Synthetic Biology

We are teaching bacteria new tricks: we have engineered E. coli cells that function like logical AND gates. These engineered bacteria produce a green flurescent protein only when we add two small chemical molecules in the bacterial culture.

We are using these bacteria in bioenergy production applications.

In order to design the synthetic gene regulatory circuits that implement the AND gate function, we first modeled and simulated them. The simulations gave us useful insight that assisted in engineering the bacteria without resorting to traditional trial and error molecular biology techniques.

Visit our publications webpage and consult the following manuscript for more details on the bacterial AND gates:

Ramalingam, KI, Tomshine, JR, Maynard, JA, Kaznessis YN. " Forward engineering of synthetic bio-logical AND gates" Biochemical Engineering Journal, 2009, 47(1-3):38-47

 

In order to assist synthetic biologists we developed the Synthetic Biology Software Suite, a suite of modeling tools that connect DNA sequences to dynamic behaviors. We have launched the Synthetic Biology Software Suite on www.synbioss.org.

SynBioSS users can now quickly design, construct and simulate synthetic gene networks. SynBioSS can also use BioBricks as input and automatically generate a reaction network that can model the dynamic behavior of the BioBrick.

SynBioSS is explained in detail in the following publications:

•  Weeding E, Houle J, Kaznessis YN “SynBioSS Designer: A Web-Based Tool for the Automated Generation of Kinetic Models for Synthetic Biological Constructs” Briefings in Bioinformatics, 2010, link

•  Kaznessis YN. "Computational Methods in Synthetic Biology", Biotechnology Journal, 2009, Volume 4(10):1392-1405.

•  A. Hill, J. Tomshine, E. Wedding, V. Sotiropoulos, Y. Kaznessis, "SynBioSS: the Synthetic Biology Modeling Suite", Bioinformatics 2008, 24(21):2551-3.

•  Kaznessis YN. "Models for synthetic biology." BMC Syst Biol. 2007 Nov 6;1(1):47

Comprehensive overview of the synthetic hybrid biological AND gates. Architecture (LTT: 1a, TLT: 1b, TTL: 1c), experimental outcome (LTT: 1d, TLT: 1e, TTL: 1f) and corresponding model predictions (LTT: 1g, TLT: 1h TTL: 1i) of the synthetic AND logic circuit. 1a-c, the promoter topology is varied by successively shifting lacO position from upstream of -35 hexamer to downstream of -10 hexamer respectively. The lacO and tetO represent the operator sites at which LacI and TetR proteins bind. 1d-f, Surface plots representing the mean of gfp fluorescence influenced by the grid of inducers concentrations (aTc, 0-200ng/ml; IPTG, 0-2mM) demonstrate excellent agreement between the experimental results and deterministic model predictions. Presence of both inducers controlled gfp expression in a dose-dependant manner saturating at high concentrations. Notably induction thresholds in the presence of aTc and IPTG absent appeared to be a function of lacO location.  The TTL promoter showed the best transcriptional regulation and AND gate phenotype of the 3 designs.