eLife

Latest preprint reviews

1. SLC1A5 provides glutamine and asparagine necessary for bone development in mice

   This article has 5 authors:

   1. Deepika Sharma
   2. Yilin Yu
   3. Leyao Shen
   4. Guo-Fang Zhang
   5. Courtney M Karner

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors report that intracellular transport of glutamine and asparagine is critical for osteoblast anabolism. The authors use a variety of in vivo and in vitro assays for the testing of their working hypothesis. The paper expands and deepens our knowledge of the role of cellular metabolism in osteoblast function and bone 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. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

2. PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans

   This article has 11 authors:

   1. Ankur V Patel
   2. Robert D Turner
   3. Aline Rifflet
   4. Adelina E Acosta-Martin
   5. Andrew Nichols
   6. Milena M Awad
   7. Dena Lyras
   8. Ivo Gomperts Boneca
   9. Marshall Bern
   10. Mark O Collins
   11. Stéphane Mesnage

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript presents the development and validation of a new tool for the characterization of peptidoglycan (PG), the essential cell wall polymer of bacteria. PG is a single large macromolecule that protects almost all bacterial cells. The newly developed open access tool will greatly facilitate comparative quantitative analyses and the determination of compositional diversity of PG, which might ultimately contribute to the development of new antibacterials that target this essential cell wall component.

     (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

3. A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

   This article has 12 authors:

   1. Robert Warneford-Thomson
   2. Parisha P Shah
   3. Patrick Lundgren
   4. Jonathan Lerner
   5. Jason Morgan
   6. Antonio Davila
   7. Benjamin S Abella
   8. Kenneth Zaret
   9. Jonathan Schug
   10. Rajan Jain
   11. Christoph A Thaiss
   12. Roberto Bonasio

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors developed an approach for surveillance screening for SARS-CoV-2, which involves the isothermic amplification of a region of the SARS-CoV-2 nucleocapsid gene using RT-LAMP, followed by detection with deep sequencing. High-throughput and cost effectiveness is achieved by two sets of barcodes that allow up to about 37,000 samples to be combined into one deep sequencing run. Moreover, the authors demonstrate they can do the detection from saliva collected on paper, which should make sample collection easier. The main strength of the work lies in solving the technical aspects for the approach to work. The main weakness is that real-world high-throughput detection is not conclusively demonstrated as only 8 clinical saliva samples are examined.

     (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, ScreenIT

4. 3D cell neighbour dynamics in growing pseudostratified epithelia

   This article has 5 authors:

   1. Harold Fernando Gómez
   2. Mathilde Sabine Dumond
   3. Leonie Hodel
   4. Roman Vetter
   5. Dagmar Iber

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors measure the three-dimensional organization within an epithelial cell monolayer and find that cell neighbors change frequently along the apicobasal axis. State-of-the-art image analysis convincingly justifies correlation, though not causation, between epithelial cell packing and nuclear position. With some stronger theoretical arguments to back up the claims made, this paper will be of interest to scientists studying tissue mechanics and packing of cells in epithelial tissues.

     (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

5. The whale shark genome reveals patterns of vertebrate gene family evolution

   This article has 10 authors:

   1. Milton Tan
   2. Anthony K Redmond
   3. Helen Dooley
   4. Ryo Nozu
   5. Keiichi Sato
   6. Shigehiro Kuraku
   7. Sergey Koren
   8. Adam M Phillippy
   9. Alistair DM Dove
   10. Timothy Read

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of interest in the field of comparative genomics as it provides novel genomic resources for the whale shark, which belongs to a group of vertebrates which has to date limited available genomic data. While the strength of this manuscript is the publication of a novel genomic resource, the importance of the conclusions and the broader impact remain unclear, particularly because the work on its own does not yet provide new insights into the biology of whale sharks.

     (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

6. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms

   This article has 20 authors:

   1. Gary KL Chan
   2. Samantha Maisel
   3. Yeonjoo C Hwang
   4. Bryan C Pascual
   5. Rebecca RB Wolber
   6. Phuong Vu
   7. Krushna C Patra
   8. Mehdi Bouhaddou
   9. Heidi L Kenerson
   10. Huat C Lim
   11. Donald Long
   12. Raymond S Yeung
   13. Praveen Sethupathy
   14. Danielle L Swaney
   15. Nevan J Krogan
   16. Rigney E Turnham
   17. Kimberly J Riehle
   18. John D Scott
   19. Nabeel Bardeesy
   20. John D Gordan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this article, global kinome profiling using fibrolamellar carcinoma and melanoma cell line models was employed to identify key effectors of protein kinase A (PKA) oncogenic signaling, which is hyperactivated in these cancer types. Based on use of molecular and cellular biology assays, authors proposed a model whereby the oncogenic effects of PKA are at least in part mediated by Aurora Kinase A (AURKA)- and PIM2-dependent regulation of MYC family members, and provide evidence that cancers with constitutive activation of PKA may be sensitive to AURKA inhibitors. Overall, it was thought that this study is of broad interest inasmuch as it provides new insights into the molecular underpinnings of oncogenic PKA signaling, and suggests the potential of using AURKA inhibitors to target malignancies characterized by aberrant PKA activation. With stronger mechanistic data linking constitutive PKA signaling to activation of AURKA and PIM2 and MYC regulation and in vivo experiments to support the conclusions, this manuscript will be of interest to researchers in the fields of cancer research, therapeutics, signal transduction and molecular and 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 agreed to share their name with the authors.)

   Reviewed by eLife

7. Group II truncated haemoglobin YjbI prevents reactive oxygen species-induced protein aggregation in Bacillus subtilis

   This article has 6 authors:

   1. Takeshi Imai
   2. Ryuta Tobe
   3. Koji Honda
   4. Mai Tanaka
   5. Jun Kawamoto
   6. Hisaaki Mihara

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of interest to microbiologists and protein biochemists who study biofilm formation, haem proteins, and cellular responses to extracellular oxidative stress. It proposes a mechanism for biofilm protection from reactive oxygen species (ROIs) through the examination of the Gram positive, Bacillus subtilis. The data support many of the conclusions of the paper and highlight the importance of cell surface-localized protein peroxidase activity for proper biofilm assembly in a model species. Further evidence is needed to fully support the proposed mechanisms.

     (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

8. Developmental change in prefrontal cortex recruitment supports the emergence of value-guided memory

   This article has 2 authors:

   1. Kate Nussenbaum
   2. Catherine A Hartley

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is a follow-up on an impactful behavioral study from the same team, characterizing age-related differences in how individuals use information about environmental regularities to guide memory encoding. This paper will be relevant to those interested in the neurodevelopment of reward learning, episodic memory, and memory-guided decision-making. The combination of a clever task and thorough data analysis make this an impactful paper, but future longitudinal studies will need to determine whether these findings reflect developmental changes or cohort effects.

     (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. Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae

   This article has 9 authors:

   1. Fabien Duveau
   2. Petra Vande Zande
   3. Brian PH Metzger
   4. Crisandra J Diaz
   5. Elizabeth A Walker
   6. Stephen Tryban
   7. Mohammad A Siddiq
   8. Bing Yang
   9. Patricia J Wittkopp

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     One key question in evolutionary biology is how traits can be affected by spontaneous mutations. This relationship between traits and mutations influences the rate and direction in which traits evolve. Here, the authors map a set of mutations that affect the expression of a focal gene in yeast, and examine their individual effects and locations in the genome and in the regulatory network. The work is rigorous and the results are well presented. The findings will be of great interest for geneticists and evolutionary biologists interested in the evolution of gene expression and of complex traits. Additional analyses and discussions will strengthen the generalization of the conclusions.

   Reviewed by eLife

10. A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia

    This article has 5 authors:

    1. Xiangyi Li
    2. Lin Jiang
    3. Chao Xue
    4. Mulin Jun Li
    5. Miaoxin Li

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This manuscript describes an improved approach (MGCA) to identify risk genes for human traits and diseases using data from genome wide association studies. The authors demonstrate the utility of their approach by analyzing data from patients with schizophrenia, and narrow in meaningful biological processes and potential drug repurposing candidates. This approach will facilitate gene prioritization from large genetic datasets for downstream applications such as functional studies.

      (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