eLife

Latest preprint reviews

1. Witnessing the structural evolution of an RNA enzyme

   This article has 5 authors:

   1. Xavier Portillo
   2. Yu-Ting Huang
   3. Ronald R Breaker
   4. David P Horning
   5. Gerald F Joyce

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The plasticity of RNA folds and their ability to response to changes in selective pressure is a key aspect of understanding the evolution of life on this planet. The Class I ligase is a remarkably fast RNA ligase ribozyme that has been harnessed by a number of laboratories to power RNA polymerization. Thought by many to be the immutable catalytic core required for polymerization, Portillo et al. demonstrate evolutionary trajectories that result in a new and catalytically enhanced ligase core. An accumulation of mutations results in a the formation of a new pseudoknot structure immediately outside the active site of the ligase core. This new structure appears to more optimally position the P7-P6-P3 coaxially stacked stems of the ligase core with respect to the primer template substrate. Tracking the emergence of this new fold, which is correlated with an enhancement in RNA polymerization activity, is novel and interesting.

     (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

2. Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

   This article has 10 authors:

   1. Angela M Phillips
   2. Katherine R Lawrence
   3. Alief Moulana
   4. Thomas Dupic
   5. Jeffrey Chang
   6. Milo S Johnson
   7. Ivana Cvijovic
   8. Thierry Mora
   9. Aleksandra M Walczak
   10. Michael M Desai

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     CR6261 and CR9114 are two antibodies that bind to the conserved stem of influenza hemagglutinin (HA) through their VH regions and differ by 14-18 mutations from their inferred germline sequences. The authors constructed large combinatorial libraries containing all combinations of 11 and 16 binding-surface mutations for CR6261 and CR9114. These were used in yeast surface display titrations to infer individual and epistatic contributions to binding diverse HAs and to infer possible evolutionary trajectories going from germline to the mature antibodies. The study provides a wealth of knowledge on amino acid contributions to binding affinity. The study informs our understanding of biochemical epistasis, and could potentially serve as a starting point for a more detailed understanding of antibody affinity maturation more generally.

     (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

3. Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

   This article has 7 authors:

   1. Julia M Kreiner
   2. George Sandler
   3. Aaron J Stern
   4. Patrick J Tranel
   5. Detlef Weigel
   6. John R Stinchcombe
   7. Stephen I Wright

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper studies the evolution of herbicide resistance in Amaranthus tuberculatus, a widespread agricultural weed. By illuminating how adaptive mutations arose and spread in this remarkable example of rapid human-induced adaptation, the study will be of interest to a broad audience, ranging from plant biologists interested in herbicide resistance to evolutionary biologists and population geneticists studying the fundamental factors and processes that govern rapid adaptation. The paper applies innovative population genetic methodology to support its primary finding that resistance mutations have evolved multiple times in parallel.

     (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. A conserved strategy for inducing appendage regeneration in moon jellyfish, Drosophila, and mice

   This article has 12 authors:

   1. Michael J Abrams
   2. Fayth Hui Tan
   3. Yutian Li
   4. Ty Basinger
   5. Martin L Heithe
   6. Anish Sarma
   7. Iris T Lee
   8. Zevin J Condiotte
   9. Misha Raffiee
   10. John O Dabiri
   11. David A Gold
   12. Lea Goentoro

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper argues that simple nutritional interventions (L-leucine / insulin / sucrose) can trigger appendage regeneration in species various that do not regenerate appendages in normal conditions. Although the data on Drosophila are not fully convincing and further evidence is needed for this species, in the jellyfish Aurelia and in mice, the results are stunning and provide novel model systems for inducing appendage regeneration in animals and for studying the mechanisms underlying regeneration. These results strengthen an old idea that animals may have an intrinsic capacity to regenerate, which could be revealed by simple (e.g. nutritional) interventions. This paper will be of interest to readers in the field of signaling in regeneration and also in regenerative medicine.

     (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

5. Piezo1 ion channels inherently function as independent mechanotransducers

   This article has 2 authors:

   1. Amanda H Lewis
   2. Jörg Grandl

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The work, when completed, will provide important mechanistic detail on how Piezo channels, the most important and versatile mechanoreceptor molecules, functionally interact in the plane of the plasma membrane. It will be of interest to the field of mechanobiology and sensory mechanotransduction.

     (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. Visualizing formation of the active site in the mitochondrial ribosome

   This article has 7 authors:

   1. Viswanathan Chandrasekaran
   2. Nirupa Desai
   3. Nicholas O Burton
   4. Hanting Yang
   5. Jon Price
   6. Eric A Miska
   7. V Ramakrishnan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Ribosomes are among the most complex molecular machines a cell makes. The work by Chandrasekaran et al. contributes to our understanding of the molecular details of mitochondrial ribosome assembly, and how disruptions to this pathway may cause human disease. Using cryo-EM, the authors identified a subpopulation of immature human mitochondrial large ribosomal subunits that interact with assembly factors NSUN4, MTERF4 and GTPBP7. Based on this structure, they introduce mutations in C. elegans orthologs of these assembly factors that are expected to disrupt binding to the large subunit, and they show that these mutants cause sterility and disrupt mitochondrial proteostasis in the mutant animals. The work does not yet establish a direct link between the putative structural defects of the mutants and the observed developmental defects in C. elegans. Additional studies are needed to test the interesting possibility that this structure represents an on-pathway intermediate of mitoribosome biogenesis and/or ribosome recycling.

     (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

7. TRPM7 is critical for short-term synaptic depression by regulating synaptic vesicle endocytosis

   This article has 11 authors:

   1. Zhong-Jiao Jiang
   2. Wenping Li
   3. Li-Hua Yao
   4. Badeia Saed
   5. Yan Rao
   6. Brian S Grewe
   7. Andrea McGinley
   8. Kelly Varga
   9. Simon Alford
   10. Ying S Hu
   11. Liang-Wei Gong

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Jiang et al. present a study on a novel role of the ion channel TRPM7 in the regulated release of neurotransmitters and hormones. Their analysis focused on TRPM7-deficient chromaffin cells and neurons, which they studied using electrophysiological and imaging techniques. The data indicate that TRPM7 is activated during the compensatory endocytotis process that follows secretory vesicle fusion. This TRPM7 activation increases Ca2+ influx into the cytosol during endocytosis, which boosts endocytosis and reduces the tendency of synapses to progressively fatigue in phases of prolonged stimulation. Multiple aspects of the present findings are novel, interesting, and important - they provide important new insights into the mechanisms by which transmitter and hormone release is fine-tuned. The mechanism of how secretory vesicles, and in particular synaptic vesicles, recycle is important to understand, as impairment in vesicle cycling in turn impairs synaptic transmission, and therefore brain function. However, there are several issues that remain to be addressed before the present data fully justify the conclusions put forward by the authors.

     (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. Individual variations in ‘brain age’ relate to early-life factors more than to longitudinal brain change

   This article has 31 authors:

   1. Didac Vidal-Pineiro
   2. Yunpeng Wang
   3. Stine K Krogsrud
   4. Inge K Amlien
   5. William FC Baaré
   6. David Bartres-Faz
   7. Lars Bertram
   8. Andreas M Brandmaier
   9. Christian A Drevon
   10. Sandra Düzel
   11. Klaus Ebmeier
   12. Richard N Henson
   13. Carme Junqué
   14. Rogier Andrew Kievit
   15. Simone Kühn
   16. Esten Leonardsen
   17. Ulman Lindenberger
   18. Kathrine S Madsen
   19. Fredrik Magnussen
   20. Athanasia Monika Mowinckel
   21. Lars Nyberg
   22. James M Roe
   23. Barbara Segura
   24. Stephen M Smith
   25. Øystein Sørensen
   26. Sana Suri
   27. Rene Westerhausen
   28. Andrew Zalesky
   29. Enikő Zsoldos
   30. Kristine Beate Walhovd
   31. Anders Fjell

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of interest to scientists within the field of lifespan developmental neuroscience. The data analysis is rigorous and the conclusions are justified by the data. The key claims of the manuscript are directly related to, and support, a more reasonable interpretation of previous known findings.

     (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

9. Rotational dynamics in motor cortex are consistent with a feedback controller

   This article has 7 authors:

   1. Hari Teja Kalidindi
   2. Kevin P Cross
   3. Timothy P Lillicrap
   4. Mohsen Omrani
   5. Egidio Falotico
   6. Philip N Sabes
   7. Stephen H Scott

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors use numerical simulations and analyses of neural data from non-human primates to investigate whether rotational dynamics in motor cortical population activity which are typically attributed to recurrent connections can alternatively be explained by sensory feedback alone. They find that neural networks performing the same tasks will produce rotational dynamics even without any internal recurrent units. Overall, this paper examines an important question in the motor control field. The authors should clarify in more detail how the case with no recurrent dynamics has been simulated and address/discuss the role of task structure in their conclusions. Once the authors address issues associated with precisely how they eliminated recurrence from their simulations, the results that rotational dynamics are not necessarily generated autonomously due to recurrent connections will be a valuable and important addition to the ongoing debate about the nature of these rotational dynamics.

     (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

10. TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs

    This article has 10 authors:

    1. Koshlan Mayer-Blackwell
    2. Stefan Schattgen
    3. Liel Cohen-Lavi
    4. Jeremy C Crawford
    5. Aisha Souquette
    6. Jessica A Gaevert
    7. Tomer Hertz
    8. Paul G Thomas
    9. Philip Bradley
    10. Andrew Fiore-Gartland

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The paper by Mayer-Blackwell et al. builds on the idea that TCRs to the same antigen often share sequence similarities, which they quantify using a bespoke tool TCRdist3. Using this tool they develop the idea of a metaclone, a set of TCRs sharing similarities and potentially recognising the same antigen. They further show that such clonotypes show increased sharing between HLA-related individuals, and explore the use of such clonotypes in characterising antigen-specific immune response across cohorts of individuals. The paper is novel and of interest to a broad range of immunologists interested in repertoire. However, as raised in a series of detailed comments by the reviewers, the message of the paper needs to be sharpened and clearly focused on the development of the metaclone concept (with less emphasis on SARS-Cov-2. The concept of the metaclone itself, which is the main message of the paper, needs to be clarified, and characterised.

      (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, ScreenIT