OpenLab

Gazette
published: Sept 28

The Scientists
What do you envision when you think of molecular biology? Maybe you see the marvels of evolution or symphonies of chemical complexity.
Mads Kaern sees spare parts.
Kaern, a member of the Ottawa Institute of Systems Biology, is a sort of biotechnology inventor. He approaches networks of genes (the units of DNA that code for proteins and, thus, set many of our phenotypes) like an electrical engineer would approach a circuit. By knowing how the component genes interact, Kaern can predict what will happen if he replaces one gene with another.

The Science
Modifying DNA is actually a fairly routine task in modern biology. Enzymes can be used to snip DNA in two, inject a new gene and stitch the chain back together again. Voila! New genes and new regulatory chunks of DNA are added to a genetic circuit. (Regulatory chunks like promoters, enhancers and terminators turn on or off different genes and link gene networks to the outside world by responding to a drugs or different types of food.)
When Kaern wants to engineer a new network, he needs these vital chunks of DNA.
But where can he get them? One answer is he can buy them. Companies exist that own genomic libraries and let scientific researchers, like Kaern, use these libraries—for a price.
But that cost can be frustratingly high and Kaern is an inventor: he needs a large toolbox.

The Solution
In response to the privatization of genetic libraries, the Registry of Standard Biological Parts was founded in 2003. It’s an open source genetic archive of over 3,400 biological parts available to everybody. Like so many open source projects, the Registry encourages users not only to take from the archive but also to give back to the community. That’s ok with Kaern.
One way that he contributes to the community is by participating in iGEM, the International Genetically Engineered Machine competition. Teams of students are sent a kit of biological parts from the Registry and given one summer to use the parts to build useful biological systems.
Kaern has led the uOttawa team for four years.  Last year it won a gold medal for contributing a new standardized sequence of DNA for eukaryotic cells. Kaern and his team are part of iGEM, which holds a Creative Commons licence. Not only do they have the community’s toolbox open to them but they also participate in a competition that encourages ideas to flow quickly throughout the scientific community. Getting to see what works and what doesn’t for other groups is invaluable to a biotech inventor like Kaern.

Note: Professor Kaern will be discussing the Registry of Standard Biological Parts and iGEM on September 30 at 11:00 a.m. at the Syn-Bio Colloquium. The all day– colloquium, which will discuss the interface between science and policy, costs only $11.30 for students.