eLife

Latest preprint reviews

1. Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes

   This article has 3 authors:

   1. Martina Milighetti
   2. John Shawe-Taylor
   3. Benny Chain

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript reports a new approach to the important and challenging problem of predicting T cell receptor:peptide-MHC interactions, one that relies on molecular model building (with previously published tools) followed by feature extraction and machine learning. The strengths of the study are more conceptual than practical: the overall framework and analytical approach; a balanced, critical assessment of the method's performance (which does not shy away from negative results); some observations on TCR:pMHC docking geometry. On the practical side, the classifier does not appear to generalize well to unseen epitopes (neither do the published tools it's compared to), so at the end of the day it's not clear that it will be preferable to simpler sequence-based approaches.

     (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

2. TALPID3/KIAA0586 Regulates Multiple Aspects of Neuromuscular Patterning During Gastrointestinal Development in Animal Models and Human

   This article has 20 authors:

   1. Jean Marie Delalande
   2. Nandor Nagy
   3. Conor J. McCann
   4. Dipa Natarajan
   5. Julie E. Cooper
   6. Gabriela Carreno
   7. David Dora
   8. Alison Campbell
   9. Nicole Laurent
   10. Polychronis Kemos
   11. Sophie Thomas
   12. Caroline Alby
   13. Tania Attié-Bitach
   14. Stanislas Lyonnet
   15. Malcolm P. Logan
   16. Allan M. Goldstein
   17. Megan G. Davey
   18. Robert M. W. Hofstra
   19. Nikhil Thapar
   20. Alan J. Burns

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, the authors used a chick and a mouse model and human tissues to analyze the role of the conserved protein TALPID3/KIAA0586, previously linked to ciliogenesis, in gut development. Using a multi-species approach, the authors conclude that TALPID3 has an evolutionary conserved role in regulating gut patterning along the radial axis, apparently orchestrated by neural crest cells in a non-cell-autonomous manner and mediated by perturbation of Sonic Hedgehog signaling and the composition of extracellular matrix.

     (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

3. All-Optical Electrophysiology in hiPSC-Derived Neurons With Synthetic Voltage Sensors

   This article has 17 authors:

   1. Francesca Puppo
   2. Sanaz Sadegh
   3. Cleber A. Trujillo
   4. Martin Thunemann
   5. Evan P. Campbell
   6. Matthieu Vandenberghe
   7. Xiwei Shan
   8. Ibrahim A. Akkouh
   9. Evan W. Miller
   10. Brenda L. Bloodgood
   11. Gabriel A. Silva
   12. Anders M. Dale
   13. Gaute T. Einevoll
   14. Srdjan Djurovic
   15. Ole A. Andreassen
   16. Alysson R. Muotri
   17. Anna Devor

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be interesting for people performing all optical electrophysiology. It describes a new combination of previously available genetic tools to allow simultaneous optogenetic manipulation and optical electrophysiology. The manuscript does not provide a major conceptual advance but provides good evidence that this assay can be employed for large-scale screening in hIPSC-derived neurons.

     (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

4. Transthyretin Promotes Axon Growth via Regulation of Microtubule Dynamics and Tubulin Acetylation

   This article has 8 authors:

   1. Jessica Eira
   2. Joana Magalhães
   3. Nídia Macedo
   4. Maria Elena Pero
   5. Thomas Misgeld
   6. Mónica M. Sousa
   7. Francesca Bartolini
   8. Márcia A. Liz

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In their manuscript, Eira et al. investigate the role of transthyretin in promoting axon elongation by modulating microtubule dynamics. The data point to a possible role of transthyretin in regulating microtubule dynamics by modulating tubulin acetylation levels during axon outgrowth. With additional support to strengthen this conclusion, the paper will be of interest to those in the neurodevelopment, neurodegeneration, and microtubule cytoskeleton 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.The reviewers remained anonymous to the authors.)

   Reviewed by eLife

5. The aversive value of pain in human decision‐making

   This article has 3 authors:

   1. Hocine Slimani
   2. Pierre Rainville
   3. Mathieu Roy

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This behavioural study in healthy participants examines how people trade-off a brief phasic pain stimulus with a monetary reward, reporting a quadratic effect of pain on decision making. It supports and adds to previous findings of a context-dependency deriving from the distribution of rewards, which is a deviation from conventional rational choice theory (which proposes that a particular level of pain should carry the same price, regardless of small context changes). Broadly, the reviewers found the work well executed and the data compelling, but there were some suggestions for alternative explanations that are not ruled out given the current 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

6. Single-cell atlas of early chick development reveals gradual segregation of neural crest lineage from the neural plate border during neurulation

   This article has 4 authors:

   1. Ruth M Williams
   2. Martyna Lukoseviciute
   3. Tatjana Sauka-Spengler
   4. Marianne E Bronner

   This article has been curated by 1 group:

   • Curated by eLife

     Public Evaluation Summary:

     Determining when cells acquire their individual identity is critical for understanding the patterning and growth of embryos. The authors use state-of-the-art methods to map the lineages of cells that emerge during the earliest stages of development in chick embryos and that contribute to the central and peripheral nervous system. The authors have characterised the gene signature of ectoderm sub-clusters and used algorithms to infer lineage trajectories using the dataset. However, the analysis of placode and neural crest emergence is not clear-cut or well supported by in vivo experiments in the embryo. The work overall will be of broad interest to developmental and stem cell biologists, as well as neurobiologists interested in the understanding of the neural and neural crest gene regulatory networks.

     (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

7. Linking spatial self-organization to community assembly and biodiversity

   This article has 4 authors:

   1. Bidesh K Bera
   2. Omer Tzuk
   3. Jamie JR Bennett
   4. Ehud Meron

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this paper, the authors use a mathematical model of plant and water dynamics in drylands to show that drylands adaptive capacity to respond to changes, via spatial self-organization in space, has also beneficial effects in preserving its biodiversity and ecosystem functions. The current study extends previous work by considering a trait diversity gradient that ranges from stress-tolerant to fast-growing plant species.

     (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 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

8. A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria

   This article has 11 authors:

   1. Sofiene Seef
   2. Julien Herrou
   3. Paul de Boissier
   4. Laetitia My
   5. Gael Brasseur
   6. Donovan Robert
   7. Rikesh Jain
   8. Romain Mercier
   9. Eric Cascales
   10. Bianca H Habermann
   11. Tâm Mignot

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this manuscript, the authors explore mechanisms involved in predation of other bacteria by Myxococcus xanthus. They identify two gene clusters, which encode proteins with homology to proteins of the Tad pilus system and some of which are important for predation. The work represents a good starting point for understanding how Myxococcus cells may engage in contact-dependent killing of other bacteria.

     (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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

9. Information content differentiates enhancers from silencers in mouse photoreceptors

   This article has 6 authors:

   1. Ryan Z Friedman
   2. David M Granas
   3. Connie A Myers
   4. Joseph C Corbo
   5. Barak A Cohen
   6. Michael A White

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest to geneticists seeking to establish rules that govern gene regulation. To explain why a sequence enhances, rather than silences, gene transcription the authors draw our attention away from the binding of a single transcription factor, to focus instead on the number and diversity of transcription factor molecules that bind to it. Using a relatively simple metric called sequence information content they appear to be able to improve the prediction of enhancer over silencer sequences. A concern is whether the silencers are true silencers, or whether they only act as such in this specific experimental paradigm.

     (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. Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS

    This article has 7 authors:

    1. Metehan Ilter
    2. Ramazan Kasmer
    3. Farzaneh Jalalypour
    4. Canan Atilgan
    5. Ozan Topcu
    6. Nihal Karakas
    7. Ozge Sensoy

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This is potentially an interesting paper in which extensive MD simulations are used to probe the effect of phosphorylation of a tyrosine residue on the conformational ensemble of Ras GTPase. The insights form the basis for a screen of small molecule(s) that disrupt interaction with its target Raf kinase, and predictions are tested experimentally. Overall, the integrated approach is of interest to a wide range of biochemist and protein scientists and could potentially be used to modulate the activities of other proteins.

      (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