eLife

Latest preprint reviews

1. 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 stronger evidence for the study's conclusions, which is currently incomplete. The authors should justify their methodological choices and provide greater detail and clarity regarding each computational layer of the pipeline.

   Reviewed by eLife

2. 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

3. 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

     This important study addresses the role of non-genetic factors in individual differences in phenotype. Using C. elegans, the study finds 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.

   Reviewed by eLife

4. 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

5. 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

6. 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

7. 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

8. 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

9. Aging-associated Increase of GATA4 levels in Articular Cartilage is Linked to Impaired Regenerative Capacity of Chondrocytes and Osteoarthritis

   This article has 10 authors:

   1. Meagan J Makarczyk
   2. Yiqian Zhang
   3. Alyssa Aguglia
   4. Olivia Bartholomew
   5. Sophie Hines
   6. Kate Li
   7. Suyash Sinkar
   8. Silvia Liu
   9. Craig Duvall
   10. Hang Lin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents an important finding on the role of GATA4 in aging- and OA-associated cartilage pathology. The conclusions are well supported by compelling in vitro and in vivo evidence. This work will be of broad interest to both cell biologists and orthopedic clinicians.

   Reviewed by eLife

10. Functional analysis across model systems implicates ribosomal proteins in growth and proliferation defects associated with hypoplastic left heart syndrome

    This article has 20 authors:

    1. Tanja Nielsen
    2. Anaïs Kervadec
    3. Jeanne L Theis
    4. Maria A Missinato
    5. James Marchant
    6. Michaela Lynott
    7. Aashna Lamba
    8. Xin-Xin I Zeng
    9. Marie Berenguer
    10. Stanley M Walls
    11. Analyne Schroeder
    12. Katja Birker
    13. Greg Duester
    14. Paul Grossfeld
    15. Timothy J Nelson
    16. Timothy M Olson
    17. Karen Ocorr
    18. Rolf Bodmer
    19. Georg Vogler
    20. Alexandre R Colas

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important study applies an innovative multi-model strategy to implicate the ribosomal protein (RP) encoding genes as candidates causing Hypoplastic Left Heart Syndrome. The evidence from the screen in stem cell-derived cardiomyocytes and whole genome sequencing of human patients, followed by functional analyses of RP genes in fly and fish models, is convincing and supports the authors' claims. This work and methodology applied would be of broad interest to medical biologists working on congenital heart diseases.

    Reviewed by eLife