synthetic biology

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 […]

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 […]

Plant Synthetic Biology

Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software that can be used for plant synthetic biology. It includes a library of plant biological parts […]

CRISPR Cas9 Synthetic Eukaryotic Transcription Factors

The CRISPR Cas9 technology is used to design synthetic transcription factors in eukaryotes. The approach is used to design activators and repressors. Data shows that this approach can work in yeast and mammalian cells. This paper comes from Tim Lu’s group at MIT. A couple of years ago, we wrote a GenoCAD grammar to represent the structure of these […]

Opiate synthesis in yeast

This article got a lot of attention because of its potential biosecurity implications. Even though the paper only describes the synthesis of an intermediate, media quickly extrapolated to envision this as an avenue to home-brewed morphine and other addictive drugs. Of course, there is a long way to go before substantial amounts of illicit substances […]

Rule-based design of synthetic transcription factors

To design and build living systems, synthetic biologists have at their disposal an increasingly large library of naturally derived and synthetic parts. These parts must be combined together in particular orders, orientations, and spacings to achieve desired functionalities. These structural constraints can be viewed as grammatical rules describing how to assemble parts together into larger […]