eLife

Latest preprint reviews

1. Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning

   This article has 6 authors:

   1. Darko Mitrovic
   2. Sarah E McComas
   3. Claudia Alleva
   4. Marta Bonaccorsi
   5. David Drew
   6. Lucie Delemotte

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This potentially important work proposes a novel approach, based on co-evolution analysis, machine-learning protocols and molecular dynamics simulations, to predict structures and energetics of the main states of the alternating access cycle of a family of membrane transporters, the sugar porters. The approach is compelling, especially the application of co-evolution and Alphafold to generate highly accurate models in different conformational states of a given protein, but the work is currently incomplete due to shortcomings in the calculation of the energy landscape. With this aspect strengthened, the manuscript will be of interest to the transporter and computational modeling communities.

   Reviewed by eLife

2. Multi-centre analysis of networks and genes modulated by hypothalamic stimulation in patients with aggressive behaviours

   This article has 18 authors:

   1. Flavia Venetucci Gouveia
   2. Jurgen Germann
   3. Gavin JB Elias
   4. Alexandre Boutet
   5. Aaron Loh
   6. Adriana Lucia Lopez Rios
   7. Cristina Torres Diaz
   8. William Omar Contreras Lopez
   9. Raquel Chacon Ruiz Martinez
   10. Erich Talamoni Fonoff
   11. Juan Carlos Benedetti-Isaac
   12. Peter Giacobbe
   13. Pablo M Arango Pava
   14. Han Yan
   15. George M Ibrahim
   16. Nir Lipsman
   17. Andres Lozano
   18. Clement Hamani

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents useful structural and functional connectivity profiles of patients receiving deep brain stimulation in the posterior hypothalamus for severe and refractory aggressive behavior. The inclusion of data from multiple centers is compelling. However, the imaging analysis is incomplete and the interpretation of the findings is not solid.

   Reviewed by eLife

3. Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales

   This article has 5 authors:

   1. Anton A Polyansky
   2. Laura D Gallego
   3. Roman G Efremov
   4. Alwin Köhler
   5. Bojan Zagrovic

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study reports a joint experimental and computational investigation of the structural features of biomolecular condensates formed by a specific intrinsically disordered protein. The authors also adapt emerging rules to discuss and physico-chemical determinants of these structures of condensates. Specifically, the authors adapt the analysis of fractal structures, co-opted from the field of colloidal chemistry / physics, and generate important insights regarding the network-like organization of disordered proteins within in silico facsimiles of condensates. The usage of these analyses in the context of studying all atom models for multi-chain assemblies intended to mimic the internal organization of condensates is very interesting. The work is of relevance to cell biology and structural biology.

   Reviewed by eLife

4. scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border

   This article has 7 authors:

   1. Alexandre P Thiery
   2. Ailin Leticia Buzzi
   3. Eva Hamrud
   4. Chris Cheshire
   5. Nicholas M Luscombe
   6. James Briscoe
   7. Andrea Streit

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The study of Thiery et al. details the heterogeneous expression of a very large number of genes presumably associated with cell fate decisions in the ectoderm at the neural plate border in early avian embryos. The authors mostly succeed in presenting their very complex strategy of data analysis in a clear way but the work is incomplete with some conceptual weaknesses in how the authors describe and interpret their results. By focusing on one of the earliest cell fate decisions in the ectoderm of a vertebrate embryo, this study will be valuable to a broad range of developmental biologists.

   Reviewed by eLife

5. Inconsistencies between human and macaque lesion data can be resolved with a stimulus-computable model of the ventral visual stream

   This article has 2 authors:

   1. Tyler Bonnen
   2. Mark AG Eldridge

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a useful application of a prior model published by the authors to a new dataset. The results from this approach were interesting and solid but the conclusions that one can make from the application of the model to only one paper are limited in scope and would depend on further probing to know if the model itself has face validity as a model of ventral visual stream function.

   Reviewed by eLife

6. Impairment of lipid homeostasis causes lysosomal accumulation of endogenous protein aggregates through ESCRT disruption

   This article has 11 authors:

   1. John Yong
   2. Jacqueline E Villalta
   3. Ngoc Vu
   4. Matthew A Kukurugya
   5. Niclas Olsson
   6. Magdalena Preciado López
   7. Julia R Lazzari-Dean
   8. Kayley Hake
   9. Fiona E McAllister
   10. Bryson D Bennett
   11. Calvin H Jan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Protein and lipid homeostasis is essential for maintaining cellular functions but their crosstalk remains largely unknown. This important manuscript deals with this interesting topic and applies the powerful unbiased tools of somatic cell genetics to discover evidence suggesting a link between sphingolipids/cholesterol ester metabolism and lysosomal protein aggregation. The authors provide compelling orthogonal evidence to support their conclusions.

   Reviewed by eLife

7. Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice

   This article has 17 authors:

   1. Elizaveta V Bashkirova
   2. Nell Klimpert
   3. Kevin Monahan
   4. Christine E Campbell
   5. Jason Osinski
   6. Longzhi Tan
   7. Ira Schieren
   8. Ariel Pourmorady
   9. Beka Stecky
   10. Gilad Barnea
   11. Xiaoliang Sunney Xie
   12. Ishmail Abdus-Saboor
   13. Benjamin M Shykind
   14. Bianca J Marlin
   15. Richard M Gronostajski
   16. Alexander Fleischmann
   17. Stavros Lomvardas

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This is an important paper that revises the canonical model of how olfactory sensory neurons choose which odor receptor to express. The data presented in the paper are convincing and the model proposed is provocative and likely to enable future work.

   Reviewed by eLife

8. The acetylase activity of Cdu1 regulates bacterial exit from infected cells by protecting Chlamydia effectors from degradation

   This article has 9 authors:

   1. Robert J Bastidas
   2. Mateusz Kędzior
   3. Robert K Davidson
   4. Stephen C Walsh
   5. Lee Dolat
   6. Barbara S Sixt
   7. Jonathan N Pruneda
   8. Jörn Coers
   9. Raphael H Valdivia

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study combines state-of-the art proteomics and genetic manipulation of Chlamydia trachomatis to study the function of a chlamydial effector, Cdu1, with deubiquitination and acetylation activities. Solid evidence is provided to show that Cdu1 is able to protect itself and three other chlamydial effectors, which are involved in the control of chlamydial egress from host cells, from ubiquitin-mediated degradation, and that this depends on the acetylation activity of Cdu1, but not on its deubiquitination activity. This work will be of interest to microbiologists and cell biologists studying host cell-pathogen interactions.

   Reviewed by eLife

9. Vangl2 suppresses NF-κB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation

   This article has 17 authors:

   1. Jiansen Lu
   2. Jiahuan Zhang
   3. Huaji Jiang
   4. Zhiqiang Hu
   5. Yufen Zhang
   6. Lian He
   7. Jianwu Yang
   8. Yingchao Xie
   9. Dan Wu
   10. Hongyu Li
   11. Ke Zeng
   12. Peng Tan
   13. Qingyue Xiao
   14. Zijing Song
   15. Chenglong Pan
   16. Xiaochun Bai
   17. Xiao Yu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable manuscript describes a novel role of Vangl2, a core planar cell polarity protein, in linking the NF-kB pathway to selective autophagic protein degradation in myeloid cells. The mechanistic studies provide convincing evidence that Vangl2 targets p65 for NDP52-mediated autophagic degradation, limiting inflammatory NF-kB response, with functional significance of the proposed mechanism in sepsis. Additional future studies dissecting autophagic Vangl2 functions in various myeloid subsets in the context of inflammation could be informative, and additional Vangl2 targets in the inflammatory pathway, including IKK2, could also be explored. Overall, this exciting study can advance our understanding of NF-kB control, particularly in the context of inflammatory diseases.

   Reviewed by eLife

10. Robust membrane protein tweezers reveal the folding speed limit of helical membrane proteins

    This article has 4 authors:

    1. Seoyoon Kim
    2. Daehyo Lee
    3. WC Bhashini Wijesinghe
    4. Duyoung Min

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This work presents an important methodological advance for single-molecule force spectroscopy of membrane proteins providing a new robust design of the linkage between a target single molecule and solid support. The data provide compelling evidence of the improved mechanical stability of the pulling system. Allowing more statistically reliable force measurements of biomolecules, this method may be broadly applicable in the field of single-molecule biophysics.

    Reviewed by eLife