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Lab News -- January 30, 2009

January 30 , 2009

LabNews 01/30/2009PDF (1 Mb)

Biorefinery in a plant — the next step in biofuel production

By Patti Koning


Sometime in the not-so-distant future, agricultural waste, weeds, and other plant products that are typically discarded or destroyed may fuel our cars. But going from the ground to the fueling station is not a simple process . . . yet. Sandia researchers are partnering with the US Department of Agriculture (USDA) on a project that aims to create a consolidated biorefinery process within plant cells.

Called “A Trojan Horse Strategy for Deconstruction of Biomass for Biofuels Production,” this project seeks to embed into the plant cells synthetic genetic circuits constructed using parts from extremophilic organisms that can break down the complex carbohydrates of plant biomass into fermentable sugars. The result would be a significant reduction in the cost and complexity of the process currently used to deconstruct biomass for biofuels processing — a savings of as much as $1 per gallon of biofuel by some estimates.

Masood Hadi (8621), principal investigator for the Trojan Horse project, explains that breaking down complex carbohydrates into biomass involves many physical processes — raising the temperature, subjecting the biomass to acid treatment followed by washing, and then enzymatic digestion.

“The pretreatment and enzymatic hydrolysis steps represent about 40 percent of the cost, which could be cut in half if the enzymes are embedded into dedicated biofuel crops,” he says. “Our idea is to consolidate this entire process and have it all take place within the plant. To put it simply, we’d move certain aspects of the biorefinery process inside the plant cells.”

The potential of the extremophile organisms is well-understood, thanks to Sandia’s research on using enzymes produced by Sulfolobus solfataricus as a means of breaking down lignocellulosic biomass (Lab News, June 22, 2007). But bringing organisms that exist only in harsh environments, such as sulfur cauldrons and hot springs, into living plants is not a natural fit.

Synthetic biology

This is where synthetic biology comes in: taking engineering design principles and applying them to the cellular structure of plants. “We’re taking a circuit that doesn’t necessarily ever exist in a tractable organism, putting it into a plant, and having that plant do something it couldn’t do before,” says Masood.

The goal is for the circuit to become part of the plant genome and be passed onto future generations through seeds. This is the Trojan Horse aspect to the project; the embedded circuits are, in a sense, stealthily brought into the plants where they lay dormant until activated by extreme heat.

Masood and his team are taking several approaches to the circuit construction — freely expressing the enzyme genes within the cell and targeting the genes to be near the complex carbohydrate material, minimizing mass transport and localization issues. Mary Bao Tran-Gyamfi (8621) and other Sandia microbiologists have developed constructs with different localization signals (kind of like zip codes) in different parts of the cell.

Two model plants

Initial work is being done on two model plants: Arabidopsis, a small flowering plant that is a member of the mustard family, and Brachypodium distachyon, a grass species related to the major cereal species (wheat, barley, oats, maize, rice, rye, sorghum, and millet). Using model systems in plants is akin to biological experiments with mice or fruit flies for translational research in humans: Model plants have well- understood genetics and are easy to transform, with small statures and short life cycles.

For help with the plant genetics side of the problem, Sandia is partnering with two scientists at the USDA’s Western Regional Research Center (WRRC) in Albany, Calif. — James Thomson, a bacteriologist and Arabidopsis expert, and Roger Thilmony, a molecular biologist and Brachypodium distachyon expert. The WRRC is home to the Brachypodium Genome Resources Project.

Thilmony and Thomson are now, through biotechnology tools, expressing these genes of interest, the engineered circuits, in the model plants. The process to grow plants with the genes will take five to six weeks with Arabidopsis and three to four months with Brachypodium.

Proof of concept

The USDA researchers already have successfully transformed onion cells as a proof of concept. Because onion cells are white and the genes are blue, it’s quickly apparent if the transformation took place and the circuit worked in the plant cell.

Getting the genes into the plants is an amazing process. For Arabidopsis, Thomson creates an agrobacterium, to which he feeds the DNA encoding the circuit. Then he literally dips the plant flowers into the bacteria solution and the bacteria take it from there.

“The bacteria serve as a shuttle vector that takes the DNA into the plant — it does the hard work. We just wait a few weeks to see if the plant seeds are transformed as we hope,” explains Thomson.

The process is more complicated with Brachypodium; the bacteria must be introduced to plant stem cells, but the general principle is the same.

Advanced imaging

Sandia is also drawing on its expertise in advanced imaging and analysis techniques developed by Jeri Timlin in Biomolecular Analysis and Imaging Dept. 8632. “Our techniques in hyperspectral fluorescence imaging with multivariate curve resolution enable researchers to remove the background of chlorophyll and locate the proteins of interest,” she says.

Her work, along with that of colleagues Michael Sinclair and Ryan Davis (both 1816), helps Masood and other researchers see results quickly and clearly. This information is then used to modify and enhance future experiments.

If the circuits are successfully introduced into the model plants, the process will be repeated with dedicated biofuel plants such as switch grass, which is closely related to Brachypodium, and poplar, a close relative of Arabidopsis. “If we are successful in Brachypodium, I’m quite confident we can express the genes in switchgrass,” says Thilmony.

In parallel, the researchers are also investigating rice straw as another potential dedicated biofuel. “About 50 percent of the world’s protein comes from rice, but rice straw is discarded and even burned,” says Blake Simmons (8655), manager of the energy systems group and the Trojan Horse project manager. “So we’d be making energy from something that typically goes to waste.”

Not competing with food crops

This is an important point — the biofuel crops do not compete with agricultural crops used for human or even animal consumption, thus avoiding the “food versus fuel” debate. Another important point is that the synthetic biology is not being done on food-source plants. In other words, these aren’t genetically engineered foods.

“With rice straw, this enzyme will not be expressed in the grain. It will only be in the stalks and leaves, which are not even used for livestock because the silica content is too high for any animal system consumption,” says Masood.

Blake explains that in this three-year project, Sandia and USDA will not create a new class of dedicated energy crops that are ready for commercialization, but rather develop a method to make that possible. “Our goal is a system and technology demonstration that shows that we can put these extremophile enzymes into plants, activate upon a thermal trigger, and achieve hydrolysis of the polysaccharides into fermentable sugars,” he says. “That would be a substantial impact to the community.” -- Patti Koning

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Sandia’s impact on the state’s economy put on display at summit

By Chris Burroughs

More than 200 business, education, and civic leaders learned firsthand Jan. 22 about Sandia’s impact on the state of New Mexico’s economy during the Labs’ first-ever Economic Impact Summit held at the Albuquerque Convention Center.

“The purpose of the summit was to make the greater Albuquerque business and civic communities aware of the economic impact Sandia has on the state, which is believed to be about three times the total amount it spends on purchases and salaries,” says Don Devoti, manager of Sandia’s Small Business Utilization Dept. 10222. “Most people attending the event already knew that Sandia plays a key role in New Mexico’s economy. They just didn’t know the extent.”

At the event Labs officials — including Matt O’Brien, chief financial officer and VP of Business Operations Div. 10000, and Carol Yarnall, Supply Chain Management Center 10200 director — rolled out the new Sandia Economic Impact brochure, which outlined the full scope of the Labs’ impact on the state’s economy last year.

Carol informed the gathering of the importance of New Mexico community and business groups to Sandia’s future.

“Sandia’s suppliers are considered strategic partners, and this is the first of many venues the supply chain center will be sponsoring,” she said.

Also on hand to provide insight to Sandia’s economic effects on the community, all outlined in the brochure, were Karen Gillings, acting director of Human Resources Center 3500; Jackie Kerby Moore, manager of Sandia’s Technology & Economic Development Dept. 1033; George Friberg, senior director of Technology Ventures Corp. (TVC); and Bruce McClure, manager of Sandia’s Community Involvement Dept. 3652.

Among the information discussed at the summit and in the brochure are:

To obtain a copy of the brochure and for more information about Sandia’s economic impact on the economy call 1-800-765-1678 or email — Chris Burroughs

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Cognition symposium boggles mind

By Chris Burroughs

More than 200 scientists from throughout the country gathered at a resort just north of Albuquerque earlier this month and spent three days peering into the future of cognition research. What they heard was mind-boggling.

It’s a future of new treatments for diseases such as Alzheimer’s, Parkinson’s, depression, and schizophrenia, and cures for people with traumatic brain injuries; the creation of new machines, like super-powerful computers that will enhance the way people perform and think; and dramatically improved robotics.

The scientists were attending the fourth Decade of the Mind symposium, sponsored by Sandia and cosponsors Krasnow Institute at George Mason University, Los Alamos National Laboratory, Santa Fe Institute, the University of New Mexico, MIND Research Network, and the Potomac Institute for Policy Studies. Subtitled “Reverse Engineering the Brain: Sowing the Seeds for Technology Innovation,” the symposium was held at the Hyatt Regency Tamaya Resort and Spa on the Santa Ana Pueblo.

“Our goal was to obtain a glimpse of the technologies emerging in the areas of reverse engineering of the brain, computational neuroscience, cognition modeling, and massive neuronal simulations,” says John Wagner (6341), manager of Sandia’s cognition department and symposium chairman. “What we got was a world-class symposium that left everyone who attended awed about how far cognition research has come — and how far it needs to go.”

Al Romig, Sandia executive VP and deputy Laboratories director for Integrated Technologies & Systems and interim chief operating officer, said at the symposium that the move to understanding the brain is not unlike what occurred 15 years ago when scientists were first interfacing biology and physics into the new science of biotechnology.

“It’s a multiscale problem that is going to take a multidisciplinary effort to solve,” he said. “A better understanding of the brain will have great benefit to the nation and humankind.”

The research may result in reducing armed conflict, countering terrorism, understanding the mechanisms of dementia, and addressing the human elements of energy security and climate change problems. Some of the disciplines that will have to come together are computing and mathematics, neuroscience, engineering sciences, micro and nano technologies, psychology, social sciences, material sciences, physics, chemistry, biology, and physiology, Al said.

Jim Olds, director of the Krasnow Institute for Advanced Study and the Shelley Krasnow University Professor of Neuroscience at George Mason University in Virginia, organized previous Decade of the Mind symposiums. He noted that his belief in an advanced cognition future is rooted in the Human Genome Project, which showed that “large challenges can be cracked.”

Olds told conference-goers that he and a team of researchers are working on establishing a cross-disciplinary and multiagency project to consolidate new science, inspire new technologies, and try a new assault on understanding how the mind emerges from the brain. The project would cost $4 billion over 10 years.

At the symposium Olds emphasized that for such a project to be successful, it has to be international in scope. And, in fact, European researchers have already joined forces with American scientists on the mind project. The next Decade of the Mind symposium will be in Berlin Sept. 10-12.

Other speakers at the New Mexico symposium talked about ethics and cognition research, what is consciousness, research on brains of fruit flies, and cognition modeling. — Chris Burroughs

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