eLife

Latest preprint reviews

1. Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics

   This article has 13 authors:

   1. Elena G. Govorunova
   2. Oleg A. Sineshchekov
   3. Hai Li
   4. Yueyang Gou
   5. Hongmei Chen
   6. Shuyuan Yang
   7. Yumei Wang
   8. Stephen Mitchell
   9. Alyssa Palmateer
   10. Leonid S. Brown
   11. François St-Pierre
   12. Mingshan Xue
   13. John L. Spudich

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study describes newly identified light-gated ion channel homologs (channelrhodopsins, ChRs) in several protist species, with a primary focus on the biophysical characterization of ChRs of ancyromonads. The authors employed a powerful combination of bioinformatics, manual and automated patch-clamp electrophysiology, absorption spectroscopy, and flash photolysis. Additionally, they evaluated the applicability of the newly discovered anion-conducting ChRs in cortical neurons of mouse brain slices and in living C. elegans worms. The evidence supporting most of the claims is convincing and this work will be of interest to the microbial rhodopsin community and neuro- and cardioscientists utilizing optogenetics in their research.

   Reviewed by eLife

2. Domain Coupling in Allosteric Regulation of SthK Measured Using Time-Resolved Transition Metal Ion FRET

   This article has 3 authors:

   1. Pierce Eggan
   2. Sharona E. Gordon
   3. William N. Zagotta

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful work employs transition-metal FRET (tmFRET) to study the cyclic nucleotide binding domain (CNBD) of a bacterial ion channel. The authors employ lifetime measurements of fluorescence to extend their own prior study and observe distance changes within the CNBD domains of a full-length channel; they base these measurements on changes in lifetimes due to tmFRET between a metal at an introduced chelator site and a fluorescent non-canonical amino acid at another site within the channel sequence. This allows the authors to show that coupling of the CNBDs to the rest of the channel stabilizes the CNBDs in their active state relative to an isolated CNBD construct. The data are compelling and of high quality, and support the authors' conclusions.

   Reviewed by eLife

3. Identification and classification of ion-channels across the tree of life: Insights into understudied CALHM channels

   This article has 10 authors:

   1. Rahil Taujale
   2. Sung Jin Park
   3. Nathan Gravel
   4. Saber Soleymani
   5. Rayna Carter
   6. Kennady Boyd
   7. Sarah Keuning
   8. Zheng Ruan
   9. Wei Lü
   10. Natarajan Kannan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The first part of this manuscript describes an interdisciplinary approach to mine the human channelome and discover further ion channel orthologues across diverse organisms. Although the findings and data curation enabled by the new approach are valuable to the ion channel community, as well as to those interested in improved methods for mining sequence space for their protein of interest, this part of the work is incomplete because critical methodological information is missing. Further validation of the improvements this approach shows over others is needed. The second part of the manuscript utilizes the approach described in the first part to delineate co-conserved amino acid patterns in CALHM channels, but the evidence provided to support the role of the identified residues in channel gating is currently inadequate.

   Reviewed by eLife

4. Spiral-eyes: A soft active matter model of in vivo corneal epithelial cell migration

   This article has 4 authors:

   1. Kaja Kostanjevec
   2. Rastko Sknepnek
   3. Jon Martin Collinson
   4. Silke Henkes

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study describes a physical mechanism for the emergence of spiral patterns in the outer epithelial layer of the mammalian cornea independent of pre-patterning or guidance cues, using an agent-based model of self-propelled particles with alignment. The model is well constructed, however the central premise of the manuscript, that the spiral patterning of epithelial corneal cells occurs without guidance cues, is incomplete and not fully supported. Several significant questions remain unanswered, such as the role of the corneal curvature or the importance of topological defects. Furthermore, comparison between the model and data are qualitative at best for the moment.

   Reviewed by eLife, preLights

5. A tissue boundary orchestrates the segregation of inner ear sensory organs

   This article has 5 authors:

   1. Ziqi Chen
   2. Magdalena Żak
   3. Shuting Xu
   4. Javier de Andrés
   5. Nicolas Daudet

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study is a first report investigating the boundary formation between sensory and non-sensory tissues of the inner ear, which has broad relevance to the developmental field in general. All three reviewers thought the results and data analyses presented are solid. However, the causal relationship between the morphological evidence and the role of Lmx1a is not well supported by the results. The mechanism linking Lmx1a to ROCK is also incomplete, considering ROCK is involved in so many processes.

   Reviewed by eLife

6. Shifting the PPARγ conformational ensemble towards a transcriptionally repressive state improves covalent inhibitor efficacy

   This article has 10 authors:

   1. Liudmyla Arifova
   2. Brian S MacTavish
   3. Zane Laughlin
   4. Mithun Nag Karadi Giridhar
   5. Jinsai Shang
   6. Min-Hsuan Li
   7. Xiaoyu Yu
   8. Di Zhu
   9. Theodore M Kamenecka
   10. Douglas J Kojetin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript presents a fundamental advance in our understanding of nuclear receptor pharmacology by expanding on previous work demonstrating dual ligand occupancy in the peroxisome proliferator-activated receptor-gamma (PPARγ). Using a compelling combination of biophysical, structural, and cellular approaches, the authors show that covalent inhibitors with inverse agonist activities modulate receptor conformation to permit co-binding with additional ligands, leading to a finely tuned transcriptional response. The data support a model of proximal, bi-directional allostery that challenges traditional views of nuclear receptor regulation. These findings will be of broad interest to researchers in structural biology, transcriptional control, and drug discovery.

   Reviewed by eLife

7. Human giant GTPase GVIN1 forms an antimicrobial coatomer around the intracellular bacterial pathogen Burkholderia thailandensis

   This article has 6 authors:

   1. Weilun Guo
   2. Shruti S Apte
   3. Mary S Dickinson
   4. So Young Kim
   5. Miriam Kutsch
   6. Jörn Coers

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a fundamental discovery revealing two independent IFNγ-induced pathways that restrict bacterial motility: one GBP1-dependent and the other GVIN1-dependent. The findings are supported by compelling evidence. While the paper is already very strong, there are a few points that could be addressed editorially or through the addition of a few key experiments.

   Reviewed by eLife

8. Protein Language Model Identifies Disordered, Conserved Motifs Driving Phase Separation

   This article has 3 authors:

   1. Yumeng Zhang
   2. Jared Zheng
   3. Bin Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study presents an analysis of evolutionary conservation in intrinsically disordered regions, identified as key drivers of phase separation, leveraging a protein language model. The strength of evidence is potentially compelling, but a clearer justification of the methods and analyses is needed to fully support the main claims.

   Reviewed by eLife

9. Repression of the Wnt pathway effector TCF7L2 reverses lethal cachexia in mice with intestinal cancers

   This article has 3 authors:

   1. Mei Ling Leong
   2. Christiane Ruedl
   3. Klaus Karjalainen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this valuable study, the authors demonstrate that TCF7L2 plays a role in the pathogenesis of cachexia in a mouse model of GI cancer. The results are solid, although future studies will need further mechanistic analyses. These data will be interesting to cancer biologists, especially those trying to understand late-stage complications such as cachexia and wasting, a major cause of cancer morbidity and mortality.

   Reviewed by eLife

10. Monocyte-derived macrophage recruitment mediated by TRPV1 is required for eardrum wound healing

    This article has 6 authors:

    1. Yunpei Zhang
    2. Pingting Wang
    3. Lingling Neng
    4. Kushal Sharma
    5. Allan Kachelmeier
    6. Xiaorui Shi

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study exploring the role of TRPV1 signaling in recruiting macrophages and promoting angiogenesis during tympanic membrane wound healing presents useful findings. However, the strength of evidence supporting the central claims is incomplete, as the mechanistic links between TRPV1 activation and immune cell recruitment remain largely correlative and rely heavily on previously published datasets without sufficient functional validation. The work will be of interest to researchers studying wound healing and sensory-immune interactions, though substantial revisions are needed to support its broader significance.

    Reviewed by eLife