1. ESPRESSO: Spatiotemporal omics based on organelle phenotyping

    This article has 7 authors:
    1. Lorenzo Scipioni
    2. Giulia Tedeschi
    3. Mariana Navarro
    4. Yunlong Jia
    5. Scott Atwood
    6. Jennifer A. Prescher
    7. Michelle Digman

    Reviewed by Arcadia Science

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  2. Semantical and Geometrical Protein Encoding Toward Enhanced Bioactivity and Thermostability

    This article has 5 authors:
    1. Yang Tan
    2. Bingxin Zhou
    3. Lirong Zheng
    4. Guisheng Fan
    5. Liang Hong
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      ProtSSN is a valuable approach that generates protein embeddings by integrating sequence and structural information, demonstrating improved prediction of mutation effects on thermostability compared to sequence-only models. The work is currently incomplete as it lacks a thorough comparison against other recent top-performing methods that also incorporate structural data, such as SaProt, EVE-based models, and GEMME. Providing a comprehensive analysis benchmarking ProtSSN against these state-of-the-art structure-based approaches would significantly strengthen the evidence supporting the utility of ProtSSN's joint sequence-structure representations.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  3. Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections

    This article has 11 authors:
    1. Mighten C. Yip
    2. Mercedes M. Gonzalez
    3. Colby F. Lewallen
    4. Corey R. Landry
    5. Ilya Kolb
    6. Bo Yang
    7. William M. Stoy
    8. Ming-fai Fong
    9. Matthew J.M. Rowan
    10. Edward S. Boyden
    11. Craig R. Forest
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This technical study presents a novel sampling strategy for detecting synaptic coupling between neurons from dual pipette patch-clamp recordings in acute slices of mammalian brain tissue in vitro. The authors present solid evidence that this strategy, which incorporates automated patch clamp electrode positioning and cleaning for reuse with strategic neuron targeting, has the potential to substantially improve the efficiency of neuronal sampling with paired recordings. This technique and the extensions discussed will be useful for neuroscientists wanting to apply or already conducting automated multi-pipette patch clamp recording electrophysiology experiments in vitro for neuron connectivity analyses.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. CYpHER: Catalytic extracellular targeted protein degradation with high potency and durable effect

    This article has 9 authors:
    1. Zachary R. Crook
    2. Gregory P. Sevilla
    3. Pamela Young
    4. Emily J. Girard
    5. Tinh-Doan Phi
    6. Monique Howard
    7. Jason Price
    8. James M. Olson
    9. Natalie W. Nairn

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  5. A three filament mechanistic model of musculotendon force and impedance

    This article has 3 authors:
    1. Matthew Millard
    2. David W. Franklin
    3. Walter Herzog
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a valuable study that develops a new model of the way muscle responds to perturbations, synthesizing models of how it responds to small and large perturbations, both of which are used to predict how muscles function for stability but also how they can be injured, and which tend to be predicted poorly by classic Hill-type models. The evidence presented to support the model is solid, since it outperforms Hill-type models in a variety of conditions. Although the combination of phenomenological and mechanistic aspects of the model may sometimes make it challenging to interpret the output, the work will be of interest to those developing realistic models of the stability and control of movement in humans or other animals.

    Reviewed by eLife

    This article has 11 evaluationsAppears in 1 listLatest version Latest activity
  6. Compositional editing of extracellular matrices by CRISPR/Cas9 engineering of human mesenchymal stem cell lines

    This article has 12 authors:
    1. Sujeethkumar Prithiviraj
    2. Alejandro Garcia Garcia
    3. Karin Linderfalk
    4. Bai Yiguang
    5. Sonia Ferveur
    6. Ludvig Nilsén Falck
    7. Agatheeswaran Subramaniam
    8. Sofie Mohlin
    9. David Hidalgo
    10. Steven J Dupard
    11. Deepak Bushan Raina
    12. Paul E Bourgine
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The study presents a potentially useful approach to genetically modify cells to produce extracellular matrices with altered compositions. The evidence supporting the authors' conclusions regarding the chondrogenicity of lyophilized constructs is considered incomplete, as the study does not adequately demonstrate the formation of a histologically identifiable cartilaginous matrix. The study also lacks several significant details and does not have sufficient power to support the conclusions.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  7. Development of a new genotype–phenotype linked antibody screening system

    This article has 9 authors:
    1. Takashi Watanabe
    2. Hikaru Hata
    3. Yoshiki Mochizuki
    4. Fumie Yokoyama
    5. Tomoko Hasegawa
    6. Naveen Kumar
    7. Tomohiro Kurosaki
    8. Osamu Ohara
    9. Hidehiro Fukuyama
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The studies described here are useful; they are broadly applicable to all antibody discovery subfields but do not add significant improvement to techniques already published. The findings are incomplete with respect to the methodology since details that are crucial in order to repeat the experiment are lacking (such as a timestamp) and they do not take into account multiple recent papers that have tested similar strategies. These studies will be of interest to a specialized audience working on making antibodies to infectious agents.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  8. HiExM: high-throughput expansion microscopy enables scalable super-resolution imaging

    This article has 8 authors:
    1. John H. Day
    2. Catherine Marin Della Santina
    3. Pema Maretich
    4. Alexander L. Auld
    5. Kirsten K. Schnieder
    6. Tay Shin
    7. Edward S. Boyden
    8. Laurie A. Boyer
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study develops a high throughput version of expansion microscopy that can be performed in 96-well plates. The engineered technology is convincing and compatible with standard microplates and automated microscopes and thus will be of broad interest. However, the application is incomplete and would benefit from additional experiments.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  9. Overcoming the nutritional immunity by engineering iron-scavenging bacteria for cancer therapy

    This article has 8 authors:
    1. Sin-Wei Huang
    2. See-Khai Lim
    3. Yao-An Yu
    4. Yi-Chung Pan
    5. Wan-Ju Lien
    6. Chung-Yuan Mou
    7. Che-Ming Jack Hu
    8. Kurt Yun Mou
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study combines proteomics and a mouse model to reveal the importance of iron uptake in bacterial therapy for cancer. The evidence presented is convincing. Notably, the authors showed upregulation of iron uptake of bacteria significantly inhibits tumor growth in vivo. This paper will be of interest to a broad audience including researchers in cancer biology, cell biology, and microbiology.

    Reviewed by eLife

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  10. Near-perfect precise on-target editing of human hematopoietic stem and progenitor cells

    This article has 7 authors:
    1. Fanny-Mei Cloarec-Ung
    2. Jamie Beaulieu
    3. Arunan Suthananthan
    4. Bernhard Lehnertz
    5. Guy Sauvageau
    6. Hilary M Sheppard
    7. David JHF Knapp
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents an important methodology to increase the efficiency and precision of gene editing in human hematopoietic stem and progenitor cells. The evidence supporting the claims is convincing in that primitive LTC-ICs were minimally affected as a result of the editing procedure and the lack of edits at predicted off-target sites. The work will be of interest to biologists studying hematopoietic stem and progenitor cells and genome editing for potential clinical applications.

    Reviewed by eLife

    This article has 6 evaluationsAppears in 1 listLatest version Latest activity