Synthetic signaling systems: half-life control as a determinant of dynamic properties. Cellular stress responses often rely on underlying regulatory processes that are highly dynamic. In the context of interconnected gene-regulatory and signaling networks, the lifetime of mRNA and protein molecules has a large effect on the overall behavior of the cell. This effect often manifests itself in the underlying network dynamics, as degradation rates can play a central role in determining the crucial timing of events. In this program, we will examine the role of degradation on signaling networks. To do this, we will utilize tools from computational biophysics and synthetic biology to design and construct novel gene signaling circuits that allow for control over the degradation rates of proteins and mRNA.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center (P50)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-CBCB-2)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
La Jolla
United States
Zip Code
Bean, Gordon J; Jaeger, Philipp A; Bahr, Sondra et al. (2014) Development of ultra-high-density screening tools for microbial "omics". PLoS One 9:e85177
Nazarko, Taras Y; Ozeki, Katharine; Till, Andreas et al. (2014) Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy. J Cell Biol 204:541-57
Hossain, Munshi Azad; Johnson, Tracy L (2014) Using yeast genetics to study splicing mechanisms. Methods Mol Biol 1126:285-98
Hui, Ashley; Pinter-Wollman, Noa (2014) Individual variation in exploratory behaviour improves speed and accuracy of collective nest selection by Argentine ants. Anim Behav 93:261-266
Tsimring, Lev S (2014) Noise in biology. Rep Prog Phys 77:026601
Mather, William; Hasty, Jeff; Tsimring, Lev S (2014) Synchronization of degrade-and-fire oscillations via a common activator. Phys Rev Lett 113:128102
Bouslimani, Amina; Sanchez, Laura M; Garg, Neha et al. (2014) Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep 31:718-29
Gorkin, David U; Leung, Danny; Ren, Bing (2014) The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14:762-75
Lee, KiYoung; Sung, Min-Kyung; Kim, Jihyun et al. (2014) Proteome-wide remodeling of protein location and function by stress. Proc Natl Acad Sci U S A 111:E3157-66
Caldwell, Andrew B; Cheng, Zhang; Vargas, Jesse D et al. (2014) Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes Dev 28:2120-33

Showing the most recent 10 out of 69 publications