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Synthetic Biology [20.80s]

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Date: TBD, 2010 | Tuition: $3,250 (tentative) | Continuing Education Units (CEUs): 2.6 (tentative)

This class is tentatively planned for 2010, depending on the level of interest. Email the Short Programs office to express your interest in taking this course. Please include your industry and learning goals.

COURSE SUMMARY

Synthetic Biology is an emerging technology that hopes to further develop biology as a substrate for engineering by adapting concepts developed in other fields of engineering. Foundational tools to meet this challenge include: ready access to off-the-shelf standardized biological parts and devices; a reliable and defined cellular chassis in which engineers can assemble and power DNA programs; and computational tools as well as measurement standards that enable the ready integration of simpler devices into many-component functional systems. By applying these engineering foundations to the richness and versatility of biology, some of the world’s most significant challenges can be addressed. For example advanced genome, protein and pathway redesign, metabolic engineering and cell-programmed therapeutics have already benefited from the tools of synthetic biology, and these developments will serve as the point of departure for many of the foundational topics. As synthetic biology matures into a robust engineering discipline, it should be capable of transforming the biotechnology, pharmaceutical, and chemical industries as well as suppliers of biotechnology tools, reagents, and services. This summer course offers an unprecedented opportunity to learn about this emerging field from its leaders as well as engage in hands-on computational and laboratory work using the latest tools and techniques.

Content

  Fundamentals: Core concepts, understandings and tools (30%)
  Latest Developments: Recent advances and future trends (30%)
  Industry Applications: Linking theory and real-world (20%)
  Other: Hands-on laboratory work (20%)

Delivery Methods

  Lecture: Delivery of material in a lecture format (50%)
  Discussion or Groupwork: Participatory learning (30%)
  Labs: Demonstrations, experiments, simulations (20%)

Level

  Introductory: Appropriate for a general audience (20%)
  Specialized: Assumes experience in practice area or field (30%)
  Advanced: In-depth explorations at the graduate level (50%)

« BACK TO TOP LEARNING OBJECTIVES By completing this short course, participants will:

Understand the motivation for and increased importance of making biology easy to engineer Grasp how foundational tools from mature engineering disciplines were game-changers in those fields and how they might be applied to the engineering of biology Identify aspects of biotechnology that inhibit and enable the faster, more reliable programming of natural systems Gain familiarity with a common vocabulary useful for synthetic biology (e.g. standard part, chassis, etc.) Analyze and apply an abstraction hierarchy to the design of biological systems Have knowledge and direct experience with state-of-the art computational approaches to protein and biocircuit design Appreciate current and future application spaces for synthetic biology Identify current scientific, engineering, and regulatory bottlenecks in the field Experience some fundamental laboratory approaches for engineering biology Have knowledge of the latest published literature in the field and insight into ongoing research « BACK TO TOP WHO SHOULD ATTEND This course is targeted for industrial leaders, in particular those in biotechnology, pharmaceutical, and chemical industries as well as suppliers of genetic tools and custom DNA synthesis companies. This course will also be of keen interest to professionals within regulatory agencies (e.g. FDA, USDA, EPA) in anticipation of technical decisions that will be faced as the products of synthetic biology come to trial and market. The class will also benefit academics with an interest in the latest advances related to biological, chemical and metabolic engineering. Members of civil society organizations and the public may also wish to consider the class as an intensive primer by which to gain access to the latest advances in synthetic biology.

« BACK TO TOP OUTLINE OF THE COURSE Day 1: Introduction to the Engineering of Biological Systems Topics will include:

Biological Engineering and Synthetic Biology Computer Science and Synthetic Biology Lab: day 1 Day 2: Biological Standards Topics will include: Engineering Principles for Parts and Devices Measurement Standards Re-design of Cellular Chassis Lab: day 2 Day 3: Computation Topics will include: Principles of Protein and Pathway Engineering Computational Re-design of Proteins Lab: day 3 Day 4: Applications and Implications Topics will include: Optimization of Microbial Chemical Factories Re-design of Metabolic Pathways Standards of Practice Lab: day 4 Day 5: Summary and Future Directions The final day of the class will cover concepts and emerging thinking on several advanced topics as well as evaluation of content delivered.

Note: Various case studies and examples will be used throughout the course to highlight concepts or demonstrate current applications of synthetic biology. Participants do not require in-depth knowledge of these cases studies for lectures or the exercises, but basic molecular biology and cell biology knowledge is assumed. Participants who are able to bring laptops to the class are encouraged to do so. Others will be provided with laptops to complete the in-class exercises.

« BACK TO TOP COURSE SCHEDULE AND REGISTRATION TIMES Class runs 10:00 am - 5:00 pm on Monday, 9:00 am - 5:00 pm Tuesday, Wednesday, and Thursday, and 8:00 am - 11:00 am on Friday.

Registration is on Monday morning from 9:00 - 9:30 am.

« BACK TO TOP ABOUT THE LECTURERS Dr. Natalie Kuldell Natalie Kuldell is currently a member of the Department of Biological Engineering at MIT and Associate Education Director of the NSF-funded Synthetic Biology Engineering Research Center (SynBERC). She is a leading authority on inquiry-driven learning approaches and has spearheaded development of synthetic biology curricula for undergraduate education. As such she sits on several scientific advisory boards and educational leadership teams, including those for Understanding Science, VisionLearning, and the Coalition for the Public Understanding of Science. She directs an educational website, BioBuilder, to engage and inform a wider audience of synthetic biology enthusiasts. Her research interests include chromatin remodeling complexes in yeast, and the development of genetic tools to study and control mitochondrial gene expression in the model organism, Saccharomyces cerevisiae. Dr. Kuldell obtained a bachelor’s degree in Chemistry from Cornell University in 1987 and a Ph.D. in Cell Biology from Harvard University in 1994. She is author of numerous educational and scientific articles as well as co-editor of a book on zinc-finger proteins.

Dr. Douglas Lauffenburger Douglas A. Lauffenburger is Uncas & Helen Whitaker Professor of Bioengineering and Head of the Department of Biological Engineering at MIT, and also holds appointments in the Department of Biology and the Department of Chemical Engineering. His major research interests are in cell engineering: the fusion of engineering with molecular cell biology. A central focus of his research program is in receptor-mediated cell communication and intracellular signal transduction, with emphasis on development of predictive computational models derived from quantitative experimental studies, for cell cue/signal/response relationships important in pathophysiology with application to drug discovery and development. Dr, Lauffenburger has served as a consultant or scientific advisory board member for Astra-Zeneca, Beyond Genomics, CellPro, Eli Lilly, Entelos, Genstruct, Insert Therapeutics, Johnson & Johnson, Merrimack Pharmaceuticals, Pfizer, Precision Therapeutics, SyStemix, the Burroughs-Wellcome Fund, and the Whitaker Foundation. His awards include the Pierre Galletti Award from AIMBE, the A.P. Colburn Award, Bioengineering Division Award, and W.H. Walker Award from AIChE, the Distinguished Lecture Award from BMES, the C.W. McGraw Award from ASEE, the Amgen Award in Biochemical Engineering from the Engineering Foundation, and a J.S. Guggenheim Fellowship, along with a number of named lectures at academic institutions. Dr. Lauffenburger’s B.S. and Ph.D. degrees are in chemical engineering from the University of Illinois and the University of Minnesota, in 1975 and 1979 respectively. He is a member of the National Academy of Engineering and of the American Academy of Arts & Sciences, and has served as President of the Biomedical Engineering Society, Chair of the College of Fellows of AIMBE, and on the Advisory Council for the National Institute for General Medical Sciences at NIH.

Dr. Jay D. Keasling Jay Keasling is the Bard Howe Distinguished Professor of Biochemical Engineering in the Departments of Chemical Engineering and Bioengineering at the University of California, Berkeley. Dr. Keasling is also Senior Faculty Scientist and Division Director in the Physical Biosciences Director at the Lawrence Berkeley National Laboratory and Chief Executive Officer of the Joint BioEnergy Institute in Emeryville, CA. Dr. Keasling was an early pioneer in synthetic biology and its application to redesigning microorganisms for production of complex chemicals and for degradation of toxic, environmental contaminants. Dr. Keasling’s laboratory at the University of California, Berkeley developed many early tools for manipulating the metabolism of microorganisms and then used these tools to develop microbial production processes for specialty chemicals, drugs, and biodegradable plastics and for degradation of nerve agents and pesticides. Dr. Keasling’s laboratory engineered both Saccharomyces cerevisiae and Escherichia coli to produce a readily-convertible precursor to the effective, anti-malarial drug artemisinin. Recently, Dr. Keasling has turned his attention to engineering microorganisms to produce biofuels, work that is performed at the Joint BioEnergy Institute. Dr. Keasling has founded three synthetic biology companies (Amyris, LS9, and Codon Devices) and has published over 150 refereed journal articles, conference proceedings, and book chapters. He has four granted patents and over 28 patents pending. Dr. Keasling has won several awards, including the Professional Progress Award from the American Institute for Chemical Engineers in 2007, the first ever Scientist of the Year award from Discover Magazine in 2006, and the Technology Pioneer award from the World Economic Forum in 2005.

Dr. Adam P. Arkin Adam Arkin is Associate Professor of Bioengineering at UC Berkeley, a senior scientist with Berkeley Lab’s Physical Biosciences Division, investigator with the Howard Hughes Medical Institute (2000-2007), and Director of Berkeley Lab’s Environmental Stress Pathway Project. He is a leading authority on the evolutionary design principles of cellular regulatory networks and how these principles aid in the prediction, control, and design of cellular behaviors. His lab develops physical theory and computational tools for understanding cellular processes such as gene expression, signal transduction cascades, and cytomechanics. The lab also analyzes genomic data relevant to the dynamics of regulatory networks in a number of viral, bacterial, and eukaryotic systems, and performs experiments to test the theories. Dr. Arkin is Editor-in-Chief of the upcoming journal “Synthetic Biology.”

Dr. George Church George Church is Professor of Genetics at Harvard Medical School and Director of the Center for Computational Genetics. With degrees from Duke University in Chemistry and Zoology, he co-authored research on 3D-software & RNA structure with Sung-Hou Kim. His Ph.D. from Harvard in Biochemistry & Molecular Biology with Wally Gilbert included the first direct genomic sequencing method in 1984; initiating the Human Genome Project then as a Research Scientist at newly-formed Biogen Inc. and a Monsanto Life Sciences Research Fellow at UCSF with Gail Martin. He invented the broadly-applied concepts of molecular multiplexing and tags, homologous recombination methods, and array DNA synthesizers. Technology transfer of automated sequencing & software to Genome Therapeutics Corp. resulted in the first commercial genome sequence (the human pathogen, H. pylori, 1994). This multiplex solid-phase sequencing evolved into polonies (1999), ABI-SOLiD (2005) & open-source Polonator.org (2007) and Personal Genomes.org. He has served in advisory roles for 12 journals (including Nature Molecular Systems Biology), 5 granting agencies and 24 biotech companies (e.g. 23andme & recently founding Codon Devices, Knome and LS9). Current research focuses on integrating biosystems-modeling with Personal Genomics & synthetic biology.

Dr. Drew Endy Drew Endy is an Assistant Professor in the Faculty of Bioengineering at Stanford University. He previously helped launch the Department of Biological Engineering at Massachusetts Institute of Technology. He serves as President of the BioBricks Foundation, a not-for-profit organization promoting open access to biological technologies, and has cofounded two biotechnology companies. Esquire magazine recently named Drew one of the 75 most influential people of the 21st century. Drew gained his doctorate in biochemical engineering from Dartmouth College and carried out postdoctoral research at University of Texas and University of Wisconsin.

Dr. Ken Oye Kenneth A. Oye is Associate Professor of Political Science at MIT. He served two terms as Director of the MIT Center for International Studies (1992-2000), and is now forming a Political Economy and Technology Policy Program within the Center. He has served on the faculties of the Kennedy School at Harvard University, the University of California, Princeton University, and Swarthmore College. He received the 1998 MIT Graduate Student Council Outstanding Teaching Award in Social Sciences, Humanities and Arts for his research seminar in international relations and the 2003 MIT Technology and Policy Program Faculty Appreciation Award for his teaching and advising in science, technology and public policy. He holds a B.A. in Political Science and Economics with Highest Honors from Swarthmore College and a Ph.D. in Political Science with the Chase Dissertation Prize from Harvard University. He has published six books including Cooperation Under Anarchy, Economic Discrimination and Political Exchange, and Eagle in a New World as well as numerous shorter pieces in international relations, political economy, as well asscience and technology policy. His current research cuts across these fields, by using theory and methods from the field of political economy to address issues in the field of science, technology and environmental policy.

Dr. Kristala L. Jones Prather Kristala L. Jones Prather is the Joseph R. Mares (1924) Career Development Assistant Professor of Chemical Engineering at MIT. Dr. Prather’s research interests are centered on the design and assembly of recombinant microorganisms for the production of small molecules. Current efforts include the development of tools and methodologies for novel biosynthetic pathway design and the investigation of gene dosage effects on the physiology and productivity of engineered microbes. Her research combines the traditions of metabolic engineering with the practices of biocatalysis to expand and optimize the biosynthetic capacity of microbial systems. A particular focus is the elucidation of design principles for the production of unnatural organic compounds within the framework of the nascent field of synthetic biology. She obtained a Bachelor of Science degree in chemical engineering from MIT in 1994, and a Ph.D. degree from the University of California, Berkeley, in 1999. Dr. Prather joined the faculty of MIT after 4 years in BioProcess Research and Development at Merck Research Labs (Rahway, NJ), first as a Senior Research Biochemical Engineer and then as a Research Fellow. While at Merck, she worked on projects in the areas of biocatalysis for small molecule transformations, high-yield production of plasmids as DNA vaccines, and mammalian cell line development for production of therapeutic proteins. Dr. Prather is the recipient of a Camille and Henry Dreyfus Foundation New Faculty Award (2004) and Office of Naval Research Young Investigator grant (2005). She has also received the chemical engineering departmental award for Outstanding Undergraduate Teaching (2006).

Dr. Tanja Kortemme Department of Biopharmaceutical Sciences, UCSF

Dr. Tom Knight Senior Research Scientist, Computer Science and Artificial Intelligence Laboratory, MIT

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