Biodefense

This course provides a comprehensive overview of the key concepts in molecular biology. Topics to be covered include nucleic acid structure and function, DNA replication, transcription, translation, chromosome structure, and the remodeling and regulation of gene expression in prokaryotes and eukaryotes. Extended topics to be covered include methods in recombinant DNA technology, microarrays, and microRNA.

This course covers cell organization and subcellular structure. Students examine the evolution of the cell, chromosome, and plasma membrane structures and behaviors, as well as the mechanics of cell division, sites of macromolecular synthesis and processing, transport across cell membranes, cell dynamics, organelle biogenesis, and cell specialization. Students are also introduced to the experimental techniques used in cell biology to study cell growth, manipulation, and evaluation. Prerequisites: 410.601 Biochemistry or equivalent.

This foundational biotechnology course provides the biotechnology student an introduction to the business of biotechnology, from scientific discovery through product launch and subsequent organizational and scientific pipeline growth. The course introduces the biotechnology student to various disciplines and activities (such as funding, research and development, biomanufacturing, commercialization) for biotechnology enterprise formation, development, and operation. A course-long project involving several assignments that include aspects of a biotechnology organizational simulation is reflected in a student learning organization (SLO) construct. Course Prerequisites: AS.410.601 Biochemistry or equivalent, AS.410.602 Molecular Biology or equivalent, AS.410.603 Advanced Cell Biology or equivalent, or approval of program committee.

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 will explore the world of chemical and biological threats ranging from the foundational scientific principles to the history of chemical and biological warfare. The chemical and biological threat methodologies for detection, identification, medical intervention, and forensic attribution will be discussed from a foreign and domestic defense standpoint. The course material covers a spectrum of topics pertaining to the use of biological and chemical agents, including the historical background of biological and chemical agents in classic and discretionary warfare, the introduction of scientific evidence in criminal proceedings and chain of custody for evidentiary materials in crimes and terrorism, quality assurance in laboratory operations, threat containment, threat characterization, toxicological assessments, decontamination and remediation, health and safety of responders and analysts, risk assessments, protection, and emerging threats. The scientific principles behind the instrumentation used to characterize, assess, and detect threats for forensic analysis of both biological (bacterial, viral, biological toxins, agricultural threats) and chemical (traditional chemical agents, toxic industrial chemicals, incapacitants) agents will be discussed. In depth molecular and chemical mechanisms of action for each chemical and biological agent will be described linking the biochemical and cellular processes responsible for the whole body symptoms observed following exposure to these threats. Medical countermeasures and/or therapeutics used to defend against chemical and biological threats will also be discussed in detail. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology or equivalent, 410.615 Applied Microbiology or undergraduate microbiology course, or consent of programming committee.

This course provides a comprehensive introduction to Biodefense. It covers the properties of the Biological Select Agents and Toxins (BSAT); their historical and potential use as biological warfare or bioterrorism weapons, their medical consequences, diagnosis, detection, identification, treatment and prevention. Relevant international and domestic policy issues are explored, along with defense strategies and the nature of existing threats to national security. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology or equivalent, 410.615 Applied Microbiology or undergraduate microbiology course, or consent of programming committee. 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

This laboratory course introduces students to methods for manipulating and analyzing nucleic acids. Students gain extensive hands-on experience with plasmid purification, restriction mapping, ligations, bacterial transformations, gel electrophoresis, and applications of the polymerase chain reaction. This course is not recommended for students with substantial experience in these methodologies. Prerequisites: 410.602 Molecular Biology. SCI

This laboratory course introduces students to the methods and techniques used for biothreat detection, surveillance, and identification. Using bio simulants and demonstrations, various bio detection platforms will be discussed and presented, such as point-of-detection devices and methods, laboratory-based screening and identification technologies (culture, quantitative PCR, immunoassays, biosensors), and high-throughput environmental surveillance methods. Statistical methods for determining diagnostic sensitivity and specificity and assay validity will be discussed. Laboratory practices and procedures for working in simulated Biosafety Level 2 and 3 environments will be practiced. Students will be introduced to the current bioinformatics genomic and proteomic databases used for select agent (category A, B, and C) identification and characterization. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I, undergraduate microbiology or 410.615 Microbiology, or approval of program committee. 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 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.

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 laboratory course introduces students to the isolation, cultivation, and differentiation of stem cells. Students are introduced to reprogramming and differentiation protocols for various stem cell and cell progenitor types and the basics of tissue engineering. Students will scale up cells into mini-bioreactors for large-scale use. The class will include industry-wide practices in cGMP. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology or equivalent; 410.603 Advanced Cell Biology or equivalent; 410.604 Cellular Signal Transduction or equivalent; 410.652 Cell Culture Techniques or permission of programming committee. SCI

Students examine cell-to-cell signaling that involves hormones and receptors, signal transduction pathways, second messenger molecules, cell adhesion, extracellular matrix, cell cycle, programmed cell death, methylation of DNA, modification of chromatin structure, and mechanisms of the cell. The roles that defects in signal transduction pathways play in the development of cancer and other disease states will be stressed. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology or equivalent; 410.603 Advanced Cell Biology or equivalent.

This course will cover the biological development of vaccines a well as the immunologic concepts and methods for vaccine delivery. Specific topics include new technologies for vaccine development, such as DNA vaccines, recombinant mucosal vaccines, dendritic cells for antigen delivery, novel adjuvants, and methods to increase vaccine stability. Both time-tested and new vaccine delivery systems, such as lipid-based systems, needle-free injection systems, and the use of genetically modified foods, will be discussed. The underlying biological role of the innate and adaptive immune systems will be explored in light of new types of vaccines and delivery systems. Finally, the process of bringing vaccines to market will be covered, including government oversight and licensure. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I, 410.613 Principles of Immunology, or undergraduate immunology course. 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 is an overview of microorganisms important to clinical diseases and biotechnology. Students are introduced to the general concepts concerning the morphology, genetics, and reproduction of these microbial agents. Lectures focus on individual organisms, with emphasis on infectious diseases, biotechnology applications, molecular and biochemical characteristics, and molecular and serological identification methods. Students will also discuss the impact that biotechnology, particularly genomics, will have on the development of antibiotics and vaccines as treatments and preventive measures. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I. SCI

This course covers the advanced study of viruses with regard to the basic, biochemical, molecular, epidemiological, clinical, and biotechnological aspects of animal viruses primarily, and bacteriophage, plant viruses, viroid’s, prions, and unconventional agents secondarily. Specific areas of virology, including viral structure and assembly, viral replication, viral recombination and evolution, virus-host interactions, viral transformation, gene therapy, antiviral drugs, and vaccines, are presented. The major animal virus families are discussed individually with respect to classification, genomic structure, viroid structure, virus cycle, pathogenesis, clinical features, epidemiology, immunity, and control. The viral vectors and their application in biotechnology are discussed. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I. SCI

The field of parasitology is immense. It covers a plethora of organisms and a multitude of disciplines. This course focuses on the parasites of medical importance that cause human morbidity and mortality throughout the world. It also introduces the student to the general aspects of parasitology. The developmental biology, natural history, and cell and molecular biology of the major eukaryotic parasites will be discussed. Also, the fundamental mechanisms of host-parasite relationships, diagnosis, pathogenesis, epidemiology, and control strategies will be emphasized. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I. SCI

This course is designed to provide an introduction to the application of recombinant DNA technology in agriculture. We will study methods for the introduction of foreign DNA into plant and animal cells and the generation of stably transformed plants and animals. We will discuss specific examples of the use of transgenic plants and animals in biotechnology, which can provide protection against insects, diseases, and tolerance to specific herbicides. We will also investigate how recombinant growth hormones can result in leaner meat, greater milk yield, and better feed utilization, as well as how transgenic plants and animals can serve as bioreactors for the production of medicinals or protein pharmaceuticals. Because recombinant agricultural products are released into the environment or consumed as foods, we will also discuss environmental safety issues. Prerequisites: 410.601 Biochemistry 410.602 Molecular Biology, 410.603 Advanced Cell Biology I.

This course focuses on infectious diseases of mankind and is presented in a system-by-system format. Basic principles of host defense and microbial virulence will be discussed. Practical, up-to-date information on the clinical presentation, symptoms, physical findings, laboratory diagnosis, treatment, and prevention of the general array of diseases caused by bacteria and viruses will be presented. The use of antibiotics, prophylactic agents, and vaccines, along with selected aspects of pathogenesis and epidemiology, will be covered. More cursory coverage will be given to the fungal and parasitic agents of human disease. The student will develop a broad understanding of the many different kinds of infectious processes to which our bodies are subjected on an ongoing basis. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology or equivalent. SCI

This course focuses on emerging infectious diseases from many different perspectives. The maladies addressed range from diseases that have reappeared in altered genetic forms, such as the influenza virus and West Nile virus, to the lethal hemorrhagic fever caused by the Ebola virus. Also discussed is the threat of recombinant and ancient infectious agents, such as Bacillus anthracis, the causative agent of anthrax, which can be used in biological warfare weapons. Opinions from noted scientists and leaders concerning emerging diseases and the prospects for battling them successfully provide scientific and social perspectives. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I. 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 will provide a practical, hands-on introduction to the study of phylogenetics and comparative genomics. Theoretical background on molecular evolution will be provided only as needed to inform the comparative analysis of genomic data. The emphasis of the course will be placed squarely on the understanding and use of a variety of computational tools designed to extract meaningful biological information from molecular sequences. Lectures will provide information on the conceptual essence of the algorithms that underlie various sequence analysis tools and the rationale behind their use. Only programs that are freely available as either downloadable executables or as Web servers will be used in this course. Students will be encouraged to use the programs and approaches introduced in the course to address questions relevant to their own work. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.633 Introduction to Bioinformatics. SCI

This course covers basic concepts and practical applications of modern laboratory diagnostic techniques. Topics include the principles of testing methodology, quality assurance, and the application of molecular methods to the clinical and research laboratory. The test methods to be covered include nucleic acid-based methods, such as hybridization, amplification, and sequencing, non-nucleic acid methods, such as HPLC, GLC, and protein analysis, and technologies such as PFGE, ribotyping, RFLP, and serological testing methodologies. In addition to the test procedures, students are exposed to aspects of statistics, quality control, and regulatory issues, as well as applications of these methods to the diagnosis and prognosis of human disease. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology. SCI

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

Epidemiology is the study of the patterns and determinants of disease in populations. It constitutes a basic science for public health and biomedical sciences, and its influence can be felt daily through the presentation of data by government, academic, and industry sources. The goal of this course is to present an introduction to epidemiological methods and inferences to biotechnology professionals with little prior experience in public health. Issues in epidemiological inference and the assessment of causal relationships from epidemiological studies will be discussed, introducing the issues of bias and confounding. Throughout the course, emphasis will be placed on the practical use of epidemiology, and lectures will be complemented by case studies and published literature. Examples will be drawn from contemporaneous issues in chronic and infectious diseases. At the conclusion of the course, students should have a greater appreciation for the role of the epidemiologic method and be able to evaluate a basic epidemiologic study, including how the study goals and research questions relate to the design, measures, and inferences. Recommended prerequisites: undergraduate statistics course or 410.645 Biostatistics. SCI

The recent revolution in DNA sequencing technologies has transformed biology within a few short years, decreasing the cost and difficulty of sequencing dramatically to the point where the “$1,000 human genome” is in sight. Armed with complete genome sequences, biologists need to identify the genes encoded within and the variation in these genes between individuals, assign functions to the genes, and put these into functional and metabolic pathways. This course will provide an overview of next-generation sequencing technologies in the historical context of DNA sequencing, the pros and cons of each technology, and the bioinformatics techniques used with this sequence information, beginning with quality control assessment, genome assembly, and annotation. Prerequisites: 410.602 Molecular Biology, 410.633 Introduction to Bioinformatics, 410.634 Practical Computer Concepts for Bioinformatics. 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 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 laboratory course introduces students to the isolation, cultivation, and differentiation of stem cells. Students are introduced to reprogramming and differentiation protocols for various stem cell and cell progenitor types and the basics of tissue engineering. Students will scale up cells into mini-bioreactors for large-scale use. The class will include industry-wide practices in cGMP. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology or equivalent; 410.603 Advanced Cell Biology or equivalent; 410.604 Cellular Signal Transduction or equivalent; 410.652 Cell Culture Techniques or permission of programming committee. SCI