eLife

Latest preprint reviews

1. Latent gammaherpesvirus exacerbates arthritis through modification of age-associated B cells

   This article has 5 authors:

   1. Isobel C Mouat
   2. Zachary J Morse
   3. Iryna Shanina
   4. Kelly L Brown
   5. Marc S Horwitz

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study could help shed light on mechanistic connections between latent infection by EBV with an age-dependent autoimmune condition, such as rheumatoid arthritis. The authors use two models: a murine model of rheumatoid arthritis (CIA), and a murine analog of human EBV: 𝜸HV68. The use of these two models allows the investigation of how latent viral infection exacerbates the autoimmune condition via the action of a special class of B cells: Age-associated B cells.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

2. A transient postnatal quiescent period precedes emergence of mature cortical dynamics

   This article has 11 authors:

   1. Soledad Domínguez
   2. Liang Ma
   3. Han Yu
   4. Gabrielle Pouchelon
   5. Christian Mayer
   6. George D Spyropoulos
   7. Claudia Cea
   8. György Buzsáki
   9. Gordon Fishell
   10. Dion Khodagholy
   11. Jennifer N Gelinas

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors use dense electrode recordings in young mice and EEG recordings in human infants to quantitatively describe the transition from immature patterns of brain activity in sleep to more mature patterns. Interestingly, they find an intervening period when overall activity declines in both species. This study is interesting because it enriches our relatively impoverished view of how mature activity patterns emerge during development. However, reviewers expressed concerns that further work was need to rule out potential artifacts of the surgical and recording techniques used in the animal experiments.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

3. Closed-loop auditory stimulation method to modulate sleep slow waves and motor learning performance in rats

   This article has 7 authors:

   1. Carlos G Moreira
   2. Christian R Baumann
   3. Maurizio Scandella
   4. Sergio I Nemirovsky
   5. Sven Leach
   6. Reto Huber
   7. Daniela Noain

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes their phase-targeted closed-loop auditory stimulation protocol to alter slow wave oscillations in rodents. This manuscript provides a set of proof-of-concept data for a rodent model of closed-loop auditory stimulation during sleep as a method for augmenting NREM sleep thalamocortical oscillations and its behavioral effect on a motor task. The strongest contribution of this study to the field is that it provides a technical basis for future studies to be carried out which actually explore the neurobiological underpinnings of CLAS in detail. Applying this tool to rodent research in future studies may allow for bridging some of the putative mechanisms underlying memory consolidation (e.g., replay during NREM sleep) and behavioral changes observed with sleep (e.g., improved hippocampus-dependent memory). It's also nice to have a non-invasive way to manipulate sleep, particularly to translate rodent research to clinical work.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

4. Phosphoproteomics of ATR signaling in mouse testes

   This article has 11 authors:

   1. Jennie R Sims
   2. Vitor M Faça
   3. Catalina Pereira
   4. Carolline Ascenção
   5. William Comstock
   6. Jumana Badar
   7. Gerardo A Arroyo-Martinez
   8. Raimundo Freire
   9. Paula E Cohen
   10. Robert S Weiss
   11. Marcus B Smolka

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study describes a phosphoproteomic analysis of the ATR kinase signaling pathway in mouse testis. The study is well designed and performed, the manuscript is properly constructed and written, and the conclusions are supported by the data. The phosphoproteomic data obtained will be very useful resource for the DNA repair, meiosis, and reproductive biology communities studying the roles of the ATR-dependent DNA damage response pathway.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

5. Relating multivariate shapes to genescapes using phenotype-biological process associations for craniofacial shape

   This article has 12 authors:

   1. Jose D Aponte
   2. David C Katz
   3. Daniela M Roth
   4. Marta Vidal-García
   5. Wei Liu
   6. Fernando Andrade
   7. Charles C Roseman
   8. Steven A Murray
   9. James Cheverud
   10. Daniel Graf
   11. Ralph S Marcucio
   12. Benedikt Hallgrímsson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper offers a new take on multivariate genotype-phenotype mapping that identifies the joint phenotypic effect of genes involved in known biological processes that impact craniofacial variation. More specifically, the work expands on the traditional idea of candidate gene investigations into candidate biological process investigations, grouping multiple genes into a single analysis. In doing so, the authors show the joint effects of three strong candidate processes, chondrocyte differentiation, determination of left/right symmetry, and palate development on multidimensional craniofacial shape in the heterogenous Diversity Outbred mouse population.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

   Reviewed by eLife

6. Exosome component 1 cleaves single-stranded DNA and sensitizes human kidney renal clear cell carcinoma cells to poly(ADP-ribose) polymerase inhibitor

   This article has 9 authors:

   1. Qiaoling Liu
   2. Qi Xiao
   3. Zhen Sun
   4. Bo Wang
   5. Lina Wang
   6. Na Wang
   7. Kai Wang
   8. Chengli Song
   9. Qingkai Yang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Targeting DNA repair pathway provides a novel approach managing malignancies and emphasizing the necessity of discovering biomarkers which could select patients who will benefit. In this research the authors performed comprehensive bioinformatic analysis and identified EXOSC1 as the endogenous source of mutation, which was then validated for its role in damaging DNA and could sensitize kidney renal clear cell carcinoma cells to DNA repair inhibitor. This research is innovative for proposing EXOSC1 role in mutagenesis and could serve as the biomarker to discriminate potential patients who would benefit from DNA repair inhibitor treatment.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

7. Novel neuroanatomical integration and scaling define avian brain shape evolution and development

   This article has 5 authors:

   1. Akinobu Watanabe
   2. Amy M Balanoff
   3. Paul M Gignac
   4. M Eugenia L Gold
   5. Mark A Norell

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Watanabe and colleagues analyse endocasts from extant (and some fossil) material to identify the distinct evolutionary and developmental patterns governing the growth and scaling relationships found in avian brains. The use of sophisticated geometric morphometrics, high-quality digital endocasts, and a suite of multivariate statistical tests robustly support the findings asserted in the paper, namely that crown birds exhibit a distinct allometric relationship that dictates their brain evolution and development. This paper is of broad interest to those working in comparative and evolutionary neuroanatomy as well as vertebrate paleontology.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

8. MBNL1 and RBFOX1 co-regulate alternative splicing events transcriptome-wide through a conserved buffering mechanism

   This article has 10 authors:

   1. Melissa Hale
   2. Joseph Ellis
   3. Ryan Meng
   4. Sunny McDaniel
   5. Amy Mahady
   6. Stacey Wagner
   7. Jared Richardson
   8. Ona McConnell
   9. Eric Wang
   10. J. Andrew Berglund

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     A major question in the field of alternative splicing regulation is how information from multiple, independently-acting splicing factors is integrated into a single signal that informs the spliceosome to include or skip an exon. This study addresses the extent of co-regulation of alternative splicing events by the two RNA binding proteins RBFOX1 and MBNL1. The work has implications for how the effects of perturbing one splicing factor can be buffered by the action of a second RNA binding protein, with broad relevance in development and disease. Additional work would provide more support for a generalized mechanism underlying regulation alternative splicing events.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

9. Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia

   This article has 17 authors:

   1. Anne-Claire Godet
   2. Emilie Roussel
   3. Florian David
   4. Fransky Hantelys
   5. Florent Morfoisse
   6. Joffrey Alves
   7. Françoise Pujol
   8. Isabelle Ader
   9. Edouard Bertrand
   10. Odile Burlet-Schiltz
   11. Carine Froment
   12. Anthony K Henras
   13. Patrice Vitali
   14. Eric Lacazette
   15. Florence Tatin
   16. Barbara Garmy-Susini
   17. Anne-Catherine Prats

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study reports a novel link by which specific cellular mRNAs, that contain internal ribosome sites (IRES), are made competent for translation in paraspeckles in the nucleus. The data showed that a long noncoding RNA, Neat1, is the major player to add transacting factors to the internal ribosome entry site located in fibroblast growth factor 1 mRNAs in the nucleus. This event occurs during hypoxia in mouse cardiomyocytes and is, thus, relevant to gene expression during angiogenesis.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

10. Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops

    This article has 5 authors:

    1. Inigo Urrutia-Irazabal
    2. James R Ault
    3. Frank Sobott
    4. Nigel J Savery
    5. Mark S Dillingham

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:
      The resolution of R-loops that form during collisions between replication and transcription machineries is crucial for cell survival. This is exemplified by the lethality of deletion of PcrA, a helicase that appears to be involved in the resolution of such collisions. Here, the authors aim to characterize the critical regions of PcrA/RNAP interactions and determine the function of such interactions. The manuscript's structural work is refined, elegant and leaves little room for doubt concerning the importance of the CTD PcrA-RNAP molecular interactions. This work moves the field forward in a meaningful way and unravels key aspects of PcrA/UvrD function with regards to interaction and function on RNAP. It will be of interest across the wide field of protein-DNA interactions, both prokaryotic and eukaryotic.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

    Reviewed by eLife