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12/11/2016 Comments (0) Views: 23 Health

Open-Source Tool is a Windfall for Optogenetics

The first low-cost, easy-to-use optogenetics hardware platform will let biologists who have little or no training in engineering or software design incorporate optogenetics testing in their labs.

The Light Plate Apparatus (LPA), which researchers created in the lab of Jeffrey Tabor, assistant professor of bioengineering at Rice University, uses open-source hardware and software. The apparatus can deliver two independent light signals to each well in a standard 24-well plate and has sockets that accept LEDs of wavelengths ranging from blue to far red.

Total component costs for the LPA are less than $400—$150 for labs with a 3D printer—and each unit can be assembled and calibrated by a non-expert in one day.

“Our intent is to bring optogenetics to any researcher interested in using it,” says Tabor, whose students created the LPA. In doing so, they found ways to make most of its parts with 3D printers and also created software called Iris that uses simple buttons and pull-down menus to allow researchers to program the instrument for a wide range of experiments.

Optogenetics, which was developed in the past 15 years, involves genetically modifying cells with light-sensing molecules so that light can be used to turn genes and other cellular processes on or off. Its most notable successes have come in neuroscience following the invention of brain-implantable optical neuro interfaces, which have explored the cells and mechanisms associated with aggression, parenting, drug addiction, mating, same-sex attraction, anxiety, obsessive-compulsive disorders, and more.

“Over the past 5-10 years, practically every biological process has been put under optogenetics control,” says bioengineering graduate student Karl Gerhardt, who works in Tabor’s lab. “The problem is that while everyone has been developing the biological tools to do optogenetics—the light-sensing proteins, gene-expression systems, protein interactions, etc.—outside of neuroscience, no one has really developed good hardware that makes it easy to use those tools.”

Making the system better and better

To demonstrate the broad applicability of LPA, Tabor, Gerhardt, and coauthors used the system to perform a series of optogenetics tests on a diverse set of model organisms, including gut bacteria, yeast, mammalian cells, and photosynthetic cyanobacteria.

A biochemist by training, Gerhardt initially was interested in simply creating something that would allow him to incorporate optogenetics in his own research. In early 2014, Gerhardt was studying the social amoeba Dictyostelium discoideum. Evan Olson, another PhD student in Tabor’s group, had just created the “light tube array,” or LTA, an automated system for doing optogenetics on up to 64 test tubes at a time.

Unfortunately for Gerhardt, D. discoideum, which biologists commonly call “dicty,” prefers to grow on flat surfaces, like Petri dishes and flat-bottomed well plates. Dicty is also sensitive to vibrations and movement. Like dicty, many organisms commonly studied in biology labs, including many animal cell lines and virtually all human cells, require similar conditions.

“I couldn’t culture dicty in the LTA, so I built a sort of plate-based version, and I used it for a couple of experiments, but it didn’t work very well,” Gerhardt says. “Then, some other people in our lab who had training in electrical engineering and Evan, with his physics background, said, ‘We can take this version and make it a lot better.’”

Gerhardt says the group kept innovating and coming up with new versions of the hardware. For example, to make it easy to change the wavelength of light, the team incorporated standard sockets so it would be easy to swap out different colored LEDs. They also added a low-cost microcontroller with an SD card reader, drivers capable of producing more than 4,000 levels of light intensity, and millisecond time control.

“We got more and more ambitious in terms of the features we wanted to add, and now we’re on version three or four of the hardware,” he says. Then others on the team “who had expertise in programming and website design, said, ‘We’ll make the software,’ and that’s where Iris came from.”

Programming isn’t a barrier

Iris makes use of a graphical user interface to allow people without specialized computer training to easily program experiments for the LPA.

“Programming is a major barrier for some biologists who want to work with this kind of hardware,” Gerhardt says. “Optogenetics hardware, most of the time, requires someone with programming experience who can go into the command line and write code. We wanted to eliminate that barrier.”

To simplify the process for getting started with LPA, Tabor and Gerhardt have published all the software, design files, and specifications for the system on GitHub, a site that caters to the do-it-yourself community by making it easy to create, share, and distinguish different versions of software and files for open-source platforms like LPA.

Gerhardt says at least a half-dozen research groups began making LPAs after an early version of the paper was posted on a biology preprint server, and he hopes many more begin using it now that the work appears in Scientific Reports.

“I hope this becomes the standard format for doing general optogenetics experiments, especially for people on the biology end of the spectrum who would never think about building their own hardware,” Gerhardt says. “I hope they’ll see this and say, ‘OK. We can do optogenetics now.’”

Additional coauthors are from Rice and the University of California, Berkeley.

The Office of Naval Research, the National Science Foundation, the National Institutes of Health, the Department of Defense, the Ford Foundation, the Department of Energy, and the Simons Foundation funded the work.

Source: Rice University

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