January 3rd, 2012 | Category: Art&Design, Blogs, Information processing, Saccharomyces, Synthetic Biology | Leave a comment


Christina Agapakis is a postdoctoral research fellow at UCLA in the lab. of James C. Liao. She writes the rather excellent synthetic biology blog Oscillator. Previous posts can still be found at her earlier Scienceblogs residence.

A good place to start is her post from December on cyborg yeast (Fig. 1) …

Fig. 1. Cyber yeast.

Fig. 1. Two cyber yeasts.

… or more precisely, in silico feedback for in vivo regulation of a gene expression circuit (linking computer-outputs with biological information processing).

Yeast cells were engineered to express two plant proteins (PhyB and PIF3) that respond to red light. In red light, these proteins are bound together, interacting to cause transcription of the gene of interest (in this case a yellow fluorescent protein (YFP)). In the absence of red light, this interaction does not occur and transcription ceases.

Christina goes on to explain the importance of feed-back and feed-forward loops in biological systems. Such loops are essential in maintaining constant levels of proteins in the cell for example. In the study in question, the researchers established such a feedback loop outside of the cell.

Christina explains,

These “cyborg yeast” cells were kept in the dark with a computer monitoring the level of yellow fluorescence. When the computer sensed that the level of fluorescence was decreasing, it flashed a red light. When it sensed that the fluorescence was too high, it flashed near-infrared light that turned the gene off. With the help of the computer the same cells could maintain the protein level constant at any arbitrarily chosen level, a task that would be nearly impossible with “traditional” synthetic biology.

She concludes her piece discussing the potential for such systems, adding,

The metaphors and mixtures of computers and biology have always been complex, and the feedback between synthetic biology and computer science will only continue to amplify itself and spin off new and weird cyborgs.

It goes without saying that it is well worth looking into her blog in more depth.

Leave a Reply




You can use these HTML tags

<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong>