eLife

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1. Purified Zymogens Reveal Mechanisms of Snake Venom Metalloproteinase Auto-Activation

   This article has 17 authors:

   1. Sophie Hall
   2. Iara Aimê Cardoso
   3. Mark C. Wilkinson
   4. Maria Molina Carretero
   5. Srikanth Lingappa
   6. Bronwyn Rand
   7. Dakang Shen
   8. Johara Boldrini-França
   9. Richard Stenner
   10. Stefanie K. Menzies
   11. Georgia Balchin
   12. Konrad Kamil Hus
   13. Renaud Vincentelli
   14. Andrew Mumford
   15. Nicholas R. Casewell
   16. Imre Berger
   17. Christiane Schaffitzel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this useful paper, the authors present a comprehensive method for the purification of recombinant Snake Venom Metalloproteinases (SVMPs) using the MultiBac expression system, explain the self-activation of the enzymes by Zn2+ incubation, and establish high-throughput screening (HTS) techniques. The authors addressed a key problem: producing a substantial amount of pure and enzymatically active SVMPs required for structural and functional studies. Altogether, this work builds a solid foundation for the large-scale production of active SVMPs for future biochemical and structural characterization as well as for drug discovery, albeit leaving certain caveats about the universal applicability of the described methodology for the production of any recombinant SVMPs.

   Reviewed by eLife

2. HUMAN SPINAL CORD ORGANOIDS REVEAL CELL INTERCALATION AS A CONSERVED MECHANISM FOR SECONDARY NEURULATION

   This article has 9 authors:

   1. José Blanco-Ameijeiras
   2. Yara El Majzoub
   3. Mar García-Valero
   4. Mariana M Faustino
   5. Elena Rebollo
   6. Javier Macho-Rendón
   7. Jorge Corbacho
   8. Juan Ramón Martínez-Morales
   9. Elisa Martí

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable human stem cell-derived organoid model that captures key morphological and cellular features of spinal cord development and provides evidence for a YAP-dependent mechanism of lumen formation relevant to secondary neurulation. Overall, the evidence is convincing, using strong and validated approaches consistent with the current state of the art, including systematic protocol optimisation across multiple cell lines and quantitative analysis of tissue architecture. However, some claims regarding precise anterior-posterior and dorsoventral spinal cord identity, as well as several novelty claims, are at times overstated and would benefit from more direct validation and more careful positioning. The work will be of interest to developmental biologists and researchers studying neural tube defects.

   Reviewed by eLife

3. Patient-specific iPSC models of neural tube defects identify underlying deficiencies in neuroepithelial cell shape regulation and differentiation

   This article has 8 authors:

   1. Ioakeim Ampartzidis
   2. Elliott M Thompson
   3. Yashica Gupta
   4. Andrea Krstevski
   5. Nicola Elvassore
   6. Eirini Maniou
   7. Paolo de Coppi
   8. Gabriel L Galea

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors used genetic mutations in VANGL2 to study cell morphological changes during differentiation of hPSCs and understand the mechanisms underlying neural tube closure defects. The findings are important as they establish a quantitative, reproducible 2D human iPSC-to-neural-progenitor platform for analyzing cell-shape dynamics during differentiation. The convincing evidence provided, combined with the relative simplicity of the model and its tractability as a patient-specific and reverse genetic platform, make it attractive.

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

   Reviewed by eLife, Review Commons

4. RAB14-dependent tubulovesicular recycling directs MET to invadopodia promoting TNBC cell invasion

   This article has 6 authors:

   1. Amrita Khamari
   2. Atreyee Guria
   3. Kiran Tak
   4. Rajiv Sharma
   5. Yannis Kalaidzidis
   6. Sunando Datta

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable paper advances understanding of the role of the HGF receptor, MET, in cancer cell invasion by demonstrating HGF-induced coordinated trafficking of MET and metalloprotease MT1-MMP into invadopodia. The results are generally solid, but there are concerns about the cell biology and whether the trafficking mechanism is clinically relevant. It's also unclear whether this is a general mechanism or specific to triple-negative breast cancer cells. The paper will be of interest to cancer cell biologists.

   Reviewed by eLife

5. Bruce suppresses autophagy-regulated caspase activity and wing tissue growth in Drosophila

   This article has 4 authors:

   1. Natsuki Shinoda
   2. Yutaro Hama
   3. Nozomi Hanawa
   4. Masayuki Miura

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study reports insights into how the caspase Dcp-1, best known for cell death, can also promote tissue growth in Drosophila, extending the authors' earlier work by identifying regulatory factors that shape this non-lethal activity. The valuable findings identify new Dcp-1-interacting proteins Sirt1, Fkbp59, Debcl, Buffy, Atg2, and Atg8a, and help broaden understanding of how growth and death pathways intersect. The evidence is solid, but some conclusions would be strengthened by additional studies, particularly regarding the nature of the cell death observed and the involvement of autophagy.

   Reviewed by eLife

6. Efficient transduction of pancreas tissue slices with genetically encoded calcium integrators

   This article has 9 authors:

   1. Charles S Lazimi
   2. Austin E Stis
   3. Julia K Panzer
   4. Helmut Hiller
   5. Maria L Beery
   6. Amelia K Linnemann
   7. Cherie L Stabler
   8. Clayton E Mathews
   9. Edward A Phelps

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable advance by enabling functional mapping of Ca²⁺ responses in live human pancreatic tissue slices, providing new opportunities to study islet heterogeneity and diabetes-related dysfunction in an intact tissue context. The evidence supporting the main conclusions is solid, based on reproducible methodology and functional validation across multiple human donor samples. Key revisions needed include clearer quantification of transduction efficiency and tissue viability, and improved clarification of how CaMPARI2 signals should be interpreted.

   Reviewed by eLife

7. Rapid evolution of fine-scale recombination during domestication: a perspective from population genomics

   This article has 17 authors:

   1. Zheng-Xi Liu
   2. Ming Li
   3. Xue-Hai Ge
   4. Kun Wang
   5. Si Si
   6. Chang-Rong Ge
   7. Jian-Hai Chen
   8. Li-Rong Hu
   9. Min-Sheng Peng
   10. Ting-Ting Yin
   11. Ali Esmailizadeh
   12. Chang Zhang
   13. Lu-Jiang Qu
   14. Xue-Mei Lu
   15. Jian-Lin Han
   16. Ya-Ping Zhang
   17. Ming-Shan Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This paper addresses valuable questions about the evolution of recombination landscape under domestication by examining recombination maps in domesticated chickens and their wild ancestor. However, despite employing a state-of-the-art deep learning method for recombination map inference, the lack of systematic benchmarking and presence of some unexpected patterns raise concerns about the reliability of the inferred maps, thus providing incomplete support for rapid evolution of recombination landscapes. Additionally, due to methodological limitations in testing for intra-genome correlations between evolutionary processes, the current evidence is inadequate to support the associations of recombination with selection and/or introgression in domesticated chickens.

   Reviewed by eLife

8. Specialisation of meiotic kinetochores revealed through a synthetic SAC strategy

   This article has 3 authors:

   1. Lori B Koch
   2. Christos Spanos
   3. Adele L Marston

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Koch et al. describe a valuable novel methodology, SynSAC, to synchronise cells to analyse meiosis I or meiosis II or mitotic metaphase in budding yeast. The authors present convincing data to validate abscisic acid-induced dimerisation to induce a synthetic spindle assembly checkpoint (SAC) arrest that will be of particular importance to analyse meiosis II. The authors use their approach to determine the composition and phosphorylation of kinetochores from meiotic metaphase I and metaphase II that will be of interest to the broader meiosis research community.

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

   Reviewed by eLife, Review Commons

9. Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching

   This article has 3 authors:

   1. Kexin Zhang
   2. Timothy Grant
   3. Nikolaus Grigorieff

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study builds on previous work from the same authors to present a conceptually distinct workflow for cryo-EM reconstruction that uses 2D template matching to enable high-resolution structure determination of small (sub-50 kDa) protein targets. The paper describes how density for small-molecule ligands bound to such targets can be reconstructed without these ligands being present in the template. However, the evidence described for the claim that this technique "significantly" improves the alignment of the reconstruction of small complexes is incomplete. The authors could better evaluate the effects of model bias on the reconstructed densities.

   Reviewed by eLife

10. Reproducibility of Scientific Claims in Drosophila Immunity: A Retrospective Analysis of 400 Publications

    This article has 30 authors:

    1. Hannah Westlake
    2. Fabrice David
    3. Yao Tian
    4. Kenan Krakovic
    5. Asya Dolgikh
    6. Liza Juravlev
    7. Thomas Esmangart de Bournonville
    8. Alexia Carboni
    9. Claudia Melcarne
    10. Tisheng Shan
    11. Yang Wang
    12. Yizhu Mu
    13. Akshata Kotwal
    14. Nadia Pirko
    15. Jean Philippe Boquete
    16. Fanny Schüpfer
    17. Samuel Rommelaere
    18. Mickael Poidevin
    19. Zhonggeng Liu
    20. Shu Kondo
    21. Girish S Ratnaparkhi
    22. Sveta Chakrabarti
    23. Guiqing Liu
    24. Florent Masson
    25. Li Xiaoxue
    26. Mark A Hanson
    27. Haobo Jiang
    28. Francesca Di Cara
    29. Estee Kurant
    30. Bruno Lemaitre

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This fundamental study is part of an impressive, large-scale effort to assess the reproducibility of published findings in the field of Drosophila immunity. In a companion article, the authors analyze 400 papers published between 1959 and 2011, and assess how many of the claims in these papers have been tested in subsequent publications. In this article, the authors report the results of validation experiments to assess a subset of the claims that, according to the literature, have not been corroborated. While the evidence reported for some of these validation studies is convincing, it remains incomplete for others.

    Reviewed by eLife