eLife

Latest preprint reviews

1. Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development

   This article has 10 authors:

   1. Scott A Rankin
   2. Jeffrey D Steimle
   3. Xinan H Yang
   4. Ariel B Rydeen
   5. Kunal Agarwal
   6. Praneet Chaturvedi
   7. Kohta Ikegami
   8. Michael J Herriges
   9. Ivan P Moskowitz
   10. Aaron M Zorn

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The formation of the cardiopulmonary circuit is a vital terrestrial adaptation, and precise mechanisms defining how the heart and lung co-develop would be interesting to a broad developmental biology audience. In this manuscript, Rankin et al. propose a nuanced model that bridges previous observations regarding the role of Tbx5 and retinoic acid in forming the cardiopulmonary circuit. This manuscript nicely utilizes forward and reverse genetic approaches in Xenopus model system to rigorously study to describe a Tbx5-Aldh1a2- Shh pathway that leads to reciprocal mesoderm-endoderm interactions and co-induction of segmental heart and lung identities.

     (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

2. Behavioral control by depolarized and hyperpolarized states of an integrating neuron

   This article has 2 authors:

   1. Aylesse Sordillo
   2. Cornelia I Bargmann

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The interneuron RIM affects many behaviours in C. elegans. Attempts to understand or manipulate its function have sometimes led to conflicting and difficult to interpret results. Sordillo and Bargmann investigate the role of the RIM in locomotion by manipulating it's signaling properties in multiple ways. The strength of this approach is that targeting multiple biological signaling mechanisms, they are able to conduct a nuanced analysis of RIM's signaling functions that goes beyond simplistic ON/OFF distinctions. They reach two primary conclusions: 1. RIM depolarization extends reversals via synaptic (glutamatergic) and secretory (tyraminergic) signaling; 2. RIM hyperpolarization promotes forward locomotion via electrical signaling through gap junctions. As a result, RIM was shown to act for stabilizing both forward and backward movement, which is important for understanding of C. elegans in general. Also, the implication that interneurons can be multifunctional in this way is intriguing and potentially impactful.

     (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

3. Competitive binding of MatP and topoisomerase IV to the MukB dimerization hinge

   This article has 11 authors:

   1. Gemma L. M. Fisher
   2. Jani R. Bolla
   3. Karthik V. Rajasekar
   4. Jarno Mäkelä
   5. Rachel Baker
   6. Man Zhou
   7. Josh P. Prince
   8. Mathew Stracy
   9. Carol V. Robinson
   10. Lidia K. Arciszewska
   11. David J. Sherratt

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of potential interest to an audience of biochemists, cell biologists, and structural biologists working in the area of chromosome organization and segregation. A wide range of in vitro methods is used to provide compelling biochemical evidence for the interaction of MatP and ParEC at the hinge of MukB, the condensin of Enterobacteria. However, the evidence supporting the significance of these interactions in vivo is less strong, limiting the biological implications of the elegant biochemical findings.

     (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. The YTHDF proteins ECT2 and ECT3 bind largely overlapping target sets and influence target mRNA abundance, not alternative polyadenylation

   This article has 8 authors:

   1. Laura Arribas-Hernández
   2. Sarah Rennie
   3. Michael Schon
   4. Carlotta Porcelli
   5. Balaji Enugutti
   6. Robin Andersson
   7. Michael D Nodine
   8. Peter Brodersen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Post-transcriptional gene regulation mediated by YTH proteins that bind N6-methyladenosine (m6A) in mRNA is a pathway that has emerged of importance in eukaryotic biology. This paper focuses on two evolutionarily close proteins of this family, ETC2 and ETC3 to find redundant, specific and divergent functions. The authors addressed previously contradictory reports regarding the subcellular location of these proteins. The paper is of general interest to scientists within the field of post-transcriptional gene regulation and RNA biology and is not limited to the plant research community. This will advance our understanding of mRNA methylation and its role in plant 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 and Reviewer #2 agreed to share their names with the authors.)

     This manuscript was co-submitted with: https://www.biorxiv.org/content/10.1101/2021.04.18.440342v2

   Reviewed by eLife

5. Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate

   This article has 5 authors:

   1. Thomas Hackl
   2. Sarah Duponchel
   3. Karina Barenhoff
   4. Alexa Weinmann
   5. Matthias G Fischer

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Approaching the search of novel viruses while in an endogenized stage, rather than as free virions, the study by Hackl et al. reveals a large diversity of complete and fragmented virophage genomes - termed EMALEs- scattered throughout the genomes of four strains of the marine protist Cafeteria. Given that the activation of the integrated virophage mavirus during infection by the giant virus, CroV, has been shown to have a protective effect on the Cafeteria population, this study provides a tantalizing window into the traces of virophage-giant virus¬-protist interactions in the marine environment. Given the enormous diversity of virophages and giant viruses that have been found in metagenomes with no known hosts, this study is a step towards deciphering the biology of these viruses.

     (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

6. Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2

   This article has 8 authors:

   1. Laura Arribas-Hernández
   2. Sarah Rennie
   3. Tino Köster
   4. Carlotta Porcelli
   5. Martin Lewinski
   6. Dorothee Staiger
   7. Robin Andersson
   8. Peter Brodersen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Gene regulation triggered by recognising N6-methyladenosine (m6A) by RNA-binding proteins emerged as a fundamental process for development and adaptation in most eukaryotes. This paper is of interest to scientists within the field of post-transcriptional gene regulation and RNA biology. In a deep and thorough analysis, the authors resolved previously contradictory reports of sequence motifs associated with methylation sites in messenger RNAs and shed light on the proteins that recognise this modification.

     (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.)

     This manuscript was co-submitted with: https://www.biorxiv.org/content/10.1101/2021.08.01.454660v1

   Reviewed by eLife

7. Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

   This article has 10 authors:

   1. Michael Jahn
   2. Nick Crang
   3. Markus Janasch
   4. Andreas Hober
   5. Björn Forsström
   6. Kyle Kimler
   7. Alexander Mattausch
   8. Qi Chen
   9. Johannes Asplund-Samuelsson
   10. Elton Paul Hudson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work combines elegant experimental approaches with modelling predictions to study of metabolic adaptations in the bacterium Cupriavidus necator, a microorganism of interest given its metabolic versatility and potential industrial applications. This manuscript will be interesting for microbiologists and systems biologists who want to understand how protein production and economy and enzyme utilization differs in a versatile microorganism in different conditions.

     (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

8. A model of preferential pairing between epithelial and dendritic cells in thymic antigen transfer

   This article has 9 authors:

   1. Matouš Vobořil
   2. Jiří Březina
   3. Tomáš Brabec
   4. Jan Dobeš
   5. Ondřej Ballek
   6. Martina Dobešová
   7. Jasper Manning
   8. Richard S Blumberg
   9. Dominik Filipp

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest to immunologists studying mechanisms of thymic central tolerance. The study elegantly makes use of multiple genetic mouse models to generate data supporting the conclusion that different dendritic cell subsets in the thymus capture self-antigens from distinct subsets of thymic epithelial cells. However, some key conclusions are not entirely novel, and the final model, as currently presented, draws from only selective analyses and thus may not accurately reflect the antigen transfer between thymic epithelial cell and dendritic cell subsets that promote central tolerance.

     (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

9. Proton transfer pathway in anion channelrhodopsin-1

   This article has 5 authors:

   1. Masaki Tsujimura
   2. Keiichi Kojima
   3. Shiho Kawanishi
   4. Yuki Sudo
   5. Hiroshi Ishikita

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors report continuum electrostatics, molecular dynamics and QM/MM simulations to probe the protonation pattern of key residues in anion channelrhodopsin (GtACR1). The findings provide new mechanistic insights into the gating mechanism of GtACR1, and the study will be of potential interest for the community focused on biophysical chemistry, protein simulations and optogenetics. More generally, the study helps highlight that due to potential compensatory effects, care needs to be exercised when interpreting absorption spectra of mutant 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 #1 agreed to share their name with the authors.)

   Reviewed by eLife

10. Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis

    This article has 20 authors:

    1. Andreas Hober
    2. Khue Hua Tran-Minh
    3. Dominic Foley
    4. Thomas McDonald
    5. Johannes PC Vissers
    6. Rebecca Pattison
    7. Samantha Ferries
    8. Sigurd Hermansson
    9. Ingvar Betner
    10. Mathias Uhlén
    11. Morteza Razavi
    12. Richard Yip
    13. Matthew E Pope
    14. Terry W Pearson
    15. Leigh N Andersson
    16. Amy Bartlett
    17. Lisa Calton
    18. Jessica J Alm
    19. Lars Engstrand
    20. Fredrik Edfors

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This study describes the addition of peptide immunoprecipitation by means of SISCAPA technology to the Sars-Cov2 mass spectrometry-based diagnostics toolbox. While MS-based viral detection has been described by several other groups, the presented method enriches SARS-CoV-2 peptides from clinical samples, thus enhancing the sensitivity and addressing one of the major limitations of this new method for viral diagnostics. The work is straightforward and of potentially great importance to the field. It shows beyond any doubt that mass spectrometry can become a clinically applied diagnostic instrument to detect (viral) infection.

      (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