Abstract: Corn or soy plant biomass is electron beam irradiation processed and saccharified to produce sugars. The sugars are then converted to products such as alcohols, organic acids, hydrocarbons, hydrogen, proteins, carbohydrates, fats, oils, lipids, amino acids, vitamins, and mixtures thereof.

Abstract: Compositions and methods relating to an alpha-amylase enzyme obtained from Halomonas variabilis WDG195 are described.

Abstract: The present invention relates to a phytase which has at least 74% identity to a phytase derived from Citrobacter braakii and comprises at least one alteration as compared to this phytase. These phytase variants have amended, preferably improved, properties, such as thermostability, temperature profile, pH profile, specific activity, performance in animal feed, reduced protease sensitiliby, and/or an amended glycosylation pattern. The invention also relates to DNA encoding these phytases, methods of their production, as well as the use thereof, e.g. in animal feed and animal feed additives.

Abstract: Method for incorporating a lysine derivative (particularly an N?-benzyloxycarbonyl-lysine (Z-Lys) derivative) having useful functional group such as heavy atom, selenium, reactive functional group, fluorescent group or crosslinker, which is suitable as a non-natural amino acid, into a desired protein in a site-specific manner. A mutant pyrrolysyl-tRNA synthetase has substitution of at least one amino acid residue selected from tyrosine residue at position 306, leucine residue at position 309 and cysteine residue at position 348 each constituting a pyrrolysine-binding site in the amino acid sequence for pyrrolysyl-tRNA synthetase of SEQ ID NO:2. The substitution of the amino acid residue is: of tyrosine residue at position 306 by glycine or alanine residue, of leucine residue at position 309 by glycine or alanine residue, and/or of a cysteine residue at position 348 by valine, serine or alanine residue.

Abstract: A Corynebacterium glutamicum transformant having the capability of producing isobutanol and the following genes (1) to (5): (1) a gene which encodes an enzyme having acetohydroxy acid synthase activity; (2) a gene which encodes an enzyme having acetohydroxy acid isomeroreductase activity; (3) a gene which encodes an enzyme having dihydroxy acid dehydratase activity; (4) a gene which encodes an enzyme having 2-keto acid decarboxylase activity; and (5) a gene which encodes an enzyme having alcohol dehydrogenase activity, at least one of the genes being endogenous, and at least one of the genes being exogenous, efficiently produces isobutanol.

Abstract: The present invention relates to genes, proteins and methods comprising molecules that alter amino acid levels. In one embodiment, the present invention relates to altering guanidino substrate hydrolysis activities in plants, arthropods and microorganisms using molecules within the arginase family and other molecules that alter an amino acid levels. In ones embodiment, the present invention relates to altering threonine substrate deamination and dehydration activities in plants, arthropods and microorganisms using molecules within the threonine deaminase family and other molecules that alter amino acid levels. In one embodiment, the present invention relates to using genes, proteins and methods comprising arginase or threonine deaminase for altering the pathophysiology of plants, arthropods and microorganisms. In a preferred embodiment, the present invention relates to altering guanidino substrate hydrolysis activity in plants, arthropods, and microorganisms using arginase.

Abstract: The present invention relates to a process for producing enzymes and single cell oil. The process comprises that microorganisms capable of producing both single cell oil and enzymes are cultivated under conditions suitable for single cell oil production and enzyme production in a single cell oil production process. A microorganism culture comprising single cell oil and enzymes is obtained and at least part of the microorganism culture, of the supernatant and/or microorganism cells separated from the microorganism culture, of protein fraction enriched from the supernatant, and/or of protein fraction obtained from the cells is used as an enzyme preparation or as a source of enzymes. Single cell oil is recovered from the microorganism cells and used as biofuel, component of biofuel or as a starting material for biofuel production. Enzymes produced according to the process are used in the same or in another industrial process.

Abstract: The present invention is related to recombinant host cells comprising: (i) at least one deletion, mutation, and/or substitution in an endogenous gene encoding a polypeptide that converts pyruvate to acetaldehyde, acetyl-phosphate or acetyl-CoA; and (ii) a heterologous polynucleotide encoding a polypeptide having phosphoketolase activity. The present invention is also related to recombinant host cells further comprising (iii) a heterologous polynucleotide encoding a polypeptide having phosphotransacetylase activity.

Abstract: The present invention relates to a method for producing polyphenol compounds, i.e. phloroglucinol or one of its derivatives, with a polyketide synthase of type III (PKSIII) from a brown marine alga. The invention also relates to recombinant nucleic acids coding for a polyketide synthase of type III (PKSIII) from the brown alga Ectocarpus siliculosus (E. siliculosus), to recombinant vectors comprising these nucleic acids, as well as to host cells comprising these vectors. Finally, the invention relates to a method for preparing of various compounds by means of polyphenol compounds produced according to the aforementioned method.

Abstract: The present invention relates to processes for producing fermentation products from starch-containing material, wherein an alpha-amylase, a thermostable protease, and optionally a carbohydrate-source generating enzyme and/or pullulanase, are present and/or added during liquefaction. The invention also relates to compositions suitable for use in a process of the invention.

Abstract: Described are compositions and methods relating to variant filamentous fungi having altered growth characteristics. Such variants are well-suited for growth in submerged cultures, e.g., for the large-scale production of enzymes and other proteins for commercial applications.

Abstract: An object of the present invention is to provide enzymes associated with equol synthesis, genes coding such enzymes, and a process for producing equol and its intermediates using the enzymes and genes. The present invention provides a dihydrodaidzein synthesizing enzyme, tetrahydrodaidzein synthesizing enzyme, equol synthesizing enzyme, and genes coding these enzymes. The present invention also provides a process for synthesizing dihydrodaidzein, tetrahydrodaidzein, and/or equol using these enzymes.

Abstract: In an alcohol fermentation process, oil derived from biomass is hydrolyzed into an extractant available for in situ removal of a product alcohol such as butanol from a fermentation broth. The glycerides in the oil can be catalytically (e.g., enzymatically) hydrolyzed into free fatty acids, which form a fermentation product extractant having a partition coefficient for a product alcohol greater than a partition coefficient of the oil of the biomass for the product alcohol. Oil derived from a feedstock of an alcohol fermentation process can be hydrolyzed by contacting the feedstock including the oil with one or more enzymes whereby at least a portion of the oil is hydrolyzed into free fatty acids forming a fermentation product extractant, or the oil can be separated from the feedstock prior to the feedstock being fed to a fermentation vessel, and the separated oil can be contacted with the enzymes to form the fermentation product extractant.

Abstract: The invention provides a non-naturally occurring microbial organism having a 2-hydroxyisobutyric acid, 3-hydroxyisobutyric acid or methacrylic acid pathway. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in a 2-hydroxyisobutyric acid, 3-hydroxyisobutyric acid or methacrylic acid pathway. The invention additionally provides a method for producing 2-hydroxyisobutyric acid, 3-hydroxyisobutyric acid or methacrylic acid. The method can include culturing a 2-hydroxyisobutyric acid, 3-hydroxyisobutyric acid or methacrylic acid producing microbial organism expressing at least one exogenous nucleic acid encoding a 2-hydroxyisobutyric acid, 3-hydroxyisobutyric acid or methacrylic acid pathway enzyme in a sufficient amount and culturing under conditions and for a sufficient period of time to produce 2-hydroxyisobutyric acid, 3-hydroxyisobutyric acid or methacrylic acid.

Abstract: The present disclosure provides methods for releasing intracellular proteins. The method allows isolation of the protein of interest from the cell without the requirement for mechanical disruption of the cells, without the need for isolation of the cells from the culture media, and without the need for removal of the cells from the culture media.

Abstract: Disclosed are compositions and methods for increasing the longevity of a cell culture and permitting the increased production of proteins, preferably recombinant proteins, such as antibodies, peptides, enzymes, growth factors, interleukins, interferons, hormones, and vaccines. Cells transfected with an apoptosis-inhibiting gene or vector, such as a triple mutant Bcl-2 gene, can survive longer in culture, resulting in extension of the state and yield of protein biosynthesis. Such transfected cells exhibit maximal cell densities that equal or exceed the maximal density achieved by the parent cell lines. Transfected cells can also be pre-adapted for growth in serum-free medium, greatly decreasing the time required to obtain protein production in serum-free medium. In certain methods, the pre-adapted cells can be used for protein production following transformation under serum-free conditions. The method preferably involves eukaryotic cells, more preferably mammalian cells.

Abstract: The present invention relates to a cell line in which an expression construct is introduced into a genomic DNA, the expression construct including: (a) a promoter operable in animal cells and heterologous to adenoviruses; and (b) a modified adenovirus E1 coding gene sequence of SEQ ID NO:1 operatively linked to the promoter. According to the present invention, the cell line of the present invention is a novel cell line which is less likely to produce a replication competent adenovirus (RCA). The adenovirus producing cell line of the present invention has a low possibility of producing RCA due to homologous recombination, when compared with conventional cell lines. Therefore, this makes it possible to regulate the required amount of virus during gene therapy using the adenovirus and prevent tissue damage and toxic effects caused by overproduction of the adenovirus.

Abstract: Novel crystal structures of human and murine glutaminyl cyclase (QC, EC 2.3.2.5), methods of preparing the crystals, as well as the use of said crystal structures for identifying inhibitors of human and murine glutaminyl cyclase.

Abstract: The invention relates to a variant of a parent Termamyl-like alpha-amylase, which variant exhibits altered properties, in particular reduced capability of cleaving a substrate close to the branching point, and improved substrate specificity and/or improved specific activity relative to the parent alpha-amylase.

Abstract: The present invention relates to a method of microbial production of L-lysine from methanol and other substrates, and particularly improving the production of L-lysine from such substrates. The invention concerns a method for producing L-lysine in B. methanolicus, said method comprising overexpressing an aspartate kinase III (AKIII) enzyme in said B. methanolicus. In particular the method may concern introducing a nucleic acid molecule comprising a nucleotide sequence encoding an AKIII enzyme into a B. methanolicus. The invention also relates to a B. methanolicus micro-organism which overexpresses an AKIII enzyme, nucleic acid molecules which encode polypeptides having AK activity, polypeptides which have AK activity and host cells and vector systems comprising the nucleic acid molecules or vector.

Abstract: Provided is a novel process for producing an L-amino acid using a microorganism belonging to the genus Escherichia. According to the present invention, a process for producing an L-amino acid comprising; culturing a microorganism in which an activity of the protein of any of the following [1]-[3] is increased compared with that of the parent strain in a medium, producing and accumulating the L-amino acid in the medium, and recovering the L-amino acid from the medium: [1] a protein comprising the amino acid sequence shown in SEQ ID NO: 2 [2] a protein consisting of an amino acid sequence in which one or more amino acids are deleted, substituted or added in the amino acid sequence shown in SEQ ID NO: 2, and having YeiG activity [3] a protein consisting of an amino acid sequence having 80% or more homology to the amino acid sequence shown in SEQ ID NO: 2, and having YeiG activity.

Abstract: The present invention provides aspartyl-tRNA synthetase derived proteins (DRS polypeptides) with altered cysteine content, compositions comprising the same, and methods of using such polypeptides and compositions for treating or diagnosing a variety of conditions. The DRS polypeptides of the invention have immunomodulatory properties, and exhibit improved activity and stability.

Abstract: The present invention provides a method of increasing protein production in a cell culture by growing cells that produce the protein (e.g., the growth phase) in a perfusion cell culture to a high cell density (i.e., at least above about 40×106 cells/mL) and then switching to a protein production phase, wherein the cells are cultured in a fed-batch cell culture. The present invention further provides a method for clarifying a protein from a cell culture by adjusting the pH of the cell culture to below neutral pH (i.e., below a pH of 7) and settling the cell culture, such that the cell culture separates to form a supernatant layer and a cell-bed layer, wherein the protein is in the supernatant layer.

Abstract: The present invention provides methods for purifying a polypeptide from a composition comprising the polypeptide and at least one contaminant by overloading a chromatography material and eluting the product.

Abstract: The invention provides methods and systems for production of recombinant protein, and particularly, for production of recombinant protein from inclusion bodies. For example, in one aspect, the method comprises providing a protein preparation comprising inclusion bodies, preparing an inclusion body dispersion, and exposing the protein preparation to high pressure in a pressure vessel, to disaggregate and refold the inclusion body protein.

Abstract: The present invention provides a method for collecting a carotenoid from a culture of a carotenoid-producing bacterium at high yield. Specifically, the present invention provides a method for separating a carotenoid comprising a step of precipitating a concentrate containing the carotenoid from a culture of a carotenoid-producing bacterium under acidic conditions; and a method for producing a carotenoid comprising the steps of precipitating a concentrate containing the carotenoid from a culture of a carotenoid-producing bacterium under acidic conditions and collecting the carotenoid from the obtained precipitate.

Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogs bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.

Abstract: Described are compositions and methods relating to variant alpha-amylases having altered biochemical properties and advantageous performance characteristics as compared to a reference alpha-amylase. The variants are suitable for use in various industrial applications such as starch conversion, ethanol production, laundry, dishwashing, pulp and paper production, textile desizing, and/or sweetener production.

Abstract: The present invention relates to modified SAK gene having amino acid SEQ ID 2. The present invention further relates to process for cloning and expressing modified SAK gene fusion protein which imparts improved stability to the heterologous protein of interest. Further the invention relates to process of purification of recombinant heterologous proteins from bacterial inclusion bodies using modified SAK.

Abstract: Disclosed herein are systems and methods that allow analysis of macromolecular structures using laserspray ionization at intermediate pressure or high vacuum using commercially available mass spectrometers with or without modification and with the application of heat. The systems and methods produce multiply-charged ions for improved analysis in mass spectrometry.

Abstract: The present invention refers to the gene cluster and genes comprised by the gene cluster which are involved in the biosynthesis of griselimycin and methylgriselimycin and to the use of the gene cluster, genes comprised thereby and proteins encoded thereby for the production of antibiotic agents.

Abstract: The present invention relates to isolated polypeptides having protease 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 for producing and using the polypeptides.

Abstract: The present invention generally relates to methods of making cDNA molecules and cDNA libraries. The invention also relates to cDNA molecules and cDNA libraries produced according to these methods, as well as to vectors and host cells containing such cDNA molecules and libraries. The invention also relates to kits for making the cDNA molecules and libraries of the invention.

Abstract: The present invention is directed to alpha-mannosidase sequences from plants and the use thereof, especially genomic nucleotide sequences containing the regulatory elements controlling their expression, intron and exon sequences and polynucleotide sequences coding for alpha-mannosidase enzymes. Such plants with modified alpha-mannosidase activity can be used for the production of glycoproteins having an altered saccharide composition of great benefit. The present invention also relates to the use of these alpha-mannosidase enzymes for hydrolyzing mannoses.

Abstract: A novel activating enzyme for ubiquitin, Uba6, is provided. Compositions and methods for inhibiting ubiquitin via the Uba6 pathway are provided. Methods of identifying novel inhibitors of ubiquitination are also provided. Novel RNAi molecules are also provided.

Abstract: The described invention provides genetically engineered microorganisms, including photosynthetic microorganisms, expressing 4-hydroxybenzoyl-CoA thioesterases and methods of using the genetically engineered microorganisms for producing free fatty acids and/or fatty acid derivatives.

Abstract: A transgenic insect cell line for production of elevated levels of recombinant glycoproteins comprising mammalian-like N-glycans is provided. Also disclosed are nucleic acid sequences encoding ?-N-acetylglucosaminidases.

Abstract: A method of producing a sugar liquid using a cellulose-containing biomass as a raw material includes (a) hydrolyzing a cellulose-containing biomass to produce an aqueous sugar solution and (b) filtering the obtained aqueous sugar solution through a reverse osmosis membrane to collect a purified sugar liquid from a feed side, while removing fermentation-inhibiting substances from a permeate side.

Abstract: A recombinant filamentous fungal cell (e.g. Aspergillus) having one or more inactivated chromosomal genes is provided. The chromosomal genes in some embodiments correspond to derA, derB, htmA, mnn9, mnn10, ochA, dpp4, dpp5, pepAa, pepAb, pepAc, pepAd, pepF and combinations thereof. The recombinant fungal cells may include further inactivated chromosomal genes which correspond to pepA, pepB, pepC and pepD. The recombinant filamentous fungal cells may include a heterologous nucleic acid encoding a protein of interest. Also provided are methods of producing a protein of interest in said recombinant filamentous fungal cell.

Abstract: This invention relates to industrial production of proteins. More specifically, the invention relates to the res-DHFR surrogate marker, which corresponds to a fusion between DHFR and a protein conferring resistance to a toxic compound or conferring a metabolic advantage. The invention further relates to the use of res-DHFR for screening cells for high expression of a protein of interest. The invention is illustrated by the Puro-DHFR surrogate marker, which corresponds to a fusion between the puromycin N-acetyltransferase and dihydrofolate reductase (DHFR).

Abstract: Hybrid alpha-amylases are provided that share a conserved 3D structure in whole or in part with a wild-type Termamyl-like ?-amylase, e.g., a Bacillus amylase. In the hybrid, an N terminal portion of a Termamyl-like ?-amylase is replaced with sequences from an archae ? amylase. The sequence similarity between the two amylase sequences may be less than 60%. Conserving the wild-type 3D structure in the hybrid facilitates obtaining enzymatically active amylases. In one embodiment, one or both amylase sequences contribute residues to the B domain, resulting in particularly advantageous properties. For instance, replacement of the Ca2+ binding site in the B domain of the Termamyl-like ?-amylase with a B domain sequence of an archae ? amylase that does not bind Ca2+ can produce a hybrid that is fully active in the absence of Ca2+.

Abstract: The invention relates to an isolated nucleic acid sequence comprising a promoter, which is a native sequence of Pichia pastoris comprising the nucleic acid sequence of pCS1 of SEQ ID NO:1, or a functionally active variant thereof which is a size variant, a mutant or hybrid of SEQ ID NO:1, or a combination thereof, expression constructs and recombinant host cells comprising the promoter, and a method of producing a protein of interest under the control of the promoter. It further relates to a method to identify a constitutive promoter from eukaryotic cells, and an isolated nucleic acid sequence comprising a promoter which when operatively linked to a nucleotide sequence encoding a protein of interest directs the expression thereof in a host cell at an expression level that is higher than under control of the native pGAP promoter at high and low growth rates.

Abstract: Fusion proteins having thermostable blunt-end ligase activity are provided. Blunt-end ligases are useful for DNA amplification, sequencing, production of recombinant DNA and recombinant fusion proteins, and other purposes. These thermostable blunt-end DNA ligases are useful in ligation schemes which include, e.g., an incubation at about 60-65° C. or higher, or as high as about 94° C., or at other temperatures. The ligases disclosed herein may enable high temperature blunt-end ligation without need for molecular crowding agents, and so may be useful for many nucleic acid ligation-amplification schemes, e.g., ones which operate at a uniform temperature (e.g., at about 60° C. or higher), including ones which require temperature cycling, e.g., from about 94° C. to about 60° C. (or higher) for one, two, three, or more cycles.

Abstract: Treating Sonic Hedgehog-Associated Medulloblastoma comprises inhibiting the synthesis or biologic activity of leukotrienes that drive Nestin expression in cancerous or precancerous granule neuron precursors and that further drive growth and proliferation of medulloblastoma cells through Nestin-mediated aberrant Sonic Hedgehog signaling.

Abstract: The invention relates to a thrombolytic enzyme referred to as Thrombinase having a molecular weight of 31,000 to 32,000. Such a thrombolytic enzyme can be used for dissolving blood clots. The process comprises culturing a filtrate of Bacillus sphaericus sero type H5a 5b, removing the cell, subjecting the cell supernatant to filtration, salting out the retentate, subjecting the precipitate to dialysis, reprecipitating the precipitate and then reconstituting in buffer and finally decolorizing, purifying and dialyzing.

Abstract: Disclosed are compositions and methods for the labeling of two or more targets with different labels. Specifically, disclosed are compositions for biotin and the protection of biotin within multilabel assays which employ the biotin-biotin binding protein binding relationship for each distinct label in relation to targets such as nucleic acids, polypeptides, antibodies or cells. These multilabel assays are enabled through the use of biotin with desthiobiotin, orthogonal protecting schemes for biotin, or a combination of the approaches.

Abstract: The present invention relates to cell wall degradative systems, in particular to systems containing enzymes that bind to and/or depolymerize cellulose. These systems have a number of applications. Some embodiments relate to a method of producing ethanol using the cell wall degradative systems of the present invention.

Abstract: Methods for producing modified polypeptides containing amino acid analogues are disclosed. The invention further provides purified dihydrofolate reductase polypeptides, produced by the methods of the invention, in which the methionine residues have been replaced with homoallylglycine, homoproparglycine, norvaline, norleucine, cis-crotylglycine, trans-crotylglycine, 2-aminoheptanoic acid, 2-butynylglycine and allylglycine.

Abstract: Provided herein are integrated continuous biomanufacturing processes for producing a therapeutic protein drug substance. Also provided are systems that are capable of continuously producing a therapeutic protein drug substance.

Abstract: The inventors have modified the amino acid sequence of a maltogenic alpha-amylase to obtain variants with improved properties, based on the three-dimensional structure of the maltogenic alpha-amylase Novamyl. The variants have altered physicochemical properties., e.g. an altered pH optimum, improved thermostability, increased specific activity, an altered cleavage pattern or an increased ability to reduce retrogradation of starch or staling of bread.