eLife

Latest preprint reviews

1. A protease-sensing circuit links neutrophil inflammation to virulence regulation in Streptococcus pyogenes

   This article has 4 authors:

   1. Stephanie Guerra
   2. Ananya Dash
   3. Doris L. LaRock
   4. Christopher N. LaRock

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors describe a valuable finding that the Streptococcus pyogenes secreted protease SpeB is expressed in response to protease activity that degrades the Vfr repressor. Proteases can be released from host neutrophils (possibly by NETosis), as well as a positive feedback mechanism by SpeB itself. The authors utilize a dual fluorescent reporter system to simultaneously read speB and capsule gene expression, providing solid evidence that demonstrates that proteases can regulate Vfr; however, the data indicating that this is physiologically relevant and that extracellular traps themselves are important is incomplete. This work will be of interest to microbiologists studying the regulation of virulence factors at the host-pathogen interface.

   Reviewed by eLife

2. Host Endoplasmic Reticulum Stress and Interferon Responses Contribute to AAV-Induced Ocular Toxicity

   This article has 5 authors:

   1. Apolonia Gardner
   2. Christin M. Hong
   3. Sophia R. Zhao
   4. Adam J. Daniels
   5. Constance L. Cepko

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental study provides convincing evidence that distinct molecular mechanisms underlie AAV-associated retinal toxicity in retinal pigment epithelial cells and photoreceptors, advancing our understanding of gene therapy-related retinal injury. The authors employ a rigorous and comprehensive experimental approach, including multiple knockout mouse models, transcriptomic analyses, and genetic loss-of-function studies, which substantially strengthen the mechanistic conclusions. Some concerns remain regarding vector characterization, the absence of procedural injection controls, and the limited interpretation of adult versus neonatal studies; nevertheless, the study makes a substantial contribution to the field and provides a strong foundation for future translational investigations.

   Reviewed by eLife

3. Early Visual Cortex Supports One-Shot Episodic Memory via Spatially Tuned Reactivation

   This article has 3 authors:

   1. Robert Woodry
   2. Jonathan Winawer
   3. Serra E. Favila

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This paper reports the findings of a neuroimaging experiment that tested the hypothesis that the cortex, specifically early visual areas, reinstates certain content from past episodic events. This is a useful study that highlights the role of early sensory cortices in supporting rapid, one-shot learning of location information for long-term memory. The strength of the evidence is solid, with the methods, data, and analyses broadly supporting the claims.

   Reviewed by eLife

4. NPAS4 refines spatial and temporal firing in CA1 pyramidal neurons

   This article has 10 authors:

   1. Anja Payne
   2. Daniel A. Heinz
   3. Chiaki Santiago
   4. Lara L. Hagopian
   5. Rolando Sceptre Ganasi
   6. Clare Quirk
   7. Andrea L. Hartzell
   8. Jill K. Leutgeb
   9. Stefan Leutgeb
   10. Brenda L. Bloodgood

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study shows that NPAS4, a gene that is switched on by neural activity, enhances the spatial and temporal precision of hippocampal neurons during navigation. These findings, based on selective and sparse gene deletion, are supported by convincing evidence. However, the experiments were performed entirely in animals exposed to long-term environmental enrichment, which leaves open the question of whether the same effects would emerge under standard housing conditions. This study will be of interest to neuroscientists studying neuronal circuits and spatial coding.

   Reviewed by eLife

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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