eLife

Latest preprint reviews

1. A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections

   This article has 6 authors:

   1. Massimo Andreatta
   2. Ariel Tjitropranoto
   3. Zachary Sherman
   4. Michael C Kelly
   5. Thomas Ciucci
   6. Santiago J Carmona

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper uses single-cell genomics to examine the heterogeneity of virus-specific CD4 T cells over time in both acute and chronic viral infection. Further, the authors build a comprehensive atlas of the transcriptional evolution of virus-specific CD4 T cell responses that could be used as a reference tool to interpret other datasets. This work characterizes how the antiviral CD4 T cell transcriptional landscape changes with time and will be of broad interest to those that study acute and chronic CD4 T cell responses.

     (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

2. Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43

   This article has 9 authors:

   1. Dongeun Heo
   2. Jonathan P Ling
   3. Gian C Molina-Castro
   4. Abraham J Langseth
   5. Ari Waisman
   6. Klaus-Armin Nave
   7. Wiebke Möbius
   8. Phil C Wong
   9. Dwight E Bergles

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript provides strong support for the concept that oligodendrocyte alterations contribute to neurological disorders that were previous thought to be primarily cell autonomous to neurons. The work is very well done, the results presented are clear and convincing, and the discussion is reasonable and interesting. The study will have considerable impact on the assessment of various neurodegenerative disorders with TDP-43 alterations.

     (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

3. Apelin signaling dependent endocardial protrusions promote cardiac trabeculation in zebrafish

   This article has 6 authors:

   1. Jialing Qi
   2. Annegret Rittershaus
   3. Rashmi Priya
   4. Shivani Mansingh
   5. Didier YR Stainier
   6. Christian SM Helker

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript describes the presence and genetic control of endocardial cell protrusions in zebrafish hearts that resemble endocardial sprouts recently described in the mouse heart, and which appear necessary for the process of trabeculation, whereby chamber cardiomyocytes undergo staged morphogenesis to form a spongy inner layer. This manuscript is of broad interest to readers who study cardiogenesis and developmental biology. This first formal dissection of endocardial protrusions in zebrafish hearts describes how they anchor to cardiomyocytes, and how they participate in signaling pathways involved in trabeculation. The work combines elegant zebrafish reporters and high-quality imaging, as well as mutant lines and pathway inhibitors to provide key findings of how mutual regulation between the myocardium and the endocardium contribute to understanding of mechanisms underlying organ development.

     (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. Particle foraging strategies promote microbial diversity in marine environments

   This article has 3 authors:

   1. Ali Ebrahimi
   2. Akshit Goyal
   3. Otto X Cordero

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript explores how microbial foraging strategies contribute to species coexistence in aquatic environments, and will be of interest to microbial ecologists and theoretical ecologists. Using mathematical modeling, the authors demonstrate that differences in particle detachment rates across bacterial species can promote coexistence. Additional explanation and documentation of methods, along with a discussion of the generality of the results, would strengthen the manuscript and ensure reproducibility.

     (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. How to assemble a scale-invariant gradient

   This article has 3 authors:

   1. Arnab Datta
   2. Sagnik Ghosh
   3. Jane Kondev

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     How biological patterns such as concentration gradient scale with the size of the cell or organism is a long-standing question in developmental and cell biology. In this study, Datta et al show theoretically that directed membrane transport of biomolecules and their release at the cell pole results in a cytoplasmic gradient that scales with cell size if two requirements are met: the cell grows while maintaining its spheroid proportions, (i.e. not by elongation), and the binding of the cytoplasmic fraction of the biomolecule to the membrane should be close to irreversible. A strength of this manuscript is that it invokes a realistic cellular mechanism that could be achieved through several biochemical implementations and can inspire experimental studies. Stronger biological examples and a deeper search in the literature or change in some of the simulation parameters would improve the study, and give the "impetus for experiments" the authors wish to provide.

     (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

6. The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells

   This article has 4 authors:

   1. Dylane Detilleux
   2. Peggy Raynaud
   3. Berengere Pradet-Balade
   4. Dominique Helmlinger

   This article has been curated by 1 group:

   • Curated by eLife

     **Evaluation Summary:
     **
     This manuscript will be of interest to those studying gene transcription and its regulation by co-activator complexes in metazoans. The identification of the large TRAPP subunit shared between two conserved histone modification complexes as a negative regulator of the interferon type I pathway in colorectal cancer cell line provides novel insights into the functions of this TRAPP subunit, which was previously known only for this positive effects on gene transcription.

     (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. MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position

   This article has 5 authors:

   1. Sean E McGeary
   2. Namita Bisaria
   3. Thy M Pham
   4. Peter Y Wang
   5. David P Bartel

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest to readers in the field of microRNA (miRNA) biology, particularly those interested in miRNA targeting. The authors interrogated non-canonical miRNA target recognition to a depth vastly exceeding any study to date. The results revealed unexpected, sequence-specific diversity in miRNA-targeting modes, providing new insights relevant for improved target prediction.

     (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

8. Nucleoporin107 mediates female sexual differentiation via Dsx

   This article has 14 authors:

   1. Tikva Shore
   2. Tgst Levi
   3. Rachel Kalifa
   4. Amatzia Dreifuss
   5. Dina Rekler
   6. Ariella Weinberg-Shukron
   7. Yuval Nevo
   8. Tzofia Bialistoky
   9. Victoria Moyal
   10. Merav Yaffa Gold
   11. Shira Leebhoff
   12. David Zangen
   13. Girish Deshpande
   14. Offer Gerlitz

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript focuses on a missense mutation of Nucleoporin107 (Nup107) gene, which encodes a nuclear pore complex protein. Phenotypic analyses demonstrate similar phenotypes compared to syndromes identified in human XX-ovarian-dysgenesis patients. Further RNA-seq analyses revealed potential targets of Nup107, through which the authors identified the doublesex (dsx) gene as a critical target with functional readouts. Both Nup107 and Dsx act in the somatic gonadal cells to regulate germ cell function, and have connections with the BMP signaling pathway. This study provides a great example to use Drosophila as a model organism to study the molecular and cellular mechanisms of a known human disease and should be of general interest.

     (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

9. Ecdysone coordinates plastic growth with robust pattern in the developing wing

   This article has 5 authors:

   1. André Nogueira Alves
   2. Marisa Mateus Oliveira
   3. Takashi Koyama
   4. Alexander Shingleton
   5. Christen Kerry Mirth

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of broad interest for biologists, in particular developmental biologists and ecologists, as it addresses essential questions on the interaction between organisms and their environment. How organisms manage to maintain a stable phenotype (robustness) or how they adjust their phenotype (plasticity) in response to environmental variations is a major issue. In this article, the authors show that the hormone ecdysone is involved in Drosophila in the plasticity of wing size and the robustness of wing pattern.

     (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

10. Cortical microtubule pulling forces contribute to the union of the parental genomes in the Caenorhabditis elegans zygote

    This article has 5 authors:

    1. Griselda Velez-Aguilera
    2. Batool Ossareh-Nazari
    3. Lucie Van Hove
    4. Nicolas Joly
    5. Lionel Pintard

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This manuscript would be interesting for cell biologists and biophysicists studying nuclear organization and mechanics. The work provides new insights into how pulling forces from the cell cortex influence the dynamics of nuclear rupture during mitosis.

      (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