Molecular Targets and Drug Discovery

This course will cover methodological approaches to bioassay development for high-throughput screening. Both cell-based (cytotoxicity, cytoprotection, high content imaging, and reporter systems) and cell-free assay systems (enzyme, FRET, time-resolved fluorescence, quenching assays, and immunological assays) will be included with discussion of the potential promise and pitfalls associated with each assay system. Various assay formats, visualization techniques, and current developments in assay technology will be discussed. Project management techniques will be utilized to aid in the process of assay development. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology or equivalent; 410.603 Advanced Cell Biology or equivalent. SCI

This course will investigate current and potential molecular targets in cancer, including kinases, DNA repair pathways, epigenetic modifications, immunotherapy approaches, and hormonal, metastasis, and angiogenesis targets. Discussion will also include topics on what defines a molecular target and the methods by which they are evaluated. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology or equivalent; 410.603 Advanced Cell Biology or equivalent; 410.604 Cellular Signal Transduction. SCI

Drug Design and Chemical Libraries explores pharmacological space with an emphasis on disciplines related to drug discovery, and an understanding of the properties desirable in a drug. Medicinal chemistry, natural product chemistry, focused synthetic libraries, and combinatorial chemistry will be covered. The application of Lipinski's rules for assessing drug-like molecules will be discussed in detail, as well as methods for chemical analysis, in silico drug design, molecular modeling, and compound storage and handling. Also, techniques used for assessing and harnessing chemical diversity for drug discovery will be discussed. Students will gain a fundamental understanding of small molecules at the atomic level as well as insights into the structure-activity relationship. Both are critical to the design and synthesis of chemical libraries that efficiently explore therapeutically useful chemical space and to drug design. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology.

This course will use hands-on instruction in automated bioassay systems for high-throughput screening as an entry point to covering pertinent aspects of HTS, such as data manipulation, storage, and analysis; liquid handling robotics, microtiter plate washing, manipulation, and barcoding; HTS assay detectors; and automated devices for assay setup, validation, and visualization. Cost considerations, HTS amenable assay systems, and miniaturization and scale-up will also be discussed. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology, and 410.696 Bioassay Development. SCI

This course covers molecular and cellular immunology. Topics include innate immunity, adaptive immunity, the development and function of B cell and T cell antigen receptors, the major histocompatibility complexes, innate effector mechanisms, humoral and cellular immune responses, and regulation of immune responses. Special topics include immunomodulation, immunodeficiency diseases, autoimmunity, evasion and subversion of the immune system by pathogens, immunotherapies, and vaccines. Students are also introduced to the applied aspects of immunology, which include protein and cellular-based immunoassays. Prerequisites: 410.601 Biochemistry; 410.602 Molecular Biology, 410.603 Advanced Cell Biology I. SCI

This course integrates and expands concepts learned in an introductory immunology course. Students will be presented with advanced topics in immunology through literature reviews, clinical case studies, and basic science and clinical research papers. Students will also receive support from leading-edge webinars. Topic areas may include, but are not limited to: acellular and cellular innate immunity, adaptive immunity, immune regulation, autoimmunity, immunosuppression, inflammation, neuroimmunology, immunobiology of pregnancy, immunogenomics, tumor immunology, standard and developing therapies for immunopathologies, and immunotherapies. Students will also be introduced to immunological tests used for disease screening and diagnoses. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cellular Biology I, and 410.613 Principles of Immunology or an undergraduate immunology course. SCI

This course begins by reviewing receptor binding and enzyme kinetics. Various cellular receptors and their physiology are discussed, as are the pharmacological agents used to define and affect the receptor’s function. Students study the pharmacology of cell surface receptors and intracellular receptors. Also considered are the drugs that affect enzymes. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I, 410.604 Advanced Cell Biology II. SCI

This course explores the theory and practice of biological database searching and analysis. In particular, students are introduced to integrated systems where a variety of data sources are connected through internet access. Information retrieval and interpretation are discussed, and many practical examples in a computer laboratory setting enable students to improve their data mining skills. Methods included in the course are searching the biomedical literature, sequence homology searching and multiple alignment, phylogeny, gene prediction, protein sequence motif analysis and secondary structure prediction, and several genome browsing methods. Introductory analysis using the R programming language is introduced. Computer access is required. Prerequisites: 410.601 Biochemistry. Corequisite: 410.602 Molecular Biology. SCI

This course provides students with knowledge of the fundamental principles of the molecular and cellular biology of cancer cells. The course explores the role of growth factors and signal transduction mechanisms, oncogenes, tumor suppressor genes, tumor viruses, and angiogenesis in tumorigenesis and metastasis. Special topics include cancer prevention and the array of cancer therapies, which include surgery, chemotherapy, radiation therapy, hormonal therapy, stem cell transplant, and immunotherapies. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology or equivalent, 410.604 Cellular Signal Transduction. SCI

Many protein-related bioinformatics databases, query tools, and data analysis software tools have been developed to organize and provide biological annotations for proteins to support sequence, structural, functional, and evolutionary analyses in the context of pathway, network, and systems biology. This course provides a working knowledge of various computer-based tools for protein science research. Topics include protein database searching, protein physicochemical properties, secondary structure prediction, statistical verification, post-translational modification (PTM) and networks analysis, protein-protein interaction (PPI) prediction, and bioinformatics approaches in proteomics. Also covered are graphic visualization of the different types of three-dimensional folds and predicting three-dimensional structures by homology methods, machine learning, and neural network analysis. Computer laboratories complement the material presented in lectures. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology; 410.633 Introduction to Bioinformatics or equivalent; 410.634 Practical Computer Concepts for Bioinformatics.

This course introduces statistical concepts and analytical methods as applied to data encountered in biotechnology and biomedical sciences. It emphasizes the basic concepts of experimental design, quantitative analysis of data, and statistical inferences. Topics include probability theory and distributions; population parameters and their sample estimates; descriptive statistics for central tendency and dispersion; hypothesis testing and confidence intervals for means, variances, and proportions; categorical data analysis; linear correlation and regression model; logistic regression; analysis of variance; and nonparametric methods. The course provides students a foundation with which to evaluate information critically to support research objectives and product claims and a better understanding of statistical design of experimental trials for biological products/devices. Prerequisites: Basic mathematics (algebra). SCI

This laboratory course illustrates the use of basic mammalian cell culture techniques for bioscience research and commercial applications. Students are introduced to mammalian cell cultivation methods, including proper use of a biological safety cabinet, sterile technique, cell enumeration and media preparation, cultivation of mammalian cell lines, detection of contamination, cryopreservation, transfection, mammalian cell culture scale-up, and bioassays. This course is designed for students with no prior knowledge or with limited knowledge of mammalian cell culture methods. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology or equivalent. SCI

The Advanced Recombinant DNA Laboratory course consists of integrated laboratory exercises designed to give students hands-on experience with various molecular techniques. This innovative hybrid course is intended for advanced learners with extensive molecular biology experience who want to use the current and emerging techniques commonly employed in government and industry. This course will review fundamental molecular biology research principles and summarize the process of converting a research-based laboratory into a clinical-level laboratory. The onsite laboratory learning experiences will include, but not be limited to, PCR optimization, quantitative real-time PCR, and control of gene expression by DNA sequencing in the clinical setup. The essential concepts discussed will include setting up a clinical lab, writing Standard Operating Protocols (SOPs) at the clinical level, and applying for a CLIA certificate. Students will also be introduced to microarray analysis and the utilization of bioinformatics pipelines. Students are required to attend the onsite laboratory period. Prerequisites: 410.601 Biochemistry; 410.602 Molecular Biology; 410.656 Recombinant DNA Laboratory; or consent of program committee. SCI

This laboratory course introduces students to methods for analyzing the immune system. Participants gain experience with various immunologic techniques used in research and biotechnology laboratories, such as immunoassays, immunofluorescence, western blot analysis, SDS-PAGE, antibody purification (protein A), and cytokine assays. Additional topics for discussion include hybridism technology phage antibody libraries, therapeutic monoclonal antibodies, and flow cytometry. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology or equivalent; 410.603 Advanced Cell Biology or equivalent; 410.613 Principles of Immunology or undergraduate immunology course highly recommended, or consent of program committee. SCI

This course will introduce students to various methods for analyzing and interpreting transcriptomics data generated from technologies such as oligonucleotides or two-channel microarrays, qRT-PCR, and RNA sequencing. Topics will include scaling/normalization, outlier analysis, and missing value imputation. Students will learn how to identify differentially expressed genes and correlate their expression with clinical outcomes such as disease activity or survival with relevant statistical tests; methods to control for multiple testing will also be presented. An introduction to linear and nonlinear dimensionality reduction methods and both supervised and unsupervised clustering and classification approaches will be provided. Open source tools and databases for biological interpretation of results will be introduced. Assignments and concepts will make use of publicly available datasets, and students will compute and visualize results using the statistical software R. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.645 Biostatistics, 410.634 Practical Computer Concepts for Bioinformatics, or an undergraduate computer programming course. SCI

This course will provide students with hands-on experience in the process development of biological products from a cell bank through purification. Students will develop products produced in bacteria, mammalian cells, and insect cells. Students will optimize growth conditions on a small scale and then produce the biologic in a larger-scale vessel. Students will then purify the product after optimizing purification conditions. Topics to be covered include microbial fermentation, cell culture production, bioassays, product purification, and the regulatory, engineering, and business principles associated with the scale-up of a biologic product. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology. 410.656 Recombinant DNA Laboratory; or consent of program committee.