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Methods & Resources

  • Estimation of crossbridge-state during cardiomyocyte beating using second harmonic generation
    Open Access
    Estimation of crossbridge-state during cardiomyocyte beating using second harmonic generation

    Hideaki Fujita, Junichi Kaneshiro, Maki Takeda, Kensuke Sasaki, Rikako Yamamoto, Daiki Umetsu, Erina Kuranaga, Shuichiro Higo, Takumi Kondo, Yoshihiro Asano, Yasushi Sakata, Shigeru Miyagawa, Tomonobu M Watanabe

    Hideaki Fujita ... Tomonobu M Watanabe

    Published 26 May 2023

    This article describes a new method to evaluate the actomyosin activity in living cardiomyocytes during beating based on nonlinear scattering microscopy, which will be useful for elucidating cardiomyopathy mechanisms, efficacy of an intervention, and others.

  • BiFCo: visualizing cohesin assembly/disassembly cycle in living cells
    Open Access
    BiFCo: visualizing cohesin assembly/disassembly cycle in living cells

    Emilio González-Martín, Juan Jiménez, Víctor A Tallada

    Emilio González-Martín ... Víctor A Tallada

    Published 9 May 2023

    A novel strategy developed in fission yeast to visualise only-assembled cohesin complex loading/unloading cycles in eukaryotic chromosomes in living cells.

  • Gapless provides combined scaffolding, gap filling, and assembly correction with long reads
    Open Access
    Gapless provides combined scaffolding, gap filling, and assembly correction with long reads

    Stephan Schmeing, Mark D Robinson

    Stephan Schmeing ... Mark D Robinson

    Published 4 May 2023

    gapless is a new tool for combined execution of correction, scaffolding and gap filling using PacBio or Oxford Nanopore reads.

  • Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method
    Open Access
    Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method

    Jianqi Yang, Alison N DeVore, Daniel A Fu, Mackenzie M Spicer, Mengcheng Guo, Samantha G Thompson, Katelin E Ahlers-Dannen, Federica Polato, Andre Nussenzweig, Rory A Fisher

    Jianqi Yang ... Rory A Fisher

    Published 10 April 2023

    A novel, precise, rapid, and generalizable method to determine transgene zygosity in mice by allele-specific restriction enzyme digestion of PCR products from transgenes or homologous endogenous genes.

  • A novel approach to measure complex V ATP hydrolysis in frozen cell lysates and tissue homogenates
    Open Access
    A novel approach to measure complex V ATP hydrolysis in frozen cell lysates and tissue homogenates

    Lucia Fernandez-del-Rio, Cristiane Benincá, Frankie Villalobos, Cynthia Shu, Linsey Stiles, Marc Liesa, Ajit S Divakaruni, Rebeca Acin-Perez, Orian S Shirihai

    Lucia Fernandez-del-Rio ... Orian S Shirihai

    Published 14 March 2023

    This novel method can be used in clinical samples to determine CV function in diseases, with the added benefit of being able to use frozen samples in a high-throughput manner and to explore ATP hydrolysis as a drug target for disease treatment.

  • A protocol for single nucleus RNA-seq from frozen skeletal muscle
    Open Access
    A protocol for single nucleus RNA-seq from frozen skeletal muscle

    Tyler GB Soule, Carly S Pontifex, Nicole Rosin, Matthew M Joel, Sukyoung Lee, Minh Dang Nguyen, Sameer Chhibber, Gerald Pfeffer

    Tyler GB Soule ... Gerald Pfeffer

    Published 13 March 2023

    The authors detail a method to isolate nuclei for single nucleus RNA sequencing from frozen, biobanked human skeletal muscle samples.

  • Efficient knock-in method enabling lineage tracing in zebrafish
    Open Access
    Efficient knock-in method enabling lineage tracing in zebrafish

    Jiarui Mi, Olov Andersson

    Jiarui Mi ... Olov Andersson

    Published 6 March 2023

    This study introduces a knock-in method in zebrafish that is cloning-free, preserves the endogenous gene, achieves high germline transmission, and useful for both cell labelling and lineage tracing.

  • New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads
    Open Access
    New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

    Laura Gonzalez-Garcia, David Guevara-Barrientos, Daniela Lozano-Arce, Juanita Gil, Jorge Díaz-Riaño, Erick Duarte, Germán Andrade, Juan Camilo Bojacá, Maria Camila Hoyos-Sanchez, Christian Chavarro, Natalia Guayazan, Luis Alberto Chica, Maria Camila Buitrago Acosta, Edwin Bautista, Miller Trujillo, Jorge Duitama

    Laura Gonzalez-Garcia ... Jorge Duitama

    Published 22 February 2023

    Innovative algorithmic approaches were used to perform assembly of complex genomes across the tree of life, from long DNA sequencing data.

  • Activation and inhibition of the C-terminal kinase domain of p90 ribosomal S6 kinases
    Open Access
    Activation and inhibition of the C-terminal kinase domain of p90 ribosomal S6 kinases

    Marlene Uglebjerg Fruergaard, Christine Juul Fælled Nielsen, Cecilia Rosada Kjeldsen, Lars Iversen, Jacob Lauwring Andersen, Poul Nissen

    Marlene Uglebjerg Fruergaard ... Poul Nissen

    Published 20 February 2023

    The design of a constitutively active form of the C-terminal kinase domain of the p90 ribosomal S6 kinase 2 (RSK2) is described, and this is based on a phosphomimetic mutation and a C-terminal truncation, yielding a high kinase activity.

  • A genome-wide CRISPR functional survey of the human phagocytosis molecular machinery
    Open Access
    A genome-wide CRISPR functional survey of the human phagocytosis molecular machinery

    Patrick Essletzbichler, Vitaly Sedlyarov, Fabian Frommelt, Didier Soulat, Leonhard X Heinz, Adrijana Stefanovic, Benedikt Neumayer, Giulio Superti-Furga

    Patrick Essletzbichler ... Giulio Superti-Furga

    Published 1 February 2023

    The validation and interpretation of a genome-wide CRISRPko FACS screen via protein–protein interaction data yield a broad view of the molecular network-regulating phagocytosis in human cells.

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