eLife

Latest preprint reviews

1. Synaptotagmin 1 and Synaptotagmin 7 promote MR1-mediated presentation of Mycobacterium tuberculosis antigens

   This article has 7 authors:

   1. Se-Jin Kim
   2. Jessie C Peterson
   3. Andrew J Olive
   4. Fikadu G Tafesse
   5. Corinna A Kulicke
   6. Elham Karamooz
   7. David M Lewinsohn

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study examines the contribution of synaptotagmin 1 and synaptotagmin 7 to metabolite antigen presentation to mucosal-associated invariant T (MAIT) cells; it begins to address a critical gap in our understanding of the antigen presentation mechanisms to these cells. Strengths of the study include the use of Mtb to study the dynamics of antigen presentation to MAIT cells instead of a synthetic antigen. However, the strength of the evidence to support the conclusion is currently incomplete. The conclusions could be enhanced by additional dissection of some of the cell biological events that lead to antigen presentation by MR1.

   Reviewed by eLife

2. Macroscopic Analyses of RNA-Seq Data to Reveal Chromatin Modifications in Aging and Disease

   This article has 6 authors:

   1. Achal Mahajan
   2. Francesca Ratti
   3. Ban Wang
   4. Hana El-Samad
   5. James H Kaufman
   6. Vishrawas Gopalakrishnan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study analyzes aging-related chromatin changes through the lens of intra-chromosomal gene correlation length, which is a novel computational metric that captures spatial correlations in gene expression along the chromosome. The authors propose that this metric reflects chromatin structure and can serve as a proxy for its changes during aging. While currently the strength of evidence is somewhat incomplete, if revised with further supporting data, this work will provide a systems-level understanding of aging and genome regulation, which is predicted to have a substantive impact on the field.

   Reviewed by eLife

3. Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development

   This article has 4 authors:

   1. César Nieto
   2. Zahra Vahdat
   3. Bomyi Lim
   4. Abhyudai Singh

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable quantitative framework for analyzing transcription dynamics data for enhancers and genes expressed in the early Drosophila embryo. By analyzing existing data across both synthetic reporters and an endogenous gene (eve), this work provides evidence that spatial gene expression patterns within the embryo are largely determined by "activity time" - the time during which a gene is bursting. The methods and evidence are solid and should be of broad interest to researchers in developmental biology and quantitative gene regulation, but the study would be significantly enhanced by clarifying the novelty of the findings relative to prior work and presenting a rigorous benchmarking of their algorithm against previously used algorithms.

   Reviewed by eLife

4. A Python Toolbox for Representational Similarity Analysis

   This article has 11 authors:

   1. Jasper JF van den Bosch
   2. Tal Golan
   3. Benjamin Peters
   4. JohnMark Taylor
   5. Mahdiyar Shahbazi
   6. Baihan Lin
   7. Ian Charest
   8. Jörn Diedrichsen
   9. Nikolaus Kriegeskorte
   10. Marieke Mur
   11. Heiko H Schütt

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a new toolbox for Representational Similarity Analysis, representing a valuable contribution to the neuroscience community. The authors offer a well-integrated platform that brings together a range of state-of-the-art methodological advances within a convincing framework, with strong potential to enable more rigorous and insightful analyses of neural data across multiple subfields.

   Reviewed by eLife

5. Canonical and phosphoribosyl ubiquitination coordinate to stabilize a proteinaceous structure surrounding the Legionella-containing vacuole

   This article has 3 authors:

   1. Adriana Steinbach
   2. Chetan Mokkapati
   3. Shaeri Mukherjee

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript presents a valuable and insightful contribution to the understanding of how Legionella pneumophila remodels its vacuolar niche through coordinated ubiquitination mechanisms. The identification of Rab5 as a target of both canonical and phosphoribosyl ubiquitination, and the demonstration of a detergent-resistant ubiquitin "cloud" surrounding the LCV, represent significant advances in the field. The findings are supported by rigorous experimental design, robust quantitative analyses, and clear mechanistic insight, meeting a standard of evidence that is compelling and exceeds current state-of-the-art approaches.

   Reviewed by eLife

6. A Priming Circuit Controls the Olfactory Response and Memory in Drosophila

   This article has 3 authors:

   1. He Yang
   2. Yang Jiang
   3. Samuel Kunes

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work, combining behavioural genetics and calcium imaging, provides evidence for a form of learning in Drosophila that derives solely from direct or (optogenetically induced) phantom experience of punishment or reward. Flies that experience foot-shock alone show a subsequent decrease in avoidance to all odorants, together with increased odor-evoked activation of reward-encoding dopaminergic neurons that innervate the mushroom body. Phantom reward, delivered via optogenetic activation of reward-encoding dopaminergic neurons, increases subsequent odour-avoidance. While the findings are valuable to the field, there are aspects of the work that are incomplete, and some of the conclusions and terminology are also not completely justified; three major issues include : (a) the use of the term "priming" to describe this form of learning seems inappropriate and inconsistent with the accepted definition of this term; (b) a key 1998 publication with an initial description of this behavioural phenomenon needs to be cited and presented as context; and (c) the work on reward induced increase in odor-aversion seems relatively preliminary.

   Reviewed by eLife

7. Transcriptional Subtypes on Immune Microenvironment and Predicting Postoperative Recurrence and Metastasis in Pheochromocytoma and Paraganglioma

   This article has 8 authors:

   1. Yang Liu
   2. Xu Yan
   3. Yibo Zhang
   4. Zhenfu Gao
   5. Fengrui Nan
   6. Siyu Shi
   7. Jingyun Chen
   8. Lingyu Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a valuable study describing transcriptome-based pheochromocytoma and paraganglioma (PPGL) subtypes and exploring the mutations, immune correlates and disease progression of cases in each subtype. The cohort is a reasonable size and a second cohort is included from the Cancer Genome Atlas (TCGA). One of the key premises of the study is that identification of driver mutations in PPGL is not complete and that compromises characterisation for prognostic purposes. This is a solid starting point on which to base characterisation using different methods.

   Reviewed by eLife

8. ATAD2 mediates chromatin-bound histone chaperone turnover

   This article has 14 authors:

   1. Ariadni Liakopoulou
   2. Fayçal Boussouar
   3. Daniel Perazza
   4. Sophie Barral
   5. Emeline Lambert
   6. Tao Wang
   7. Florent Chuffart
   8. Ekaterina Bourova-Flin
   9. Charlyne Gard
   10. Denis Puthier
   11. Sophie Rousseaux
   12. Christophe Arnoult
   13. André Verdel
   14. Saadi Khochbin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study explores the role of the chromatin regulator ATAD2 in mouse spermatogenesis. It convincingly demonstrates that ATAD2 is essential for proper chromatin remodeling in haploid spermatids, influencing gene accessibility, H3.3-mediated transcription, and histone eviction. Using Atad2 knockout (KO) mice, the authors link ATAD2 to the DNA-replication-independent incorporation of sperm-specific proteins like protamines and histone H3.3. Although the findings highlight chromatin abnormalities and impaired in vitro fertilization in KO mice, natural fertility remains unaffected, suggesting possible in vivo compensatory mechanisms. However, in its current form, the study lacks mechanistic insight and provides only partial evidence for ATAD2's molecular role, limiting its functional conclusions.

   Reviewed by eLife

9. Altered cognitive processes shape tactile perception in autism

   This article has 4 authors:

   1. Ourania Semelidou
   2. Mathilde Tortochot-Megne Fotso
   3. Adinda Winderickx
   4. Andreas Frick

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides valuable insights with solid evidence into altered tactile perception in a mouse model of ASD (Fmr1 mice), paralleling sensory abnormalities in Fragile X and autism. Its main strength lies in the use of a novel tactile categorization task and the careful dissection of behavioral performance across training and difficulty levels, suggesting that deficits may stem from an interaction between sensory and cognitive processes. However, while the experiments are well executed, the reported effects are subtle and sometimes non-significant. The interpretation of results may be over-extended given the nature of the data (solely behavioral) and the absence of mechanistic, causal, or computational approaches limits the strength of the broader conclusions. The work will be relevant to those interested in autism, cognition, and/or sensory processing.

   Reviewed by eLife

10. Fitting bifurcation structure, not voltage traces: A biophysically inspired derivation of reduced neuron models exemplified by potassium dynamics

    This article has 4 authors:

    1. Louisiane Lemaire
    2. Mahraz Behbood
    3. Jan-Hendrik Schleimer
    4. Susanne Schreiber

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This work demonstrates an objective way to select parameter values for a quadratic integrate-and-fire model so that its bifurcation diagram matches a specific target diagram, generated from the Wang-Buzsaki model. The method is useful for the field and is presented with convincing evidence. The method is currently limited in its ability to be applied to data, but improves our mathematical tools to treat a rarely studied type of bifurcation.

    Reviewed by eLife