eLife

Latest preprint reviews

1. Quantifying chromosomal instability from intratumoral karyotype diversity using agent-based modeling and Bayesian inference

   This article has 5 authors:

   1. Andrew R Lynch
   2. Nicholas L Arp
   3. Amber S Zhou
   4. Beth A Weaver
   5. Mark E Burkard

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study seeks to develop a mathematical framework for estimating rates of chromosome missegregation based on known chromosomal properties and observed aneuploidy rates. A derived model is validated using live-cell imaging before being applied to several previously-described datasets from tumors and organoids. The subject matter is of high interest to aneuploidy and genome evolution researchers.

     (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. First-principles model of optimal translation factors stoichiometry

   This article has 2 authors:

   1. Jean-Benoît Lalanne
   2. Gene-Wei Li

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper presents a theoretical analysis of the abundance of components of the translation machinery (ribosomes, initiation, elongation and release factors, tRNA synthetases) in bacteria. These proteins make up a large fraction of the total proteome and their abundance is closely linked to cell growth. That the stoichiometry of the different components is adjusted such as to maximize the growth rate has been postulated a long time ago, but was so far only studied in detail for ribosomes and EF-Tu, the most abundant elongation factor. Here, the authors extend these earlier works to an unprecedented level of detail and provide a complete analysis based on this idea and derive the optimal stoichiometry for all these factor, which they find to be in good agreement with the observed abundance in different bacteria. This provides new evidence supporting the idea of proteome optimization for maximal growth.

     (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 names with the authors.)

   Reviewed by eLife

3. Acquisition of cellular properties during alveolar formation requires differential activity and distribution of mitochondria

   This article has 9 authors:

   1. Kuan Zhang
   2. Erica Yao
   3. Biao Chen
   4. Ethan Chuang
   5. Julia Wong
   6. Robert I Seed
   7. Stephen L Nishimura
   8. Paul J Wolters
   9. Pao-Tien Chuang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper explores the under-investigated role of mitochondrial activity and subcellular distribution for alveolar formation by using a variety of transgenic mouse models to delete two specific mitochondrial proteins. The data suggest a new concept for mitochondrial dysfunction driving lung injury and potentially human disease. With some further evidence to support the potential cell-specific role for the observed outcomes and additional mitochondrial assessment, this paper will be of interest to a large group of scientists interested in mitochondrial metabolism in general as well as lung development and disease in particular.

     (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

4. Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

   This article has 6 authors:

   1. Katelyn Mika
   2. Mirna Marinić
   3. Manvendra Singh
   4. Joanne Muter
   5. Jan Joris Brosens
   6. Vincent J Lynch

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The study by Mika and colleagues uses a comparative transcriptomics approach to identify changes in the expression of genes that specifically occurred during the evolution of the human endometrium. The authors find that hundreds of genes gained or lost endometrial expression in the human lineage and that several of these genes are potentially implicated in the pathophysiology of human pregnancy. The study contributes to ongoing interest in the effect of human evolution on the pathophysiology of human pregnancy, and has the potential to serve as a model of how to study the evolution of pregnancy-associated genomic changes in particular species and 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 #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

5. Variation in human herpesvirus 6B telomeric integration, excision, and transmission between tissues and individuals

   This article has 15 authors:

   1. Michael L Wood
   2. Colin D Veal
   3. Rita Neumann
   4. Nicolás M Suárez
   5. Jenna Nichols
   6. Andrei J Parker
   7. Diana Martin
   8. Simon PR Romaine
   9. Veryan Codd
   10. Nilesh J Samani
   11. Adriaan A Voors
   12. Maciej Tomaszewski
   13. Louis Flamand
   14. Andrew J Davison
   15. Nicola J Royle

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Human Herpesvirus 6A (HHV6A) and 6B are common herpesviruses that establish lifelong infection in latent form and can cause severe disease upon reactivation. They are spread by acquired infection of free virus and by germ-line transmission of inherited chromosomally-integrated HHV-6A/6B in telomeres. The authors develop an approach to analyse a hypervariable region of the HHV-6B genome and exploit it to investigate the relationship between acquired and inherited virus, presenting evidence that HHV-6B can readily transition between telomere-integrated and free virus forms.

     (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. Persistent Firing Neurons in the Medial Septum Drive Arousal and Locomotion

   This article has 8 authors:

   1. Endre Levente Marosi
   2. Karolina Korvasova
   3. Felix Ludwig
   4. Hiroshi Kaneko
   5. Liudmila Sosulina
   6. Tom Tetzlaff
   7. Stefan Remy
   8. Sanja Mikulovic

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper suggest that that intrinsically generated persistent firing activity of medial septal glutamatergic (VGluT2+) neurons underlies initiation of locomotor activity. In this work, the authors provide evidence for a non-canonical role for persistent firing in initiating locomotion by performing a series of technically difficult experiments to dissect the circuit mechanisms of the persistent firing. This manuscript will be of interest to readers in the field of spatial navigation, motor control, and neural network dynamics.

     (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

7. Pneumococcal genetic variability in age-dependent bacterial carriage

   This article has 14 authors:

   1. Philip HC Kremer
   2. Bart Ferwerda
   3. Hester J Bootsma
   4. Nienke Y Rots
   5. Alienke J Wijmenga-Monsuur
   6. Elisabeth AM Sanders
   7. Krzysztof Trzciński
   8. Anne L Wyllie
   9. Paul Turner
   10. Arie van der Ende
   11. Matthijs C Brouwer
   12. Stephen D Bentley
   13. Diederik van de Beek
   14. John A Lees

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Strain variability in bacterial infections is a confounding factor in the treatment and prevention of the associated diseases. Pneumococcal disease is widespread, and the current vaccine targets only a subset of circulating strains, with disease and vaccine efficacy likely varying with the age of the host. Using two large databases of pneumococcal genomes, this study explores the associations between genomic factors and the age of the human host. Ultimately, these data and related studies will establish whether and how vaccines should be differentially designed for children and the elderly. This work will be of interest to those working in bacterial infections and host-pathogen genomics.

     (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

8. The need for high-quality oocyte mitochondria at extreme ploidy dictates mammalian germline development

   This article has 3 authors:

   1. Marco Colnaghi
   2. Andrew Pomiankowski
   3. Nick Lane

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Non-nuclear genomes, such as those of mitochondria, contribute to many aspects of cellular function, organismal function, and fitness. Understanding their biology and evolutionary dynamics is thus an essential component eukaryotic evolution. The manuscript addresses an important and complex problem regarding the relationship between mitochondrial mutations, their impacts on gamete function, and the attendant evolutionary processes. The authors present a computational approach to distinguish between three hypotheses about the level of selection most likely to explain the distribution of mitochondrial mutations in human populations. They propose that selection among mitochondria is the most likely process to match empirical, clinical data, for mitochondrial mutation loads. There is, however, currently a mismatch between the fact that the data are derived from numerous different species whose biology is not always comparable, the model, and the title of the paper.

     (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

9. Homotopic contralesional excitation suppresses spontaneous circuit repair and global network reconnections following ischemic stroke

   This article has 11 authors:

   1. Annie R Bice
   2. Qingli Xiao
   3. Justin Kong
   4. Ping Yan
   5. Zachary Pollack Rosenthal
   6. Andrew W Kraft
   7. Karen P Smith
   8. Tadeusz Wieloch
   9. Jin-Moo Lee
   10. Joseph P Culver
   11. Adam Q Bauer

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Bice et al. present new work using an optogenetics-based stimulation to test how this affects stroke recovery in mice. Namely, can they determine if contralateral stimulation of S1 would enhance or hinder recovery after a stroke? They found that stimulation of the cortex contralateral to the site of stroke impairs recovery from this stroke, and impairs the brain mapping and the connectivity that normally emerges in recovery from stroke. This unexpected finding in a mouse model relates to clinical literature on the role of the contralateral cortex in recovery.

     (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. Multiple timescales of sensory-evidence accumulation across the dorsal cortex

    This article has 3 authors:

    1. Lucas Pinto
    2. David W Tank
    3. Carlos D Brody

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Previous studies have indicated that neurons in different cortical areas have different intrinsic timescales. In this study, Pinto and colleagues aimed at establishing the functional significance of intrinsic timescales across cortical regions by performing optogenetic silencing of cortical areas in an evidence accumulation task in mice. The results are of broad interest, but the reviewers identified a few important issues that need to be addressed to validate the authors' conclusions.

      (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