The NIH Training Grant in Biotechnology Traineeships are awarded to Ph.D. degree seeking graduate students. Traineeships cover nine units of graduate level tuition and a partial stipend, are for two years or eight quarters, and run consecutively, including summer quarter, unless an internship is taken during the training period. In this case, the remaining quarter(s) of the award will be held, and training resumed by the trainee at the conclusion of the internship. It is expected that trainees will have broad interests in the area of biotechnology. The Program Director and Faculty Affiliates actively seek to provide an exposure to the broad scope of "Biotechnology" that goes beyond what a single department offers.
The key aspects of the program are:
Coursework
Trainees must take three of the following courses:
BIOC 202 - (3 units) Metabolic Biochemistry: Structure, Metabolism, and Energetics
Structure and function of biological molecules, enzyme kinetics and mechanisms, bioenergetics, pathways of intermediary metabolism and their control, and membrane structure and function. Course offered via online lectures and problem sets, with weekly small-group review sessions.
Offered Autumn, Summer (Pfeiffer, Theriot, Harbury)
BIOC 214 - (3-5 units) Physical & Chemical Principles of Enzyme Function
Enzymatic mechanisms, with emphasis on the fundamental behavior of biochemical systems and the properties that emerge due to the complex nature of these systems. Student presentations on specific enzymes based on classic and current literature, developed in consultation with the instructor. Prerequisites: BIOC/SBIO 241 and a course in organic chemistry.
(Herschlag) not given 2004-05
BIOC 218 - (3 units) Computational Molecular Biology
Online course; see http://biochem218.stanford.edu. For molecular biologists and computer scientists. Major issues, existing methods, and future directions concerning biological sequences and structure. Topics: accessing molecular databases, pattern search, classification of sequence and structure, alignment of sequences, rapid similarity searching, phylogenies, automated pattern learning, representing protein structure, gene expression profiling, clustering expressed genes, and discovering transcription factor binding sites. Lecture/lab. Final project. Enrollment limited to 40. Prerequisite: BIOSCI 52 or equivalent, or consent of instructor.
(Brutlag) not given 2004-05
BIOC 220 - (4 units) Chemistry of Biological Processes
(Same as MPHA 200.) The principles of organic and physical chemistry as applied to biomolecules. Goal is a working knowledge of chemical principles that underlie biological processes, and chemical tools used to study and manipulate biological systems. Prerequisites: organic chemistry and biochemistry, or consent of instructor.
Offered Autumn (Wandless, Herschlag, Chen, Bogyo)
BIOC 241 - (5 units) Biological Macromolecules (Enroll in SBIO 241.)
Introduction to the physical and chemical basis of macromolecular function. The forces that stabilize biopolymers with three-dimensional structures and their functional implications. Thermodynamics, molecular forces, and kinetics of enzymatic and diffusional processes, and relationship to their practical application in experimental design and interpretation. Biological function at the level of individual molecular interactions and at the level of complex processes.
Offered Autumn (Puglisi, Block, Herschlag, Kirkegaard, McKay, Pande, Garcia)
CHEMENG 350 - (3 units) Principles of Cellular Systems
Biochemistry and cell biology for engineering students with no training in biology. Recommended: undergraduate physical and organic chemistry.
Offered Winter (Kao)
CHEMENG 355 - (3 units) Advanced Biochemical Engineering
(Same as BIOE 355.) The technological tools for exploiting the power offered by modern biology. Review of relevant biochemistry. How a cell interacts with and influences its environment, how a production organism is optimized, what technology is used for large scale production, how products are isolated and purified, how proteins can be made without living cells, how biopharmaceutical is formulated and delivered, and what the regulatory requirements are for drug approval and sale. Prerequisite: 350 or BIOSCI 41 or equivalent.
Offered Spring (Swartz)
CHEMENG 452 - (3 units) Protein Science and Engineering
(Same as CHEM 232.) The physio-chemical interactions that govern the structure and function of proteins. Topics: protein function and structure, techniques for probing protein structure and function, mechanisms of protein function, design of proteins with novel properties. Examples fro literature on enzymes. Recommended: background in physical and organic chemistry.
(Khosla) Not give 2004-05
CHEMENG 454 - (3 units) Metabolic Engineering Methods and Applications
(Same as BIOE 454.) The analysis and optimization of industrial organisms. Applications illustrate the basic principles of metabolic pathway regulation, metabolic flux analysis, and traditional and new methods for genetic engineering. Examples: production of amino acids, protein synthesis and post-translational modification, and the production of isoprenoids, peptides, and polyketides. Prerequisites: 250, 255 or equivalent.
Offered Spring (Swartz) alternate years, not given 2005-06
BIOE 200A - (3 units) Molecular and Cellular Engineering
Preference to Bioengineering graduate students. Molecular and cellular bases of life from an engineering perspective. Metabolism, information flow and feedback, signal transduction, and means for engineering these processes. Clinical motivations and practical applications.
Offered Autumn (Kovacs, Staff)
BIOE 200B - (3 units) Systems Biology and Tissue Engineering
Preference to Bioengineering graduate students. The interaction, communication, and disorders of organ systems, Major organ systems and engineering means of probing them. Relevant developmental biology and tissue engineering from cells to complex organs.
Offered Winter (Kovacs, Staff)
BIOE 200C - (3 units) Medical Devices, Diagnostics, and Pharmaceuticals: Technologies, Regulation, and Applications
Preference to Bioengineering graduate students. Design, regulatory matters, and applications in practical settings. Major classes of technologies, practical limitations, and feature trade-offs in clinical settings.
Offered Spring (Kovacs, Staff)
BIOE 214 - (4 units) Representations and Algorithms for Computational Molecular Biology
(Same as BIOMEDIN 214, CS 274.) Topics: algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, computing with networks of genes, basic structural computations on proteins, protein structure prediction, protein threading techniques, homology modeling, molecular dynamics and energy minimization, statistical analysis of 3D biological data, integration of data sources, knowledge representation and controlled terminologies for molecular biology, graphical display of biological data, and genetic algorithms and programming applied to biological problems. Prerequisites: programming skills and matrix algebra.
Offered Spring (Altman)
BIOE 360A - (2 units) Tissue Engineering
(Same as ME 385A.) Tissue engineering is an expanding discipline that applies biological and engineering principles to create substitutes or replacements for defective tissues or organs. The principles of cell biology as a foundation for using engineering approaches to generate tissue structure and function. Emphasis is on how scaffolds, smart polymers, and mechanical forces can be used to reproduce the physical environment that acts, at the whole organ system level, to maintain specialized cellular function through molecular and genetic mechanisms.
Offered Winter (Smith, Carter)
Trainees who have already completed the equivalent courses are exempt from this requirement.
Each trainee is expected to complete a one-quarter course in graduate level biotechnology
Chemical Engineering 450 - (3 units) Introduction to Biotechnology
Introduction to Biotechnology is offered in spring quarter. (3 Units) (Cross Listed as BIOC 450, BIOPHYS 450, BIOSCI 450, CEE 237, MPHA 450, NBIO 450, SBIO 450)
Chemical Engineering 450 - [formerly 237] is a course that originated with this training grant. It is taught by the faculty affiliates in the program as well as by staff scientists and engineers from local biotechnology organizations. On occasion, faculty outside of the program are recruited to present lectures if their fields of expertise are not well represented in the program.
Topics: protein structure and dynamics, protein engineering, biocatalysis, gene expression, rDNA protein production, cellular metabolism and metabolic engineering, protein production from transgenic animals, gene therapy, genomic mapping, fermentation technology, purification methods, agricultural biotechnology, environmental biotechnology and bioremediation, rational drug design, molecular devices and biosensors, diagnostic device design.
Each trainee is expected to attend the ongoing seminar series Frontiers in Interdisciplinary Biosciences [Chemical Engineering 459]
Chemical Engineering 459 - (1 unit) Frontiers in Interdisciplinary Biosciences
An introduction to cutting-edge research involving interdisciplinary approaches to bioscience and biotechnology intended for both specialists and non-specialists. Associated with Stanford's new Clark Center and the Bio-X Programs. Leading investigators from Stanford and from throughout the world speak on their research. Students meet separately to present and discuss the every-changing subject matter, related literature, and future directions.
Med 255 - (1 unit) The Responsible Conduct of Research
An overview of the major ethical issues in research: authorship, intellectual property, and peer review; conflicts of interest, and commitment in the relationship between academia and industry; research involving human subjects; ethics and the use of animals in research, and the responsible conduct of science. Offered in the winter quarter.
Trainees must take at least one course in the biotechnology field that is outside of their department and at the graduate level. Also, trainees must take at least one course in the biotechnology field that is outside of their school.
Meetings
Trainees must attend the Trainees Meetings held approximately twice each month for one hour.
Biotechnology Symposium
Trainees must participate in the NIH Training Grant in Biotechnology Industrial Biotechnology Symposium and Poster Session held annually.
Reading Committee
Trainees must establish a Reading Committee and meet with their committees at least once each year. One member of the Reading Committee must be from outside the trainee's primary department.
Internships
Trainees must set aside one quarter for their industrial internship, usually in the San Francisco Bay Area; There are approximately 35 industrial affiliates associated with this training grant. Internships are to be arranged with the approval of the trainee's advisor with regards to timing. The NIH grant Program Director will assist with the arrangements. During their internship, trainees take a one-quarter or 3-month leave of absence from the university, and the Industrial Affiliate Biotechnology Company, providing the internship, pays their normal quarterly stipend.
