eLife

Latest preprint reviews

1. Circuit mechanisms underlying embryonic retinal waves

   This article has 6 authors:

   1. Christiane Voufo
   2. Andy Quaen Chen
   3. Benjamin E Smith
   4. Rongshan Yan
   5. Marla B Feller
   6. Alexandre Tiriac

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     This paper should be of high interest to scientists within the field of developmental neuroscience. The authors characterize the earliest spontaneous waves of the retina - a topic that is poorly understood. The ability to monitor waves over the entire retina at high resolution is a strength of the work. Weaknesses include reliance on pharmacology and some missing details in the analysis.

     (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 name with the authors.)

   Reviewed by eLife

2. Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment

   This article has 11 authors:

   1. Simon Rosowski
   2. Caroline Remmert
   3. Maren Marder
   4. Misao Akishiba
   5. Judith Bushe
   6. Annette Feuchtinger
   7. Alina Platen
   8. Siegfried Ussar
   9. Fabian Theis
   10. Sandra Wiedenmann
   11. Matthias Meier

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     A comprehensive single-cell transcriptomic study was performed in this study to gain insight into the development of endothelial cells and other co-developing mural cells derived from human induced pluripotent stem cells (hiPSCs) in 3D environment. This study gave us important information about signature genes, trajectories, and cell-cell interactions at various stages of vessel formation. Accordingly, the results of this study could potentially be of valuable interest to scientists working in the fields of stem cells, regenerative medicine, and tissue engineering.

     (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. Internally generated time in the rodent hippocampus is logarithmically compressed

   This article has 5 authors:

   1. Rui Cao
   2. John H Bladon
   3. Stephen J Charczynski
   4. Michael E Hasselmo
   5. Marc W Howard

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     This is a rigorous evaluation of whether the compression of time cells in the hippocampus follows the Weber-Fechner Law, using a hierarchical Bayesian model that simultaneously accounts for the firing pattern at the trial, cell, and population levels. The two key results are that the time field width increases linearly with delay, even after taking into account the across trial response variability, and that the time cell population is distributed evenly on a logarithmic time scale. Overall, the paper is well written, the experiment and data analysis are technically sound, and the conclusions are mostly well supported.

     (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. Defining function of wild-type and three patient-specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma

   This article has 22 authors:

   1. Jiangfei Chen
   2. Kunal Baxi
   3. Amanda E Lipsitt
   4. Nicole Rae Hensch
   5. Long Wang
   6. Prethish Sreenivas
   7. Paulomi Modi
   8. Xiang Ru Zhao
   9. Antoine Baudin
   10. Daniel G Robledo
   11. Abhik Bandyopadhyay
   12. Aaron Sugalski
   13. Anil K Challa
   14. Dias Kurmashev
   15. Andrea R Gilbert
   16. Gail E Tomlinson
   17. Peter Houghton
   18. Yidong Chen
   19. Madeline N Hayes
   20. Eleanor Y Chen
   21. David S Libich
   22. Myron S Ignatius

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     This manuscript sheds light on the biology of embryonal rhabdomyosarcoma, a common pediatric muscle tumor, by exploiting an established zebrafish model. Specifically, new knowledge is revealed of how the p53 tumor suppressor contributes to progression and extent of disease. This paper will be of interest not only to pediatric oncologists but also the broader cancer research community given the frequency of TP53 mutations as secondary lesions in human cancer.

     (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. Phage resistance profiling identifies new genes required for biogenesis and modification of the corynebacterial cell envelope

   This article has 2 authors:

   1. Amelia C McKitterick
   2. Thomas G Bernhardt

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     The authors perform a Transposon-Sequencing screen to determine bacterial factors (including receptors) important for infection by two phages in the model bacterium Corynebacterium glutamicum. Using their established high-density transposon library, they identify genes required for infection with the phages Cog and CL31. They also identified a spontaneous phage-resistant mutant that led to the discovery of a gene involved in mycolic acid synthesis. Overall, the work is of broad interest to scientists in the field of cell wall biogenesis, phage infection, and bacterial cell 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. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

6. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution

   This article has 20 authors:

   1. Inês Gomes Castro
   2. Shawn P Shortill
   3. Samantha Katarzyna Dziurdzik
   4. Angela Cadou
   5. Suriakarthiga Ganesan
   6. Rosario Valenti
   7. Yotam David
   8. Michael Davey
   9. Carsten Mattes
   10. Ffion B Thomas
   11. Reut Ester Avraham
   12. Hadar Meyer
   13. Amir Fadel
   14. Emma J Fenech
   15. Robert Ernst
   16. Vanina Zaremberg
   17. Tim P Levine
   18. Christopher Stefan
   19. Elizabeth Conibear
   20. Maya Schuldiner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     In this manuscript, the authors perform an extensive systematic analysis of membrane contacts sites to uncover novel proteins required for tethering organelles and modulation of membrane contacts. The authors identify over 100 new potential contact site proteins and effectors including proteins associated with the recently discovered plasma membrane-LD (pClip) and Golgi-peroxisome (GoPo) contact sites. Further, the authors identify and characterize novel lipid transport proteins associated with the pClip as well as Lec1, an ER-Lipid droplet contact site associated protein which contains a novel putative lipid binding domain and may facilitate ergosterol transport between the plasma membrane and lipid droplets.

     (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

7. Mechanosensitive pore opening of a prokaryotic voltage-gated sodium channel

   This article has 8 authors:

   1. Peter R Strege
   2. Luke M Cowan
   3. Constanza Alcaino
   4. Amelia Mazzone
   5. Christopher A Ahern
   6. Lorin S Milescu
   7. Gianrico Farrugia
   8. Arthur Beyder

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     This manuscript presents a biophysical study of the nature of the mechanosensitivity of voltage-gated sodium channels. The identification of a voltage-independent mechanosensitive step is well founded, the proposal that this step is the intracellular gate is plausible speculation. It is expected to be of interest to scientists studying the physical basis of mechanosensitivity in electrophysiology.

     (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

8. Structural basis of Yta7 ATPase-mediated nucleosome disassembly

   This article has 5 authors:

   1. Feng Wang
   2. Xiang Feng
   3. Qing He
   4. Hua Li
   5. Huilin Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     This manuscript presents the cryo-EM structure of the Yta7 chromatin remodeler, which provides new mechanistic insight into how this AAA+ protein unfolds histone H3 in yeast for DNA replication. The study details the putative role of the C-terminal bromodomains, as well as an N-terminal bromo-interaction motif, in engaging nucleosomes for subsequent capture of the H3 tail for ATP-driven translocation by the upper AAA1 ring. The accompanying functional work helps establish the proposed nucleosome recognition mechanism, providing a structural framework that may be generally used by AAA+ nucleosome remodelers. The work will be of interest to colleagues in chromatin biology as well as all who study the very large family of AAA-ATPases.

     (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 name with the authors.)

   Reviewed by eLife

9. Translational rapid ultraviolet-excited sectioning tomography for whole-organ multicolor imaging with real-time molecular staining

   This article has 6 authors:

   1. Wentao Yu
   2. Lei Kang
   3. Victor TC Tsang
   4. Yan Zhang
   5. Ivy HM Wong
   6. Terence TW Wong

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment:

     This paper demonstrates an integrated labeling and block face fluorescence imaging method that enables the rapid evaluation of biological specimens as large as an E18 mouse embryo with single cell resolution. Such capabilities will likely be of great interest to developmental biologists and pathologists. While the approach can be considered a major step forward, additional experimental support is necessary to gauge how quantitative the method is.

     (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. Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors

    This article has 18 authors:

    1. Joseph M Replogle
    2. Jessica L Bonnar
    3. Angela N Pogson
    4. Christina R Liem
    5. Nolan K Maier
    6. Yufang Ding
    7. Baylee J Russell
    8. Xingren Wang
    9. Kun Leng
    10. Alina Guna
    11. Thomas M Norman
    12. Ryan A Pak
    13. Daniel M Ramos
    14. Michael E Ward
    15. Luke A Gilbert
    16. Martin Kampmann
    17. Jonathan S Weissman
    18. Marco Jost

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment:

      Replogle et al. present their design of a compact and functionally validated dual sgRNA libary and dCas9-effector protein that will enable new forms of CRISPRi-based screening in mammalian cells. Quantitative comparisons to previously published standards demonstrate strengths and weaknesses, which, along with the protocols and design strategies outlined, should enable end users to rapidly adopt their approach.

      (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