reactions and adjust the computer model accordingly. In the lab, she “I was always interested in how things work,” says Associate Professor studies the ubiquitous bacterium Escherichia coli (E. coli), found in the Jennifer Reed, a 2014 recipient of the Presidential Early Career Award gut of humans and animals; cyanobacteria, a familiar sight as blue-green for Scientists and Engineers and a scientist at the Great Lakes Bioenergy “algae” in freshwater lakes; and Zymomonas mobilis, a bacterium found Research Center (GLBRC). “As a kid, I would look at the washing in the sap of sugar-rich plants. machine and wonder how it knew when the door was closed and it should Studying a variety of microbes could prove important to the biofuels start its cycle. But it wasn’t until college that I discovered it was much industry, where specific more interesting to apply microbes could be used engineering solutions to to match the specific biological problems.” characteristics of different After learning that the locales. Cyanobacteria, wide array of chemical for example, which require reactions inside a living cell only sunlight and carbon could be modeled with a dioxide to produce biocomputer, Reed became fuels, could be an ideal fit hooked on the field of for sun-drenched states metabolic engineering, the like Arizona. practice of optimizing cell But Reed’s computaprocesses to increase the tional design goes well production of desirable beyond matching the chemicals such as ethanol. industry’s geography “I discovered that a with natural variation in cell’s metabolism is this a microbe’s preferred incredibly complex system, environment. Increasing but with all kinds of the economic viability of controls in place to make the biofuel pipeline will sure it doesn’t go awry,” require creating valuable Reed says. “It all seemed co-products along the very logical. The cell is not way. To that end, Reed some random thing that also works on converting just happened to emerge. cellulosic, or non-edible, This engineer-minded plant material to the kinds description of biology of chemicals used to make really appealed to me.” plastic soda bottles, In her lab at UW– pesticides and pharmaMadison, Reed focuses on ceuticals, creating noncontrolling thousands of petroleum derived sources reactions inside a cell by Jennifer Reed working with a GLBRC team member in her lab. of a host of commercially changing the genes that valuable chemicals. help produce a specific “E. coli can be designed to produce hundreds of compounds that it chemical. For example, in her GLBRC research, she tweaks certain strains doesn’t produce in nature,” Reed says. “So you can make large amounts of yeast and bacteria so that they can better access and convert the sugar of biofuel with a small profit margin, and supplement that with smaller molecules contained in corn stover—the stalks, leaves, husks and cobs that volumes of commodity chemicals that are much more profitable.” remain in fields after the harvest—to ethanol and advanced biofuels. Long-term, Reed’s goal is to be able to feed any arbitrary DNA And yet engineering challenges like these are not simple, nor are they sequence into a computer and predict not only the function of the genes limited to studying just one particular pathway within a cell. As Reed contained in that sequence, but also the levels, inside a living cell, of the explains it, if you want a cell to produce a different kind of biofuel, such as various products they control. isobutanol, you need to turn off the ethanol pathway and enhance flow “I’m really interested in how DNA encodes the behavior of cells, into the pathway that makes isobutanol. Knowledge of the entire biological whether we’ve engineered them or they occur naturally,” she says. system is required to develop these kinds of strategies, which is why “Right now, I have to do a lot of tinkering with various DNA elements metabolism modelers like Reed are also called systems biologists. to introduce a new pathway. But the more computational design that Reed’s research approach is unique in that it combines computational you can do, the less of that trial-and-error strategy is needed.” modeling and lab work. Running experiments with living microbes allows her to compare their observed behavior to the computer’s predicted
MODELING METABOLISM FOR
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