eLife

Latest preprint reviews

1. Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children

   This article has 28 authors:

   1. Alvin X Han
   2. Zandra C Felix Garza
   3. Matthijs RA Welkers
   4. René M Vigeveno
   5. Nhu Duong Tran
   6. Thi Quynh Mai Le
   7. Thai Pham Quang
   8. Dinh Thoang Dang
   9. Thi Ngoc Anh Tran
   10. Manh Tuan Ha
   11. Thanh Hung Nguyen
   12. Quoc Thinh Le
   13. Thanh Hai Le
   14. Thi Bich Ngoc Hoang
   15. Kulkanya Chokephaibulkit
   16. Pilaipan Puthavathana
   17. Van Vinh Chau Nguyen
   18. My Ngoc Nghiem
   19. Van Kinh Nguyen
   20. Tuyet Trinh Dao
   21. Tinh Hien Tran
   22. Heiman FL Wertheim
   23. Peter W Horby
   24. Annette Fox
   25. H Rogier van Doorn
   26. Dirk Eggink
   27. Menno D de Jong
   28. Colin A Russell

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work offers an in-depth exploration of within-host influenza evolution that helps untangle the process by which global trends arise from host-level dynamics. The manuscript will be of interest to virologists and evolutionary biologists alike, and the dataset provides a unique opportunity to explore evolutionary dynamics late in acute infections of both endemic and emerging viruses. Technical concerns relating to data interpretation and modeling assumptions suggest that some results might change after further investigation.

     (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. Systematic morphological and morphometric analysis of identified olfactory receptor neurons in Drosophila melanogaster

   This article has 8 authors:

   1. Cesar Nava Gonzales
   2. Quintyn McKaughan
   3. Eric A Bushong
   4. Kalyani Cauwenberghs
   5. Renny Ng
   6. Matthew Madany
   7. Mark H Ellisman
   8. Chih-Ying Su

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Nava Gonzales et al. have reconstructed in unprecedented detail the morphology of olfactory sensory neurons (OSNs) and supporting cells within the sensilla in D. melanogaster, characterising the majority of sensory hairs, and OSN types. The morphometric dataset collected will be a reference point for the field of olfaction research in Drosophila, and furthermore might inspire similar analyses of other sensory systems, building our understanding of how peripheral morphological features contribute to sensory neuron processing.

     (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

3. Activity-dependent modulation of synapse-regulating genes in astrocytes

   This article has 10 authors:

   1. Isabella Farhy-Tselnicker
   2. Matthew M Boisvert
   3. Hanqing Liu
   4. Cari Dowling
   5. Galina A Erikson
   6. Elena Blanco-Suarez
   7. Chen Farhy
   8. Maxim N Shokhirev
   9. Joseph R Ecker
   10. Nicola J Allen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper describes the transcriptome and synaptogenic function of astrocytes in the developing visual cortex (VC), a widely used model for neural development. The central questions examined are two-fold: 1) deciphering layer specific organization of astrocytes and 2) how neuronal activity can influence layer specific astrocyte profiles that relate to synaptogenic gene families. Using bulk RNAseq and detailed histology, they demonstrate that expression of key synaptogenic genes are timepoint and layer specific during development, providing an essential resource for understanding how astrocytes change and impact the development of VC circuits. Moreover, the authors revealed that expression of synapse-regulating genes is also regulated by input from thalamic neuronal activity (using vGlut2 KO mice) and astrocyte calcium activity in vivo (using IP3R2 KO mice). They further demonstrate astrocyte molecular changes using snRNA-seq in VGlut2 cKO and Ip3r2 cKO mice. Collectively, these results show that neuronal activity drives the changes in astrocyte function and layer-specific expression of synaptogenic secreted proteins. Overall, this a rigorous and well conducted study that provides important and new information on astrocyte diversity, neuron-astrocyte interactions during development, and mechanisms underlying the expression of key astrocyte synaptogenic genes.

     (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. PARROT is a flexible recurrent neural network framework for analysis of large protein datasets

   This article has 2 authors:

   1. Daniel Griffith
   2. Alex S Holehouse

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors report a user-friendly software package (PARROT) that allows non-experts to use machine learning approaches to analyze high-throughput experiments on proteins. This package will allow more scientists to apply these powerful machine learning methods, thus increasing our ability to understand the chemistry and biological function of proteins.

     (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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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