eLife

Latest preprint reviews

1. Transcription initiation at a consensus bacterial promoter proceeds via a ‘bind-unwind-load-and-lock’ mechanism

   This article has 3 authors:

   1. Abhishek Mazumder
   2. Richard H Ebright
   3. Achillefs N Kapanidis

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work aims to provide insight into the molecular mechanism by which RNA polymerase separates the two strands of DNA, generating a single-stranded template for RNA synthesis. Using single-molecule analysis, the authors examined two conformational transitions taking place during RNA transcription initiation: DNA unwinding and RNAP clamp movements. Pending addition of some important controls, the paper will help to distinguish between two competing hypotheses within the literature. The work will be of relevance to a wide range of researchers interested in the molecular basis of gene expression and gene regulation.

     (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. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth

   This article has 4 authors:

   1. Marco Marconi
   2. Marcal Gallemi
   3. Eva Benkova
   4. Krzysztof Wabnik

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper describes the development of a mechano-chemical model for plant root development. As such, it presents a significant advance relative to other root models that have focussed predominantly on either the mechanical or auxin patterning aspects of root development, as evidenced by the potential of the model to reproduce a series of hormonal and mechanical perturbation experiments. The current conclusion that a set of minimal principles for self-organized root tip patterning is revealed must be moderated, as patterning inputs are essential to produce the reported observations.

     (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

3. Tightly coupled inhibitory and excitatory functional networks in the developing primary visual cortex

   This article has 4 authors:

   1. Haleigh N Mulholland
   2. Bettina Hein
   3. Matthias Kaschube
   4. Gordon B Smith

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Mulholland et al show that there is a very close relationship between the development of excitatory and inhibitory networks in the developing cortex. This paper makes an important contribution to our understanding of the structure of inhibition during an early stage in cortical development. It is therefore of great interest to scientists interested in development, and in computation in cortical circuits. The work has been carefully performed and analysed.

     (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. Virtual mouse brain histology from multi-contrast MRI via deep learning

   This article has 10 authors:

   1. Zifei Liang
   2. Choong H Lee
   3. Tanzil M Arefin
   4. Zijun Dong
   5. Piotr Walczak
   6. Song-Hai Shi
   7. Florian Knoll
   8. Yulin Ge
   9. Leslie Ying
   10. Jiangyang Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper demonstrates how MRI can be used to mimic histological measures. This is something that the field of MRI has dubbed virtual histology (or MR-histology) for a while, but to my knowledge this paper is the first convincing demonstration that it can be achieved. The paper combines open access mouse histology data from the Allen Institute with their own multimodal post-mortem MRI, and using deep convolutional networks, are able to build models that map MRI data onto multiple histological contrasts. Some of the results are impressive, such as predicting the outcome of histology on mutant shiverer mice.

     (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. Proof of concept for multiple nerve transfers to a single target muscle

   This article has 12 authors:

   1. Matthias Luft
   2. Johanna Klepetko
   3. Silvia Muceli
   4. Jaime Ibáñez
   5. Vlad Tereshenko
   6. Christopher Festin
   7. Gregor Laengle
   8. Olga Politikou
   9. Udo Maierhofer
   10. Dario Farina
   11. Oskar C Aszmann
   12. Konstantin Davide Bergmeister

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The study uses a novel rodent surgical model for establishing that dual nerve transfer in the upper extremity improves neuromuscular regeneration in comparison to single nerve transfer. The authors provide a detailed description of how the model is developed and they characterize neuromuscular regeneration through nerve crush, neurotomy, behavioral analysis, and retrograde labeling. The nerve transfer method is clearly delineated for researchers to use in future scientific and clinical applications. The evidence clearly support the main study conclusions. Thus, this manuscript is of great interest to readers in the field of peripheral nerve repair and neural interfaces.

     (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

6. STING mediates immune responses in the closest living relatives of animals

   This article has 6 authors:

   1. Arielle Woznica
   2. Ashwani Kumar
   3. Carolyn R Sturge
   4. Chao Xing
   5. Nicole King
   6. Julie K Pfeiffer

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors addressed the role of a STING ortholog in antimicrobial defense of choanoflagellates. The analysis of the response of the choanoflagellate Monosiga brevicollis to a variety of bacterial species revealed that exposure of M. brevicollis to Pseudomonas aeruginosa conditioned medium results in choanoflagellate death and the authors found that this is dependent on the newly discovered ortholog of STING. Characterization reveals that the STING response can be induced by 2'3' cGAMP, which parallels the activation of STING in diverse species. In addition, the finding that cyclic dinucleotide treatment induces autophagy also has parallels with the effector pathways observed in other organisms. There are a number of strengths as outlined by the Reviewers. First, the development of a Choanaoflagellate model system to study innate immunity, second with the development of genetics for M. brevicollis, third, the demonstration of a functional STING system in one of the closest relatives to animals and fourth, that cell death occurs in response to cyclic dinucleotides.

     (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, preLights

7. Fast and accurate annotation of acoustic signals with deep neural networks

   This article has 5 authors:

   1. Elsa Steinfath
   2. Adrian Palacios-Muñoz
   3. Julian R Rottschäfer
   4. Deniz Yuezak
   5. Jan Clemens

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper presents and evaluates a machine learning method for segmenting and annotating animal acoustic communication signals. The paper presents results from applying the method to signals from Drosophila, mice, and songbirds, but the method should be useful for a broad range of researchers who record animal vocalizations. The method appears to be easily generalizable and has high throughput and modest training times.

     (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

8. Causal roles of prefrontal cortex during spontaneous perceptual switching are determined by brain state dynamics

   This article has 1 author:

   1. Takamitsu Watanabe

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     By combining real-time closed-loop EEG-TMS and computational modelling, this study ambitiously examined the causal role of prefrontal cortex in resolving perceptual ambiguity. It impressively demonstrates brain-state-dependent effects on bistable perception.

     (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. Experimental evidence that chronic outgroup conflict reduces reproductive success in a cooperatively breeding fish

   This article has 2 authors:

   1. Ines Braga Goncalves
   2. Andrew N Radford

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper uses controlled exposure to territorial intrusion to show that repeated exposure to conflict between groups compromises fitness in social fish. With a host of results relating to fertility, behavior, and parental investment, its findings will increase confidence in the argument that intergroup conflict is an important factor in social evolution. There are several statistical issues that should be addressed to minimize the possibility of false-positive 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

10. An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation

    This article has 4 authors:

    1. Rui Fang
    2. Jason Hon
    3. Mengying Zhou
    4. Ying Lu

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      AAA+ ATPases consume chemical energy in form of ATP to catalyze essential cellular reactions. Here, computational and biochemical approaches are used to model how the six subunits of the AAA+ ATPase Rpt1-6 coordinate their enzymatic activity with each other to exert unidirectional pulling forces on target polypeptide chains that promote protein unfolding. Although the technical aspects of the work are sometimes difficult to follow, the findings indicate that the order in which ATPase active sites fire is generally sequential, much like a rotary engine. The system can tolerate "misfires" - instances in which a subunit fails to hydrolyze ATP - by skipping the problematic subunit. The work should appeal to the broad AAA+ community and researchers trying to understand the biophysical principles by which complex biological machines operate.

      (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