eLife

Latest preprint reviews

1. Improvement of muscle strength in a mouse model for congenital myopathy treated with HDAC and DNA methyltransferase inhibitors

   This article has 10 authors:

   1. Alexis Ruiz
   2. Sofia Benucci
   3. Urs Duthaler
   4. Christoph Bachmann
   5. Martina Franchini
   6. Faiza Noreen
   7. Laura Pietrangelo
   8. Feliciano Protasi
   9. Susan Treves
   10. Francesco Zorzato

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper describes improvement in muscle phenotype of a congenital myopathy mouse model by a combined treatment with pharmacological inhibitors of Class IIa histone deacetylases and DNA methylases. The paper demonstrates in principle that there are treatment avenues to pursue but their application could be limited as phenotypic rescue appears to be restricted to particular muscle fiber types.

     (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

2. Novel insights from a multiomics dissection of the Hayflick limit

   This article has 20 authors:

   1. Michelle Chan
   2. Han Yuan
   3. Ilya Soifer
   4. Tobias M Maile
   5. Rebecca Y Wang
   6. Andrea Ireland
   7. Jonathon J O'Brien
   8. Jérôme Goudeau
   9. Leanne JG Chan
   10. Twaritha Vijay
   11. Adam Freund
   12. Cynthia Kenyon
   13. Bryson D Bennett
   14. Fiona E McAllister
   15. David R Kelley
   16. Margaret Roy
   17. Robert L Cohen
   18. Arthur D Levinson
   19. David Botstein
   20. David G Hendrickson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript presents a well-done integrative analysis of data from many genome-wide technologies for the study of replicative senescence, contrasting the data to non-senescence and acute senescence controls. The time-course study design and the combinatorial analyses have revealed many interesting features of senescence that were previously unknown. Data mining by scientists in the future promises to unlock other aspects of senescence biology and hence this study serves as a great resource to the community. This paper and resource will be invaluable not only for researchers specifically studying the molecular biology of cell senescence but should also be more broadly relevant for researchers studying aging, inflamm-aging, cancer, regeneration, and other fields where senescence plays a role.

     (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 name with the authors.)

   Reviewed by eLife

3. The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates

   This article has 5 authors:

   1. Keith J Mickolajczyk
   2. Paul Dominic B Olinares
   3. Brian T Chait
   4. Shixin Liu
   5. Tarun M Kapoor

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Mickolajczyk et al. report the development of a new optical tweezers-based unbinding-force assay to characterize the interaction between the MIDAS domain of the mechanoenzyme Mdn1 and the ubiquitin-like (UBL) domain-containing ribosomal proteins Rsa1 and Ytm1. The authors show that the bond between MIDAS and Rsa1/Ytm1 can be best explained by a catch-slip bond behavior. The observations suggest that catch bonding between MIDAS and UBL domains plays a key role in the Mdn1-mediated ribosomal biogenesis. The reported results will be of interesting for the ribosomal and single-molecule biophysics communities and the developed DNA-tether-based optical tweezers assay will be useful for characterizing other molecular bonds.

     (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

4. The molecular mechanism of load adaptation by branched actin networks

   This article has 5 authors:

   1. Tai-De Li
   2. Peter Bieling
   3. Julian Weichsel
   4. R Dyche Mullins
   5. Daniel A Fletcher

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This in vitro study proposes to explain why branched actin filament networks, similar to the ones encountered in migrating cells, become denser when they grow against a mechanical load. This question is of broad interest, and has long been waiting for a molecular-scale explanation. Building on their previously published tools and results, the authors perform a series of elegant and clever experiments, and convincingly identify key molecular mechanisms. Importantly, the results also confirm the Brownian ratchet model for actin assembly. This study captures several important features of branched filament networks, and should become a reference on the topic.

     (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. µ-Theraphotoxin Pn3a inhibition of CaV3.3 channels reveals a novel isoform-selective drug binding site

   This article has 5 authors:

   1. Jeffrey R McArthur
   2. Jierong Wen
   3. Andrew Hung
   4. Rocio K Finol-Urdaneta
   5. David J Adams

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Low voltage-activated T-type calcium channels (CaV3.1-3.3) are important for several physiological processes. It is challenging to distinguish their specific physiological / pathophysiological roles as they share similar biophysical properties, expression profiles and there is a lack of subtype selective pharmacology. This study reports a spider toxin, Pn3a, which exhibits 100-fold selectivity for inhibiting CaV3.3 over CaV3.1 and CaV3.2 isoforms, and which therefore makes for an excellent reagent for the physiological study of CaV3.3.

     (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. Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

   This article has 4 authors:

   1. Richard J White
   2. Eirinn Mackay
   3. Stephen W Wilson
   4. Elisabeth M Busch-Nentwich

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Zebrafish strains are typically considerably polymorphic. White and colleagues tested the hypothesis that genes in linkage with a mutant allele might show allele-specific expression differences and thus potentially confound the interpretation of mutant effects. Using a variety of mutant and wild-type alleles with sophisticated analysis of RNA-seq data in zebrafish embryos they demonstrate over-representation of gene expression changes from genes that are in linkage with the mutant allele on the same chromosome. The data are extensive, carefully analyzed and of sufficient depth and quality to support their main claim of frequent occurrence of allele-specific gene expression in outcross experiments. These allele-specific expression differences may impact on the interpretation of differential gene expression caused by a specific mutation. The findings of this study will be of interest to genetics working not only with zebrafish, but potentially also other polymorphic species.

     (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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

7. aCPSF1 cooperates with terminator U-tract to dictate archaeal transcription termination efficacy

   This article has 7 authors:

   1. Jie Li
   2. Lei Yue
   3. Zhihua Li
   4. Wenting Zhang
   5. Bing Zhang
   6. Fangqing Zhao
   7. Xiuzhu Dong

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study presents new evidence that support a model of aCPSF1-dependent transcription termination in Archaea. Archaeal transcription termination is shown to rely on both poly-U tract terminator signals and the endoribonuclease aCPSF1 of the β-CASP family. This mechanism resembles the eukaryal RNAP II termination process. These new insights fill a gap in our understanding of the mechanism of transcription termination in Archaea and they are of general importance for the RNA biology community.

     (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

8. Using positional information to provide context for biological image analysis with MorphoGraphX 2.0

   This article has 22 authors:

   1. Sören Strauss
   2. Adam Runions
   3. Brendan Lane
   4. Dennis Eschweiler
   5. Namrata Bajpai
   6. Nicola Trozzi
   7. Anne-Lise Routier-Kierzkowska
   8. Saiko Yoshida
   9. Sylvia Rodrigues da Silveira
   10. Athul Vijayan
   11. Rachele Tofanelli
   12. Mateusz Majda
   13. Emillie Echevin
   14. Constance Le Gloanec
   15. Hana Bertrand-Rakusova
   16. Milad Adibi
   17. Kay Schneitz
   18. George W Bassel
   19. Daniel Kierzkowski
   20. Johannes Stegmaier
   21. Miltos Tsiantis
   22. Richard S Smith

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript reports advances in the image analysis software package MorphGraphX (MGX). designed to capture the developmental dynamics of growing tissues at cellular resolution. This version, MGX2.0, includes new tools for precise quantitation of cellular behaviors, such as cell division and expansion, within the context of positional information in the growing organs. To illustrate multiple functionalities of MGX2.0, various tissues are analyzed. This presentation style highlights the power and broad applicability of MGX2.0, but leads to a somewhat disjointed narrative, and how it can provide insight into specific biological questions is less clear.

     (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

9. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

   This article has 19 authors:

   1. Alba Pacheco-Moreno
   2. Francesca L Stefanato
   3. Jonathan J Ford
   4. Christine Trippel
   5. Simon Uszkoreit
   6. Laura Ferrafiat
   7. Lucia Grenga
   8. Ruth Dickens
   9. Nathan Kelly
   10. Alexander DH Kingdon
   11. Liana Ambrosetti
   12. Sergey A Nepogodiev
   13. Kim C Findlay
   14. Jitender Cheema
   15. Martin Trick
   16. Govind Chandra
   17. Graham Tomalin
   18. Jacob G Malone
   19. Andrew W Truman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work uses large-scale genome sequencing and analysis, mass spectrometry and bioassays to investigate the genomic diversity of Pseudomonas strains and their potential role in plant protection. The authors identified a novel group of cyclic lipopeptides that could inhibit Streptomyces scabies, the causal agent of potato scab, and showed how genomic diversity in closely related bacterial strains can contribute to plant pathogen suppression 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. Characterization of the endogenous DAF-12 ligand and its use as an anthelmintic agent in Strongyloides stercoralis

    This article has 11 authors:

    1. Zhu Wang
    2. Mi Cheong Cheong
    3. Jet Tsien
    4. Heping Deng
    5. Tian Qin
    6. Jonathan DC Stoltzfus
    7. Tegegn G Jaleta
    8. Xinshe Li
    9. James B Lok
    10. Steven A Kliewer
    11. David J Mangelsdorf

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This work reveals the pathway by which an important human parasite synthesizes a nuclear hormone receptor ligand critical for progression through its life cycle and demonstrates the potential therapeutic implications of perturbing this pathway. The experiments are insightfully and expertly conceived, designed and executed, and the data support the conclusions. This manuscript will be of general interest to parasitologists, nematode biologists, and those studying transcriptional regulatory networks governed by ligand-gated nuclear receptors.

      (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