MEDFORD, Mass.--In this densely populated city outside Boston without a farm in sight, agriculture researchers are engineering corn and other crops to become better biofuels.

U.S. Secretary of Agriculture Tom Vilsack last week visited Agrivida, a small company working on a method it hopes will help deliver on the biofuels industry's promise of economically making fuel and chemicals from non-food crops. Vilsack toured the lab of Agrivida to draw attention to federal investments in renewable energy research and development.

Cheaper biofuels will help lower fuel costs and provide economic development in rural areas of the U.S., he said. The company received about $6.8 million in grants from the USDA and the Department of Energy's ARPA-E program, in addition to venture capital.

Agrivida's is using genetic engineering and other techniques from the biotech industry to create proteins with specific traits designed for rapid, and cheaper, biofuel production from sorghum, switchgrass, and corn stover, the residual material from corn harvesting.

Company scientists are identifying proteins, or enzymes, that rapidly break down cellulose, the compound in cell walls that gives plants structure. Those enzymes are then inserted inside plants. After the transgenic plants are harvested, the enzymes are "switched on" and begin breaking down the crop's cell walls faster than traditional biofuel methods.

The end goal, as is with many biofuels processes, is to make sugars that can be fermented into ethanol or turned into different products, such as specialty chemicals, through existing methods.

"We've tested 600,000 enzymes this year and over 2 million since we started," said Agrivida CEO Mark Wong during the tour. "Plants make the enzymes to chop up the cellulose but they are in a dormant form. Then we activate (the enzymes) by heating them to high temperatures."

Sorghum, which is often used as animal feed, could be a feedstock to make sugars for fuels or chemicals, according to Agrivida.

If it works, the company's GreenGenes method will be cheaper than the traditional processes of breaking plant matter into sugars by adding enzymes after crops are harvested and milled. The production price target is 80 cents a gallon, Wong said.

Agrivida is planning to deliver three "plant expressed" enzymes for corn this fall and have them tested with its seed partners by the end of the year. It would take a few years for USDA approval and the earliest it would reach the market is four to six years, Wong said.

Lab bench robots One of the primary challenges that protein engineering companies like Agrivida face is isolating the genes that are most effective at a desired trait. In its case, Agrivida scientists are drawing on traits found in organisms, including fungi and bacteria, that break down plants, explained senior scientist Philip Lessard.

But the sheer number of genes means that the company needs to rely on automation to sort through different enzymes. In its lab, it uses robots to sort through thousands of enzymes and then to monitor their growth in assay plates, which can hold dozens of colonies in a single tray.

Once genes are isolated, scientists then grow the enzymes in a type of bacteria that can be inserted into plants, explained Lessard, one of the 20 PhDs in a company of 40 people. That allows them to grow and be tested in plants, rather than testing the enzymes in microbes.

In its lab, Agrivida has a section dedicated to incubating plant tissue and growing a variety of these transgenic plants. In the final stage of its testing, it measures how much sugar different varieties produce. Some of its genetically engineered plants, such as sorghum or switch grass, can produce 50 percent more sugar than traditional processes, Lessard said.

"There are many companies willing to turn sugars into ethanol, biogasoline or even chemicals," he said.

Beyond testing the thousands of possible gene combinations, the biggest technical challenge is inserting and controlling the switch that activates the cellulose-chopping enzymes, Wong said. After growing and testing 600,000 enzymes this year, the company has about 10 engineered enzymes. "It's a big numbers game," said Wong.