eLife

Latest preprint reviews

1. Pinpointing the tumor-specific T cells via TCR clusters

   This article has 13 authors:

   1. Mikhail M Goncharov
   2. Ekaterina A Bryushkova
   3. Nikita I Sharaev
   4. Valeria D Skatova
   5. Anastasiya M Baryshnikova
   6. George V Sharonov
   7. Vadim Karnaukhov
   8. Maria T Vakhitova
   9. Igor V Samoylenko
   10. Lev V Demidov
   11. Sergey Lukyanov
   12. Dmitriy M Chudakov
   13. Ekaterina O Serebrovskaya

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript presents a computational approach to identify T-cells which can mount an immune response against tumors. The authors examine the presence of clusters of T cells with similar sequence as a surrogate for tumor antigen specific responses. The identification of tumor-specific responses within the background of bystander T cell infiltration is an area of great current interest. This study provides solid support for the concept that T cell sequence clustering can be used to quantify the tumor specific response in vivo and in vitro.

     (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. All reviewers agreed to share their name with the authors.)

   Reviewed by eLife

2. BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking

   This article has 14 authors:

   1. Christopher J Gabriel
   2. Zachary Zeidler
   3. Benita Jin
   4. Changliang Guo
   5. Caitlin M Goodpaster
   6. Adrienne Q Kashay
   7. Anna Wu
   8. Molly Delaney
   9. Jovian Cheung
   10. Lauren E DiFazio
   11. Melissa J Sharpe
   12. Daniel Aharoni
   13. Scott A Wilke
   14. Laura A DeNardo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of potential interest to researchers performing animal behavioral quantification with computer vision tools. The manuscript introduces 'BehaviorDEPOT', a MATLAB application and GUI intended to facilitate quantification and analysis of freezing behavior from behavior movies, along with several other classifiers based on movement statistics calculated from animal pose data. The paper describes how the tool can be applied to several specific types of experiments, and emphasizes the ease of use - particularly for groups without experience in coding or behavioral quantification. While these aims are laudable, and the software is relatively easy to use, further improvements to make the tool more automated would substantially broaden the likely user base.

     (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

3. Reorganization of postmitotic neuronal chromatin accessibility for maturation of serotonergic identity

   This article has 5 authors:

   1. Xinrui L Zhang
   2. William C Spencer
   3. Nobuko Tabuchi
   4. Meagan M Kitt
   5. Evan S Deneris

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to developmental biologists who study the gene regulatory mechanisms necessary for induction and maintenance of postmitotic neuronal identity. The study generated a useful resource of genomic data and provided new insights into the dynamic regulation of accessible chromatin regions in post-mitotic serotonin (5-HT) neurons of the mouse hindbrain. This work proposes two transcription factors (Pet1, Lmx1b) as necessary for establishment and maintenance of accessible chromatin regions in serotonin (5-HT) neurons. The study is a major technical achievement but some of the central claims are not yet fully demonstrated.

     (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

4. MAF1, a repressor of RNA polymerase III-dependent transcription, regulates bone mass

   This article has 11 authors:

   1. Ellen Phillips
   2. Naseer Ahmad
   3. Li Sun
   4. James Iben
   5. Christopher J Walkey
   6. Aleksandra Rusin
   7. Tony Yuen
   8. Clifford J Rosen
   9. Ian M Willis
   10. Mone Zaidi
   11. Deborah L Johnson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Johnson et al. have used several complementary in vivo and in vitro approaches to analyze the effects of regulated MAF1 expression or inhibition of RNA pol III transcription on osteogenesis and adipocyte differentiation. The data are well controlled and of excellent quality, providing novel insights into Maf1 and RNA polymerase-mediated transcriptions in skeleton biology.

     (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

5. An improved organ explant culture method reveals stem cell lineage dynamics in the adult Drosophila intestine

   This article has 3 authors:

   1. Marco Marchetti
   2. Chenge Zhang
   3. Bruce A Edgar

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Marchetti and colleagues present a promising, ex vivo culture method for the Drosophila adult midgut and other abdominal organs. There are numerous advantages of the authors' method that will attract broad interest and enable real-time analysis of new and important scientific questions. There are concerns about the authors' interpretations of asymmetric/symmetric fate outcomes and terminal differentiation, more information about midgut viability is needed, and comparison of ex vivo vs in vivo regeneration would be useful.

     (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 name with the authors.)

   Reviewed by eLife

6. Magnetic stimulation allows focal activation of the mouse cochlea

   This article has 7 authors:

   1. Jae-Ik Lee
   2. Richard Seist
   3. Stephen McInturff
   4. Daniel J Lee
   5. M Christian Brown
   6. Konstantina M Stankovic
   7. Shelley Fried

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study provides a demonstration that magnetic stimulation of the cochlea is feasible and suggests it could be more precise than electrical stimulation for cochlear implants. The conclusions of the paper are mostly well supported by data, but some aspects of the experimental procedure, the neuronal response acquisition, and the data analysis need to be clarified and extended.

     (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 name with the authors.)

   Reviewed by eLife

7. Macrophage inflammation resolution requires CPEB4-directed offsetting of mRNA degradation

   This article has 12 authors:

   1. Clara Suñer
   2. Annarita Sibilio
   3. Judit Martín
   4. Chiara Lara Castellazzi
   5. Oscar Reina
   6. Ivan Dotu
   7. Adrià Caballé
   8. Elisa Rivas
   9. Vittorio Calderone
   10. Juana Díez
   11. Angel R Nebreda
   12. Raúl Méndez

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study examined the role of CEBP4 in resolution of immune inflammatory responses. The manuscript uses genetic and pharmacologic approaches to demonstrate requirement of CEBP4 for survival following LPS administration and outlines certain downstream details of the mechanism. However, certain conclusions pertaining to this mechanism are either weak or not fully clarified. Further, the study proposes that RNA-binding proteins CPEB4 and TTP play important roles in regulating inflammation-associated mRNA transcripts by binding to CPEs or AREs to promote RNA stability or degradation. There is general agreement that most of the claims in the paper appear reasonably well-supported by the experimental data. However, there are some concerns regarding the robustness and significance of the presented data and conclusions as indicated in the individual reviews that require revision.

     (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

8. Generation of a CRF1-Cre transgenic rat and the role of central amygdala CRF1 cells in nociception and anxiety-like behavior

   This article has 9 authors:

   1. Marcus M Weera
   2. Abigail E Agoglia
   3. Eliza Douglass
   4. Zhiying Jiang
   5. Shivakumar Rajamanickam
   6. Rosetta S Shackett
   7. Melissa A Herman
   8. Nicholas J Justice
   9. Nicholas W Gilpin

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes, characterizes, and validates a novel transgenic tool that will be useful for the study of stress neurobiology and the function of the stress-related neuropeptide corticotropin releasing factor. This tool will be especially relevant to the study of stress and related fields, such as addiction, in which rats are a critical model system. There is comprehensive histochemical and functional validation of the novel rat that broadly supports its proposed utility for visualizing and providing access to central amygdala CRF1 receptor-expressing neurons.

     (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 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

9. Distinct representations of body and head motion are dynamically encoded by Purkinje cell populations in the macaque cerebellum

   This article has 2 authors:

   1. Omid A Zobeiri
   2. Kathleen E Cullen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Zobeiri and Cullen address the important question of how the cerebellum transforms multiple streams of sensory information into an estimate of the motion of the body in the world. They find that Purkinje cells, the inhibitory principal neurons of the cerebellar cortex, have multimodal and highly diverse responses to vestibular and neck proprioceptive inputs. Notably, this information is combined in a way that is different than what is seen in downstream fastigial neurons, which reflect either head or body motion, but not both. The experiments are well executed, generating data that provide important and novel insights, but there are shortcomings in the model put forward to account for these results.

     (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

10. Automated, high-dimensional evaluation of physiological aging and resilience in outbred mice

    This article has 9 authors:

    1. Zhenghao Chen
    2. Anil Raj
    3. GV Prateek
    4. Andrea Di Francesco
    5. Justin Liu
    6. Brice E Keyes
    7. Ganesh Kolumam
    8. Vladimir Jojic
    9. Adam Freund

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Chen et al. develop a comprehensive platform to score aging-dependent changes in mouse physiology and behavior using a multi-dimensional longitudinal phenotyping approach. Their thorough data collection and analysis reveals a diversity of trajectories in aging-related physiological and behavioral changes and helps disentangle biological aging from chronological aging, providing a reference pioneering work for future studies aimed at large-scale aging multi-dimensional phenotyping.

      (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