It’s a thrilling time in history for this new field, and synthetic biology promises to trigger the next golden age of technological discovery.
The Autodesk Distinguished Scholar honor was established to support the next generation of scientists by recognizing individuals in academia or industrial research who display innovation and excellence in their use of technology for the advancement of their research.
“Patrick Cai is the ideal candidate to be honored as the first Autodesk Distinguished Scholar for his research at one of the best medical and bioengineering schools in the country. The JHU synthetic yeast genome team is working toward building the world’s first synthetic eukaryotic genome and its success has revolutionary potential,” said Dr. Gordon Kurtenbach, Autodesk senior director of research. “It’s a thrilling time in history for this new field, and synthetic biology promises to trigger the next golden age of technological discovery.”
Yizhi Cai is a Johns Hopkins University School of Medicine Postdoctoral Research Fellow under the supervision of Dr. Jef Boeke, as well as an adjunct professor at Tianjin University and a senior scientific consultant to the Beijing Genomics Institute. Dr. Cai recently accepted a prestigious Chancellor’s Fellowship from the University of Edinburgh to start his own research lab there in the summer 2013. Funded by the National Science Foundation (NSF), the synthetic yeast project (Sc2.0 PROJECT) seeks to design, construct and integrate an entirely synthetic version of the yeast genome. The practical goal of the synthetic yeast team is to develop generic platforms for biotechnology as well as solutions to societal problems such as the looming energy crisis and bioremediation (environmental cleanup by biological agents). Supported by NSF, Drs. Cai and Boeke organized the first Synthetic Yeast Consortium meeting in Beijing on April 17, 2012, that was attended by researchers and founding agencies from the U.S., U.K., China, Hong Kong, France, India and Belgium.
The team chose yeast, Saccharomyces cerevisiae (a.k.a. ‘sugar fungus’ ‘found in beer’), for the synthetic genome project because it is a well-understood compact eukaryote genome with just 16 chromosomes (by way of comparison, humans have 46). Synthetic yeast also has the potential to become a preeminent genome for a wide variety of practical industrial uses including ethanol production from agricultural products and by-products. Archaeologists have found yeast use for fermentation and baking as early as 7,000 years ago, and Saccharomyces cerevisiae continues to be consumed daily, in various forms, by billions of people in the form of beer, wine and bread. To learn more about the Synthetic Yeast Genome project, visit the Synthetic Yeast 2.0 website.
Recognizing the potential dangers and the need for additional levels of protection when creating synthetic code, Dr. Cai is also embarking a project called “K-plex integrated safety switch (KISS)” recently funded by DARPA. The goal of KISS is to embed multiple orthogonal safety switches into engineered microorganisms, such that they can only survive on a “special sauce” of small molecules. KISS will help mitigate the risks associated with accidental or intentional release of engineered species into the environment.
AutoGene: A Design Suite for Synthetic Biology
This summer Autodesk also piloted a unique collaboration with Dr. Cai and Johns Hopkins University which will help propel this innovative research and inform future software development. Dr. Cai supervised a JHU undergraduate student project with the Autodesk IDEA Studio, a San Francisco-based residency program for designers, engineers, artists and scholars who are pursuing innovation projects that push technology to its limits to solve real-life problems.
Under the direction of a team of JHU advisors: Yizhi Cai, Giovanni Stracquadanio, Jef Boeke and Joel Bader, the students worked to create one of the first cloud-based computational facilities for the visualization, design and fabrication of synthetic biological sequences. The project, entitled “AutoGene: A Design Suite for Synthetic Biology,” utilized Autodesk cloud technology to run AutoGene, a management system for biological data. By using the cloud to optimize and parallelize the algorithms used by AutoGene, the students successfully developed an AutoGene API for DNA sequence manipulation. The JHU AutoGene student team just won the iGem 2012 Jamboree World Championship for Best Software.
Autodesk Distinguished Scholar
The Autodesk Distinguished Scholar honor is selected by the Autodesk Research team and will be bestowed upon researchers with whom the company plans to collaborate. Autodesk Research is dedicated to innovation and discovery ranging from methods to help users learn powerful digital prototyping tools, to visualization and simulation techniques that enable designers to achieve new levels of performance. Advancing the state of the art in human-computer interaction, computer graphics and digital design technology, Autodesk Research collaborates openly with researchers at leading universities around the world. The Bio/Nano Programmable Matter group within Autodesk Research is extending this expertise by developing software for the design and simulation of molecular systems and living systems.
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