eLife

Latest preprint reviews

1. SMAD4 and TGFβ are architects of inverse genetic programs during fate determination of antiviral CTLs

   This article has 9 authors:

   1. Karthik Chandiran
   2. Jenny E Suarez-Ramirez
   3. Yinghong Hu
   4. Evan R Jellison
   5. Zeynep Ugur
   6. Jun Siong Low
   7. Bryan McDonald
   8. Susan M Kaech
   9. Linda S Cauley

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors set out to investigate the roles of SMAD4 and TGFbeta in regulating memory CD8 T cell differentiation during viral infection. To achieve their goal, the authors utilized a variety of available tools including, gene expression, mice that lack certain regulatory genes, and different tissue tissue culture approaches. Although the in vitro experiments yielded interesting results that will interest students of T cell immunology/biology, there is an absence of results from in vivo studies that would validate the in vitro observations.

     (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. Activation of targetable inflammatory immune signaling is seen in myelodysplastic syndromes with SF3B1 mutations

   This article has 31 authors:

   1. Gaurav S Choudhary
   2. Andrea Pellagatti
   3. Bogos Agianian
   4. Molly A Smith
   5. Tushar D Bhagat
   6. Shanisha Gordon-Mitchell
   7. Srabani Sahu
   8. Sanjay Pandey
   9. Nishi Shah
   10. Srinivas Aluri
   11. Ritesh Aggarwal
   12. Sarah Aminov
   13. Leya Schwartz
   14. Violetta Steeples
   15. Robert N Booher
   16. Murali Ramachandra
   17. Maria Samson
   18. Milagros Carbajal
   19. Kith Pradhan
   20. Teresa V Bowman
   21. Manoj M Pillai
   22. Britta Will
   23. Amittha Wickrema
   24. Aditi Shastri
   25. Robert K Bradley
   26. Robert E Martell
   27. Ulrich G Steidl
   28. Evripidis Gavathiotis
   29. Jacqueline Boultwood
   30. Daniel T Starczynowski
   31. Amit Verma

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is an outstanding manuscript evaluating a mutation commonly seen in AML and MDS in a spliceosome protein called SF3B1. The authors link this spliceosome mutation to altered transcripts and ultimately to cell cycle proteins and differentiation. This paper will be of high interest for oncologists in that it demonstrates that AML and MDS cells with this mutation can be targeted in a precision medicine approach.

     (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

3. HIF-1α induces glycolytic reprograming in tissue-resident alveolar macrophages to promote cell survival during acute lung injury

   This article has 10 authors:

   1. Parker S Woods
   2. Lucas M Kimmig
   3. Kaitlyn A Sun
   4. Angelo Y Meliton
   5. Obada R Shamaa
   6. Yufeng Tian
   7. Rengül Cetin-Atalay
   8. Willard W Sharp
   9. Robert B Hamanaka
   10. Gökhan M Mutlu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study provides important new information regarding the functions and behavior of lung tissue-resident alveolar macrophages in the context of acute lung injury. New data regarding the impact of hypoxia via HIF-1 on biology of these critical cells are provided and importantly suggesting an impact on the outcome of lung injury.

     (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 model of egocentric to allocentric understanding in mammalian brains

   This article has 8 authors:

   1. Benigno Uria
   2. Borja Ibarz
   3. Andrea Banino
   4. Vinicius Zambaldi
   5. Dharshan Kumaran
   6. Demis Hassabis
   7. Caswell Barry
   8. Charles Blundell

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper presents an artificial neuronal network which, from action and visual inputs, develops representations of space comparable to those found in the navigational system of the brain. They show that the representations developed by this network can be used in novel environments and in a reinforcement learning task. This demonstration of representations in absolute coordinates from agent-centered information is a significant contribution to neuroscientists as well as machine learning.

     (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. Whole-brain comparison of rodent and human brains using spatial transcriptomics

   This article has 6 authors:

   1. Antoine Beauchamp
   2. Yohan Yee
   3. Ben C Darwin
   4. Armin Raznahan
   5. Rogier B Mars
   6. Jason P Lerch

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of interest to readers interested in how brain gene expression patterns differ between humans and other animals. The authors develop an innovative approach to map correspondences between the gene expression profiles of human and mouse brains, finding that the profiles of sensorimotor areas are more similar than those of transmodal association cortex. This thus contributes to our understanding of the genetic mechanisms that may drive differences in brain organization across species. The study is methodologically sound and the key claims are supported by the data.

     (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

6. High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly

   This article has 15 authors:

   1. Martin H Berryer
   2. Gizem Rizki
   3. Anna Nathanson
   4. Jenny A Klein
   5. Darina Trendafilova
   6. Sara G Susco
   7. Daisy Lam
   8. Angelica Messana
   9. Kristina M Holton
   10. Kyle W Karhohs
   11. Beth A Cimini
   12. Kathleen Pfaff
   13. Anne E Carpenter
   14. Lee L Rubin
   15. Lindy E Barrett

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Berryer et al. report on an automated and quantitative platform to study the number of synaptic inputs formed in networks of human excitatory neurons and astrocytes in vitro. The authors tested the utility of the platform by screening a large collection of small molecules and identified several modulators of synapse density, which were validated in follow-up experiments. The automated platform substantially extends what is currently available, particularly with respect to the automation of the initial analysis steps. The positive hits identified here, the inhibitors of bromodomain and extraterminal (BET) family of gene expression regulators, are important, and will likely contribute to the understanding of the mechanisms of human synapse assembly.

     (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

7. p75NTR prevents the onset of cerebellar granule cell migration via RhoA activation

   This article has 2 authors:

   1. Juan P Zanin
   2. Wilma J Friedman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to neurobiologists and developmental biologists. Identifying novel mechanisms that prevent excessive neuronal migration is an important contribution to the field of neural development. The key conclusions of the paper are well supported by the data.

     (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. Specific binding of Hsp27 and phosphorylated Tau mitigates abnormal Tau aggregation-induced pathology

   This article has 15 authors:

   1. Shengnan Zhang
   2. Yi Zhu
   3. Jinxia Lu
   4. Zhenying Liu
   5. Amanda G Lobato
   6. Wen Zeng
   7. Jiaqi Liu
   8. Jiali Qiang
   9. Shuyi Zeng
   10. Yaoyang Zhang
   11. Cong Liu
   12. Jun Liu
   13. Zhuohao He
   14. R Grace Zhai
   15. Dan Li

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors found elevated Hsp 27 levels in brains from Alzheimer disease patients. Hsp27 co-localized with p-Tau, efficiently prevented pTau fibrillation in vitro, and mitigated neuropathology of pTau aggregation in a Drosophila tauopathy model. A series of biochemical assays is presented to supporrt the claim that Hsp27 prevents abnormal Tau aggregation and p-Tau pathology. Overall, the study is well designed and presented, and the data convincingly support this major conclusion, which is relevant to colleagues studying neurodegeneration.

     (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

9. Live-cell imaging in human colonic monolayers reveals ERK waves limit the stem cell compartment to maintain epithelial homeostasis

   This article has 11 authors:

   1. Kelvin W Pond
   2. Julia M Morris
   3. Olga Alkhimenok
   4. Reeba P Varghese
   5. Carly R Cabel
   6. Nathan A Ellis
   7. Jayati Chakrabarti
   8. Yana Zavros
   9. Juanita L Merchant
   10. Curtis A Thorne
   11. Andrew L Paek

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Pond et al. established a 2D patient-derived organoid screening platform to study tissue patterning and kinase pathway dynamics. They aim to understand how the spacing of different colonic cell types and their communication are regulated. They found that apoptosis induces Erk signaling waves that prime cell movement and are essential to maintain tissue patterning in the organoid monolayers. The work presented here is of importance to the field and provides insights into how Erk waves driven by apoptosis can help maintain gut homeostasis.

     (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. DetecDiv, a generalist deep-learning platform for automated cell division tracking and survival analysis

    This article has 3 authors:

    1. Théo Aspert
    2. Didier Hentsch
    3. Gilles Charvin

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This article introduces "DetecDiv", a high throughput, deep learning method to perform automated cell-division tracking in yeast. The performance of the method, estimated to be 100 times faster than manual annotation, overcomes current time processing limitations that are inherent to large single cell datasets. In particular, DetecDiv allows to automatically get quantitative measurements of replicative life span in yeast. The method is of broad interest for quantitative biology as it can be used to study yeast cells dynamics across their lifespan.

      (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