eLife

Latest preprint reviews

1. Lipid packing contributes to the confinement of caveolae to the plasma membrane

   This article has 10 authors:

   1. Elin Larsson
   2. Aleksei Kabedev
   3. Hudson Pace
   4. Jakob Lindwall
   5. Fouzia Bano
   6. Robert G Parton
   7. Christel AS Bergström
   8. Ingela Parmryd
   9. Marta Bally
   10. Richard Lundmark

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study reports the important finding that the dynamin inhibitor Dyngo-4a broadly affects lipid packing and plasma membrane dynamics, independently of its action on dynamin. While solid computational, biophysical, and cell-based evidence supports this conclusion, there is incomplete support for the authors' main claim on the role of lipid packing in caveolae internalization, as the causal relationship remains unclear and direct analyses are lacking. With stronger evidence, this work would be of significant interest to cell biologists, biophysicists, and chemists interested in membrane remodeling and drug-membrane interactions.

     [Editors' note: this paper was reviewed by Review Commons.]

   Reviewed by eLife, Review Commons

2. Stall force measurement of the kinesin-3 motor KIF1A using a programmable DNA origami nanospring

   This article has 5 authors:

   1. Nobumichi Takamatsu
   2. Hiroko Furumoto
   3. Takayuki Ariga
   4. Mitsuhiro Iwaki
   5. Kumiko Hayashi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript describes a novel method for determining the mechanical parameters of the kinesin, KIF1A, that uses fluorescence microscopy and does not require an optical tweezer apparatus. The length of a tethered fluorescent DNA nanospring is measured as the kinesin moves processively along the microtubule and then stalls. The work reports important findings, and (barring a few exceptions) the evidence supporting the claims is generally convincing.

   Reviewed by eLife

3. 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 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 made fundamental findings that the Pipsqueak domain-containing transcription factor Eip93F is central to the specification of a later-born neuronal subtype and in inhibiting gene expression for earlier subtypes.

   Reviewed by eLife

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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