eLife

Latest preprint reviews

1. Noise in Competing Representations Determines the Direction of Memory Biases

   This article has 2 authors:

   1. Andrey Chetverikov
   2. Sabrina Hansmann-Roth

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study investigates the mechanisms underlying inter-item biases in visual working memory. By experimentally manipulating the relative noise levels of target and non-target items, the authors report bias patterns that are broadly consistent with predictions of their previously proposed normative demixing theory. However, the supporting evidence remains incomplete, as the manuscript lacks a sufficient description of the underlying theory, key assumptions, and a quantitative link between the model and behavioral data. The manuscript would be substantially strengthened by clearer exposition and stronger tests, including analyses of the full error distributions and comparisons with alternative models, which would increase its potential interest to the cognitive neuroscience and computational cognitive science communities.

   Reviewed by eLife

2. Rehabilitation drives functional reorganization of intact corticospinal-supraspinal projections following partial spinal cord injury

   This article has 5 authors:

   1. James Bonanno
   2. Sheel Trivedi
   3. Ciara F. O’Brien
   4. Sharna Saha
   5. William B.J. Cafferty

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study investigates the neural basis for recovery of complex wheel running behaviour following a unilateral spinal cord injury in mice. By combining behavioural analyses, whole-brain mapping, and tracing techniques, the authors provide incomplete evidence that new cortico-medullary connections can drive effective motor recovery. The paper could be strengthened with manipulations to establish causality, a more fine-grained analysis of the behaviour, and some reorganisation of how the data are presented and discussed.

   Reviewed by eLife

3. Central carbon metabolism switching in lytic versus temperate coral reef viral communities

   This article has 32 authors:

   1. Jacob Kelman
   2. Meena Khan
   3. Chibundu Umunna
   4. Russell Brainard
   5. Grace Donohue
   6. Rob Edwards
   7. Natalie A Falta
   8. Emma George
   9. Eleanor Gorham
   10. Juris Grasis
   11. Kevin Green
   12. Andreas Haas
   13. Kimberly Halsey
   14. Eric Hester
   15. Summer Jacob
   16. Aydin Loid Karatas
   17. Yan Wei Lim
   18. Mark Little
   19. Stuart Sandin
   20. Jessie Segnitz
   21. Maya Serota
   22. Natalia Shahwan
   23. Giselle Simmons
   24. Jennifer E Smith
   25. Isha Tripathi
   26. Linda Wegley Kelly
   27. Lauren Woodward
   28. Nickie Yang
   29. Charles Young
   30. Brian Zgliczynski
   31. Forest Rohwer
   32. Ben Knowles

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The worldwide decline in the health of coral reefs is well documented, and overgrowth by microbial consortia can be a contributing factor. Kelman and colleagues used metagenomic analysis to interrogate potential changes in phage-associated genes predicted to be involved in central carbon metabolism. The study addresses the hypothesis that metabolic genes associated with carbon metabolism that are encoded by viruses reflect the health of the corals. The study contributes a valuable perspective on the potential role of phages in coral health, although limitations of the data and analyses offer an exploratory examination rather than a definitive result. Overall, the evidence supporting the major findings is incomplete, in part because the conceptual model relies on qualitative assumptions rather than empirical data.

   Reviewed by eLife

4. 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 have a functional role are incomplete. This work will be of interest to microbiologists studying the regulation of virulence factors at the host-pathogen interface.

   Reviewed by eLife

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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