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More articles from Methods

  • Genome-wide profiling of histone modifications in <em>Plasmodium falciparum</em> using CUT&amp;RUN
    Open Access
    Genome-wide profiling of histone modifications in Plasmodium falciparum using CUT&RUN

    Riward Campelo Morillo, Chantal T Harris, Kit Kennedy, Samuel R Henning, Björn FC Kafsack

    Riward Campelo Morillo ... Björn FC Kafsack

    Published 15 November 2022

    We present a detailed step-wise protocol for reliable genome-wide profiling of histone modifications using CUT&RUN that requires only low numbers of Plasmodium falciparum blood stages.

  • A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology
    Open Access
    A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology

    Alexis Diaz-Vegas, Dougall M Norris, Sigrid Jall-Rogg, Kristen C Cooke, Olivia J Conway, Amber S Shun-Shion, Xiaowen Duan, Meg Potter, Julian van Gerwen, Harry JM Baird, Sean J Humphrey, David E James, Daniel J Fazakerley, James G Burchfield

    Alexis Diaz-Vegas ... James G Burchfield

    Published 25 October 2022

    The authors describe a high-throughput method for measuring endogenous GLUT4 and transferrin receptor translocation in adipocytes. They reveal that this method has advantages over studying GLUT4 trafficking using overexpressed GLUT4 reporters, which are commonly used in the field.

  • Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia
    Open Access
    Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia

    Gimano D Amatngalim, Lisa W Rodenburg, Bente L Aalbers, Henriette HM Raeven, Ellen M Aarts, Dounia Sarhane, Sacha Spelier, Juliet W Lefferts, Iris AL Silva, Wilco Nijenhuis, Sacha Vrendenbarg, Evelien Kruisselbrink, Jesse E Brunsveld, Cornelis M van Drunen, Sabine Michel, Karin M de Winter-de Groot, Harry G Heijerman, Lukas C Kapitein, Magarida D Amaral, Cornelis K van der Ent, Jeffrey M Beekman

    Gimano D Amatngalim ... Jeffrey M Beekman

    Published 3 August 2022

    This work describes an optimized assay to determine CFTR drug responses in people with cystic fibrosis, using nasal-airway organoids that are generated from 2D differentiated epithelial monolayers.

  • Workflow for high-dimensional flow cytometry analysis of T cells from tumor metastases
    Open Access
    Workflow for high-dimensional flow cytometry analysis of T cells from tumor metastases

    Cristina Faccani, Gianluca Rotta, Francesca Clemente, Maya Fedeli, Danilo Abbati, Francesco Manfredi, Alessia Potenza, Achille Anselmo, Federica Pedica, Guido Fiorentini, Chiara Villa, Maria P Protti, Claudio Doglioni, Luca Aldrighetti, Chiara Bonini, Giulia Casorati, Paolo Dellabona, Claudia de Lalla

    Cristina Faccani ... Claudia de Lalla

    Published 3 June 2022

    We describe an improved method for the high-dimensional flow cytometry analysis of conventional and rare unconventional T cells infiltrating tumor liver metastases.

  • Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing
    Open Access
    Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing

    Chu Cheng, Pengfeng Xiao

    Chu Cheng ... Pengfeng Xiao

    Published 14 April 2022

    This article proposed the correctable decoding sequencing technology with conservative theoretical error rate of 0.0009%, and evaluated its robustness by simulation. This technology can provide a powerful new protocol for NGS platforms, enabling accurate identification of rare mutations in medicine.

  • Tracking connectivity maps in human stem cell–derived neuronal networks by holographic optogenetics
    Open Access
    Tracking connectivity maps in human stem cell–derived neuronal networks by holographic optogenetics

    Felix Schmieder, Rouhollah Habibey, Johannes Striebel, Lars Büttner, Jürgen Czarske, Volker Busskamp

    Felix Schmieder ... Volker Busskamp

    Published 13 April 2022

    Holographic optogenetic stimulation of human iPSC–derived neuronal networks was exploited to map precise functional connectivity motifs and their long-term dynamics during network development.

  • A FIJI macro for quantifying pattern in extracellular matrix
    Open Access
    A FIJI macro for quantifying pattern in extracellular matrix

    Esther Wershof, Danielle Park, David J Barry, Robert P Jenkins, Antonio Rullan, Anna Wilkins, Karin Schlegelmilch, Ioannis Roxanis, Kurt I Anderson, Paul A Bates, Erik Sahai

    Esther Wershof ... Erik Sahai

    Published 27 January 2021

    This work provides a quantitative tool for the analysis of fibrillar patterns in biology. We demonstrates its utility on in vitro generated extracellular matrices, mouse tissues, and patient samples. The tool is already publicly available to the research community.

  • Quantification of cristae architecture reveals time-dependent characteristics of individual mitochondria
    Open Access
    Quantification of cristae architecture reveals time-dependent characteristics of individual mitochondria

    Mayuko Segawa, Dane M Wolf, Nan W Hultgren, David S Williams, Alexander M van der Bliek, David B Shackelford, Marc Liesa, Orian S Shirihai

    Mayuko Segawa ... Orian S Shirihai

    Published 4 June 2020

    A novel, machine-learning approach to quantify cristae density and architecture in live-cell super-resolution imaging characterizes the ultrastructural parameters of individual mitochondria over time.

  • Robust production of uniform human cerebral organoids from pluripotent stem cells
    Open Access
    Robust production of uniform human cerebral organoids from pluripotent stem cells

    Adam A Sivitilli, Jessica T Gosio, Bibaswan Ghoshal, Alesya Evstratova, Daniel Trcka, Parisa Ghiasi, J Javier Hernandez, Jean Martin Beaulieu, Jeffrey L Wrana, Liliana Attisano

    Adam A Sivitilli ... Liliana Attisano

    Published 17 April 2020

    By leveraging advances in 3D stem cell culture techniques, the authors describe, characterize and validate a novel platform to efficiently generate morphologically consistent human forebrain cerebral organoids.

  • Simultaneous multiple allelic replacement in the malaria parasite enables dissection of PKG function
    Open Access
    Simultaneous multiple allelic replacement in the malaria parasite enables dissection of PKG function

    Konstantinos Koussis, Chrislaine Withers-Martinez, David A Baker, Michael J Blackman

    Konstantinos Koussis ... Michael J Blackman

    Published 16 March 2020

    This work combines the use of an inducible Cre recombinase and different lox sites to simultaneously create multiple allelic replacements. We show that an essential malarial cGMP-dependent protein kinase functions exclusively during the release of the parasite from its host cell.

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