Instructors – 2014

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Karmella Haynes

ARIZONA STATE UNIVERSITY
School of Biological and Health Systems Engineering

http://haynes.lab.asu.edu

Karmella Haynes is an Assistant Professor of Biomedical Engineering at Arizona State University. She earned her Ph.D. studying epigenetics and chromatin in Drosophila at Washington University, St. Louis. Postdoctoral fellowships at Davidson College and Harvard Medical School introduced her to synthetic biology. Today, her research aims to identify how the intrinsic properties of chromatin, the DNA-protein structure that packages eukaryotic genes, can be used to control cell development in tissues. Her HHMI postdoctoral fellowship project on bacterial computers was featured on NPR’s Science Friday and was recognized as “Publication of the Year” in 2008 by the Journal of Biological Engineering. She is currently a SynBERC Affiliated PI, a SynBioLEAP fellow, and Head Judge for the International Genetically Engineered Machines competition. CSHL topic: Dr. Haynes will lead the module on unconventional methods for specific, targeted transgene manipulation in human cells: Cas9-mediated DNA editing and artificial (ectopic) chromatin. Students will learn about the relevant molecular mechanisms for these methods, human cell culturing techniques, probabalistic modeling of gene expression, and methods for quantitative analysis of transgene expression states.
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Julius Lucks

CORNELL UNIVERSITY
School of Chemical and Biomolecular Engineering

http://luckslab.org

Julius B. Lucks is Assistant Professor of Chemical and Biomolecular Engineering at Cornell University. His research combines both experiment and theory to ask fundamental questions about the design principles that govern how RNAs fold and function in living organisms, and how these principles can be used to engineer biomolecular systems. As a Miller Fellow, he pioneered the development of first RNA-based synthetic genetic circuits, and was the leader of the team that created SHAPE-Seq – a technology that uses next generation sequencing to characterize RNA structures in unprecedented throughput, and that is now being used to uncover the role of RNA structure in regulating fundamental cellular processes across the genome. His lab focuses on dynamically programming cellular behavior with synthetic RNA circuitry, and using/developing SHAPE-Seq to understand RNA folding dynamics in the cell. For his pioneering research efforts, he has been named a DARPA Young Faculty Awardee, an Alfred P. Sloan Foundation Research Fellow, an ONR Young Investigator, and an NIH New Innovator. CSHL topic: In the Cold Spring Harbor Synthetic Biology Course, Lucks leads the module on the rapid design and characterization of synthetic RNA circuitry. In this module, students learn to i) use cell-free transcription-translation (TX-TL) systems to rapidly characterize the dynamics of genetic circuitry, ii) use computational modeling to interpret experiments, and iii) to design genetic circuitry to perform a specific task (i.e. turn genes on in a specified temporal order). The module is fast paced, with the design-test cycle lasting only a matter of hours, allowing students to rapidly explore and test circuit architectures. The module moves from idea to test in a matter of a few hours! In past courses, research from this module has generated some of the first evidence of the speed of RNA genetic circuits, which were shown to propagate signals in a mere matter of minutes.
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Pamela Peralta-Yahya

GEORGIA INSTITUTE OF TECHNOLOGY
School of Chemistry and Biochemistry
School of Chemical and Biomolecular Engineering

http://peralta-yahya.gatech.edu/

Pamela Peralta-Yahya is an Assistant Professor of Chemistry and Biochemistry as well as Chemical and Biomolecular Engineering at the Georgia Institute of Technology. Research in her laboratory focuses on developing technologies to accelerate the engineering of microbes for the production of chemicals. Specifically, her lab focuses on the engineering of baker’s yeast, due to its robustness during the fermentation processes and the limited number of synthetic biology tools available to rapidly engineer this organism. CSHL topic: Prof. Peralta-Yahya will lead the yeast metabolic engineering module at the Cold Spring Harbor Course. In this module, participants will learn a) key computational tools used for the design of metabolic pathways, c) yeast molecular biology, and d) quantification of the microbially-produced product.
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David Savage

UNIVERSITY OF CALIFORNIA, BERKELEY
Departments of Molecular & Cell Biology and Chemistry

http://www.savagelab.org

Dave Savage is Assistant Professor of Biochemistry, Biophysics, and Structural Biology in the Departments of Molecular & Cell Biology and Chemistry at the University of California, Berkeley. His lab is broadly interested in microbial physiology and in developing new tools for the understanding and engineering of biology. For this work, he has been named a Sloan Research Fellow, a DOE Early Career Awardee, and a NIH New Innovator. CSHL Topic: At Cold Spring Harbor, Dave leads a module focused on the engineering of metabolic pathways and applying novel genome engineering tools to rapidly manipulate and improve metabolism.
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Jeff Tabor

RICE UNIVERSITY
Department of Bioengineering

http://www.taborlab.rice.edu/

Jeff Tabor is currently an Assistant Professor in the Department of Bioengineering at Rice University. He received his Ph.D. in molecular biology from UT-Austin in 2006, studying with Andy Ellington. There, he demonstrated that synthetic genetic circuits can compete for ribosomes, and increase noise in global gene expression in E. coli. He also led a collaboration with Chris Voigt’s group at UCSF to engineer E. coli to function as a photographic film. He then joined the Voigt lab as an NIH postdoctoral fellow, where he reprogrammed the bacterial film to function as an edge detector, and engineered the first two-channel optical gene regulatory system, also in E. coli. CSHL topic: A current major limitation in synthetic biology is that even well characterized genetic devices (sensors, transcription factors, promoters,) often fail to compose in a predictable manner, and new compositions require significant time and effort to debug. My group is working to make synthetic biology more predictable. Our approach is to develop novel ‘optogenetic’ methods – based upon genetically encoded light-switchable proteins – to measure and control biochemical processes inside the cell with unprecedented accuracy and precision. Our current focus is using light switchable proteins to generate gene expression signals, such as linear ramps or sine waves, that can be used to study the dynamical properties of genetic circuits. Then, with more complete models of component circuits in hand, we aim to assemble them into larger systems, with predictable outcomes. We are applying the discoveries gained from our methods to program cell differentiation, synthetic multicellular patterns, and tissue growth, as well as novel cellular sense/respond behaviors for a range of applications.

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