Paris Bettencourt

Biosensors are a common theme in iGEM and synthetic biology. However there are not many nucleotide biosensors in the registry. This year team Calgary developed a pathogenic E. coli biosensor and Paris Bettencourt is developing a M. tuberculosis sensor. Both the teams are using relatively new technology to create these sensors, namely, Transcription Activator Like Effector (TALE) and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and these are both DNA sensor.

TALEs are modular in nature and they contain domains called repeat variable domains (RVD) which are 34 amino acid repeats with and amino acid number 12 and 13 are variable which determines which nucleotide the TALE binds to. The specificity of these amino acids have been solved and therefore making custom TALEs targeting any sequence is very easy. CRISPRS are small extrachromosomal DNA that binds to DNA recognition protein called Cas9. The CRISPR/Cas9 complex target a sequence called protospacer which can be any sequence starting with NGG.

One of the binding elements of both these projects is the modular nature of both the TALEs and CRISPRs and the fact that they are both nucleotide sensors. These elements can be customized to detect any DNA of interest we desire. Therefore, we can use both of these systems to detect pathogenic E. coli or M. tuberculosis and any other oligonucleotide sequence we desire. However, the striking differences between the systems are how the teams are using these systems. Calgary is developing an in vitro biosensor that can be used by people in the field and Paris-Bettencourt is developing an in vivo biosensor that is used as a diagnostic tool in a laboratory environment.

This collaboration started when Paris and Calgary met at SB 6.0 in Imperial College London. We quickly figured out that both the teams are investigating platform technologies for nucleic acid biosensors. We looked through the registry and found that there were only 6 nucleic acid biosensors submitted to the registry in the six years that iGEM has been alive. This helped us identify a need for more nucleic acid biosensors and made us wonder what other types of biosensors are out there in the registry. This gave birth to SensiGEM, a collaborative biosensor database developed by Calgary and Paris Bettencourt[LINK].

To begin our collaboration both the teams reviewed biosensors that are already in the registry and has been part of iGEM thus far. Both the teams had video conferences weekly to think about basic questions regarding our projects as well as biosensors such as:

What is a biosensor? After an extensive literature review we settled on the definition being a biological or biologically derived system which contains a sensor element (DNA, RNA and protein) and a reporter element (visual, pH, colour, gene expression).

What are the elements of a biosensor? A biosensor can contain in vitro sensory elements such as TALEs, isolated transcription factors, repressors and/or they could contain in vivo sensory elements such as promoters, riboswitches and aptamers. In addition to the sensory element the biosensor must have a reporter element such as change in colour, florescence and gene expression.

What are some of the biosensors that are already in the registry? Some of the most common types of biosensors found in the registry thus far are chemical biosensors, followed by abiotic biosensors. However there is are only 6 nucleic acid biosensors in the registry thus far. Given the large number of projects in iGEM (963) and a vast array of biosensor projects (227) the number of nucleic acid sensor is microscopic.

What are some of our strengths (for both projects) and weaknesses (both projects)? <-- MAYBE THIS IS NOT A NECCESSITY

WE NEED TO ANSWER ALL THESE QUESTIONS AND THE STATS WILL FIT IN NICELY I THINK.

To extend the scope of this collaboration and to further show that the TALEs and CRISPRs are indeed modular in nature. Also list some characterization idea/ studies we might do as a future direction.