Researchers in Dr. Buchler’s lab are working to better understand the regulatory mechanisms that occur naturally within the gene networks of organisms. The bulk of their research goes toward answering three basic questions. Firstly, how do these mechanisms function? Secondly, how do these mechanisms influence the large-scale workings of an organism’s gene networks(s)? Thirdly, how can these mechanisms be utilized or manipulated in order to give greater control over inter-gene regulation to researchers?
To investigate these questions, members of Dr. Buchler’s rely heavily on synthetic biology, which in their case involves building synthetic gene circuits–small clusters of genes that influence one another’s expression through a regulatory mechanism of interest in either a natural or controllable way–that are then inserted into budding yeast. Once inserted into yeast, these gene circuits and the effects of their substituent regulatory components can be monitored using well-established techniques and equipment common to yeast molecular biology.
Like the majority of the research occurring in Dr. Buchler’s lab, my project is to further develop our understanding and ability to utilize two powerful classes of regulatory mechanism: bi-stable switches and oscillators. But what exactly are these?
A regulatory mechanism is called a bi-stable switch if it can be used to switch “on” or “off” the expression of a gene (or genes) in a manner that is both highly controllable and highly stable (I use quotation marks because the expression of a gene can never be fully on or fully off, but rather in a state of relatively high or low expression, high being “on” and low being “off”.) In other words, a bi-stable switch allows a researcher to “turn on” the expression of a gene and have that gene stay “on” indefinitely, and then “turn off” the expression of that gene and have it stay “off” indefinitely.
An oscillator, on the other hand, is a regulatory mechanism that, once initiated, turns “on” and “off” the expression of a gene at regular intervals of time without the need for interference by an outside force (like a researcher). A synthetic biologist might, for instance, design an oscillator that turns a gene “on” for ten minutes, then turns it “off” for ten minutes, then turns it back “on” for ten minutes, and then back “off” again for ten minutes… and so on (I chose the interval of ten minutes arbitrarily).
Returning back to describing my project, I am working to develop a gene circuit that functions as a bistable switch and another that functions as an oscillator in E. coli bacteria. Although the Buchler lab does not typically work with E. coli, the circuits that I am helping to design are based on circuits that my secondary mentor, Sargis Karapetyan, successfully created for yeast. Controlling those circuits in yeast, however, proved to be more difficult than expected, so Sargis and Dr. Buchler decided to try and make use of them in bacteria, which have been shown to better cooperate with regulatory mechanisms like bistable switches and oscillators.
I cannot say exactly how we have designed these circuits, but, if our experiments and designs fare well, I’m hopeful that my work will contribute a small fraction to the writing of a research paper that reveals all.
