Cell Biology

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    Protocols in Current Issue
    Measurements of Root Colonized Bacteria Species
    Authors:  Vílchez Juan Ignacio, Yu Yang, Dian Yi and Huiming Zhang, date: 04/05/2021, view: 203, Q&A: 0

    Root-associated bacteria are able to influence plant fitness and vigor. A key step in understanding the belowground plant-bacteria interactions is to quantify root colonization by the bacteria of interest. Probably, genetic engineering with

    ...
    Brain-localized and Intravenous Microinjections in the Larval Zebrafish to Assess Innate Immune Response
    Authors:  Alison M. Rojas and Celia E. Shiau, date: 04/05/2021, view: 222, Q&A: 0

    Creating a robust and controlled infection model is imperative for studying the innate immune response. Leveraging the particular strengths of the zebrafish model system, such as optical transparency, ex utero development, and large clutch size,

    ...
    Ex vivo Assessment of Mitochondrial Function in Human Peripheral Blood Mononuclear Cells Using XF Analyzer
    Authors:  Alica Schöller-Mann, Katja Matt, Barbara Hochecker and Jörg Bergemann, date: 04/05/2021, view: 121, Q&A: 0

    Cellular health and function, as we know today, depend on a large extent on mitochondrial function. The essential function of mitochondria is the energy production, more precisely ATP production, via oxidative phosphorylation. Mitochondrial energy

    ...
    A Workflow for High-pressure Freezing and Freeze Substitution of the Caenorhabditis elegans Embryo for Ultrastructural Analysis by Conventional and Volume Electron Microscopy
    Authors:  Mohammad M. Rahman, Irene Y. Chang, Orna Cohen-Fix and Kedar Narayan, date: 04/05/2021, view: 130, Q&A: 0

    The free-living nematode Caenorhabditis elegans is a popular model system for studying developmental biology. Here we describe a detailed protocol to high-pressure freeze the C. elegans embryo (either ex vivo after dissection, or within the intact

    ...
    Measurements of Root Colonized Bacteria Species
    Authors:  Vílchez Juan Ignacio, Yu Yang, Dian Yi and Huiming Zhang, date: 04/05/2021, view: 203, Q&A: 0
    [Abstract]

    Root-associated bacteria are able to influence plant fitness and vigor. A key step in understanding the belowground plant-bacteria interactions is to quantify root colonization by the bacteria of interest. Probably, genetic engineering with fluorescence markers is the most powerful way to monitor bacterial strains in plant. However, this could

    ...
    Brain-localized and Intravenous Microinjections in the Larval Zebrafish to Assess Innate Immune Response
    Authors:  Alison M. Rojas and Celia E. Shiau, date: 04/05/2021, view: 222, Q&A: 0
    [Abstract]

    Creating a robust and controlled infection model is imperative for studying the innate immune response. Leveraging the particular strengths of the zebrafish model system, such as optical transparency, ex utero development, and large clutch size, allows for the development of methods that yield consistent and reproducible results. We created a

    ...
    Ex vivo Assessment of Mitochondrial Function in Human Peripheral Blood Mononuclear Cells Using XF Analyzer
    Authors:  Alica Schöller-Mann, Katja Matt, Barbara Hochecker and Jörg Bergemann, date: 04/05/2021, view: 121, Q&A: 0
    [Abstract]

    Cellular health and function, as we know today, depend on a large extent on mitochondrial function. The essential function of mitochondria is the energy production, more precisely ATP production, via oxidative phosphorylation. Mitochondrial energy production parameters therefore represent important biomarkers. Studies on human cells have mainly

    ...
    A Workflow for High-pressure Freezing and Freeze Substitution of the Caenorhabditis elegans Embryo for Ultrastructural Analysis by Conventional and Volume Electron Microscopy
    Authors:  Mohammad M. Rahman, Irene Y. Chang, Orna Cohen-Fix and Kedar Narayan, date: 04/05/2021, view: 130, Q&A: 0
    [Abstract]

    The free-living nematode Caenorhabditis elegans is a popular model system for studying developmental biology. Here we describe a detailed protocol to high-pressure freeze the C. elegans embryo (either ex vivo after dissection, or within the intact worm) followed by quick freeze substitution. Processed samples are suitable for ultrastructural

    ...
    Intestinal Co-culture System to Study TGR5 Agonism and Gut Restriction
    Authors:  Snehal N. Chaudhari and A. Sloan Devlin, date: 03/20/2021, view: 679, Q&A: 0
    [Abstract]

    The activation of the Takeda G-protein receptor 5 (TGR5, also known as the G protein-coupled bile acid receptor 1, GPBAR1) in enteroendocrine L-cells results in secretion of the anti-diabetic hormone Glucagon-Like Peptide 1 (GLP-1) into systemic circulation. Consequently, recent research has focused on identification and development of TGR5

    ...
    A Spectrofluorophotometrical Method Based on Fura-2-AM Probe to Determine Cytosolic Ca2+ Level in Pseudomonas syringae Complex Bacterial Cells
    [Abstract]

    Calcium signaling is an emerging mechanism by which bacteria respond to environmental cues. To measure the intracellular free-calcium concentration in bacterial cells, [Ca2+]i, a simple spectrofluorometric method based on the chemical probe Fura 2-acetoxy methyl ester (Fura 2-AM) is here presented using Pseudomonad bacterial cells. This is an

    ...
    Liposomal Clodronate-mediated Macrophage Depletion in the Zebrafish Model
    Authors:  Linlin Yang, Alison M. Rojas and Celia E. Shiau, date: 03/20/2021, view: 579, Q&A: 0
    [Abstract]

    The ability to conduct in vivo macrophage-specific depletion remains an effective means to uncover functions of macrophages in a wide range of physiological contexts. Compared to the murine model, zebrafish offer superior imaging capabilities due to their optical transparency starting from a single-cell stage to throughout larval development.

    ...
    Real-time Base Excision Repair Assay to Measure the Activity of the 8-oxoguanine DNA Glycosylase 1 in Isolated Mitochondria of Human Skin Fibroblasts
    Authors:  Daniel Schniertshauer, Daniel Gebhard and Jörg Bergemann, date: 03/20/2021, view: 484, Q&A: 0
    [Abstract]

    7,8-dihydro-8-oxoguanine (8-oxoG) is one of the most common and mutagenic oxidative DNA damages induced by reactive oxygen species (ROS). Since ROS is mainly produced in the inner membranes of the mitochondria, these organelles and especially the mitochondrial DNA (mtDNA) contained therein are particularly affected by this damage. Insufficient

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    An Image-based Dynamic High-throughput Analysis of Adherent Cell Migration
    [Abstract]

    In this protocol, we describe a method to monitor cell migration by live-cell imaging of adherent cells. Scratching assay is a common method to investigate cell migration or wound healing capacity. However, achieving homogenous scratching, finding the optimal time window for end-point analysis and performing an objective image analysis imply, even

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    Retention Using Selective Hooks (RUSH) Cargo Sorting Assay for Live-cell Vesicle Tracking in the Secretory Pathway Using HeLa Cells
    Authors:  Mehrshad Pakdel, Natalia Pacheco-Fernandez and Julia von Blume, date: 03/20/2021, view: 714, Q&A: 0
    [Abstract]

    More than 30% of the total amount of proteins synthesized in mammalian cells follow the secretory pathway in order to mature and be properly sorted to their final destinations. Among several methodologies that describe live-cell monitoring of vesicles, the Retention Using Selective Hooks (RUSH) system is a powerful one that allows to visualize

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