Cancer Biology

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    Protocols in Current Issue
    Fe-NTA Microcolumn Purification of Phosphopeptides from Immunoprecipitation (IP) Eluates for Mass Spectrometry Analysis
    Authors:  Ethan J. Sanford and Marcus B. Smolka, date: 08/05/2021, view: 14, Q&A: 0

    Protein phosphorylation is a nearly universal signaling mechanism. To date, a number of proteomics tools have been developed to analyze phosphorylation. Phosphoproteome-wide analyses using whole cell extracts suffer from incomplete coverage, often

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    A Genetically Engineered Mouse Model of Venous Anomaly and Retinal Angioma-like Vascular Malformation
    Authors:  Xudong Cao, Beibei Xu, Xiao Li, Taotao Li and Yulong He, date: 08/05/2021, view: 16, Q&A: 0

    Characterization of key regulators in vein development will advance our understanding of mechanisms underlying venous anomalies and provide therapeutic targets for the treatment of vascular malformations. Here, we provide a detailed protocol for the

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    A Genetically Engineered Mouse Model of Venous Anomaly and Retinal Angioma-like Vascular Malformation
    Authors:  Xudong Cao, Beibei Xu, Xiao Li, Taotao Li and Yulong He, date: 08/05/2021, view: 16, Q&A: 0
    [Abstract]

    Characterization of key regulators in vein development will advance our understanding of mechanisms underlying venous anomalies and provide therapeutic targets for the treatment of vascular malformations. Here, we provide a detailed protocol for the generation of genetically engineered mouse models targeting the Tek gene for the analysis of vein

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    Fe-NTA Microcolumn Purification of Phosphopeptides from Immunoprecipitation (IP) Eluates for Mass Spectrometry Analysis
    Authors:  Ethan J. Sanford and Marcus B. Smolka, date: 08/05/2021, view: 14, Q&A: 0
    [Abstract]

    Protein phosphorylation is a nearly universal signaling mechanism. To date, a number of proteomics tools have been developed to analyze phosphorylation. Phosphoproteome-wide analyses using whole cell extracts suffer from incomplete coverage, often missing phosphorylation events from low-abundance proteins. In order to increase coverage of

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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: 948, 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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    Antisense Oligo Pulldown of Circular RNA for Downstream Analysis
    Authors:  Debojyoti Das, Aniruddha Das and Amaresh C. Panda, date: 07/20/2021, view: 456, Q&A: 0
    [Abstract]

    Circular RNAs (circRNAs) are a large family of noncoding RNA molecules that have emerged as novel regulators of gene expression by sequestering microRNAs (miRNAs) and RNA-binding proteins (RBPs). Several computational tools have been developed to predict circRNA interaction with target miRNAs and RBPs with a view to studying their potential effect

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    Analysis of the Effects of Hexokinase 2 Detachment From Mitochondria-Associated Membranes with the Highly Selective Peptide HK2pep
    Authors:  Francesco Ciscato, Federica Chiara, Riccardo Filadi and Andrea Rasola, date: 07/20/2021, view: 818, Q&A: 0
    [Abstract]

    The crucial role of hexokinase 2 (HK2) in the metabolic rewiring of tumors is now well established, which makes it a suitable target for the design of novel therapies. However, hexokinase activity is central to glucose utilization in all tissues; thus, enzymatic inhibition of HK2 can induce severe adverse effects. In an effort to find a selective

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    Monitoring Changes in the Oxidizing Milieu in the Endoplasmic Reticulum of Mammalian Cells Using HyPerER
    Authors:  Julia Birk, Beata Lizak, Christian Appenzeller-Herzog and Alex Odermatt, date: 07/05/2021, view: 1292, Q&A: 0
    [Abstract]

    The production of reactive oxygen species (ROS) and endoplasmic reticulum (ER) stress are tightly linked. The generation of ROS can be both the cause and a consequence of ER stress pathways, and an increasing number of human diseases are characterized by tissue atrophy in response to ER stress and oxidative injury. For the assessment of modulators

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    Intravenous and Non-invasive Drug Delivery to the Mouse Basal Forebrain Using MRI-guided Focused Ultrasound
    [Abstract]

    Basal forebrain cholinergic neurons (BFCNs) regulate circuit dynamics underlying cognitive processing, including attention, memory, and cognitive flexibility. In Alzheimer’s disease and related neurodegenerative conditions, the degeneration of BFCNs has long been considered a key player in cognitive decline. The cholinergic system thus

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    Multi-color Flow Cytometry for Comprehensive Analysis of the Tumor Immune Infiltrate in a Murine Model of Breast Cancer
    Authors:  Ana S. Almeida, Miriam R. Fein and Mikala Egeblad, date: 06/05/2021, view: 1418, Q&A: 0
    [Abstract]

    Flow cytometry is a popular laser-based technology that allows the phenotypic and functional characterization of individual cells in a high-throughput manner. Here, we describe a detailed procedure for preparing a single-cell suspension from mammary tumors of the mouse mammary tumor virus-polyoma middle T (MMTV-PyMT) and analyzing these cells by

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    Surface Engineering and Multimodal Imaging of Multistage Delivery Vectors in Metastatic Breast Cancer
    Authors:  Shreya Goel, Mauro Ferrari and Haifa Shen, date: 05/20/2021, view: 3447, Q&A: 0
    [Abstract]

    The design of effective nanoformulations that target metastatic breast cancers is challenging due to a lack of competent imaging and image analysis protocols that can capture the interactions between the injected nanoparticles and metastatic lesions. Here, we describe the integration of in vivo whole-body PET-CT with high temporal resolution, ex

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    ATAC-Seq-based Identification of Extrachromosomal Circular DNA in Mammalian Cells and Its Validation Using Inverse PCR and FISH
    Authors:  Zhangli Su, Shekhar Saha, Teressa Paulsen, Pankaj Kumar and Anindya Dutta, date: 05/05/2021, view: 3170, Q&A: 0
    [Abstract]

    Recent studies from multiple labs including ours have demonstrated the importance of extrachromosomal circular DNA (eccDNA) from yeast to humans (Shibata et al., 2012; Dillon et al., 2015; Møller et al., 2016; Kumar et al., 2017; Turner et al., 2017; Kim et al., 2020). More recently, it has been found that cancer cells obtain a selective

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