eLife

Latest preprint reviews

1. Translation of dipeptide repeat proteins in C9ORF72 ALS/FTD through unique and redundant AUG initiation codons

   This article has 8 authors:

   1. Yoshifumi Sonobe
   2. Soojin Lee
   3. Gopinath Krishnan
   4. Yuanzheng Gu
   5. Deborah Y Kwon
   6. Fen-Biao Gao
   7. Raymond P Roos
   8. Paschalis Kratsios

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study by Sonobe et al uses transfected cells and patient iPSC-derived neurons to define mechanisms underlying translation of the antisense C4G2 RNA strand expressed in C9orf72-associated ALS and FTD. The authors design a series of constructs to explore the start codon required to produce toxic PR and prominent PG dipeptides in disease. Using these constructs they provide solid data that translation in the PR and PG reading frames occur due to the presence of AUG codons within the 5'UTR of the RNA strand. However, in its current form the paper is incomplete and the conclusions require additional experimental support.

   Reviewed by eLife

2. We couldn't get details of this article at this time:
   10.1101/2022.09.17.508382

3. Competitive interactions between culturable bacteria are highly non-additive

   This article has 3 authors:

   1. Amichai Baichman-Kass
   2. Tingting Song
   3. Jonathan Friedman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study presents an interesting example of how complexities of communities may be reduced by showing that the joint effects of two or more species on a focal species are generally not additive, but rather dominated by the strongest single effect. The evidence, enabled by over 14,000 measurements using nanodroplet-based microfluidics, is compelling, although the generality of the conclusion awaits further studies. This paper is of interest to microbial ecologists.

   Reviewed by eLife

4. Structure of Dunaliella photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes

   This article has 4 authors:

   1. Ido Caspy
   2. Maria Fadeeva
   3. Yuval Mazor
   4. Nathan Nelson

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The work of Caspy and coworkers resolves the cryo-EM structures of stacked and unstacked PSII supercomplexes of Dunaliella, revealing unexpected connectivity and conformational flexibility, with intriguing implications for the function and regulation of photosynthesis.

   Reviewed by eLife

5. Multimodal mapping of cell types and projections in the central nucleus of the amygdala

   This article has 11 authors:

   1. Yuhan Wang
   2. Sabine Krabbe
   3. Mark Eddison
   4. Fredrick E Henry
   5. Greg Fleishman
   6. Andrew L Lemire
   7. Lihua Wang
   8. Wyatt Korff
   9. Paul W Tillberg
   10. Andreas Lüthi
   11. Scott Sternson

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study uses top-notch spatial profiling methods to present a valuable account of the number of different neuron types in the central nucleus of the amygdala of the mouse. The approaches and evidence presented are compelling, but the analysis is incomplete and would benefit from increases in sample size. With this aspect strengthened, this paper would be of interest to neuroscientists investigating the function of the central amygdala.

   Reviewed by eLife

6. 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

7. 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

8. 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

9. 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

10. 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