Abstract: This invention describes discovery and development of a biological system of plant growth promotion and environmental improvement by carbon sequestration and/or nitrogen utilization by application of a microbial agent, e.g., a highly effective strain of T. viride, particularly strains NRRL B-50520 and/or K5. This strain outperforms the best current strains of Trichoderma used for this purpose available commercially. The highly active products also are expected to increase plant productivity and improve quality of fruits, vegetables, flowers or other plant products. The invention also describes and demonstrates that strain combinations including Bacillus amyloliquifaciens AS2 or AS3, as well as disclosed metabolites, promote plant growth. This is true across monocots and dicots, seed treatments and foliar sprays.

Abstract: Disclosed herein are plant propagation materials, methods of manufacturing, formulations and uses thereof. The plant propagation materials disclosed herein may comprise a strigolactone obtained by a biosynthetic process. The plant propagation material may comprise a chemical mimic of a strigolactone. The strigolactone may be 5-deoxystrigol. Methods of manufacturing the plant propagation materials may comprise a chemical process. Alternatively, methods of manufacturing the plant propagation material may comprise a biosynthetic process. The methods may comprise use of one or more polynucleotides. The polynucleotides may encode a metabolite. The polynucleotides may comprise one or more genes encoding one or more components of a strigolactone pathway.

Abstract: The present invention provides methods, compositions and articles of manufacture useful for the prophylactic and therapeutic amelioration and treatment of gram-positive bacteria, including Streptococcus and Staphylococcus, and related conditions. The invention provides compositions and methods incorporating and utilizing Streptococcus suis derived bacteriophage lysins, particularly PlySs2 and/or PlySs1 lytic enzymes and variants thereof, including truncations thereof. Methods for treatment of humans are provided.

Abstract: The present invention relates to novel biosensors that are based on bioluminescence resonance energy transfer (BRET). These biosensors may be used to monitor rapid interaction and conformational changes within G protein-coupled receptor/G protein complexes and, in this way, reflect the activation status of the receptor. Advantageously, the biosensors may be used as a highly sensitive and quantitative assay for the identification of ligands (agonists, antagonists, inverse agonists, partial agonists, etc.) targeting G protein-coupled receptors (GPCRs) as well as for the analysis of the activation status of these receptors. Moreover, multiplexing different biosensors within receptors/G protein complexes allows for mapping ligand textures. Additionally, the biosensors permit the direct, real-time examination of interactions between receptors and G protein in their natural environment, the living cell.

Abstract: The present disclosure provides engineered transaminase enzymes having improved properties as compared to a naturally occurring wild-type transaminase enzyme. Also provided are polynucleotides encoding the engineered transaminase enzymes, host cells capable of expressing the engineered transaminase enzymes, and methods of using the engineered transaminase enzymes to synthesize a variety of chiral compounds.

Abstract: The present invention relates to enzyme preparations consisting essentially of an enzyme which has cellulytic activity, which perform very well in industrial applications such as laundry compositions, for biopolishing of newly manufactured textiles, for providing an abraded look of cellulosic fabric or garment, and for treatment of paper pulp. Further, the invention relates to DNA constructs encoding such enzymes, a method for providing a gene encoding for such enzymes, a method of producing the enzymes, enzyme preparations containing such enzymes, and the use of these enzymes for a number of industrial applications.

Abstract: A composition is provided that includes Bacillus subtilis 2084 (NRRL B-50013) or a strain having all of the identifying characteristics of the Bacillus subtilis 2084 (NRRL B-50013), B. subtilis 27 (NRRL B-50105) or a strain having all of the identifying characteristics of the B. subtilis 27 (NRRL B-50105), and B. licheniformis 21 (NRRL B-50134) or a strain having all of the identifying characteristics of the B. licheniformis 21 (NRRL B-50134). Animal bedding that includes the Bacillus strains is also provided, as well as a method of making the animal bedding. Also provided are methods of controlling odors from animal waste. A method of making a composition including the Bacillus strains is also provided.

Abstract: A method for producing ?-glucanase and xylanase which includes the step of culturing a microorganism classified under the genus Trichoderma using a liquid culture medium which contains (a) a pulp derived from paper which has not been subjected to heat treatment nor alkali treatment as a carbon source, and (b) an ammonia nitrogen or an amino nitrogen as a nitrogen source.

Abstract: The invention relates to complement inhibitors that inhibit both the classical and alternative complement pathways. In particular, the invention relates to complement inhibitors derived from the salivary glands of haematophagous arthropods that inhibit both the classical and alternative complement pathways. The invention also relates to the use of such complement inhibitors in the treatment and prevention of diseases.

Abstract: The present invention provides compositions and methods for the expression of recombinant ?-glucosidase variants, as well as their use in the production of fermentable sugars from cellulosic biomass.

Abstract: The present invention relates to methods for improving the yield of microbial processes that use lignocellulose biomass as a nutrient source. The methods comprise conditioning a composition comprising lignocellulose biomass with an enzyme composition that comprises a phenol oxidizing enzyme. The conditioned composition can support a higher rate of growth of microorganisms in a process. In one embodiment, a laccase composition is used to condition lignocellulose biomass derived from non-woody plants, such as corn and sugar cane. The invention also encompasses methods for culturing microorganisms that are sensitive to inhibitory compounds in lignocellulose biomass. The invention further provides methods of making a product by culturing the production microorganisms in conditioned lignocellulose biomass.

Abstract: The invention relates to processes and biocatalysts for producing ethanol and other useful products from biomass and/or other materials. Initial processing of lignocellulosic biomass frequently yields methylglucuronoxylose (MeGAX) and related products which are resistant to further processing by common biocatalysts. Strains of Enterobacter asburiae are shown to be useful in bioprocessing of MeGAX and other materials into useful bioproducts such as ethanol, acetate, lactate, and many others. Genetic engineering may be used to enhance production of desired bioproducts.

Abstract: Disclosed are microorganisms of the genus Cupriavidus or Ralstonia, which are genetically modified to express phosphomannose isomerase (EC5.3.1.8) and facilitated diffusion protein (EC1.3.1.74) for mannose uptake, and optionally mannofructokinase (EC2.7.1.4). The microorganisms also may be genetically modified to express xylose isomerase (EC 5.3.1.5), xylulokinase (E 2.7.1.17) and xylose proton symporter E or a high affinity ABC-transporter. The genetically modified microorganisms are capable of growing on mannose, xylose, arabinose, glucose, or galactose, or a combination thereof as the carbon source.

Abstract: New strains of microalgae belonging to the Euglena genus, allow production of lipids, in particular of EPA and/or ARA, in mixotrophic mode, and a method for selecting and culturing such strains, using a variable and/or discontinuous light source, in particular a flashing light.

Abstract: New strains of microalgae belonging to the Nitzschia genus, allow high-yield production of lipids, in particular of docosahexaenoic acid (DHA) and/or eicosapentaenoic acid (EPA) and/or carotenoids, in particular fucoxanthin, in mixotrophic mode, and a method for selecting and culturing such strains, using a variable and/or discontinuous light source, in particular a flashing light.

Abstract: A method of growing a microorganism by culturing the microorganism in a an aqueous solution of carbohydrates containing C6-sugar monomers or C5-sugar monomers, wherein the aqueous solution of carbohydrates is made by reacting biomass or a biomass-derived reactant with a solvent system including a lactone and water, and an acid catalyst. The reaction yields a product mixture containing water-soluble C6-sugar-containing oligomers, C6-sugar monomers, C5-sugar-containing oligomers, C5-sugar monomers, or any combination thereof. The product mixture is then partitioned or extracted to yield an aqueous layer containing the carbohydrates and a substantially immiscible organic layer containing the lactone. The aqueous layer is used for growing the microorganisms.

Abstract: The present invention relates to variants (mutants) of polypeptides, in particular Termamyl-like alpha-amylases, which variant has alpha-amylase activity and exhibits an alteration in at least one of the following properties relative to said parent alpha-amylase: substrate specificity, substrate binding, substrate cleavage pattern, thermal stability, pH/activity profile, pH/stability profile, stability towards oxidation, Ca2+ dependency, specific activity, and solubility, in particular under production conditions.

Abstract: The present invention relates to a method for enhancing growth of plants which comprises contacting a Trichoderma strain with the plant or a plant seed under conditions effective for the Trichoderma strain to colonize the roots of the plant or a plant grown from the plant seed, thereby creating a plant-Trichoderma system. The plant or plant seed is grown under conditions effective to sustain the plant-Trichoderma system in a planting medium and to enhance plant growth, where the Trichoderma strain is selected from the group consisting of Trichoderma atroviride strain WW10TC4 (ATCC accession number PTA 9707), Trichoderma harzianum strain RR17Bc (ATCC accession number PTA 9708), Trichoderma harzianum strain F11Bab (ATCC accession number PTA 9709), and combinations thereof.

Abstract: The present invention relates to a method for enhancing growth of plants which comprises contacting a Trichoderma strain with the plant or a plant seed under conditions effective for the Trichoderma strain to colonize the roots of the plant or a plant grown from the plant seed, thereby creating a plant-Trichoderma system. The plant or plant seed is grown under conditions effective to sustain the plant-Trichoderma system in a planting medium and to enhance plant growth, where the Trichoderma strain is selected from the group consisting of Trichoderma atroviride strain WW10TC4 (ATCC accession number PTA 9707), Trichoderma harzianum strain RR17Bc (ATCC accession number PTA 9708), Trichoderma harzianum strain F11Bab (ATCC accession number PTA 9709), and combinations thereof.

Abstract: The invention relates to a method for multiplying a strain of Trichoderma, which includes the preparation of substantially contaminant-free culture media, containing disinfected wood fibers obtained by means of a twin-screw extruder, the amplification of Trichoderma via a series of steps for manufacturing a primary inoculum and then a secondary inoculum from said primary inoculum, and the multiplication of the microorganisms in each step, wherein the multiplication of the propagules reaches 2×104 to 105. The invention also relates to a plant growing medium containing a secondary inoculum of Trichoderma.

Abstract: The present invention provides isolated or genetically modified strains of microorganisms that display enhanced resistance to acetate as a result of increased expression of a sodium proton antiporter. The present invention also provides methods for producing such microbial strains, as well as related promoter sequences and expression vectors. Further, the present invention provides methods of producing alcohol from biomass materials by using microorganisms with enhanced resistance to acetate.

Abstract: The present disclosure provides a method for pre-treating non-wood lignocellulosic material containing less than 5 % (w/w) starch or sugar in a process for production of ethanol from lignocellulose, comprising the steps of: adding organic acid or organic acid-producing bacteria to the lignocellulosic material; storing the lignocellulosic material in the presence of the organic acid for a period of at least two weeks in an atmosphere of less than 5% oxygen to obtain organic acid-impregnated material; and heating the organic acid-impregnated material at a temperature of at least 160° C. to obtain pre-treated lignocellulosic material, wherein no, or substantially no, inorganic acid or base, including SO2, is added in the method.

Abstract: The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

Abstract: Microorganism compositions are described that comprise combinations of genetic modifications that include a genetic modification to increase oxaloacetate alpha-decarboxylase enzymatic activity. By such genetic modification a 3-hydroxypropionic acid (“3-HP”) production pathway is provided or improved. In various embodiments, comprising other genetic modifications, including selected gene disruptions, 3-HP production is greater than in a control microorganism lacking such combinations of genetic modifications.

Abstract: The invention provides methods of cultivating oil-bearing microbes using cellulosic material. Also provided are microorganisms that manufacture non-alcohol-based fuels and fuel feedstocks through a process of converting cellulosic materials into oils. Also provided are compositions comprising depolymerized cellulosic materials and oil-bearing microbes. Some methods of microbial fermentation are provided that comprise combining depolymerized cellulosic materials with other non-cellulosic feedstocks to enhance the economics of renewable fuel manufacturing. Particular advantages of the processes provided herein include production of oils rather than alcohols through cellulosic processes. Additional advantages include methods for manufacturing high nutrition oils from non-edible feedstocks such as wood chips, switchgrass, and bagasse.

Abstract: The invention provides improved methods for the production of isoprene from biological materials using a membrane bioreactor to culture isoprene-producing cells.

Abstract: The invention relates to sialate-O-acetyltransferase (SOAT) polypeptides, nucleic acids that encode the polypeptides, and methods of using the polypeptides.

Abstract: The present invention provides, inter alia, an improvement in the production of a desired product from yeast, wherein the growth rate and fermentation rate of the yeast are maintained at excellent levels. The present invention also provides, inter alia, for the introduction of a foreign gene into a yeast host cell, wherein the foreign gene encodes an enzyme involved in the production of a desired product. The yeast may also constitutively express a HAP4 gene, or a homologous gene thereof, to significantly improve the ability of the yeast to produce the desired product while maintaining its growth rate and fermentation rate. In some embodiments, a yeast mutant is used which is a mutant strain having lowered alcohol productivity vis-à-vis a wild-type strain.

Abstract: Disclosed are recombinant host cells suitable for degrading an oligosaccharide that have been optimized for growth and production of high yields of ethanol, and methods of making and using these cells. The invention further provides minimal media comprising urea-like compounds for economical production of ethanol by recombinant microorganisms. Recombinant host cells in accordance with the invention are modified by gene mutation to eliminate genes responsible for the production of unwanted products other than ethanol, thereby increasing the yield of ethanol produced from the oligosaccharides, relative to unmutated parent strains. The new and improved strains of recombinant bacteria are capable of superior ethanol productivity and yield when grown under conditions suitable for fermentation in minimal growth media containing inexpensive reagents. Systems optimized for ethanol production combine a selected optimized minimal medium with a recombinant host cell optimized for use in the selected medium.

Abstract: Provided herein is a transgenic bacteria engineered to accumulate carbohydrates, for example disaccharides. Also provided is a photobioreactor for cultivating photosynthetic microorganisms comprising a non-gelatinous, solid cultivation support suitable for providing nutrients and moisture to photosynthetic microorganisms and a physical barrier covering at least a portion of the surface of the cultivation support. Devices for the large scale and continuous cultivation of photosynthetic microorganisms incorporating photobioreactors and methods of use are disclosed. Also disclosed are methods of producing fermentable sugar from photosynthetic microorganisms using a photobioreactor of the invention.

Abstract: The present invention relates to the field of bacteriology. In particular, the invention relates to compositions of probiotic microbes and methods for making and using such compositions, e.g. in the treatment and prevention of catheter associated urinary tract infections.

Abstract: A method for enhancing growth of plants comprising contacting a Trichoderma strain with the plant or a plant seed under conditions effective for the Trichoderma strain to colonize the roots of the plant or a plant grown from the plant seed, thereby creating a plant-Trichoderma system. The plant or plant seed is grown under conditions effective to sustain the plant-Trichoderma system in a planting medium and to enhance plant growth. The Trichoderma strain is selected from the group consisting of Trichoderma atroviride strain WW10TC4 (ATCC accession number PTA 9707), Trichoderma harzianum strain RR17Bc (ATCC accession number PTA 9708), Trichoderma harzianum strain F11 Bab (ATCC accession number PTA 9709), and combinations thereof. Methods of enhancing resistance of plants to abiotic stress, increasing nitrogen use efficacy in plants, reducing nitrous oxide emissions in air, reducing leaching of nitrates into soil and water, and enhancing sequestration of carbon from air are disclosed.

Abstract: Provided is a method for producing corn gluten hydrolysate comprising: (a) separating corn gluten protein by removing carbohydrate, water soluble sugars, inorganic materials and fiber material; (b) preparing corn gluten protein lysate by carrying out acid hydrolysis, enzymatic hydrolysis or natural fermentation; and (c) increasing a content of branch chain amino acid (BCAA) which is included in the hydrolysate by isolating, concentrating, precipitating, desalting and filtering the resultant corn gluten protein lysate. With improved pre-treatment and concentration processes as compared with the conventional method, the hydrolysate prepared according to the present invention is rich in amino acids and low-molecular-weight peptides. In particular, free amino acids and branched-chain amino acids (BCAA) are included in large quantity.

Abstract: The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

Abstract: The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6 (SEQ ID NO:1 encodes the full length endoglucanase; SEQ ID NO:4 encodes the mature form), and the corresponding endoglucanase VI amino acid sequence (“EGVI”; SEQ ID NO:3 is the signal sequence; SEQ ID NO:2 is the mature sequence). The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

Abstract: The present invention is directed to methods of using nucleic acid molecules encoding for fusion peptides to produce the fusion peptides. The methods can include preparing or providing the nucleic acid molecules that having a fungal targeting agent (e.g., a fungal pheromone, such as alpha-mating pheromone) and a channel-forming domain consisting essentially of amino acids 451-626 of colicin Ia. The nucleic acid molecules can be transfected into host cells to produce the fusion peptide. The fusion peptides of the peptides of the present invention are particularly useful for the treatment of fungal infections in a wide variety of organisms.

Abstract: Compositions and methods for producing hydrocarbons such as aldehydes, alkanes, and alkenes are described herein. Certain hydrocarbons can be used in biofuels.

Abstract: The problem addressed by the present invention is to provide a method of treating an organic substance-containing waste liquid, and a treatment apparatus therefor, and an additive for treating an organic substance-containing waste liquid, and a bacterium for degrading an organic substance component or the like in the waste liquid, capable of accomplishing at least one of treatment of the organic substance-containing waste liquid with a high efficiency and a high treatment rate, without substantially generating a foul odor, and obtainment of water quality that is suitable for releasing to sewage, a public water area, or the like. This problem is solved by providing a method of treating an organic substance-containing waste liquid characterized by contacting an activated sludge containing a specified bacterium with an organic substance-containing waste liquid.

Abstract: Described are recombinant yeast which ferment xylose to ethanol and which maintain their ability to do so when cultured for numerous generations in non-selective media. The preferred yeast contain multiple copies of integrated genes encoding xylose reductase, xylitol dehydrogenase, and xylulokinase fused to promoters which are non-glucose inhibited and which do not require xylose for induction. Also described are preferred methods for integrating multiple copies of exogenous DNA into host cells by transforming cells with replicative/integrative vectors, and then replicating the cells a number of times under selective pressure to promote retention of the vector in subsequent generations. The replicated vectors thus serve to integrate multiple copies of the exogenous DNA into the host cells throughout the replication/selection phase. Thereafter the selective pressure can be removed to promote loss of the vector in subsequent generations, leaving stable integrants of the exogenous DNA.

Abstract: The present invention is directed to nucleic acids encoding for fusion peptides comprising a fungal targeting agent and a channel-forming domain consisting essentially of amino acids 451-626 of colicin Ia, as well as vectors having the nucleic acids of the invention and host cells having the vectors. The fusion peptides of the peptides of the present invention are particularly useful for the treatment of fungal infections in a wide variety of organisms. The fusion peptides can be prepared from the nucleic acids, such as when a vector having the nucleic acid is included in a host cell.

Abstract: Described are engineered strains of the oleaginous yeast Yarrowia lipolytica capable of producing an oil comprising greater than 50 weight percent of eicosapentaenoic acid [“EPA”], an ?-3 polyunsaturated fatty acid, measured as a weight percent of total fatty acids [“% TFAs”] and having a ratio of at least 3.1 of EPA % TFAs, to linoleic acid, measured as % TFAs. These strains over-express at least one ?9 elongase/?8 desaturase multizyme, in addition to other heterologous ?9 elongases, ?8 desaturases, ?5 desaturases, ?17 desaturases, ?12 desaturases, C16/18 elongases, and optionally over-express diacylglycerol cholinephosphotransferases, malonyl CoA synthetases and/or acyl-CoA lysophospholipid acyltransferases. The expression of at least one peroxisome biogenesis factor protein is down-regulated. Methods for producing EPA within said host cells, oils obtained from the cells, and products therefrom are claimed.

Abstract: Provided herein are methods and compositions for bacterial cellulose production. In some embodiments, the methods and compositions involve or are made from distiller's grain.

Abstract: The present invention provides a novel UDP-glucuronosyltransferase and a polynucleotide encoding the same, for example, a polynucleotide comprising nucleotides 1 to 1359 of SEQ ID NO: 4, nucleotides 1 to 1365 of SEQ ID NO: 10, nucleotides 1 to 1371 of SEQ ID NO: 12, and nucleotides 1 to 1371 of SEQ ID NO: 22; or a polynucleotide encoding a protein having the amino acid sequence of SEQ ID NOS: 5, 11, 13 or 23. The invention provides a novel UDP-glucuronosyltransferase with a broad substrate specificity.

Abstract: The present invention relates to novel polypeptides according to caroase 01-05 or any functional equivalents of any of them, suitable for use in a method for preparing a food products having increased whiteness, the use of the enzyme to increase whiteness of at least part of a food product, a process for preparing a food product wherein the enzyme is used and the food product obtained.

Abstract: The invention provides a method for designing a nucleic acid binding protein of the Cys2-His2 zinc finger class capable of binding to a nucleic acid quadruplet in a target nucleic acid sequence, wherein binding to base 4 of the quadruplet by an alpha-helical zinc finger nucleic acid binding motif in the protein is determined as follows: if base 4 in the quadruplet is A, then position +6 in the alpha-helix is Glu, Asn or Val; if base 4 in the quadruplet is C, then position +6 in the alpha-helix is Ser, Thr, Val, Ala, Glu or Asn; if base 4 of the quadruplet is G, the position +6 in the alpha helix is Arg or Lys; if position 4 in the quadruplet is T, then position +6 in the alpha helix is Ser, Thr, Val or Lys.

Abstract: The present invention relates material that is useful in culturing and transferring cells as well as delivering cells. The material comprises plant derived cellulose nanofibers or derivatives thereof, wherein the cellulose nanofibers are in a form of a hydrogel or membrane. The invention also provides methods for producing these materials and compositions and uses thereof.

Abstract: Contamination was controlled in fermentations using Zymomonas mobilis as the biocatalyst, without negative impact on fermentation production, by the addition of virginiamycin. The effective concentration of virginiamycin was found to be dependent upon the type of fermentation medium used.

Abstract: A cellulose gel medium having good visibility of microbial colonies, a cellulose gel culture substrate for manufacturing the cellulose gel medium, a method for manufacturing the cellulose gel culture substrate, a method for screening cellulase-producing microorganisms or cellulase activity with greater efficiency and rapidity, and a culture substrate, which includes a cellulose gel containing cellulose and water as medium-solidifying components, the cellulose has the viscosity of 12 to 35 mPa·S as measured at 26° C. with a solution prepared by dissolving the cellulose at a concentration of 2.5 mg/mL in dimethylacetamide containing 8% (W/V) lithium chloride.

Abstract: Provided herein is a transgenic bacteria engineered to accumulate carbohydrates, for example disaccharides. Also provided is a photobioreactor for cultivating photosynthetic microorganisms comprising a non-gelatinous, solid cultivation support suitable for providing nutrients and moisture to photosynthetic microorganisms and a physical barrier covering at least a portion of the surface of the cultivation support. Devices for the large scale and continuous cultivation of photosynthetic microorganisms incorporating photobioreactors and methods of use are disclosed. Also disclosed are methods of producing fermentable sugar from photosynthetic microorganisms using a photobioreactor of the invention.

Abstract: Provided herein is a transgenic bacteria engineered to accumulate carbohydrates, for example disaccharides. Also provided is a photobioreactor for cultivating photosynthetic microorganisms comprising a non-gelatinous, solid cultivation support suitable for providing nutrients and moisture to photosynthetic microorganisms and a physical barrier covering at least a portion of the surface of the cultivation support. Devices for the large scale and continuous cultivation of photosynthetic microorganisms incorporating photobioreactors and methods of use are disclosed. Also disclosed are methods of producing fermentable sugar from photosynthetic microorganisms using a photobioreactor of the invention.