Cancer Biology

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    Protocols in Current Issue
    Conditional Human BRD4 Knock-In Transgenic Mouse Genotyping and Protein Isoform Detection
    Authors:  Michael Paul Lewis, Shwu-Yuan Wu and Cheng-Ming Chiang, date: 04/05/2022, view: 441, Q&A: 0
    [Abstract]

    Bromodomain-containing protein 4 (BRD4) is an acetyl-lysine reader protein and transcriptional regulator implicated in chromatin dynamics and cancer development. Several BRD4 isoforms have been detected in humans with the long isoform (BRD4-L, aa 1-1,362) playing a tumor-suppressive role and a major short isoform (BRD4-S, aa 1-722) having

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    A Cell-based Screening Method Using an Intracellular Antibody for Discovering Small Molecules Targeting Hard-to-drug Proteins
    Authors:  Nicolas Bery and Terry H. Rabbitts, date: 02/20/2022, view: 1859, Q&A: 0
    [Abstract] Targeting hard-to-drug proteins, such as proteins functioning by protein-protein interactions (PPIs) with small molecules, is difficult because of the lack of well-defined pockets. Fragment or computational-based methods are usually employed for the discovery of such compounds, but no generic method is available to quickly identify small molecules ...
    Developing Clinically Relevant Acquired Chemoresistance Models in Epithelial Ovarian Cancer Cell Lines
    Authors:  Priti S. Shenoy, Sourav Chakraborty, Snehal M. Gaikwad, Asmita Sakpal and Pritha Ray, date: 02/05/2022, view: 1406, Q&A: 0
    [Abstract]

    Chemoresistance, the ability of cancer cells to overcome therapeutic interventions, is an area of active research. Studies on intrinsic and acquired chemoresistance have partly succeeded in elucidating some of the molecular mechanisms in this elusive phenomenon. Hence, drug-resistant cellular models are routinely developed and used to mimic the

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    ATAC Sequencing Protocol For Cryopreserved Mammalian Cells
    Authors:  Juan Manuel Caravaca, Monika Mehta, Sujatha Gowda and Bao Tran, date: 01/20/2022, view: 1438, Q&A: 0
    [Abstract]

    ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) is a powerful method to evaluate chromatin accessibility and nucleosome positioning at a genome-wide scale. This assay uses a hyperactive Tn5 transposase, to simultaneously cut open chromatin and insert adapter sequences. After sequencing, the reads generated

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    Urea Denaturation, Zinc Binding, and DNA Binding Assays of Mutant p53 DNA-binding Domains and Full-length Proteins
    Authors:  Jeung-Hoi Ha, Xin Yu, Darren R. Carpizo and Stewart N. Loh, date: 10/20/2021, view: 932, Q&A: 0
    [Abstract]

    In the cell, the thermodynamic stability of a protein – and hence its biological activity – can change dramatically as a result of perturbations in its amino acid sequence and the concentration of stabilizing ligands. This interplay is particularly evident in zinc-binding transcription factors such as the p53 tumor suppressor, whose

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    Analysis of Leukemia Cell Metabolism through Stable Isotope Tracing in Mice
    Authors:  Nick van Gastel, Jessica B. Spinelli, Marcia C. Haigis and David T. Scadden, date: 10/05/2021, view: 1947, Q&A: 0
    [Abstract]

    Once thought to be a mere consequence of the state of a cell, intermediary metabolism is now recognized as a key regulator of mammalian cell fate and function. In addition, cell metabolism is often disturbed in malignancies such as cancer, and targeting metabolic pathways can provide new therapeutic options. Cell metabolism is mostly studied in

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    Modeling the Nonlinear Dynamics of Intracellular Signaling Networks
    Authors:  Oleksii S. Rukhlenko and Boris N. Kholodenko, date: 07/20/2021, view: 2073, Q&A: 0
    [Abstract]

    This protocol illustrates a pipeline for modeling the nonlinear behavior of intracellular signaling pathways. At fixed spatial points, nonlinear signaling dynamics are described by ordinary differential equations (ODEs). At constant parameters, these ODEs may have multiple attractors, such as multiple steady states or limit cycles. Standard

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    Atomic Force Microscopy to Characterize Ginger Lipid-Derived Nanoparticles (GLDNP)
    Authors:  Dingpei Long, Chunhua Yang, Junsik Sung and Didier Merlin, date: 04/05/2021, view: 3799, Q&A: 0
    [Abstract]

    We have demonstrated that a specific population of ginger-derived nanoparticles (GDNP-2) could effectively target the colon, reduce colitis, and alleviate colitis-associated colon cancer. Naturally occurring GDNP-2 contains complex bioactive components, including lipids, proteins, miRNAs, and ginger secondary metabolites (gingerols and shogaols).

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    Intestinal Co-culture System to Study TGR5 Agonism and Gut Restriction
    Authors:  Snehal N. Chaudhari and A. Sloan Devlin, date: 03/20/2021, view: 3467, Q&A: 1
    [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

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    RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
    Authors:  Juan Pablo Tosar, Fabiana Gámbaro, Mauricio Castellano and Alfonso Cayota, date: 02/20/2021, view: 3158, Q&A: 0
    [Abstract]

    Exosomes and other extracellular vesicles (EVs) are considered the main vehicles transporting RNAs in extracellular samples, including human bodily fluids. However, a major proportion of extracellular RNAs (exRNAs) do not copurify with EVs and remain in ultracentrifugation supernatants of cell-conditioned medium or blood serum. We have observed

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