eLife

Latest preprint reviews

1. Evolutionary divergence of anaphase spindle mechanics in nematode embryos constrained by antagonistic pulling and viscous forces

   This article has 4 authors:

   1. Dhruv Khatri
   2. Thibault Brugière
   3. Chaitanya A. Athale
   4. Marie Delattre

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work will be of interest to cell biologists studying the mechanism of asymmetric cell division and its diversity across species. Building on their earlier work, the authors show that that there is considerable variability in the mechanics of the spindle among six nematode species studied here. While the authors' main conclusion is plausible - that spindle oscillations require high force and low viscosity - stronger support by the data would be needed.

     (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. Discovery of Fungus-Specific Targets and Inhibitors Using Chemical Phenotyping of Pathogenic Spore Germination

   This article has 3 authors:

   1. Sébastien C. Ortiz
   2. Mingwei Huang
   3. Christina M. Hull

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study is an extension of previous work by the same authors, which established a two step high-throughput screening approach to monitor germination and growth of fungal spores of the human pathogen Cryptococcus neoformans and identified an FDA-approved drug with antifungal activity (DOI: 10.1128/AAC.00994-19). The current work extends this approach to three libraries of drug-like molecules comprising 75,000 candidate compounds and employs automated image analysis methods to identify classes of inhibition phenotypes. The key result of this work is the identification of 191 inhibitors, of which 76 could be grouped in to 8 classes based on chemical structure - inhibitors that share structural similarities tend to share phenotypic impact.

     (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. Pseudomonas aeruginosa C-Terminal Processing Protease CtpA Assembles into a Hexameric Structure That Requires Activation by a Spiral-Shaped Lipoprotein-Binding Partner

   This article has 5 authors:

   1. Hao-Chi Hsu
   2. Michelle Wang
   3. Amanda Kovach
   4. Andrew J. Darwin
   5. Huilin Li

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper demonstrates an inactive protease in Pseudomonas aeruginosa, CtpA, is regulated by am outer membrane lipoprotein LbcA. Using crystallization and EM strategies, they also provide a complex structure; however, the precise mechanism of regulation is speculative due to the flexible arrangement of protein domains.

     (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

4. Force-Induced Changes of PilY1 Drive Surface Sensing by Pseudomonas aeruginosa

   This article has 10 authors:

   1. Shanice S. Webster
   2. Marion Mathelié-Guinlet
   3. Andreia F. Verissimo
   4. Daniel Schultz
   5. Albertus Viljoen
   6. Calvin K. Lee
   7. William C. Schmidt
   8. Gerard C. L. Wong
   9. Yves F. Dufrêne
   10. George A. O’Toole

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study demonstrates that a cysteine residue (C152) in the vWA domain of the type-iV pili tip-associated protein, PilY1 impacts surface sensing, biofilm formation and cyclic-di-GMP signaling in Pseduomonas aeruginosa. Well-executed experiments provide insight into the events that initiate cell adhesion and colonisation, the understanding of which has important implications for human health. The work will be of interest to microbiologists in general.

     (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. Deciphering early-warning signals of SARS-CoV-2 elimination and resurgence from limited data at multiple scales

   This article has 3 authors:

   1. Kris V. Parag
   2. Benjamin J. Cowling
   3. Christl A. Donnelly

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study is timely and important for all scientists and policymakers with an interest in producing, using or interpreting estimates of the effective reproductive number, R, as an indicator of epidemic growth when case counts are low (e.g. at the very beginning or end of an epidemic). However, the utility and accuracy of these methods is not evaluated in the context of less-than-ideal surveillance, including time-varying case observation and long delays, which is currently the case in most countries and they fail to evaluate the performance of the metrics in real time.

     (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, ScreenIT

6. Reinvestigation of Classic T Cell Subsets and Identification of Novel Cell Subpopulations by Single-Cell RNA Sequencing

   This article has 8 authors:

   1. Xuefei Wang
   2. Xiangru Shen
   3. Shan Chen
   4. Hongyi Liu
   5. Ni Hong
   6. Hanbing Zhong
   7. Xi Chen
   8. Wenfei Jin

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of broad interest to readers interested in heterogeneity in immune cell populations with single-cell RNA sequencing, and for students of human T cell biology. It uses and reanalyses published single-cell RNA sequencing data dataset for this purpose. However, it does not adequately address major technical concerns, and therefore the interpretations are not robustly 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

7. Immunoelectron Microscopic Characterization of Vasopressin-Producing Neurons in the Hypothalamo-Pituitary Axis of Non-Human Primates by Use of Formaldehyde-Fixed Tissues Stored at −25 °C for Several Years

   This article has 8 authors:

   1. Akito Otubo
   2. Sho Maejima
   3. Takumi Oti
   4. Keita Satoh
   5. Yasumasa Ueda
   6. John F. Morris
   7. Tatsuya Sakamoto
   8. Hirotaka Sakamoto

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript shows that it is possible to detect high-abundance peptide antigens in nerve cells at the electron microscope (EM) level in sections of formaldehyde-fixed monkey brain after the sections have been stored for several years in an antifreeze solution in the freezer. The topic of utilizing formalin fixed tissue for research, especially with the numerous "brain banks" worldwide, is an important topic especially if one wishes to conduct studies in post mortem human tissue. The authors used antibodies to detect the presence of vasopressin gene-related products (i.e., neurophysin II and copeptin) in the hypothalamus and pituitary of the monkey brain. This paper is of interest to anatomists who work on AVP neurons in non-human primate. Due to issues with tissue quality, methodology and interpretation, the experimental approach described in this paper may not be as useful for studying fixed and archived brain sections as the authors conclude.

     (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

8. Social media study of public opinions on potential COVID-19 vaccines: informing dissent, disparities, and dissemination

   This article has 7 authors:

   1. Hanjia Lyu
   2. Junda Wang
   3. Wei Wu
   4. Viet Duong
   5. Xiyang Zhang
   6. Timothy D. Dye
   7. Jiebo Luo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study uses social media data (namely twitter) to analyse factors of covid-vaccine acceptance. It first trains a classifier to detect whether a tweets pro-vaccine, neutral, or against. Using then a large corpus of accounts, it investigates multiple factors explaining this position in a light counterfactual analysis. The central finding is that the most socioeconomically disadvantaged groups are more likely to hold polarized opinions on COVID-19 vaccines; other findings inclduing that personal pandemic experience has an important impact on acceptance, or that interest in politics modulates acceptance. This study a good example of what machine learning can do with social media data; however it is also a good example of the high data-demands and limitations of a machine learning approach. The correlations found are plausible but the causal implications are not evidenced strongly enough to guide public policy.

     (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, ScreenIT

9. Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

   This article has 3 authors:

   1. Alexandre Laverré
   2. Eric Tannier
   3. Anamaria Necsulea

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper addresses a subject of potential great interest regarding the evolution of gene regulation and of enhancer landscapes. Available chromatin looping and gene expression data in mouse and human are analyzed to compare diverse properties of genome-wide promoter-centered maps, including associations with gene expression. It is shown that there is conservation of regulatory landscape across the two species, and that the extent of conservation in the TSS-distal landscape is associated with gene expression similarities. These overall results are in agreement with a large body of work 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.The reviewers remained anonymous to the authors.)

   Reviewed by eLife

10. Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

    This article has 17 authors:

    1. Francisco Rodriguez-Algarra
    2. Robert A. E. Seaborne
    3. Amy F. Danson
    4. Selin Yildizoglu
    5. Harunori Yoshikawa
    6. Pui Pik Law
    7. Zakaryya Ahmad
    8. Victoria A. Maudsley
    9. Ama Brew
    10. Nadine Holmes
    11. Mateus Ochôa
    12. Alan Hodgkinson
    13. Sarah J. Marzi
    14. Madapura M. Pradeepa
    15. Matthew Loose
    16. Michelle L. Holland
    17. Vardhman K. Rakyan

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This manuscript extends the evidence that ribosomal DNA has substantial interindividual variation, and presents evidence that variants are associated with differences in DNA methylation. The authors show that some rDNA types respond to environmental signals during in utero development, whereas others are changed during the aging process - thus broadening the known communication between development/nutrition/aging and the cellular protein synthesis machinery. These findings have relevance for the influence of such epialleles on gene expression and disease risk.

      (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