eLife

Latest preprint reviews

1. Genetic Network Shaping Kenyon Cell Identity and Function in Drosophila Mushroom Bodies

   This article has 5 authors:

   1. Pei-Chi Chung
   2. Kai-Yuan Ku
   3. Sao-Yu Chu
   4. Chen Chen
   5. Hung-Hsiang Yu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental study uses the Drosophila mushroom body as a model to understand the molecular machinery that controls the temporal specification of neuronal cell types. With convincing experimental evidence, the authors make the finding that the Pipsqueak domain-containing transcription factor Eip93F plays a central role in specifying a later-born neuronal subtype while repressing gene expression programs for earlier subtypes.

   Reviewed by eLife

2. Treacle and MDC1 coordinate rDNA break repair by homologous recombination

   This article has 3 authors:

   1. Andrea Haenel
   2. Johannes Leyrer
   3. Manuel Stucki

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript reports valuable results on the role of MDC1 and Treacle in DSB repair in rDNA repeats. It has been previously established that MDC1 is replaced by Treacle as the main adaptor in the nucleolar DNA damage response. This work provides convincing evidence that MDC1 is required for the recruitment of RAD51 and BRCA1 to DSBs in rDNA. The work involves multiple MDC1 knockout models and establishes that RFN8-RNF168 act downstream of MDC1 in the recruitment of the HR machinery to nucleolar DSBs.

   Reviewed by eLife

3. Importance of higher-order epistasis in protein sequence-function relationships

   This article has 2 authors:

   1. Palash Sethi
   2. Juannan Zhou

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this important work, the authors present a new transformer-based neural network designed to isolate and quantify higher-order epistasis in protein sequences. They provide solid evidence that higher-order epistasis can play key roles in protein function. This work will be of interest to the communities interested in modeling biological sequence data and understanding mutational effects.

   Reviewed by eLife

4. Ω-Loop mutations control dynamics of the active site by modulating the hydrogen-bonding network in PDC-3 β-lactamase

   This article has 6 authors:

   1. Shuang Chen
   2. Andrew R Mack
   3. Andrea M Hujer
   4. Christopher R Bethel
   5. Robert A Bonomo
   6. Shozeb Haider

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript uses adaptive-bandit simulations to describe the dynamics of the Pseudomonas-derived chephalosporinase PDC-3 β-lactamase and its mutants to better understand antibiotic resistance. The finding, that clinically observed mutations alter the flexibility of the Ω- and R2-loops, reshaping the cavity of the active site, is valuable to the field. The evidence is considered incomplete, however, with the need for analysis to demonstrate equilibrium weighting of adaptive trajectories and related measures of statistical significance.

   Reviewed by eLife

5. Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity

   This article has 12 authors:

   1. Eric Greene
   2. Richard Muniz
   3. Hiroki Yamamura
   4. Samuel E Hoff
   5. Priyanka Bajaj
   6. D John Lee
   7. Erin M Thompson
   8. Angelika Arada
   9. Gyun Min Lee
   10. Massimiliano Bonomi
   11. Justin M Kollman
   12. James S Fraser

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript employs cryo-EM, mutational analysis, and biochemical assays to explore the molecular basis by which glutamine promotes filamentation and regulates the activity of human glutamine synthetase (hGS) by stabilizing interactions between hGS decamers. The studies supporting this mechanism are solid, but could be improved by providing more clarity and by addressing methodological issues in the cryoEM data processing workflow. This work will be of particular interest and useful to groups interested in understanding the molecular basis of nutrient sensing, cellular metabolism, and structural regulation of enzyme activity.

   Reviewed by eLife

6. Heterozygote advantage cannot explain MHC diversity, but MHC diversity can explain heterozygote advantage

   This article has 1 author:

   1. Joshua L Cherry

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The is a valuable evaluation of a previously published simulation model on the role of heterozygote advantage in shaping MHC diversity, showing that the conclusions from this model hold only within a narrow parameter range that might be unrealistic. The author presents an alternative model, in which MHC homozygotes with duplicated MHC genes outperform heterozygotes with single genes, thereby challenging the explanation that heterozygote advantage will lead to high allelic variation at a given MHC gene. The topic is highly relevant for eco-immunology and evolutionary genetics, but several major aspects of the author's claim need to be clarified to make the model interpretable. While the work has the potential to improve our understanding of the question of how the extraordinary diversity at the MHC locus evolves, without this addition, the conclusions remain incomplete.

   Reviewed by eLife

7. Starvation transforms signal encoding in C. elegans thermoresponsive neurons and suppresses heat avoidance via bidirectional glutamatergic and peptidergic signaling

   This article has 2 authors:

   1. Saurabh Thapliyal
   2. Dominique A Glauser

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study shows how hunger alters avoidance of harmful heat in C. elegans by reconfiguring the activity of key sensory neurons. The evidence is convincing, with well-designed behavioural, genetic, and imaging experiments that support the main conclusions. The work will be of interest to neuroscientists studying how internal states shape sensory processing and behaviour across species.

   Reviewed by eLife

8. Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition

   This article has 5 authors:

   1. Natalie Gonzaga-Saavedra
   2. Eleanor A Degen
   3. Isabella V Soluri
   4. Corinne Croslyn
   5. Shelby A Blythe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study employed state-of-the-art quantitative imaging and genomics approaches to address a fundamental question regarding the establishment of Polycomb domains during Drosophila embryogenesis. The critical developmental stage was pinpointed to the maternal-to-zygotic transition, rather than earlier stages, providing clarification for the field. The roles of two factors, Zelda and GAGA-factor, were investigated, which reveal that Zelda, but not GAGA-factor, contributes to this process. These compelling findings have implications for chromatin and developmental biology.

   Reviewed by eLife

9. Synaptotagmin 1 and Synaptotagmin 7 promote MR1-mediated presentation of Mycobacterium tuberculosis antigens

   This article has 7 authors:

   1. Se-Jin Kim
   2. Jessie C Peterson
   3. Andrew J Olive
   4. Fikadu G Tafesse
   5. Corinna A Kulicke
   6. Elham Karamooz
   7. David M Lewinsohn

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study examines the contribution of synaptotagmin 1 and synaptotagmin 7 to metabolite antigen presentation to mucosal-associated invariant T (MAIT) cells; it begins to address a critical gap in our understanding of the antigen presentation mechanisms to these cells. Strengths of the study include the use of Mtb to study the dynamics of antigen presentation to MAIT cells instead of a synthetic antigen. However, the strength of the evidence to support the conclusion is currently incomplete. The conclusions could be enhanced by additional dissection of some of the cell biological events that lead to antigen presentation by MR1.

   Reviewed by eLife

10. Macroscopic Analyses of RNA-Seq Data to Reveal Chromatin Modifications in Aging and Disease

    This article has 6 authors:

    1. Achal Mahajan
    2. Francesca Ratti
    3. Ban Wang
    4. Hana El-Samad
    5. James H Kaufman
    6. Vishrawas Gopalakrishnan

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This valuable study analyzes aging-related chromatin changes through the lens of intra-chromosomal gene correlation length, which is a novel computational metric that captures spatial correlations in gene expression along the chromosome. The authors propose that this metric reflects chromatin structure and can serve as a proxy for its changes during aging. While currently the strength of evidence is somewhat incomplete, if revised with further supporting data, this work will provide a systems-level understanding of aging and genome regulation, which is predicted to have a substantive impact on the field.

    Reviewed by eLife