For the past few months, a team of students from the Hijacking Microbial Factories for Synthetic Biology stream has worked to keep bacteria from doing what they do best: evolving.
One of the biggest problems that synthetic biologists face today is ensuring that the changes they make to bacteria continue working for as many generations as needed. A group of student researchers from the stream manipulated the bacterium E.coli to look for the mutations that ‘break’ artificial modifications, and in turn keep cells from producing the proteins that they were programmed to make.
The researchers presented their work in Boston for the International Genetically Engineered Machine, or iGEM, competition this September. The event, called the Giant Jamboree, included the work of 280 teams from universities worldwide.
Minimizing the mutations that cause cells to change over time would be a huge benefit to synthetic biology research. Dennis Mishler, the Research Educator for the Synthetic Biology Stream, explained that “evolution is great for things that want to live and grow and survive,” but is “really bad for people who want to reprogram bacteria.” When mutations cause cells to stop doing what researchers program them to do, they tend to be able to save more energy, making them better at surviving than their modified counterparts. Even small changes to their genetic programming can change entire populations over short spans of time.
The basic procedure the team used was to create plasmids, loops of DNA that contain the sequence of DNA that scientists choose to modify, or the genetic device. These plasmids are then introduced to cells within a culture. Students programmed these cells to produce fluorescent proteins, which can be measured by the intensity of light they give off.
Once a significant amount of the florescence had decreased, researchers knew that the genetic device was no longer working correctly, and that most likely many of the cells had stopped producing these proteins. They then chose a representative colony of the bacteria to send out for DNA sequencing, which allowed them to check for mutations.
After testing, Computer Science Major Tyler Rocha says that the team found two groups of devices, those that were “either very unstable or very stable.”
This research has helped improve the Evolutionary Failure Mode Calculator, an online form developed by the Barrick lab in the Department of Chemistry that allows users to insert the genetic sequences of their cultures and detect mutational hotspots. “Our hope is to make this calculator available to a lot of synthetic researchers,” said Sanjana Reddy, a Biology Major on the team.
Continuing with research from previous years, the 2015 iGEM team also worked to build genetic devices with real world applications. In 2012 students from the stream’s iGEM team pioneered a plasmid that would allow bacteria to break down methylxanthine compounds, with the intention of determining how much caffeine different beverages contain. This plasmid works well for artificial drinks like sodas, which contain pure caffeine solutions, but organic beverages like tea and coffee contain other methylxanthine compounds that are highly similar to caffeine, making it hard to measure exact amounts of caffeine. This year’s team, led by senior Alex Gutierrez, created a set of plasmids which together can determine the concentrations of each compound, including caffeine.
To meet iGEM community outreach recommendations, researchers set up a booth at the South by Southwest festival, encouraging people to ‘paint’ with modified bacteria and sending back pictures of their glowing plates afterwards. “Synthetic biology is something that not everyone is on board with,” Neuroscience Major Natalie Schulte said, “a lot of that comes from people not understanding what it is.”
The team presented their findings this September alongside groups from other US and international institutions. They team completed a 20 minute presentation and a ten minute Q & A session. Schulte accredited the large audience to the fundamental nature of the project, explaining that “all of those projects are in a way dependent on evolutionary stability.” The aptly named ‘Breaking is Bad’ project received an individual gold standard, awarded to fewer than half of the competing teams.
Looking forward to next year, the students are excited about starting on ideas from the spring semester which warrant more attention, or continuing with current projects, such as evolutionary stability, which still have potential for improvement. Dr. Mishler described plans for projects turning bacteria into living sensors for pH and temperature, and making bees more resilient to external chemicals like pesticides.
UT Journalism Student