eLife

Latest preprint reviews

1. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain

   This article has 12 authors:

   1. Aleksandra Białas
   2. Thorsten Langner
   3. Adeline Harant
   4. Mauricio P Contreras
   5. Clare EM Stevenson
   6. David M Lawson
   7. Jan Sklenar
   8. Ronny Kellner
   9. Matthew J Moscou
   10. Ryohei Terauchi
   11. Mark J Banfield
   12. Sophien Kamoun

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Convergent evolution is often observed in nature, but the molecular mechanisms allowing similar functions to independently emerge are rarely understood. This work determines how the high-affinity recognition of a pathogenic effector produced by the rice blast fungus, Avr-PikD, evolved in the immune receptor Pik-1. The integration of molecular evolution analyses with structure-function biochemical testing is novel to the field and the data quality is exceptional. In addition to advancing knowledge of host-microbe co-evolution, this work is exemplary in its transparency and the breadth of approaches utilized to understand protein evolution, and we expect that this study will provide a conceptual framework for similar studies in the future.

     (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, PREreview

2. RSC primes the quiescent genome for hypertranscription upon cell-cycle re-entry

   This article has 4 authors:

   1. Christine E Cucinotta
   2. Rachel H Dell
   3. Keean CA Braceros
   4. Toshio Tsukiyama

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Cucinotta et al. describe mechanisms that support an intense burst of transcription from many genes within minutes of nutrient repletion as Saccharomyces cerevisiae cells emerge from quiescence. They focus primarily on the role of the nucleosome remodeler RSC in managing chromatin architecture over promoters during quiescence and as cells re-enter the cell cycle using a broad range of genome-wide measurements that strongly support the conclusions. This important process of cell cycle re-entry from quiescence is understudied but impacts areas as diverse as development and carcinogenesis in multicellular organisms to long-term survival and adaptation of microorganisms to environmental cues, so the results will be of interest to a broad audience.

     (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

3. Repression by the Arabidopsis TOPLESS corepressor requires association with the core Mediator complex

   This article has 9 authors:

   1. Alexander R. Leydon
   2. Wei Wang
   3. Hardik P. Gala
   4. Sabrina Gilmour
   5. Samuel Juarez-Solis
   6. Mollye L. Zahler
   7. Joseph E. Zemke
   8. Ning Zheng
   9. Jennifer L. Nemhauser

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, Leydon et al. use an elegant multi-component genetic system to address the mechanisms of repression by the Arabadopsis TOPLESS (Tpl) protein. Taking advantage of the genetic tools and knowledge of the structure of the Tpl protein, the authors determine two short alpha helical regions that act as independent repression domains, with the target of one of these domains being the N-terminal region of the Med21 subunit of the mediator complex. Experiments are presented that indicate that Tpl mediated repression involves formation of a promoter complex comprising the mediator complex along with several general transcription factors, but lacking RNA polymerase II. The experimental data comes from both heterologous experimental systems in yeast and the native plant setting and involves diverse but complementary experimental approaches that converge towards a model for gene repression. This paper will be of interest to researchers investigating the mechanisms regulating gene expression, in particular how specific protein-protein interactions repress gene expression.

     (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

4. High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing

   This article has 3 authors:

   1. William S Hart
   2. Philip K Maini
   3. Robin N Thompson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript uses a new approach to model the infectiousness profile of COVID-19 infected individuals. The work suggests a higher proportion of pre-symptomatic infectiousness in COVID-19 than the current evidence. The findings are of great interest to public health policy makers. The methodology is of general interest to modellers working on COVID-19.

     (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 names with the authors.)

   Reviewed by eLife, ScreenIT

5. Optical analysis of the action range of glutamate in the neuropil

   This article has 19 authors:

   1. E.A. Matthews
   2. W. Sun
   3. S.M. McMahon
   4. M. Doengi
   5. L. Halka
   6. S. Anders
   7. J.A. Müller
   8. P. Steinlein
   9. N. Vana
   10. G. van Dyk
   11. J. Pitsch
   12. A.J. Becker
   13. A. Pfeifer
   14. E.T. Kavalali
   15. A. Lamprecht
   16. C. Henneberger
   17. V. Stein
   18. S. Schoch
   19. D. Dietrich

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors address the spatial spread of glutamate outside of synapses, with the surprising conclusion that glutamate released at one synapse can strongly activate receptors at neighboring synapses. This manuscript should interest those studying neural signaling and techniques associated with that field. However, caveats of the advanced techniques used to address this difficult question limit the strength of the main conclusion.

     (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

6. Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree

   This article has 20 authors:

   1. Audrey M Hendley
   2. Arjun A Rao
   3. Laura Leonhardt
   4. Sudipta Ashe
   5. Jennifer A Smith
   6. Simone Giacometti
   7. Xianlu L Peng
   8. Honglin Jiang
   9. David I Berrios
   10. Mathias Pawlak
   11. Lucia Y Li
   12. Jonghyun Lee
   13. Eric A Collisson
   14. Mark S Anderson
   15. Gabriela K Fragiadakis
   16. Jen Jen Yeh
   17. Chun Jimmie Ye
   18. Grace E Kim
   19. Valerie M Weaver
   20. Matthias Hebrok

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, the authors present a high-resolution single-cell transcriptomic atlas of the pancreatic ductal tree. Their analysis unveiled important heterogeneity within the pancreatic ductal tree and identified unique cellular states. Overall, the results presented here suggest distinct functional roles for subpopulations of duct cells in maintenance of duct cell identity and implication in chronic pancreatic inflammation. Finally, such detailed analysis of the pancreatic duct tree is relevant also in the context of cancer biology and might help elucidating the transition from pancreatitis to pancreatic cancer and/or different predisposition to cancer.

     (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

7. Local adaptation and archaic introgression shape global diversity at human structural variant loci

   This article has 7 authors:

   1. Stephanie M Yan
   2. Rachel M Sherman
   3. Dylan J Taylor
   4. Divya R Nair
   5. Andrew N Bortvin
   6. Michael C Schatz
   7. Rajiv C McCoy

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The technical challenges of identifying and quantifying the frequency of structural variants (SV) on a population scale has been a major limitation to the study of recent human adaptation. This manuscript applies a recent graph-based genotyping method that leverages a library of SVs identified by long-read sequencing to identify SVs in large short-read based cohorts. This is a sensible and powerful approach that highlights several examples of likely adaptive SV evolution in different human populations. The key findings and examples are well supported by the data and methods used. However, the manuscript would benefit from further comparisons and context from previous studies, and deeper exploration of the biological significance. In addition to providing novel examples of adaptive SV evolution, this analysis may serve as a template for future analyses that merge long-read and short-read datasets.

     (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. Rules for the self-assembly of ESCRT-III on endosomes

   This article has 6 authors:

   1. Simon Sprenger
   2. Simona M. Migliano
   3. Florian Oleschko
   4. Marvin Kobald
   5. Michael Hess
   6. David Teis

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     ESCRT-III is a conserved hetero-oligomeric membrane remodeling machine known to impact a number of cellular phenomena, yet mechanistic details of its function have remained enigmatic. This work identifies critical inter-subunit contact sites critical for ESCRT-III assembly and function.

     (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

9. Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection

   This article has 7 authors:

   1. Kunal Sharma
   2. Neeraj Dhar
   3. Vivek V Thacker
   4. Thomas M Simonet
   5. Francois Signorino-Gelo
   6. Graham W Knott
   7. John D McKinney

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Reviewers value the development and characterization of a bladder-on-chip infection model for recapitulating the multiples factors involved in UPEC driven UTIs. Notably, it consists of human bladder epithelial cells, bladder microvascular endothelial cells, neutrophils and urine that are also subjected to mechanical changes mimicking those occurring during bladder filling and micturition. This model is a lot more complex than in vitro tissue culture models and more amenable to analysis such as imaging than animal models and therefore constitute a distinct advance for in vitro modeling of UTI that has potential to reveal key aspects of UTIs and reasons for the difficulty to clear these infections with antibiotics.

     (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. Mechanisms underlying neonate-specific metabolic effects of volatile anesthetics

    This article has 14 authors:

    1. Julia Stokes
    2. Arielle Freed
    3. Rebecca Bornstein
    4. Kevin N Su
    5. John Snell
    6. Amanda Pan
    7. Grace X Sun
    8. Kyung Yeon Park
    9. Sangwook Jung
    10. Hailey Worstman
    11. Brittany M Johnson
    12. Philip G Morgan
    13. Margaret M Sedensky
    14. Simon C Johnson

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This manuscript reports that Volatile anesthetics VA induce a rapid depletion of circulating ß-HB and the induction of hypoglycemia by VA in neonates, but not in adults. The phenomenon is very interesting and robust, however it has already been described. Whats new here is that through a metabolomics analysis they demonstrate a role of ACC and CPT1 in this phenomenon.

      (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