Journal Club

Noise in synthetic genetic oscillators

This paper focuses on characterizing the stochastic dynamics of previously described synthetic genetic oscillators. It is a very nice combination of experimental and computational work. The computational aspect includes both image analysis and parameter estimation. They breakdown the noise into different components including intrinsic noise, cell cycle noise, and parameter variability by looking at the expression […]

Entrainment of a genetic oscillator

This paper from Bill Mather group in the Physics Department at Virginia Tech shows how a genetic oscillator responds to noisy signals. The authors show that the oscillator gets entrained despite the noise affecting the input signal. This is a nice use of an existing oscillator developed in Jeff Hasty’s group. After demonstrating this property […]

Modeling a Minimal CDK Network

This paper reports a computational analysis of the minimal CDK network engineered in fission yeast (doi:10.1038/nature09543). It had been observed that a Cdk-inhibitory mechanism working through tyrosine phosphorylation of the kinase subunit, which is essential for modern fission yeast, is dispensable in the minimal Cdk network. Developing both deterministic and stochastic models of the minimal Cdk […]

Minimal Cell Cycle

This is a great example of a paper where synthetic biology meets systems biology. The authors developed a minimal cell cycle regulatory network by engineering a synthetic CDK. To simplify the cell cycle control machinery, a cassette expressing a fusion of cdc13 and cdc2under the control of the cdc13 regulatory elements was integrated into the genome. They show that oscillation of a […]

Big data reproducibility issues

This piece explains the inherent challenge of providing statistical significant results out of high dimensional data sets. It also suggests a number of strategies to mitigate the problem.

Bacterial tape recorder

This paper describes a bacterial tape recorder. E.coli engineered to be a bacterial tape recorder by allowing it change its genome in response to chemical signals. This is one of these mind-blowing papers that the Lu’s lab is known for. It’s a very nice combination of biology with engineering. This may be a way of using […]

Universal genetic parts for bacteria

This paper describes UBER, a set of universal genetic parts for bacteria.  This gene expression system for bacteria relying on a self-regulated T7 promoter. The advantage of this system is that it can be ported across species. The system is primed by using degenerate promoter sequences that works in many bacteria. The sequences were also […]