Abstract: The invention generally relates to methods, devices, and microbes involved in performing redox imbalanced fermentations. In one aspect, the invention provides a device that generally includes an electrode and at least one microbe in electron communication with the electrode. The microbe generally can exhibit increased activity of at least one enzyme involved in converting a substrate to a redox imbalanced product. In another aspect, the invention provides a method for performing redox imbalanced fermentation. Generally, the method includes providing a substrate to a microbe under conditions effective for the microbe to metabolize the substrate to a redox imbalanced product. At least one microbe may be in contact with an electrode. In some cases, metabolic conversion of the substrate to the redox imbalanced product can include transferring electrons between the electrode and the microbe.

Abstract: The invention provides non-naturally occurring microbial organisms having a propylene pathway. The invention additionally provides methods of using such organisms to produce propylene.

Abstract: Disclosed are methods and systems for treating cellulose to make it more accessible for enzymatic or chemical modification. The invention includes treating cellulose with an alkali in an alcohol/water co-solvent system. The treatment decrystallizes or deaggregates the cellulosic material. The methods and systems increase the efficiency of enzymatic or chemical modifications of cellulose for use as biofuels or cellulose derivatives.

Abstract: The present invention is directed to variant squalene synthase enzymes, including Saccharomyces cerevisiae squalene synthase enzymes, and to nucleic acid molecules encoding these variant enzymes. These variant enzymes produce squalene at a lower rate than the wild-type enzyme, allowing more farnesyl pyrophosphate to be utilized for production of isoprenoid compounds, while still producing sufficient squalene to allow the S. cerevisiae cells to grow without the requirement for supplementation by sterols such as ergosterol. These variant enzymes, therefore, are highly suitable for the efficient production of isoprenoids.

Abstract: Method for preparing a mono-unsaturated alkene comprising contacting an aliphatic mono-unsaturated carboxylic acid with an Fdc1 polypeptide comprising an amino acid sequence with at least 21% sequence identity to SEQ ID NO: 1 and a Pad1 polypeptide comprising an amino acid sequence with at least 17% sequence identity to SEQ ID NO: 2.

Abstract: The present invention provides for novel metabolic pathways to convert biomass and other carbohydrate sources to malonyl-CoA derived products, such as hydrocarbons and other bioproducts, under anaerobic conditions and with the net production of ATP. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to achieve conversion of a carbohydrate source to, e.g., long-chain hydrocarbons and hydrocarbon derivatives, wherein the one or more native and/or heterologous enzymes is activated, upregulated, downregulated, or deleted. The invention also provides for processes to convert biomass to malonyl-CoA derived products which comprise contacting a carbohydrate source with a recombinant microorganism of the invention.

Abstract: Embodiments of the present invention provide for efficient and economical production and recovery of volatile organic compounds and hydrocarbons. One embodiment comprises contacting a solid component of a biomass material with a solution adapted to facilitate saccharification, and contacting the at least one fermentable sugar with a microorganism capable of using the at least one fermentable sugar to generate a hydrocarbon. The solid component is generated by introducing a biomass material to a compartment of a solventless recovery system, wherein the biomass material contains one or more volatile organic compounds; contacting the biomass material with a superheated vapor stream in the compartment to vaporize at least a portion of an initial liquid content in the biomass material; separating a vapor component and a solid component from the heated biomass material; and retaining at least a portion of the gas component for use as part of the superheated vapor stream.

Abstract: Provided are methods for degrading or converting a cellulosic material, comprising: treating the cellulosic material with an enzyme composition in the presence of a polypeptide having catalase activity; and enzyme composition used for degrading or converting a cellulosic material comprising one or more (e.g., several) enzymes having cellulolytic and/or hemicellulolytic activity and a polypeptide having catalase activity.

Abstract: A method of producing at least one terpene in a yeast cell is disclosed. The method comprises exogenously expressing within the mitochondria of the yeast cell or directing localization thereto a terpene synthase.

Abstract: The NonA alkene synthase in Synechococcus sp. displays selective synthesis of 1-nonadecene. Heterologous recombination of a domain, i.e. the acyl binding domain, with other acyl binding proteins, affects acyl substrate chain-length binding selectivity and therefore the chain-length of the synthesized 1-alkenes. Compositions and methods are provided to selectively synthesize 1-alkenes of various chain lengths.

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: 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: Provided herein are compositions and methods related to the direct conversion of the starch in a ground or fractionated grain into a fermentable sugar feedstock capable of serving as a carbon source for the industrial production of one or more products by a fermenting organism, such as isoprene, isoprenoid precursor molecules, and/or isoprenoids. Such conversions may be performed at temperatures at or below the initial gelatinization temperature of the starch present in the grain and may utilize one or more isolatable endogenous enzymes present in certain unrefined grains.

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: 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: 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: The present invention provides for a polyketide synthase (PKS) capable of synthesizing an ?-olefin, such as 1-hexene or butadiene. The present invention also provides for a host cell comprising the PKS and when cultured produces the ?-olefin.

Abstract: Disclosed herein a process for upgrading the liquid hydrocarbon fuels by reducing aromatic content, sulfur content and nitrogen content wherein the process comprising isolating polycyclic aromatic hydrocarbon (PAH) transforming microbes and preparing biocatalyst by mutagenesis, contacting the biocatalyst with the liquid hydrocarbon fuel in an aqueous medium for transforming the aromatic, sulfur, and nitrogen containing compounds to polar substances, subjecting the mixture of biocatalyst and the liquid hydrocarbon fuel to a process of bioconversion, removing the polar substances by liquid-liquid extraction with a polar solvent to obtain dearomatized, desulphurised and denitrogenated liquid hydrocarbon fuel and recovering the upgraded liquid hydrocarbon fuel.

Abstract: The invention relates to nucleic acids encoding a zingiberene synthase that enables host cells and plants to make zingiberene that is useful in fragrances and for repelling or killing insects. The invention also relates to isolated zingiberene synthases and to methods for making zingiberenes.

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

Abstract: A method for producing at least one compound selected from the group consisting of 1,8-cineole, and 1-methyl-1,4-cyclohexadiene is also described. The method includes culturing a microorganism on or within a culturing media in a container under conditions sufficient for producing the at least one compound.

Abstract: Methods for forming hydrocarbon products from bacteria, namely, bacteria which produce fatty acids, are disclosed. The methods involve the bacterial production of fatty acids, the thermal decarboxylation of the resulting fatty acids, the hydrocracking and isomerization of the decarboxylation product, and the distillation to yield the desired hydrocarbon fractions. The products can be isolated in the gasoline, jet and/or diesel fuel ranges. Thus, bacteria can be used to produce products in the gasoline, jet and/or diesel fuel ranges which are virtually indistinguishable from those derived from their petroleum-based analogs.

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: Methods of manufacturing fuels are provided. These methods use often difficult to process lignocellulosic materials, for example crop residues and grasses. The methods can be readily practiced on a commercial scale in an economically viable manner, in some cases using as feedstocks materials that would otherwise be discarded as waste.

Abstract: The present invention is directed to variant squalene synthase enzymes, including Saccharomyces cerevisiae squalene synthase enzymes, and to nucleic acid molecules encoding these variant enzymes. These variant enzymes produce squalene at a lower rate than the wild-type enzyme, allowing more farnesyl pyrophosphate to be utilized for production of isoprenoid compounds, while still producing sufficient squalene to allow the S. cerevisiae cells to grow without the requirement for supplementation by sterols such as ergosterol. These variant enzymes, therefore, are highly suitable for the efficient production of isoprenoids.

Abstract: The present invention provides a method for producing a fermentation product from lignocellulose-containing material, a method for converting lignocellulose-containing material into a hydrolyzate comprising mono- and oligo-saccharides, and a method for treating lignocellulose-containing material, all of which comprise the step of mixing an acid pre-treated lignocellulose-containing material and an alkaline pre-treated lignocellulose-containing material. The present invention further provides a fermentation product made according to the method for producing a fermentation product.

Abstract: Provided herein are compositions and methods for the heterologous production of acetyl-CoA-derived isoprenoids in a host cell. In some embodiments, the host cell is genetically modified to comprise a heterologous nucleotide sequence encoding an acetaldehyde dehydrogenase, acetylating (ADA, E.C. 1.2.1.10) and an MEV pathway comprising an NADH-using HMG-CoA reductase. In some embodiments, the host cell is genetically modified to comprise a heterologous nucleotide sequence encoding an ADA and an MEV pathway comprising an acetoacetyl-CoA synthase. In some embodiments, the genetically modified host cell further comprises one or more heterologous nucleotide sequences encoding a phosphoketolase and a phosphotransacetylase. In some embodiments, the genetically modified host cell further comprises a functional disruption of the native PDH-bypass. The compositions and methods described herein provide an energy-efficient yet redox balanced route for the heterologous production of acetyl-CoA-derived isoprenoids.

Abstract: A process for producing ethylene from a carbonaceous containing feedstock the process comprising the steps of a) reforming the carbonaceous containing feedstock into a first product stream comprising carbon dioxide, carbon monoxide and hydrogen; b) fermenting the first product stream with an acetogenic anaerobic bacteria to produce a second product stream comprising ethanol; c) concentrating ethanol from the second product stream into a third product stream and; d) dehydrating ethanol in the third product stream to produce ethylene.

Abstract: The present invention provides for the improved production of fatty acid products in a recombinant microorganism or host cell engineered to express a non-native gene encoding a thioesterase and a non-native gene encoding a lysophosphatidic acid acyltransferase (LPAAT), in which the LPAAT is overexpressed in the recombinant microorganism compared to an otherwise identical microorganism that does not include the non-native LPAAT gene. The invention also provides methods of producing fatty acid products using such recombinant microorganisms.

Abstract: The present invention relates to polypeptide having cellulolytic enhancing activity variants. 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: The present invention relates to the production of a isoprenoid products from a lignocellulosic feedstock. Specifically at least triple mutant of filamentous fungi having the isoprenoid pathway results in production of isoprenoid products in commercial quantities. One embodiment of the invention relates to producing the isoprenoid products at the site of the lignocellulosic feedstock to reduce costs of shipping the feedstock.

Abstract: Hydrocarbon and hydrogen fuels and other products may be produced by a process employing a combination of fermentation and electrochemical stages. In the process, a biomass contained within a fermentation medium is fermented with an inoculum comprising a mixed culture of microorganisms derived the rumen contents of a rumen-containing animal. This inoculated medium is incubated under anaerobic conditions and for a sufficient time to produce volatile fatty acids. The resultant volatile fatty acids are then subjected to electrolysis under conditions effective to convert said volatile fatty acids to hydrocarbons and hydrogen simultaneously. The process can convert a wide range of biomass materials to a wide range of volatile fatty acid chain lengths and can convert these into a wide range of biobased fuels and biobased products.

Abstract: In one aspect, a method for rendering biomass-derived pyrolysis oil miscible with refinery hydrocarbons comprises mixing a high oxygen content bio-oil having an oxygen content of at least about 10 wt. % with a low oxygen content bio-oil having an oxygen content of less than about 8 wt. % to produce a blended oil. The blended oil may be hydrotreated to produce a deoxygenated hydrotreated mixture from which water is removed using a separator, resulting in a low oxygen content hybrid bio-oil intermediate miscible in refinery process streams. A portion of the low oxygen content hybrid bio-oil intermediate may be recycled with the high oxygen content bio-oil or removed for use in a refinery process stream for further hydroprocessing.

Abstract: The present disclosure relates to oxidative decarbonylase enzymes, methods of making hydrocarbons with such enzymes, hydrocarbons produced therefrom and uses thereof. More particularly, the present disclosure relates to isolated polypeptide sequences that are cytochrome P450 enzymes with oxidative decarbonylase activity and methods of their use to generate hydrocarbon products, such as biofuels.

Abstract: The present invention relates to variants of a parent beta-glucosidase. 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: The invention relates to recombinant expression of a taxadiene synthase enzyme and a geranylgeranyl diphosphate synthase (GGPPS) enzyme in cells and the production of terpenoids.

Abstract: The present invention provides isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also provides 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 an integrated method and system for the simultaneous production of biodiesel from free fatty acids (via esterification) and from triglycerides (via transesterification) within the same reaction chamber. More specifically, one preferred embodiment of the invention relates to a method and system for the production of biodiesel using an electrodeionization stack, wherein an ion exchange resin matrix acts as a heterogeneous catalyst for simultaneous esterification and transesterification reactions between a feedstock and a lower alcohol to produce biodiesel, wherein the feedstock contains significant levels of free fatty acid. In addition, because of the use of a heterogeneous catalyst, the glycerol and biodiesel have much lower salt concentrations than raw biodiesel produced by conventional transesterification processes. The present invention makes it much easier to purify glycerol and biodiesel.

Abstract: Methods and systems for the production of hydrocarbon products, including providing a substrate comprising CO to a bioreactor containing a culture of one or more micro-organisms; and fermenting the culture in the bioreactor to produce one or more hydrocarbon products. The substrate comprising CO is derived from a CO2 reforming process.

Abstract: Embodiments of the present disclosure relate to a process for producing isoprenoid precursor molecules and/or isoprenoids from a starch substrate by saccharification and/or fermentation. The saccharification is effectively catalyzed by a glucoamylase at a pH in the range of 5.0 to 8.0. At a pH of 6.0 or above, the glucoamylase possesses at least 50% activity relative to its maximum activity. The saccharification and fermentation may be performed as a simultaneous saccharification and fermentation (SSF) process.

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

Abstract: Provided are ATP-binding cassette transporters (ABC transporters). More specifically, the present disclosure relates to ABC terpenoid transporters, nucleic acid sequences, amino acids, proteins, vectors, cells, transgenic organisms, uses, compositions, methods, processes, and kits thereof.

Abstract: The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a sulfur-containing compound. The present invention also relates to methods of using the compositions.

Abstract: Methods and systems to achieve clean fuel processing systems in which carbon dioxide emissions (1) from sources (2) may be processed in at least one processing reactor (4) containing a plurality of chemoautotrophic bacteria (5) which can convert the carbon dioxide emissions into biomass (6) which may then be used for various products (21) such as biofuels, fertilizer, feedstock, or the like. Sulfate reducing bacteria (13) may be used to supply sulfur containing compounds to the chemoautotrophic bacteria (5).

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

Abstract: The present invention is directed to variant squalene synthase enzymes, including Saccharomyces cerevisiae squalene synthase enzymes, and to nucleic acid molecules encoding these variant enzymes. These variant enzymes produce squalene at a lower rate than the wild-type enzyme, allowing more farnesyl pyrophosphate to be utilized for production of isoprenoid compounds, while still producing sufficient squalene to allow the S. cerevisiae cells to grow without the requirement for supplementation by sterols such as ergosterol. These variant enzymes, therefore, are highly suitable for the efficient production of isoprenoids.

Abstract: The present invention is directed to variant squalene synthase enzymes, including Saccharomyces cerevisiae squalene synthase enzymes, and to nucleic acid molecules encoding these variant enzymes. These variant enzymes produce squalene at a lower rate than the wild-type enzyme, allowing more farnesyl pyrophosphate to be utilized for production of isoprenoid compounds, while still producing sufficient squalene to allow the S. cerevisiae cells to grow without the requirement for supplementation by sterols such as ergosterol. These variant enzymes, therefore, are highly suitable for the efficient production of isoprenoids.

Abstract: A process for production of biofuels from algae can include cultivating an oil-producing algae by promoting sequential photoautotrophic and heterotrophic growth. The method can further include producing oil by heterotrophic growth of algae wherein the heterotrophic algae growth is achieved by introducing a sugar feed to the oil-producing algae. An algal oil can be extracted from the oil-producing algae, and can be converted to form biodiesel.

Abstract: According to the present invention, organic material is converted to biogas through anaerobic digestion and the biogas is purified to yield a combustible fluid feedstock comprising methane. A fuel production facility utilizes or arranges to utilize combustible fluid feedstock to generate renewable hydrogen that is used to hydrogenate crude oil derived hydrocarbons in a process to make transportation or heating fuel. The renewable hydrogen is combined with crude oil derived hydrocarbons that have been desulfurized under conditions to hydrogenate the liquid hydrocarbon with the renewable hydrogen or alternatively, the renewable hydrogen can be added to a reactor operated so as to simultaneously desulfurize and hydrogenate the hydrocarbons. The present invention enables a party to receive a renewable fuel credit for the transportation or heating fuel.

Abstract: According to the present invention, organic material is converted to biogas through anaerobic digestion and the biogas is purified to yield a combustible fluid feedstock comprising methane. A fuel production facility utilizes or arranges to utilize combustible fluid feedstock to generate renewable hydrogen that is used to hydrogenate crude oil derived hydrocarbons in a process to make liquid transportation or heating fuel. The renewable hydrogen is combined with crude oil derived hydrocarbons that have been desulfurized under conditions to hydrogenate the hydrocarbons with the renewable hydrogen.