eLife

Latest preprint reviews

1. Somatic hypermutation patterns in immunoglobulin variable regions are established independently of the local transcriptional landscape

   This article has 15 authors:

   1. Ursula E Schoeberl
   2. Johanna Fitz
   3. Kimon Froussios
   4. Renan Valieris
   5. Iordanis Ourailidis
   6. Marina Makharova
   7. Bernd Bauer
   8. Tobias Neumann
   9. Eva-Maria Wiedemann
   10. Monika Steininger
   11. Adriana Cantoran Garcia
   12. Marialaura Mastrovito
   13. Hugo Mouquet
   14. Israel Tojal Da Silva
   15. Rushad Pavri

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study clarifies that stalled RNA pol II is not sufficient for AID targeting, which is important to the field. The authors provide solid experimental evidence that RNA poll II stalling is not the driving mechanism for AID targeting, and even though the results are generally "negative", they are highly relevant to our current understanding of SHM. The authors propose premature transcription termination as a possible mechanism to determine V gene mutability, but the study does not experimentally address such possibilities. This paper makes investigators rethink the model with which AID finds single-strand DNA in the genome.

   Reviewed by eLife

2. Structural mechanism of strand exchange by the RAD51 filament

   This article has 4 authors:

   1. Luay Joudeh
   2. Robert E Appleby
   3. Joseph D Maman
   4. Luca Pellegrini

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This landmark study describes the structure of the human RAD51 filament with a recombination intermediate called the displacement loop (D-loop). Using cryogenic structural, biochemical, and single-molecule analyses, the authors provide compelling evidence on how the RAD51 filament promotes strand exchange between single-stranded and double-stranded DNAs. The findings are highly relevant to the fields of homologous recombination, DNA repair, and genome stability.

   Reviewed by eLife

3. Hatching with Numbers: Pre-natal Light Exposure Affects Number Sense and the Mental Number Line in young domestic chicks

   This article has 4 authors:

   1. Rosa Rugani
   2. Matteo Macchinizzi
   3. Yujia Zhang
   4. Lucia Regolin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental study demonstrates how a left-right bias in the relationship between numerical magnitude and space depends on brain lateralization. The evidence is compelling and will be of interest to researchers studying numerical cognition, brain lateralization, and cognitive brain development more broadly.

   Reviewed by eLife

4. Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models

   This article has 6 authors:

   1. Abolfazl Ziaeemehr
   2. Marmaduke Woodman
   3. Lia Domide
   4. Spase Petkoski
   5. Viktor Jirsa
   6. Meysam Hashemi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This paper presents a valuable software package, named "Virtual Brain Inference" (VBI), that enables faster and more efficient inference of parameters in dynamical system models of whole-brain activity, grounded in artificial network networks for Bayesian statistical inference. The authors have provided solid evidence, across several case studies, for the utility and validity of the methods using simulated data from several commonly used models, but more thorough benchmarking could be used to demonstrate the reliability, generalizability, and practical utility of the toolkit. This work will be of interest to computational neuroscientists interested in modelling large-scale brain dynamics.

   Reviewed by eLife

5. Population-level morphological analysis of paired CO2- and odor-sensing olfactory neurons in D. melanogaster via volume electron microscopy

   This article has 7 authors:

   1. Jonathan Choy
   2. Shadi Charara
   3. Kalyani Cauwenberghs
   4. Quintyn McKaughan
   5. Keun-Young Kim
   6. Mark H Ellisman
   7. Chih-Ying Su

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study reveals surprising morphological diversity of Drosophila sensory neurons. Using serial block-face electron microscopy, the authors created detailed 3D reconstructions of large neuronal populations, convincingly finding significant structural variation both within and across distinct classes. These results form the basis for testable hypotheses on how neuronal arborization is optimized for particular sensory functions. This research will be highly relevant to biologists in the fields of physiology, insect chemosensation, and neuroscience.

   Reviewed by eLife

6. Cerebellar Purkinje cell stripe patterns reveal a differential vulnerability and resistance to cell loss during normal aging in mice

   This article has 6 authors:

   1. Sarah G Donofrio
   2. Cheryl Brandenburg
   3. Amanda M Brown
   4. Tao Lin
   5. Hsiang-Chih Lu
   6. Roy V Sillitoe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable findings on the patterned loss of Purkinje cells in the mouse cerebellum during aging. Convincing evidence shows that Purkinje cell loss with aging occurs in a pattern of parasagittal stripes in relationship with the zebrin-II expression pattern. Further evidence supporting the Purkinje cell aging loss pattern as it relates to human cerebellar aging would strengthen the study.

   Reviewed by eLife

7. Locus coeruleus modulation of single-cell representation and population dynamics in the mouse prefrontal cortex during attentional switching

   This article has 5 authors:

   1. Marco Nigro
   2. Lucas Silva Tortorelli
   3. Machhindra Garad
   4. Natalie E Zlebnik
   5. Hongdian Yang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding on how the locus coeruleus modulates the involvement of medial prefrontal cortex in set shifting using calcium imaging. The evidence supporting the claims was viewed as incomplete, although a more rigorous statistical comparison of intradimensional vs. extradimensional stages of the task, either in behavior or in the calcium imaging data, would help to address this concern. The work is of broad interest to those studying flexible cognition.

   Reviewed by eLife

8. Atherosclerosis, Intracranial Aneurysms, and Intermediate Biomarkers: Real-World Observational and Mendelian Randomization Research

   This article has 10 authors:

   1. Wei Liu
   2. Zhaoxu Zheng
   3. Chenglong Liu
   4. Yuanren Zhai
   5. Shuang Wang
   6. Liangran Huang
   7. Rong Wang
   8. Yan Zhang
   9. Peicong Ge
   10. Dong Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is valuable work with theoretical implications for possible mediation by MMP12 in the link between atherosclerosis and intracranial aneurysms, using Mendelian Randomization for causal inference. Additional analysis would be required to verify the claims, which currently have incomplete support in terms of the strength of evidence. Given that most of the identified causal associations do not hold after correcting for multiple tests, the conclusions should be carefully reviewed in order to be fully supported by the results.

   Reviewed by eLife

9. Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes

   This article has 4 authors:

   1. Vikram Dalal
   2. Brandon K Tan
   3. Hanrui Xu
   4. Wayland WL Cheng

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The reported cryo-EM imaging of a pentameric ligand-gated ion channel in liposomes as opposed to nanodiscs has both broad implications and contributes valuable methodological advances to the structural investigation of membrane receptors. The comparison of structures assigned to distinct functional states in liposomes versus nanodiscs is convincing and will aid membrane protein structural biologists in selection of functionally relevant membrane reconstitution environments.

   Reviewed by eLife

10. Chemostat culturing reduces fecal eukaryotic virus load and delays diarrhea after virome transplantation

    This article has 13 authors:

    1. Simone Margaard Offersen
    2. Signe Adamberg
    3. Malene Roed Spiegelhauer
    4. Xiaotian Mao
    5. Torben Sølbeck Rasmussen
    6. Frej Larsen
    7. Jingren Zhong
    8. Duc Ninh Nguyen
    9. Dennis Sandris Nielsen
    10. Lise Aunsholt
    11. Thomas Thymann
    12. Kaarel Adamberg
    13. Anders Brunse

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      In this valuable study, the authors report on an innovative chemostat propagation system to reduce eukaryotic viruses while retaining phages in mixtures used for FVTs (fecal virome transplant). The authors hypothesized that chemostat-propagated viromes could modulate the gut microbiota and reduce necrotizing enterocolitis (NEC) lesions while avoiding potential side effects, such as earlier onset of diarrhea. The study is solid in that it integrates in vitro fermentation, high-resolution metagenomics, immunogenicity assays, and in vivo validation, demonstrating the potential of FVT using eukaryotic-free virome-based therapeutics. However, the study overall has some conceptual and technical limitations.

    Reviewed by eLife