eLife

Latest preprint reviews

1. The DNA sensors AIM2 and IFI16 are SLE autoantigens that bind neutrophil extracellular traps

   This article has 13 authors:

   1. Brendan Antiochos
   2. Daniela Trejo-Zambrano
   3. Paride Fenaroli
   4. Avi Rosenberg
   5. Alan Baer
   6. Archit Garg
   7. Jungsan Sohn
   8. Jessica Li
   9. Michelle Petri
   10. Daniel W Goldman
   11. Christopher Mecoli
   12. Livia Casciola-Rosen
   13. Antony Rosen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript identifies the DNA sensor AIM2 as a target of auto-antibodies in the human autoimmune disease systemic lupus erythematosus. Importantly, the authors provide evidence that AIM2 protects extracellular DNA from destruction and propose that this property may enhance the autoimmune response to the DNA and associated proteins. The work may therefore provide an important underlying mechanism for a prevalent and important human autoimmune disease.

     (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

2. Columnar processing of border ownership in primate visual cortex

   This article has 2 authors:

   1. Tom P Franken
   2. John H Reynolds

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is a milestone towards understanding the formation and representation of visual object structure in the brain. It shows that in the pivotal area V4, border ownership selectivity emerges in the deep layers earlier than in the granular layers which receive the input from V1/V2, indicating that border ownership is not inherited from the input, but computed by deep-layer neurons using visual context information possibly provided through horizontal connections, cortico-cortical feedback or thalamic input. They further report that the preferred side of border ownership across layers is similar, i.e. it is organized in a columnar fashion. The study is elegantly done, with the outstanding questions clearly laid out and the results presented in a clear and informative fashion.

     (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

3. Initial ciliary assembly in Chlamydomonas requires Arp2/3 complex–dependent endocytosis

   This article has 3 authors:

   1. Brae M. Bigge
   2. Nicholas E. Rosenthal
   3. Prachee Avasthi

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript addresses the role of the Arp2/3 complex in endocytic retrieval of ciliary precursors from the plasma membrane for use in assembly of Chlamydomonas cilia, a topic of broad interest to cell biologists. The manuscript can serve as basis for future research addressing whether Arp2/3 affects cilium biogenesis solely via endocytic retrieval or through additional mechanisms, and whether these findings apply to species other than Chlamydomonas.

     (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

4. Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae

   This article has 15 authors:

   1. Aftab Nadeem
   2. Alexandra Berg
   3. Hudson Pace
   4. Athar Alam
   5. Eric Toh
   6. Jörgen Ådén
   7. Nikola Zlatkov
   8. Si Lhyam Myint
   9. Karina Persson
   10. Gerhard Gröbner
   11. Anders Sjöstedt
   12. Marta Bally
   13. Jonas Barandun
   14. Bernt Eric Uhlin
   15. Sun Nyunt Wai

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Proteins that form pores in biological membranes are found in diverse contexts, including pathogenic toxins that help infect or lyse target cells and organelles. The study by Nadeem et al. reports on the properties of an α-pore-forming toxin, MakA, produced by the human pathogen, V. cholerae. The study is a remarkable example of a pH-induced structural mechanism of membrane remodeling. The insights reported here will be of interest to a wide range of scientists studying host-pathogen interactions, membrane remodeling, and macromolecular structure.

     (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 names with the authors.)

   Reviewed by eLife

5. A bacterial derived plant- mimicking cytokinin hormone regulates social behaviour in a rice pathogen

   This article has 10 authors:

   1. Sohini Deb
   2. Chandan Kumar
   3. Rahul Kumar
   4. Amandeep Kaur
   5. Palash Ghosh
   6. Gopaljee Jha
   7. Prabhu B. Patil
   8. Subhadeep Chatterjee
   9. Hitendra K. Patel
   10. Ramesh V. Sonti

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The major finding of this manuscript is that cytokinin produced by a bacterial plant pathogen affects bacterial growth and physiology. Production of cytokinin is linked to the well-known type three effector XopQ, which has primarily been studied for its function inside plant cells. The authors provide evidence that XopQ is required for the pathogen Xanthomonas oryzae to produce cytokinin in culture, and that cytokinin production controls whether or not the bacterium engages in planktonic growth or biofilm formation (i.e., biofilms form in the absence of cytokinin). These data indicate that bacterially produced cytokinins affect bacterial physiology, indicating that these hormones control signaling beyond photosynthetic organisms. The findings are of interest both to those studying plant-pathogen interactions and to microbiologists in general.

     (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. Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9

   This article has 7 authors:

   1. Lukasz Nierzwicki
   2. Kyle W East
   3. Uriel N Morzan
   4. Pablo R Arantes
   5. Victor S Batista
   6. George P Lisi
   7. Giulia Palermo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is a comprehensive study combining solution NMR with molecular dynamics simulations to uncover the effects of three key mutations in the Cas9 HNH domain that increase CRISP-Cas9 complex specificity and reduce off-target activity. Through the analysis of these three different mutations, the authors concluded that by tuning the conformational dynamics of the HNH module in the CRISP-Cas9 complex, it is possible to control the function and specificity of the system. Combined these findings could have important implications for the design of new variants for this important gene editing complex.

     (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. Assessing target engagement using proteome-wide solvent shift assays

   This article has 5 authors:

   1. Jonathan G Van Vranken
   2. Jiaming Li
   3. Dylan C Mitchell
   4. José Navarrete-Perea
   5. Steven P Gygi

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of broad interest to readers in the field of proteomics and drug discovery. It describes a potentially robust method for the identification of biological targets of small molecules, a substantial hurdle in drug discovery. The experiments described are rigorous and this manuscript provides a useful template for the broad implementation of this method. One conclusion that needs further support is the one of the complementarity of CPP and TPP (as in "these two approaches share much in common, they remain distinct and likely serve to complement one another").

     (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. Physical observables to determine the nature of membrane-less cellular sub-compartments

   This article has 5 authors:

   1. Mathias L Heltberg
   2. Judith Miné-Hattab
   3. Angela Taddei
   4. Aleksandra M Walczak
   5. Thierry Mora

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     There has been a lively debate recently concerning the multiplicity of reported observations of phase-separated compartments inside of cells. Specifically, some claims of phase separation have been challenged, and an alternative model put forward in which clustering of observed particles is due to a clustering of binding sites with no phase separation. The current study does an admirable job of proposing and analyzing ways of distinguishing these two scenarios.

     (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. Gated recurrence enables simple and accurate sequence prediction in stochastic, changing, and structured environments

   This article has 2 authors:

   1. Cédric Foucault
   2. Florent Meyniel

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     There has been a longstanding interest in developing normative models of how humans handle latent information in stochastic and volatile environments. This study examines recurrent neural network models trained on sequence-prediction tasks analogous to those used in human cognitive studies. The results demonstrate that such models lead to highly accurate predictions for challenging sequences in which the statistics are non-stationary and change at random times. This is a novel and remarkable result that opens up new avenues for cognitive modelling.

     (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

10. Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon hepatitis B vaccination

    This article has 19 authors:

    1. George Elias
    2. Pieter Meysman
    3. Esther Bartholomeus
    4. Nicolas De Neuter
    5. Nina Keersmaekers
    6. Arvid Suls
    7. Hilde Jansens
    8. Aisha Souquette
    9. Hans De Reu
    10. Marie-Paule Emonds
    11. Evelien Smits
    12. Eva Lion
    13. Paul G Thomas
    14. Geert Mortier
    15. Pierre Van Damme
    16. Philippe Beutels
    17. Kris Laukens
    18. Viggo Van Tendeloo
    19. Benson Ogunjimi

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      By using modern high-throughput sequencing this paper demonstrates the antibody mediated immune responses that are elicited by vaccination are improved by pre-existing memory CD4 T cell responses. Moreover, the experimental data are an important contribution and may also be useful as a data resource for future research. All reviewers agree that the findings are of great interest. However, there are still some clarifications needed in statistical analytical and validations so they convincingly support the conclusions.

      (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