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Technology Transfer Opportunities: Biological and Environmental Research

Program Area OverviewOffice of Biological and Environmental Research  The Biological and Environmental Research (BER) Program supports fundamental, peer_reviewed research on complex systems in climate change, subsurface biogeochemistry, genomics, systems biology, radiation biology, radiochemistry, and instrumentation. BER funds research at public and private research institutions and at DOE laboratories. BER also supports leading edge National Scientific User Facilities including the DOE Joint Genome Institute (JGI), the Environmental Molecular Science Laboratory (EMSL), the Atmospheric Radiation Measurement (ARM) Climate Research Facility and instrumentation for structural biology research at the DOE Synchrotron Light and Neutron sources.  BER has interests in the following areas:   1)    Biological Systems Science integrates discovery_ and hypothesis_driven science with technology development on plant and microbial systems relevant to DOE bioenergy mission needs. Systems biology is the multidisciplinary study of complex interactions specifying the function of entire biological systems?from single cells to multicellular organisms?rather than the study of individual components. The Biological Systems Science subprogram focuses on utilizing systems biology approaches to define the functional principles that drive living systems, from microbes and microbial communities to plants and other whole organisms. Key questions that drive this research include: What information is encoded in the genome sequence? How is information exchanged between different sub_cellular constituents? What molecular interactions regulate the response of living systems and how can those interactions be understood dynamically and predictively? The approaches employed include genome sequencing, proteomics, metabolomics, structural biology, high resolution imaging and characterization, and integration of information into predictive computational models of biological systems that can be tested and validated.   The subprogram supports operation of a scientific user facility, the DOE Joint Genome Institute (JGI), and access to structural biology facilities at the DOE Synchrotron Light and Neutron Sources. Support is also provided for research at the interface of the biological and physical sciences and in radiochemistry and instrumentation to develop new methods for real_time, high_resolution imaging of dynamic biological processes.   2)    The Climate and Environmental Sciences subprogram focuses on a predictive, systems_level understanding of the fundamental science associated with climate change and DOE?s environmental challenges?both key to supporting the DOE mission. The subprogram supports an integrated portfolio of research from molecular level to field_scale studies with emphasis on multidisciplinary experimentation and use of advanced computer models. The science and research capabilities enable DOE leadership in climate_relevant atmospheric_process research and modeling, including clouds, aerosols, and the terrestrial carbon cycle; large_scale climate change modeling; integrated analysis of climate change impacts; and advancing fundamental understanding of coupled physical, chemical, and biological processes controlling contaminant mobility in the environment.  The subprogram supports three primary research activities and two national scientific user facilities.  Atmospheric System Research seeks to resolve the two major areas of uncertainty in climate change model projections: the role of clouds and the effects of aerosols on the atmospheric radiation balance.  Environmental System Science supports research that provides scientific understanding of the effects of climate change on terrestrial ecosystems, the role of terrestrial ecosystems in global carbon cycling, and the role of subsurface biogeochemistry in controlling the fate and transport of energy_relevant elements.  Climate and Earth System Modeling focuses on development, evaluation, and use of large scale climate change models to determine the impacts of climate change and mitigation options.   Two scientific user facilities the Atmospheric Radiation Measurement (ARM) Climate Research Facility and the Environmental Molecular Sciences Laboratory (EMSL) provide the broad scientific community with technical capabilities, scientific expertise, and unique information to facilitate science in areas integral to the BER mission and of importance to DOE.   For additional information regarding the Office of Biological and Environmental Research priorities, click here. TOPIC 20:  Technology Transfer Opportunities: Biological and Environmental Research  Maximum Phase I Award Amount:  $225,000 Maximum Phase II Award Amount:  $1,500,000 Accepting SBIR Phase I Applications:  YES Accepting SBIR Fast_Track Applications:  NO Accepting STTR Phase I Applications:  YES Accepting STTR Fast_Track Applications:  NO  Applicants to TECHNOLOGY TRANSFER OPPORTUNITIES (TTO) should review the section describing these opportunities on page 7 of this document prior to submitting applications.   DOE’s Office of Biological and Environmental Research (BER) Genomic Science Program supports DOE missiondriven fundamental research to identify the foundational principles that drive biological systems. Development of innovative approaches for sustainable bioenergy production will be accelerated by a systems biology understanding of non_food plants that can serve as dedicated cellulosic biomass feedstocks and microbes capable of deconstructing biomass into their sugar subunits and synthesizing next generation biofuels from cellulosic biomass. Genomic Science Program research also brings the _omics driven tools of modern systems biology to bear for analyzing interactions among organisms that form biological communities and between organisms and their surrounding environments.  BER established three Bioenergy Research Centers (BRCs) in 2007 to pursue the basic research underlying a range of high_risk, high_return biological solutions for bioenergy applications. Advances resulting from the BRCs are providing the knowledge needed to develop new biobased products, methods, and tools that the emerging biofuel industry can use. The three Centers are based in the Southeast, the Midwest, and the West Coast, with partners across the nation. DOE?s Lawrence Berkeley National Laboratory leads the DOE Joint BioEnergy Institute (JBEI) in California, DOE?s Oak Ridge National Laboratory leads the BioEnergy Science Center (BESC) in Tennessee, and the University of Wisconsin_Madison leads the Great Lakes Bioenergy Research Center (GLBRC).  The goal for the three BRCs is to understand  the biological mechanisms underlying biofuel production from cellulosic biomass so that these mechanisms can be  improved, and used to develop novel, efficient bioenergy strategies that can be replicated on a mass scale. Detailed understanding of many of these mechanisms form the basis for the BRCs? inventions and tech_transfer opportunities, which enable the development of technologies that are critical to the growth of a biofuels industry.  Successful applicants will propose R&D that will lead to biofuel commercialization utilizing one of the TTOs listed below. Applications that propose technologies related to a TTO but that do not directly utilize a TTO will not be funded. Applications should include sufficient preliminary data and scientific detail so that expert reviewers will understand both the potential benefits and the challenges that may be encountered in carrying out the proposed research. Challenges should be identified, and solutions should be proposed that will explain how the PI?s team will overcome the challenges. Applications should address potential risks such as biocontainment challenges as well as strategies to mitigate those risks.  Questions ? Contact: Prem Srivastava, prem.srivastava@science.doe.gov  Grant applications are sought in the following subtopics:   a. Technology Transfer Opportunity: Engineering Polyketide Synthases for Production of Fuels Joint BioEnergy Institute (JBEI) researchers are using synthetic biology to engineer polyketide synthases (PKSs) that can be used to produce carboxylic acids and lactones for biofuel production. Carboxylic acids can easily be converted to an ester biofuel. The JBEI team is the first to design PKSs to synthesize biofuels or their immediate precursors. Some of the longer_chain esters that can be produced by the JBEI PKSs could be used in biodiesel blends. Shorter chain esters and the lactones could be used as petroleum additives or in non_hydrophilic, advanced biofuel blends compatible with current fuel infrastructure.  Because the JBEI process allows controlled engineering, ester linkages can be placed so that combustion properties of the resulting biofuel are enhanced. b. Technology Transfer Opportunity: Irreversible, Low Load Genetic SwitchesRecombinases that have been conclusively demonstrated to work orthogonally are non_cross_reacting and do not cause unpredictable recombination events.  Researchers at the Joint BioEnergy Institute (JBEI) have developed novel nucleic acid constructs containing matched orthogonal site selective recombinases. The JBEI invention removes the ability of a cell to access certain genes and enables the concurrent use of multiple recombinases. This system enables multiple genes to be turned on or off at different states of an organism?s lifecycle, which has both research and industrial applications. It offers improved reliability over other approaches by ensuring that circuits proceed to completion rather than equilibrating. Potentially, these devices could be used to construct an expression system with low load on the cell, a very low level of basal expression and an extremely high level of expression after induction. This could be useful where a growth phase and a production/manipulation phase need to be kept distinct. Using this sort of toggle, many changes can be made at once to cell physiology.  c. Technology Transfer Opportunity: Directed Evolution of Microbe Producing Biofuels Using In Vivo Transcription Factor Based Biosensors JBEI researchers developed a method of using transcription factors expressed in vivo to evolve, screen, and select for microorganisms producing an intracellular small molecule of interest, such as a short chain alcohol. Biosensors composed of transcription factors and their cognate promoters are designed and constructed to be capable of binding the particular molecule of interest. For the biofuels industry, an in vivo biosensor in a microorganism, such as E. coli, for the detection of short_chain alcohols can be used to develop high_throughput selections and screens to engineer microorganisms producing alcohol_based biofuel molecules. This approach provides an alternative to low throughput methods, such as chromatography, for metabolite detection. The JBEI invention improves screening throughput and exhibits greater sensitivity as compared to high_throughput colorimetric screens. Downstream application of the invention as a selection method could allow for direct, dynamic evolution of strains without the need for screening. The JBEI technology focuses on bacterial transcription factors and their cognate promoters. This class of transcription factors has been shown to bind to a broad range of industrial and commercial molecules.  d. Technology Transfer Opportunity: Biosynthetically Produced Pinene for Jet Fuel or Chemical Applications  A Joint BioEnergy Institute (JBEI) research team has constructed a metabolic pathway to produce the monoterpene pinene, an immediate chemical precursor to a potential jet fuel. Pinene is typically derived from turpentine, a byproduct of pine resin distillation. The JBEI technology could open the door to more economical and sustainable production of a vital transportation fuel. The researchers modified host cells, rerouting the isoprenoid pathway to produce geranyl pyrophosphate and then pinene, using selected synthases. Researchers confirmed that their technology is capable of producing pinene from either xylan or cellobiose.  e. Technology Transfer Opportunity: Enhancing Fatty Acid Production by Regulation of fadR ExpressionResearchers at the DOE Joint BioEnergy Institute (JBEI) have developed a genetically modified host cell that increases production of fatty acids and their derivatives. Specifically, the JBEI team found that increased concentration of cellular fadR, a transcriptional factor protein that regulates genes responsible for fatty acid activation and several genes in the fatty acid degradation pathway, lowers fatty acid degradation rate and enhances unsaturated fatty acid biosynthesis, resulting in an increase in total fatty acid production.   f. Technology Transfer Opportunity: Transcription Factor_based Biosensors for Detection of Dicarboxylic Acids  This invention comprises a biosensor_based system for accurate detection of exogenous dicarboxylic acids in liquid or solid media and in vivo detection of endogenously produced diacids within a single host. Microorganisms are highly adept at sensing and responding to small_molecules in their environment. For example, transcription factors binding dicarboxylic acids can modulate expression of one or more reporter genes downstream of the transcription factor’s cognate promoter. By monitoring the expression of the reporter genes dicarboxylic acid concentration can be readily measured. Exemplary reporter genes may encode for beta_galactosidase, a fluorescent protein, an antibiotic resistance protein, or a biosynthetic pathway. This strategy has been implemented for detection of short_chain alcohols using an E. coli strain heterologously expressing a short_chain alcohol responsive transcription factor. In addition to transcription factors, a dicarboxylic acid specific catabolic operon can couple exogenous dicarboxylic acid concentration to the specific growth rate of a biosensor microorganism.  g. Technology Transfer Opportunity: Bacterial Overproduction of Methyl Ketones from Sugar Researchers at the Joint BioEnergy Institute (JBEI) have developed a bacterial strain that can overproduce medium_chain (such as C11 to C15) methyl ketones from glucose. The methyl ketones could be blended with diesel fuel to yield a viable transportation fuel derived, in part, from renewable resources. Methyl ketones, such as 2_undecanone and 2_tridecanone, are also used in the flavor and aroma industries.  h. Technology Transfer Opportunity: Long alkyl Chain Alcohols as Co_solvent, Precipitant and Extraction Medium in Ionic Liquid Pretreatment  JBEI researchers developed a method to use long chain alcohols such as octanol or hexanol as anti_solvents to precipitate dissolved cellulose in ionic liquids. This method is advantageous compared with the most commonly used water anti_solvents. Water is miscible with ionic liquids, hampering, recycling and reuse of both ionic liquids and anti_solvents. Longer chain alcohols are immiscible with ionic liquids, enabling easier separation of both ionic liquids and octanol. The invented method provides multiple potential technical advantages: Recycle of ionic liquids and possible extraction of depolymerized lignin fractions in octanol. The resulting solids after solid/liquid separation are highly digestible by cellulolytic enzymes and no wash is needed before loading of enzymes. Recycled IL can directly reused for pretreatment without further purification and concentration.  i. Technology Transfer Opportunity: Production of Fatty_Acid_Derived Biofuels and Chemicals in Saccharomyces Cerevisiae  Joint BioEnergy Institute (JBEI) researchers have developed a method of genetically engineering budding yeast Saccharomyces cerevisiae (S. cerevisiae) to produce free fatty acids, fatty alcohols and biodiesels directly from simple sugars. As indicated in their Metabolic Engineering publication, the researchers demonstrated that S. cerevisiae provides a platform for a scalable route to key chemicals.  Rather than swap out individual fatty acid biosynthesis genes to enhance production, the Berkeley Lab team replaced the native promoters of all fatty acid biosynthesis genes with a strong constitutive promoter, yielding a strain that overproduces fatty acid. To augment triacylglycerol (TAG) accumulation, the researchers also overexpressed key fatty acid and TAG biosynthesis enzymes. Depending on the choice of converting enzyme, this engineered strain could produce and secrete directly into the culture medium fatty acid ethyl esters (biodiesel), free fatty acids, or fatty alcohols.  j. Technology Transfer Opportunity: Gene Modification to Increase Drought and Flood Tolerance in Plants  Researchers at the Joint BioEnergy Institute (JBEI) have used recombinant nucleic acid techniques to overexpress a gene ? SAB18 ? to increase plants? tolerance to both drought and flooding. SAB18, found in rice and other grass plants, is involved in carbohydrate and nucleotide metabolism and is responsible for a plant?s natural tolerance to variations in water availability. Plants that are modified to over_express this gene have been shown to remain greener, taller, and more erect when subjected to extreme water conditions. When compared to natural plants under similar conditions, the viability and health of SAB18 modified rice plants increased substantially.  k. Technology Transfer Opportunity: Production of 1_Deoxyxylulose_5_Phosphate (DXP)  Host Cells and Methods for Producing 1_deoxyxylulose_5_phosphate. Novel routes into the microbial DXPbased isoprenoid pathway have been discovered that increase the theoretical yield of isoprenoid_based fuels and chemicals from sugars. These routes allow more direct conversion of carbon to terpenoid compounds circumventing the typical, but inherently inefficient, route to DXP. Terpenoids are key ingredients in flavors and fragrances and offer a pathway to naturally derived isoprenoid_based biofuels and materials.  l. Technology Transfer Opportunity: Transgenic Cyanobacteria: A Novel Direct Secretion of Glucose for the Production of Biofuels  A direct secretion of glucose by transgenic cyanobacteria creates an extremely efficient, cost effective feedstock for the production of ethanol. The cells can be recycled for repeated glucose harvest.  m. Technology Transfer Opportunity: Ethanol Tolerant Yeast for Improved Production of Ethanol from Biomass  UW?Madison researchers have developed a method to impart ethanol tolerance to yeast. The toxicity of alcohol to microbes such as yeast is a bottleneck in the production of ethanol from biomass_derived sugars through fermentation. The Elongase 1 gene encodes ELO1, an enzyme involved in the biosynthesis of unsaturated fatty acids in yeast. This gene could be incorporated into an industrial yeast strain to increase the amount of ethanol produced from biomass. An industrial fermentation yeast strain with increased ethanol tolerance could be widely applicable in reducing costs and energy consumption.  n. Technology Transfer Opportunity: Genes for Xylose Fermentation, Enhanced Biofuel Production in Yeast  UW?Madison researchers have identified 10 genes in yeast that are involved in xylose fermentation. Efficient fermentation of biofuels and biorenewable chemicals from biomass_derived sugars would benefit from microbes that can utilize both glucose and xylose. These genes could be used to create an organism by modifying one that normally utilizes glucose to one that can ferment both xylose and glucose for enhanced biofuel production. These genes may be used in various combinations to produce useful industrial strains.  o. Technology Transfer Opportunity: Production of Polyhydroxyalkanoates with a Defined Composition from an Unrelated Carbon Source UW?Madison researchers have developed recombinant E. coli capable of producing high yields of medium chain length polyhydroxyalkanoates from non_lipid, carbohydrate sources. The researchers previously designed and built a bacterial strain that produces high levels of C12 fatty acids (see WARF reference number P09329US02). This strain has been further modified by deleting various fad genes implicated in the breakdown of fatty acids. Also, the bacteria cells incorporate several genes taken from other species to increase conversion efficiency.  p. Technology Transfer Opportunity: Organic Acid_Tolerant Microorganisms and Uses Thereof for Producing Organic Acids UW?Madison researchers have genetically modified microorganisms to better tolerate organic acids like 3HP, acrylic acid and propionic acid. In the modified bacteria, the acsA gene is replaced or deleted. This leads to increased organic acid tolerance. The modified microorganisms are cyanobacteria such as HP or acrylic acid.  q. Technology Transfer Opportunity: Fatty Acid_Producing HostsUW?Madison researchers have developed genetically modified E. coli that are capable of overproducing fatty acid precursors for medium_ to long_chain hydrocarbons. The modified bacteria were transformed with exogenous nucleic acids to increase the production of acyl_ACP or acyl_CoA, reduce the catabolism of fatty acid products and intermediates, and/or reduce feedback inhibition at specific points in the biosynthetic pathway. The modified bacteria can be cultured in the presence of sugars to produce fatty acids. The fatty acid products formed during fermentation then can be separated from the fermentation media via a two_phase separation process or other method. The separated products can be used directly or as feedstock for subsequent reactions, including conversion to medium_ and long_chain hydrocarbons. Production of medium_chain and long_chain hydrocarbons for use as biofuels or specialty chemicals.  r. Technology Transfer Opportunity: High Calorie and Nutritional Content Plants or Plant Seeds MSU researchers have developed a suite of technologies that may be used for several purposes, depending on implementation. The technolgies include i) the wrinkle 1 regulatory gene, which switches on expression of enzymes involved in lipid production; ii) pyruvate kinase genes downstream of wrinkle 1, which may be used to increase lipids or certain amino acids, and iii) diacylglycerol acyl transferase (DAGAT) genes, which may be used to increase lipid production. This suite of technologies may be used to increase oil content in plant seeds or alternatively plant leafy tissues. High oil leafy tissues may be used as enhanced forage crops or for vegetable and biodiesel production Leaf oil contents of greater than 10% have been demonstrated. Forage crops may also be enhanced by increased production of amino acids.  s. Technology Transfer Opportunity: A Method to Produce 3_Acetyl_1, 2_Diacyl_sn_glycerols (ac_TAGs) Michigan State University?s inventions provide a source and production method for novel plant oils, acetyltriacylglycerols (ac_TAGs), with possible uses as biodiesel_like biofuel and/or as low_fat food ingredients. By combining an ac_TAG_related enzyme with a method for catalyzing large_scale synthesis of ac_TAGs, in a single crop, many benefits can be obtained. The inventions have lower viscosity and fewer calories per mole than TAGs. Pilot experiments by the inventors have achieved approximately a 60 mole percent accumulation of ac_TAGs in seed oil.  t. Technology Transfer Opportunity: A Novel Integrated Biological Process for Cellulosicethanol Production Featuring High Ethanol Productivity, Enzyme Recycling, and Yeast Cells Reuse  MSU’s technology provides a method of recycling unhydrolized recalcitrant solids in a biomass processing facility. The recycling process addresses current biomass processing issues that lead to high enzyme loading, slow xylose fermentation, and low ethanol productivity. Recycling of unhydrolyzed solids after a short enzymatic digestion enables use of 33% less enzyme, and increases ethanol productivity 2_3X in comparison to standard processes.  u. Technology Transfer Opportunity: Advanced Biomass Tree Crops Cellulose is a complex carbohydrate that serves as the basic structural component of plant cell walls. It accounts for roughly one_third of all vegetal matter, making it the most common organic compound on earth. Due to its ubiquitous nature, cellulose and its derivatives are key resources for the agriculture, forestry, textile, and paper industries. For these industries that rely on plant biomass, profitability is directly related to the quantity and quality of cellulose harvested from crops. However, until now, there have been no known methods of genetically controlling the quantity or quality of cellulose synthesized in plant species through direct regulation. MSU’s suite of technologies provide genes for increasing cellulose and/or hemicellulose production in trees, and promoter “switches” that turn on expression of the trait genes in woody tissues.    v. Technology Transfer Opportunity: Switchable Ionic Liquids for Biomass Pretreatment and Enzymatic Hydrolysis  This invention addresses the challenge that current ionic liquids are excellent at pretreating biomass, but are generally incompatible with enzymatic hydrolysis.  JBEI researchers identified properties of ionic liquids that have the greatest impact on enzyme performance and how to manipulate these.  The ionic liquid can be switched to a form compatible with enzymatic hydrolysis of cellulose following pretreatment, and then switched back to efficiently pretreat biomass. By switching from one form to another, this novel ionic liquid can be used to efficiently pretreat biomass, and then?without having to remove the ionic liquid? be used in its enzyme compatible form for saccharification of the resulting cellulose.  w. Technology Transfer Opportunity: Cell_Free System for Combinatorial Discovery of Enzymes Capable of Transforming Biomass for BiofuelsUW_Madison researchers have developed compositions and methods that expand the ability to make, express and identify target polypeptides, including enzymes capable of enhancing the deconstruction of biomass into fermentable sugars. This approach uses a cell_free system to express enzymes and other polypeptides in a combinatorial manner. Because the system is cell_free, the enzymes can be assayed without intermediate cloning steps or purification of the protein products.  This system also is more reliable than conventional methods for analyzing biomass transformation because it does not utilize living systems, which could rapidly consume soluble sugars. This system could be used to efficiently screen enzyme combinations for effective deconstruction of biomass from different feedstocks and under different conditions.  x. Technology Transfer Opportunity: Multifunctional Cellulase and HemicellulaseUW?Madison researchers have engineered a multifunctional polypeptide capable of hydrolyzing cellulose, xylan and mannan. It is made of the catalytic core of Clostridium thermocellum Cthe_0797 (also called CelE), a linker region and a cellulose_specific carbohydrate binding module (CBM3). C. thermocellum is a well_known cellulose_degrading bacterium whose genome has been sequenced, annotated and published. Multifuncional enzymes could simplify the enzyme cocktail needed for biomass conversion, thereby reducing costs.  

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