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  1. No Access

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    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

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    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)

  3. No Access

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    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)

  4. No Access

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    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)

  5. No Access

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    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)

  6. 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)

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. No Access

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    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)

  13. 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)

  14. 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)

  15. No Access

    Protocol

    Maize Transformation Using the Morphogenic Genes Baby Boom and Wuschel2

    Despite the fact that maize transformation has been available for over 25 years, the technology has remained too specialized, labor-intensive, and inefficient to be useful for the majority of academic labs. Co...

    Todd Jones, Keith Lowe, George Hoerster, Ajith Anand, Emily Wu in Transgenic Plants (2019)

  16. No Access

    Protocol

    Myoblast Phosphoproteomics as a Tool to Investigate Global Signaling Events During Myogenesis

    Protein phosphorylation is a universal covalent chemical modification of amino acids involved in a large number of biological processes including cell signaling, metabolism, proliferation, differentiation, sur...

    Fiona K. Jones, Gemma E. Hardman, Samantha Ferries, Claire E. Eyers in Myogenesis (2019)

  17. No Access

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    Computational Methods for Analysis of Tumor Clonality and Evolutionary History

    Cancer is an evolutionary process. Recent advances in sequencing technologies have allowed us to investigate intratumor heterogeneity at the single nucleotide level. Here, we describe computational methods tha...

    Gerald Goh, Nicholas McGranahan, Gareth A. Wilson in Cancer Bioinformatics (2019)

  18. No Access

    Protocol

    Proteomic Detection of Carbohydrate-Active Enzymes (CAZymes) in Microbial Secretomes

    Secretomes from microorganisms growing on biomass contain carbohydrate-active enzymes (CAZymes) of potential biotechnological interest. By analyzing such secretomes, we may discover key enzymes involved in deg...

    Tina R. Tuveng, Vincent G. H. Eijsink, Magnus Ø. Arntzen in Functional Proteomics (2019)

  19. No Access

    Protocol

    Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates

    Gene duplication is an important process in the evolution of gene content in eukaryotic genomes. Understanding when gene duplicates contribute new molecular functions to genomes through molecular adaptation is...

    Laurel R. Yohe, Liang Liu, Liliana M. Dávalos in Computational Methods in Protein Evolution (2019)

  20. No Access

    Protocol

    Measuring Human Lipid Metabolism Using Deuterium Labeling: In Vivo and In Vitro Protocols

    Stable isotopes are powerful tools for tracing the metabolic fate of molecules in the human body. In this chapter, we focus on the use of deuterium (2H), a stable isotope of hydrogen, in the study of human lipid ...

    Katherine E. Pinnick, Pippa J. Gunn, Leanne Hodson in Metabolic Signaling (2019)

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