eLife

Latest preprint reviews

1. 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

2. 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

3. 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

4. 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

5. 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

6. Kinesin-1, -2, and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport

   This article has 7 authors:

   1. Allison M Gicking
   2. Tzu-Chen Ma
   3. Qingzhou Feng
   4. Rui Jiang
   5. Somayesadat Badieyan
   6. Michael A Cianfrocco
   7. William O Hancock

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In their study, Gicking et al. study the physical properties of artificial complexes composed of the dynein-dynactin-BicD2 (DDB) complex linked to one of three classes of kinesins (1, 2, or 3) via a DNA scaffold. They find that all three kinesins can move to the plus-end of microtubules when coupled to the DDB complex. This is surprising because motors in the kinesin-2 and kinesin-3 families have been shown to have a higher load sensitivity. However, the authors show that the faster reattachment kinetics of these motors compensate for their faster detachment rates under load. This work is relevant to both the biophysics field for advancing knowledge in fundamental science, and in the neuroscience field since disruption of neuronal transport leads to a variety of neurodegenerative 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

7. Chronic Ca2+ imaging of cortical neurons with long-term expression of GCaMP-X

   This article has 15 authors:

   1. Jinli Geng
   2. Yingjun Tang
   3. Zhen Yu
   4. Yunming Gao
   5. Wenxiang Li
   6. Yitong Lu
   7. Bo Wang
   8. Huiming Zhou
   9. Ping Li
   10. Nan Liu
   11. Ping Wang
   12. Yubo Fan
   13. Yaxiong Yang
   14. Zengcai V Guo
   15. Xiaodong Liu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper addresses the toxicity of fluorescent calcium indicators, comparing two series of indicators (GCaMPs and GCaMP-Xs) in mouse neurons. The paper documents GCaMP toxicity during development and following prolonged strong expression, and establishes that GCaMP-X indicators are less toxic. The paper will be of interest primarily to neuroscientists who use fluorescence calcium indicators to monitor calcium dynamics during neuronal development.

     (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

8. Landmark-based spatial navigation across the human lifespan

   This article has 8 authors:

   1. Marcia Bécu
   2. Denis Sheynikhovich
   3. Stephen Ramanoël
   4. Guillaume Tatur
   5. Anthony Ozier-Lafontaine
   6. Colas N Authié
   7. José-Alain Sahel
   8. Angelo Arleo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is an important study that investigates whether older adults have selective impairments in allocentric navigation (using distal cues to navigate). Using a combination of ecologically inspired real-world navigation, virtual reality, eye tracking, and body-tracking, the study reports, for the first time, that older adults show no difference from younger adults when using geometry to navigate a Y maze. Instead, their deficits appear to relate to perceptual difficulties with processing individual landmarks. This large sample study therefore provides somewhat compelling evidence of age-related difficulties in processing landmarks visually rather than a selective deficit in allocentric navigation.

     (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

9. Hepatic AMPK signaling dynamic activation in response to REDOX balance are sentinel biomarkers of exercise and antioxidant intervention to improve blood glucose control

   This article has 10 authors:

   1. Meiling Wu
   2. Anda Zhao
   3. Xingchen Yan
   4. Hongyang Gao
   5. Chunwang Zhang
   6. Xiaomin Liu
   7. Qiwen Luo
   8. Feizhou Xie
   9. Shanlin Liu
   10. Dongyun Shi

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     There is a debate whether ROS (reactive oxygen species) generated through redox signaling could be a friend or foe. There are several paradoxical studies (both animal and human) wherein exercise health benefits were reported to be accompanied by increases in ROS generation. Utilizing the in-vitro studies as well as mice model work, this manuscript illustrates the different regulatory mechanisms of exercise and antioxidant intervention on redox balance and blood glucose level in diabetes. The manuscript does address some advancements in the area of research specialization.

     (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. High-throughput automated methods for classical and operant conditioning of Drosophila larvae

    This article has 10 authors:

    1. Elise C Croteau-Chonka
    2. Michael S Clayton
    3. Lalanti Venkatasubramanian
    4. Samuel N Harris
    5. Benjamin MW Jones
    6. Lakshmi Narayan
    7. Michael Winding
    8. Jean-Baptiste Masson
    9. Marta Zlatic
    10. Kristina T Klein

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      A new and interesting operant conditioning paradigm is established for the Drosophila larva. A novel role for serotonergic pathways in the VNC in operant learning points to new circuits and mechanisms for learning and memory. Impressive technology opens doors for new and exciting studies on learned behavior in the small and tractable circuits of the larva.

      (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