By: Kathryne Metcalf
Digital memory versus analog: it’s a question that’s plagued music lovers for years. In biology, however, the focus is overwhelmingly digital: 0 or 1, on or off, genes expressed or not expressed. But what would analog memory look like in a cell, and how might it be useful?
This past summer, the UIUC_Illinois International Genetically Engineered Machine (iGEM) team set out to create a novel genetic part that would allow bacteria to record their environment in analog. Their completed project, SCRIBE (Synthetic Cellular Recorders Integrating Biological Events), was presented over the weekend at the iGEM Giant Jamboree in Boston, where it received a silver medal.
The International Genetically Engineered Machine (iGEM) Foundation is a non-profit organization that promotes synthetic biology technologies and collaborative, open-sourced study in the context of high school and undergraduate education. Teams comprising 6-10 students compete in an annual competition and submit a genetic part, or “BioBrick,” to be added to iGEM’s Registry of Standard Biological Parts, which then becomes available to researchers around the world.
“If you want a truly fundamental and yet frontier-pressing extracurricular as an undergraduate, and are interested in molecular biology or genetic engineering,” said team member Sameer Andani, “there’s nothing else you can do that’s more beneficial for your education than participating in iGEM.”
iGEM teams design their own study and manage research tasks over the course of the spring and summer. The competition culminates in the annual Jamboree, where teams attend lectures and present their findings for a chance to win medals in various subjects, including their BioBrick, Wiki site, and outreach efforts. The 2015 Jamboree attracted more than 250 teams from 35 countries.
The University of Illinois iGEM team, hosted by the Carl R. Woese Institute for Genomic Biology, is now in its eighth year, and has won several medals at both the regional and international level. The 2015 team consists of ten undergraduate students from six departments, including three returning members. Their research was conducted in the Biosystems Design theme laboratory under faculty advisor Dr. Yong-Su Jin, with the mentorship and assistance of graduate advisors from a number of departments.
The team’s work was built on research by Dr. Timothy Lu at the Massachusetts Institute for Technology, redesigned to function as a modular system inside a bacterium for recording the level of certain substances in their environment. Team member Caroline Blassick described SCRIBE’s memory as “far more specific than other biosensors […] it’s able to hold the values [of the inducing substance], and doesn’t ‘turn off’ or forget.”
Whereas traditional biosensors only test in binary—often through bioluminescence, glowing to indicate presence, dark for absence—SCRIBE causes the cell to add a telling mutation to its chromosome, which is then passed to its daughter cells. By plating and sequencing cells from the trial sites, it would be possible to extrapolate the number of recombination events, and determine how much of the inducing substance was in their environment.
“In human history,” said Andani, “the most energetically conserved form of data is DNA. And that’s what we’re manipulating—we’re encoding DNA. We’re keeping ‘memories’ inside a genetic tape recorder, inside the genome of the cell itself.”
Blassick suggested one potential application for SCRIBE: testing for groundwater contaminants. The expense and expertise required to use testing kits are what made traditional biosensors popular in the first place, she explained, “but what if there’s a remote water source people want to measure the contaminants in—maybe it’s periodically flooded but not consistently contaminated, or it drains completely during different seasons—that could slip by regular tests.” SCRIBE, however, could survive in the groundwater for weeks, and “remember” having encountered contaminants that are no longer present.
“SCRIBE could become a cost-effective, long term, and durable solution for testing environmental contaminants,” concluded Blassick.
Funding for the UIUC_Illinois iGEM team was provided in part by the IGB, the Departments of Bioengineering, Agricultural & Biological Engineering, Chemical and Biomolecular Engineering, and the Roy J. Carver Biotechnology Center. Applications for undergraduates to join the 2016 iGEM team will be released this winter. To find out more about SCRIBE and iGEM, visit the UIUC_Illinois iGEM page here.
By: Kathryne Metcalf