Gel Imaging on a Budget

Winter is coming.

It’s not just a popular phrase from a television program. It’s a motivating force for Drs. Erik Sacks and Lindsay Clark.

Sacks, Associate Professor of Perennial Grass Breeding and Genetics, and Clark, a Research Specialist, both work in the department of Crop Sciences at the University of Illinois at Urbana-Champaign. Winter in Illinois is hard on crops, particularly on Miscanthus giganteus, a hybrid grown as a source of renewable energy.

There are several problems with the strain of Miscanthus giganteus grown in Illinois.

“The current type that is grown for biomass is all one clone, which is a bad idea to begin with,” Clark says. “It is also not quite winter hardy for Illinois.”

Sacks explains that the main clone is from much warmer climes: central or southern Japan. It was brought to Denmark in the 1930s and then it made its way around Europe and North America. Most winters in central Illinois are mild enough that Miscanthus giganteus can survive.

“But if we have a really tough winter here, like we did a few years ago, what was that, 2014? 2013? New plantings that were planted in the spring of the previous year will suffer greatly. Even a mature stand will have reduced yields,” Sacks says.

And so instead of waiting for winter to come to us, they went to winter.

Sacks journeyed to the Russian far east, to be more precise, as part of a 2012 plant collection expedition funded by the USDA and in collaboration with the Vavilov Institute in Russia. Winter temperatures there regularly dip to -30 Celsius (-22 Fahrenheit).

“So, it keeps your ice cream pretty solid at that temperature. And these plants survive there. That is where they are from,” Sacks says.

The goal of that expedition was to analyze cold-resistant plant genes. With these genes, Sacks and Clark can help Miscanthus giganteus survive any winter that Illinois can throw at it.

The Russian Miscanthus dataset is available for download at the Illinois Data Bank, a public access repository operated by the Research Data Service at the University Library: https://doi.org/10.13012/B2IDB-4084515_V1.

 
‘I finally did it’

As you might imagine, analyzing plant genes requires specialized equipment like gel imagers. Gel imagers are widely used in laboratories to see and document the molecules in DNA and RNA.

These things are expensive. Imagers tend to cost upwards of $10,000.

But Clark is a tinkerer. She had been playing with the idea of building an imager using a Raspberry Pi for a while. Raspberry Pis are small, single-board computers usually available for under $100. So when the imager that Clark had been using in a colleague’s lab stopped working, she didn’t put in for a new one. Instead, she took her chance.

Clark built her own gel imager using just a Raspberry Pi, a styrofoam box, an orange camera filter, and a pair of reading glasses she bought from a pharmacy.

Total cost? $150.

Clark built a complicated piece of lab equipment for just a little over 1% of what it normally costs to buy one.

What’s more, she details how she built the Raspberry Pi gel imager on her blog, for other tinkerers to follow. That information can be found here: https://sites.google.com/site/lindsayvclarkgenetics/science-blog/cheapandlazygelimagerusingraspberrypi.

Seeds of the future

In one version of the near future, sugarcane sprouts in Illinois.

It’s a bit off, to be sure, given that Sacks can only get some to grow in a greenhouse right now.

“Just a little bit of winter hardiness improvement with sugarcane would really increase where we can grow it in the U.S., because right now it is now just south Florida, coastal Louisiana a little bit, and southern coastal Texas,” Clark says.

But it’s possible. Sugarcane is, after all, closely related to Miscanthus.

Making sugarcane more resistant to cold would do more than just provide an interesting challenge to researchers.

It would make a lot of land in the U.S. more usable. Even more importantly, hardier sugar cane could change how we relate to both fuel and food on both national and global scales.

“It could have implications for the food supply, or energy, whatever people use sugar for. I was just in Brazil at a meeting and they like to say there, ‘We drink the best and we drive the rest’,’” Sacks says.

Winter is coming. But we’re ready for it.