eLife

Latest preprint reviews

1. 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

2. 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

3. 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

4. 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

5. Morphometric analysis of lungfish endocasts elucidates early dipnoan palaeoneurological evolution

   This article has 7 authors:

   1. Alice M Clement
   2. Tom J Challands
   3. Richard Cloutier
   4. Laurent Houle
   5. Per E Ahlberg
   6. Shaun P Collin
   7. John A Long

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Clement and colleagues describe and illustrate the endocasts of six Palaeozoic lungfish genera from superb 3D fossil material, which are very informative for the understanding of brain evolution of lungfishes, the extant sister group to land vertebrates. Rendering important anatomical details regarding brain evolution in lungfishes, and sarcopterygians in general, this work will be of broad interest to zoologists, including vertebrate paleontologists and neuroanatomists.

     (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 #, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

6. The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield

   This article has 14 authors:

   1. Alejandro Villalta
   2. Alain Schmitt
   3. Leandro F Estrozi
   4. Emmanuelle RJ Quemin
   5. Jean-Marie Alempic
   6. Audrey Lartigue
   7. Vojtěch Pražák
   8. Lucid Belmudes
   9. Daven Vasishtan
   10. Agathe MG Colmant
   11. Flora A Honoré
   12. Yohann Couté
   13. Kay Grünewald
   14. Chantal Abergel

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Giant dsDNA viruses, with genomes in excess of 1Mb that encode more than a thousand genes, were only recently discovered and their study offers new opportunities to understand life's evolved mechanisms. In this manuscript, Villalta and colleagues report results on one of the most complex known viruses, the Mimivirus. Its genome is compacted into magnificent fibers comprising apparently repurposed GMC-type oxidoreductase paralogs assembled as a helical coat around genomic dsDNA. Cryo-EM and cryo-ET image analysis yielded a structural model of the fiber in multiple states. The authors also provide some evidence that additional viral enzymes, including RNA polymerases, exist within the fiber assemblies. Pending the resolution of certain issues that emerged in peer review, the study will be of broad interest to biologists.

     (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

7. Therapeutic deep brain stimulation disrupts movement-related subthalamic nucleus activity in parkinsonian mice

   This article has 8 authors:

   1. Jonathan S Schor
   2. Isabelle Gonzalez Montalvo
   3. Perry WE Spratt
   4. Rea J Brakaj
   5. Jasmine A Stansil
   6. Emily L Twedell
   7. Kevin J Bender
   8. Alexandra B Nelson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper would be of interest to neuroscientists and clinician scientists interested in better understanding the mechanism of deep brain stimulation (DBS) in the treatment of Parkinson's disease. Using a combination of electrical artifact-free calcium imaging and electrical stimulation, it probes the effects of stimulation on the neural dynamics of basal ganglia structures that correlate with motor improvement. The key claims are well supported with a convincing discussion of the caveats of the methods used.

     (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

8. Shared mechanisms of auditory and non-auditory vocal learning in the songbird brain

   This article has 6 authors:

   1. James N McGregor
   2. Abigail L Grassler
   3. Paul I Jaffe
   4. Amanda Louise Jacob
   5. Michael S Brainard
   6. Samuel J Sober

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     McGregor et al. establish a new reinforcement learning paradigm for songbirds, where instead of auditory feedback (white noise) they use mild cutaneous electrical stimulation as a reinforcer. Their data shows that this somatosensory stimulus can aversively drive pitch changes of a targeted syllable in similar manners as an auditory stimulus does. They further show that the anterior forebrain pathway (AFP) and dopaminergic projections to the AFP are necessary for this non-auditory vocal learning by electrolytically lesioning the output nucleus of the AFP and by depleting dopaminergic input to Area X. Their analysis is rigorous and their data convincingly show shared mechanisms for vocal reinforcement learning using white noise (auditory) or cutaneous electrical stimulation (non-auditory).

     (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. Machine learning-assisted discovery of growth decision elements by relating bacterial population dynamics to environmental diversity

   This article has 4 authors:

   1. Honoka Aida
   2. Takamasa Hashizume
   3. Kazuha Ashino
   4. Bei-Wen Ying

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Aida et al use a combination of novel experimental measurements and data processing to wrangle the complexity of bacterial growth for different media conditions. This study represents a clear example tackling the complexity of biological systems from the condition sides (~13,000 growth curves were measured) influencing the growth of a well-defined single specie of bacterium and with a reasonable first pass at data processing. The findings are ultimately simple (with essentially 3 conditions accounting all variability in the system) and easily interpretable.

     (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

10. Effects of dopamine D2/3 and opioid receptor antagonism on the trade-off between model-based and model-free behaviour in healthy volunteers

    This article has 10 authors:

    1. Nace Mikus
    2. Sebastian Korb
    3. Claudia Massaccesi
    4. Christian Gausterer
    5. Irene Graf
    6. Matthäus Willeit
    7. Christoph Eisenegger
    8. Claus Lamm
    9. Giorgia Silani
    10. Christoph Mathys

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This study provides novel evidence that a dopamine D2 receptor antagonist enhances model-based control of behavior, whereas blocking opioid receptors has no effect on the trade-off between habitual responding and goal-directed planning. These conclusions are based on compelling behavioral and computational modeling data and will be of interest to cognitive neuroscientists and computational psychiatrists.

      (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