eLife

Latest preprint reviews

1. Fluidics system for resolving concentration-dependent effects of dissolved gases on tissue metabolism

   This article has 7 authors:

   1. Varun Kamat
   2. Brian M Robbings
   3. Seung-Ryoung Jung
   4. John Kelly
   5. James B Hurley
   6. Kenneth P Bube
   7. Ian R Sweet

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper presents a flow method for measuring the effects of dissolved gases on tissues while having control over tissue concentration. Working with gases can be challenging. The improvements reported here incorporate technology that allows for metabolic characterization of mammalian tissues while precisely controlling the concentration of abundant gases (e.g., oxygen), as well as trace gases (e.g., hydrogen sulfide). The authors utilize their technology to investigate the metabolic impacts of dissolved hydrogen sulfide, at physiological concentrations. This method should be a powerful tool for the field and enable further experimentation.

     (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

2. A unified framework for measuring selection on cellular lineages and traits

   This article has 5 authors:

   1. Shunpei Yamauchi
   2. Takashi Nozoe
   3. Reiko Okura
   4. Edo Kussell
   5. Yuichi Wakamoto

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript by Wakamoto and colleagues presents a general statistical framework to infer selection on a quantitative trait based on measurements of the values of this trait along related cell lineages. The manuscript provides both a detailed explanation of the mathematical underpinnings of the method and an illustration of its application to existing and new cell lineage datasets. The framework is widely applicable to general exponentially growing populations and is not tailored to particular growth models or environmental 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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

3. Arginine-vasopressin mediates counter-regulatory glucagon release and is diminished in type 1 diabetes

   This article has 24 authors:

   1. Angela Kim
   2. Jakob G Knudsen
   3. Joseph C Madara
   4. Anna Benrick
   5. Thomas G Hill
   6. Lina Abdul Kadir
   7. Joely A Kellard
   8. Lisa Mellander
   9. Caroline Miranda
   10. Haopeng Lin
   11. Timothy James
   12. Kinga Suba
   13. Aliya F Spigelman
   14. Yanling Wu
   15. Patrick E MacDonald
   16. Ingrid Wernstedt Asterholm
   17. Tore Magnussen
   18. Mikkel Christensen
   19. Tina Vilsbøll
   20. Victoria Salem
   21. Filip K Knop
   22. Patrik Rorsman
   23. Bradford B Lowell
   24. Linford JB Briant

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Although the cellular and molecular mechanisms for insulin secretion regulation are relatively well defined, the precise control of glucagon secretion remains poorly understood. This paper is an elegant and thorough investigation into the role of Arginine-vasopressin (AVP) in glucagon secretion. It is known that AVP is a robust activator of calcium response in pancreatic alpha cells leading to glucagon release. The physiological relevance and regulation of this AVP-induced glucagon secretion is unclear. This manuscript goes a long way in closing this gap.

     (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. A B-cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation

   This article has 8 authors:

   1. Jia C Wang
   2. Yang-In Yim
   3. Xufeng Wu
   4. Valentin Jaumouille
   5. Andrew Cameron
   6. Clare M Waterman
   7. John H Kehrl
   8. John A Hammer

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of interest to immunologists studying mechanisms of lymphocyte activation and scientists in the broader field of cell mechanics. The work provides new insight into the cooperation among receptors, the actin cytoskeleton, and myosin motors that is required for the formation of a B cell immune synapse. The data support the key claims of the manuscript.

     (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. Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

   This article has 11 authors:

   1. Nicolás Mongiardino Koch
   2. Jeffrey R Thompson
   3. Avery S Hiley
   4. Marina F McCowin
   5. A Frances Armstrong
   6. Simon E Coppard
   7. Felipe Aguilera
   8. Omri Bronstein
   9. Andreas Kroh
   10. Rich Mooi
   11. Greg W Rouse

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The study by Koch et al presents new phylogenomic and molecular clock analyses of echinoids. The study uses state of the art phylogenetic approaches and includes 17 newly sequenced genomes and transcriptomes, which are used to estimate the tree topology and divergence times of major groups of echinoids. The molecular clock-estimated times of origin of particular echinoid lineages predate the lineages' appearance on the fossil record by tens of millions of years, prompting re-evaluation of the early evolution of echinoid diversity.

     (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

6. A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

   This article has 13 authors:

   1. Chen Yang
   2. Hailin Zhang
   3. Mengnuo Chen
   4. Siying Wang
   5. Ruolan Qian
   6. Linmeng Zhang
   7. Xiaowen Huang
   8. Jun Wang
   9. Zhicheng Liu
   10. Wenxin Qin
   11. Cun Wang
   12. Hualian Hang
   13. Hui Wang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to scientists across translational medicine and cancer treatment. It describes a standardized method to identify drugs that could be potentially repositioned for tumor treatment. In addition, using this new method and experimental manipulations the authors identify homoharringtonine as a new potential therapy for liver cancer and the underlying liver disease. However, while bioinformatic analysis was really comprehensive, the results and conclusions obtained are based on public datasets and therefore limited by the data available. In addition, the experimental approach to test the potential new treatments are currently based on in vitro assays and would be strengthened by in vivo validations.

     (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

7. Visually induced changes in cytokine production in the chick choroid

   This article has 2 authors:

   1. Jody A Summers
   2. Elizabeth Martinez

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of general interest to basic researchers and clinician-scientists working on the eye and vision, developmental and inflammatory eye disorders, and cell-cell signalling in vascular tissue. Experiments are well designed, the resulting data are of very high quality, and their significance is not over-interpreted. The approach and findings with regard to myopia are quite novel, revealing exciting new possibilities for understanding the visual regulation of eye growth, with some overlap into understanding regulatory mechanisms in inflammation.

     (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

8. Sequence features of retrotransposons allow for epigenetic variability

   This article has 7 authors:

   1. Kevin R Costello
   2. Amy Leung
   3. Candi Trac
   4. Michael Lee
   5. Mudaser Basam
   6. J Andrew Pospisilik
   7. Dustin E Schones

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors aim to understand how certain transposable elements escape chromatin-based silencing. Focusing on variably methylated copies of IAP (VM-IAPs) in the mouse, the authors show that elements that can escape silencing share sequence variations that alter KRAB zinc finger protein (KZFP) binding and KAP1 recruitment, proximity to expressed genes and high CpG content. Analysis of human elements in human KZFP-free mouse cells recapitulates some of these observations. The authors propose that ZF-CxxxC proteins play a role in establishing permissive chromatin at transposable elements that harbor high CpG content and weak KZFP binding. The data are mostly correlative and open the path for further mechanistic analyses. The paper is of interest to readers in the field of epigenetics, genome biology and transposable elements.

     (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. Regeneration of the larval sea star nervous system by wounding induced respecification to the Sox2 lineage

   This article has 3 authors:

   1. Minyan Zheng
   2. Olga Zueva
   3. Veronica F Hinman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript presents a careful study of nervous system regeneration in the larval sea star using new transgenic tools for marking and following cells involved in regeneration. The authors find that these animals can regenerate their nervous system by the re-specification of existing cells, which are induced to express the embryonic neurogenesis program. The experimental approach is robust and creative and the data interpretation sound. For its contribution to our understanding of how cells are induced to contribute to specific cell lineages during regeneration, this work will be of interest to the broad community of researchers inregenerative and developmental 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. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

10. Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies

    This article has 2 authors:

    1. Matthew Osmond
    2. Graham Coop

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The relationship between homologous chromosomes sampled in a population can be described by an "ancestral recombination graph" or as a "forest" of correlated coalescent trees describing the relationship at each locus on the chromosome. It has long been clear that this graph contains enormous amounts of information about the history of the population, and should be used in analysis. Hitherto this has been computationally infeasible, but recently developed methods are starting to make it possible, and this paper is one of the first attempts to do so. The paper should be of interest to anyone working with population genetic inference, although there are concerns about possible bias in the estimates from the 1001 Arabidopsis Genomes that need to be resolved.

      (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 names with the authors.)

    Reviewed by eLife