William Brady, whose been at chemical company Cabot Corporation for 23 years, will take over as CEO as it tries to go commercial.

The transition has been expected. Bruce Jamerson, the former CEO, took over Frontier Renewable Resources last year. Frontier will build plants based around Mascoma's microbial formulas for cellulosic ethanol and is in the midst of raising a few hundred million to build the plant. Jamerson's background is in finance and Mascoma wanted someone more familiar with R&D and chemical processing. Frontier is aiming to get the plant running in 2011 or 2012. Cellulosic ethanol is taking longer than expected: The Energy Information Administration estimates that the U.S. won't likely hit its goal of 36 billion gallons of cellulosic ethanol a year mark until 2030. The early goal was 2022.

The company, a spin-out of Dartmouth College, exploits genetically enhanced microbes to turn vegetable matter into fuel. The process typically takes three stages: cellulose has to be separated for vegetable matter, cellulose then has to be converted to sugar, and the sugar then has to be converted to alcohol. Mascoma hopes to combine those last two stages into one and thereby save time and money.

However, it hasn't been easy. Despite landing around $100 million in grants from the federal government various states and $100 million in equity investments from Khosla Ventures and others, Mascoma has missed a few deadlines and scaled back some projects. It's par for the cellulosic ethanol course, but Mascoma was more visible than many competitors so the delays have been a bit embarrasing.

Last September, it signed a deal with Chevron Technology Ventures. Under that deal, Chevron (CVX) will supply feedstocks to Mascoma, and then Mascoma's microbes will convert the material into ethanol and lignin, the tough protein that protects plants. Chevron will then evaluate the results. To survive and thrive, biofuel startups will invariably have to partner with the major fuel companies. Chevron already has an R&D alliance with Solazyme, which makes algal biodiesel. Shell has deals with 70 or so different alternative fuel companies, according to sources.