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  • richardmitnick 7:40 am on March 31, 2016 Permalink | Reply
    Tags: , Biofuels, Ee-Been Goh, , woman scientist   

    From LBL: “From Near-Dropout to PhD, Berkeley Lab Scientist Now at Forefront of Biofuels Revolution” 

    Berkeley Logo

    Berkeley Lab

    March 30, 2016
    Julie Chao
    (510) 486-6491

    Ee-Been Goh works with summer intern Joshua Borrajo in 2013. (Credit: Roy Kaltschmidt/Berkeley Lab)

    To see biochemist Ee-Been Goh in the lab today, figuring out how to rewire bacteria to produce biofuels, one would never guess she was once so uninterested in school that she barely made it through junior high.

    “My mom would say, ‘You used to be the worst in school—why would you want to go for more school?’” Goh said. “That was the joke when I was going into grad school.”

    Today Goh is a project scientist at the Joint BioEnergy Institute (JBEI), a Department of Energy Bioenergy Research Center led by Lawrence Berkeley National Laboratory (Berkeley Lab). She has been lead author on two important publications on methyl ketones, a compound found in blue cheese that has also turned out be one of the most promising and high-performing biofuels at JBEI.

    Her path into science is an object lesson she likes to share with the high school students she mentors through a JBEI summer program called Introductory College Level Experience in Microbiology (iCLEM). “I always tell the iCLEM kids how I was a terrible student in Singapore,” she said. “I was a tomboy, and I just loved goofing off on the streets and playing sports. I really hated school. I would’ve loved to have had a career in professional sports.”

    At the age of 14, her parents moved the entire family to Vancouver, largely for a better educational experience for Goh and her two sisters. Getting to do hands-on science activities in high school, such as animal dissections, sparked her interest in science. “When you do it yourself, you understand things a lot better than when you’re being bombarded with words on a board or an overhead projector,” she said. “That’s something that really caught on for me.”

    Likewise, she encourages students to take advantage of any opportunity they might have. “I think some of these students get really dejected when they don’t do well in school, and as you get more dejected, you just don’t want to put in any more effort,” she said. “That’s how I felt when I was a little kid. The most important thing for me is to fan their interest.”

    As an undergrad at the University of British Columbia, her opportunity was an internship in the microbiology lab of Julian Davies, a renowned scientist in the field of antibiotics and drug resistance. “He was retired and in his 70s, but he really loved science so he was still taking on undergrad students who liked to do research,” she said. “He was very hands-on and got very excited even with small results, and it got me excited too.”

    With encouragement from Davies, Goh decided to pursue an advanced career in science. She did her graduate work in microbiology at UC Davis, where her research focused on understanding how bacteria communicate with each other. This work in the basic sciences taught Goh useful research techniques, but she realized she wanted to pursue a career in the applied sciences.

    “With applied science it impacts more people and has broader reach,” she said. “People can take it and use it. That’s what science is about, right?”

    Landing a job at JBEI fit that requirement perfectly.

    From blue cheese to climate change

    “Many valuable commodity chemicals and fragrances are often derived from petroleum,” Goh said. “At JBEI we’re aiming not just to make biofuels but also to replace a lot of everyday products that come from that barrel of crude oil. We’re trying to do our part in slowing down climate change—that’s the ultimate goal.”

    The focus of her research has been methyl ketones, which are derived from fatty acids and show great promise for biodiesel fuels. Not only are methyl ketones a potential biodiesel, there is a market for these compounds as flavors and fragrances. Working with Harry Beller, director of Biofuels Pathways at JBEI, Goh’s research is aimed at engineering E. coli bacteria to produce methyl ketones as efficiently as possible.

    “Ee-Been has made significant scientific contributions to the development of new biofuels at JBEI,” Beller said. “Her two first-author publications on engineering and optimizing a novel methyl ketone pathway in E. coli have made a notable impact in the area of fatty acid-derived biofuels—medium-chain methyl ketones are among our best performing biofuels at JBEI.”

    Beller elaborated on what made Goh good at what she does: “Qualities that have helped Ee-Been be a successful scientist are her persistence and intelligent approach to troubleshooting. In biotechnology, as in many areas of science and technology, only a fraction of scientific avenues we follow lead to clear success. Ee-Been has the fortitude and ability to learn from things that didn’t work to eventually pursue things that do.”

    And although she occasionally likes to pull pranks in the lab—switching out medium-sized gloves for small ones is a perennial favorite—her JBEI colleagues have voted her “JBEI Citizen” for two consecutive years for “fostering a positive working environment through helping colleagues.”

    “Perhaps Ee-Been’s most lasting legacy at JBEI is all the people she has helped along the way,” Beller said. “She’s been very generous with her time, including ongoing involvement in the iCLEM summer internship program for economically disadvantaged high-school students.”

    See the full article here .

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  • richardmitnick 10:53 am on February 3, 2016 Permalink | Reply
    Tags: , Biofuels, ,   

    From Sandia: “Algae raceway paves path from lab to real-world applications” 

    Sandia Lab

    February 2, 2016
    Patti Koning
    (925) 294-4911

    Sandia algae raceway testing facility

    In a twist of geometry, an oval can make a line. The new algae raceway testing facility at Sandia National Laboratories may be oval in shape, but it paves a direct path between laboratory research and solving the demand for clean energy.

    As the nation and California adopt policies to promote clean transportation fuels, that path could help bring the promise of algal biofuels closer to reality. As one of the fastest growing organisms on the planet, algae are an ideal source of biomass, but researchers have not yet found a cost-competitive way to use algae for fuels.

    “This facility helps bridge the gap from the lab to the real world by giving us an environmentally controlled raceway that we can monitor to test and fine tune discoveries,” said Ben Wu, Sandia’s Biomass Science and Conversion Technology manager.

    “The success of moving technologies from a research lab to large outdoor facilities is tenuous. The scale-up from flask to a 150,000-liter outdoor raceway pond is just too big.”

    The new Sandia algae testing facility consists of three 1,000-liter raceway ponds with advanced monitoring provides new advantages to researchers:

    Easy scale-up to larger, outdoor raceways
    Customizable lighting and temperature controls, operational by year end, to simulate the conditions of locations across the country
    Fully contained for testing genetic strains and crop protection strategies
    Advanced hyperspectral monitoring 24 hours a day

    Several ongoing projects will use the algae raceway right away. Researchers Todd Lane and Anne Ruffing will test genetically modified algae strains as part of a project funded by Sandia’s Laboratory Directed Research and Development (LDRD) program. The algae raceway will allow the researchers to more quickly identify strains that promise improved performance.

    Lane is also part of a project partnership with Lawrence Livermore National Laboratory funded by the Department of Energy’s Bioenergy Technologies Office (BETO) that is investigating a probiotic approach to algae crop protection.

    Another BETO project seeks to convert algae proteins into useful chemical compounds such as butanol. Wu expects the facility will expand opportunities for Sandia researchers to develop algae as a robust source of biofuels and increase collaborations and partnerships with the private sector, particularly in California where efforts to transform transportation energy are prevalent.

    “The bioeconomy is gaining momentum,” he said. “Biofuels from algae may be further off, but algae has sugar and proteins that can make fuel or higher valued products, such as butanol or nylon — products that currently come from fossil fuels.”

    See the full article here .

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    Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major R&D responsibilities in national security, energy and environmental technologies, and economic competitiveness.

  • richardmitnick 6:20 pm on January 4, 2016 Permalink | Reply
    Tags: , Biofuels, Indiana U   

    From IU: “IU scientists create ‘nano-reactor’ for the production of hydrogen biofuel” 

    Indiana U bloc

    Indiana University

    Jan. 4, 2016
    Kevin Fryling
    Office 812-856-2988

    Temp 1
    An artist’s rendering of P22-Hyd, a new biomaterial created by encapsulating a hydrogen-producing enzyme within a virus shell. | Photo by Trevor Douglas

    Temp 2
    Illustration showing the release of NiFe-hydrogenase from inside the virus shell, or “capsid,” of bacteriophage P22. | Photo by Trevor Douglas

    Scientists at Indiana University have created a highly efficient biomaterial that catalyzes the formation of hydrogen — one half of the “holy grail” of splitting H2O to make hydrogen and oxygen for fueling cheap and efficient cars that run on water.

    A modified enzyme that gains strength from being protected within the protein shell — or capsid — of a bacterial virus, this new material is 150 times more efficient than the unaltered form of the enzyme.

    The process of creating the material was recently reported in Self-assembling biomolecular catalysts for hydrogen production in the journal Nature Chemistry.

    “Essentially, we’ve taken a virus’s ability to self-assemble myriad genetic building blocks and incorporated a very fragile and sensitive enzyme with the remarkable property of taking in protons and spitting out hydrogen gas,” said Trevor Douglas, the Earl Blough Professor of Chemistry in the IU Bloomington College of Arts and Sciences’ Department of Chemistry, who led the study.

    Trevor Douglas | Photo by Montana State University

    “The end result is a virus-like particle that behaves the same as a highly sophisticated material that catalyzes the production of hydrogen.”

    Other IU scientists who contributed to the research were Megan C. Thielges, an assistant professor of chemistry; Ethan J. Edwards, a Ph.D. student; and Paul C. Jordan, a postdoctoral researcher at Alios BioPharma, who was an IU Ph.D. student at the time of the study.

    The genetic material used to create the enzyme, hydrogenase, is produced by two genes from the common bacteria Escherichia coli, inserted inside the protective capsid using methods previously developed by these IU scientists. The genes, hyaA and hyaB, are two genes in E. coli that encode key subunits of the hydrogenase enzyme. The capsid comes from the bacterial virus known as bacteriophage P22.

    The resulting biomaterial, called “P22-Hyd,” is not only more efficient than the unaltered enzyme but also is produced through a simple fermentation process at room temperature.

    The material is potentially far less expensive and more environmentally friendly to produce than other materials currently used to create fuel cells. The costly and rare metal platinum, for example, is commonly used to catalyze hydrogen as fuel in products such as high-end concept cars.

    “This material is comparable to platinum, except it’s truly renewable,” Douglas said. “You don’t need to mine it; you can create it at room temperature on a massive scale using fermentation technology; it’s biodegradable. It’s a very green process to make a very high-end sustainable material.”

    In addition, P22-Hyd both breaks the chemical bonds of water to create hydrogen and also works in reverse to recombine hydrogen and oxygen to generate power. “The reaction runs both ways — it can be used either as a hydrogen production catalyst or as a fuel cell catalyst,” Douglas said.

    The form of hydrogenase is one of three occurring in nature: di-iron (FeFe)-, iron-only (Fe-only)- and nitrogen-iron (NiFe)-hydrogenase. The third form was selected for the new material due to its ability to easily integrate into biomaterials and tolerate exposure to oxygen.

    NiFe-hydrogenase also gains significantly greater resistance upon encapsulation to breakdown from chemicals in the environment, and it retains the ability to catalyze at room temperature. Unaltered NiFe-hydrogenase, by contrast, is highly susceptible to destruction from chemicals in the environment and breaks down at temperatures above room temperature — both of which make the unprotected enzyme a poor choice for use in manufacturing and commercial products such as cars.

    These sensitivities are “some of the key reasons enzymes haven’t previously lived up to their promise in technology,” Douglas said. Another is their difficulty to produce.

    “No one’s ever had a way to create a large enough amount of this hydrogenase despite its incredible potential for biofuel production. But now we’ve got a method to stabilize and produce high quantities of the material — and enormous increases in efficiency,” he said.

    The development is highly significant according to Seung-Wuk Lee, professor of bioengineering at the University of California-Berkeley, who was not a part of the study.

    “Douglas’ group has been leading protein- or virus-based nanomaterial development for the last two decades. This is a new pioneering work to produce green and clean fuels to tackle the real-world energy problem that we face today and make an immediate impact in our life in the near future,” said Lee, whose work has been cited in a U.S. Congressional report on the use of viruses in manufacturing.

    Beyond the new study, Douglas and his colleagues continue to craft P22-Hyd into an ideal ingredient for hydrogen power by investigating ways to activate a catalytic reaction with sunlight, as opposed to introducing elections using laboratory methods.

    “Incorporating this material into a solar-powered system is the next step,” Douglas said.

    This research was supported by the U.S. Department of Energy.

    See the full article here .

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  • richardmitnick 9:03 am on December 17, 2015 Permalink | Reply
    Tags: , , Biofuels,   

    From Sandia: “Sandia, ASU collaborate on algae computational modeling, look for algae pond predators” 

    Sandia Lab

    December 17, 2015
    Michael Padilla
    (925) 294-2447

    Sandia National Laboratories researcher Jerilyn Timlin serves as a principal investigator for the Algal Predator and Pathogen Signature Verification project. (Photo by Randy Montoya)

    Work part of a broader framework for funding energy-related science, technology

    Sandia National Laboratories and Arizona State University (ASU) have teamed up to further improve computational models of algae growth in raceway ponds that can predict performance, improve pond design and operation and discover ways to improve algae yield outdoors.

    Such ponds consist of an oval-shaped closed-loop channel — or raceway — in which the cultivation mixture of water and algae is propelled to flow around the raceway and undergo mixing by a paddlewheel powered by an electric motor.

    In addition, Sandia and ASU will further develop spectroradiometric techniques to optically monitor the growth and health of algae pond cultivation in real-time and detect early warnings of predators and pathogens in outdoor algal ponds.

    The work is part of a newly signed Cooperative Research and Development Agreement (CRADA) between ASU and Sandia to collaborate on algae-based biofuels, solar fuels, concentrating solar technologies, photovoltaics, electric grid modernization and the energy-water nexus. The umbrella CRADA also covers international applications of the technologies and science and engineering education. The topics were first identified in a 2013 memo of understanding between Sandia and ASU focusing on collaborations to support science, technology, engineering and mathematics, or STEM, fields.

    This is the first CRADA Sandia has executed with a university in nearly 15 years and is currently the only active umbrella CRADA with an institution of higher education. The algae cultivation modeling and monitoring projects are the first two efforts funded under this umbrella CRADA.

    Sandia researcher Ron Pate said Sandia brings distinctive capabilities for physics-based modeling of algae cultivation systems performance and for remote spectroradiometric monitoring and diagnostics of algae growth and state of health, while ASU has a variety of algae species under cultivation in outdoor ponds in a range of scales in which to take measurements.

    “Sandia is excited about the collaboration with ASU,” Pate said. “This agreement allows Sandia to continue modeling and monitoring work that we have been pursuing with ASU since 2013 under the original ATP3 (Algae Testbed Public-Private Partnership) project.” Pate serves as deputy director for ATP3, overseeing Sandia technical tasks under the project.

    The ATP3 project was established to support the algae research and development community and industry to advance the field and help accelerate progress toward more rapid and successful commercialization of algae-based technologies for fuels and products. ATP3 is funded by the DOE’s Energy Efficiency and Renewable Energy Bioenergy Technologies Office. ATP3 partners include Sandia, ASU, the National Renewable Energy Laboratory, California Polytechnic State University in San Luis Obispo, the Georgia Institute of Technology in Atlanta and the algae companies San Diego-based Cellana Inc. with algae cultivation facilities in Kona, Hawaii, Commercial Algae Management in Franklin, North Carolina and Florida Algae in Vero Beach, Florida.

    Two projects exercise new Sandia, ASU CRADA

    The first project under the agreement, Algal Cultivation Growth Dynamic Modeling and Analysis, focuses on the further development of a Sandia algae growth model based on the effect of light, temperature, nutrients, pH and salinity integrated into an open raceway pond hydrodynamic computational fluid dynamics model. The algae growth model has been partially validated utilizing multiple data sets from partners involved in ATP3. Under the CRADA, the modeling will be further refined through improvement of the paddlewheel driven pond circulation flow and mixing portion of the model based on the application of hydrodynamic measurement data taken from experimental testing with progressively larger scale outdoor ponds operated by ATP3 partners.

    The 12-month project, led by principal investigators Patricia Gharagozloo from Sandia and John McGowen from ASU, will be conducted in two phases. The first phase will study the flow dynamics of turbulence models and control parameters in open raceway ponds, which are currently the most promising outdoor cultivation system approach for cost-effectively growing algae at the large scales required for producing fuels. In this phase, ASU will measure the spatial variations in velocity of the flow of algae-water mix in the ponds at various paddlewheel speeds.

    The second phase will calibrate the model and verify the appropriate turbulence physics to be accounted for at certain scales of ponds for one paddlewheel speed. After the two phases, a study will be conducted to compare the data with model results at additional paddlewheel speeds.

    The second 12-month project, Algal Predator and Pathogen Signature Verification, looks at exploring and exploiting the various detailed optical signatures that arise when the algae cultivation pond surface is monitored using Sandia’s optical spectroradiometric techniques. These techniques can differentiate algae growth and state of health and provide an early warning of the active presence of predators and pathogens in outdoor algal ponds. Sandia researcher Jerilyn Timlin and McGowen are the principal investigators for this project. Sandia researcher Tom Reichardt, who pioneered the original technology as part of a bioscience Laboratory Directed Research & Development project, also serves as technical contributor to the project.

    During the first phase of this project, controlled experiments will be conducted in the laboratory with a host-pathogen-predator pair that the team has seen cause problems in the field in order to understand the parameters that control culture collapse and identify spectral markers that indicate the presence of the pathogen or predator. The second phase will consist of experiments in the field to determine how well the identified spectral markers predict the presence of the pathogen or predator in the challenges of an outdoor environment.

    “The continuation of the technical work related to algae biofuels, which began under the ATP3 project, is a great opportunity to exercise this new Sandia-ASU CRADA,” Pate said. “However, collaborative work on the other STEM topic areas could also be pursued in the future as funding becomes available and the mutual interest exists at ASU and Sandia.”

    See the full article here .

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  • richardmitnick 10:43 am on August 21, 2015 Permalink | Reply
    Tags: , Biofuels,   

    From EPFL: Using fungi to harvest microalgae for biofuels 

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    École Polytechnique Fédérale de Lausanne EPFL

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    Microalgae are a promising feedstock for biofuels, but current methods of harvesting and dewatering them are unsustainable. Now researchers have shown that growing the algae with certain filamentous fungi to form lichens can reduce both cost and the energy input.

    Biofuels produced using microalgae could play an important role in the transition from a fossil fuel-based to a sustainable economy. While researchers have optimized the transformation of microalgae into biogas, harvesting and drying the algae continue to consume too much energy, accounting for 20-30% of the cost of biofuel production. Now, scientists from EPFL and the Universities of the Western Cape and Stellenbosch in South Africa have come across a filamentous fungus that could cut the cost of biomass harvesting. They presented their findings in the journal Bioresource Technology in June.

    Burning biogas made from microalgae only releases as much carbon into the air as the algae absorb during their growth, making algal biogas a potential carbon neutral substitute for natural gas. Curiously, the bottleneck to making the technology competitive is not in the technologically challenging process of transforming the algae into biogas, a mixture of methane (CH4) and carbon dioxide (CO2). Researchers have solved this step using a highly efficient process called hydrothermal gasification as part of the SunCHem project . Instead, the bottleneck lies in the technologically much simpler step of harvesting the algae.

    Researchers Stephan Mackay and Eduardo Gomes may have serendipitously stumbled a potential solution to harvesting problem. When testing different types of microalgae, they noticed that in one of their samples, the algae lumped together into little pellets. Upon close investigation, they identified the culprit: a filamentous fungus, Isaria fumosorosea that had contaminated their samples. The pellets that they observed were in fact lichens, hybrid structures made up of algae and fungi. A few millimeters in diameter, the pellets are large enough to be harvested from the water with a simple filter, with much lower energy expenditure than conventional approaches such as drying and dewatering.

    According the Jean-Paul Schwitzguébel from EPFL’s Laboratory for Environmental Biotechnology and the principal investigator of the study, the next steps would be to assess the energy savings that could be made using the approach if it were to be scaled up.

    This work builds on the output of the SunCHem project, carried out by the Swiss Competence Center for Energy and Mobility (CCEM), in collaboration with EPFL, the Paul Scherrer Institut (PSI) and other partners.

    See the full article here.

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  • richardmitnick 2:18 pm on October 10, 2014 Permalink | Reply
    Tags: , , Biofuels,   

    From BNL: “Researchers Pump Up Oil Accumulation in Plant Leaves” 

    Brookhaven Lab

    October 7, 2014
    Karen McNulty Walsh, (631) 344-8350 or Peter Genzer, (631) 344-3174

    Increasing the oil content of plant biomass could help fulfill the nation’s increasing demand for renewable energy feedstocks. But many of the details of how plant leaves make and break down oils have remained a mystery. Now a series of detailed genetic studies conducted at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and published in The Plant Cell reveals previously unknown biochemical details about those metabolic pathways—including new ways to increase the accumulation of oil in leaves, an abundant source of biomass for fuel production.

    Using these methods, the scientists grew experimental Arabidopsis plants whose leaves accumulated 9 percent oil by dry weight, which represents an approximately 150-fold increase in oil content compared to wild type leaves.

    “This is an unusually high level of oil accumulation for plant vegetative tissue,” said Brookhaven Lab biochemist Changcheng Xu, who led the research team. “In crop plants, whose growth time is longer, if the rate of oil accumulation is the same we could get much higher oil content—possibly as high as 40 percent by weight,” he said.

    And when it comes to growing plants for biofuels, packing on the calories is the goal, because energy-dense oils give more “bang per bushel” than less-energy-dense leaf carbohydrates.
    Deciphering biochemical pathways

    The key to increasing oil accumulation in these studies was to unravel the details of the biochemical pathways involved in the conversion of carbon into fatty acids, the storage of fatty acids as oil, and the breakdown of oil in leaves. Prior to this research, scientists did not know that these processes were so intimately related.

    “Our method resulted in an unusually high level of oil accumulation in plant vegetative tissue.”
    — Brookhaven Lab biochemist Changcheng Xu

    “We previously thought that oil storage and oil degradation were alternative fates for newly synthesized fatty acids—the building blocks of oils,” said Brookhaven biochemist John Shanklin, a collaborator on the studies.

    To reveal the connections, Brookhaven’s Jillian Fan and other team members used a series of genetic tricks to systematically disable an alphabet soup of enzymes—molecules that mediate a cell’s chemical reactions—to see whether and how each had an effect in regulating the various biochemical conversions. They also used radiolabeled versions of fatty acids to trace their paths and learn how quickly they move through the pathway. They then used the findings to map out how the processes take place inside different subcellular structures, some of which you might recognize from high school science classes: the chloroplast, endoplasmic reticulum, storage droplets, and the peroxisome.

    Brookhaven researchers Jilian Fan, John Shanklin, and Changcheng Xu have developed a method for getting experimental plants to accumulate more leaf oil. Their strategy could have a significant impact on the production of biofuels.

    “Our goal was to test and understand all the components of the system to fully understand how fatty acids, which are produced in the chloroplasts, are broken down in the peroxisome,” Xu said.

    Key findings

    Details of the oil synthesis and breakdown pathways within plant leaf cells: Fatty acids (FA) synthesized within chloroplasts go through a series of reactions to be incorporated into lipids (TAG) within the endoplasmic reticulum (ER); lipid droplets (LD) store lipids such as oils until they are broken down to release fatty acids into the cytoplasm; the fatty acids are eventually transported into the peroxisome for oxidation. This detailed metabolic map pointed to a new way to dramatically increase the accumulation of oil in plant leaves — blocking the SDP1 enzyme that releases fatty acids from lipid droplets in plants with elevated fatty acid synthesis. If this strategy works in biofuel crops, it could dramatically increase the energy content of biomass used to make biofuels.

    The research revealed that there is no direct pathway for fatty acids to move from the chloroplasts to the peroxisome as had previously been assumed. Instead, many complex reactions occur within the endoplasmic reticulum to first convert the fatty acids through a series of intermediates into plant oils. These oils accumulate in storage droplets within the cytoplasm until another enzyme breaks them down to release the fatty acid building blocks. Yet another enzyme must transport the fatty acids into the peroxisome for the final stages of degradation via oxidation. The amount of oil that accumulates at any one time represents a balance between the pathways of synthesis and degradation.

    Some previous attempts to increase oil accumulation in leaves have focused on disrupting the breakdown of oils by blocking the action of the enzyme that transports fatty acids into the peroxisome. The reasoning was that the accumulation of fatty acids would have a negative feedback on oil droplet breakdown. High levels of fatty acids remaining in the cytoplasm would inhibit the further breakdown of oil droplets, resulting in higher oil accumulation.

    That idea works to some extent, Xu said, but the current research shows it has negative effects on the overall health of the plants. “Plants don’t grow as well and there can be other defects,” he said.

    Based on their new understanding of the detailed biochemical steps that lead to oil breakdown, Xu and his collaborators explored another approach—namely disabling the enzyme one step back in the metabolic process, the one that breaks down oil droplets to release fatty acids.

    “If we knock out this enzyme, known as SDP1, we get a large amount of oil accumulating in the leaves,” he said, “and without substantial detrimental effects on plant growth.”

    “This research points to a new and different way to accumulate oil in leaves from that being tried in other labs,” Xu said. “In addition, the strategy differs fundamentally from other strategies that are based on adding genes, whereas our strategy is based on disabling or inactivating genes through simple mutations. This work provides a very promising platform for engineering oil production in a non-genetically modified way.”

    “This work provides another example of how research into basic biochemical mechanisms can lead to knowledge that has great promise to help solve real world problems,” concluded Shanklin.

    This research was conducted by Xu in collaboration with Jilian Fan and Chengshi Yan and John Shanklin of Brookhaven’s Biosciences Department, and Rebecca Roston, now at the University of Nebraska, Lincoln. The work was funded by the DOE Office of Science and made use of a confocal microscope at Brookhaven Lab’s Center for Functional Nanomaterials, a DOE Office of Science user facility.

    See the full article here.

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  • richardmitnick 1:41 pm on August 29, 2014 Permalink | Reply
    Tags: , , Biofuels, ,   

    From LBL: “Going to Extremes for Enzymes” 

    Berkeley Logo

    Berkeley Lab

    August 29, 2014
    Lynn Yarris (510) 486-5375

    In the age-old nature versus nurture debate, Douglas Clark, a faculty scientist with Berkeley Lab and the University of California (UC) Berkeley, is not taking sides. In the search for enzymes that can break lignocellulose down into biofuel sugars under the extreme conditions of a refinery, he has prospected for extremophilic microbes and engineered his own cellulases.

    Extremophiles thriving in thermal springs where the water temperature can be close to boiling can be a rich source of enzymes for the deconstruction of lignocellulose.

    Speaking at the national meeting of the American Chemical Society (ACS) in San Francisco, Clark discussed research for the Energy Biosciences Institute (EBI) in which he and his collaborators are investigating ways to release plant sugars from lignin for the production of liquid transportation fuels. Sugars can be fermented into fuels once the woody matter comprised of cellulose, hemicellulose, and lignin is broken down, but lignocellulose is naturally recalcitrant.

    “Lignocellulose is designed by nature to stand tall and resist being broken down, and lignin in particular acts like a molecular glue to help hold it together” said Clark, who holds appointments with Berkeley Lab’s Physical Biosciences Division and UC Berkeley’s Chemical and Biomolecular Engineering Department where he currently serves as dean of the College of Chemistry. “Consequently, lignocellulosic biomass must undergo either chemical or enzymatic deconstruction to release the sugars that can be fermented to biofuels.”

    Douglas Clark holds joint appointments with Berkeley Lab and UC Berkeley and is a principal investigator with the Energy Biosciences Institute. (Photo by Roy Kaltschmidt)

    For various chemical reasons, all of which add up to cost-competitiveness, biorefineries could benefit if the production of biofuels from lignocellulosic biomass is carried out at temperatures between 65 and 70 degrees Celsius. The search by Clark and his EBI colleagues for cellulases that can tolerate these and even harsher conditions led them to thermal springs near Gerlach, Nevada, where the water temperature can be close to boiling. There they discovered a consortium of three hyperthermophilic Archaea that could grow on crystalline cellulose at 90 degrees Celsius.

    “This consortium represents the first instance of Archaea able to deconstruct lignocellulose optimally above 90°C,” Clark said.

    Following metagenomic studies on the consortium, the most active high-temperature cellulase was identified and named EBI-244.

    “The EBI-244 cellulase is active at temperatures as high as 108 degrees Celsius, the most extremely heat-tolerant enzyme ever found in any cellulose-digesting microbe,” Clark said.

    The most recent expedition of Clark and his colleagues was to thermal hot springs in Lassen Volcanic National Park, where they found an enzyme active on cellulose up to 100°C under highly acidic conditions – pH approximately 2.2.

    “The Lassen enzyme is the most acidothermophilic cellulase yet discovered,” Clark said. “The final products that it forms are similar to those produced by EBI244.”

    A consortium of three hyperthermophilic Archaea that could grow on crystalline cellulose at 90 degrees Celsius yielded EBI-244, the most active high-temperature cellulase ever identified.

    In addition to bioprospecting for heat tolerant enzymes, Clark and his colleagues have developed a simple and effective mutagenesis method to enhance the properties of natural enzymes. Most recently they used this technique to increase the optimal temperature and enhance the thermostability of Ce17A, a fungal cellulase that is present in high concentrations in commercial cellulase cocktails. They engineered yeast to produce this enzyme with encouraging results.

    “The yeast Saccharomyces cerevisiae has often been used both in the engineering and basic study of Cel7A; however, Cel7A enzymes recombinantly expressed in yeast are often less active and less stable than their native counterparts,” Clark said. “We discovered that an important post-translational modification that was sometimes absent in the yeast-expressed enzyme was the underlying cause of this disparity and successfully carried out the post-translational modification in vitro. After this treatment, the properties of Cel7A recombinantly expressed in yeast were improved to match those of the native enzyme.”

    Collaborators in this research include Harvey Blanch, who also holds joint appointments with Berkeley Lab and UC Berkeley, and Frank Robb from the University of Maryland.

    EBI, which provided the funding for this research, is a collaborative partnership between BP, the funding agency, UC Berkeley, Berkeley Lab and the University of Illinois at Urbana-Champaign.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 4:44 pm on August 18, 2014 Permalink | Reply
    Tags: , Biofuels,   

    From Berkeley Lab: “Bionic Liquids from Lignin” 

    Berkeley Logo

    Berkeley Lab

    August 18, 2014
    Lynn Yarris (510) 486-5375

    While the powerful solvents known as ionic liquids show great promise for liberating fermentable sugars from lignocellulose and improving the economics of advanced biofuels, an even more promising candidate is on the horizon – bionic liquids.

    Researchers at the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI) have developed “bionic liquids” from lignin and hemicellulose, two by-products of biofuel production from biorefineries. JBEI is a multi-institutional partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab) that was established by the DOE Office of Science to accelerate the development of advanced, next-generation biofuels.

    “What if we could turn what is now a bane to the bioenergy industry into a boon?” says Blake Simmons, a chemical engineer who is JBEI’s Chief Science and Technology Officer and heads JBEI’s Deconstruction Division. “Lignin is viewed as a waste stream that is typically burned to generate heat and electricity for the biorefinery, but if other uses for lignin could be found with higher economic value it would significantly improve the refinery’s overall economics. Our concept of bionic liquids opens the door to realizing a closed-loop process for future lignocellulosic biorefineries, and has far-reaching economic impacts for other ionic liquid-based process technologies that currently use ionic liquids synthesized from petroleum sources.”

    Simmons and Seema Singh, who directs JBEI’s biomass pretreatment program, are the corresponding authors of a paper describing this research in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose. The lead author is Aaron Socha. Other co-authors are Ramakrishnan Parthasarathi, Jian Shi, Sivakumar Pattathil, Dorian Whyte, Maxime Bergeron, Anthe George, Kim Tran, Vitalie Stavila, Sivasankari Venkatachalam and Michael Hahn.

    Blake Simmons and Seema Singh of the Joint BioEnergy Institute (JBEI) are leading an effort to improve the economics of biofuel production through improved deconstruction of lignocellulosic biomass.

    The cellulosic sugars stored in the biomass of grasses and other non-food crops, and in agricultural waste, can be used to make advanced biofuels that could substantially reduce the use of the fossil fuels responsible for the release of nearly 9 billion metric tons of excess carbon into the atmosphere each year. More than a billion tons of biomass are produced annually in the United States alone and fuels from this biomass could be clean, green and renewable substitutes for gasoline, diesel and jet fuel on a gallon-for-gallon basis. Unlike ethanol, “drop-in” transportation fuels derived from biomass have the potential to be directly dropped into today’s engines and infrastructures at high levels – greater than 50-percent – without negatively impacting performance.

    However, if biofuels, including cellulosic ethanol, are to be a commercial success, they must be cost-competitive with fossil fuels. This means economic technologies must be developed for extracting fermentable sugars from cellulosic biomass and synthesizing them into fuels and other valuable chemical products. A major challenge has been that unlike the simple sugars in corn grain, the complex polysaccharides in biomass are deeply embedded within a tough woody material called lignin. Researchers at JBEI have been cost-effectively deconstructing biomass into fuel sugars by pre-treating the biomass with ionic liquids – salts that are composed entirely of paired ions and are liquid at room temperature. The ionic liquids that have emerged from this JBEI effort as a benchmark for biomass processing are imidazolium-based molten salts, which are made from nonrenewable sources such as petroleum or natural gas.

    “Imidazolium-based ionic liquids effectively and efficiently dissolve biomass, and represent a remarkable platform for biomass pretreatment, but imidazolium cations are expensive and thus limited in their large-scale industrial deployment,” says Singh. “To replace them with a renewable product, we synthesized a series of tertiary amine-based ionic liquids from aromatic aldehydes in lignin and hemicellulose.”

    Aaron Socha directs the Center for Sustainable Energy at the Bronx Community College in NYC.

    The JBEI researchers tested the effectiveness of their bionic liquids as a pre-treatment for biomass deconstruction on switchgrass, one of the leading potential crops for making liquid transportation fuels. After 73 hours of incubation with these new bionic liquids, sugar yields were between 90- and 95-percent for glucose, and between 70- and 75-percent for xylose. These yields are comparable to the yields obtained after pre-treatment with the best-performing imidazolium-based ionic liquids.

    “Lignin and hemicellulose are byproducts from the agricultural industry, biofuel plants and pulp mills, which not only makes these abundant polymers inexpensive, but also allows for a closed-loop bio-refinery, in which the lignin in the waste stream can be up-cycled and reused to make more bionic liquid,” says lead author Socha, who is now the Director of the Center for Sustainable Energy at the Bronx Community College in New York City.

    The current batch of bionic liquids was made using reductive amination and phosphoric acid, but Socha says the research team is now investigating the use of alternative reducing agents and acids that would be less expensive and even more environmentally benign.

    “Our results have established an important foundation for the further study of bionic liquids in biofuels as well as other industrial applications,” he says.

    This research was supported by the DOE Office of Science.

    See the full article here.

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  • richardmitnick 12:05 pm on July 28, 2014 Permalink | Reply
    Tags: , , Bioenergy, Biofuels, ,   

    From Berkeley Lab: “How Sweet It Is: New Tool for Characterizing Plant Sugar Transporters Developed at Joint BioEnergy Institute” 

    Berkeley Lab

    July 28, 2014
    Lynn Yarris

    A powerful new tool that can help advance the genetic engineering of “fuel” crops for clean, green and renewable bioenergy, has been developed by researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), a multi-institutional partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab). The JBEI researchers have developed an assay that enables scientists to identify and characterize the function of nucleotide sugar transporters, critical components in the biosynthesis of plant cell walls.

    The Joint BioEnergy Institute (JBEI) is one of three Bioenergy Research Centers established by DOE’s Office of Science to accelerate the development of advanced, next-generation biofuels. (Photo by Roy Kaltschmidt)

    A family of six nucleotide sugar transporters never before described have been characterized in Arabidopsis, a model plant for research in advanced biofuels. (Photo by Roy Kaltschmidt)

    “Our unique assay enabled us to analyze nucleotide sugar transporter activities in Arabidopsis and characterize a family of six nucleotide sugar transporters that has never before been described,” says Henrik Scheller, the leader of JBEI’s Feedstocks Division and a leading authority on cell wall biosynthesis. “Our method should enable rapid progress to be made in determining the functional role of nucleotide sugar transporters in plants and other organisms, which is very important for the metabolic engineering of cell walls.”

    Scheller is the corresponding author, along with Ariel Orellana at the Universidad Andrés Bello, Santiago, Chile, of a paper describing this research in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis. The lead authors are Carsten Rautengarten and Berit Ebert, both of whom hold appointments with JBEI, and both of whom, like Scheller, also hold appointments with Berkeley Lab’s Physical Biosciences Division. (See below for the full list of co-authors.)

    The sugars in plant biomass represent an enormous potential source of environmentally benign energy if they can be converted into transportation fuels – gasoline, diesel and jet fuel – in a manner that is economically competitive with petroleum-based fuels. One of the keys to success in this effort will be to engineer fuel crops whose cells walls have been optimized for sugar content.

    With the exception of cellulose and callose, the complex polysaccharide sugars in plant cell walls are synthesized in the Golgi apparatus by enzymes called glycosyltransferases. These polysaccharides are assembled from substrates of simple nucleotide sugars which are transported into the Golgi apparatus from the cytosol, the gel-like liquid that fills a plant cell’s cytoplasm. Despite their importance, few plant nucleotide sugar transporters have been functionally characterized at the molecular level. A big part of the holdup has been a lack of substrates that are necessary to carry out such characterizations.

    “Substrates of mammalian nucleotide sugar transporters are commercially available because of the medical interest but have not been available for plants, which made it difficult to study both nucleotide sugar transporters and glycosyltransferases,” Scheller says.

    For their assay, Scheller, Rautengarten, Ebert and their collaborators, created several artificial substrates for nucleotide sugar transporters, then reconstituted the transporters into liposomes for analysis with mass spectrometry. The researchers used this technique to characterize the functions of the six new nucleotide sugar transporters they identified in Arabidopsis, a relative of mustard that serves as a model plant for research in advanced biofuels.

    “We found that these six new nucleotide sugar transporters are bispecific, which is a surprise since the two substrates are not very similar from a physical standpoint to the human eye,” Scheller says. “We also found that limiting substrate availability has different effects on different polysaccharide products, which suggests that cell wall polysaccharide biosynthesis in the Golgi apparatus of plants is also regulated by substrate transport mechanisms.”

    In addition to these six nucleotide sugar transporters, the assay was used to characterize the functions of 20 other transporters, the details of which will soon be published.

    “Thanks largely to the efforts these past two years of Carsten Rautengarten and Berit Ebert, we now know the activity of three times more nucleotide sugar transporters than are known in humans, and we have determined the function of two-thirds of the plant transporters as compared to one-quarter of the human ones,” Scheller says. “This is a tremendous accomplishment and we are already using this information at JBEI to improve biomass sugar composition for biofuel production.”

    Other co-authors of the PNAS paper reporting this research were Ignacio Moreno, Henry Temple, Thomas Herter, Bruce Link, Daniela Doñas-Cofré, Adrián Moreno, Susana Saéz-Aguayo, Francisca Blanco, Jennifer Mortimer, Alex Schultink, Wolf-Dieter Reiter, Paul Dupre, Markus Pauly and Joshua Heazlewood.

    (From left) Berit Ebert, Carsten Rautengarten and Henrik Scheller at JBEI have developed an assay for characterizing the functions of nucleotide sugar transporters in plant cell walls. (Photo by Irina Silva, JBEI)

    This research was supported by the DOE Office of Science.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 11:36 am on April 8, 2013 Permalink | Reply
    Tags: , , Biofuels,   

    From Berkeley Lab: “Sweet Success” 

    Berkeley Lab

    Berkeley Lab Researchers Find Way to Catalyze More Sugars from Biomass

    April 07, 2013
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    Catalysis may initiate almost all modern industrial manufacturing processes, but catalytic activity on solid surfaces is poorly understood. This is especially true for the cellulase enzymes used to release fermentable sugars from cellulosic biomass for the production of advanced biofuels. Now, researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) through support from the Energy Biosciences Institute (EBI) have literally shed new light on cellulase catalysis.

    PALM – for Photo-Activated Localization Microscopy – enables researchers to quantify how and where enzymes are binding to the surface of cellulose in heterogeneous surfaces, such as those in plant cell walls.

    Using an ultrahigh-precision visible light microscopy technique called PALM – for Photo-Activated Localization Microscopy – the researchers have found a way to improve the collective catalytic activity of enzyme cocktails that can boost the yields of sugars for making fuels. Increasing the sugar yields from cellulosic biomass to help bring down biofuel production costs is essential for the widespread commercial adoption of these fuels.

    From left, Jan Liphardt, Harvey Blanch and Doug Clark led the development of a way to improve the collective catalytic activity of enzyme cocktails that can boost the yields of sugars for making advanced biofuels. (Photo by Roy Kaltschmidt)

    ‘The enzymatic breakdown of cellulosic biomass into fermentable sugars has been the Achilles heel of biofuels, a key economic bottleneck,’ says chemical engineer Harvey Blanch, one of the leaders of this research. ‘Our research provides a new understanding of how multiple cellulase enzymes attack solid cellulose by working in concert, an action known as enzyme synergy, and explains why certain mixtures of cellulase enzymes work better together than each works individually.’”

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California


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