Showing page 2 of 369 pages of list content

  1. Effects of Arginine Vasopressin on Islet Cells in Pancreatic Tissue Slices: Glucose-Dependent Modulation of IP3 Receptor-Specific Responses

    This article has 14 authors:
    1. Jasmina KerÄŤmar
    2. Nastja Murko
    3. Lidija Križančić Bombek
    4. Eva ParadiĹľ Leitgeb
    5. Johannes Pfabe
    6. Sandra Postić
    7. Ya-Chi Huang
    8. AndraĹľ StoĹľer
    9. Dean Korošak
    10. Xaver Kozisek
    11. Monika Perisic
    12. Markus Muttenthaler
    13. Christian W Gruber
    14. Marjan Slak Rupnik
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a useful finding on the effects of arginine vasopressin (AVP) on islet cells in pancreatic tissue slices, using technically sophisticated spatio-temporal calcium recordings to confirm that AVP influences α and β cells differently depending on glucose concentrations. While the study’s methods – particularly the calcium imaging techniques and peptide ligand design targeting V1b receptors – are strong, the reviewers were concerned about several aspects of the experimental design. The results on β-cell responses are incomplete and insufficient to support the manuscript’s claims, especially due to the high variability of islet responses and lack of mechanistic and functional (hormone release) data. There are also concerns about the possibility of off-target effects and suboptimal receptor specificity: the study would be significantly strengthened by inclusion of signaling pathway interrogation, hormone output assays, genetic validation (e.g., β cell-specific deletion of V1br), and receptor localization. The work will still be of interest to researchers studying islet physiology in the context of health and diabetes.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  2. Identifying a novel mechanism of L-leucine uptake in Mycobacterium tuberculosis using a chemical genomic approach

    This article has 8 authors:
    1. Nisheeth Agarwal
    2. Himanshu Gogoi
    3. Eeba
    4. Linus Augustin
    5. Md. Younus Khan
    6. Yashwant Kumar
    7. Sayan Kumar Bhowmick
    8. Bappaditya Dey
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      By performing a chemical screen of an FDA-approved library of small molecules against a leucine-dependent Mtb strain, this work discovered that semapimod inhibits Mtb growth by impairing leucine import. The work is useful because it connects leucine uptake with the cell wall lipids in Mtb; however, it remains incomplete as the evidence supporting semapimod's ability to target leucine uptake needs more substantial proof. The work requires significant experimental evidence to identify leucine transporter(s) and determine how PDIM participates in leucine uptake.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  3. Temperature-based MHC class-I multimer peptide exchange for human HLA-A, B and C

    This article has 13 authors:
    1. Cilia R Pothast
    2. Ian Derksen
    3. Anneloes van der Plas - van Duijn
    4. Angela el Hebieshy
    5. Wesley Huisman
    6. Kees LMC Franken
    7. Jacques Neefjes
    8. Jolien J Luimstra
    9. Marieke Griffioen
    10. Michel Kester
    11. Maarten H Vermeer
    12. Mirjam HM Heemskerk
    13. Ferenc A Scheeren
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents an alternative to conventional and UV-based tetramers, which are easy to use and reliable for the identification of antigen-specific CD8 T cells. The authors demonstrate that tetramers for HLA alleles A0301, A1101, B0702, and C0702 can be subjected to specific temperatures that facilitate peptide exchange, whilst maintaining structural integrity. Whilst the strength of the evidence is currently incomplete, further development and validation of this approach is likely to provide a useful alternative to generating reagents for examining T cell specificities.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Type I interferon responses contribute to immune protection against mycobacterial infection

    This article has 14 authors:
    1. Andrea Szydlo-Shein
    2. Blanca Sanz-MagallĂłn Duque de Estrada
    3. Joshua Rosenheim
    4. Carolin T Turner
    5. Aneesh Chandran
    6. Evdokia Tsaliki
    7. Marc CI Lipman
    8. Heinke Kunst
    9. Gabriele Pollara
    10. Philip M Elks
    11. Jean-Pierre Levraud
    12. Elspeth M Payne
    13. Mahdad Noursadeghi
    14. Gillian S Tomlinson
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This useful study shows a protective role of type 1 IFN during Mycobacterium tuberculosis infection. It shows that the type 1 IFN response in human skin TST inversely correlates with TB severity, suggesting its protective role. Considering that type I IFN is usually shown to be pro-pathogenic, the higher vulnerability of zebrafish larvae lacking stat2 to M marinum infection is a strong result. However, the conclusion that IFN-I is protective during mycobacterial infection remains indirect and incomplete; the study requires additional mechanistic insights and validation.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  5. Synonymous mutations in AAV Rep enhance genome packaging in a library selection

    This article has 3 authors:
    1. Tasfia Azim
    2. Dru Myerscough
    3. Jonathan J Silberg
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Engineering of adeno-associated virus (AAV) replication proteins may provide new insights into Parvoviral replication. The authors created a useful collection of Rep protein variants with changes that alter the amino acid sequence, but these did not lead to clear improvements in how the virus worked. Instead, their screen showed that changes that do not alter the protein ("synonymous" mutations) and changes to the promoter were more common. As it stands the results are incomplete due to potential issues with the screening design. We encourage a more complete characterization, which may enhance the translational potential of the approach.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  6. Vascular endothelial-specific loss of TGF-beta signaling as a model for choroidal neovascularization and central nervous system vascular inflammation

    This article has 5 authors:
    1. Yanshu Wang
    2. Amir Rattner
    3. Zhongming Li
    4. Philip M Smallwood
    5. Jeremy Nathans
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Endothelial cell-specific loss of TGF-beta signaling in mice leads to CNS vascular defects, specifically impairing retinal development and promoting immune cell infiltration. The data are solid, showing that loss of TGF-beta signaling triggers vascular inflammation and attracts immune cells specific to CNS vasculature, but there are issues with the single-nucleus RNA sequencing of immune cells. These findings are valuable, highlighting TGF-beta's role in maintaining vascular-immune homeostasis and its therapeutic potential in neurovascular inflammatory diseases.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  7. Gut Microbe-Derived Trimethylamine Shapes Circadian Rhythms Through the Host Receptor TAAR5

    This article has 27 authors:
    1. Kala K Mahen
    2. William J Massey
    3. Danny Orabi
    4. Amanda L Brown
    5. Thomas C Jaramillo
    6. Amy C Burrows
    7. Anthony J Horak
    8. Sumita Dutta
    9. Marko Mrdjen
    10. Nour Mouannes
    11. Venkateshwari Varadharajan
    12. Lucas J Osborn
    13. Xiayan Ye
    14. Dante M Yarbrough
    15. Treg Grubb
    16. Natalie Zajczenko
    17. Rachel Hohe
    18. Rakhee Banerjee
    19. Pranavi Linga
    20. Dev Laungani
    21. Adeline M Hajjar
    22. Naseer Sangwan
    23. Mohammed Dwidar
    24. Jennifer A Buffa
    25. Garth R Swanson
    26. Zeneng Wang
    27. J Mark Brown
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents an important finding linking the bacterial metabolite trimethylamine and its receptor to circadian rhythms and olfaction. The current evidence supporting the claims of the authors is convincing, although further data and improvements to the presentation would further increase the impact of these results. This work will be of broad interest to researchers interested in nutrition, microbial metabolism, circadian rhythms, and host-microbiome interactions.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  8. Sphingolipid imbalance aggravates tau pathology by endomembrane rigidification and rupture

    This article has 7 authors:
    1. Jessica Tittelmeier
    2. Carl Alexander Sandhof
    3. Nicole Martin
    4. Deike El-Kabarity
    5. Soki-Bradel Ngonza-Nito
    6. Ronald Melki
    7. Carmen Nussbaum-Krammer
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study addresses the role of sphingolipid metabolism in maintaining endolysosomal membrane integrity and its impact on tau pathology in Caenorhabditis elegans and human cell culture models. The methods are solid and the proposed mechanisms are conceivable. However, the current evidence is incomplete and could be strengthened, due to reliance on imaging data and insufficient biochemical validation. The work will be of broad interest to cell biologists and biologists working on Alzheimer's disease and related proteinopathies.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. A geometric shape regularity effect in the human brain

    This article has 8 authors:
    1. Mathias Sablé-Meyer
    2. Lucas Benjamin
    3. Cassandra Potier Watkins
    4. Chenxi He
    5. Maxence Pajot
    6. Théo Morfoisse
    7. Fosca Al Roumi
    8. Stanislas Dehaene
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study provides converging results from complementary neuroimaging and behavioral experiments to identify human brain regions involved in representing regular geometric shapes. Geometric shape concepts are universally present across diverse human cultures and possibly essential for unique human capabilities such as numerical cognition and symbolic reasoning, and identifying the brain networks involved in geometric shape representation is of broad interest to researchers studying human visual perception, reasoning, and cognitive development. The provided experimental evidence regarding the presence of geometric shape regularity representation in dorsal parietal and prefrontal cortex is solid, but the claimed link with mathematical reasoning, the influence of experimental tasks, and the role of experience in driving geometric shape representation in both humans and artificial vision models require further elucidation.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  10. Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers

    This article has 10 authors:
    1. Fereshteh Sadeqi
    2. Dexin Dong
    3. Kai Stroh
    4. Marian Vache
    5. Jutta Metz
    6. Dietmar Riedel
    7. Andreas Janshoff
    8. Herre Jelger Risselada
    9. Caroline Kolenda
    10. Michael Meinecke
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This fundamental study combines in vitro reconstitution experiments and molecular dynamics simulations to elucidate how membrane lipids are transported from the outer to the inner membrane of mitochondria. The authors provide convincing evidence that a positive membrane curvature is critical for membrane lipid extraction. The work will be of broad interest to cell biologists and biochemists.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  11. 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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  12. 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 EM 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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  13. 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

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  14. 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

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  15. 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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  16. 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

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  17. 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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  18. 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

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  19. 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

    This article has 6 evaluationsAppears in 2 listsLatest version Latest activity
  20. 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

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity