eLife

Latest preprint reviews

1. Neural underpinning of a respiration-associated resting-state fMRI network

   This article has 2 authors:

   1. Wenyu Tu
   2. Nanyin Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to researchers studying control of respiration and also those developing functional magnetic resonance imaging methodology. The work provides insight into the relationship between brain activity (measured directly) and non-invasive functional magnetic resonance imaging measures. The authors find that the respiration signal is associated with the gamma band in the cingulate cortex, and both the gamma signal and respiration signal correlate with distributed neuronal networks across the brain. This contributes to our knowledge of the contribution of respiration on neuro and neuro-vascular signals during resting conditions.

     (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. A DARPin-based molecular toolset to probe gephyrin and inhibitory synapse biology

   This article has 5 authors:

   1. Benjamin FN Campbell
   2. Antje Dittmann
   3. Birgit Dreier
   4. Andreas Plückthun
   5. Shiva K Tyagarajan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors developed a set of synthetic proteins, Designed Ankyrin Repeat Proteins (DARPins), that bind gephyrin, the main scaffold protein at inhibitory postsynaptic sites, and characterize them extensively to study gephyrin cluster morphology and biochemistry. In several aspects, DARPins outperform traditional antibodies. This study is clear, well organized and well written, demonstrating that DARPins can be important tools synaptic, cellular and circuit neuroscience 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. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

3. Molecular mechanism of Afadin substrate recruitment to the receptor phosphatase PTPRK via its pseudophosphatase domain

   This article has 6 authors:

   1. Iain M Hay
   2. Katie E Mulholland
   3. Tiffany Lai
   4. Stephen C Graham
   5. Hayley J Sharpe
   6. Janet E Deane

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     These studies establish a role for the D2 pseudophosphatase domain of the PTPRK receptor-like phosphotyrosine phosphatase in recruiting Afadin, a cell-cell junction protein that is reported to be a PTPRK substrate, for dephosphorylation by the active D1 phosphatase domain. These findings suggest that the D2 pseudophosphatase domains of RPTPKs might have a general function as platforms to recruit specific phosphotyrosine substrates.

     (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

4. Visual experience has opposing influences on the quality of stimulus representation in adult primary visual cortex

   This article has 4 authors:

   1. Brian B Jeon
   2. Thomas Fuchs
   3. Steven M Chase
   4. Sandra J Kuhlman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The present manuscript examines cortical representations of basic visual attributes following a manipulation shown to enhance plasticity in the adult brain: binocular dark exposure for several days, followed by light re-introduction. The work has fundamental therapeutic and conceptual implications, and will be of potential interest to a broad readership of vision scientists, neuroscientists, clinicians and modelers. The paper is well-written and based on sophisticated experiments. The evidence provided convincingly supports the authors' contention that dark exposure does not have a negative impact on visual representations in V1. The study uses a generally appropriate study design. However, it would benefit from the addition of some key experimental details, and additional analyses and statistical tests to explore alternative interpretations of results.

     (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

5. The circadian clock controls temporal and spatial patterns of floral development in sunflower

   This article has 4 authors:

   1. Carine M Marshall
   2. Veronica L Thompson
   3. Nicky M Creux
   4. Stacey L Harmer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This paper, of relevance to a broad range of plant biologists and colleagues in the circandian field, reports important results that demonstrate circadian coordination of characteristic floral development in sunflower. The current manuscript includes convincing observations and possible hypotheses, but the ecological relevance of the temporally-controlled flower development is incompletely shown.

   Reviewed by eLife

6. Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis

   This article has 12 authors:

   1. Andrew I Wong
   2. Tiago Beites
   3. Kyle A Planck
   4. Rachael A Fieweger
   5. Kathryn A Eckartt
   6. Shuqi Li
   7. Nicholas C Poulton
   8. Brian C VanderVen
   9. Kyu Y Rhee
   10. Dirk Schnappinger
   11. Sabine Ehrt
   12. Jeremy Rock

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Bacteria living in stressful and fluctuating environments need to respond to changing conditions. Many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis, use cAMP as a secondary messenger to sense and respond to specific stimuli. What distinguishes M. tuberculosis, is that its genome encodes for at least 15 adenylate cyclases, enzymes that synthesize cAMP from ATP. The authors characterized one specific adenylate cyclase, Rv3645, and demonstrate that it is the most significant contributor to cAMP levels and mediates fatty acid metabolism and antibiotic resistance. This manuscript will be of broad interest to readers in the field of tuberculosis drug discovery and bacterial metabolism.

     (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

7. Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq

   This article has 36 authors:

   1. Sara E Vazquez
   2. Sabrina A Mann
   3. Aaron Bodansky
   4. Andrew F Kung
   5. Zoe Quandt
   6. Elise MN Ferré
   7. Nils Landegren
   8. Daniel Eriksson
   9. Paul Bastard
   10. Shen-Ying Zhang
   11. Jamin Liu
   12. Anthea Mitchell
   13. Irina Proekt
   14. David Yu
   15. Caleigh Mandel-Brehm
   16. Chung-Yu Wang
   17. Brenda Miao
   18. Gavin Sowa
   19. Kelsey Zorn
   20. Alice Y Chan
   21. Veronica M Tagi
   22. Chisato Shimizu
   23. Adriana Tremoulet
   24. Kara Lynch
   25. Michael R Wilson
   26. Olle Kämpe
   27. Kerry Dobbs
   28. Ottavia M Delmonte
   29. Rosa Bacchetta
   30. Luigi D Notarangelo
   31. Jane C Burns
   32. Jean-Laurent Casanova
   33. Michail S Lionakis
   34. Troy R Torgerson
   35. Mark S Anderson
   36. Joseph L DeRisi

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work presents a series of enhancements to the PhIP-seq method of autoantibody discovery, with the goal of improving scaling to larger cohorts and increasing disease specificity. The strength of the paper is the validation of the high throughput format, although results from screening patient samples confirm or only modestly extend previous 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 #1 agreed to share their name with the authors.)

   Reviewed by eLife, ScreenIT

8. Inhibited KdpFABC transitions into an E1 off-cycle state

   This article has 10 authors:

   1. Jakob M Silberberg
   2. Charlott Stock
   3. Lisa Hielkema
   4. Robin A Corey
   5. Jan Rheinberger
   6. Dorith Wunnicke
   7. Victor RA Dubach
   8. Phillip J Stansfeld
   9. Inga Hänelt
   10. Cristina Paulino

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     KdpFABC is a bacterial potassium uptake transporter made up of a channel-like subunit (KdpA) and a P-type ATPase (KdpB). When potassium levels are low (< 2 mM), the transporter actively and selectively uptakes potassium, but must be switched off again to prevent excessive K+ accumulation. Although structures of KdpFABC have been determined before, the structural basis for inhibition by phosphorylation is unknown. Here, the authors have determined the structure of KdpABC in an arrested (off-state) that is in a distinct conformation from previously determined P-type ATPase structures. More detailed structural comparisons are needed to more convincingly show this, however, and the protein required to inhibit KdpABC by phosphorylation remains unknown. This paper will be of interest to researchers in the microbiology and transporter communities.

     (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. Targeting RNA:protein interactions with an integrative approach leads to the identification of potent YBX1 inhibitors

   This article has 14 authors:

   1. Krystel El Hage
   2. Nicolas Babault
   3. Olek Maciejak
   4. Bénédicte Desforges
   5. Pierrick Craveur
   6. Emilie Steiner
   7. Juan Carlos Rengifo-Gonzalez
   8. Hélène Henrie
   9. Marie-Jeanne Clement
   10. Vandana Joshi
   11. Ahmed Bouhss
   12. Liya Wang
   13. Cyril Bauvais
   14. David Pastré

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Protein-RNA interactions are involved in many diseases and targeting them with drugs can be valuable. Because protein-RNA complexes are considered difficult to target both computationally and experimentally, an integrated computational-experimental approach to solve this limitation is introduced. The approach is demonstrated by targeting the mRNA-binding protein YB-1, which works remarkably well. Inhibitors in the micromolar range are detected, including a previously approved drug. The main strength here is the proof of concept that protein-RNA interactions are targetable. However, additional data are required to support the central claims of the paper.

     (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. EZ Clear for simple, rapid, and robust mouse whole organ clearing

    This article has 8 authors:

    1. Chih-Wei Hsu
    2. Juan Cerda
    3. Jason M Kirk
    4. Williamson D Turner
    5. Tara L Rasmussen
    6. Carlos P Flores Suarez
    7. Mary E Dickinson
    8. Joshua D Wythe

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The manuscript reports a new tissue clearing procedure that is faster (clearing within 48 hours), uses less hazardous chemicals, and importantly appears to result in less tissue volume change compared to other methods. The simple protocol adds further to the toolbox of tissue clearing methods and is one that is likely to be even more popular than many current methods, although the scope of tissue on which it can be used and rigorous comparisons to existing protocols have not been fully investigated.

      (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