eLife

Latest preprint reviews

1. High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors

   This article has 8 authors:

   1. Mingrui Duan
   2. Smitha Sivapragasam
   3. Jacob S Antony
   4. Jenna Ulibarri
   5. John M Hinz
   6. Gregory MK Poon
   7. John J Wyrick
   8. Peng Mao

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest for researchers interested in DNA repair and transcriptional regulation. The authors provide a series of well-executed and designed high-resolution sequencing data demonstrating that transcription factor (TF) binding perturbs alkylation base damage formation as well as inhibits its repair via base excision repair (BER) at TF binding sites. Moreover, they demonstrate differences between nucleotide excision repair and BER at TF binding sites that are consistent with the different repair mechanism of these two pathways. These results should have an important and timely impact on the field.

     (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 name with the authors.)

   Reviewed by eLife

2. Hippocampal-hypothalamic circuit controls context-dependent innate defensive responses

   This article has 7 authors:

   1. Jee Yoon Bang
   2. Julia Kathryn Sunstrum
   3. Danielle Garand
   4. Gustavo Morrone Parfitt
   5. Melanie Woodin
   6. Wataru Inoue
   7. Junchul Kim

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to neuroscientists, particularly those studying defensive behaviors. The authors provide novel insights into the mechanisms by which the brain computes contextual information associated with innate threats in mice. The experimental approach and data analysis are mostly adequate and the study provides the first causal evidence of a hippocampus-anterior hypothalamic pathway mediating spatial fear memory of ethological threats. The implementation of more robust statistical tests, as well as more detailed Methods and Discussion sections should serve to strengthen an already elegant study.

     (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 name with the authors.)

   Reviewed by eLife

3. Spatial signatures of anesthesia-induced burst-suppression differ between primates and rodents

   This article has 10 authors:

   1. Nikoloz Sirmpilatze
   2. Judith Mylius
   3. Michael Ortiz-Rios
   4. Jürgen Baudewig
   5. Jaakko Paasonen
   6. Daniel Golkowski
   7. Andreas Ranft
   8. Rüdiger Ilg
   9. Olli Gröhn
   10. Susann Boretius

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study reveals that anesthesia-induced burst suppression's spatial patterns differ across humans, macaques, marmosets, and rats. Given that burst suppression is considered a hallmark of unconscious states, these findings are potentially important for us to understand the evolution of the neural correlates of consciousness. In addition, a novel, purely MR-based method is presented to identify and map burst suppression, which may have relevance in both clinical and experimental studies.

     (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 name with the authors.)

   Reviewed by eLife

4. A neural network model of when to retrieve and encode episodic memories

   This article has 3 authors:

   1. Qihong Lu
   2. Uri Hasson
   3. Kenneth A Norman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper addresses an important problem in control of episodic memory. This paper develops a computationally-based proposal about how semantic, working memory, and episodic memory systems might learn to interact so that stored episodic memories can optimally contribute to reconstruction of semantic memory for event sequences. This is an understudied area and this present work can make a major theoretical contribution to this domain with new predictions. The reviewers were positive about the contribution.

     (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 name with the authors.)

   Reviewed by eLife

5. Evolution of binding preferences among whole-genome duplicated transcription factors

   This article has 4 authors:

   1. Tamar Gera
   2. Felix Jonas
   3. Roye More
   4. Naama Barkai

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors applied original approaches to explore the evolution of transcription factors following duplication and subsequent divergence among duplicates. This paper should generate broad interest among evolutionary biologists as it addresses the long-standing question of how newly evolved transcription factors acquire new binding specificity. By combining genome editing with high-precision DNA binding profiling, this study provides extensive in vivo data showing how the binding profiles of transcription factor paralog pairs diverge.

     (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. Structural basis for cytoplasmic dynein-1 regulation by Lis1

   This article has 7 authors:

   1. John P Gillies
   2. Janice M Reimer
   3. Eva P Karasmanis
   4. Indrajit Lahiri
   5. Zaw Min Htet
   6. Andres E Leschziner
   7. Samara L Reck-Peterson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     LIS1 is a key regulator of the microtubule motor cytoplasmic dynein. Here the authors use yeast proteins and streptavidin-coated grids to solve the first high-resolution (3.1Å) structure of the dynein-Lis1 complex. The two beta-propellors in a Lis1 dimer make contact with different sites on a single dynein motor domain. Mutagenesis shows both sites are important for yeast and human dynein and uncover how they modulate motor function.

     (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

7. Systematic investigation of the link between enzyme catalysis and cold adaptation

   This article has 4 authors:

   1. Catherine Stark
   2. Teanna Bautista-Leung
   3. Joanna Siegfried
   4. Daniel Herschlag

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Are enzymes found in organisms that optimally grow at colder temperatures are more active than the same enzymes found in organisms that optimally grow at warmer temperatures? Here, an assessment of the catalytic constants for approximately 2200 enzymes (obtained from the BRENDA database) showed no correlation between the relative catalytic activity and the optimum growth temperature. Further support for this conclusion was obtained from the measurement of the catalytic constant from a selection of ketosteroid isomerases from organisms that optimally grow between 15 and 46 degrees centigrade. These are interesting results, although the significance with respect to earlier studies has not been clearly explained.

     (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. Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

   This article has 8 authors:

   1. Angela McLaughlin
   2. Vincent Montoya
   3. Rachel L Miller
   4. Gideon J Mordecai
   5. Canadian COVID-19 Genomics Network (CanCOGen) Consortium
   6. Michael Worobey
   7. Art FY Poon
   8. Jeffrey B Joy

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study measures the transmission of SARS-CoV-2 lineages in Canada and the rate at which lineages were imported into Canada from other countries during the first year of the pandemic. This information is critical for understanding basic SARS-CoV-2 evolution and epidemiology, but the impacts of sampling biases in space and time might weaken the conclusions.

     (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, ScreenIT

9. Sampling motion trajectories during hippocampal theta sequences

   This article has 2 authors:

   1. Balazs B Ujfalussy
   2. Gergő Orbán

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to neuroscientists interested in predictive coding and planning. It presents a novel analysis of hippocampal place cells during exploration of an open arena. It performs a comprehensive comparison of real and synthetic data to determine which encoding model best explains population activity in the hippocampus.

     (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. Monkey plays Pac-Man with compositional strategies and hierarchical decision-making

    This article has 7 authors:

    1. Qianli Yang
    2. Zhongqiao Lin
    3. Wenyi Zhang
    4. Jianshu Li
    5. Xiyuan Chen
    6. Jiaqi Zhang
    7. Tianming Yang

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This report presents findings of broad interest to behavioral, systems, and cognitive neuroscientists. The combination of a complex behavioral paradigm and sophisticated modeling provides significant insight and a novel approach to studying higher cognition in primates. Key clarifications are needed that have to do with better justification for the modeling strategy, selective comparisons within the data, and a more thorough consideration that subjects may employ a more passive strategy.

      (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