eLife

Latest preprint reviews

1. ahctf1 and kras mutations combine to amplify oncogenic stress and restrict liver overgrowth in a zebrafish model of hepatocellular carcinoma

   This article has 16 authors:

   1. Kimberly J Morgan
   2. Karen Doggett
   3. Fansuo Geng
   4. Stephen Mieruszynski
   5. Lachlan Whitehead
   6. Kelly A Smith
   7. Benjamin M Hogan
   8. Cas Simons
   9. Gregory J Baillie
   10. Ramyar Molania
   11. Anthony T Papenfuss
   12. Thomas E Hall
   13. Elke A Ober
   14. Didier YR Stainier
   15. Zhiyuan Gong
   16. Joan K Heath

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Here, Morgan and colleagues report a novel synthetic lethal interaction between nucleoporin inhibition and KRAS-driven hepatocyte hyperproliferation. The authors show that nucleoporin inhibitor treatment or heterozygosity of nucleoporin genes (ahctf1 and/or ranbp2) suppresses KRAS-driven zebrafish larval liver overgrowth, providing impetus for developing Nup inhibitors as hepatocellular carcinoma treatment. Their data provide insights into the consequences of nucleoporin inhibition in cancer, demonstrating that disrupting ahctf1 decreases proliferation and promotes apoptosis by impairing nuclear pore formation and mitotic spindle assembly through a mechanism that may be at least partially dependent on tp53.

   Reviewed by eLife

2. Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota

   This article has 16 authors:

   1. Daniel Hoces
   2. Giorgia Greter
   3. Markus Arnoldini
   4. Melanie L Stäubli
   5. Claudia Moresi
   6. Anna Sintsova
   7. Sara Berent
   8. Isabel Kolinko
   9. Florence Bansept
   10. Aurore Woller
   11. Janine Häfliger
   12. Eric Martens
   13. Wolf-Dietrich Hardt
   14. Shinichi Sunagawa
   15. Claude Loverdo
   16. Emma Slack

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study addresses whether the composition of the microbiota influences the intestinal colonization of encapsulated vs unencapsulated Bacteroides thetaiotaomicron, a resident micro-organism of the colon. This is an important question because factors determining the colonization of gut bacteria remain a critical barrier in translating microbiome research into new bacterial cell-based therapies. To answer the question, the authors develop an innovative method to quantify B. theta population bottlenecks during intestinal colonization in the setting of different microbiota. Their main finding that the colonization defect of an acapsular mutant is dependent on the composition of the microbiota is valuable and this observation suggests that interactions between gut bacteria explains why the mutant has a colonization defect. The evidence supporting this claim is currently insufficient. Additionally, some of the analyses and claims are compromised because the authors do not fully explain their data and the number of animals is sometimes very small.

   Reviewed by eLife

3. Prediction of diabetic kidney disease risk using machine learning models: A population-based cohort study of Asian adults

   This article has 7 authors:

   1. Charumathi Sabanayagam
   2. Feng He
   3. Simon Nusinovici
   4. Jialiang Li
   5. Cynthia Lim
   6. Gavin Tan
   7. Ching Yu Cheng

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     There is an urgent need to improve prognostication of diabetic kidney disease in different diverse populations so this study is valuable in identifying specific predictive factors in a cohort of South East Asian populations whose baseline risk is higher. There are some limitations: the assumptions the authors make and the methods would benefit from some more investigation/validation.

   Reviewed by eLife

4. Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation

   This article has 12 authors:

   1. Marco Caligaris
   2. Raffaele Nicastro
   3. Zehan Hu
   4. Farida Tripodi
   5. Johannes Erwin Hummel
   6. Benjamin Pillet
   7. Marie-Anne Deprez
   8. Joris Winderickx
   9. Sabine Rospert
   10. Paola Coccetti
   11. Jörn Dengjel
   12. Claudio De Virgilio

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This is an important study that shows how Snf1/AMP Kinase fine-tunes TORC1 signaling in response to glucose starvation. Their observation that Snf1 phosphorylation of the TORC regulator Pib1 and the TORC effector kinase Sch9 provides new mechanistic information on this important pathway involved in cell growth. The combination of phosphoproteomics, genetic, biochemical, and physiological experiments is generally convincing, although the results with the Pib2 SA and SE mutants are somewhat inconsistent.

   Reviewed by eLife

5. Chloride ions evoke taste sensations by binding to the extracellular ligand-binding domain of sweet/umami taste receptors

   This article has 7 authors:

   1. Nanako Atsumi
   2. Keiko Yasumatsu
   3. Yuriko Takashina
   4. Chiaki Ito
   5. Norihisa Yasui
   6. Robert F Margolskee
   7. Atsuko Yamashita

   This article has been curated by 2 groups:

   • Curated by eLife

     eLife assessment

     This fundamental study presents solid evidence for T1r (sweet /umami) taste receptors as chloride (Cl-) receptors, based on a combination of state-of-the-art techniques to demonstrate that T1r receptors from Medaka fish bind chloride and that this binding induces a conformational change in the heteromeric receptor. This conformational change leads to low-concentration chloride-specific action potential firing in nerves from neurons containing these receptors in mice, results that represent an important advance in our understanding of the logic of taste perception.

   • Curated by Biophysics Colab

     Endorsement statement (17 November 2022)

     The preprint by Atsumi et al. describes how chloride binding to sweet- and umami-sensing proteins (T1R taste receptors) can evoke taste sensation. The authors use an elegant combination of structural, biophysical and electrophysiological approaches to locate a chloride binding site in the ligand-binding domain of medaka fish T1r2a/3 receptors. They convincingly show that low mM concentrations of chloride induce conformational changes and, using single fiber recordings, establish that mouse chorda tympani nerves are activated by chloride in a T1R-dependent manner. This suggests that chloride binding to sweet receptors could mediate the commonly reported sweet taste sensation following ingestion of low concentrations of table salt. The findings will be of broad relevance to those studying taste sensation and ligand recognition in GPCRs.

     (This endorsement by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

   Reviewed by eLife, Biophysics Colab

6. Smart squirrels use a mortise-tenon structure to fix nuts on understory twigs

   This article has 10 authors:

   1. Han Xu
   2. Lian Xia
   3. John R. Spence
   4. Mingxian Lin
   5. Chunyang Lu
   6. Yanpeng Li
   7. Jie Chen
   8. Tushou Luo
   9. Yide Li
   10. Suqin Fang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study presents a potentially interesting contribution on animal caching behaviour. At present, evidence that the flying squirrels themselves modified the nuts is incomplete, but there are clear video observations of them associating with the nuts. Either way, the images of the modified nuts and the detailed descriptions of the caching behaviour describe a new technique for storing nuts in a tropical rainforest.

   Reviewed by eLife

7. Ancient trans-species polymorphism at the Major Histocompatibility Complex in primates

   This article has 2 authors:

   1. Alyssa Lyn Fortier
   2. Jonathan K Pritchard

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important manuscript presents a thorough analysis of trans-specific polymorphism (TSP) in Major Histocompatibility Complex gene families across primates. The analysis makes the most of currently available genomic data and methods to substantially increase the amount and evolutionary time that TSPs can be observed. Both false negative TSPs due to missing genes at the assembly and/or annotation level, as well as false positives due to read mismapping with missing paralogs, are well assessed and discussed. Overall the evidence provided is compelling, and the manuscript clearly delineates the path for future progress on the topic.

   Reviewed by eLife

8. A frameshift in Yersinia pestis rcsD alters canonical Rcs signalling to preserve flea-mammal plague transmission cycles

   This article has 7 authors:

   1. Xiao-Peng Guo
   2. Hai-Qin Yan
   3. Wenhui Yang
   4. Zhe Yin
   5. Viveka Vadyvaloo
   6. Dongsheng Zhou
   7. Yi-Cheng Sun

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study substantially advances our understanding of the phenotypic divergence of the plague-causing bacterium, Yersinia pestis, from a closely related species, Yersinia pseudotuberculosis, which causes much milder disease. The authors provide convincing evidence that a frameshift mutation in the Y. pestis rcsD gene changes a signaling pathway that contributes to the flea-mammal transmission of plague. The work shows how small genetic differences can alter pathogenicity and stress survival.

   Reviewed by eLife

9. Synchronous multi-segmental activity between metachronal waves controls locomotion speed in Drosophila larvae

   This article has 5 authors:

   1. Yingtao Liu
   2. Eri Hasegawa
   3. Akinao Nose
   4. Maarten F Zwart
   5. Hiroshi Kohsaka

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Exploiting the power of the Drosophila larva as a model, Liu et al.'s important study sheds light on the neuronal mechanisms of speed regulation during locomotion. The data obtained using a combination of functional and structural approaches are mostly rigorous and convincing, but there are concerns about the small number of animals analysed in some of the behavioural experiments.

   Reviewed by eLife

10. Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis

    This article has 8 authors:

    1. Sana Naderi
    2. Peter E Chen
    3. Carmen Lia Murall
    4. Raphael Poujol
    5. Susanne Kraemer
    6. Bradley S Pickering
    7. Selena M Sagan
    8. B Jesse Shapiro

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This important study offers compelling evidence, in the form of a rigorous and clear analysis of SARS-CoV-2 mutations observed within non-human animal hosts, of viral mutations that may provide an adaptive advantage within hosts. The authors could, however, improve the description of some elements of their methods and analysis approach, and they should cite additional relevant literature. The findings are relevant to those interested in the ecology of infectious disease, epidemiology, and specifically those who are interested in the genetic underpinnings of pandemic potential.

    Reviewed by eLife