Biotechnology & Genomics Course Descriptions/ Elective Courses


Core Courses

16:115:511 Molecular Biology and Biochemistry (Fall, 3)
Disciplines of biochemistry and molecular biology as interlocking and mutually complementary fields of study. Protein structure and function, lipids, membranes and carbohydrates, catalysis of biochemical reactions, intermediary metabolism, oxidative phosphorylation, membrane transport, lipid metabolism, signal transduction, photosynthesis, protein secretion, targeting and turnover, nitrogen, amino acid, and nucleotide metabolism. 


16:115:512 Molecular Biology and Biochemistry (Spring 3)
Disciplines of biochemistry and molecular biology as interlocking and mutually complementary fields of study. Recombinant DNA approaches, DNA replication, repair and recombination, mobile genetic elements, transcription and gene regulation, RNA splicing, translation, viral gene expression. 


16:115:503/504 Biochemistry (Fall, 4; Spring, 3)
A comprehensive survey of the chemistry and metabolism of biological compounds, including proteins, polysaccharides, lipids, and nucleic acids. Enzyme kinetics, bioenergetics, organelles, and cellular organization. Expression and processing of biological information, including DNA replication; transcription into RNA; translation into protein, regulation, and recombinant DNA techniques. A detailed computer laboratory study of structural biology, including protein and nucleic acid three-dimensional structures and the interactions between these and ligands. 


16:137:615 Concepts in Biotechnology and Genomics (Fall, 3)
This will be the introductory survey course. It will cover a broad range of topics with an emphasis on applications in research and industry, along with a focus on the impact of these technologies on science and society. Mike Lawton will develop this course and be the instructor. 


16:137:616 NextGen Biotechnology & Genomics (Spring, 3)

This course will comprise 5-6 modules, each focused on a particular technology (DNA sequencing, proteomics, metabolomics, imaging, synthetic biology (for example -these will change each year)). The course will bring in experts from industry and academia to discuss the scientific foundations of the technology and its applications. Students will work in teams of ~5 on one of the module subjects to develop a project that will be set up by the instructor (e.g. develop a genomics-based approach to identify non-responders to a drug; develop and design scale-up plant for algal-based biofuels). These projects will take into account scientific, economic, market, business and social factors. Prerequisites: Completion of the three core courses listed above.


16:765:585 Bioinformatics (Fall, 3)
This course is designed to introduce biologists to utilizing UNIX, perl and R in bioinformatics. The concepts, principles and tools of bioinformatics will be introduced in the framework of basic shell scripting. Students will learn how to script, install programs and navigate in the UNIX shell. Students will learn how to setup and use command line BLAST. Students will learn basic perl scripting and handling of large datasets. Finally, students will be introduced to the statistical package R, and learn basic functions such as file handling, analysis and graphing.



01:447:451 (F) Genomes (Fall, 3)
Examination of genome structure and function in humans and other organisms. Topics include genome structure and function, the evolution of genomes and the role of genome analysis in medicine, pharmacology, and agriculture.

01:447:481 Topics in Human Genetics (Fall, 3)
Genetics aspects of human health and disease. Topics include birth defects, immunogenetics, cytogenetics, metabolic disorders, pattern of inheritance, and genetic counseling.


01:447:486 Evolutionary Genetics (Fall, 3)
Principles of evolution as revealed in DNA sequences. The effects of natural selection, genetic drift, and speciation on DNA, and the inference of histories from comparative DNA sequence data. 


01:694:412 Proteomics and Functional Genomics (Spring, 3)
Survey of modern techniques of protein biochemistry, bioinforatics, proteomics, and functional genomics, including basic concepts of protein structure and function, protein folding, protein characterization and purification, enzyme kinetics, NMR and X-ray crystallography, mass spectrometry, RNAi, yeast two hybrid, and various techniques and approaches to functional and structural genomics. 


01:694:413 Chromatin and Epigenomics (Fall, 3)
Introduction to chromatin dynamics, particularly the structural and biochemical modifications of chromatin that underlie epigenetic states and their effects on gene expression and development.


01:694:492 Gene Regulation and Cancer Development (Spring, 3)
Molecular biology is an experimental science, and a major goal of this course is to explain not just what molecular biologists know, but how they know it. Thus, while covering selected topics in gene regulation, development, and cancer, we will emphasize the methods, experimental design, history, and deductive reasoning that has led to the current state of understanding of these topics. Pre- or co-requisites: 16:115:403/404 or 16:115:511/512.


11:126:407 Comparative Virology (Fall, 3)
Biology of viruses and approaches to control through antivirals and genetic engineering. Genome organization, gene expression, replication, movement, and transmission across kingdoms. Prerequisites: Two semesters of biology and organic chemistry. Offered in odd-numbered years


11:126:481 Molecular Genetics (Fall, 3)
Principles of genetics at the molecular level, including the chemical nature of hereditary material, the genetic code, regulatory mechanisms, the molecular basis of mutation, DNA replication and recombination. 


11:680:480 Microbial Genomics (Spring, 3)
This course covers the principles of genetics and genomics and their application to the study of fundamental biological functions at the molecular and cellular level in microbial organisms. Topics include: mutations and genetic analysis of mutants; genetic elements and their role in horizontal gene transfer; control of gene expression, global regulatory mechanisms; intercellular signaling, quorum sensing, two-component systems; structure and function of prokaryotic genomes; genome-wide expression analysis; applications of genomic data; evolution of prokaryotic genomes – what makes a prokaryotic species?; inferring microbial physiology, pathogenicity, resistance from genomic sequences.


16:125:509 Medical Device Development (Spring, 3)
Development of medical devices that employ primarily polymeric materials in their construction. Materials selection, feasibility studies, prototype fabrication, functionality testing, prototype final selection, biocompatibility considerations, efficacy testing, sterilization validation, FDA regulatory approaches, writing of IDE, SID(K) and PMAs, device production, and record keeping.


16:125:586 Structure and Dynamics in Adult and Stem Cell Biology (Fall, 3)
The interface between stem cell biology and bioengineering is central to the application of developmental biology to problems in biomedicine and biotechnology. This course will provide a basic understanding of the science behind stem cell research, its applications and potential, and its ethic and social implications. The course will begin by highlighting important fundamental aspects of stem cell biology: embryonic and adult stem cells, including origin, regulation, self-renewal, differentiation, fate, and relationship to cancer; biological mechanisms and methods to translate findings to therapeutic applications; this is to be followed by a consideration of the role that bioengineering can play in advancing research into stem cell biology. Each class will include a lecture on a fundamental topic (traditional lecture format), followed by an extended discussion about a paper of particular significance in the current stem cell biology and bioengineering literature (a journal club format). After completion of this course, students will have enough knowledge to understand and participate in stem cell research activities on campus and be informed about the political and ethical stances surrounding this developing field. The course is geared primarily toward broadly trained graduate students (for example, students of the IGERT program). Students will be expected to take an active role in both lectures and discussion periods


16:148:514 Molecular Biology of Cells (Fall, 3)
Fundamentals of the molecular organization and functions of cells. Co-requisite: Graduate course in biochemistry.


16:375:510 (S) Environmental Microbiology (Spring, 3)
Microorganisms in carbon, nitrogen, sulfur cycling, biogeochemical processes, and water and wastewater treatment systems; biodegradation strategies and pathways; and bioremediation of toxic contaminants in the environment. Prerequisite: One semester of microbiology.


16:400:514 (S) Food Biology Fundamentals (Spring, 3)
Mechanistic examinations of food-borne microbes, enzymology, biotechnology, postharvest physiology, nutrition, and current concepts in food safety as related to food composition and processing. Prerequisite: General microbiology or biochemistry.


16:710:555 Neurobiology (Fall, 3)
Introductory survey emphasizing experimental approaches to the study of invertebrate and vertebrate nervous systems. Molecular, biophysical, and biochemical bases of nerve cell function. Higher-level functions shown as emerging from nerve cell properties, anatomical development, and mature connections. See also 16:830:555. Recommended: Biochemistry, physiology, or animal behavior.



16:137:510 Drug Development from Concept to Market (Fall, 3)
The first part of the course will be an industry overview and orientation of the process of the development of a pharmaceutical product. An interactive case study format will be used to study the developmental history of specific drug candidates throughout the course, starting with the target identification and method of drug discovery, through the development of lead compounds, patent filings, drug refinement, clinical trials, regulatory approvals and marketing processes. These sessions will be led by members of the pharmaceutical industry who will discuss their roles in the developmental pipeline


16:137:511 Drug Discovery Through Preclinical Development (Spring, 3)

This course provides an in-depth study of the pharmaceutical industry from target identification through preclinical development. In addition to lectures led by the instructor and several guest lecturers, students will participate on project teams to evaluate a potential drug target, and then advance the project through lead discovery, lead optimization and preclinical development to the IND stage. Students will participate in a series of group presentations where project teams will discuss how they dealt with real-life problems encountered by drug discovery and development teams and assemble a summary IND document.


16:137:580 Practical Aspects of Clinical Trial Design (Fall, 3)
This course is designed to provide extensive training in clinical research and clinical data management.  It incorporates end-to-end training for all Clinical research areas with a special focus on clinical data management processes, documentation and clinical data management systems.  The course includes extensive practical sessions to provide rigorous hands-on experience on a Clinical Data Management system (CDMS), which is widely used in the pharmaceutical industry today. It also provides hands-on experience in Protocol Development, Case Report Form development, clinical database planning, database design, clinical data entry, clinical data definition, discrepancy management, and writing validation procedures. 


16:137:581 Statistics in Clinical and Translational Research (Spring, 3)
This course provides extensive training in the use of statistical procedures to analyze data from clinical and translational research studies using a standard statistical package. Through writing and executing program in SAS, students will gain an appreciation of the concepts of random variation and bias. The course provides opportunities to gain experience with a wide range of bio-statistical methods, and applying these methods to problems in medicine and public health. In addition, students will learn to recognize pitfalls in interpreting biomedical and public health data.

16:137:582 Fundamentals of Regualtory Affairs (Spring, 3)
An overview of the laws, regulations, and regulatory agencies governing Pharmaceuticals, Devices, Biologics and Combination Products marketed in the US and in the world. The course also discusses the historical context in which the FDA evolved; its structure and its relationship with other US regulatory agencies. The course will provide an overview of market clearance pathways for drugs, biologics, medical devices and combination products so that the development and delivery of safe and effective healthcare products can be expedited. This course will emphasize teamwork, oral communication skills, and written communication skills.


Biotechnology & Food

16:400:514 Food Biology Fundamentals (Spring, 3)
Mechanistic examinations of food-borne microbes, enzymology, biotechnology, postharvest physiology, nutrition, and current concepts in food safety as related to food composition and processing.


16:400:610 (S) Nutragenics and Nutraceuticals (3)
Host-immune responses in diseases, signal transduction pathways in cancer and inflammation, transcription factors, proteomics, bioavailability of nutraceuticals, signaling molecules and their interactions with nutraceuticals. Role of nutraceuticals in health promotion and its mechanism of action. Isolation and identification of health promoting nutraceuticals and separation techniques. Beneficial and questionable effects of nutraceuticals and the development of future foods. Prerequisite: 16:400:514 or biochemistry or permission of instructor.


16:400:613 Nanotechnology and Its Applications in Biotechnology and Food (Fall, 3)
Basic concepts, investigation tools, and fundamental issues of nanotechnology, with emphasis on the applications of nanotechnology in agricultural and food systems, health care, food safety, and food packaging. Self-assembly, scanning probe microscopy, micro- and nanoencapulation, organic/inorganic nanocomposites, DNA, and protein chips. Prerequisites: Physical chemistry or permission of instructor.


Plant Biotechnology

16:765:513 Plant Molecular Biology (Fall, 3)
Fundamental and applied aspects of plant molecular biology, including isolation, structure, and regulation of nuclear and organellar genes, molecular biology of plant-microbe interactions, molecular biology of plant development, and plant biotechnology. Prerequisites: one semester of genetics and organic chemistry. Course in molecular genetics or molecular biology recommended.


16:765:520 Plant Biochemistry and Metabolism (Spring, 3)
Physiological significance of principal metabolic systems, including photosynthesis, photorespiration, sulfate and nitrate reduction, and hexose metabolism; synthesis of lipids and lipid pigments, photochemical, and hormonal controls, chloroplast development, and biochemistry of secondary plant products. Prerequisite: Plant physiology or equivalent.


16:765:528 Advanced Plant Breeding (Fall, 3)

Breeding, self-pollinated, cross-pollinated, and apomictic plants; role of mutation, polyploidy, and interspecific hybridization in plant improvement; inheritance of adaptive plant characters; developing and maintaining improved varieties.