When biologists create a new microorganism to fulfill a certain task, it can sometimes be hard to accurately predict its behavior, even if you understand what each of its component parts do. A new study outlines how virtual reality can help to better test the future functioning of the microorganism.
The approach takes a lead from the software development industry, where unit and integration testing is a fundamental part of application development. It sees each individual component tested both on its own and on its interaction with the surroundings. This usually involves simulating its behavior in a virtual environment. It’s an approach the research believe has merits in the biological world.
“Biological systems are complex, and we would benefit if we could debug them like a computer code. In unit and integration testing, you simulate the environment and plug each of the components in separately to verify that they function as intended. Then you combine them in pairs and start all over. In this way, you will see at which point feedback and interference start to disturb the system, and adjust it appropriately,” the authors say.
Put to the test
The researchers demonstrated the potential for this approach via a bio-digital oscillator, whereby they modified E.coli cells to produce a specific protein capable of glowing blue-violet. This light formed the interface with the digital component, with measurements taken every six minutes of the light produced by the cell. A virtual signal molecule was then generated in proportion to the reading. If the signal exceeded a certain threshold, the production of the fluorescent protein was stopped.
“The cells are interacting with the simulated environment. What they do influences what the computer does, and what the computer does influences the reaction of the cells. If you know Star Trek, you have certainly heard of the Holodeck. What we have built is essentially a simple Holodeck for genes of microorganisms,” the team say.
When the hybrid circuits were tested, they uncovered some interesting results. Whilst the population of cells glowed in blue violet—and the glow oscillated, albeit with variations between the individual bacteria, this differed from their expectations. The team hoped for the bacteria to oscillate in synchrony, so they altered the digital component and set up a virtual communication network between the bacteria. In this set-up, some of the virtual signal is distributed between neighbors and the group of bacteria display different types of collective oscillation.
The team hope that their work will help other researchers develop microorganisms more effectively.