Biotechnology Science and Laboratory Elective Courses

Knowledge about neuronal structure, function, and circuitry will be applied in order to understand the genetic and molecular bases of a wide variety of diseases that affect the central and/or peripheral nervous systems. This course will incorporate explorations of the recent primary literature, as it relates to specific disease pathologies and treatments, and innovative research tools used in their study. The particular pathologies covered will vary by semester, but will include some of the following: brain/spinal cord injury, epilepsy, stroke, multiple sclerosis, Parkinson’s disease, Alzheimer’s disease, schizophrenia, depression/bipolar disorder, amyotrophic lateral sclerosis, Huntington’s disease, infectious disease, prion-based disease, addiction, autism spectrum disorder, and disorders of neural development. This course is a natural continuation of, and builds upon the foundations provided in, the Neurobiology course. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I, 410.604 Advanced Cell Biology II, 410.628 Neurobiology. SCI

This course will explore the cellular and molecular mechanisms involved in the growth and development of complex organisms. In particular, students will be introduced to the mechanisms of fertilization, formation of the early body plan, cell type determination, organogenesis, morphogenesis, and stem cell niches. The course will examine the cellular and morphological changes during development, as well as the molecular signals responsible for development of organisms. SCI

Students use genetic analysis and molecular biology techniques to investigate chromosome organization, chromatin structure, functional genomics, and mechanisms of differential gene expression. Other topics include DNA methylation, silencers, enhancers, genomic imprinting, and microarray analysis. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology. SCI

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

In this course, students learn to use the tools of modern genomics to elucidate phenotypic variation within populations. The course uses human disease (from simple Mendelian disorders to common, complex disorders) to exemplify the types of studies and tools that can be used to characterize cellular pathophysiology as well as to provide genetic diagnostics and therapies. Students become facile with linkage analysis, cancer genetics, microarray analysis (oligo and DNA arrays), gene therapy, SNP studies, imprinting, disequilibrium mapping, and ethical dilemmas associated with the Human Genome Project. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology. 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

Lecture and discussion are augmented by guided readings on pathogenic bacteria, with special attention being given to the microorganisms that cause human disease. The course is designed to impart to the student an appreciation and knowledge of the history, epidemiology, cultivation, morphology, serology, biochemistry, and clinical description of the major disease-producing bacteria. Discussion of therapeutic considerations and vaccination will also be included in this course. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, undergraduate microbiology course, or permission of program committee. SCI

This course examines the principles of applied microbiology and microbial technology 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 or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology or equivalent. 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 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 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 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 provides an extensive overview of a process for the development of a pharmaceutical by a biotechnology company or pharmaceutical company. The course emphasizes the importance of intellectual property, the basic sciences underpinning the development of a product, and the importance of the interaction between a company and the Food and Drug Administration. Students learn to appreciate the importance of quality control and assurance, good manufacturing practices, preclinical and clinical testing, and the lengthy regulatory processes that govern the development, manufacturing, and eventual sale of biotechnological products. Hands-on solving of practical problems and guest lecturers who are experts in the field familiarize students with the intricacies of the process. Prerequisites: 410.303 Bioscience for Regulatory Affairs, OR 410.601 Biochemistry and 410.603 Advanced Cell Biology I or admission to the MS in Regulatory Science OR Master of Biotechnology Enterprise and Entrepreneurship programs. SCI

This course provides a framework for understanding the molecular physiology of neuronal structure, signaling, and circuitry, and how this cellular design is ultimately integrated to achieve higher cognitive functions, such as perception, control of movement, learning, and memory. The course introduces the students to various current neuroscience topics, including but not limited to membrane physiology and electrical excitability of neurons, neurotransmitters and synaptic transmission, signaling at the neuromuscular junction, cellular and higher-order aspects of perception and motor control, molecular mechanisms of neural development, and the molecular basis of learning and memory. This course places particular emphasis on the genetic and molecular bases of a wide variety of neurological and neurodegenerative diseases, such as multiple sclerosis, amyotrophic lateral sclerosis, Parkinson’s, and Alzheimer’s. 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

Because of recent advances, powerful diagnostic tests now detect genetic diseases, and there is promise of gene replacement therapy. In this course, students cover general genetic principles, DNA tools for genetic analysis, cytogenetics, gene mapping, the molecular basis of genetic diseases, animal models, immunogenetics, genetics of development, genetics of cancer, and treatment of genetic diseases. Molecular methods of analysis are emphasized. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I. SCI

In this course, students learn about how gene therapy can be used to treat or prevent genetic disease in the human population. This course is centered around how disease-causing variations in the human genome, including inherited diseases, mutations, epigenetic modifications, and viral infections, can be targeted using molecular technologies. Students will learn about the benefits and limitations of gene therapy and the bioethical concerns involved with this field of research and medicine. Prerequisites: 410.601 Biochemistry or equivalent, 410.602 Molecular Biology or equivalent, 410.603 Advanced Cell Biology or equivalent. SCI

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

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 introduces students with a background in the life sciences to the basic computing concepts of the UNIX operating system, relational databases, structured programming, object-oriented programming, and the Internet. Included is an introduction to SQL and the Python scripting language. The course emphasizes relevance to molecular biology and bioinformatics. It is intended for students with no computer programming background but with a solid knowledge of molecular biology. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology. SCI

Large-scale DNA sequencing efforts have resulted in increasingly large numbers of DNA sequences being deposited in public databases. Assigning annotations, such as exon boundaries, repeat regions, and other biologically relevant information accurately in the feature tables of these sequences requires a significant amount of human intervention. This course instructs students on computer analytical methods for gene identification, promoter analysis, and introductory gene expression analysis using software methods. Additionally, students are introduced to comparative genomics and proteomic analysis methods. Students will become proficient in annotating large genomic DNA sequences. This course covers customizing genome browsers with novel data. Next-generation sequence analysis is covered through sequence quality control and assembly and analysis of ChIP-seq and RNA-seq data. Students complete two large sequence analysis projects during the course. Prerequisites: 410.601 Biochemistry; 410.602 Molecular Biology; 410.633 Introduction to Bioinformatics or equivalent. 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 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

Through a case study approach, this course will cover the basic design issues of clinical trials, specifically targeting protocol, case report forms, analysis plans, and informed consent. The design of a specific trial will be studied to illustrate the major issues in the design of a study, such as endpoint definition, control group selection, and eligibility criteria. The course will also cover the analysis plan for a study, including approaches that are central to clinical trials, such as stratified analysis, adjustment factors, and “intention-to-treat” analysis. The planned analytical techniques will include the analysis of correlated data (i.e., clustered data and longitudinal data), survival analysis using the proportional hazards (Cox) Regression model, and linear models. A semester-long project will include the creation of a protocol, case report forms, and informed consent. Prerequisites: 410.645 Biostatistics or equivalent (recommended), 410.651 Clinical Development of Drugs and Biologics (recommended). SCI

This course introduces students to the planning and work required to develop potential new drugs and biologics efficiently. Students gain a thorough appreciation of FDA and International Council for Harmonisation regulations and guidelines. Because the course emphasizes the importance of planning before the execution of any of the necessary steps, lectures use a “backward” approach, discussing the final analysis and report before developing protocols. Topics also include an overview of preclinical investigations, NDA/BLA format and content, clinical development plans, product and assay development, the IND, and trial design, implementation, and management. Prerequisites: 410.303 Foundations of Bioscience OR 410.601 Biochemistry and 410.603 Advanced Cell Biology OR admission to the MS in Regulatory Science Program OR Master of Biotechnology Enterprise and Entrepreneurship programs. SCI

Regenerative Medicine is a multidisciplinary field developing next-generation therapies that aim to augment, repair, replace or regenerate tissues and organs. This field can be broadly defined by three overlapping technology domains: cell therapy, gene therapy, and tissue engineering. In this course, we will explore these regenerative medicines from bench to bedside. We will discuss relevant biological, engineering, clinical, legal, regulatory, and ethical principles and perspectives to understand the emerging field of regenerative medicine. Specific topics will include induced pluripotent stem cells, bioartificial organs, cell-based immunotherapy, and gene editing techniques such as a CRISPR/Cas-9. In addition to gaining a scientific foundation, students will become familiar with the current state of the industry and the process of bringing these regenerative medicine products to market, including market trends and opportunities, process development and manufacturing, and commercialization challenges and successes. Readings will be drawn primarily from scientific journals. Prerequisites: 410.601 Biochemistry; 410.602 Molecular Biology; 410.603 Advanced Cell Biology I. 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

This course is a literature-driven exploration of current topics and methodologies employed in cell biology research. By closely examining both fundamental and innovative experimental approaches as well as cutting-edge technologies, we will explore a broad range of cell biology topics, many of which most students have previously encountered, at least at some level, in the core courses. The particular subjects and technologies discussed may vary widely from semester to semester; topics may include but are not limited to expression profiling (microarray analysis), “knock-down” with RNAi, the use of transgenic and knockout mice, proteomics and mass spectrometry, microscopy applications (epifluorescence, confocal, and/or EM), characterizing protein/protein interactions, and detection methods for the movement of small molecules and ions. Students enrolling in this course are expected to already have some experience in critical reading and evaluation of the primary scientific literature. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I, 410.604 Advanced Cell Biology II. 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 provides an overview of the biological processes and laboratory techniques utilized for the discovery, development, and evaluation of therapeutic drugs. Students investigate drug development processes, such as gene cloning, culture scale-up, downstream processing, and product purification. Emphasis is placed on the theory and application of laboratory methods used in drug development, such as recombinant DNA techniques, antibody technology, protein purification, immunoassays, high- throughput drug screening, chromatography, electrophoresis cell receptor characterization, pharmacokinetics, drug toxicity testing and evaluation of therapeutic drugs, diagnostics, and vaccines. Prerequisites: 410.303 Bioscience for Regulatory Affairs, OR 410.601 Biochemistry and 410.603 Advanced Cell Biology OR admissions to the MS in Regulatory Science OR Master of Biotechnology Enterprise and Entrepreneurship programs. SCI

Food microbiology encompasses the study of microorganisms that have both beneficial and deleterious effects on the quality and safety of raw and processed meat, poultry, and egg products. Food microbiology focuses on the general biology of the microorganisms that are found in foods, including their growth characteristics, identification, and pathogenesis. Specifically, areas of interest that concern food microbiology are food poisoning, food spoilage, food preservation, and food legislation. Pathogens in products, or harmful microorganisms, result in major public health problems in the United States and worldwide, and are the leading causes of illnesses and death. 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 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 builds on the Perl concepts taught in 410.634 Practical Computer Concepts for Bioinformatics. Perl has emerged as the language of choice for the manipulation of bioinformatics data. Bioperl, a set of object-oriented modules that implements common bioinformatics tasks, has been developed to aid biologists in sequence analysis. The course will include an overview of the principal features of Bioperl and give students extensive opportunity to use Perl and the tools of Bioperl to solve problems in molecular biology sequence analysis. Prerequisites: 410.601 Biochemistry, 410.60 Molecular Biology, 410.634 Practical Computer Concepts for Bioinformatics. SCI

The emerging field of nanobiotechnology utilizes developments in nanotechnology and molecular biology for applications to biomedical science and clinical practice, fundamental cell biology research, and industrial biotechnology. Nanobiotechnology is an interdisciplinary field that exploits the unique functional properties of natural and synthetic biomolecular-sized (nanometer-scale) constructs, such as quantum dots, carbon nanotubes, nanostructured surfaces, liposomes, artificial membranes, and molecular machines for biotechnology and medicine. This course will survey the research, development, and applications of nanotechnology to medical diagnostics, imaging, and therapeutics (including drug delivery and anti-cancer treatments), cell biology and single-cell analysis, nanofluidics, bioassays, biosensors, and bio-inspired engineering. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology or equivalent; 410.603 Advanced Cell Biology or equivalent. SCI

Whether tackling business challenges in a clinic or creating global initiatives, being a healthcare provider, scientist, engineer, or entrepreneur means being a problem solver. This course focuses on helping students develop the problem-solving strategies and innovation development models necessary to more effectively tackle challenges in medical, industrial, and environmental areas of biotechnology. Students will develop a working knowledge of design thinking principles, lean startup, storytelling, and human-centered techniques, as well as an understanding of how they can be utilized to create positive change in any context. While evaluating real-world problems, students will consider how these techniques can be utilized to turn an innovative idea into an effective solution. Students will work individually and collaboratively on real-world projects, turn their ideas into practical action, and demonstrate their ability to leverage science, health care, technology, and social innovation to bring change through community-based and global initiatives.

In order to provide the best care possible, health care professionals are working together more now than ever before. As a result, strong leadership and teamwork skills are becoming necessities in joining the health care field. This course will provide hands-on activities to help students develop problem-solving skills, learn basic negotiation and mediation strategies, and understand their own tendencies as leaders and team members. Using real-world examples, students will explore how strong leadership and teamwork can drive innovative solutions to public health issues.

In this capstone course, students will learn basic diagnostic techniques and use case studies to explore the relationship between physiological illnesses and diagnostic output. Through discussions and guided interviews, students will explore the role of psychology and sociology in patient care choices as well as physician recommendations to patients. Students will practice cultural sensitivity through group activities and discussion of pressing public health issues. Students will undertake final group projects that identify needs in the local community and attempt to create solutions that could feasibly be completed with limited resources.

Alterations to the genome are the basis of cancer development, but not all mutations cause cancer. Cancer genomics is the study of cancer cell genomes to elucidate how changes from the normal host genome drive cancer development and how these changes can be targeted for better prevention, diagnosis, and treatment of cancer. In this course, students learn about the multi-step process of tumorigenesis and the confounding development of passenger mutations that challenge the use of genomics to inform therapies. Students will use bioinformatics tools to analyze human cancer genomic data sets to understand the genetic basis of cancer and how to identify genetic signatures in tumors to guide treatment. Topics also include the development of drug resistance, biological sample acquisition, the technologies used to identify and distinguish pathogenic alleles, and how data is stored, referenced, and shared. Discussions about clinical trials and standards of care based on cancer genomics, and about the ethical challenges raised by the use of genomic information to make personal care decisions, are included in the course. Prerequisites: 410.601 Biochemistry or equivalent; 410.602 Molecular Biology; 410.603 Advanced Cell Biology; 410.638 Cancer Biology; 410.633 Introduction to Bioinformatics is recommended.

This intermediate-to-advanced-level course, intended as a follow-on to 410.634 Practical Computer Concepts for Bioinformatics (a prerequisite for this new class), will integrate and expand on the concepts from that introductory class to allow students to create working, Web-based bioinformatics applications in a project-based course format. After a review of the concepts covered in 410.634, students will learn how to create functional Web applications on a UNIX system, using Python and CGI to create forms that can be acted upon, and using the Perl DBI module to interface with MySQL relational databases that they will create and populate to retrieve and present information. This will be demonstrated by building an in-class, instructor-led project. More advanced SQL concepts and database modeling will also be covered, as well as introductions to HTML5, CSS3, and Javascript/JQuery. Class time in the latter weeks of the class will be devoted to individual assistance on student projects and to short lectures on advanced topics. Once again, whenever possible, this course will emphasize relevance to solving problems in molecular biology and bioinformatics. Prerequisites: 410.601 Biochemistry; 410.602 Molecular Biology; 410.634 Practical Computer Concepts. SCI

The next generation of array and sequencing technologies provides the ability to investigate large quantities of genomics information with higher sensitivity, greater throughput, and lower costs. This also introduces new challenges in data management, novel algorithmic approaches, and general interpretation. This course builds on the topics in 410.671 Gene Expression Data Analysis and Visualization to address analysis of both genetic variation and genomics content, including splice variants, single nucleotide polymorphisms (SNPs) with family-based and case/control genome-wide association, copy number variation, somatic and germline single nucleotide variants, tumor clonality and ploidy estimates, and transcription factor binding sites. Data types will include array, RNA sequencing, and DNA sequencing (targeted and whole exome) with sequence assembly methods presented,?such as de novo and reference-based.?Prerequisites: 410.602 Molecular Biology, 410.633 Introduction to Bioinformatics, 410.671 Gene Expression Data Analysis and Visualization. SCI

Food toxicology is the study of the nature, properties, effects, and detection of toxic substances in food, and their disease manifestation in humans. This course will provide a general understanding of toxicology related to food and the human food chain. Fundamental concepts will be covered, including dose-response relationships, absorption of toxicants, distribution and storage of toxicants, biotransformation and elimination of toxicants, target organ toxicity, teratogenesis, mutagenesis carcinogenesis, food allergy, and risk assessment. The course will examine chemicals of food interest, such as food additive mycotoxins and pesticides, and how they are tested and regulated. SCI

This class examines animal physiology from an evolutionary and comparative viewpoint. The goal is to examine the commonalities and unique differences in how various animal organisms address the necessary life functions. Topics will include homeostatic mechanisms as an overarching theme, integrating the following systems: nervous, endocrine, muscle, circulatory, defense, respiratory, excretory, fluid and acid-base balance, digestive, energy balance and thermal, and reproductive. SCI

The emerging field of metagenomics allows for the study of entire communities of microorganisms at once, with far-reaching applications in a wide array of fields, such as medicine, agriculture, and bioremediation. Students will learn the principles of metagenomics through the exploration of published project data and guided readings of recent literature. Using data from the Human Microbiome Project, students will explore practical analysis tasks, including sequence assembly, gene prediction and annotation, metabolic reconstruction, taxonomic community profiling, and more. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.633 Introduction to Bioinformatics, 410.634 Practical Computer Concepts for Bioinformatics. SCI

With the advent of rapid, low-cost whole-genome sequencing, the field of personalized medicine is growing from a niche field to becoming the new standard of practice in medicine. Already, oncology makes use of genomic sequencing to inform treatment decisions based on tumor types, and patients are seeking knowledge about their genetic and environmental risk factors to make informed health decisions. This class explores the evolving field of personalized medicine, examining genomics as well as proteomics, metabolomics, epigenetics, and the microbiome. Students will read and discuss new developments in pharmacogenomics, rare and complex diseases, genomics for the healthy person, and the ethical, economic, and social implications of these new technologies. These topics will be approached with a view toward application in clinical practice. Prerequisites: 410.602 Molecular Biology; 410.633 Introduction to Bioinformatics. 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 involve discussion and debate on current topics concerning stem cell biology and the use of stem cells in biotechnology and therapeutics. Topics will include review and discussion of developmental and cell biology, stem cell characteristics, stem cell preparation and therapeutic uses, tissue engineering, global regulatory and ethical issues, and commercialization of stem cell therapy. The course will also detail state-of-the-art techniques for the experimental study of stem cells for biotechnology and biomedical applications. Current peer-reviewed literature and guest experts in the field will provide up-to-date information for discussion. 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

In this course, students are introduced to the current technologies used in the production of alternative energies. These technologies include first and second-generation biomass biofuels, carbon-neutral synthetic fuels, microbial fuel cells, algae fuel, and biological hydrogen production. The study of biomass biofuels will include technologies using agriculture, cellulosic, and waste feedstocks. Carbon-neutral synthetic fuels will include biobutanol, acetone-butanol-ethanol, methane, and biogas. Students will study the methods used to produce these types of fuels, the by-products produced, and the sustainability of energy production. In addition to studying the techniques used to produce alternative energy, students will also discuss the economic and environmental impacts of producing and using alternative energy sources. Prerequisites: 410.601 Biochemistry, 410.602 Molecular Biology, 410.603 Advanced Cell Biology I. SCI

Students in Center for Biotechnology Education (CBE) MS programs have the opportunity to enroll in an independent research course. This elective course is an option after a student has completed at least eight graduate-level courses and has compiled a strong academic record. Prior to proposing a project, interested students must have identified a research topic and a mentor who is familiar with their prospective inquiry and is willing to provide guidance and oversee the project. The research project must be independent of current work-related responsibilities as determined by the project mentor. The mentor may be a faculty member teaching in the biotechnology program, a supervisor from the student’s place of work, or any expert with appropriate credentials. Students are required to submit a formal proposal for review and approval by the biotechnology program committee. The proposal must be received by the instructors ideally one month prior to, and no later than one week after, the beginning of the term in which the student wants to enroll in the course. Students must meet with a member of the program committee periodically for discussion of the project’s progress, and a written document, poster, and oral presentation must be completed and approved by the program committee and project mentor for the student to receive graduate credit. Additional guidelines can be obtained from the AAP administrative office. Prerequisites: All core courses for your degree program and four additional courses.

Students wishing to complete a thesis may do so by embarking on a two-semester thesis project, which includes the 410.800 Independent Research Project and 410.801 Biotechnology Thesis courses. This project must be a hypothesis-based, original research study. The student must complete 410.800 Independent Research Project and fulfill the requirements of that course, including submission of a project proposal, final paper, and poster presentation, before enrolling in the subsequent thesis course. For the thesis course, students are required to submit a revised proposal (an update of the 410.800 proposal) for review and approval by the faculty adviser and biotechnology program committee one month prior to the beginning of the term. Students must meet with the faculty adviser periodically for discussion of the project’s progress. Graduation with a thesis is subject to approval by the thesis committee and program committee and requires the student to present his/her project to a faculty committee both orally and in writing. Prerequisites: Successful completion of 410.800 Independent Research Project and 410.645 Biostatistics. 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