eLife

Latest preprint reviews

1. Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer’s model

   This article has 18 authors:

   1. Felicia Reinitz
   2. Elizabeth Y Chen
   3. Benedetta Nicolis di Robilant
   4. Bayarsaikhan Chuluun
   5. Jane Antony
   6. Robert C Jones
   7. Neha Gubbi
   8. Karen Lee
   9. William Hai Dang Ho
   10. Sai Saroja Kolluru
   11. Dalong Qian
   12. Maddalena Adorno
   13. Katja Piltti
   14. Aileen Anderson
   15. Michelle Monje
   16. H Craig Heller
   17. Stephen R Quake
   18. Michael F Clarke

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is interesting and potentially impactful work uncovering mechanisms of stem cell exhaustion and impaired self-renewal that precede inflammatory phenotypes in Alzheimer's disease. The authors describe a mechanism converging on BMP signaling that may represent an early therapeutic target. The reviewers of this manuscript were excited about the potential impact but had some concerns which, if addressed, will strengthen the conclusions reached in this work.

     (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 name with the authors.)

   Reviewed by eLife

2. Heterogeneity of the GFP fitness landscape and data-driven protein design

   This article has 10 authors:

   1. Louisa Gonzalez Somermeyer
   2. Aubin Fleiss
   3. Alexander S Mishin
   4. Nina G Bozhanova
   5. Anna A Igolkina
   6. Jens Meiler
   7. Maria-Elisenda Alaball Pujol
   8. Ekaterina V Putintseva
   9. Karen S Sarkisyan
   10. Fyodor A Kondrashov

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript dives into how protein structure/function robustness to mutation or polymorphism relates across evolutionary distance. The work indicates that evolutionarily related genes will have different shapes of robustness to variation, and that this will not necessarily track with phylogenetic relationships. The conclusions have potential ramifications for protein engineering, protein structure as well as population genetics and phylogenetics.

     (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

3. Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data

   This article has 5 authors:

   1. Nighat Noureen
   2. Zhenqing Ye
   3. Yidong Chen
   4. Xiaojing Wang
   5. Siyuan Zheng

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Single-cell RNA sequencing allows us to quantify variability of gene expression patterns within a population, and thus devise patterns with prognostic, diagnostic and predictive potential, called "gene expression signatures". Here, Noureen and collaborators benchmark four methods used for identifying these gene expression signatures, and evaluate their performance at overcoming a number of analytical challenges. They conclude that caution should be exercised when using bulk sample-based methods in single-cell data analyses, and cellular contexts should be taken into consideration. With strengthening of some statistical and methodological aspects to support the validity of the conclusions, this paper will be an informative and potentially valuable addition 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. Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

4. SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

   This article has 6 authors:

   1. Michela Zaffagni
   2. Jenna M Harris
   3. Ines L Patop
   4. Nagarjuna Reddy Pamudurti
   5. Sinead Nguyen
   6. Sebastian Kadener

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper makes the provocative claim that SARS-CoV-2 Nsp14 is the key protein that mediates the effects of viral infection on the host cell transcriptome. The current evidence for this claim is good, but the paper would benefit from a few additional experiments. If confirmed by these experiments, the conclusion is unexpected and important, especially in these COVID times.

     (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 name with the authors.)

   Reviewed by eLife, ScreenIT

5. Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation

   This article has 15 authors:

   1. Jaime James
   2. Yifei Chen
   3. Clara M Hernandez
   4. Florian Forster
   5. Markus Dagnell
   6. Qing Cheng
   7. Amir A Saei
   8. Hassan Gharibi
   9. Gonzalo Fernandez Lahore
   10. Annika Åstrand
   11. Rajneesh Malhotra
   12. Bernard Malissen
   13. Roman A Zubarev
   14. Elias SJ Arnér
   15. Rikard Holmdahl

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation summary:

     This paper documents a novel aspect of how T cell activation is regulated by the PTPN22 phosphatase, namely reversible oxidation which transiently reduces the activity of PTPN22 to allow the T cell antigen receptor to drive a strong activation signal. This compelling work adds to our understanding of how an immune response is initiated and provides new insights that could be exploited for the development of new drugs to treat immune-mediated diseases.

     (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. Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike

   This article has 8 authors:

   1. Marco A Díaz-Salinas
   2. Qi Li
   3. Monir Ejemel
   4. Leonid Yurkovetskiy
   5. Jeremy Luban
   6. Kuang Shen
   7. Yang Wang
   8. James B Munro

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes timely work on the structural dynamics of the SARS-CoV-2 spike protein that will be of importance to a broad range of scientists with interests in the biology of SARS-CoV-2 and COVID-19 and the function of anti-COVID-19 vaccines and antibodies as well as to molecular biophysicists generally interested in single-molecule imaging, protein dynamics, allostery, and molecular mechanisms. The experiments were very well-designed, controlled, and executed, and the data are of very high quality. Nonetheless, although the conclusions seem to be generally supported by the data and consistent with expectations based on previous findings, there are some concerns regarding the modeling and error analysis of some of 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, ScreenIT

7. TUBA1A tubulinopathy mutants disrupt neuron morphogenesis and override XMAP215/Stu2 regulation of microtubule dynamics

   This article has 5 authors:

   1. Katelyn J Hoff
   2. Jayne E Aiken
   3. Mark A Gutierrez
   4. Santos J Franco
   5. Jeffrey K Moore

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Tubulin mutations underlie a number of neurodevelopmental diseases, but their effect on microtubule function remains largely unknown. Using a combination of approaches and model systems, the authors provide evidence that the disease-associated alpha-tubulin mutations V409A and V409I may perturb microtubule polymerization. In addition, the mutations in alpha tubulin directly impact Tumor Overexpressed Gene domain proteins from recruiting tubulins to regulate microtubule dynamics. This study demonstrates a link between regulators of microtubule dynamics and disease pathogenesis. It will be of interest to the cytoskeleton and neurobiology fields.

     (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. Boosting of cross-reactive antibodies to endemic coronaviruses by SARS-CoV-2 infection but not vaccination with stabilized spike

   This article has 17 authors:

   1. Andrew R Crowley
   2. Harini Natarajan
   3. Andrew P Hederman
   4. Carly A Bobak
   5. Joshua A Weiner
   6. Wendy Wieland-Alter
   7. Jiwon Lee
   8. Evan M Bloch
   9. Aaron AR Tobian
   10. Andrew D Redd
   11. Joel N Blankson
   12. Dana Wolf
   13. Tessa Goetghebuer
   14. Arnaud Marchant
   15. Ruth I Connor
   16. Peter F Wright
   17. Margaret E Ackerman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study is aimed to determine whether infection or vaccination affects activation of pre-existing cross-reactive memory B cells. The data are clear and have implications for further development of new-generation of vaccines.

     (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, ScreenIT

9. Tom70-based transcriptional regulation of mitochondrial biogenesis and aging

   This article has 6 authors:

   1. Qingqing Liu
   2. Catherine E Chang
   3. Alexandra C Wooldredge
   4. Benjamin Fong
   5. Brian K Kennedy
   6. Chuankai Zhou

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors test the hypothesis that components of the TOM complex regulate efficient mitochondrial biogenesis by coordinating the synthesis (via controlling transcription of the corresponding RNAs) of mitochondrial proteins with the rate of mitochondrial protein import. It has previously been established that failure to import mitochondrial proteins results in the accumulation of toxic protein aggregates in the cytosol. The authors conclude that Tom70 fulfills this role and find that Tom70 expression declines as cells age, which contributes to age-associated mitochondrial dysfunction.

     (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. Sleep EEG in young people with 22q11.2 deletion syndrome: A cross-sectional study of slow-waves, spindles and correlations with memory and neurodevelopmental symptoms

    This article has 10 authors:

    1. Nicholas A Donnelly
    2. Ullrich Bartsch
    3. Hayley A Moulding
    4. Christopher Eaton
    5. Hugh Marston
    6. Jessica H Hall
    7. Jeremy Hall
    8. Michael J Owen
    9. Marianne BM van den Bree
    10. Matt W Jones

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The authors quantified sleep oscillations and their coordination in young people with 22q11.2 Deletion Syndrome and their siblings. This was done to identify potential biomarkers of later neurodevelopmental diagnoses in 22q11.2DS. The core findings demonstrate that sleep rhythms in 22q11.2DS are altered in comparison to the control group, as is their relationship with the behavioural expressions of memory consolidation.

      (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