eLife

Latest preprint reviews

1. NUDT2 loss defines quantitative limits for dinucleoside polyphosphate action on the cGAS–STING–TBK1 axis

   This article has 10 authors:

   1. Paul Weiland
   2. Renuka Dharani Shivakumar
   3. Ekaterina Jalomo-Khayrova
   4. Julia Schmidt
   5. Victor Zegarra
   6. Ying Wang
   7. Nicole Paczia
   8. Stephan Kiontke
   9. Andreas Burchert
   10. Gert Bange

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study investigates the role of dinucleoside polyphosphates in regulating the cGAS-STING-TBK1 axis of innate immunity. The data collected using multiple biochemical and cellular assays, plus X-ray crystallography, are solid, but testing additional polyphosphates and using NUDT2KO cells will further strengthen the main conclusion. This paper will be broadly relevant to those studying various innate immune pathways.

   Reviewed by eLife

2. Multimodal temporal modeling of behavioral reorganization across threat learning and extinction in rats

   This article has 3 authors:

   1. Bin Yin
   2. Jiaojiao Rao
   3. X.T. (XiaoTian) Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study applies a hidden Markov model to freezing, ultrasonic vocalizations, and lever pressing in male rats to ask whether fear extinction restores normal behavior or only suppresses defensive responding. The evidence is incomplete because the model states are not related back to raw behavior or group manipulations, and the states are not tested as predictors of relapse. The work will be of interest to researchers studying fear extinction and computational approaches to behavior.

   Reviewed by eLife

3. Phylogenomics of free-living neobodonids reveals they are a paraphyletic group from which all other metakinetoplastids are descended

   This article has 6 authors:

   1. Daryna Zavadska
   2. Julia A Packer
   3. Daria Tashyreva
   4. Ryoma Kamikawa
   5. Alastair Simpson
   6. Daniel J Richter

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study substantially improves the phylogenetic framework for Kinetoplastea through greatly expanded sampling of free-living neobodonids; the phylogenomic analyses provide convincing evidence that neobodonids are paraphyletic and establish a substantially revised framework for deep relationships within Metakinetoplastina. The work forms the foundation for future comparative studies of kinetoplastid evolution and systematics, although its implications for the origins of parasitism should not be overstated. An 18S rRNA phylogeny documenting the placement of the newly sampled strains within previously recognized neobodonid lineages and/or confirmation of the principal topology using a well-documented phylogenomic set of marker genes would further strengthen the study. The work will be of particular interest to researchers studying protist evolution and the evolutionary context of trypanosomatids.

   Reviewed by eLife

4. Phosphorylation and pocket-binding ligands rewire the coupled networks in multidomain protein condensate

   This article has 3 authors:

   1. Yu Cao
   2. Jinyu Chen
   3. Xiakun Chu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study uses coarse-grained molecular simulations to investigate how phosphorylation and small-molecule ligands reshape the interactions underlying condensation and multidomain assembly of HDAC6. The findings provide mechanistic insights into how modifications of intrinsically disordered regions and ligand binding may regulate protein condensation. The evidence is solid: although the simulations broadly agree with previous experimental observations, concerns about model robustness and sampling in full-length assemblies limit support for the proposed mechanism and its pharmacological implications.

   Reviewed by eLife

5. Penumbria: Advanced 3D cell segmentation for biomedical imaging

   This article has 3 authors:

   1. Laurids Stockert
   2. Joseph Donovan
   3. Herwig Baier

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study presents Penumbria, a method for segmenting cells in three-dimensional microscopy images, released with publicly available code and documentation. The implementation is technically sound, and the reported performance gains would be a welcome contribution; the advance is incremental, since regression on distances to boundaries is already widespread in the field. The evidence is incomplete: the main text does not state which setting it used for the main competing method, and the setting used is the one that handles data of this kind poorly, so the central claim of better accuracy is unsettled; current leading methods are missing from the comparison; and five architectural and training choices are combined without attributing the gains to any of them. Every evaluation dataset labels nuclei, so the work should present itself as nuclei segmentation; describing and completing the comparisons, and attributing the gains, would raise the strength of evidence.

   Reviewed by eLife

6. Wnt/beta-catenin signaling regulates Vascular Endothelial Growth Factor (VEGF) receptors in central nervous system endothelial cells

   This article has 5 authors:

   1. Yanshu Wang
   2. Ningyu Zhu
   3. Amir Rattner
   4. Philip M Smallwood
   5. Jeremy Nathans

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides important novel insight into how Wnt/beta-catenin signaling may regulate the responsiveness of blood vessels in the brain and retina to vascular endothelial growth factor, with potential relevance to Wnt surrogate therapies aimed at restoring vascular barriers. Solid evidence that Wnt/beta-catenin signaling changes the protein abundance and relative balance of two vascular endothelial growth factor receptors in brain blood vessels is provided by informative genetic mosaic experiments; in the retina, however, regulation of VEGFR2 was difficult to establish because expression by neighboring cells obscured its detection in blood vessels. Physiological implications are discussed, but evidence remains incomplete because the observed changes in receptor abundance were not directly linked to altered signaling or vascular function in living animals. A second mechanism, in which Wnt/beta-catenin signaling suppresses signaling through VEGFR2 with little or no change in receptor abundance, was inferred from reporter experiments in cell-based systems.

   Reviewed by eLife

7. Gene function and expression profiling in yeast spores, killifish diapause embryos, and their post-dormant offspring cells

   This article has 9 authors:

   1. Shaimaa Hassan
   2. Maria Rodriguez-López
   3. StJohn Townsend
   4. Büşra Köksal
   5. Sezin Akkus
   6. Alessandro Ori
   7. Alessandro Cellerino
   8. Markus Ralser
   9. Jürg Bähler

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study used several genome-wide approaches to compare dormancy in S. pombe spores and killifish diapause embryos. The findings include a trade-off between longevity and heat resistance in yeast spores and, in both these systems, a relatively higher expression of ribosomal-protein mRNAs but not proteins. While the evidence for the findings is overall solid, some interpretations should still be tempered. The large-scale datasets provide an excellent resource for future research in the dormancy field.

     [Editors' note: this paper was reviewed by Review Commons.]

   Reviewed by eLife

8. P95-HER2 promotes metastatic progression by biasing MRTFA dependent signaling

   This article has 15 authors:

   1. Joseph D Fernandes
   2. Erin Bresnahan
   3. Hillary Zawada
   4. Joshua D Ginzel
   5. H Kim Lyerly
   6. Bruce W Rogers
   7. Shyam M Kavuri
   8. Allison J Introne
   9. Melanie R Sadecki
   10. Hidetoshi Mori
   11. Glenn Doherty
   12. Alexander D Borowsky
   13. Kevin B Flores
   14. Jose Javier Bravo-Cordero
   15. Joshua C Snyder

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study with implications for signal transduction, breast cancer, and metastasis research. The study uses cell lines from the innovative HER2BOW model mouse to compare and contrast properties of mouse mammary tumors induced by wt-HER2, dex16-HER2, and p95-HER2. The study involves mechanistic approaches that are convincing for distinguishing signaling from dex16-HER2 and p95-HER2; this will be of interest to the cancer field.

   Reviewed by eLife

9. Whole human organ clearing and multimodal mapping

   This article has 10 authors:

   1. Héloïse Policet-Bétend
   2. Tomàs Jordà-Siquier
   3. Geraldine Cuenu
   4. Maeva Badré
   5. Sami Schranz
   6. Julien Da Costa
   7. Céline Brockmann
   8. Pascal Senn
   9. Daniel Huber
   10. Christophe M Lamy

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important paper introduces a generalisable tissue-clearing method to study human anatomy and the organisation of complex tissues and organs. The evidence for its broad applicability is compelling, based on results from 15 diverse human tissues, including highly heterogeneous specimens, with successful labelling using five antibodies and five fluorescent dyes. The method has broad potential applications across multiple disciplines.

   Reviewed by eLife

10. Structures of LolB bound to LolA or lipoprotein provide insight into the final steps of bacterial lipoprotein trafficking

    This article has 4 authors:

    1. Abigail E Jepson
    2. Elise Kaplan
    3. Nicholas P Greene
    4. Vassilis Koronakis

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This is a valuable study that aims to resolve the mechanistic details of the final steps of bacterial lipoprotein trafficking. The evidence supporting the conclusions is mostly solid but support for other claims is incomplete. This work will be of interest to biochemists and microbiologists studying the bacterial cell envelope and those aiming to develop novel antibacterial molecules.

    Reviewed by eLife