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!"#$%&'%())*+%, THIS SPECIAL ISSUE OF THE EBINSIDER IS DEVOTED TO THE HISTORIC FIRST INCLUSIVE -*#.%/001 RETREAT OF THE ENERGY BIOSCIENCES INSTITUTE, HELD AT THE IHOTEL AND HOSTED BY THE UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN JUNE 19 - 22. IN WORDS AND IMAGES, THIS EDITION IS DESIGNED TO CONVEY THE EXCITEMENT AND TEAM-

!"#$#%&'()*+, BUILDING SPIRIT THAT WAS FELT BY THOSE WHO ATTENDED.

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EBI SCIENTISTS, STUDENTS, STAFF USE RETREAT TO RECALIBRATE EFFORTS AND COMPARE NOTES NEW RESEARCH They came from across the country conference center in Urbana. And the PREPROPOSALS and across the campus—agronomists event was the first inclusive retreat DUE AUGUST 10 and biochemists, physiologists since the EBI was established in late and chemical engineers, economists 2007. The Energy Biosciences Institute has and climatologists, professors and issued a call for new research proposals students—to engage in a weekend of The host of this historic gathering, in the areas of 1) novel aspects of energy around-the-clock conversations about Illinois professor and EBI Deputy biosciences, and 2) development of where they are and where they go Director Steve Long, outlined the lignocellulosic . Funding of up to from here. purpose of the program at the opening $7.5 million is available for the period of session on June 20: “…to figure out 2010–2013, and three-page preproposals are due from faculty no later than August “They” were the members of a how we work together as a team, 10. To be eligible, faculty must have potentially world-changing research to find the opportunities where one- primary appointments at one of the partnership called the Energy plus-one is more than two, and to see partner EBI institutions. Biosciences Institute. The location where we can find synergy in place of was the University of Illinois’ IHotel duplication. This (retreat) will help us Faculty submitting preproposals !"#$%&$'()*#$*+,-*./0 considered a good fit for the EBI’s goals will be invited to submit a more detailed proposal, including a proposed budget INSIDE THE INSIDER and timelines. A confidential peer-review process will identify successful proposals for funding consideration by the EBI Executive Committee.

Preproposals should be submitted online at www.ebiweb.org/cgi-bin/admin/logon. 2 5 8 cfm. More information about the scope, format, timelines, procedures, and related Feedstocks 2 Chemistry 6 matters can be found on the EBI public web site (www.energybiosciencesinstitute. Depolymerization 3 MEHR 6 org) under “Funding Opportunities.” Questions should be addressed to EBI Ecosystem Services 4 Bioconversion 10 Assistant Director Susan Jenkins at [email protected]. The View from BP 5 Socioeconomics 11

. FEEDSTOCKS: MINIMUM INPUT, MAXIMUM YIELD PLANT DEPOLYMERIZATION: 57#87 :$;!#7#$256< BREAKING DOWN WHAT NATURE HAS EVOLVED yield—how much can be produced per varying conditions. Comparative trials hectare of land,” he said. “The biofuels are set up throughout the U.S. 57#87 :$B/0&#$./!# we seek don’t need large nutritional said, he “hit the wall.” He lacked rate-limiting. And to achieve efficient The agriculture specialists from Illinois or energy inputs.” Long said the ideal the genetic tools to manipulate the depolymerization, we need a lot of crop will also have a high energy are focusing on four aspects of biofuel genome, and the interplay of enzymes. So how can we increase conversion efficiency; for example, the in the EBI program: feedstock in the hydrolysis was more complex the quantity by at least an order of highly regarded perennial production and agronomy, engineering than he imagined. magnitude?” grass has a solar conversion rate of solutions for production, 70 percent, which is 60 percent more pests and pathogens, and feedstock Now, in a collaboration with EBI He said the depolymerization investigator Louise Glass and team is “casting a wide net.” One productive than corn. genomics. colleagues, he and his team are group, led by DOE Joint Genome 8%(9(*C#$, Miscanthus giganteus, a sterile , As a relatively new crop, Miscanthus focusing on Neurospora crassa, a Institute (JGI) Director Eddy Rubin model fungus that breaks down in collaboration with University of EBI Deputy Director Steve Long has other advantages, according hasn’t developed large populations of DA5&(*>A%( woody fiber, and the way its enzymes, Illinois microbiologists Rod Mackie and outlined the criteria that new to Long: a root system that binds pests and pathogens yet. However, as the acreage increases, such problems transporters, and regulators function. Isaac Cann, is studying cow rumen biofuel feedstocks had to meet: no the soil and prevents erosion while If anyone knows how difficult it will The excellent genetic resources microbes. Cann is also investigating will arise, so understanding them at displacement of food crops, no major providing to the plant, high be to rapidly depolymerize cellulose available in Neurospora have allowed thermophylic organisms that produce water requirements, and a reduction in productivity in temperate climates, and this stage will to preventative care and lignin into fermentable sugars, the researchers to undertake a . UC Berkeley’s Doug Clark and net greenhouse gas (GHG) emissions. via carbon sequestration. and possible resistant strains. Viruses, it’s Jamie Cate. The UC Berkeley systematic analysis of what each gene Harvey Blanch are leading the efforts Researchers are modeling Miscanthus bacteria, nematodes, and insects biochemist spent the first year of contributes to biomass degradation. to improve enzymes by building a “One of the most important for solar radiation, water content, are all possible candidates being his EBI program trying to study model system of how they work. And the function of cellulosomes, an characteristics for feedstocks is and soil depth to predict yields under investigated. “Any given organism secretes dozens other groups are probing the physical, assembled group of enzymes that of proteins to break down plant biological, and chemical basis for appear to be key to the genetic cell walls,” Cate said. “We don’t cellulase activity. =/6#2:$;!#7#$055;#$/64$3>.>$!&6<1$?6&7#8;&!-$5@$&22&65&;A$ breakdown. But when it came to understand many of them. To try to manipulating those proteins, he manipulate a given organism can be ;"#&2/$0..580&.31$?.$%#83#2#-

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“We are developing system &;//.$./661$?6&7#8;&!-$5@$&22&65&;$ informatics and decision support throughput sequencing program, Rubin systems to see how all of these things noted. “The challenge now is analysis affect the future efficiencies,” Ting of the data. It takes huge amounts said. “We set up scenarios to identify of data-intensive computing to pull missing links and help managers out the genes we are interested in. determine the best supply and value Eventually we can begin to assemble chain.” whole microbial genomes.”

!34#5*6(7%0*8%(9(*:##;(<*=-*>-*?&$,<*8@(&6A*:">#45&"B A plant reproduction specialist, And he added, “Nature has evolved McCormick said she is tending to through the millennia the ability to Moose, who the feedstock genome “reads,” with genetic markers 150 plants break down biomass, so we are genomics program, is looking at the in the thousands. That’s still only about in an Albany, CA, greenhouse and just scratching the surface. We need to move from genomic data to genes that underlie interesting traits. 2 percent of the entire Miscanthus studying their pollination and self- enzymological data.” Through , the good traits genome, but he hopes to complete a incompatibility. Since the pollen is very !34#5*6(7%0*:&"@(66(*>@A$,<*E))F*G'H&$<*I;AA"*>A$$ might be enhanced, the bad ones draft of it over the next year. short-lived, only a few of the plants are Chang explained the challenges of Rubin said his JGI team is developing Cann’s discovery group is eliminated. But it’s a challenge. He’s usable for study on any one day. decomposing lignin, the complex a large catalogue of full-length seeking effective cellulases and Ting is studying the biomass cycle spent much of his career studying the binding compound in plant cells that lignocellulolytic genes. “We are hemicellulases. “Our strategy is to genetic characteristics of corn, but from crop to refinery, looking for Through genetic mapping and can constitute up to 30 percent of the looking at microbes that participate use isolated organisms and make Miscanthus giganteus has a genome improvements in efficiency along the comparisons with the maps of cellulosic biomass. She is studying in the deconstruction of energy a set of enzymes that break down the size of three corn genomes. way. They could come in crop health ryegrass and , she said, she hopes the relationship between the lignin feedstocks and finding the genes cellulose, and another set that break and growth, harvesting, transportation, to find the key to overcoming self- structure and the multi-enzyme relevant to the process,” he said. down ,” he said. “So So far, thanks to new sequencing or storage. He uses state-of-the-art incompatibility in order to enhance breakdown pathways, looking at both Much of that data comes from it’s an enzyme mix for hydrolysis technology, he and his team have monitoring tools that include a rotating plant fertility and rise above the fungal and bacterial systems. the rumen of cows that are fed to monosaccharides.” Early results captured about 63,000 genes or tower camera and a mini-helicopter reproductive barriers that Miscanthus switchgrass. are proving the principle with small “We don’t understand the chemistry amounts of substrate by increasing the fragments, about 12,000 of those with remote sensing equipment. By and other feedstocks might face. yet,” she said, “but when we do, we “We’ve done 18 billion base pairs release of xylose and arabinose, two of long enough to use in experiments. the end of this year, a 40-by-60-foot can look at it in terms of chemical of switchgrass-associated rumen the fermentable sugars in cellulose. Computers have produced 73 million feedstock storage research facility will reactions and breakdowns.” microbes” within the JGI’s high-

1 2 ECOSYSTEM SERVICES: SEEKING SUSTAINABILITY, ENVIRONMENTAL INTEGRITY 57#87 :$#7/6$4#2?.&/ ecosystems, we can measure the and sensors rapidly capture the carbon intake and release of these elements going in and out of a planted zone. A in the plants, in the soil, and in the tile drainage system has been installed atmosphere.” In doing so, they hope under the plots, which, he explained, to find a feedstock that adds nitrogen directs the leached runoff into wells and carbon to soil fertility, balances for automated sampling and chemical carbon uptake and outgo, and minimizes analysis. Towers equipped with sonic greenhouse gases and water use. anemometers, infrared gas analyzers, laser-based nitrogen flux probes, and soil Those measurements will largely be respiration monitors are all technologies E9A$*O(C'"&A made on the EBI Energy Farm in Illinois. crucial to the search for a “green” “There are no major studies yet on biofuel feedstock. How will the deployment of biofuel adjacent plots of systems,” DeLucia feedstocks on the landscape affect said. “But in our experimental plots, His colleagues are also looking at land, water, and air? That’s what we will be studying corn, Miscanthus, the non-plant biology of the system. THE VIEW FROM BP: Illinois environmental scientist Evan switchgrass, and restored prairie side-by- Microbial ecologist Angela Kent is DeLucia and his EBI colleagues in the side.” focusing on nitrogen-fixing bacteria. PROMISING FUTURE FOR EBI, BIOFUELS Environmental Impact and Sustainability Others are studying microbes and group are trying to predict. The instrumentation in those fields is arthropods. Some 14,000 insects have Eyton presented his vision of BP’s the strategy, policy and technology extensive and sophisticated. DeLucia been collected in three different types of energy portfolio, indicating the division, was the final evening’s dinner “We want to close the biochemical described one system called “eddy traps and are being identified, possibly company is “quite bearish in the speaker and offered a PowerPoint cycles for carbon, nitrogen, and water,” covariance,” in which air moves over enriching the biodiversity in new biofuel short term, given the fluctuation in oil “tour” of the company’s biofuel he told his EBI colleagues. “By studying a surface in giant ovals, up and down, feedstocks. prices.” His prediction: “The world is business units. looking to, and believing in, a more =/6#2:$./82$%#86/.."&1$?6&7#8;&!-$5@$&22&65&;A$6580$0&22#81$?.$%#83#2#-$ renewable and “Biofuels is actually a great business above and beyond fossil fuels. But to be working in, because so much /64$%#83#2#-$2/%A$/8=/4$"587/!"1$?.$%#83#2#- (fossil fuels) will continue to comprise in energy companies is not high- growth these days,” Dobson said. Horvath, environmental engineering a large portion of the energy industry.” “Technology is absolutely essential to colleague Tom McKone, and a team He said he expected to see significant this industry.” of 17 are studying the entire life cycle progress on of a biofuel and are working to provide OA9&)*EF%#$ technologies by 2030, but that BP BP’s biofuel plan between now and models and realistic numbers for each David Eyton, BP’s Vice President for is more interested in what happens 2020, he said, calls for producing new stage of development and use. “We Research and Technology, was one between now and then—will there fuels equivalent in energy to 4½ giant will rely on the entire EBI for good of the more interested attendees at be more in the oil fields. Through both corporate numbers, in production, conversion the EBI retreat, not just because he’s atmosphere? And what does that and academic partnerships, he said, and processing, storage, transport, the new chairman of the Institute’s mean for the energy future of the the company is hoping to produce 70 !34#5*6(7%0*>A46*K(4$A""@&<*L#45*:&66(4<*M4+A)*N#49A%@ distribution, and combustion and use,” governance board, but also because planet? billion gallons of biofuel by the end of he said. “All of these will result in human his energy company likes to see profit the next decade. Plant biologist Bernacchi explained conduct geospatial analysis, health and ecosystem impacts.” from its investments. The EBI happens “We are focusing on places that we how he is trying to extend the plot- crop modeling, and agro-economic believe will have government support, According to Dobson, several hurdles The challenge comes in what he termed to be one of its largest, at $500 million. sized investigations at the Energy Farm analysis around the globe. One of the on where we are most confident we have to be overcome for the endeavor the “uncertainty” of the data and into a regional modeling of potential first tasks is looking at marginal lands, And he likes what he sees. can make things work,” Eyton said. “In to be successful—including the “scalability issues.” The overarching environmental impacts of feedstock which are prospective targets for order of potential, we are investing in “blend wall” limits of current auto metric is money—the total cost of production. Those models use inputs growing Miscanthus and switchgrass. “This is a very grand scale of biofuels, carbon management, solar, engines, the underinvestment by ecosystem services and environmental from the atmosphere, land surface, In coordination with a United Nations enterprise,” he told the conferees on and wind. BP is taking equity interest other members of the global energy impacts. Metrics will be developed for natural vegetation, and below-ground group studying bioenergy and earth the first day of meetings, “and I have in (biofuel) companies, (but) we are market, the emerging issues related to human health, natural environments, carbon and nitrogen. sustainability, he said, they are exploring no doubt whatsoever that (the EBI) will more comfortable with more open environmental impacts and land use, natural resources, man-made new and better modeling techniques make a large impact on the world. You collaborations and believe in their and the tariff walls being imposed by environments, and life-support systems. “We will incorporate our measurements by assimilating the elements of existing cannot underestimate the importance ability to make a difference in the some countries. Access to affordable in Illinois and scale them up to the systems. of a broad holistic understanding of world—like the EBI.” feedstock will be key, he added. region, shifting them throughout an “We are also tasked with tracking the impact of biofuels on society. emissions, from source to impact, how annual time cycle,” he said. “The Energy “EBI is now evaluating the models,” Politicians and the public need to know Eyton added that the EBI is a new “Regulatory support is solid, and they bioaccumulate, uptakes and doses,” Farm will give us a more reliable data Miller said. “There are 43 parameters what is and is not fact-based.” model for BP, and “we have to learn by the market is going to be big,” he he said. “In protecting these services, set. Then we can incorporate fluxes that potentially vary by vegetation type. doing as things arise, and try them out concluded. “Technology is advancing we have to worry about biodiversity, at other sites throughout the United We need to develop decision support He added a hearty “well-done to for real. We are very excited about this quite apace. Renewable fuels should air cleaning, water retention, erosion States.” tools to help identify prioritized land everyone for coming out of the block journey.” be competitive with fossil alternatives based on crop value, pasture value, and control, and carbon sequestration. so quickly. We are very proud of what by 2020. (Biofuel) has a healthy, long- Climatologist Miller is also using optimization of soils.” Agriculture systems should be optimized has been achieved here.” Ian Dobson, Eyton’s BP colleague in term future.” models—five of them, in fact—to by using this life cycle analysis.”

/ J MEHR: ENLISTING MICROBES IN EFFORTS TO ACCESS ‘LOST’ ENERGY 57#87 :$!#88-$"/C#6 MEHR program principal investigator amount of sulfur compounds such Terry Hazen, senior earth scientist as H2S) and reduce the viscosity, or at Lawrence Berkeley National convert it to methane and then push Laboratory, said his team’s objective it out of the formation. If we could is “to understand the microbial improve the oil recovery by just 5 A VISIT TO THE FARM community and function” in the deep percent, it would mean a tremendous !"#$%&'(&)*#+,- subsurface wells that yield petroleum. amount of oil.” He noted that nearly 65 percent of the oil discovered in reservoirs They have already begun field testing throughout the world is inaccessible at a Decatur, IL, injection well on and unrecoverable. Those untapped the Archer Daniels Midland ethanol ?(44F*NAR($ reserves are the target for MEHR. plant site. The well was drilled for The mission of the newest EBI carbon storage and capture tests, and program, Microbially Enhanced “Sometimes it works, sometimes it Illinois geologist Bruce Fouke and his Hydrocarbon Recovery (MEHR), might doesn’t, and we don’t know why,” team are getting ready to study the at first glance seem to run counter to he said of the use of microbes to underground geobiology networks. EBI’s primary search for alternatives extract the difficult deposits. “The Members of the Berkeley contingent at to fossil fuels. But BP Technology Vice variables are the science we have to the retreat took a June 22 field trip to President and EBI Associate Director pursue.” The core study areas include the site. Paul Willems doesn’t see it that way. reservoir geology and geochemistry, ecogenomics, and flow rate and Hazen said that the expected “We won’t be turning carbon off mechanisms. outcomes of the program include the completely,” he told the retreat identification of pertinent novel model attendees about the world’s future “We hope to identify pertinent species, the quantitative understanding energy needs. “But we need to get novel model species and gain of the deep subsurface environment, energy from carbon-friendly sources. an understanding of in situ and the development of predictive In the transition (from fossil to biorefinement,” Hazen said. “We will models for use by the oil industry. biofuels), we need a low-energy way try to find bacteria we could stimulate of recovering oil.” to ‘sweeten’ the oil (i.e., reduce the BIOFUEL CHEMISTRY: BIOLOGY’S INVALUABLE PARTNER 57#87 :$/2#D$%#22 UC Berkeley chemical engineer requirements for a biofuel. Alex Bell discussed one of those approaches: the potential use of ionic “It is too early to assess the ultimate !?#+0*X4&,&$A6*:&;"A$%@';*;&%(*(;%AH6&;@()*&$*1YY1Z*!K(6#U0*T$5A$$()*M(4&A6*[(@&"6(*!TM[0*5#$&%#4;*"4#+;*74#5*%@(*A&4 liquids (IL) to dissolve cellulose. He viability of the approach and its explained that the advantage of ILs— cost,” he noted of the non-enzyme Those attending the research retreat salts containing organic cations—is depolymerization technique. But early who had not yet been to the EBI that at or near room temperature, they research results indicate the option Energy Farm piled into buses on a can dissolve virtually all components of is certainly worth pursuing, either as spring afternoon in central Illinois biomass. a stand-alone chemical process or in to get up close and personal with conjunction with biological methods. Miscanthus, switchgrass, prairie grasses, and . Approximately M6(S*K(66 “Cellulose is a crystalline solid held together by strongly interacting 100 different species and varieties While the EBI mission is to explore hydroxyl groups,” he explained. “Ionic of feedstocks are being grown and “the application of advanced liquids break up these interactions. monitored in the 280-acre outdoor knowledge of biological processes, Once the cellulose is dissolved, it can laboratory, Feedstock Production/ materials and mechanisms to the be hydrolyzed with the aid of an acid Agronomy Program leader Tom Voigt energy sector,” the Institute’s catalyst to produce glucose.” The of the University of Illinois told the leadership has not forgotten glucose produced can be converted to visitors. chemistry’s role. The EBI has also a variety of products by combinations funded non-biological approaches to of acid and metal catalysts. Bell and his The Energy Farm will eventually deconstructing biomass and converting team are exploring how this approach become a one-half-square-mile living the products into biofuel alternatives. can be used to produce fuel molecules M6(S*K(66*!4&,@%0*A$)*T>*K(4B(6(F* that meet the energy and performance "@(5&"A6*($,&$((4*M6(S*=A%R*)&;"';;* !"#$%&$'()*#$*+,-*\0 +#;%(4*U&%@*KVW;*E4&"*:A"B*!6(7%0 P Q library of potential biofuel feedstock—a test site for plant yield, planting and harvesting equipment, and agronomy techniques, as well as a classroom for visiting schools, extension groups, and service organizations. And as the crops grow, EBI researchers maintain constant surveillance above and below ground. Berkeley city slickers touched leaves of the young (Mxg) plants, which were standing at roughly half the height of their eventual 13 vertical feet and by October would yield as much as 30 tons of feedstock per hectare, according to EBI Deputy Director Steve Long. Mxg isn’t the only thing growing. The Farm itself will be 340 acres in size when the final plot of land is acquired next year. And by the end of 2009, a new permanent building at the Energy Farm will have been constructed to host a feedstock preparation lab, equipment storage, sample archives, and staff offices. O(+'%F*O&4("%#4*8%(9(*C#$,*%A6B;* M,4&"'6%'4A6*($,&$((4*M6A$*NA$;($* AH#'%*:&;"A$%@'; )&;+6AF;*A*@A$)7'6*#7*7(();%#"B* ^:&"4#_+6#%;W*;%')F*&$;("%*A77("%;*#$*HA;; :&;"A$%@';<*H(7#4(*A$)*A7%(4*@A49(;% 4@&R#5(;*A;*+A4%*#7*%@(*@A49(;%&$,* (`'&+5($%*)&;+6AF A VISIT TO THE FARM (CONT’D)

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] \ BIOCONVERSION: SOCIOECONOMICS: ENGINEERING MICROBES TO BUILD A BETTER FUEL MAKING SURE BIOFUEL IMPACTS ON SOCIETY ARE POSITIVE 57#87 :$/4/0$/83&6 57#87 :$0/4"?$3"/66/ fermentation of feedstock sugars that will lead to the efficient production into energy fuels. “Existing biofuels of ethanol or other high-density fuels. support should be provided, and about security benefits they can provide.” what policies are needed to support are not optimally produced,” said These policies, however, may have the UC Berkeley systems biologist. Few natural bacterial systems hold biofuels.” the promise of efficient conversion unintended consequences. Biofuel “The fuel has to be scalable, it has Not all biofuels are the same. Biofuels policies like the Renewable Fuels to use the full value of the , of biomass to fuel, but Zymomonas mobilis is one of them. Arkin said Z. from crop residues and perennial Standard and tax credits for biofuels and has to be less energy-intensive to grasses, such as switchgrass and encourage a switch away from gasoline produce. Current fuels are often toxic mobilis is known for its high ethanol yields, high tolerance levels, and high Miscanthus, are considered more and towards biofuels, but do not create in high concentrations and are not sustainable than corn ethanol. They have incentives for fuel conservation, Khanna transportable by traditional means.” fermentation selectivity. His team’s next steps will be to create a full Z. a milder carbon footprint and will have a explained. If gasoline supply is fairly That’s a tall order, and it’s made more mobilis library, to genetically screen smaller impact on food prices because responsive to price, these policies could they require less diversion of cropland lower the price of gasoline and create complicated by the fact that the strains “like crazy,” and to identify :A)@'*=@A$$A M)A5*M4B&$ also have to overcome relevant genes and fermentation from food production to fuels, according perverse incentives for increasing the presence of toxic inhibitors, the pathways. Results will be posted Underlying the prospect of a promising to Khanna. fuel use, reducing the extent to which biofuels displace gasoline and thus Adam Arkin titled his talk “An result of pretreatments of the cellulose on Microbes Online, a functional biofuel industry is a host of critical Market forces will drive the costs, as reducing their energy security and Idiosyncratic View of Fuel Synthesis prior to deconstruction. But a team of database that features tools to enable questions regarding its economic and environmental impacts, a complicated will land and resource input prices, environmental benefits. Challenges,” but there’s nothing quirky researchers, including Illinois’ Yong-Su comparisons of genes and genomes. regulations, trade agreements, and fuel about the goal of EBI’s bioconversion Jin, Huimin Zhao, and Chris Rao, and Tools are also being built for enzyme chain of influences that EBI researchers are trying to sort out. Illinois agricultural competitors. , “Yields will be very important,” she program—to engineer new strains the Joint Genome Institute’s Thanos and pathway engineering once the water quality, and biodiversity are also said. “There will be spatial differences of microbes that can maximize the Lykidis, are looking for the pathways predictive analysis is completed. economist Madhu Khanna explained that the Institute’s programs fall within four in the mix of factors that will determine in costs (based upon where and how areas: land use, adoption and market the viability of biofuels. For that reason, the feedstocks are grown). There is not impact of biofuels, laws and regulation, Khanna said EBI is engaging in “a likely to be one winner (biofuel type), but =/6#2:$"?&0&6$C"/5$/64$."8&;$8/51$?6&7#8;&!-$5@$&22&65&;A$ and life cycle analysis. very interdisciplinary approach, with more than one. Policies will be critical !"/65;$2-3&4&;1$B5&6!$<#650#$&6;!&!?!# economists, soil scientists, atmospheric to determining what impact biofuels “There are three grand challenges for scientists, and engineers” working will have on food and fuel prices and E. coli, Rao and his team have already biofuels,” she said. “First, to compete together “to determine the sustainable on land use. Market effects can have studied nearly 30 sugar transporters to with food for land; second, to compete mix of biofuel feedstocks. Government a big impact on the environmental the point where “we now understand with crude oil as a fuel; and third, to policies are needed because the market effects of biofuels—the market will the regulation, and now we must try to be environmentally sustainable. So left to itself will price all biofuels based determine how many gallons of biofuel crack the hierarchy.” there are questions about the types on their energy content relative to will be consumed versus other fuels of feedstocks, about the type of gasoline and not value the different and therefore the overall reduction in He has focused on the sugars technology, about where government environmental benefits and energy greenhouse gas emissions.” arabinose and xylose, studying gene expression at single-cell resolution. =/6#2:$4/7&4$C&2%#80/61$?.$%#83#2#-A$B/-$3#;/61$?6&7#8;&!-$5@$&22&65&; Lykidis is interested in another and standards. With this much volatility bacterial path to biofuels—the in the market, he said “the challenge transition of sugar into lipid molecules, is how to develop contracts that will like fatty acid esters. From a list of provide fiscal viability to processors and genomes, he found one enzyme that growers.” !34#5*6(7%0*N'&5&$*a@A#<*>@4&;*GA#<*?@A$#;*CFB&)&; seemed to do the job. “Now we are looking at bacterial response to lipid The EBI groups will closely watch two Brewer’s is an effective agent modification method for removing accumulation, and the genetic basis policies that will impact the future of in , robust and and inserting a gene rapidly, and a for this,” said the JGI biochemist. “We biofuels: the federal Renewable Fuels tolerant, with a well-known physiology. metabolic flux analysis tool. Also, know why we humans accumulate Standard, which requires 36 billion It can work on so-called C6 sugars— genome-scale modeling helps in triglycerides, but we don’t know how it gallons of biofuel to be blended with those with six carbon atoms, like assembling pentose sugar utilization happens in certain bacteria.” gasoline by 2022, and the state Low glucose—but it can’t break down pathways.” !34#5*6(7%0*OA9&)*a&6H(45A$<*DAF*=(;A$ Carbon Fuel Standard, which calls C5 sugars like xylose and pentose. Their goal is to be able to generate for a reduction of at least 10 percent Huimin Zhao’s group is working to Biomolecular chemist Rao is also enough lipids for production of diesel One of the things David Zilberman and to understand how fuel prices are likely in the carbon intensity of California’s engineer a pathway that will also work working to engineer microbial strains and gasoline extenders by microbial his team are considering is the influence to be determined in the future with transportation fuels by 2020. EBI on the residual sugars in cellulose to optimized for large-scale fermentation, cultures. Approximately 60 percent of that OPEC, the cartel of oil-producing biofuels.” researchers will evaluate the impacts of maximize yield. specifically tracking the transport of the transportation fleet in Europe and nations, will have on biofuel prices. The price of energy is extremely flexible, these policies on the economics of the sugars “and trying to understand gene a third in the U.S. is dependent upon “OPEC tries to raise prices in the rest energy sector and the environment. “We’ve developed quite a few tools,” dynamics which could lead to a strain diesel fuel, which cannot be blended of the world but keep those in their own he noted, and future biofuel pricing will Zhao told the group, “like a pathway for efficient multiple sugar utilization,” with ethanol. countries low,” he said. “We need to be dependent on imports and exports (DNA) assembler, a one-step genome he said. Using the model organism develop a theory of how OPEC operates of fuel, corn and oil costs, demand for !"#$%&$'()*#$*+,-*.J0 foreign oil, and government mandates .Y .. WHAT’S NEEDED: MORE COMMUNICATING, DATA MANAGEMENT, PRIORITIZATION Standard 2, indirect land use impacts in EPA regulations, and carbon pricing. “Be strategic rather than reactive,” EBI Associate Director Paul Willems told the group. And Somerville reminded them that researchers, while unable to advocate as EBI members, can comment freely in their roles as faculty members. “(The EBI) should produce good academic papers that policymakers can rely on,” he said. Berkeley Lab’s Paul Adams and BP’s Steve Pietsch summarized the dozens of suggestions made by the “what are we missing?” group and clustered them into four main categories: communications (intra-institutional and with outside groups, sharing of !34#5*6(7%0*>@4&;*8#5(49&66(<*8%(9(*C#$,<*VA'6*b&66(5; research results, videoconferencing of presentations, workshops); tools Some common themes emerged The challenge for all, he noted, is the efforts towards studying structural (analysis of things like pretreatment when five focus groups gave retreat- scarcity of data to provide a common homology, perhaps through the chemistry and plant composition); concluding reports from their set of inputs. Group chair and EBI use of new tools such as X-ray centralization (core capabilities like 90-minute brainstorming sessions. Deputy Director Steve Long said that crystallography and Nuclear Magnetic genetic sequencing, standardized Virtually all of them expressed a when they talked about the needs of Resonance (NMR) to narrow the biomass sample library); and new desire for greater cross-disciplinary the “downstream” process modelers, targets of research. directions (chemical analysis of communications, both within the “the major issue was quality of the enzymes, international biomass EBI and with outside groups. They biomass. It varies by site and by year, UC Berkeley’s Adam Arkin identified transport issues, woody biomass professed the need for more and but it will be important. Toughness of the bioconversion group’s biggest deconstruction, hydrogen issues, and better data and the ability to archive the material will determine the amount collective need as the need to know so on). it for inter-project uses. And they harvested. (Feedstock) yield and which fuels molecules will be created Recognizing the value of the focus asked for Institute help in refining their composition are important.” and to really understand their issues, group exercise, Somerville promised efforts through prioritization of areas properties, regulatory challenges, co- that a similar conference will be held like preferred feedstocks, fuel type, Miller added the consensus that products, and so forth. “We need to !K(6#U0*T>*K(4B(6(F*+#;%)#"*N(&)&*8R(5($F(&*;%')&(;*4(%4(A%*+#;%(4 annually as a learning and sharing and pre-treatment efforts. the data should be recorded in one build our knowledge base in terms of resource, accessible via the web chemicals, organisms and pathways of opportunity. “We’re not sure what Additional manipulation and visual site. The group also vowed to have interest,” he said. “We have to know the format will be next year,” he tools and chemical analyses were also teleconferences and some in-person where our edge is.” told them, “but we need some joint requested. meetings to maintain a tighter team thinking about what would be most during model evaluations. Somerville suggested they convene useful for you.” EBI Director Chris Somerville had a workshop of experts to educate convened the groups as a way “to The group prospecting for effective EBI researchers about making fuels, look at where we have duplication microbial organisms (co-chair Doug especially experts from industries that and convert that into collaborations, Clark of UC Berkeley called it “Fuels have been doing it for years. Possible to look at what the opportunities are Gold”) said its main focus will be on chemical-biological hybrid processing that we’re missing, where can we be functional analysis of current samples, approaches and the use of more exotic combining our different components and expressed an interest in finding molecules are among the ideas the together, and what opportunities better lignocellulases from untapped team will pursue. should be our priorities.” natural sources. The primary suggestions that emerged Participants selected their “We need to reduce the complexity from the socioeconomic discussion discussion group from among five of the samples, establish standard group were program collaborations topics: modeling, bioprospecting, assays and methods for determining and contributions to the policy bioconversion, economics- and comparing activity, develop development process. Berkeley environment-policy, and “what’s methods for high-throughput gene economist David Zilberman reported missing?” expression and activity assays, and that the EBI can play an educational better characterize the physiochemical role in upcoming policy debates like Berkeley Lab’s Norm Miller of the properties of relevant feedstocks,” the Low Carbon Fuel Standard, cap- modeling group noted the significant Clark reported. and-trade programs, Renewable Fuel number of programs in the EBI that are dependant on predictive modeling. The group also encouraged greater !"#$%&$'()*#$*$(S%*+A,(0 .1 .2 EBI SCIENTISTS, STUDENTS, STAFF USE RETREAT TO RECALIBRATE EFFORTS (CONT’D - FROM PAGE 1)

of enhancing interactions within the 2030, increasing a gigawatt every 1.6 in cellulosic fuels. EBI. days. “But where will it come from? And what will it do to our climate?” he Somerville said the overriding goal “When you think about resources— asked. of the EBI is “to create coherent money, people, equipment,” he told knowledge in the field” by making them, “you won’t just think about The Institute, which is dedicated to discoveries and educating via the people you see every day, but studying the applications of biology interdisciplinary collaboration. The about the people who were here. The to the energy sector, was established presence of BP, he noted, “gives us Institute brings the resources and the with certain principles in mind, he a real-world perspective, a greater capabilities, and we all need to get out said: investing broadly across a understanding of the industry than any of the box of traditional research and complete spectrum of issues to other academic group can attain.” He think about what’s available through create capability and a coherent view, said he felt “uniquely privileged” to the EBI in general.” supporting competing approaches work with BP and help them “make to a problem, and identifying future good choices, and help society make One of Long’s opening slides was opportunities as they arise. No other good choices.” a cartoon depiction of the “golden research organization of its type has spike” transcontinental railway the technical and thematic reach of the He added, “We have a real chance to ceremony, in which the converging EBI, which handles 24 different topics change the world.” sets of tracks were connected but misaligned. “We want to avoid this EKI*"#$7(4((;*A%*%@(*IN#%(6*6&;%($*%#*I66&$#&;W*>A46*K(4$A""@&*)&;"';;*($9&4#$5($%A6*&5+A"%*5#)(6&$, kind of situation (in the EBI),” he joked. Then he instructed that individuals were prohibited from sitting next to people from their own institutions at subsequent lunches and dinners, a kind of enforced alignment that proved to be a popular socializing technique.

In his opening remarks, Somerville framed the importance of the EBI’s task within the context of future energy demand: the world’s energy V#;%(4*;(;;&#$*9&;&%#4;*&$"6')()*!74#5*6(7%0*I66&$#&;*4(;(A4"@(4;*I;AA"*>A$$*A$)* use is predicted to nearly double by M$,(6A*=($%<*A$)*D#&$%*c($#5(*I$;%&%'%(W;*:A%%@&A;*N(;;

SOCIOECONOMICS: MAKING SURE BIOFUEL IMPACTS ON SOCIETY ARE POSITIVE (CONT’D - FROM PAGE 11)

Law professor Jay Kesan said his and participating in efforts to shape focus is “understanding the legal and standards for sustainable biofuels. regulatory environment and public policy d#'$,*K(4B(6(F*4(;(A4"@(4;*($e#F*HA4H("'(*)&$$(4*A%*%@(*4(%4(A%*f*!A4#'$)*%AH6(<*74#5*6(7%0*>6A4&;A*K(eA4<*D(4#5(*3#S<* issues that will result in an economically Their search will take them beyond VA)5A*c'$)A<*:A$'(6*N#(46<*IA$*bA66A"(<*8A4A@*N'77(4<*D#$*cA6AR"A<*N(&)&*8R(5($F(&<*d&$,*c' viable, sustainable biofuel industry.” He the processing plant to issues such as described three approaches: looking carbon sequestration and the associated at all regulatory requirements, from property rights, liability issues, and to formulate our future directions at understand the complexity of what briefings, farm and facility tours, and feedstock to consumer; analyzing and utilization agreements, according the Institute.” we’re trying to accomplish and poster sessions. Sunday afternoon was critiquing laws; and proposing solutions to Kesan. At the farm level, issues understand that we are a lot more than devoted to five breakout focus groups where gaps appear. might involve carbon credits, cap-and- And that it did, according to EBI the sum of the parts of the people in that discussed what the EBI needs trade schemes, and so on. The legal Director Chris Somerville. At the this room. It was important to give to advance its mission. A common One of his team’s efforts has been infrastructure for biofuels is a work in closing session on Sunday, he everyone exposure to what everyone and unifying theme of this discussion an empirical study of data from 166 progress at both the state and federal reminded the attendees that “most else is doing.” was the search for additional cross- ethanol plants in the period from 2000 to levels. EBI’s legal experts will follow 2008, in which they found that through developments closely with a view to of you by definition work in a narrow disciplinary communications, which duration analysis, medium-sized plants identifying topics where additional field of science, but the things Nearly 250 conferees—from Illinois, Somerville said was “music to our you do collectively comprise the the campus and federal lab at have the greatest chance of continuing academic research would be useful in I$;%4'5($%A%&#$*A5#$,*%@(* ears” and reflected the retreat’s goal operation, compared to small-sized and helping resolve emerging issues. broad arena of what the EBI is set Berkeley, and BP—participated in 7(();%#"B*+6#%; large-sized plants. The team is also up to accomplish. It’s important to a program of thematic research !"#$%&$'()*#$*$(S%*+A,(0 studying frameworks for sustainability ./ .J THE PEOPLE BEHIND THE SCENES

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EBI Director Chris Somerville broke the specialists Melissa Edwards and Haley silence. At the closing dinner on June Ahlers. He also acknowledged farm 21, he expressed his appreciation for a manager Tim Mies and his helpers on flawless research gathering, crediting the tour. both the IHotel staff and the University of Illinois hosts for “a fantastic job.” “They set a really high standard,” he From the sumptuous meals to the said. “It will be a challenge for us to endless administrative challenges that replicate the success of the meeting mark a conference of this magnitude, next year in Berkeley.” the retreat came off without a hitch. EBI-Berkeley’s Trisha Togonon, whose It is said that event management is In his champagne toast, Somerville arrangements for getting nearly 120 a thankless task, the planners being cited EBI-Illinois Assistant Deputy people to and from Champaign on time acknowledged only if something goes Director Jenny Kokini for her overall were likewise flawless, is probably wrong. Success is generally reflected by management, assisted by Becky Heid already thinking about 2010. silence. A good meeting is one without and Connie Wilder, Illinois lab manager complaint. Rachel Shekkar, and communications

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