Abstract: The present invention provides enriched polynucleotides, and enriched polypeptides having pectinase activity. The present invention also includes methods of using the polynucleotides and polypeptides described herein. For instance, the methods include producing a metabolic product, such as ethanol.

Abstract: A stable continuous method for producing ethanol from the anaerobic bacterial fermentation of a gaseous substrate containing at least one reducing gas involves culturing in a fermentation bioreactor anaerobic, acetogenic bacteria in a liquid nutrient medium; supplying the gaseous substrate to the bioreactor; and manipulating the bacteria in the bioreactor by reducing the redox potential, or increasing the NAD(P)H TO NAD(P) ratio, in the fermentation broth after the bacteria achieves a steady state and stable cell concentration in the bioreactor. The free acetic acid concentration in the bioreactor is maintained at less than 5 g/L free acid. This method allows ethanol to be produced in the fermentation broth in the bioreactor at a productivity of greater than 10 g/L per day. Both ethanol and acetate are produced in a ratio of ethanol to acetate ranging from 1:1 to 20:1.

Abstract: A stable continuous method for producing ethanol from anaerobic fermentation of a gaseous substrate containing at least one reducing gas in a liquid nutrient medium; supplying the gaseous substrate to the bioreactor. The free acetic acid concentration in the bioreactor is maintained at less than 5 g/L free acid. This method allows ethanol to be produced in the fermentation broth in the bioreactor at a productivity of greater than 10 g/L per day. Both ethanol and acetate are produced in a ratio of ethanol to acetate ranging from 1:1 to 20:1.

Abstract: A stable continuous method for producing ethanol from anaerobic fermentation of a gaseous substrate containing at least one reducing gas in a liquid nutrient medium; supplying the gaseous substrate to the bioreactor. The free acetic acid concentration in the bioreactor is maintained at less than 5 g/L free acid. This method allows ethanol to be produced in the fermentation broth in the bioreactor at a productivity of greater than 10 g/L per day. Both ethanol and acetate are produced in a ratio of ethanol to acetate ranging from 1:1 to 20:1.

Abstract: A stable continuous method for producing ethanol from anaerobic fermentation of a gaseous substrate containing at least one reducing gas in a liquid nutrient medium; supplying the gaseous substrate to the bioreactor. The free acetic acid concentration in the bioreactor is maintained at less than 5 g/L free acid. This method allows ethanol to be produced in the fermentation broth in the bioreactor at a productivity of greater than 10 g/L per day. Both ethanol and acetate are produced in a ratio of ethanol to acetate ranging from 1:1 to 20:1.

Abstract: The invention provides recombinant GH61 proteins obtained from Myceliophtora thermophila, and nucleic acids that encode such proteins. The invention also provides protein fractions isolated from M. thermophila supernatant that have GH61 protein activity. These preparations can be used to increase yield of products from reactions in which a cellulose-containing substrate undergoes saccharification by one or more cellulase enzymes, such as endoglucanase, ?-glucosidase, or cellobiohydrolase. Combinations of GH61 protein and cellulases can be used to break down cellulosic biomass into fermentable sugars in the production of ethanol.

Abstract: The present invention aims to develop a pretreatment technology for performing efficient saccharification without losing carbohydrates (in particular, free carbohydrates, starch, xylan, or the like) due to solid-liquid separation and washing steps, as a pretreatment for enzymatic saccharification of a lignocellulosic biomass feedstock (including a lignocellulosic biomass feedstock containing readily degradable carbohydrates).

Abstract: Processes for removing water from organic solvents, such as ethanol. The processes include distillation in two columns operated at sequentially higher pressure, followed by treatment of the overhead vapor by one or two membrane separation steps.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed to produce useful intermediates and products, such as energy, fuels, foods or materials. For example, methods are described that can use feedstock materials, such as cellulosic and/or lignocellulosic materials, to produce an intermediate or product, e.g., by fermentation.

Abstract: The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

Abstract: The presently disclosed subject matter related to methods of converting lignocellulosic materials to alcohol that include increasing the fiber consistency of enzymatic hydrolysis mixtures. More particularly, the methods involve contacting lignocellulosic biomass with an enzyme composition for a period of time, and then thickening the mixture and further hydrolyzing the thickened mixture. The thickening can be performed by filtration, optionally reusing the filtrate and/or any enzymes contained therein during the lignocellulose conversion process to increase the efficiency of the process. Hydrolysis of the thickened mixture provides a fermentable sugar mixture having a higher concentration of sugar than fermentable sugar mixtures provided from less concentrated biomass/enzyme mixtures. Compositions comprising alcohol prepared according to the presently disclosed methods are also provided.

Abstract: The present invention relates to a process for the production of ethanol and butanol from biomass, and in particular to a process for the production of ethanol and butanol using two separate fermentation steps, said process comprising: a) passing a biomass feedstock to a first fermentation step, b) in said first fermentation step subjecting the biomass feedstock to anaerobic fermentation at a pH below 6.0 and at a temperature in the range 20 to 700° C.

Abstract: Biomass is converted to short chain alcohols such as butanol by a process which comprises (1) reacting biomass with an oxidizing agent to produce unoxidized aromatic and/or phenolic compounds and C1-6 linear and branched, saturated and unsaturated carboxylic acids; (2) separating the unoxidized aromatic and/or phenolic compounds from the C1-6 carboxylic acids; (3) anaerobically fermenting the C1-6 carboxylic acids in the presence of an anaerobic bacterium in its solventogenesis phase to produce a solvent comprised of butanol and non-fermentable carboxylic acids. The products of the process can be used as fuel and/or fuel additives.

Abstract: Processes for removing water from organic solvents, such as ethanol. The processes include distillation in two columns operated at sequentially higher pressure, followed by treatment of the overhead vapor by one or two membrane separation steps.

Abstract: Embodiments of the present disclosure relate to a process for producing downstream products, such as fermentable sugars and end products, 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: This invention relates to novel enzymes and novel methods for producing the same. More specifically this invention relates to a variety of fungal enzymes. Nucleic acid molecules encoding such enzymes, compositions, recombinant and genetically modified host cells, and methods of use are described. The invention also relates to a method to convert lignocellulosic biomass to fermentable sugars with enzymes that degrade the lignocellulosic material and novel combinations of enzymes, including those that provide a synergistic release of sugars from plant biomass. The invention also relates to methods to use the novel enzymes and compositions of such enzymes in a variety of other processes, including washing of clothing, detergent processes, deinking and biobleaching of paper and pulp, and treatment of waste streams.

Abstract: A process and system for converting animal waste to useful biofuel products, and more particularly a process and system for converting excrement from lactating dairy cattle to a combination of ethanol, methane, carbon dioxide and fertilizer is presented. The system uses a continuous process to place the animal waste into an aqueous mixture with a starter sugar and a digestive microorganism into a heated anaerobic digester. The products of the reactions within the digester include methane, which is extracted in a gaseous form, and ethanol and carbon dioxide, which are separated out of an aqueous solution in a distillation column. The water from the solution is recycled and the solid residue remaining in the digester is dried in a rotary kiln and granulated to form a fertilizer material.

Abstract: This invention relates to novel enzymes and novel methods for producing the same. More specifically this invention relates to a variety of fungal enzymes. Nucleic acid molecules encoding such enzymes, compositions, recombinant and genetically modified host cells, and methods of use are described. The invention also relates to a method to convert lignocellulosic biomass to fermentable sugars with enzymes that degrade the lignocellulosic material and novel combinations of enzymes, including those that provide a synergistic release of sugars from plant biomass. The invention also relates to methods to use the novel enzymes and compositions of such enzymes in a variety of other processes, including washing of clothing, detergent processes, deinking and biobleaching of paper and pulp, and treatment of waste streams.

Abstract: The present invention relates to a process for enzymatic hydrolysis of granular starch into a soluble starch hydrolysate at a temperature below the initial gelatinization temperature of said granular starch.

Abstract: A method includes operating an apparatus having a mash circulating and recirculating system with pump and fermentation tank, an atmosphere circulating and recirculating system with blower for recirculating atmosphere between the tank and an ethanol-removal station, and an integrated refrigerating heat-transfer system with first coils remote from the tank for condensing out ethanol from the atmosphere, and second coils for warming the mash. The entire apparatus can be up-sized or down-sized for specific applications. In one form, the system includes electrically-driven pump, blower, and refrigeration compressors, with the external energy consumption being entirely electrical and kept surprisingly low.

Abstract: The present invention provides a modular ethanol production plant constructed of a number of identically sized modules each having a supporting structure main framework to which the components contained in the modules are attached. The plurality of modules includes a fermentation module, a distillation module, a ground grain module, and an optional heating module. Each of the modules are sized to occupy the same approximate space as a standard sized ocean going shipping container. Also, each of the modules has a central walkway including piping and electrical control boxes that are aligned for each connection to the next adjacent module.

Abstract: The invention provides variants of the Clostridium thermocellum endoglucanase (CeIG) that have improved endoglucanase activity compared to the wild type enzyme. Also provided are related polynucleotides, compositions, vectors, host cells, and methods of use.

Abstract: Methods are disclosed for the production of high concentrations of ethanol from biomass using Zymomonas as the ethanologen. Zymomonas is grown under conditions of low impeller agitation with high concentration of insoluble solids in a saccharification-fermentation mixture during a simultaneous saccharification and fermentation reaction for the production of high concentrations of ethanol.

Abstract: Techniques, systems, apparatus and material are disclosed for generating multi-purpose H2-dense fuel for isolating contaminants and storing energy. In one aspect, a method of producing a renewable multi-purpose biomaterial for isolating a hazardous contaminant from an environment and storing energy includes dissociating biomass waste using a thermochemical reaction to produce at least one of hydrocarbon and alcohol by applying waste heat recovered from an external heat source. The method includes dissociating the at least one of hydrocarbon and alcohol to generate carbon and hydrogen. Carbon dioxide emitted from an industrial process is harvested and reacted with the hydrogen to generate the hydrogen-dense fuel. A hazardous contaminant is dissolved in the hydrogen-dense fuel operating as a solvent to generate a liquid mixture that isolates the hazardous contaminant from the environment. The hazardous contaminant includes at least one of a carbon donor and a hydrogen donor.

Abstract: The present disclosure relates to hydrolysis of mannan-containing poly- or oligo-saccharides by use of a polypeptide having endo-?-mannanase activity. In particular the present disclosure relates to compositions comprising a bacterial endo-?-mannanase, polynucleotides encoding the endo-?-mannanase, and methods of use thereof.

Abstract: The present invention relates to an enzyme blend composition comprising a glucoamylase, an acid stable alpha amylase, and an acid fungal protease. The present invention is further directed to a method for producing end products such as alcohols from fermentable sugars, comprising the steps of: (a) contacting a slurry comprising a milled grain that contains starch with an alpha amylase to produce a liquefact; (b) contacting the liquefact with a glucoamylase, an acid stable alpha amylase, and an acid fungal protease, to produce fermentable sugars; and (c) fermenting the fermentable sugars in the presence of a fermenting organism to produce end products.

Abstract: Ethanol and other liquid products are produced by contacting syngas components such as CO or a mixture of CO2 and H2 with a surface of a membrane under anaerobic conditions and transferring these components into contact with a biofilm on the opposite side of the membrane. These steps provide a stable system for producing liquid products such as ethanol, butanol and other chemicals. The gas fed on the membrane's gas contact side transports through the membrane to form a biofilm of anaerobic microorganisms that converted the syngas to desired liquid products. The system can sustain production with a variety of microorganisms and membrane configurations.

Abstract: The present invention relates to a process for the production of second generation biofuels and/or sugar based chemicals—for example ethanol, butanol etc—and/or materials—for example plastics, single cell proteins etc.—together with sulfonated lignin from lignocellulosic biomass, in particular from lignocellulosic biomass comprising, among others, annual plants, agricultural waste, or wood. In particular, the present invention relates to a process for the production of sugar based chemicals, biofuels or materials together with sulfonated lignin from lignocellulosic biomass comprising the pretreatment of a lignocellulosic biomass in a sulfite cooking step.

Abstract: Methods for treating biomass for release of fermentable sugars with an improved inhibitor profile are provided. Specifically, a hydrolysate comprising fermentable sugars with an improved inhibitor profile is obtained by saccharification of a reaction product obtained by pretreating biomass with ammonia under suitable reaction conditions. The pretreated biomass reaction product has an acetamide to acetate molar ratio greater than about 1 and an acetyl conversion of greater than 60%. The acetamide to acetate molar ratio is maintained greater than about 1 throughout saccharification. The hydrolysate may be fermented to a target compound.

Abstract: A system for making biofuels comprising methane, ethanol, and biodiesel comprises a tank (100) with a sealable lid (120). An algae mass (105), water, and either a yeast or bacterial culture (106) is added to the tank. Under high temperature conditions, sour (CO2-containing) methane is produced and stored in a container (130). Under lower temperature conditions, ethanol and CO2 are produced. Heated or cooled water passed through a water jacket (160) that surrounds the tank maintains the proper temperature within the tank. The CO2 is stored in a second container (270). The sour methane and the CO2 are optionally passed through a scrubber. Scrubbed methane is suitable for use as a fuel and drives a generator (275) that supplies power to various parts of the system. Carbon credits will be available for CO2 that is trapped in the scrubber. A still (185) separates ethanol and water for later use. Biodiesel can also be made in the apparatus by first making ethanol, then employing a transesterification process.

Abstract: A resource production system using a byproduct from the production of ethanol for efficiently producing biogas and fertilizer from the byproducts of ethanol production. The resource production system using a byproduct of a production of ethanol generally includes a plurality of processes for producing an inorganic renewable fertilizer, such as struvite and a non-fossil fuel source of energy, such as biogas, by using various types of byproducts produced by the ethanol plant, such as but not limited to whole stillage, thin stillage and thin stillage solubles. The process also produces an organic fertilizer, such as biosolids and a liquid stream suitable for further processing to produce recyclable water at the ethanol plant.

Abstract: The present invention provides a pretreatment method which enables the promotion of the enzymatic glycosylation of lignocellulose under relatively mild conditions by using a tree bark as a raw material with less energy. Specifically the present invention provides a step for producing a sugar from a tree bark, which is characterized by having the following steps: an alkali treatment step of immersing the tree bark in an alkali compound solution; a refining treatment step of refining the alkali treated tree bark mechanically into fine pieces; and an enzymatic glycosylation step of glycosylating the refined tree bark with an enzyme. The present invention also provides a method of producing an ethanol.

Abstract: Provided herein are methods for producing fermentable sugar obtained from a plant tissue. The methods include providing transgenic plant material comprising one or more locked carbohydrates and contacting plant material with an enzyme capable of converting the locked carbohydrate into a fermentable sugar. The methods are useful for providing sugar or sugar pre-cursors for several industrial purposes including ethanol production. The invention also encompasses plants and plant parts that produce a lock enzyme to yield a locked carbohydrate, with the consequence of accumulating the locked carbohydrate in the plant. The invention also encompasses providing a key enzyme able to convert locked carbohydrates to fermentable sugars. Key enzymes can be provided by transgenic plants or plant parts, transgenic microbes, transgenic yeast, microbes or yeast.

Abstract: The present invention relates to a process for enzymatic hydrolysis of granular starch into a soluble starch hydrolysate at a temperature below the initial gelatinization temperature of said granular starch.

Abstract: This invention provides systems and methods for the production of compounds by C. phytofermentans. C. phytofermentans is genetically-engineered for hydrolysis and fermentation of carbonaceous biomass to synthesize compounds of commercial value.

Abstract: Some aspects of this invention provide methods and bioreactors for converting a carbon source into a lipid. In some embodiments, lipid production is carried out in an aerobic fermentor and carbon dioxide generated during lipid production is converted into a carbon substrate by CO2 fixation in an anaerobic fermentor. In some embodiments, the carbon substrate generated by CO2 fixation is used as the carbon source for lipid production, thus achieving total carbon utilization in lipid production.

Abstract: An apparatus includes a mash circulating system with pump and fermentation tank, an atmosphere circulating system with blower for circulating atmosphere between the tank and an ethanol-removal station, and an integrated refrigerating heat-transfer system with first coils for condensing out ethanol from the atmosphere, and second coils for warming the mash. A support frame supports portions of the above components, making it a transportable modular unit to facilitate installation, minimize cost, and provide for efficient operation. The entire apparatus can be up-sized or down-sized for specific applications. In one form, the system includes electrically-driven pump, blower, and refrigeration compressors, with the external energy consumption kept surprisingly low. Methods related to the above are also disclosed.

Abstract: Provided herein are methods for producing a fermentation product, such as ethanol, by co-culture of a member of the genus Paenibacillus and an ethanologenic microbe, such as yeast or E. coli. Also provided are methods for making enzymes useful in the saccharification of a pretreated lignocellulosic material. The enzymes may be made by culturing a member of the genus Paenibacillus in a composition suitable for production of such enzymes. An example of such a composition is a pretreated lignocellulosic material, for example, spent hydrolysates. Also provided are genetically modified members of the genus Paenibacillus that have been genetically modified to not produce an antimicrobial, for instance, a polymyxin E.

Abstract: A process for producing ethanol including a combination of biochemical and synthetic conversions results in high yield ethanol production with concurrent production of high value coproducts. An acetic acid intermediate is produced from carbohydrates, such as corn, using enzymatic milling and fermentation steps, followed by conversion of the acetic acid into ethanol using esterification and hydrogenation reactions. Coproducts can include corn oil, and high protein animal feed containing the biomass produced in the fermentation.

Abstract: The present invention is directed to the enhanced production of ethanol from fermentation using an ethanol producing microorganism. In particular, the present invention provides a process for the enhanced growth and metabolism of an ethanol producing microorganism (e.g., yeast), for the purpose of increasing or enhancing ethanol production, both in terms of total ethanol produced and in terms of the time required for ethanol producing microorganisms to convert carbohydrates and/or sugars to end products (i.e., ethanol). In accordance with this invention bicarbonate ions are used to enhance ethanol fermentation and/or reduce the time required for ethanol producing microorganisms to convert carbohydrates and/or sugars to end products, i.e., ethanol. The present invention can also be used for enhancing fermentation end products in, for example, the fuel ethanol, industrial, cheese, brewing, and wine making industries.

Abstract: Provided are methods for the efficient and cost-reduced production of ethanol or other fermentation products or both from cellulosic biomass, which methods exploit the optimal features of yeasts, fungi, and bacteria while simultaneously minimizing their limitations. For example, one aspect of the present invention relates to methods of producing ethanol or other fermentation products or both from lignocellulosic biomass via progressive fermentation using in series or parallel two or more of yeast, fungus, and bacteria.

Abstract: Disclosed are methods for producing high levels of alcohol during fermentation of plant material, and to the high alcohol beer produced.

Abstract: A method to reduce enzyme usage for the break down of lignocellulosic material by enzymatic hydrolysis. Enzyme activity is retained and enzymes are recycled back for the hydrolysis of new lignocellulosic material after removal of fermentation products using low temperature distillation.

Abstract: A process for producing ethanol by the conversion of carbohydrates from a corn dry milling process in which the bottoms fraction from distillation of ethanol in a conventional yeast fermentation is used in a process including a combination of biochemical and synthetic conversions. The process results in high yield ethanol production with concurrent production of high value coproducts. An acetic acid intermediate is produced from bottoms fraction, followed by conversion of the acetic acid into ethanol using esterification and hydrogenation reactions. Coproducts of the process include a high protein content solids fraction produced in the fermentation.

Abstract: A process is disclosed for converting complex plant polysaccharides, including cellulosic materials, into fuels and other chemicals.

Abstract: Processes and systems for production of bioproducts such as biofuels are provided. The bioproduct production processes and systems utilize pretreatment of a carbohydrate-containing feedstock to produce soluble sugar molecules and continuous conversion of the pretreated feedstock to a bioproduct by an immobilized fermenting microorganism.

Abstract: The present invention relates to a process for the production of ethanol comprising both gasification and fermentation of feedstocks, and, in particular to a process for the production of ethanol comprising: a) passing a biomass feedstock to a first fermentation step wherein it is subjected to anaerobic fermentation at a pH below 6.0 and at a temperature in the range 20 to to convert the biomass to a solution comprising acetic acid as the predominant product, b) passing a gasifiable feedstock to a gasification step wherein it is subjected to gasification to produce a gaseous mixture comprising carbon monoxide and hydrogen, and c) passing the solution comprising acetic acid from step (a) and the gaseous mixture from step (b) to one or more further fermentation steps wherein they are subject to fermentation to produce ethanol.

Abstract: A method of increasing the rate of conversion of reactants to reaction product of enzyme catalyzed, reversible, i.e., equilibrium, reactions having water or methanol as byproduct includes removing water and/or methanol from the reaction mass during reaction by permeation of the reaction mass through a selectively permeable perfluorinated polymer or copolymer membrane.

Abstract: A process for pretreating a lignocellulosic plant raw material in order to obtain a pretreated material that is capable of being hydrolyzed and fermented for the production of bioethanol, includes the following successive steps: (i) destructuring the lignocellulosic plant raw material by placing it in the presence of a mixture containing formic acid and water, at a reaction temperature between 95° C. and 110° C.; (ii) then, at atmospheric pressure and prior to any hydrolysis then fermentation action, separating: on the one hand, the solid phase, mainly composed of the cellulose, constituting a first co-substrate, capable of then being hydrolyzed and fermented for the production of bioethanol; and on the other hand, the liquid phase, containing, in particular in aqueous solution, the formic acid, the lignins, and the hemicelluloses, constituting a second co-substrate, capable of then being hydrolyzed and fermented for the production of bioethanol.

Abstract: The invention relates to uses of polypeptides having amylase activity, nucleic acids encoding them, and methods for making and using them. For example, in one aspect, the invention provides methods for making alcohol using polypeptides of the invention. In one aspect, the polypeptides having amylase activity have increased activity and stability at acidic, neutral and alkaline pH and increased temperature. In one aspect, the invention provides methods for producing an alcohol, for producing a high-maltose or a high-glucose syrup or a mixed syrup, for liquifying a starch-comprising composition, for hydrolyzing a starch, comprising use of polypeptides of the invention, or polypeptides encoded by the nucleic acids of this invention.