eLife

Latest preprint reviews

1. Active regulation of the epidermal growth factor receptor by the membrane bilayer

   This article has 6 authors:

   1. Shwetha Srinivasan
   2. Xingcheng Lin
   3. Xuyan Chen
   4. Raju Regmi
   5. Bin Zhang
   6. Gabriela S Schlau-Cohen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors describe an interesting approach to studying the dynamics and function of membrane proteins in different lipid environments. The fundamental findings have theoretical and practical implications beyond the study of EGFR to all membrane signalling proteins. The evidence supporting the conclusions is compelling, based on the use of a nanodisk system to study membrane proteins in vitro, combined with state-of-the-art single-molecule FRET. The work will be of broad interest to cell biologists and biochemists.

   Reviewed by eLife

2. Explainable machine learning-assisted exploration of chromatin dynamics reveals chromosome-specific response to serum starvation

   This article has 6 authors:

   1. Taras Redchuk
   2. Antti Pennanen
   3. Harri Jäälinoja
   4. Olli Natri
   5. Lassi Paavolainen
   6. Maria K Vartiainen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This interesting study adapts machine learning tools to analyze movements of a chromatin locus in living cells in response to serum starvation. The machine learning approach developed is useful, the experiments are well controlled, and the data are solid. The study would be greatly strengthened by testing key predictions made using perturbation experiments. This work will be of interest to those studying chromosome biology and gene expression patterns.

   Reviewed by eLife

3. Dietary sulfur amino acid restriction elicits a cold-like transcriptional response in inguinal but not epididymal white adipose tissue of male mice

   This article has 5 authors:

   1. Philip MM Ruppert
   2. Aylin S Güller
   3. Marcus Rosendal
   4. Natasa Stanic
   5. Jan-Wilhelm Kornfeld

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The present study employed transcriptomics to investigate the impact of methionine restriction (MR) and cold exposure (CE) on liver and adipose tissues in mice. The authors demonstrate that responses to MR and CE are tissue-specific, while both MR and CE have a similar effect on beige adipose tissue. While these findings are somewhat descriptive, this work is considered important, as it provides a comprehensive resource for enhancing our understanding of these lifestyle interventions. The study is of high scientific quality, and the analyses are convincing.

   Reviewed by eLife

4. Organelle membrane-associated proteins recruit cGAS via phase separation to facilitate its membrane localization

   This article has 4 authors:

   1. Chengrui Shi
   2. Chaofei Su
   3. Kaixiang Zhang
   4. Hang Yin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study investigates how intrinsically disordered domains can interact to dictate the sub-cellular localization of a major innate immune sensor termed cGAS. The data from various cellular and biochemical assays are mostly solid, but the main conclusions from these experiments need to be validated further. This paper is relevant to immunologists, especially those interested in cytosolic DNA-sensing pathways.

   Reviewed by eLife

5. Death receptor 6 does not regulate axon degeneration and Schwann cell injury responses during Wallerian degeneration

   This article has 3 authors:

   1. Bogdan Beirowski
   2. Haoran Huang
   3. Elisabetta Babetto

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this valuable study, through carefully executed and rigorously controlled experiments, the authors challenged a previously reported role of the Death Receptor 6 (DR6/Tnfrsf21) in Wallerian degeneration (WD). Using two DR6 knockout mouse lines and multiple WD assays, both in vitro and in vivo, the authors provided convincing evidence that loss of DR6 in mice does not protect peripheral axons from WD after injury. Questions remain about whether this conclusion is generalizable to CNS axonal degeneration in disease models such as ALS, AD, and prion diseases. In addition, the authors need to provide information about the sex, age, and genetic background of their animal studies to allow readers to better assess the basis for inconsistencies from previous reports on the protective effects of DR6.

   Reviewed by eLife

6. Dynamic Architecture of Mycobacterial Outer Membranes Revealed by All-Atom Simulations

   This article has 3 authors:

   1. Turner P Brown
   2. Matthieu Chavent
   3. Wonpil Im

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In their study, Brown et. al. provide an important advance in understanding the architecture of the mycobacterial outer membrane. Using all-atom simulations of model mycomembranes, the work reports compelling structural insights into how α-mycolic acids and outer leaflet lipids (PDIM and PAT) shape membrane organisation. The work revealed membrane heterogeneity with ordered inner leaflets and disordered outer leaflets that provide a molecular explanation for the resilience of the mycobacterial envelope.

   Reviewed by eLife

7. TrueProbes: Quantitative Single-Molecule RNA-FISH Probe Design Improves RNA Detection

   This article has 5 authors:

   1. Jason J Hughes
   2. Benjamin K Kesler
   3. John E Adams
   4. Blythe G Hospelhorn
   5. Gregor Neuert

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study introduces a computational pipeline for designing RNA in situ fluorescence hybridization probes that could improve the sensitivity and specificity of RNA detection in cells. While the approach is novel and the preliminary data suggestive, the evidence supporting a clear advantage over existing probe design strategies is incomplete. The work will be of interest to researchers developing or using molecular tools for imaging RNA in cells.

   Reviewed by eLife

8. Evolutionary Adaptations of IRG1 Refines Itaconate Synthesis and Mitigates Innate Immunometabolism Trade-offs

   This article has 6 authors:

   1. Richard V Szeligowski
   2. Francois Miros
   3. Andres Saez
   4. Marisa DeCiucis
   5. Gunter P Wagner
   6. Hongying Shen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study addresses the timely and interesting question of how itaconate generation emerged in evolution, using taxonomic analysis of the gene and enzyme cis-aconitate decarboxylase (CAD). The authors provide solid evidence identifying three CAD branches in metazoans and showing that the early metazoan paleo-form indeed generates aconitate and is already linked to innate immunity. They further provide limited evidence suggesting that taxonomic differences in subcellular localisation of this enzyme may allow for innate immune signalling without compromising cellular energetics. The implications of the study will be of high interest to the field of innate host defence and immunometabolism.

   Reviewed by eLife

9. Backward Conditioning Reveals Flexibility in Infralimbic Cortex Inhibitory Memories

   This article has 6 authors:

   1. Nura W Lingawi
   2. Billy C Chieng
   3. R Frederick Westbrook
   4. Nathan M Holmes
   5. Mark E Bouton
   6. Vincent Laurent

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This set of experiments provides important knowledge for how the infralimbic cortex is recruited to inhibit behavior after extinction training. The evidence supporting the conclusions is convincing with multiple sophisticated behavioral designs providing converging lines of evidence, though reviewers note possible alternative interpretations and limitations of small group sizes in some cases. This work will be of interest to those interested in cortical function, learning and memory, aversive behavior, and/or related psychiatric factors.

   Reviewed by eLife

10. When word order matters: human brains represent sentence meaning differently from large language models

    This article has 3 authors:

    1. James Fodor
    2. Carsten Murawski
    3. Shinsuke Suzuki

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This work provides a valuable comparison of sentence structure representations in the human brain and state-of-the-art Large Language Models (LLMs). Based on solid analysis of 7T fMRI data, it systematically identifies sentences in which LLMs underperform relative to models that explicitly code for syntactic structure. The study will be of significant interest to both cognitive neuroscientists and artificial intelligence researchers.

    Reviewed by eLife