eLife

Latest preprint reviews

1. Representational integration and differentiation in the human hippocampus following goal-directed navigation

   This article has 5 authors:

   1. Corey Fernandez
   2. Jiefeng Jiang
   3. Shao-Fang Wang
   4. Hannah Lee Choi
   5. Anthony D Wagner

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is a carefully designed and analysed fMRI study investigating how neural representations in the hippocampus, entorhinal cortex, and ventromedial prefrontal cortex change as a function of local and global spatial learning. It will be of much interest to researchers studying the differentiation and integration of memories and the formation of cognitive maps. The results provide new insight into how local and global knowledge about our environment is represented, but some of the conclusions and interpretations could be strengthened with additional analyses.

     (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

2. Neural signatures of auditory hypersensitivity following acoustic trauma

   This article has 10 authors:

   1. Matthew McGill
   2. Ariel E Hight
   3. Yurika L Watanabe
   4. Aravindakshan Parthasarathy
   5. Dongqin Cai
   6. Kameron Clayton
   7. Kenneth E Hancock
   8. Anne Takesian
   9. Sharon G Kujawa
   10. Daniel B Polley

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study uses a mouse model of hyperacusis to further explore the hypothesis that this condition may be mediated by cortical hyperactivity. The authors here provide interesting optogenetic and calcium imaging experiments that reinforce this hypothesis and refine our understanding of the related plastic changes that are involved.

     (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

3. Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single-cell resolution

   This article has 24 authors:

   1. Marina Ainciburu
   2. Teresa Ezponda
   3. Nerea Berastegui
   4. Ana Alfonso-Pierola
   5. Amaia Vilas-Zornoza
   6. Patxi San Martin-Uriz
   7. Diego Alignani
   8. Jose Lamo-Espinosa
   9. Mikel San-Julian
   10. Tamara Jiménez-Solas
   11. Felix Lopez
   12. Sandra Muntion
   13. Fermin Sanchez-Guijo
   14. Antonieta Molero
   15. Julia Montoro
   16. Guillermo Serrano
   17. Aintzane Diaz-Mazkiaran
   18. Miren Lasaga
   19. David Gomez-Cabrero
   20. Maria Diez-Campelo
   21. David Valcarcel
   22. Mikel Hernaez
   23. Juan P Romero
   24. Felipe Prosper

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The present manuscript provides a valuable single-cell transcriptomic resource to understand normal hematopoiesis in humans and the age-dependent cellular and molecular alterations. It addresses very important questions in hematopoietic stem cell biology, such as the molecular changes underlying their aging and their perturbation in the context of myelodysplastic syndrome, and will be of interest to readers in the field of hematopoiesis and associated diseases, aging, and single-cell RNA sequencing.

     (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

4. Temporal and thermal profiling of the Toxoplasma proteome implicates parasite Protein Phosphatase 1 in the regulation of Ca2+-responsive pathways

   This article has 5 authors:

   1. Alice L Herneisen
   2. Zhu-Hong Li
   3. Alex W Chan
   4. Silvia NJ Moreno
   5. Sebastian Lourido

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Herneisen et al provide a comprehensive and thorough exploration of Ca2+ responsive changes in the Toxoplasma proteome and the resulting phosphorylation events during the transition from intracellular residing parasites to egress from the host cell. Furthermore, a novel temperature stability profiling method of all proteins responding to Ca2+ concentration with a change in stability is a novel applicable tool that here is used to map Ca2+-responsive proteins in the parasites. They provide a compelling analysis of the complex data and carefully validate their findings using genetics and cell biology. This work is of the highest quality in the field.

     (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. Phosphoproteomic mapping reveals distinct signaling actions and activation of muscle protein synthesis by Isthmin-1

   This article has 13 authors:

   1. Meng Zhao
   2. Niels Banhos Danneskiold-Samsøe
   3. Livia Ulicna
   4. Quennie Nguyen
   5. Laetitia Voilquin
   6. David E Lee
   7. James P White
   8. Zewen Jiang
   9. Nickeisha Cuthbert
   10. Shrika Paramasivam
   11. Ewa Bielczyk-Maczynska
   12. Capucine Van Rechem
   13. Katrin J Svensson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript presents evidence that the adipocyte-derived protein Ism1, which signals through a typical receptor tyrosine kinase, induces unique phosphoproteome signatures when compared to insulin, and regulates skeletal muscle force production. The manuscript should be of interest to those who study integrated physiology and skeletal muscle physiology. While the data suggest there may be some effects on myofiber size, further study is needed before any conclusions can be made as to what, if any, effects Ism1 has on myofiber size.

     (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. Limitations of principal components in quantitative genetic association models for human studies

   This article has 2 authors:

   1. Yiqi Yao
   2. Alejandro Ochoa

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This simulation study is of interest to geneticists, especially those carrying out Genome-wide Association Studies (GWAS). It compares two major approaches for dealing with "population structure"in GWAS: Principal Component Analysis (PCA) and Linear Mixed-effects Models (LMMs). This is a subject of considerable practical importance and the study nicely reviews the theoretical underpinnings and concludes - based on the review and the extensive simulations - that there is every reason to believe LMMs to be superior (although PCA is more widely used). Although this point has been made before, it is worth making again given the ubiquity of these analyses. There are some concerns about the general validity of the claim given that the simulations fail to address several real-world problems.

     (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

7. An Atypical F-Actin Capping Protein Modulates Cytoskeleton Behaviors Crucial for Trichomonas vaginalis Colonization

   This article has 9 authors:

   1. Kai-Hsuan Wang
   2. Jing-Yang Chang
   3. Fu-An Li
   4. Kuan-Yi Wu
   5. Shu-Hao Hsu
   6. Yen-Ju Chen
   7. Tse-Ling Chu
   8. Jessica Lin
   9. Hong-Ming Hsu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Trichomonas vaginalis is a sexually transmitted protist that colonizes its host by transitioning from flagellar locomotion to an adherent ameboid movement. In this manuscript, Wang and coauthors use a wide range of experimental approaches to investigate the function of a novel actin capping protein in T. vaginalis cytoadherence and cell motility. The work provides an intriguing example of how an unusual capping protein may impact cytoskeletal organization and cell behavior.

     (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 names with the authors.)

   Reviewed by eLife

8. Experimental evidence that group size generates divergent benefits of cooperative breeding for male and female ostriches

   This article has 7 authors:

   1. Julian Melgar
   2. Mads F Schou
   3. Maud Bonato
   4. Zanell Brand
   5. Anel Engelbrecht
   6. Schalk WP Cloete
   7. Charlie K Cornwallis

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of broad interest to readers in the field of animal behavior and the evolution of cooperation. This work experimentally investigates the effect of differences in group size and group composition on reproductive behavior, by using an impressive sample of semi-wild populations of ostriches. While the paper does not address some aspects of groups, such as relatedness and parentage, overall, this paper is a complete analysis of the breeding ecology of this system and can serve as a blueprint for more of such work in the fields of cooperation, group living and breeding ecology.

     (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

9. Activity-based CRISPR scanning uncovers allostery in DNA methylation maintenance machinery

   This article has 9 authors:

   1. Kevin Chun-Ho Ngan
   2. Samuel M Hoenig
   3. Hui Si Kwok
   4. Nicholas Z Lue
   5. Pallavi M Gosavi
   6. David A Tanner
   7. Emma M Garcia
   8. Ceejay Lee
   9. Brian B Liau

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This highly interesting manuscript will be relevant to colleagues studying cancer and those developing cancer therapies. The work describes the use of a large-scale CRISPR screen to identify mechanisms underlying resistance to the hypomethylating anti-cancer agent decitabine, which acts by inhibiting the DNA methyltransferase DNMT1. A specific focus is given to allosteric mechanisms of resistance that emerge, including those that appear to act as gain-of-function mutations in both DNMT1 and its interacting partner UHRF1. These findings showcase the power of large-scale genomic editing screens for the discovery of novel drug resistance mechanisms, which may guide the development of next-generation cancer therapies.

     (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. A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers

    This article has 3 authors:

    1. Marc de Manuel
    2. Felix L Wu
    3. Molly Przeworski

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This paper challenges a fundamental view concerning why males of most animals have a higher germline mutation rate than females. Evidence is provided to show that it is not simply the fact that males have more cell divisions in the germline, but instead, most of the mutations arise from a different balance of DNA damage vs. DNA repair. The case is supported by data from multiple species, from de novo mutation rate estimates from pedigrees, and from fits to a simple heuristic model. This work will be of interest to the broad field of DNA mutations and DNA repair, as well as evolutionary and phylogenomics researchers.

      (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