Abstract: The present invention relates to methods of diagnosing, prognosing, preventing or delaying onset of or treating rheumatoid arthritis, methods of distinguishing between different types or stages of rheumatoid arthritis, of identifying an individual at risk of developing rheumatoid arthritis, and of monitoring efficacy of a treatment regime in an individual being treated for rheumatoid arthritis, using a citrullinated enolase peptide to detect or capture antibodies associated with rheumatoid arthritis.

Abstract: Methods for synthesizing isopentenyl pyrophosphate are provided. A first method comprises introducing into a host microorganism a plurality of heterologous nucleic acid sequences, each coding for a different enzyme in the mevalonate pathway for producing isopentenyl pyrophosphate. A related method comprises introducing into a host microorganism an intermediate in the mevalonate pathway and at least one heterologous nucleic acid sequence, each sequence coding for an enzyme in the mevalonate pathway necessary for converting the intermediate into isopentenyl pyrophosphate. The invention also provides nucleic acid sequences, enzymes, expression vectors, and transformed host cells for carrying out the methods.

Abstract: R-hydroxynitrile lyases having an improved substrate acceptance, increased activity and increased selectivity, in which there is replacement in the amino acid sequence of R-hydroxynitrile lyases from the Rosaceae family either a) of the amino acid residue which corresponds to position 360 of the mature PaHNL5 protein by another apolar amino acid or a neutral amino acid and/or b) of the amino acid residue which corresponds to position 225 of the mature PaHNL5 protein by another polar amino acid, it also being possible where appropriate for 1 to 20 further residues in the active center or in the hydrophobic channel leading to the active center to be replaced.

Abstract: The invention relates to chondroitinase ABC I and uses thereof. In particular, the invention relates to recombinant and modified chondroitinase ABC I, their production and their uses. The chondroitinase ABC I enzymes of the invention are useful for a variety of purposes, including degrading and analyzing polysaccharides such as glycosaminoglycans (GAGs). These GAGs can include chondroitin sulfate, dermatan sulfate, unsulfated chondroitin and hyaluronan. The chondroitinase ABC I enzymes can also be used in therapeutic methods such as promoting nerve regeneration, promoting stroke recovery, treating spinal cord injury, treating epithelial disease, treating infections and treating cancer.

Abstract: The present invention provides novel human protein antigens and related antibodies that have been identified as being specifically expressed in association to human Pancreatic Ductal Adenocarcinoma (PDA). In particular, novel phosphorylated isoforms of alpha-enolase have been identified in transformed cell lines of pancreatic origin and antibodies binding such isoforms are specifically present in the sera of PDA patients. These proteins and antibodies can be useful for the diagnosis and the treatment of PDA and other cancers having common molecular features.

Abstract: The invention is directed to polypeptides having pectate lyase (pectinase) activity, polynucleotides encoding the polypeptides, and methods for making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used as pectate lyases to catalyze the beta-elimination or hydrolysis of pectin and/or polygalacturonic acid, such as 1,4-linked alpha-D-galacturonic acid. The invention provides methods of treating fibers, fabrics or any pectate- or polygalacturonic acid-comprising material using one or more pectate lyases of the invention.

Abstract: Improved systems and methods for reducing costs and increasing yields of cellulosic ethanol including compositions of matter comprising plant biomass and cell wall-modifying enzyme polypeptides and transgenic plants expression cell wall-modifying enzyme polypeptides.

Abstract: The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. Polypeptides, including enzymes and antibodies, and nucleic acids of the invention can be used in industrial, experimental, food and feed processing, nutritional and pharmaceutical applications, e.g., for food and feed supplements, colorants, neutraceuticals, cosmetic and pharmaceutical needs.

Abstract: The present invention provides: a protein having an improved nitrile hydratase activity, whereby heat resistance has been improved when compared with a wild-type nitrile hydratase activity, wherein the amino acid sequence of a nitrile hydratase is modified; a gene DNA encoding the above protein; a recombinant vector having the above gene DNA; a transformant or transductant having the above recombinant vector; a nitrile hydratase collected from a culture of the above transformant or transductant, and a production method thereof; and a method for producing an amide compound.

Abstract: The present invention provides methods and compositions comprising at least one isoprene synthase enzyme with improved catalytic activity and/or solubility. In particular, the present invention provides variant plant isoprene synthases for increased isoprene production in microbial host cells. Biosynthetically produced isoprene of the present invention finds use in the manufacture of rubber and elastomers.

Abstract: The invention generally relates to polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) systems, to homologues thereof, to isolated nucleic acid molecules and recombinant nucleic acid molecules encoding biologically active domains of such a PUFA PKS system, to genetically modified organisms comprising PUFA PKS systems, to methods of making and using such systems for the production of bioactive molecules of interest, and to novel methods for identifying new bacterial and non-bacterial microorganisms having such a PUFA PKS system.

Abstract: Methods and materials related to producing 3-HP as well as other organic compounds are disclosed. Specifically, isolated nucleic acids, polypeptides, host cells, and methods and materials for producing 3-HP and other organic compounds are disclosed.

Abstract: The present invention relates to a process for the microbial production of L-valine in which the dihydroxy acid-synthase (ilvD) activity and/or the ilvD gene expression is intensified in a microorganism. As an alternative or in combination with this, the acetohydroxy acid-synthase (ilvBN) activity and isomeroreductase (ilvC) activity and/or the ilvBNC gene expression are intensified in a microorganism. The process according to the invention preferably makes use of microorganisms in which the activity of at least one enzyme that is involved in a metabolic pathway that reduces the formation of L-valine is weakened or eliminated. Thus, for instance, the process according to the invention preferably makes use of microorganisms having a defect mutation in the threonine dehydratase (ilvA) gene and/or a defect mutation in one or more genes of the pantothenate synthesis.

Abstract: Isolated nucleic acid fragments encoding galactinol synthase are disclosed. Recombinant DNA construct(s) for use in altering expression of endogenous genes encoding galactinol synthase are also disclosed.

Abstract: The invention provides recombinant B. thetaiotaomicron GAG lyase polypeptides. The invention also provides nucleic acid molecules encoding such polypeptides, recombinant expression vectors containing B. thetaiotaomicron GAG lyase nucleic acid molecules, and host cells into which the expression vectors have been introduced. Characterization, diagnostic and therapeutic methods utilizing compositions of the invention are also provided.

Abstract: The present invention is in the field of plant biochemistry. More specifically the invention relates to nucleic acid sequences from plant cells, in particular, nucleic acid sequences from maize and soybean associated with the tetrapyrrole pathway. The invention encompasses nucleic acid molecules that encode proteins and fragments of proteins. In addition, the invention also encompasses proteins and fragments of proteins so encoded and antibodies capable of binding these proteins or fragments. The invention also relates to methods of using the nucleic acid molecules, proteins and fragments of proteins and antibodies, for example for genome mapping, gene identification and analysis, plant breeding, preparation of constructs for use in plant gene expression and transgenic plants.

Abstract: Methods for synthesizing isopentenyl pyrophosphate are provided. A first method comprises introducing into a host microorganism a plurality of heterologous nucleic acid sequences, each coding for a different enzyme in the mevalonate pathway for producing isopentenyl pyrophosphate. A related method comprises introducing into a host microorganism an intermediate in the mevalonate pathway and at least one heterologous nucleic acid sequence, each sequence coding for an enzyme in the mevalonate pathway necessary for converting the intermediate into isopentenyl pyrophosphate. The invention also provides nucleic acid sequences, enzymes, expression vectors, and transformed host cells for carrying out the methods.

Abstract: Methods for synthesizing isopentenyl pyrophosphate are provided. A first method comprises introducing into a host microorganism a plurality of heterologous nucleic acid sequences, each coding for a different enzyme in the mevalonate pathway for producing isopentenyl pyrophosphate. A related method comprises introducing into a host microorganism an intermediate in the mevalonate pathway and at least one heterologous nucleic acid sequence, each sequence coding for an enzyme in the mevalonate pathway necessary for converting the intermediate into isopentenyl pyrophosphate. The invention also provides nucleic acid sequences, enzymes, expression vectors, and transformed host cells for carrying out the methods.

Abstract: A polynucleotide (hpa) encoding a polypeptide having heparanase activity, vectors including same, genetically modified cells expressing heparanase, a recombinant protein having heparanase activity and antisense oligonucleotides and constructs for modulating heparanase expression.

Abstract: Detergent composition comprising a surfactant and a pectate lyase (EC 4.2.2.2) enzyme en-coded by a DNA sequence endogeneous to a strain of Bacillus subtilis or a stabilized variant thereof provides superior cleaning and stain removal.

Abstract: A microorganism which is Rhodococcus rhodochrous strain NCIMB 41164 or a mutant thereof. A method of culturing the microorganism in a culture medium comprising urea or urea derivative is claimed. A nitrile hydratase obtainable from the microorganism is claimed. Also claimed is a process of preparing an amide from the corresponding nitrile wherein the nitrile is subjected to a hydration reaction in an aqueous medium in the presence of a biocatalyst selected from the group consisting of a microorganism which is a Rhodococcus rhodochrous strain NCIMB 41164, a mutant thereof and a nitrile hydratase obtainable from Rhodococcus rhodochrous strain NCIMB 41164 or a mutant thereof. Also claimed is a method of storing the Rhodococcus rhodochrous NCIMB 41164.

Abstract: Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for modulating or altering metabolism in a cell using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

Abstract: The invention generally relates to polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) systems isolated from or derived from non-bacterial organisms, to homologues thereof, to isolated nucleic acid molecules and recombinant nucleic acid molecules encoding biologically active domains of such a PUFA PKS system, to genetically modified organisms comprising PUFA PKS systems, to methods of making and using such systems for the production of bioactive molecules of interest, and to novel methods for identifying new bacterial and non-bacterial microorganisms having such a PUFA PKS system.

Abstract: The invention provides methods and materials related to producing flavonoids as well as other organic compounds. For example, the invention provides isolated nucleic acids, polypeptides, host cells, and methods and materials for producing flavonoids and other organic compounds.

Abstract: The present invention provides DNA molecules that constitute fragments of the genome of a plant, and polypeptides encoded thereby. The DNA molecules are useful for specifying a gene product in cells, either as a promoter or as a protein coding sequence or as an UTR or as a 3? termination sequence, and are also useful in controlling the behavior of a gene in the chromosome, in controlling the expression of a gene or as tools for genetic mapping, recognizing or isolating identical or related DNA fragments, or identification of a particular individual organism, or for clustering of a group of organisms with a common trait.

Abstract: The present invention relates to pectate lyase variants exhibiting alterations relative to a parent enzyme exhibiting pectate lyase activity as its major enzymatic activity; to a method of producing such enzymes; and to methods for using such enzymes in the textile, detergent and cellulose fiber processing industries. Compared to the parent enzyme, the pectate lyase variants of the present invention exhibit improved stability in detergents.

Abstract: The present invention relates to pectate lyase variants exhibiting alterations relative to a parent enzyme exhibiting pectate lyase activity as its major enzymatic activity; to a method of producing such enzymes; and to methods for using such enzymes in the textile, detergent and cellulose fiber processing industries. Compared to the parent enzyme, the pectate lyase variants of the present invention exhibit improved stability in detergents.

Abstract: The amino acid sequence of a mutant which is obtained by introducing a novel mutation into a Pseudonocardia thermophila JCM3095-derived nitrile hydratase consisting of two types of heterogeneous subunits, and the base sequence of the gene are provided. The nitrile hydratase is modified by specifying the region to be modified in the stereostructure/amino acid sequence of the nitrile hydratase, and applying alteration such as substitution, insertion, deletion or the like, to the amino acids in the amino acid sequence which are corresponding to the amino acid residues forming the region. Also provided is a method for modifying an enzyme having a nitrile hydratase activity.

Abstract: The present invention relates to a novel thermostable gluconate dehydratase from the thermoacidophilic archaeon Sulfolobus solfataricus, a coding sequence, and an expression system. The gluconate dehydratase has a molecular weight of about 320,000 to 380,000 daltons as the native protein, and about 40,000 to 50,000 daltons as the monomer protein, and catalyzes the dehydration reaction of aldonic acids to 2-keto-3-deoxy derivatives at temperatures of less than 120° C. The gluconate dehydratase can be produced from native or recombinant host cells and thereby used in the pharmaceutical, agricultural, and other industries.

Abstract: This invention relates to a novel high-activity modified S-hydroxynitrile lyase (SHNL). More particularly, this invention relates to novel high-activity modified SHNL that is obtained by substituting amino acids at given sites (14, 44, 66, 94, 103, 118, 122, 125, 127, 129, 147, 148, 152, 212, and 216) or inserting amino acid at a given site (between amino acids 128 and 129) of the amino acid sequence (SEQ ID NO: 2) of wild-type SHNL.

Abstract: The present invention provides thermostable polypeptides related to Arabidopsis Rubisco Activase polypeptides. Nucleic acids encoding the polypeptides of the invention are also provided. Methods for using the polypeptides and nuclei acids of the invention to enhance resistance of plants to heat stress are encompassed.

Abstract: The invention is directed to polypeptides having pectate lyase (pectinase) activity, polynucleotides encoding the polypeptides, and methods for making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used as pectate lyases to catalyze the beta-elimination or hydrolysis of pectin and/or polygalacturonic acid, such as 1,4-linked alpha-D-galacturonic acid. The invention provides methods of treating fibers, fabrics or any pectate- or polygalacturonic acid-comprising material using one or more pectate lyases of the invention.

Abstract: The present invention relates to novel halohydrin dehalogenase polypeptides and the polynucleotides that encode them. These polypeptides are useful in the production of 4-substituted-3-butyric acid derivatives and vicinal cyano, hydroxyl substituted carboxylic acid esters. The invention also provides related vectors, host cells and methods.

Abstract: The present invention provides insecticidal polypeptides related to shuffled Bacillus thuringiensis Cry1 polypeptides. Nucleic acids encoding the polypeptides of the invention are also provided. Methods for using the polypeptides and nucleic acids of the invention to enhance resistance of plants to insect predation are encompassed.

Abstract: The present invention relates to an improved method for the specific production of unsaturated ?-3 fatty acids and a method for the production of triglycerides having an increased content of unsaturated fatty acids, in particular ?-3 fatty acids having more than three double bonds. The invention relates to the production of a transgenic organism, preferably a transgenic plant or a transgenic microorganism, having an increased content of fatty acids, oils or lipids having ?6 double bonds due to the expression of a ?6-desaturase from Primulaceae. The invention additionally relates to expression cassettes containing a nucleic acid sequence, a vector and organisms containing at least one nucleic acid sequence or an expression cassette. The invention further relates to unsaturated fatty acids and triglycerides having an increased content of unsaturated fatty acids and use thereof.

Abstract: The invention provides nucleic acids, and variants and fragments thereof, obtained from strains of Bacillus thuringiensis encoding polypeptides having pesticidal activity against insect pests, including Lepidoptera. Particular embodiments of the invention provide isolated nucleic acids encoding pesticidal proteins, pesticidal compositions, DNA constructs, and transformed microorganisms and plants comprising a nucleic acid of the embodiments. These compositions find use in methods for controlling pests, especially plant pests.

Abstract: The invention relates to isolated mutants of enzymes from the group of 2-deoxy-D-ribose 5-phosphate aldolase wild-type enzymes having a productivity factor (as determined by a specific test) which is at least 10% higher than the productivity factor for the corresponding wild-type enzyme from which it is a mutant. The mutants have at least one amino acid substitution at one or more of the positions corresponding to K13, T19, Y49, N80, D84, A93, E127, A128, K146, K160, I166, A174, M185, K196, F200, and S239 in Escherichia coli K12 (EC 4.1.2.4) wild-type enzyme sequence, and/or a deletion of at least one amino acid at the positions corresponding to S258 and Y259 therein, optionally combined with, specific, C-terminal extension and/or N terminal extension.

Abstract: The present invention relates to methods for the production of pectin hydrolysis products, the pectin hydrolysis products produced in this manner, as well as their use.

Abstract: Bacterial polynucleotides and polypeptides are provided in which the polypeptides have a dehydrogenase activity, such as an alcohol dehydrogenase (ADH) activity, an uronate, a 4-deoxy-L-erythro-5-hexoseulose uronate (DEHU) ((4S,5S)-4,5 dihydroxy-2,6-dioxohexanoate) hydrogenase activity, a 2-keto-3-deoxy-D-gluconate dehydrogenase activity, a D-mannuronate hydrogenase activity, and/or a D-mannnonate dehydrogenase activity. Methods, enzymes, recombinant microorganism, and microbial systems are also provided for converting polysaccharides, such as those derived from biomass, into suitable monosaccharides or oligosaccharides, as well as for converting suitable monosaccharides or oligosaccharides into commodity chemicals, such as biofuels. Commodity chemicals produced by the methods described herein are also provided.

Abstract: The invention relates to R-hydroxynitrillyases from the family of Rosaceae that are characterized by an improved substrate tolerance and increased stability. In the active center of the R-hydroxynitrillyases either a) an alanine group is substituted by glycine, valine, leucine, isoleucine, or phenylalanine or b) a phenylalanine group is substituted by alanine, glycine valine, leucine or isoleucine, or c) a leucine group is substituted by alanine, glycine, valine, isoleucine or phenylalanine, or d) an isoleucine group is substituted by alanine, glycine, valine, leucine or phenylalanine. The invention also relates to the use of these lyases in the production of enantiomer-pure R- or S-cyanohydrines.

Abstract: Modified heparinases having altered binding specificity and activity are provided. Isolated nucleic acids encoding the same as well as vectors and host cells are provided. Methods for using the modified heparinases are also provided.

Abstract: The present invention is directed to phenylalanine ammonia-lyase (PAL) variants produced by prokaryotes, wherein such prokaryotic PAL variant has a greater phenylalanine-converting activity and/or a reduced immunogenicity as compared to a wild-type PAL. The invention provides compositions of prokaryotic PAL and biologically active fragments, mutants, variants or analogs thereof, as well as methods for the production, purification, and use of such compositions for therapeutic purposes, including the treatment of cancer.

Abstract: A novel biotechnological process for the preparation of nitriles, starting from amides, is described. Micro-organisms of the genus Amycolatopsis, Actinomadura or Rhodococcus are employed for this process.

Abstract: An improved hydroxynitrile lyase characterized by having a mutation of substitution of at least one amino acid residue in the amino acid sequence of a wild-type hydroxynitrile lyase with another amino acid and by its hydroxynitrile lyase activity per transformant being higher than the hydroxynitrile lyase activity per transformant into which the wild-type hydroxynitrile lyase gene is introduced; and a method for producing a hydroxynitrile lyase, comprising expressing the improved hydroxynitrile lyase in a host and recovering the improved hydroxynitrile lyase from the resultant culture.

Abstract: The present invention pertains to the use of the protein phenylalanine ammonia-lyase, as well as the biologically-active derivatives of the said protein for preventing or treating diseases associated with a phenylalanine imbalance in a human or animal body. More particularly, the present invention relates to the therapeutic use of the above-cited molecules for preventing or treating a phenylalanine imbalance in vivo. This invention also deals with therapeutic compositions comprising a pharmaceutically active amount of the above-described therapeutic molecules as well as with therapeutic methods using the said therapeutic compositions. Finally, the present invention relates to processes for selecting more therapeutically-effective variants of said protein as well as to the selected variants themselves.

Abstract: Compositions and methods for conferring herbicide resistance to plants, plant cells, tissues and seeds are provided. Compositions comprising a coding sequence for a polypeptide that confers resistance or tolerance to glyphosate herbicides are provided. The coding sequences can be used in DNA constructs or expression cassettes for transformation and expression in plants. Compositions also comprise transformed plants, plant cells, tissues, and seeds. In particular, isolated nucleic acid molecules corresponding to glyphosate resistant nucleic acid sequences are provided. Additionally, amino acid sequences corresponding to the polynucleotides are encompassed. In particular, the present invention provides for isolated nucleic acid molecules comprising nucleotide sequences encoding an amino acid sequence shown in SEQ ID NO:3, 6, 8, 11, 19, or 21, or a nucleotide sequence set forth in SEQ ID NO:1, 2, 4, 5, 7, 9, 10, 18, or 20, as well as variants and fragments thereof.

Abstract: The present invention relates to an isolated DNA sequence encoding a polypeptide having the biological activity of amorpha-4,11-diene synthase. This DNA sequence can be used for the transformation of bacteria, yeasts and plants for the production of amorpha-4,11-diene, a specific precursor in the synthesis of artemisinin, in the respective organisms. The invention also relates to these organisms.

Abstract: The present invention relates to novel halohydrin dehalogenase polypeptides and the polynucleotides that encode them. These polypeptides are useful in the production of 4-substituted-3-butyric acid derivatives and vicinal cyano, hydroxyl substituted carboxylic acid esters. The invention also provides related vectors, host cells and methods.

Abstract: The present invention is directed to phenylalanine ammonia-lyase (PAL) variants produced by prokaryotes, wherein such prokaryotic PAL variant has a greater phenylalanine-converting activity and/or a reduced immunogenicity as compared to a wild-type PAL. The invention provides compositions of prokaryotic PAL and biologically active fragments, mutants, variants or analogs thereof, as well as methods for the production, purification, and use of such compositions for therapeutic purposes, including the treatment of cancer.

Abstract: The present invention is directed to phenylalanine ammonia-lyase (PAL) produced by prokaryotes, wherein such prokaryotic PAL wherein the PAL variant has a greater phenylalanine-converting activity and/or a reduced immunogenicity as compared to a wild-type PAL. The invention thus provides compositions of bacterial PAL and biologically active fragments, mutants, variants and analogs thereof, as well as methods for the production, purification, and use of such compositions for therapeutic and industrial purposes.