eLife

Latest preprint reviews

1. A membrane insertion code for intrinsically disordered proteins

   This article has 2 authors:

   1. Fidha Nazreen Kunnath Muhammedkutty
   2. Huan-Xiang Zhou

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides a valuable advance in understanding how disordered proteins interact with cell membranes by identifying the sequence rules that enable aromatic residues to penetrate deeply into the membrane interior. The integration of complementary computational approaches, including molecular simulations, large-scale sequence analysis, and the development of an online prediction server, makes the work potentially impactful for the membrane protein and intrinsically disordered protein communities. The evidence supporting the main conclusions is generally convincing, although its transferability across diverse membrane compositions and its validity as a prediction tool for real protein-membrane systems remain to be further established.

   Reviewed by eLife

2. Membrane contact site resident PTP1B limits superoxide production by suppressing a Syk-Shc1-Phagocyte Oxidase relay

   This article has 9 authors:

   1. Minhyoung Lee
   2. Haggag S. Zein
   3. Mahlegha Ghavami
   4. Kuiru Wei
   5. Murtaza Lokhandwala
   6. Kaitlin Chan
   7. Leanne Wybenga-Groot
   8. Michael F. Moran
   9. Gregory D. Fairn

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study showing the interaction of the endoplasmic reticulum (ER)-resident tyrosine phosphatase PTP1B with the developing phagocytic cup in macrophages, and its role in inhibiting microbicidal superoxide production. The authors show convincing evidence that PTP1B interacts with Syk, a plasma membrane tyrosine kinase that plays an essential role in phagocytosis, and that ablation of PTP1B increases superoxide production and Syk phosphorylation without affecting phagocytosis. Further evidence suggests that PTP1B may inhibit a Syk/Shc1/NOX2 axis; however, robust demonstration of the proposed chain of events and of the actual role of ER-plasma membrane contact sites in the PTP1B-dependent downregulation of NOX2 activity will require additional experimental evidence. The integration of advanced imaging methods to study contact site formation with functional assays related to phagocytosis and signaling is inspiring.

   Reviewed by eLife

3. Genome-wide discovery of cis- regulatory elements in a large genome

   This article has 11 authors:

   1. Gillian Forbes
   2. Emilia Skafida
   3. Irene Karapidaki
   4. Savannah Moinet
   5. Mowgli Dandamudi
   6. Çağrı Çevrim
   7. Farzaneh Momtazi
   8. Chryssa Anastasiadou
   9. Sabrina Lo Brutto
   10. Michalis Averof
   11. Mathilde Paris

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study combines chromatin accessibility and genomic DNA sequence conservation data from low-coverage genome sequencing of related species (without assembly), for the in silico identification of cis-regulatory elements in large genomes. The approach and results are compelling and well supported by the experimental validations. The work will be of interest to researchers working in the field of gene regulation and evolution, particularly because the methodology proposed can be applied to a large variety of experimental organisms.

   Reviewed by eLife

4. Application of Engineered NK-92 Cell Extracellular Vesicles in the Treatment of Systemic Lupus Erythematosus

   This article has 9 authors:

   1. Yu Sun
   2. Zeyu Tang
   3. Mengting Guo
   4. Zimeng Zhai
   5. Zixian Wu
   6. Xia Wang
   7. Fang Li
   8. Weiling An
   9. Xiaowei Dou

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study presents the first application of engineered NK-92 cell-derived extracellular vesicles displaying CD19 scFv for the treatment of systemic lupus erythematosus (SLE). The concept of using targeted extracellular vesicles as a "cell-free" alternative to CAR-T/CAR-NK therapies is good. However, the current results are incomplete and do not provide strong support for the experimental hypothesis, particularly with respect to EV purification, characterization, mechanistic validation, and adherence to current EV field standards. Several major concerns should be addressed to strengthen the translational relevance, reproducibility, and biological interpretation of the study.

   Reviewed by eLife

5. A battery of image classification challenges reveals shared and distinct object categorization behavior across monkeys, humans, and deep networks

   This article has 8 authors:

   1. Han Zhang
   2. Zhihao Zheng
   3. Jiaqi Hu
   4. Qiao Wang
   5. Mengya Xu
   6. Zhaojiayi Zhou
   7. Zixuan Li
   8. Gouki Okazawa

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides fundamental insights into the mechanisms of visual object categorization in primates through a scalable behavioral framework for assessing category learning and generalization in macaque monkeys. The evidence is compelling, based on extensive behavioral characterization, rigorous control experiments, and comprehensive comparisons with humans and computational models, although extending the model analyses to the secondary monkey experiments would further strengthen the conclusions.

   Reviewed by eLife

6. DUAL: deep unsupervised simultaneous simulation and denoising for cryo-electron tomography

   This article has 6 authors:

   1. Xiangrui Zeng
   2. Yizhe Ding
   3. Yueqian Zhang
   4. Mostofa Rafid Uddin
   5. Ali Dabouei
   6. Min Xu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study presents a computational framework inspired by cycleGAN that enables denoising and realistic simulation of cryo-electron tomography data, addressing central challenges in tomogram cleaning, simulation, and downstream annotation. The approach coherently links several key problems in the field and demonstrates strong performance across benchmark datasets, with additional benefits for particle detection and missing-wedge completion, indicating broad relevance across electron tomography. The evidence is solid, with appropriate quantitative benchmarks and applications to diverse datasets supporting the main claims, although validation on additional, more recent tomograms would further strengthen the conclusions.

   Reviewed by eLife

7. Ectopic hAMH-driven SOX17 expression induces hyperplastic Sertoli valve formation in mouse testes

   This article has 11 authors:

   1. Xiao Han
   2. Aya Uchida
   3. Seohyeon Lee
   4. Kosuke Nakamura
   5. Katsuki Takahashi
   6. Tsutomu Endo
   7. Ayaka Yanagida
   8. Ryuji Hiramatsu
   9. Akihiko Kudo
   10. Masami Kanai-Azuma
   11. Yoshiakira Kanai

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study clearly demonstrates that Sox17 is key for the formation and function of the Sertoli valve, a transition region between the rete testis and seminiferous tubules, which remains an understudied domain of testicular biology. The supporting data are generally convincing but remain incomplete. This work will be of interest to reproductive biologists and andrologists who work on male fertility and men's health.

   Reviewed by eLife

8. Wunen(s) help navigate Primordial Germ Cells by attenuating Hedgehog signaling

   This article has 9 authors:

   1. Amrita Roy
   2. Adheena Elsa Roy
   3. Airat Ibragimov
   4. Juliana DaSilva
   5. Kundan Kumar
   6. Paul Schedl
   7. Siddhesh S Kamat
   8. Girish S Ratnaparkhi
   9. Girish Deshpande

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this valuable manuscript, the authors tackle a highly relevant question in biology: how cells integrate attractive and repulsive cues to achieve directed migration. They present solid data demonstrating that two wunen genes act as negative regulators of Hedgehog signalling, thereby enabling efficient primordial germ cell (PGC) migration in Drosophila embryos. Beyond its immediate scope, this work has broader implications, particularly for understanding key mechanisms underlying complex processes such as cancer metastasis, where the coordinated interpretation of guidance cues is critical.

   Reviewed by eLife

9. RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions

   This article has 3 authors:

   1. Alexandre Laverré
   2. Thibault Latrille
   3. Marc Robinson-Rechavi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The focus of this manuscript is a computational procedure to reveal signatures of selection on transcription factor binding sites through assessing changes in predicted binding affinity, setting out to avoid biases inherent in previous tests. The general approach could become a valuable resource for the community that can also be used for a broader range of questions. However, in its current implementation, the methods are inadequate to sufficiently support the primary claims.

   Reviewed by eLife

10. Developmental bias explains the evolutionary trend towards simple leaf shapes

    This article has 5 authors:

    1. James S Malone
    2. Nora S Martin
    3. Samuel HA von der Dunk
    4. Liliana M Dávalos
    5. Ard A Louis

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This paper presents important findings on how the shapes of leaves might be biased towards simpler shapes due to biases in how variation is generated by developmental processes rather than selection. The authors present solid evidence that combines image analysis of a herbarium dataset and computational analysis of a model of leaf development. The paper should be of interest to diverse researchers, ranging from plant development to the evolution of complexity more broadly.

    Reviewed by eLife