eLife

Latest preprint reviews

1. Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression

   This article has 11 authors:

   1. Georgia M Cook
   2. Katherine Brown
   3. Pengcheng Shang
   4. Yanhua Li
   5. Lior Soday
   6. Adam M Dinan
   7. Charlotte Tumescheit
   8. AP Adrian Mockett
   9. Ying Fang
   10. Andrew E Firth
   11. Ian Brierley

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper presents the first comprehensive gene expression analysis of two species of porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that causes economically important diseases of pigs. By applying ribosome profiling to arterivirus-infected cells the authors discovered a substantial number of efficiently translated open reading frames in viral RNAs and obtained compelling evidence of changes in ribosome frameshifting efficiencies over the course of infection. The paper is of interest to virologists and researchers studying mRNA decoding, recoding, and translation.

     (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. Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN

   This article has 7 authors:

   1. Martin A Spacek
   2. Davide Crombie
   3. Yannik Bauer
   4. Gregory Born
   5. Xinyu Liu
   6. Steffen Katzner
   7. Laura Busse

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Spacek et al. study the corticothalamic feedback of different visual stimuli on visual thalamus. With optogenetic suppression of visual cortex feedback and simultaneous multi-channel recordings in visual thalamus, the authors succeeded to acquire important data about this essential feedback loop in awake, behaving animals. The authors impressively show that the cortical feedback acts as a gain factor in thalamus for the transmission of signals from retina to cortex, specifically for natural scenes. These careful measurements performed in a well-defined circuit also advance our understanding of the role of feedback more generally in the brain.

     (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. A transcriptome atlas of the mouse iris at single-cell resolution defines cell types and the genomic response to pupil dilation

   This article has 3 authors:

   1. Jie Wang
   2. Amir Rattner
   3. Jeremy Nathans

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Using single nucleus RNA sequencing, the authors have characterized all major cell types in the mouse iris and ciliary body, defined new types of iris stromal and sphincter cells, and shown cell-specific transcriptome responses in the resting, constricted, and dilated states and identified and validated antibodies and in situ hybridization probes for visualization of major iris cell types. This work will be a valuable reference for investigations of iris development, disease, and pharmacology.

     (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. Double-μPeriscope, a tool for multilayer optical recordings, optogenetic stimulations or both

   This article has 3 authors:

   1. Mototaka Suzuki
   2. Jaan Aru
   3. Matthew E Larkum

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This Tools and Resources article presents an innovative method for simultaneously stimulating and imaging two cortical layers in tandem while causing minimal damage to brain tissue. The method substantially builds on existing methods in several ways, while still pinpointing the limitations of existing methods that are overcome in this new approach. Three well-described sets of experiments demonstrate the method's reliability and versatility, and highlight its promise in tackling big questions about cortical microcircuit functions.

     (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

5. Distinguishing different modes of growth using single-cell data

   This article has 5 authors:

   1. Prathitha Kar
   2. Sriram Tiruvadi-Krishnan
   3. Jaana Männik
   4. Jaan Männik
   5. Ariel Amir

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest to the community of quantitative biologists aiming to understand the basic mechanisms of cell growth. By demonstrating, and then resolving, the problem that a common test for exponential growth can make exponential growth appear non-exponential, and can make linear growth appear exponential, the authors introduce valuable insights and analysis tools to this active 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. Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

6. The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function

   This article has 6 authors:

   1. Marianthi Kiparaki
   2. Chaitali Khan
   3. Virginia Folgado-Marco
   4. Jacky Chuen
   5. Panagiotis Moulos
   6. Nicholas E Baker

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     A growing body of literature substantiates the physiological importance of the phenomenon of 'cell competition' induced by differences in the copy number of ribosomal proteins (Rp) in adjacent cells. Yet, the molecular players that effect cell competition in 'loser' cells have been elusive and poorly studied; the current study by Kiparaki et al makes significant headway in the field by demonstrating that a little known transcription factor, Xrp1, is the common effector of cell death in loser cells when competition is induced by Rp haplo-insufficiency. While differences in cellular translation levels were thought to be the main driver of cell death in loser cells, this work dissects this premise in detail to unequivocally show that in the absence of Xrp1, translation differences alone is not sufficient to induce loser cell death.

     (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. Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids

   This article has 17 authors:

   1. Debdeep Chatterjee
   2. Reeba S Jacob
   3. Soumik Ray
   4. Ambuja Navalkar
   5. Namrata Singh
   6. Shinjinee Sengupta
   7. Laxmikant Gadhe
   8. Pradeep Kadu
   9. Debalina Datta
   10. Ajoy Paul
   11. Sakunthala Arunima
   12. Surabhi Mehra
   13. Chinmai Pindi
   14. Santosh Kumar
   15. Praful Singru
   16. Sanjib Senapati
   17. Samir K Maji

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study sheds light on the formation of Prolactin/Galanin functional amyloids and their storage in secretory granules of the anterior pituitary gland. This study sharpens our understanding of the regulation of hormonal release from the pituitary gland. It will be of interest to the fields of endocrinology, neurobiology and 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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

8. Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children’s blood

   This article has 22 authors:

   1. Carlos Ruiz-Arenas
   2. Carles Hernandez-Ferrer
   3. Marta Vives-Usano
   4. Sergi Marí
   5. Ines Quintela
   6. Dan Mason
   7. Solène Cadiou
   8. Maribel Casas
   9. Sandra Andrusaityte
   10. Kristine Bjerve Gutzkow
   11. Marina Vafeiadi
   12. John Wright
   13. Johanna Lepeule
   14. Regina Grazuleviciene
   15. Leda Chatzi
   16. Ángel Carracedo
   17. Xavier Estivill
   18. Eulàlia Marti
   19. Geòrgia Escaramís
   20. Martine Vrijheid
   21. Juan R González
   22. Mariona Bustamante

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript reports for the first time associations between DNA methylation and gene expression in blood samples from 832 children. These associations are important for understanding the regulation of genes in the genome. The importance of this study is underlined by two surprising results: a minority of these associations are also observed in adult blood samples, and only half of the associations were with the nearest gene. These findings are critical for understanding the biological effects of DNA methylation changes caused by exposures and phenotypes.

     (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. Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization

   This article has 11 authors:

   1. Gabriel Renaud
   2. Maibritt Nørgaard
   3. Johan Lindberg
   4. Henrik Grönberg
   5. Bram De Laere
   6. Jørgen Bjerggaard Jensen
   7. Michael Borre
   8. Claus Lindbjerg Andersen
   9. Karina Dalsgaard Sørensen
   10. Lasse Maretty
   11. Søren Besenbacher

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work describes a shallow WGS sequencing approach (<1x) for genome‐wide cell‐free DNA fragmentation analysis using non-negative matrix factorization (NMF). The concept of utilizing 'fragmentomics' as an early cancer detection tool is a subject of intense investigation and there have been multiple recent publications in the field. This work adds an interesting unsupervised 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

10. Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription

    This article has 9 authors:

    1. Gonçalo Fernandes
    2. Huy Tran
    3. Maxime Andrieu
    4. Youssoupha Diaw
    5. Carmina Perez Romero
    6. Cécile Fradin
    7. Mathieu Coppey
    8. Aleksandra M Walczak
    9. Nathalie Dostatni

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The authors combine the study of synthetic transcriptional enhancers with theoretical models to understand the role of Bicoid, Hunchback and Zelda during syncytial cycles. They conclude that Bcd exists in active and inactive forms; that Hb regulates transcription during some stage after initiation; and that an equilibrium model captures the relevant behaviors, implying energy expenditure during DNA binding/transcription interaction with RNAP is theoretically unnecessary.

      (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