eLife

Latest preprint reviews

1. Mitochondrial redox adaptations enable alternative aspartate synthesis in SDH-deficient cells

   This article has 9 authors:

   1. Madeleine L Hart
   2. Evan Quon
   3. Anna-Lena BG Vigil
   4. Ian A Engstrom
   5. Oliver J Newsom
   6. Kristian Davidsen
   7. Pia Hoellerbauer
   8. Samantha M Carlisle
   9. Lucas B Sullivan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Hart et al show that loss of mitochondrial complex I rescues succinate dehydrogenase deficient (SDH) cells. The experiments are well performed and the phenotype is potentially very interesting to researchers of cancer metabolism. The authors propose that rescue of SDH deficiency by complex I inhibition is caused by an increase in mitochondrial NADH which leads to a restoration of aspartate levels, which in turn rescues proliferation. To support the model, the authors do demonstrate that there are possible correlations of this phenotype to restored aspartate biosynthesis. However, they do not unambiguously establish a mechanism that fully defines how complex I inhibition rescues the proliferation of SDH deficient cells.

     (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

2. The unmitigated profile of COVID-19 infectiousness

   This article has 6 authors:

   1. Ron Sender
   2. Yinon Bar-On
   3. Sang Woo Park
   4. Elad Noor
   5. Jonathan Dushoff
   6. Ron Milo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     A pathogen's generation interval directly affects estimates of its transmissibility (R), and the period of self-isolation or quarantine needed to prevent transmission. This study shows that the unmitigated generation interval of the original variant of SARS-CoV-2 is several days longer than previously estimated and that interventions have substantially decreased the effective generation interval. These findings improve our ability to model counterfactual intervention-free scenarios. Overall technically sound analyses support the conclusions, and extensive sensitivity analyses show that the findings are robust. However, sampling or ascertainment bias in this relatively small pre-intervention dataset or biased inputs could affect the accuracy of the reported estimates.

     (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, ScreenIT

3. Rescue of Escherichia coli auxotrophy by de novo small proteins

   This article has 9 authors:

   1. Arianne M Babina
   2. Serhiy Surkov
   3. Weihua Ye
   4. Jon Jerlström-Hultqvist
   5. Mårten Larsson
   6. Erik Holmqvist
   7. Per Jemth
   8. Dan I Andersson
   9. Michael Knopp

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes randomly generated small proteins of <50 amino acids that can rescue the growth of an auxotrophic mutant of Escherichia coli. The authors suggest that these proteins function by binding specifically to a regulatory element in the 5' UTR of the his operon RNA, altering RNA structure to increase expression. The study suggests that functional small proteins can evolve de novo and that newly evolved small proteins can function as regulators by binding RNA. This is an exciting idea, but the suggested mechanism involving the binding of the small proteins to RNA requires additional experimental support.

     (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

4. Semaphorin3F reduces vascular endothelial and smooth muscle cell PI3K activation and decreases neointimal plaque formation

   This article has 20 authors:

   1. Chutima Rattanasopa
   2. David Castano-Mayan
   3. Chengxun Su
   4. Aaron J. Farrugia
   5. Maria Corlianò
   6. Pakhwan Nilcham
   7. Crystal Pang
   8. Monalisa Hota
   9. Koh Ser Mei
   10. Wendy Lee
   11. Dasan Mary Cibi
   12. Atsu Aiba
   13. Manvendra K. Singh
   14. Siew Cheng Wong
   15. Olaf Rotzschke
   16. Alexander Bershadsky
   17. Han Wei Hou
   18. Elisa A. Liehn
   19. Sujoy Ghosh
   20. Roshni R. Singaraja

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors provide novel evidence that semaphorin signaling (SEMA3F) is engaged in the vascular endothelium and smooth muscle to confer atheroprotection. They show that SEMA3F reduces the activity of key enzyme Phosphoinositide 3-kinase to decrease smooth muscle cell proliferation, migration, and phenotype switching, which contributes to atheroprotection. The study has significant translational potential and yields a new therapeutic target.

     (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. Genomic landscape of lymphatic malformations: a case series and response to the PI3Kα inhibitor alpelisib in an N-of-1 clinical trial

   This article has 19 authors:

   1. Montaser F Shaheen
   2. Julie Y Tse
   3. Ethan S Sokol
   4. Margaret Masterson
   5. Pranshu Bansal
   6. Ian Rabinowitz
   7. Christy A Tarleton
   8. Andrey S Dobroff
   9. Tracey L Smith
   10. Thèrése J Bocklage
   11. Brian K Mannakee
   12. Ryan N Gutenkunst
   13. Joyce Bischoff
   14. Scott A Ness
   15. Gregory M Riedlinger
   16. Roman Groisberg
   17. Renata Pasqualini
   18. Shridar Ganesan
   19. Wadih Arap

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript could be of interest to physicians and researchers in the field of vascular anomalies. The cohort of patients with lymphatic malformations is reasonably sized (n=30) and the claims made by the authors are supported by the data as well as by current knowledge 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. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

6. Unbiased mosaic variant assessment in sperm: a cohort study to test predictability of transmission

   This article has 7 authors:

   1. Martin W Breuss
   2. Xiaoxu Yang
   3. Valentina Stanley
   4. Jennifer McEvoy-Venneri
   5. Xin Xu
   6. Arlene J Morales
   7. Joseph G Gleeson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript analyzes human blastocysts from in vitro fertilization for three subjects (a total of 55 blastocysts), demonstrating transmission of mosaic mutations at close to expected frequencies. These studies are the first of their kind and of translational relevance for the field of clinical genetics and prenatal genetic testing, with the potential to contribute to strategies to reduce genetic disease risk in future offspring.

     (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. The integrated stress response remodels the microtubule-organizing center to clear unfolded proteins following proteotoxic stress

   This article has 10 authors:

   1. Brian Hurwitz
   2. Nicola Guzzi
   3. Anita Gola
   4. Vincent F Fiore
   5. Ataman Sendoel
   6. Maria Nikolova
   7. Douglas Barrows
   8. Thomas S Carroll
   9. H Amalia Pasolli
   10. Elaine Fuchs

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This interesting study identifies why or how the integrated stress response pathway regulates cell recovery upon proteotoxic stress, which is especially interesting in cancer cells resistant to proteasome inhibitors. The authors conclude that translation initiation of mRNAs encoding microtubule cytoskeleton, centrosome and ATF5 proteins is necessary to recover from proteotoxic stress. This paper will make a strong contribution to the literature.

     (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

8. A scalable and modular automated pipeline for stitching of large electron microscopy datasets

   This article has 22 authors:

   1. Gayathri Mahalingam
   2. Russel Torres
   3. Daniel Kapner
   4. Eric T Trautman
   5. Tim Fliss
   6. Shamishtaa Seshamani
   7. Eric Perlman
   8. Rob Young
   9. Samuel Kinn
   10. JoAnn Buchanan
   11. Marc M Takeno
   12. Wenjing Yin
   13. Daniel J Bumbarger
   14. Ryder P Gwinn
   15. Julie Nyhus
   16. Ed Lein
   17. Steven J Smith
   18. R Clay Reid
   19. Khaled A Khairy
   20. Stephan Saalfeld
   21. Forrest Collman
   22. Nuno Macarico da Costa

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Mahalingam et al. report on a new software suite, ASAP, the assembly stitching and alignment pipeline, capable of montaging and aligning serial sections at a speed leading to total time shorter than image acquisition time. The software applies to both electron microscopy and array tomography, and more generally to any data set consisting of collections of 2D images in need of in-section montaging and cross-section registration. The result is a coarsely registered volume, ready for refining with existing software suits such as SEAMLESS by Macrina et al. (2021) towards subsequent processing, such as image segmentation and neuronal arbor reconstruction for cellular connectomics. This paper will be of special interest to researchers within the field of connectomics, but also to the broad class of scientists who perform large-scale microscopy. The establishment of fast, reliable and scalable image alignment software to process the millions of images produced by modern microscopes at the same speed as they are acquired is key to accelerate research in neuroscience and other fields. The key claims of the manuscript are well supported by the data, and the approaches used are thoughtful and rigorous.

     (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

9. Sequential addition of neuronal stem cell temporal cohorts generates a feed-forward circuit in the Drosophila larval nerve cord

   This article has 7 authors:

   1. Yi-wen Wang
   2. Chris C Wreden
   3. Maayan Levy
   4. Julia L Meng
   5. Zarion D Marshall
   6. Jason MacLean
   7. Ellie Heckscher

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Wang et al., present a thorough analysis of specific neuronal lineages in the early larval ventral nervous system with the objective to relate the birth order to circuit connectivity and function. The stated key findings of the work are (1) the identification of sharp temporal cohort divisions for the lineages under investigation, (2) synapse formation between neurons of different lineages and temporal cohorts, and (3) the observation that output neurons in this instance are born prior to input neurons. The study raises the question of to what extent these findings can be generalized.

     (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. PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors

    This article has 9 authors:

    1. Divya Khattar
    2. Sharlene Fernandes
    3. John Snowball
    4. Minzhe Guo
    5. Matthew C Gillen
    6. Suchi Singh Jain
    7. Debora Sinner
    8. William Zacharias
    9. Daniel T Swarr

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This manuscript is one of the first broad epigenetic analyses in lung development and will be of interest to not only lung biologists but also to the field of epithelial developmental biology. Using paired transcriptomic and epigenetic data, they have uncovered a vast repertoire of signaling mechanisms underlying lung development. These findings have opened up the field's opportunities to understand and study novel pathways and have further defined a role for PI3 kinase signaling in lung development.

      (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