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  1. No Access

    Protocol

    Image-based Identification of Chemical Compounds Capable of Trapping FOXO in the Cell Nucleus

    Forkhead box O (FOXO) factors are tumor suppressor proteins commonly inactivated in human tumors. Furthermore, genetic variation within the FOXO3a gene is consistently associated with human longevity. FOXO pro...

    Susana Machado, Catarina Raposo, Bibiana I. Ferreira in FOXO Transcription Factors (2019)

  2. No Access

    Protocol

    High-Resolution Mapping of N 6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-Seq)

    N 6-Methyladenosine, an abundant chemical modification in mRNA, plays crucial roles in regulating gene expression and biological processes. Research on m6A and its functions has progressed rapidly in the past fe...

    Phillip J. Hsu, Chuan He in Epitranscriptomics (2019)

  3. No Access

    Protocol

    Transgene Recombineering in Bacterial Artificial Chromosomes

    Bacterial Artificial Chromosome (BAC) libraries are a valuable research resource. Any one of the clones in these libraries can carry hundreds of thousands of base pairs of genetic information. Often the entire...

    Michael G. Zeidler, Thomas L. Saunders in Microinjection (2019)

  4. No Access

    Protocol

    Chemical Synthesis of an Asymmetric Mimic of the Nitrogenase Active Site

    The synthetic inorganic chemistry of metal–sulfur (M-S, M = metals) clusters has played an important, complementary role to the biochemical analyses of nitrogenase toward a better understanding of the enzyme a...

    Kazuki Tanifuji, Yasuhiro Ohki in Metalloproteins (2019)

  5. No Access

    Protocol

    An In Vitro Three-Dimensional Organotypic Model to Analyze Peripancreatic Fat Invasion in Pancreatic Cancer: A Culture System Based on Collagen Gel Embedding

    Three-dimensional culture systems reflect biological environments better than conventional two-dimensional culture. Additionally, three-dimensional culture is a strong experimental tool to analyze direct inter...

    Takashi Okumura, Kenoki Ohuchida, Masafumi Nakamura in Pancreatic Cancer (2019)

  6. No Access

    Protocol

    Interface-Based Structural Prediction of Novel Host-Pathogen Interactions

    About 20% of the cancer incidences worldwide have been estimated to be associated with infections. However, the molecular mechanisms of exactly how they contribute to host tumorigenesis are still unknown. To e...

    Emine Guven-Maiorov, Chung-Jung Tsai in Computational Methods in Protein Evolution (2019)

  7. No Access

    Protocol

    In Silico-Directed Evolution Using CADEE

    Recent years have seen an explosion of interest in both sequence- and structure-based approaches toward in silico-directed evolution. We recently developed a novel computational toolkit, CADEE, which facilitat...

    Beat Anton Amrein, Ashish Runthala in Computational Methods in Protein Evolution (2019)

  8. No Access

    Protocol

    Rare Variant Quantitation Using Droplet Digital PCR

    Droplet digital PCR (ddPCR) allows precise quantitation of individual copies of DNA. Using allele-specific fluorescent oligonucleotide probes, ddPCR can enumerate both mutant and wild-type alleles enabling hig...

    Brian Parkin in Chronic Lymphocytic Leukemia (2019)

  9. No Access

    Protocol

    Genome Sequencing and Analysis Methods in Chronic Lymphocytic Leukemia

    The genomic sequencing of chronic lymphocytic leukemia (CLL) samples has provided exciting new venues for the understanding and treatment of this prevalent disease. This feat is possible thanks to high-through...

    Víctor Quesada, Miguel Araujo-Voces, José G. Pérez-Silva in Chronic Lymphocytic Leukemia (2019)

  10. No Access

    Protocol

    Identification of Proteins on Archived 2D Gels

    Separation technology of proteins from a complex mixture by two-dimensional gel (2D gel) was invented more than 40 years ago. With a good laboratory practice, the 2D gels are likely to be dried and stored at a...

    Hiroyuki Matsumoto, Nobuaki Takemori in Electrophoretic Separation of Proteins (2019)

  11. No Access

    Protocol

    Tumor-Associated Macrophage Isolation and In Vivo Analysis of Their Tumor-Promoting Activity

    Characterization of individual cell populations from the tumor microenvironment is critical to understand their functional contribution to tumor progression. Magnetic bead enrichment and fluorescence-activated...

    Nicholas M. Clark, Paula D. Bos in Cancer Immunosurveillance (2019)

  12. No Access

    Protocol

    Use of Liquid Chromatography–Mass Spectrometry-Based Metabolomics to Identify Biomarkers of Tuberculosis

    Liquid chromatography–mass spectrometry (LC-MS) based metabolomics has proven to be a powerful analytical tool for biomarker screening. Here we describe two workflows which employ untargeted metabolomics to st...

    Juntuo Zhou, Yuxin Yin in Microbial Metabolomics (2019)

  13. No Access

    Protocol

    Reprogramming of Human Melanocytes and Melanoma Cells with Yamanaka Factors

    The expression of Yamanaka factors (Oct3/4, Klf-4, Sox-2, c-Myc) can reprogram cancer cells to a pluripotent stage. This may cause the removal of their epigenetic memory and result in altered tumorigenicity. V...

    Hadiseh Taheri, Umut Cagin, Açelya Yilmazer in Pre-Clinical Models (2019)

  14. No Access

    Protocol

    Expression, Purification, and Activity Analysis of Chlorophyllide Oxidoreductase and Ni2+-Sirohydrochlorin a,c-Diamide Reductase

    Nitrogenase-like enzymes play a vital role in the reduction of the conjugated ring systems of diverse tetrapyrrole molecules. The biosynthesis of all bacteriochlorophylls involves the two-electron reduction of...

    Jürgen Moser, Jan Jasper, José Vazquez Ramos, Sven T. Sowa in Metalloproteins (2019)

  15. No Access

    Protocol

    Transcriptomic Analyses of Phytoplasmas

    Transcriptomic analyses addressed to study phytoplasma gene expression may present few difficulties due to the uncultivable nature of these intracellular, obligate pathogens. While RNA extraction from insect v...

    Davide Pacifico, Simona Abbà, Sabrina Palmano in Phytoplasmas (2019)

  16. No Access

    Protocol

    Immuno-Northern Blotting: Detection of Modified RNA Using Gel Separation and Antibodies to Modified Nucleosides

    Immuno-northern blotting is a method for detecting modified RNAs using gel separation and specific antibodies to modified nucleosides. This method was developed by combining two commonly used molecular biology...

    Eikan Mishima, Takaaki Abe in Epitranscriptomics (2019)

  17. No Access

    Protocol

    Basic Procedures for Detection and Cytotoxicity of Chimeric Antigen Receptors

    Chimeric antigen receptors against CD19 (anti-CD19-CAR) are widely recognized and used by not only researchers associated with immunology, molecular biology, and cell biology but also physicians to treat B-cel...

    Keichiro Mihara, Tetsumi Yoshida, Joyeeta Bhattacharyya in Human Monoclonal Antibodies (2019)

  18. No Access

    Protocol

    DAPI and Confocal Laser-Scanning Microscopy for In Vivo Imaging of Phytoplasmas

    As phytoplasmas are located inside the phloem tissue, always surrounded by numerous layers of other cells, they can result difficult candidates for microscopical investigations. Moreover, the necessity to kill...

    Rita Musetti, Stefanie Vera Buxa in Phytoplasmas (2019)

  19. No Access

    Protocol

    Generation and Identification of Genetically Modified Mice for BMP Receptors

    BMP signaling is critical in embryogenesis and in the development of numerous tissues. Many genetically modified (knockout and transgenic) mice have been established to study BMP function in development and di...

    Jingwen Yang, Yuji Mishina in Bone Morphogenetic Proteins (2019)

  20. No Access

    Protocol

    Examining Cellular Responses to Kinase Drug Inhibition Through Phosphoproteome Mapping of Substrates

    This chapter provides a detailed description for mass spectrometry-based phosphoproteomics analysis. We describe sample preparation, phosphopeptide enrichment, mass spectrometry acquisition, label-free data an...

    Daniel Bucio-Noble, Crystal Semaan, Mark P. Molloy in Systems Chemical Biology (2019)

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