eLife

Latest preprint reviews

1. Quantifying concordant genetic effects of de novo mutations on multiple disorders

   This article has 10 authors:

   1. Hanmin Guo
   2. Lin Hou
   3. Yu Shi
   4. Sheng Chih Jin
   5. Xue Zeng
   6. Boyang Li
   7. Richard P Lifton
   8. Martina Brueckner
   9. Hongyu Zhao
   10. Qiongshi Lu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Lu et al. provide a new method that looks at whether disorders tend to share excess de novo mutations in genes across the genome. The authors apply the method to nine disorders including a developmental disorder, autism spectrum disorder, congenital heart disease, schizophrenia, and intellectual disability, finding statistically significant overlap between 12 pairs of disorders in de novo mutations that cause a loss of gene function. This method will be of interest to researchers working on disorders caused by de novo mutations, but further clarification of its strengths and weaknesses compared to alternative approaches (mTADA in particular) would strengthen the paper.

     (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

2. Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory

   This article has 5 authors:

   1. Bethany Sump
   2. Donna G Brickner
   3. Agustina D'Urso
   4. Seo Hyun Kim
   5. Jason H Brickner

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Transcriptional memory is a phenomenon via which certain genes are activated more robustly in response to repeated stimulation and in this manner, are able to "remember" previous experiences. This report dissects the molecular mechanism of inositol-driven transcriptional memory and highlights the key role of the histone mark H3K4 di-methylation, which is deposited independently from RNA Polymerase II activity. This memory-specific H3K4 di-methylation is found to be inherited over multiple cell divisions and to require specific transcription factors and chromatin machinery components to be established and maintained. The work will be of interest to those studying transcriptional regulation and epigenetics.

     (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. Evolutionary convergence of a neural mechanism in the cavefish lateral line system

   This article has 4 authors:

   1. Elias T Lunsford
   2. Alexandra Paz
   3. Alex C Keene
   4. James C Liao

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This important and exciting paper demonstrates that the blind cavefish, known for its lack of eyes and increased number of lateral line hair cells, also exhibit physiological adaptations to increase lateral line sensitivity. The authors demonstrate that these adaptations have convergently evolved in multiple populations that have independently colonized cave environments. By leveraging the numerous strengths of the cavefish model, the authors are able to show precisely how neural circuits can be affected by adaptation to the environment.

     (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 name with the authors.)

   Reviewed by eLife

4. High-resolution secretory timeline from vesicle formation at the Golgi to fusion at the plasma membrane in S. cerevisiae

   This article has 4 authors:

   1. Robert M Gingras
   2. Abigail M Sulpizio
   3. Joelle Park
   4. Anthony Bretscher

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The process of secretory vesicle formation, transport, and fusion in yeast has mainly been characterized through biochemical and genetic means. Only limited information was available about the detailed timeline and order of events. This study fills the gap with a high-resolution temporal analysis, which provides new insights into when key components arrive and depart and how they promote vesicle tethering and fusion. The work is experimentally strong, and improvements to the presentation will ensure that the findings are communicated effectively.

     (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. Viscoelastic properties of suspended cells measured with shear flow deformation cytometry

   This article has 23 authors:

   1. Richard Gerum
   2. Elham Mirzahossein
   3. Mar Eroles
   4. Jennifer Elsterer
   5. Astrid Mainka
   6. Andreas Bauer
   7. Selina Sonntag
   8. Alexander Winterl
   9. Johannes Bartl
   10. Lena Fischer
   11. Shada Abuhattum
   12. Ruchi Goswami
   13. Salvatore Girardo
   14. Jochen Guck
   15. Stefan Schrüfer
   16. Nadine Ströhlein
   17. Mojtaba Nosratlo
   18. Harald Herrmann
   19. Dorothea Schultheis
   20. Felix Rico
   21. Sebastian Johannes Müller
   22. Stephan Gekle
   23. Ben Fabry

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper describes a microfluidic approach to determine the viscoelastic properties of living cells from their deformation in a fluid flow. Its implementation seems accessible and the method offers the possibility to perform measurements on a large number of cells. This technique could eventually be used in many laboratories, including those not specialized in cell mechanics.

     (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. Macroscopic quantities of collective brain activity during wakefulness and anesthesia

   This article has 7 authors:

   1. Adrián Ponce-Alvarez
   2. Lynn Uhrig
   3. Nikolas Deco
   4. Camilo M. Signorelli
   5. Morten L. Kringelbach
   6. Béchir Jarraya
   7. Gustavo Deco

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The premise behind this manuscripts is that concepts from thermodynamics and statistical mechanics can be used to understand brain states and the transitions between such states, just like it is done with transitions between solid and liquid states in well define thermodynamic systems. While this is an interesting attempt to use thermodynamic concepts and equations to analyze fMRI signals, the legwork needed to meaningfully translate those concepts to understand their actual physiological meaning and their relationship to brain function has not yet been achieved.

     (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. Episodic memory in aspects of brain information transfer by resting-state network topology

   This article has 11 authors:

   1. Tianyi Yan
   2. Gongshu Wang
   3. Li Wang
   4. Tiantian Liu
   5. Ting Li
   6. Luyao Wang
   7. Dingjie Suo
   8. Shintaro Funahashi
   9. Duanduan Chen
   10. Bin Wang
   11. Jinglong Wu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper describes a re-analysis of a public fMRI data set which includes measures of resting state connectivity and separate task-based scans of memory encoding and memory retrieval tasks. The paper proposes an analysis method termed "information transfer" that reveals functional interactions between various brain networks during encoding and retrieval as well as differences in these interactions during encoding vs. retrieval. While the methods are potentially interesting, the payoff-or new insight afforded by these methods compared to existing methods-is not fully established.

     (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. Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis

   This article has 7 authors:

   1. Limin Jiang
   2. Hui Yu
   3. Scott Ness
   4. Peng Mao
   5. Fei Guo
   6. Jijun Tang
   7. Yan Guo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper provides a comprehensive co-mutation analysis of over 30 thousand cancer patients and 1700+ cancer cell lines to identify associations with prognosis and drug resistance that could have translational value for clinical practice. Once validated, it would provide a useful framework for precision oncology.

     “(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. Alternation emerges as a multi-modal strategy for turbulent odor navigation

   This article has 4 authors:

   1. Nicola Rigolli
   2. Gautam Reddy
   3. Agnese Seminara
   4. Massimo Vergassola

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work provides an insightful analysis of how animals can use different types of sniffing to quickly find the sources of odorants in natural, often turbulent, environments. As it turns out, the air near the ground is less turbulent but does not provide high precision information about the location of sources that are far away. To get that kind of information, animals have to pause and sniff in the air. Authors show that the relative balance between sniffing near the ground and in the air shifts as the animals approach the source and that this shift matches optimal strategies that can be pursued based on partially observable statistical models of the environment. The paper also includes a very useful set of simulations of odorant flow in the presence of obstacles that will be made publicly available.

     (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. CXCR4high megakaryocytes regulate host-defense immunity against bacterial pathogens

    This article has 8 authors:

    1. Jin Wang
    2. Jiayi Xie
    3. Daosong Wang
    4. Xue Han
    5. Minqi Chen
    6. Guojun Shi
    7. Linjia Jiang
    8. Meng Zhao

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The manuscript studies the heterogeneity of megakaryocytes using single cell RNA-seq and identifies a subpopulation of CXCR4-high megakaryocytes with immune modulatory roles. The authors also perform functional studies which show that this subpopulation of megakaryocytes promotes bacterial phagocytosis by macrophages and neutrophils. This work would be of significant interest to researchers in the fields of immunology and host defense as well as researchers studying hematopoiesis and megakaryocyte biology because it provides new perspectives on megakaryocyte heterogeneity as well as the role of megakaryocytes in host defense and immune function.

      (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