eLife

Latest preprint reviews

1. GMCL1 Controls 53BP1 Stability and Modulates Paclitaxel Sensitivity in Cancer

   This article has 11 authors:

   1. Yuki Kito
   2. Tania J. González-Robles
   3. Sharon Kaisari
   4. Juhee Pae
   5. Sheena Faye Garcia
   6. Juliana Ortiz-Pacheco
   7. Beatrix Ueberheide
   8. Ruth Lehmann
   9. Antonio Marzio
   10. Gergely Rona
   11. Michele Pagano

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study identifies 53BP1 as an interaction partner of GMCL1 (a likely CUL3 substrate receptor). The study seeks to link this finding to regulation of the mitotic surveillance pathway and paclitaxel resistance in cancer. The evidence for these claims is currently inadequate; concerns include the use of cell lines that have been reported to lack the mitotic surveillance pathway, insufficient consideration of paclitaxel mechanisms of action, and an overinterpretation of correlative results.

   Reviewed by eLife

2. Progressive mural cell deficiencies across the lifespan in a foxf2 model of Cerebral Small Vessel Disease

   This article has 3 authors:

   1. Merry Faye E. Graff
   2. Emma E.M. Heeg
   3. Sarah J. Childs

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable findings that advance our understanding of mural cell dynamics and vascular pathology in a zebrafish model of cerebral small vessel disease. The authors provide compelling evidence that partial loss of foxf2 function leads to progressive, cell-intrinsic defects in pericytes and associated endothelial abnormalities across the lifespan, leveraging powerful in vivo imaging and genetic tools. The strength of evidence could be further improved by additional mechanistic insight and quantitative or lineage-tracing analyses to clarify how pericyte number and identity are affected in the mutant model.

   Reviewed by eLife

3. Deep Learning Reveals Endogenous Sterols as Allosteric Modulators of the GPCR-Gα Interface

   This article has 18 authors:

   1. Sanjay Kumar Mohanty
   2. Aayushi Mittal
   3. Namra
   4. Aakash Gaur
   5. Subhadeep Duari
   6. Saveena Solanki
   7. Anmol Kumar Sharma
   8. Sakshi Arora
   9. Suvendu Kumar
   10. Vishakha Gautam
   11. Nilesh Kumar Dixit
   12. Karthika Subramanian
   13. Tarini Shankar Ghosh
   14. Debarka Sengupta
   15. Shashi Kumar Gupta
   16. Natarajan Arul Murugan
   17. Deepak Sharma
   18. Gaurav Ahuja

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors present a computational pipeline for the identification of endogenous allosteric modulators of GPCRs, with experimental validation performed in a yeast system. This approach is valuable for a broad audience, including GPCR structural biologists, molecular pharmacologists, and computational biophysicists. However, the rigor of the computational methods needs to be strengthened to provide more convincing evidence for the study's conclusions. The authors should justify their methodological choices and provide greater detail and clarity regarding each computational layer of the pipeline.

   Reviewed by eLife

4. Mapping of in vivo cleavage sites uncovers a major role for yeast RNase III in regulating protein-coding genes

   This article has 4 authors:

   1. Lee-Ann Notice-Sarpaning
   2. Mathieu Catala
   3. Sherif Abou Elela
   4. Ambro van Hoof

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study expands the inventory of polyadenylated RNAs cleaved by the double-stranded RNA endonuclease Rnt1 in budding yeast, using solid methodology based on high-throughput sequencing. Previous studies had anecdotally discovered mRNA substrates, and this global characterization is comprehensive with multiple complementary controls. However, the study would be stronger with a deeper investigation into the biological function of Rnt1, as well as experiments directly probing the interaction between Rnt1 and its putative substrates.

   Reviewed by eLife

5. Gene expression variation across genetically identical individuals predicts reproductive traits

   This article has 5 authors:

   1. Amy K. Webster
   2. John H. Willis
   3. Erik Johnson
   4. Peter Sarkies
   5. Patrick C. Phillips

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Complex traits are influenced by genes and the environment, but especially the latter is difficult to pin down. This important study uses C. elegans to demonstrate that non-genetic differences in gene expression, partly influenced by the environment, correlate with individual differences in two reproductive traits. This supports the use of gene expression data as a key intermediate for understanding complex traits. The clever study design makes for compelling evidence, which is further strengthened by experimental confirmation that identified differentially expressed genes indeed influence these traits.

   Reviewed by eLife

6. Extracellular vesicle-mediated release of bis(monoacylglycerol)phosphate is regulated by LRRK2 and Glucocerebrosidase activity

   This article has 12 authors:

   1. Elsa Meneses-Salas
   2. Marianna Arnold
   3. Moises Castellá
   4. Frank Hsieh
   5. Ruben Fernández-Santiago
   6. Mario Ezquerra
   7. Alicia Garrido
   8. María-José Martí
   9. Carlos Enric
   10. Suzanne R. Pfeffer
   11. Kalpana Merchant
   12. Albert Lu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study presents the potentially interesting concept that LRRK2 regulates cellular BMP levels and their release via extracellular vesicles, with GCase activity further modulating this process in mutant LRRK2-expressing cells. However, the evidence supporting the conclusions remains incomplete, and certain statistical analyses are inadequate. This work would be of interest to cell biologists working on Parkinson's disease.

   Reviewed by eLife

7. Forecasting protein evolution by integrating birth-death population models with structurally constrained substitution models

   This article has 4 authors:

   1. David Ferreiro
   2. Luis Daniel González-Vázquez
   3. Ana Prado-Comesaña
   4. Miguel Arenas

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript introduces a useful protein-stability-based fitness model for simulating protein evolution and unifying non-neutral models of molecular evolution with phylogenetic models. The model is applied to four viral proteins that are of structural and functional importance. The justification of some hypotheses regarding fitness is incomplete, as well as the evidence for the model's predictive power, since it shows little improvement over neutral models in predicting protein evolution.

   Reviewed by eLife

8. Sending mixed signals: convergent iridescence and divergent chemical signals in sympatric sister-species of Amazonian butterflies

   This article has 7 authors:

   1. Joséphine Ledamoisel
   2. Bruno Buatois
   3. Rémi Mauxion
   4. Christine Andraud
   5. Melanie McClure
   6. Vincent Debat
   7. Violaine Llaurens

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable assessment of increased similarity in visual appearance combined with an increased chemical difference between two butterfly species in sympatry compared with differences between three populations of one of the two species in allopatry. While the evidence is solid, its interpretation in terms of evolutionary responses to shared predators (visual signals) and avoiding between-species mating (chemical signals) is overstated due to the lack of direct experimental evidence.

   Reviewed by eLife

9. Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells

   This article has 7 authors:

   1. Roozbeh Dehghannasiri
   2. George Henderson
   3. Rob Bierman
   4. Tavor Baharav
   5. Kaitlin Chaung
   6. Peter Wang
   7. Julia Salzman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable advance for the analysis of gene expression variation at the level of individual cells by introducing a novel reference-free framework that can detect splicing, fusion, editing, immune-receptor diversity and repeated elements in sequencing data. The evidence supporting these claims is solid, with rigorous validation on simulated datasets and extensive analysis of full-length single-cell sequencing data demonstrating improved performance over existing methods. This work will be of particular interest to researchers developing methods for high-resolution transcriptome analysis and to those studying cellular heterogeneity in health and disease.

   Reviewed by eLife, Arcadia Science

10. Towards a unified molecular mechanism for ligand-dependent activation of NR4A-RXR heterodimers

    This article has 4 authors:

    1. Xiaoyu Yu
    2. Yuanjun He
    3. Theodore M Kamenecka
    4. Douglas J Kojetin

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important study investigated whether the nuclear receptor Nur77 is regulated by a non-canonical mechanism of ligand-induced disruption of its interaction with RXRg, similar to the family member Nurr1. The overall evidence is solid, but additional mechanisms that have not been fully explored in this study might contribute as well. This manuscript will be of interest to scientists focusing on mechanisms of transcriptional regulation.

    Reviewed by eLife