platform across multiple datasets and species, although a clearer discussion of model interpretability, current performance limitations, and data quality standards would strengthen the resource.

   Reviewed by eLife

3. Essential role for plasma membrane glutamate transporters in stimulus intensity coding in auditory neurons

   This article has 2 authors:

   1. Tenzin Ngodup
   2. Laurence O. Trussell

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this manuscript, the authors describe a cell-specific mechanism by which glutamate transporters regulate the fidelity with which T-stellate cells in the mouse ventral cochlear nucleus relay information from auditory nerve inputs. The study is supported by solid electrophysiological data. It provides valuable insights into how the rapid binding of glutamate to transporters shapes auditory information processing at specific synapses.

   Reviewed by eLife

4. Comparative single-cell transcriptomic roadmap of mammalian fetal ovarian development

   This article has 9 authors:

   1. Yifei Fang
   2. Shiyao Han
   3. Junmei Zhang
   4. Shengcan Xie
   5. Yue Su
   6. IISAGE Consortium
   7. Yulei Wei
   8. Young Tang
   9. Jingyue Ellie Duan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study provides a cross-species single-cell transcriptomic resource for early female gonadal development in mammals. The data supporting the main conclusion remain incomplete, and experimental validation is needed to strengthen the conclusions. The work will be of interest to reproductive biologists and developmental biologists.

   Reviewed by eLife

5. Opto-MDMi: a dual-lock optogenetic system for robust activation of endogenous p53

   This article has 5 authors:

   1. Tatsuki Tsuruoka
   2. Takashi Sumikama
   3. Sachiya Nakashima
   4. Yuhei Goto
   5. Kazuhiro Aoki

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript describes an important development of several variants of optogenetic tools to control endogenous p53 activity. They are based on peptides competing with Mdm2/MdmX for binding to p53, thus releasing p53 from its negative regulators and stabilizing its cellular levels. In principle, the data are convincing but should be complemented by investigations of p53 target genes at endogenous levels (instead of only reporter constructs). The study therefore remains incomplete but will be of interest to scientists working on optogenetics as well as the p53 field.

   Reviewed by eLife

6. A mitochondrial quality control mechanism reverses the phagosome maturation arrest caused by Mycobacterium tuberculosis

   This article has 20 authors:

   1. Surbhi Verma
   2. Shweta Thakur
   3. Mrinmoy Das
   4. Raman D Sharma
   5. Vikas Yadav
   6. Priya Sharma
   7. Mardiana Marzuki
   8. Shihui Foo
   9. Giulia M Piperno
   10. Mehak Z Khan
   11. Babu Mathew
   12. Meenu Bajpai
   13. Jaswinder Singh Maras
   14. Shanshan Howland
   15. Sovan Sarkar
   16. Federica Benvenuti
   17. Amit Singh
   18. Vinay Nandicoori
   19. Amit Singhal
   20. Dhiraj Kumar

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Verma and colleagues interrogate the mechanisms of phagosome maturation arrest during Mycobacterium tuberculosis infection. While cellular events that culminate in this arrest have been largely elucidated, involvement of other organelles, such as mitochondria, has not been highlighted mechanistically. In this valuable study, elements of mitochondrial quality control, such as mitophagy and mitochondrial-derived vesicles involvement, are shown to be paramount in the host-pathogen tussle. The evidence supporting the main conclusions is solid, based on multiple complementary approaches and appropriate controls, although some central mechanistic aspects of the proposed pathway remain only partially resolved.

   Reviewed by eLife

7. Distinct cell-type contributions and network topography of theta-nested gamma oscillations in the medial entorhinal cortex

   This article has 9 authors:

   1. Brandon Williams
   2. Riya Dahal
   3. Ananth Vedururu Srinivas
   4. Sheng Xiao
   5. Maria V Moya
   6. Carmen C Canavier
   7. Xue Han
   8. Michael N Economo
   9. John A White

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study investigates the cellular mechanisms underlying theta-nested gamma oscillations in the medial entorhinal cortex; the experiments are rigorous, and the analyses and modeling provide potentially useful insights into cell-type-dependent circuit dynamics. However, the evidence supporting several key conclusions remains incomplete. The study is limited by conceptual constraints in the experimental design and a modeling approach that does not fully address underlying physiological mechanisms. Overall, this is a careful study that addresses how distinct neuronal populations in superficial MEC participate in theta-gamma coordination and provides new data linking cell-type-specific activity patterns to oscillatory network structure.

   Reviewed by eLife

8. A stable cryogenic fluorescence microscope for correlative super-resolution light and electron microscopy

   This article has 6 authors:

   1. Soheil Mojiri
   2. Joseph M Dobbs
   3. Ricardo Sánchez Loayza
   4. Anna Kreshuk
   5. Julia Mahamid
   6. Jonas Ries

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this useful Tools & Resources article, the authors describe a new cryogenic light microscopy design and characterize its temperature and spatial stability. This compelling system avoids the challenges associated with vacuum-based designs, particularly vacuum transfer systems, which are difficult to engineer. A key advantage of the system is that it reduces ice contamination and drift, which are the primary challenges in open cryostat systems.

   Reviewed by eLife

9. A genetic screen reveals dosage-sensitive effects of ASD genes and identifies domino as a regulator of synaptic and behavioral phenotypes

   This article has 9 authors:

   1. Ellen Stirtz
   2. Zachary B Madaj
   3. Brejnev Muhire
   4. Robert Fillinger
   5. Joe Roy
   6. Dmitri Martirosov
   7. Daniel Bautista
   8. Sreeja Varanasi
   9. Adelheid Lempradl

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents an important large-scale behavioral and transcriptomic analysis of Drosophila that are heterozygous for putative loss-of-function alleles of homologs of human genes that have been linked to autism spectrum disorders. The authors consider 48 genes as hits from their screen, which show significant behavioral alterations in sleep, basal activity, and/or social behavior, and significant sexual dimorphism. The authors then focus on the domino/SRCAP gene as a candidate regulator of sleep, social behavior, transcriptional programs, and RNA splicing. The work generates a solid dataset and applies quantitative analytical approaches that will be of interest to researchers in the field, yet the evidence presented remains incomplete because issues of genetic background need to be further addressed.

   Reviewed by eLife

10. Structural basis for site-specific histone H3 acetylation-dependent regulation of RNAPII transcription through nucleosomes

    This article has 13 authors:

    1. Takumi Oishi
    2. Suguru Hatazawa
    3. Tomoya Kujirai
    4. Sae Suzuki
    5. Koki Nakatsu
    6. Gosuke Hayashi
    7. Junko Kato
    8. Yuki Kobayashi
    9. Mitsuo Ogasawara
    10. Haruhiko Ehara
    11. Shun-ichi Sekine
    12. Yoshimasa Takizawa
    13. Hitoshi Kurumizaka

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This manuscript describes a valuable study of the mechanism by which acetylation on the histone H3 core domain regulates RNA polymerase II transcription passing through nucleosomes. The authors provide convincing evidence that acetylation influences transcription in a context-specific fashion. Some questions relating to the static nucleosome structures and the polymerase passage remain, but this manuscript will be of considerable interest to researchers in the chromatin and transcription fields.

    Reviewed by eLife