eLife

Latest preprint reviews

1. Bayesian inference of kinetic schemes for ion channels by Kalman filtering

   This article has 4 authors:

   1. Jan L Münch
   2. Fabian Paul
   3. Ralf Schmauder
   4. Klaus Benndorf

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: The manuscript is well written and overall clear, and the mathematical treatment is a rigorous tour-de-force. However, the reviewers raised a number of points that need further clarification, better discussion or amendment. These concerns are likely to be addressable largely by changes to the main text and software documentation along with some additional analyses. The study is very nice and ambitious, but clarity is a bit impaired by dealing with perhaps too many issues. The state inference and the bayesian model selection are very important but completely different issues. The authors should consider whether they may be better treated separately, or for a more specialized audience.

   Reviewed by eLife

2. Local circuit allowing hypothalamic control of hippocampal area CA2 activity and consequences for CA1

   This article has 11 authors:

   1. Vincent Robert
   2. Ludivine Therreau
   3. Vivien Chevaleyre
   4. Eude Lepicard
   5. Cécile Viollet
   6. Julie Cognet
   7. Arthur JY Huang
   8. Roman Boehringer
   9. Denis Polygalov
   10. Thomas J McHugh
   11. Rebecca Ann Piskorowski

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: The study describes the properties of inputs from the supramammillary nucleus (SuM) to the CA2 area of the hippocampus. Novel information is presented by the influence of the SuM input on the local hippocampal network in the CA2 and what the effect of this input is on network activity in the CA1. The authors use complementary methods to address this question including patch-clamp recordings and optogenetics. Overall the reviewers found this study important, the experiments well-designed and the data of high quality. However, there are several key points raised by the reviewers to strengthen the data in order to fully support the authors' conclusions, and addressing these will require additional experimental work. The list below summarizes the list of required experiments reviewers agreed would be necessary for having full confidence in the authors' conclusions:

     1. The authors would need to show the effect of SuM stimulation on synaptically triggered APs and not only on Aps evoked with a current step.

     2. The change in the balance of EPCs and IPSCs in a train should be demonstrated in a single cell.

     3. The properties of monosynaptic/disynaptic events should be compared and the lack of direct GABAergic input from the SuM demonstrated. The authors should quantify the delay time to light-evoked IPSCs to address whether the SuM-CA2 inputs are forming monosynaptic or disynaptic GABAergic connections to pyramidal neurons, as it is possible SuM neurons co-release glutamate and GABA to CA2. Given the importance of the mono vs. disynaptic innervation of different types of cells, the authors should go beyond the TTX experiments (as TTX would block a disynaptic EPSC) and also use 4-AP to recover the TTX blocked current to unequivocally prove that they inputs are monosynaptic.

     4. The preferential role of PV+ cells should be shown with a more selective pharmacological approach.

     5. The authors should elaborate on how SuM stimulation influences theta/gamma rhythms in the CA1 area.

     This manuscript is under revision at eLife.

   Reviewed by eLife

3. Expansin-controlled cell wall stiffness regulates root growth in Arabidopsis

   This article has 10 authors:

   1. Marketa Samalova
   2. Kareem Elsayad
   3. Alesia Melnikava
   4. Alexis Peaucelle
   5. Evelina Gahurova
   6. Jaromir Gumulec
   7. Ioannis Spyroglou
   8. Elena V. Zemlyanskaya
   9. Elena V. Ubogoeva
   10. Jan Hejatko

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: The reviewers felt that this is important work because in vivo characterization of expansins has lagged far behind their in vitro characterization. However, both reviewers also made important points about additional controls and statistical comparisons that are required to fully interpret and appreciate the results that are presented here. It seems that the role of expansins in the plant cell wall may be complex and nuanced. However, it is clear from the author's discussion of their results that significant further experimentation is required to bring new insight to the function of expansins in mediating plant root growth.

   Reviewed by eLife

4. Auditory detection is modulated by theta phase of silent lip movements

   This article has 5 authors:

   1. Emmanuel Biau
   2. Danying Wang
   3. Hyojin Park
   4. Ole Jensen
   5. Simon Hanslmayr

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: The reviewers agreed that the paradigm proposed in this work is elegant, and the question timely and important. However, as detailed below, they highlighted several concerns about analysis choices and the interpretation of the data. While some of these can be addressed, it was felt that a major drawback of the present manuscript is that the behaviour and EEG are obtained separately and any links are hence only circumstantial.

   Reviewed by eLife

5. Detecting fine and elaborate movements with piezo sensors, from heartbeat to the temporal organization of behavior

   This article has 11 authors:

   1. Maria Isabel Carreño-Muñoz
   2. Maria Carmen Medrano
   3. Thomas Leinekugel
   4. Maelys Bompart
   5. Fabienne Martins
   6. Enejda Subashi
   7. Franck Aby
   8. Andreas Frick
   9. Marc Landry
   10. Manuel Grana
   11. Xavier Leinekugel

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: The need to easily measure spontaneous behaviors in a robust fashion in experimental animals is an important problem in behavioral neuroscience. Thus, while this study is timely, the reviewers found fundamental flaws that substantially dampen enthusiasm for this work. The collective major concerns are: 1) the advance provided by this system, relative to already existing and commercially available software based on similar principles, was not clear, 2) critical technical details describing this system are missing 3) the diverse biological applications were not explored with sufficient depth and many of the related claims had potential alternative explanations.

   Reviewed by eLife

6. Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

   This article has 41 authors:

   1. Xavier A. Harrison
   2. Allan D. McDevitt
   3. Jenny C. Dunn
   4. Sarah Griffiths
   5. Chiara Benvenuto
   6. Richard Birtles
   7. Jean P. Boubli
   8. Kevin Bown
   9. Calum Bridson
   10. Darren Brooks
   11. Samuel S. Browett
   12. Ruth F. Carden
   13. Julian Chantrey
   14. Friederike Clever
   15. Ilaria Coscia
   16. Katie L. Edwards
   17. Natalie Ferry
   18. Ian Goodhead
   19. Andrew Highlands
   20. Jane Hopper
   21. Joseph Jackson
   22. Robert Jehle
   23. Mariane da Cruz Kaizer
   24. Tony King
   25. Jessica M. D. Lea
   26. Jessica L. Lenka
   27. Alexandra McCubbin
   28. Jack McKenzie
   29. Bárbara Lins Caldas de Moraes
   30. Denise B. O’Meara
   31. Poppy Pescod
   32. Richard F. Preziosi
   33. Jennifer K. Rowntree
   34. Susanne Shultz
   35. Matthew J. Silk
   36. Jennifer E. Stockdale
   37. William O. C. Symondson
   38. Mariana Villalba de la Pena
   39. Susan L. Walker
   40. Michael D. Wood
   41. Rachael E. Antwis

   Reviewed by eLife

7. Cardiolipin targets a dynamin-related protein to the nuclear membrane

   This article has 3 authors:

   1. Usha Pallabi Kar
   2. Himani Dey
   3. Abdur Rahaman

   Reviewed by eLife, Review Commons

8. Integron activity accelerates the evolution of antibiotic resistance

   This article has 3 authors:

   1. Célia Souque
   2. José Antonio Escudero
   3. R Craig MacLean

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: In this manuscript, the authors test the long-standing "evolution-on-demand" hypothesis of integrons. Using a combination of genetic construction work, experimental evolution, and WGS the authors present a convincing body of work favoring the presented hypothesis. They introduce three antibiotic gene cassettes into an integron and use an "evolutionary ramp" approach with gentamicin and demonstrate that the gentamicin resistance cassette shuffles towards the start of the integron. This provides compelling evidence favoring the evolutionary effects of an active class 1 integrase.

     The paper is clear, well written and demonstrates neatly the benefits of integron shuffling. The authors should also be given credit for including experimental data from an integron containing a clinical plasmid including resistance cassettes to the last resort antibiotics carbapenems. This is largely missing in the field.

     Our overall assessment of the manuscript is positive. However, a number of questions have been raised regarding the mechanistic aspects and conclusions of the paper. We are therefore suggesting additional assays to measure phenotypic effects of evolved integrons, and possibly data analyses on the negative controls. If these are not possible to perform, the main conclusions could be slightly altered instead to focus more on the genomics. Finally, we provide some suggestions on making the discussion more balanced and in clarifying the role of chromosomal mutations in the integron-facilitated evolution.

   Reviewed by eLife

9. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells

   This article has 8 authors:

   1. Juan Carlos Jado
   2. Michelle Dow
   3. Krypton Carolino
   4. Adam Klie
   5. Gregory J. Fonseca
   6. Trey Ideker
   7. Hannah Carter
   8. Elizabeth A. Winzeler

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: The authors examined the genomic basis of resistance evolution in human chronic myelogenous leukemia (CML) near-haploid cell lines to 5 separate chemotherapeutic agents.

     Using either whole genome or whole exome analysis, they found numerous instances of single nucleotide polymorphisms and copy number variants, including amplifications and deletions, among lines. They then used subsequent knockdown or knockout experiments to confirm that these variants, in fact, lead to increased resistance in these lines.

     The work is interesting, timely, and has potential clinical implications. For example, the resistance alleles identified here could be closely examined in future studies in order to develop treatment strategies. However, the experimental design has certain limitations, advances in understanding chemotherapy resistance mechanisms is currently modest, and the presentation of results can be improved. We feel overall that these could be addressed, but that they will require significant extra experimental work.

   Reviewed by eLife

10. All-trans retinoic acid induces synaptic plasticity in human cortical neurons

    This article has 7 authors:

    1. Maximilian Lenz
    2. Pia Kruse
    3. Amelie Eichler
    4. Jakob Straehle
    5. Jürgen Beck
    6. Thomas Deller
    7. Andreas Vlachos

    This article has been curated by 1 group:

    • Curated by eLife

      Summary: All three reviewers are highly enthusiastic about the study reporting the acute effects of retinoic acid on excitatory synaptic transmission and its underlying mechanisms. The experiments are well executed and the results convincing. Aside from some minor comments that require minimal additional experiments or further clarification, the reviewers expressed one major concern regarding the dentate gyrus LTP data. Although further experiments are required to clarify the concerns, the reviewers recommended removing the LTP figure from the present study as it is not well connected with the rest of the study.

    Reviewed by eLife