Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed to produce useful products, such as fuels. For example, systems can use feedstock materials, such as cellulosic and/or lignocellulosic materials and/or starchy materials, to produce ethanol and/or butanol, e.g., by fermentation.

Abstract: The present invention relates to processes and systems for the production of fermentative alcohols such as ethanol and butanol. The present invention also provides methods for separating feed stream components for improved biomass processing and productivity.

Abstract: The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

Abstract: A fermentation liquid feed including water and a product alcohol and optionally CO2 is at least partially vaporized such that a vapor stream is produced. The vapor stream is contacted with an absorption liquid under suitable conditions wherein an amount of the product alcohol is absorbed. The portion of the vapor stream that is absorbed can include an amount of each of the water, the product alcohol and optionally the CO2. The temperature at the onset of the absorption of the vapor stream into the absorption liquid can be greater than the temperature at the onset of condensation of the vapor stream in the absence of the absorption liquid. The product alcohol can be separated from the absorption liquid whereby the absorption liquid is regenerated. The absorption liquid can include a water soluble organic molecule such as an amine.

Abstract: An improved process for alcohol production includes microbial fermentation using a genetically modified microorganism to produce substantial quantities of aldehydes that are stripped from the fermentation medium and condensed. So produced aldehydes are converted in an ex vivo process to corresponding alcohols.

Abstract: A non-naturally occurring microbial organism includes a microbial organism having a reductive TCA or Wood-Ljungdahl pathway in which at least one exogenous nucleic acid encoding these pathway enzymes is expressed in a sufficient amount to enhance carbon flux through acetyl-CoA. A method for enhancing carbon flux through acetyl-CoA includes culturing theses non-naturally occurring microbial organisms under conditions and for a sufficient period of time to produce a product having acetyl-CoA as a building block. Another non-naturally occurring microbial organism includes at least one exogenous nucleic acid encoding an enzyme expressed in a sufficient amount to enhance the availability of reducing equivalents in the presence of carbon monoxide or hydrogen, thereby increasing the yield of redox-limited products via carbohydrate-based carbon feedstock.

Abstract: A process for preparing optically active 2-methylalkan-1-ol of the general formula (III) comprising the following steps: (i) carbonyl-selective reduction of 2-methylalk-2-en-1-al of the general formula (I) to 2-methylalk-2-en-1-ol of the general formula (II), (ii) enantioselective hydrogenation of 2-methylalk-2-en-1-ol to the general formula (iii), (iii) increasing the optical yield of the optically active 2-methylalkan-1-ol (III) obtained in step (ii) by a lipase-catalyzed acylation reaction, where the radical R means C1-C10-alkyl.

Abstract: The present invention relates to producing chemicals and biofuels from wood material, e.g. mixed forest biomass. Specifically, the invention concerns a process for conditioning spent liquor produced by SO2-ethanol-water (SEW) fractionation of wood chips for fermentation to butanol, ethanol and acetone/isopropanol (so called ABE process) by Clostridia bacteria.

Abstract: Methods and systems for producing a biofuel using genetically modified iron-oxidizing bacteria (IOB) are disclosed. In some embodiments, the methods include the following: providing an IOB that have been genetically modified to include a particular metabolic pathway to enable them to generate a particular biofuel or chemical; feeding a first source of ferrous iron to the IOB; feeding water, carbon dioxide, and oxygen to the IOB; and producing at least the biofuel or chemical, ferric iron, and an IOB biomass. In some embodiments, the methods and systems include the following: a bioreactor including IOB that have been genetically modified to include a particular metabolic pathway to enable them to generate a particular biofuel; a first source of ferrous iron; sources of water, carbon dioxide, and oxygen; and a electrochemical reactor that is configured to electrochemically reduce ferric iron produced in the bioreactor to a second source of ferrous iron.

Abstract: The present disclosure identifies methods and compositions for modifying photoautotrophic organisms as hosts, such that the organisms efficiently convert carbon dioxide and light into n-alkanes, and in particular the use of such organisms for the commercial production of n-alkanes and related molecules.

Abstract: Designer Calvin-cycle-channeled and hydrogenotrophic biofuel-production pathways, the associated designer genes and designer transgenic organisms for autotrophic production of butanol and related higher alcohols from carbon dioxide, hydrogen, and/or water are provided. The butanol and related higher alcohols include 1-butanol, 2-methyl-1-butanol, isobutanol, 3-methyl-1-butanol, 1-hexanol, 1-octanol, 1-pentanol, 1-heptanol, 3-methyl-1-pentanol, 4-methyl-1-hexanol, 5-methyl-1-heptanol, 4-methyl-1-pentanol, 5-methyl-1-hexanol, and 6-methyl-1-heptanol. The designer autotrophic organisms such as designer transgenic oxyphotobacteria and algae comprise designer Calvin-cycle-channeled and hydrogenotrophic pathway gene(s) and biosafety-guarding technology for enhanced autotrophic production of butanol and related higher alcohols from carbon dioxide and water.

Abstract: The microorganism-containing biocatalysts disclosed have a large population of the microorganisms irreversibly retained in the interior of the biocatalysts. The biocatalysts possess a surprisingly stable population of microorganisms and have an essential absence of debris generation from metabolic activity of the microorganisms. The biocatalysts are composed of highly hydrophilic polymer and have an internal, open, porous structure that promotes community phenotypic changes.

Abstract: Described are novel S. stipitis strains that were obtained by UV-C irradiation of wild-type S. stipitis NRRL Y-7124 cultures, followed by 5-month anaerobic growth on xylose at 28° C. The UV-C-mutagenized strains were able to grow anaerobically on xylose or glucose medium with higher ethanol production than a Saccharomyces cerevisiae yeast strain under comparable fermentation conditions. The mutagenized strains were identified by DNA fingerprinting to be unique strains closely related to wild-type Scheffersomyces stipitis. These mutagenized strains have potential application in large-scale industrial conversion of lignocellulosic sugars to fuel ethanol.

Abstract: A process that generates sulfide in production of liquid products from syngas and a system for syngas fermentation including a sulfide generation process to convert feed gas to liquid product, the process including: partially oxidizing high-temperature gas, input gas, and molten sulfur to generate sulfide gas, the high-temperature gas containing oxygen, the input gas containing carbonaceous fuel and the sulfide gas containing hydrogen sulfide, CO, CO2, and H2; mixing the sulfide gas with the feed gas to generate mixed gas having a predetermined hydrogen sulfide concentration; providing at least a portion of the mixed gas to a production fermentor containing microorganisms; and converting the mixed gas to the liquid product by contact with the microorganisms.

Abstract: The present disclosure relates to an improved process of producing a fermentation product, in particular ethanol. The present disclosure relates also to the use of enzymes for improving the quality of by-products in the fermentative production process and to compositions comprising enzymes capable of degrading components in the fermented mash in the fermentation process.

Abstract: The present invention provides genes, polypeptides and expression constructs therefor, recombinant photosynthetic microorganisms, and method of use thereof, such as for the production of branched-chain alcohols (including 2-methyl-1-butanol, 3-methyl-1-butanol, and isobutanol) and derivatives thereof for a variety of uses.

Abstract: The invention provides an improved method for the production, separation and recovery of one or more fermentation products from a fermentation broth. Further, the invention provides a method for increasing efficiency of a fermentation reaction.

Abstract: The invention relates to a process of producing a fermentation product in the presence of pyridoxamine.

Abstract: The invention relates to recombinant microorganisms that have been engineered to produce various chemicals using genes that have been repurposed to create a reverse beta oxidation pathway. Generally speaking, the beta oxidation cycle is expressed and driven in reverse by modifying various regulation points for as many cycles as needed, and then the CoA thioester intermediates are converted to useful products by the action of termination enzymes.

Abstract: One or more genes in a biosynthesis pathway for a vitamin or other essential nutrient which is needed for the survival of a microorganism can be used as an effective selective marker to identify cells transformed with an exogenous nucleic acid. The microorganism does not naturally contain or express the one or more gene. This permits genetic manipulations to be performed. It permits lower cost fermentations to be performed. It permits production of the essential nutrient for subsequent commodity use.

Abstract: The present invention is directed to improvements in gasification for use with synthesis gas fermentation. Further, the present invention is directed to improvements in gasification for the production of alcohols from a gaseous substrate containing at least one reducing gas containing at least one microorganism.

Abstract: The present invention relates to novel enzymes and the uses thereof. The invention also relates to methods of producing such enzymes, coding nucleic acid molecules, recombinant cells and methods of modifying biomass from such materials. The invention is particularly suited to degrade biomass and/or to improve biomass degradation. The invention also relates to various applications of the enzymes of the invention for the production of bioenergy (such as bioethanol), as well as in the field of chemistry, paper industry, textile industry and beverage industry.

Abstract: Embodiments of the present invention provide for efficient and economical production and recovery of ethanol or other volatile organic compounds, such as acetic acid, from solid biomass material, particularly on a larger scale, such as on the commercialization or industrial scale. According to one aspect of the invention, the method comprises (a) generating at least about 10 tons of prepared biomass material by adding a microbe, optionally an acid, and optionally, an enzyme to a solid biomass; (b) storing the prepared biomass material for at least about 24 hours in a storage facility to allow production of at least one volatile organic compound from at least a portion of the sugar in the solid biomass; and (c) capturing the at least one volatile organic compound by using a solventless recovery system.

Abstract: The present disclosure provides engineered halohydrin dehalogenase (HHDH) polypeptides having improved enzyme properties as compared to the wild-type HHDH enzyme HheC and other reference engineered HHDH polypeptides. Also provided are polynucleotides encoding the engineered HHDH enzymes, host cells capable of expressing the engineered HHDH enzymes, and methods of using the engineered HHDH enzymes to synthesize a variety of chiral compounds including chiral epoxides and chiral alcohols.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed to produce useful products, such as fuels. For example, systems can use feedstock materials, such as cellulosic and/or lignocellulosic materials, to produce ethanol and/or butanol, e.g., by fermentation.

Abstract: Fermentable sugar useful for the production of biofuels is produced from biomass in a continuous or semi-continuous manner by providing pumpable biomass.

Abstract: Disclosed is a process for producing 2-methyl-3-buten-2-ol (MBO). The process is carried out by fermenting a hydrocarbon in a fermentation medium in the presence of a MBO-producing microorganism to produce the MBO. The MBO is removed from the fermentation medium to maintain a concentration of MBO non-toxic to the MBO-producing microorganism by flowing a gas through or across the fermentation medium to effectively remove at least a portion of the MBO into a vapor phase region of the fermentation medium. The rate of removal is measured according to the amount of MBO maintained in the vapor phase region, which is measured according to the vapor pressure of the MBO in the vapor phase region.

Abstract: Substance productivity is improved by introducing a metabolic pathway for synthesis of acetyl-CoA or acetic acid from glucose-6-phosphate into yeast. Acetic acid productivity, acetyl-CoA productivity, and productivity of a substance made from acetyl-CoA-derived are improved by attenuating genes involved in the glycolytic system of yeast and introducing a phosphoketolase gene into the yeast.

Abstract: The present disclosure provides methods useful for producing fatty alcohol compositions from recombinant host cells. The disclosure further provides variant fatty acyl-CoA reductase (FAR) enzymes, polynucleotides encoding the variant FAR enzymes, and vectors and host cells comprising the same.

Abstract: Provided herein are metabolically modified microorganisms characterized by having an increased keto-acid flux when compared with the wild-type organism and comprising at least one polynucleotide encoding an enzyme that when expressed results in the production of a greater quantity of a chemical product when compared with the wild-type organism. The recombinant microorganisms are useful for producing a large number of chemical compositions from various nitrogen containing biomass compositions and other carbon sources.

Abstract: Provided are isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. Also provided are nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: The present invention relates to methods of degrading or converting a cellulosic material pretreated with a composition comprising one or more GH61 polypeptides.

Abstract: The present invention relates to extracted lipid with high levels, for example 90% to 95% by weight, oleic acid. The present invention also provides genetically modified plants, particularly oilseeds such as safflower, which can used to produce the lipid. Furthermore, provided are methods for genotyping and selecting plants which can be used to produce the lipid.

Abstract: An isolated nucleic acid molecule that encodes a terpene synthase and is selected from among: a) a nucleic acid molecule comprising the sequence of nucleotides set forth in SEQ ID NO: 1, SEQ ID NO: 3 or SEQ ID NO: 5; b) a nucleic acid molecule that is a fragment of (a); c) a nucleic acid molecule comprising a sequence of nucleotides that is complementary to (a)- or (b); and d) a nucleic acid molecule that encodes a terpene synthase having at least or at least about or at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity to any one of (a)-(c); wherein the nucleic acid molecule encodes a terpene synthase.

Abstract: The present invention relates to methods of producing n-propanol, isopropanol, and coproducing n-propanol with isopropanol. The present invention also relates to methods for producing propylene, as well as host cells capable of n-propanol and isopropanol production.

Abstract: A process for converting a feed gas containing at least one of CO, CO2, and/or H2 to a liquid product using biomass that grow on the surface of carriers suspended in a fermentation broth within the vessel of a moving bed bioreactor (MMBR). An injector is used to at least partially dissolved the feed gas in the fermentation broth, at least partially entrain the gas in the broth as microbubbles and to introduce the mixture of the entrained gas and broth into the vessel in a substantially horizontal direction. The injection of the mixture creates eddy current in the surrounding liquid for thoroughly mixing the fermentation broth in the vessel and for keeping the biomass carrier moving to provide sufficient shear so as to maintain a biofilm thickness on the carrier in a desirable range.

Abstract: One aspect of the invention relates to a genetically modified thermophilic or mesophilic microorganism, wherein a first native gene is partially, substantially, or completely deleted, silenced, inactivated, or down-regulated, which first native gene encodes a first native enzyme involved in the metabolic production of an organic acid or a salt thereof, thereby increasing the native ability of said thermophilic or mesophilic microorganism to produce lactate or acetate as a fermentation product. In certain embodiments, the aforementioned microorganism further comprises a first non-native gene, which first non-native gene encodes a first non-native enzyme involved in the metabolic production of lactate or acetate. Another aspect of the invention relates to a process for converting lignocellulosic biomass to lactate or acetate, comprising contacting lignocellulosic biomass with a genetically modified thermophilic or mesophilic microorganism.

Abstract: The present disclosure identifies pathways and mechanisms to confer improved industrial fitness on engineered organisms. It also discloses engineered organisms having improved industrial fitness. Synthetic biologic engineering modules are disclosed that provide for light capture, carbon dioxide fixation, NADH production, NADPH production, thermotolerance, pH tolerance, flue gas tolerance, salt tolerance, nutrient independence and near infrared absorbance. The disclosed engineered organisms can include one or more of these modules. Also provided are methods of using the engineered organism to produce carbon-based products of interest, biomass or pharmaceutical agents.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed to produce useful products, such as fuels. For example, systems can use feedstock materials, such as cellulosic and/or lignocellulosic materials and/or starchy materials, to produce ethanol and/or butanol, e.g., by fermentation.

Abstract: Cytochrome P450 BM-3 from Bacillus megaterium was engineered using a combination of directed evolution and site-directed mutagenesis to hydroxylate linear alkanes regio- and enantioselectively using atmospheric dioxygen as an oxidant. Mutant 9-10A-A328V hydroxylates octane primarily at the 2-positio to form S-2-octanol (40% ee). Another mutant, 1-12G, hydroxylates alkanes larger than hexane primarily at the 2-position, but forms R-2-alcohols (40-55% ee). These biocatalysts are highly active for alkane substrates and support thousands of product turnovers. These regio- and enantio-selectivities are retained in whole-cell biotransformations with E. coli, where the engineered P450s can be expressed at high levels and the expensive cofactor is supplied endogenously.

Abstract: Provided herein are methods for the increased production of intracellular acetyl-CoA, mevalonate, isoprenoid precursors, isoprene and/or isoprenoids by recombinant microorganisms via co-metabolism of substrates with varied oxidation levels.

Abstract: A method and system for efficiently producing a fermentative product alcohol such as butanol utilizing in situ product extraction are provided. The efficiency is obtained through separating undissolved solids after liquefying a given feedstock to create a feedstock and prior to fermentation, for example, through centrifugation. Removal of the undissolved solids avoids problems associated with having the undissolved solids present during in situ production extraction, and thereby increases the efficiency of the alcohol production.

Abstract: Genetically engineered plants having altered levels of one or more starch regulation enzymes and a polysaccharide degrading enzyme are provided. Methods of genetically engineering plants to express products altering expression of one or more starch regulation enzymes and polysaccharide degrading enzymes, and genetic constructs are provided. Methods of agricultural processing and animal feed using the genetically engineered plants are described.

Abstract: Integrated processes are provided for syngas refining and bioconversion of syngas to oxygenated organic compound. In the integrated processes ammonia contained in the syngas is recovered and used as a source of nitrogen and water for the fermentation. The integrated processes first remove tars from syngas by scrubbing using a first aqueous medium under conditions that ammonium bicarbonate is unstable. With tars removed, contact between the syngas and a second aqueous medium enables ammonia and carbon dioxide to be removed from the syngas without undue removal of components adverse to the fermentation, processing or oxygenated product such as benzene, toluene, xylene, ethylene, acetylene, and hydrogen cyanide. At least a portion of the second aqueous medium is supplied as a source of water and ammonia for the fermentation.

Abstract: A method of operating a fermentation zone for the production of ethanol from syngas uses a crotonate derivative to prevent or reverse the effects of butyrigen contamination. The crotonate compound works in continuous fermentation processes to reduce or eliminate contamination from butyrate and butanol in the syngas derived ethanol product.

Abstract: The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: The present invention relates to methods of saccharifying the trash (leaf) fraction of sugar cane using enzymes.

Abstract: Methods for producing an isoprenoid are provided. A plurality of bacterial or fungal host cells is obtained. These cells comprise a heterologous nucleic acid encoding one or more enzymes of a mevalonate pathway for making isopentenyl pyrophosphate. Expression of the one or more enzymes is under control of at least one heterologous transcriptional regulator. The mevalonate pathway comprises (i) an enzyme that condenses acetoacetyl-CoA with acetyl-CoA to form HMG-CoA, (ii) an enzyme that converts HMG-CoA to mevalonate, (iii) an enzyme that phosphorylates mevalonate to mevalonate 5-phosphate, (iv) an enzyme that converts mevalonate 5-phosphate to mevalonate 5-pyrophosphate, and (v) an enzyme that converts mevalonate 5-pyrophosphate to isopentenyl pyrophosphate. The host cells are cultured in a medium under conditions that are suboptimal as compared to conditions. Temperature is maintained at a level below that which would provide for a maximum specific growth rate for the host cells.

Abstract: This invention provides a recombinant yeast that can produce branched alcohol appropriate for automotive fuel and the like and a branched alcohol production method whereby branched alcohol can be produced at low cost with the use of the recombinant yeast. A recombinant yeast in which a hydroxymethyl glutaryl-CoA reductase gene has been expressed to a high degree and the ADP-ribose pyrophosphatase gene and/or the yhfR gene are introduced so as to be expressed therein is provided.

Abstract: A stable system for producing liquid products such as ethanol, butanol and other chemicals from syngas components contacts CO or a mixture of CO2 and H2 with a hydrophilic membrane under anaerobic conditions and transfers these components into contact with microorganisms contained as a biofilm on the membrane. Maintaining the microorganisms as a biolayer on the surface of the membrane facilitates cleaning of the membrane surface that retains the biofilm. In addition the shell gas space that surrounds the membranes may be flooded to reduce or remove the biofilm. Agitation of the liquid, by for example the bubbling of gas in the surrounding shell space, can fully or partially remove the biofilm from the membrane.