Abstract: The present invention relates to methods of diagnosing and predicting organ transplant rejection. In particular, the present invention relates to the detection and prediction of kidney transplant rejection by detection of CXCR3 and CCL chemokines in urine. The present invention provides improved methods of diagnosing organ rejection and determining the efficacy of anti-rejection drugs.

Abstract: It is intended to identify and provide a novel carnitine transporter gene participating in carnitine transport in the testis and epididymis and carnitine transporter which is a protein encoded by the gene. A protein comprising the amino acid sequence represented by SEQ ID NO:2 or an amino acid sequence derived therefrom by deletion, substitution or addition of one to several amino acids and being capable of transporting carnitine or its analog; and a gene encoding this protein.

Abstract: The present invention relates to intracellular signaling molecules, in particular the Nod1 protein. The present invention provides methods of identifying modulators of Nod1 signaling. The present invention further provides methods of altering Nod1 signaling.

Abstract: The present invention concerns cDNAs for making attentuated, infectious Newcastle disease virus (NDV). Another aspect of the invention relates to methods of making the cDNAs. Another aspect of the invention is a vector containing the cDNA optionally linked to an operable promoter. Within the scope of the invention are vaccines comprising the attenuated, infectious NDV. Also disclosed are methods of making the vaccines and methods of using the vaccines to prevent or treat Newcastle disease in an avian host. The present invention also concerns the nucleotide sequences of the entire genome of NDV, the leading region, the trailing region, and the NP region, as well as proteins encoded by these nucleotide sequences.

Abstract: Disclosed herein are methods and apparatuses for sequencing a nucleic acid. These methods permit a very large number of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of a very large number (>10,000) of different oligonucleotides.

Abstract: The present invention provides compositions and methods for recombinational cloning. The compositions include vectors having multiple recombination sites and/or multiple topoisomerase recognition sites. The methods permit the simultaneous cloning of two or more different nucleic acid molecules. In some embodiments the molecules are fused together while in other embodiments the molecules are inserted into distinct sites in a vector. The invention also generally provides for linking or joining through recombination a number of molecules and/or compounds (e.g., chemical compounds, drugs, proteins or peptides, lipids, nucleic acids, carbohydrates, etc.) which may be the same or different.

Abstract: A solution for treating a nucleic acid duplex having a pH of from 3 to 11, comprising a soluble protein or mixture of proteins; and 0.1 mM to 10 mM divalent cations; wherein the nature and concentration of the protein or mixture of proteins is selected so that the solution is capable of inhibiting heat denaturation of a nucleic acid duplex.

Abstract: A method for detecting a specific sequence, a mutation and/or a polymorphisms, including a single nucleotide polymorphism (SNP), is based on the use of RecA-like recombinase protein and primer extension (PE) or oligonucleotide ligation assays (OLA). RecA coated, specific DNA oligonucleotide probes (RecA filaments) are used for homology searching in duplex DNA. Location of homologous sequences results in the formation of D-loop or double D-loop structures containing a duplex regions comprising the oligonucleotide probe and one strand of the target DNA. In the case of the PE methods, probes are selected to terminate with their 3? end adjacent to the site of mutation or SNP such that a single nucleotide or terminator addition to the primer will be diagnostic of the mutation or SNP.

Abstract: The preparation and use of nucleic acid fragments encoding plant fatty acid modifying enzymes associated with conjugated double bond formation or functionally equivalent subfragments thereof are disclosed. Chimeric genes incorporating such nucleic acid fragments or functionally equivalent subfragments thereof or complement thereof and suitable regulatory sequences can be used to create transgenic plants having altered lipid profiles.

Abstract: Disclosed herein are genetic markers for animal growth, fatness, meat quality, and feed efficiency, methods for identifying such markers, and methods of screening animals to determine those more likely to produce desired growth, fatness, meat quality, and feed efficiency and preferably selecting those animals for future breeding purposes. The markers are based upon the presence or absence of certain polymorphisms in an HMGA nucleotide sequence.

Abstract: The invention provides a SHINC-3 polynucleotide, which can be a nucleic acid encoding all or a portion of a SHINC-3 protein, or a complementary polynucleotide or antisense polynucleotide. In another aspect, the invention provides a SHINC-3 polypeptide, which can be a full-length SHINC-3 protein or a fragment thereof or an analog or homolog thereof. Desirably, the SHINC-3 polypeptide modulates apoptosis. In another aspect, the invention provides an antibody that specifically binds a SHINC-3 polypeptide. In another aspect, the invention provides diagnostic methods. For example, the method affords a method for identifying compounds that modulate apoptosis. In another aspect, the invention provides a method for detecting or evaluating the prognosis of a cancer. In another aspect, the invention provides diagnostic compositions for detection of cancer.

Abstract: A method of characterizing an analyte sample is provided that includes the steps of: (a) anchoring the analyte to a nucleic acid template of known sequence; (b) conducting a DNA polymerase reaction that includes the reaction of a template, a non-hydrolyzable primer, at least one terminal phosphate-labeled nucleotide, DNA polymerase, and an enzyme having 3??5? exonuclease activity which reaction results in the production of labeled polyphosphate; (c) permitting the labeled polyphosphate to react with a phosphatase to produce a detectable species characteristic of the sample; (d) detecting the detectable species. The method may include the step of characterizing the nucleic acid sample based on the detection. Also provided are methods of analyzing multiple analytes in a sample, and kits for characterizing analyte samples.

Abstract: This invention relates to methods of sequencing DNA. More specifically, this invention relates to methods of sequencing both the sense and antisense strands of DNA through the use of blocked and unblocked sequencing primers. In brief, these methods include the steps of annealing an unblocked primer to a first strand of nucleic acid; annealing a second blocked primer to a second strand of nucleic acid; elongating the nucleic acid along the first strand with a polymerase; terminating the first sequencing primer; deblocking the second primer; and elongating the nucleic acid along the second strand.

Abstract: Provided is a preparative method for isolating RNA comprising an oligo-or polynucleotide from a sample, which method comprises: (a) treating the sample with a reactant capable of covalently modifying the 2?-OH position of the ribose rings of the RNA under conditions so that a proportion of the 2?-OH positions of the ribose rings bear a substituent; and (b) preparing isolated RNA therefrom by separating material containing the substituent from the sample on the basis of a property of the substituent.

Abstract: A plasmid isolatable from Corynebacterium thermoaminogenes, which comprises a gene coding for a Rep protein having the amino acid sequence shown in SEQ ID NO: 8 or an amino acid sequence having homology of 90% or more to the amino acid sequence shown in SEQ ID NO: 8, and has a size of about 4.4 kb or about 6 kb, or a derivative thereof.

Abstract: The invention relates to the field of molecular biology, nucleic acid chemistry and medical diagnostics. More specifically, it relates to methods and compositions for promoting the hybridization of a nucleic acid probe with a target nucleic acid sequence which is not perfectly matched to the probe.

Abstract: The invention relates to methods for inducing a pro-asthma/pro-inflammatory like state in a resident tissue cell, comprising contacting the cell with one or more cytokines, e.g., IL-1?, TNF? or both. Methods are also disclosed for identifying genes that regulate responses to anti-inflammatory drugs, to methods for drug screening, and to methods for identifying genes that correlate with various pro-asthma/pro-inflammatory disease phenotypes.

Abstract: Linear arrays of chemosensors or chemical compounds are supported by an optical fiber that allows one to rapidly assay the entire array using changes in optical properties such as fluorescence. The location of the agent along the fiber determines the identity of the agent in these linear arrays. Combinatorial libraries may be constructed on the fiber as well as assayed on the optical fiber. A system and method of analyzing the entire array of agents on an optical fiber using a light source, an optical fiber, and a detector are also described. The time delay between the excitation and detection determines the location being assayed along the fiber and therefore the identity of the agent being assayed. The present invention may find uses in the medical, pharmaceutical, environmental, defense, and food industries.

Abstract: The present invention is directed to polynucleotides encoding polypeptides associated with the development of rheumatoid arthritis and homologs thereof. The invention further relates to diagnostic and therapeutic methods for utilizing these polynucleotides and polypeptides in the diagnosis, treatment, and/or prevention of rheumatoid arthritis and related disease states. The invention further relates to screening methods for identifying agonists and antagonists of the polynucleotides and polypeptides of the present invention, and compounds identified thereby.

Abstract: A monoclonal antibody having inhibitory activity on blood coagulation reactions, which reacts with prothrombin forming a complex with phosphatidylserine but does not react with prothrombin not forming a complex with phosphatidylserine; and a method for measuring inhibitory activity of test plasma on blood coagulation reactions, which comprises the steps of (1) measuring inhibitory activity of the test plasma on the blood coagulation reactions and inhibitory activity of this on the blood coagulation reactions, and (2) comparing the inhibitory activity of the test plasma with the inhibitory activity of this antibody.

Abstract: The present invention relates to the diagnosis of HIV infections. It especially teaches the production of a soluble retroviral surface glycoprotein-(or transmembrane glycoprotein)-chaperone complex and the advantageous use of a chaperone-antigen complex especially in the detection of antibodies to HIV in immunoassays, preferably according to the double antigen bridge concept, or as an immunogen. The invention also discloses soluble complexes comprising a variant of HIV-1 gp41 or a variant of HIV-2 gp36, respectively, and a chaperone selected from the peptidyl-prolyl-isomerase class of chaperones. Variants comprising specific amino-acid substitutions in the N-helical domain of HIV-1 gp41 or of HIV-2 gp36, respectively, are also described.

Abstract: The present invention relates to regulation of angiogenesis. More particularly, the present invention is directed to nucleic acids encoding C1-angiogenesis protein, also called integrin-linked kinase associated protein (“ILKAP”) and ILKAP protein, which is involved in modulation of angiogenesis. The invention further relates to methods for identifying and using agents, including small organic molecules, antibodies, peptides, cyclic peptides, nucleic acids, antisense nucleic acids, and ribozymes, that modulate angiogenesis via modulation of ILKAP and ILKAP-related cascades; as well as to the use of expression profiles and compositions in diagnosis and therapy of angiogenesis.

Abstract: A novel receptor, “LDL-receptor-related protein-5” (“LRP-5”), is provided, along with encoding nucleic acid. The gene is associated with type 1 diabetes (insulin dependent diabetes mellitus), and experimental evidence provides indication that it is the IDDM susceptibility gene IDDM4. In various aspects the invention provides nucleic acid, including coding sequences, oligonucleotide primers and probes, polypeptides, pharmaceutical compositions, methods of diagnosis or prognosis, and other methods relating to and based on the gene, including methods of treatment of diseases in which the gene may be implicated, including autoimmune diseases, such as glomerulonephritis, diseases and disorders involving disruption of endocytosis and/or antigen presentation, diseases and disorders involving cytokine clearance and/or inflammation, viral infection, elevation of free fatty acids or hypercholesterolemia, osteoporosis, Alzheimer's disease, and diabetes.

Abstract: The present invention provides methods for utilizing a form of optimized suspension culture to examine the infectivity of pathogenic organisms and agents in human cells and tissues. Also provided are methods using a rotating wall vessel to predict chemosensitivity of cells and tissues to toxins and chemotherapeutic agents. These culture conditions potentiate spatial colocalization and three-dimensional assembly of individual cells into large aggregates which more closely resemble the in vivo tissue equivalent. In this environment, dissociated cells can assemble and differentiate into macroscopic tissue aggregates several millimeters in size. These culture conditions allow for better cellular differentiation and formation of three-dimensional cellular aggregates, more efficient cell-to-cell interactions, the in in vivo-like exchange of growth factors and greater molecular scaffolding facilitating mechanical stability for cells.

Abstract: The invention provides methods and materials for diagnosing an angina condition in a patient. Specifically, the invention provides methods and materials for classifying an angina condition as either stable or unstable. In addition, the invention provides methods and materials for determining an individual's predisposition to have a stable or unstable angina condition. The invention also provides kits for classifying an angina condition as either stable or unstable as well as kits for determining an individual's predisposition to have a stable or unstable angina condition.

Abstract: The present invention relates to identification of polypeptides useful for generating antibodies specific for non-human IgE, particularly equine IgE. The invention, therefore, also relates to antibodies that specifically bind to IgE and methods to detect IgE using the antibodies. The invention also provides a kit for detection of IgE.

Abstract: Disclosed is a modified glucose dehydrogenase having pyrroloquinoline quinone as a coenzyme, wherein one or more amino acid residues in a region of amino acid 349-377 of water-soluble PQQGDH derived from Acinetobacter calcoaceticus is replaced with other amino acid residues and has an inhibition constant (Ksi) of 200 mM or more. The modified water-soluble PQQGDH of the invention can be utilized for measuring glucose levels in the presence of high concentrations of glucose because of the low substrate inhibition by glucose.

Abstract: A biosensor in which a carbohydrate or a derivative of a carbohydrate is used to generate a detectable signal by way of the specific binding to a protein, a virus or a cell.

Abstract: A device and method for detecting the presence or absence of a prokaryotic microorganism are provided, comprising the steps of identifying a protein, such as a microbial-specific protease that characterizes the presence of a specific prokaryotic microbe and thereby provides a marker for that microbe; detecting the protease that is a marker for the presence of a specific prokaryotic microbe by cleaving a substrate when the protease is present; and signaling the presence of that protease when cleavage has occurred. More specifically, the method comprises identifying at least one outer membrane protein or a secreted protein that is unique to a particular microbial pathogen such as for example Listeria monocytogenes and that is substrate specific.

Abstract: The invention provides nucleic acid and amino acid sequences for a novel family of taste transduction G-protein coupled receptors, antibodies to such receptors, methods of detecting such nucleic acids and receptors, and methods of screening for modulators of taste transduction G-protein coupled receptors.

Abstract: The present invention relates generally to the fields of biochemistry, molecular biology, and virology. More particularly, it relates to the identification of 259 nucleotides located at the 3? end of the GB virus B (GBV-B) genome. The invention involves nucleic acid constructs and compositions encoding GBV-B sequence, including the 3? end of the sequence, which has allowed an infectious GBV-B clone to be constructed. This construct, and chimeric versions of it, may be employed to study GBV-B and related hepatitis family members, such as hepatitis C virus. The invention thus includes methods of preparing GBV-B-containing sequences, constructs, and viruses, as well as methods of employing these compositions.

Abstract: The present invention relates in part to isolated nucleic acid molecules (polynucleotides) which encode Drosophila melanogaster ligand-gated ion channel proteins. The present invention also relates to recombinant vectors and recombinant hosts which contain a DNA fragment encoding Drosophila ligand-gated ion channel proteins, substantially purified forms of associated Drosophila ligand-gated ion channel proteins and recombinant membrane fractions comprising these proteins, associated mutant proteins, and methods associated with identifying compounds which modulate associated Drosophila melanogaster ligand-gated ion channel proteins, which will be useful as insecticides.

Abstract: Expression vectors encoding bacteriophage signal peptides are described. The vectors may be used for the heterologous expression and secretion of polypeptides such as antibodies in bacterial host cells.

Abstract: A vector having a region encoding a cold shock protein gene mRNA-origin 5?-nontranslated region, characterized in that the 5?-nontranslated region has a mutation having been transferred therein so as to change the distance of the stem structure formed by the region.

Abstract: Multimeric hybrid genes encoding the corresponding chimeric protein comprise a gene sequence coding for an antigenic region of a protein from a first pathogen linked to a gene sequence coding for an antigenic region of a protein from a second pathogen. The pathogens particularly are parainfluenza virus (PIV) and respiratory syncytial virus (RSV). A single recombinant immunogen is capable of protecting infants and similar susceptible individuals against diseases caused by both PIV and RSV.

Abstract: The present invention relates to nucleotides encoding for the production of novel regulatory proteins for Nox enzymes involved in generation of reactive oxygen intermediates that affect cell division. The present invention also provides vectors containing these nucleotides, cells transfected with these vectors, antibodies raised against these novel proteins, kits for detection, localization and measurement of these nucleotides and proteins, and methods to determine the activity of drugs to affect the biological activity of the regulatory proteins of the present invention.

Abstract: Novel Saccharomyces Cerevisiae mutant strains are provided for producing human parathyroid hormone. The novel strains acre genetically disrupted in at least one of the genes encoding the yapsin family of proteases Yapsin 1, Yapsin 2 and Yapsin 3 and harbor a human parathyroid hormone gene in their genomes. Culturing the novel strains results in the secretion of intact hPTH into culture media at high yield.

Abstract: Disclosed is a method that includes: (i) providing a plurality of initial nucleic acid cassettes that include: a) a first coding region encoding a first immunoglobulin variable domain, b) a second coding region encoding a second immunoglobulin variable domain, and c) a ribosomal binding site disposed between the first and second coding regions for translation of the second polypeptide in a first expression system, wherein the first and second coding regions are in the same translational orientation; (ii) modifying each nucleic acid cassette of the plurality in a single reaction mixture so that it is functional in a second expression system, wherein the first and second region remain physically attached during the modifying; (iii) introducing each modified nucleic acid cassette into a mammalian cell to produce a mixture of transfected cells; and (iv) expressing each modified nucleic acid cassette in the transfected cells.

Abstract: The present invention features improved methods for the enhanced production of pantoate and pantothenate utilizing microorganisms having modified pantothenate biosynthetic enzyme activities and having modified methylenetetrahydrofolate (MTF) biosynthetic enzyme activities. In particular, the invention features methods for enhancing production of desired products by increasing levels of a key intermediate, ketopantoate by enzymes that contribute to its synthesis. Recombinant microorganisms and conditions for culturing same are also are featured. Also featured are compositions produced by such microorganisms.

Abstract: A microbial method for the preparation of an epothilone containing a terminal hydroxyalkyl group, comprising contacting at least one epothilone having a terminal alkyl group with an enzyme or microorganism capable of catalyzing the selective hydroxylation of said alkyl group to a hydroxyalkyl group, and effecting said hydroxylation.

Abstract: The object of this invention is to provide a method which not only maintains the nitrile hydratase activity of a nitrile hydratase-containing cell or a treated material of the cell under conditions where the cell does not grow, but also improves the nitrile hydratase activity of a nitrile hydratase-containing cell or a treated material of the cell whose activity was once reduced. This invention relates to a method of maintaining or improving a nitrile hydratase activity which comprises bringing a nitrile hydratase-containing cell or a treated material of the cell into contact with an oxidizing agent under conditions where the cell does not grow, as well as a method of producing an amide compound from a nitrile compound, which comprises using the cell brought into contact with an oxidizing agent or a treated material of the cell.

Abstract: The present invention is in the field of the preparation of lactic acid by means of fermentation, more particularly it is directed to processes to separate the biomass from the lactic acid-containing fermentation product by means of flocculation. We have found that for the separation of biomass from lactate and lactic acid-containing fermentation broth the following process is very convenient and suitable; a) Subjecting the fermentation broth to an alkalifying step, b) adding one or more flocculants, and c) separating the biomass flocs from the lactate and lactic acid-containing fermentation broth. With this process even bacteria-based fermentation broths can be suitably handled efficiently and economically.

Abstract: The invention relates to a method of producing ethanol by fermentation, said method comprising a secondary liquefaction step in the presence of a thermostable acid alpha-amylase or, a thermostable maltogenic acid alpha-amylase.

Abstract: Array systems that facilitate the simultaneous monitoring of many interactions between biological molecules and the analysis of cellular protein interactions with high throughput. The present invention provides methods and arrays for analyzing biochemical pathways by forming an array of immobilized biomolecules; exposing the array to biomolecules in solution; and detecting modification of the immobilized biomolecules, modification of the biomolecules in solution, and/or binding of biomolecules in solution to immobilized biomolecules.

Abstract: The invention relates generally to isolated leucoanthocyanidin reductase LAR polypeptides of the Reductase-Epimerase-Dehydrogenase (RED) protein family, and nucleic acid molecules encoding same and their use in regulating the biosynthesis and accumulation of proanthocyanidins in plants. The invention is further directed to isolated nucleic acid molecules of plants, which encode leucoanthocyanidin reductases of the RED protein family. The isolated polypeptides and nucleic acid molecules of the present invention are useful for modifying the pasture quality of legumes, and, in particular, for producing bloat-safe forage crops, or crops having enhanced nutritional value, enhanced disease resistance or pest resistance, or enhanced malting qualities.

Abstract: Disclosed is a water-soluble PQQGDH wherein two subunits are linked together via a disulfide bond. The water-soluble PQQGDH of the invention exhibits improved thermal stability.

Abstract: This invention provides fusion polypeptides that include a glycosyltransferase catalytic domain and a catalytic domain from an accessory enzyme that is involved in making a substrate for a glycosyltransferase reaction. Nucleic acids that encode the fusion polypeptides are also provided, as are host cells for expressing the fusion polypeptides of the invention.

Abstract: The invention concerns polymerase chimeras which are composed of amino acid fragments representing domains and which combine properties of naturally occurring polymerases that are advantageous with regard to a particular application. It has surprisingly turned out that the domains from the various enzymes are active in the chimeras and exhibit cooperative behavior. In addition the present invention concerns a process for the production of the chimeras according to the invention and the use of these chimeras for the synthesis of nucleic acids e.g. during a polymerase chain reaction. Moreover the present invention concerns a kit which contains the polymerase chimeras according to the invention.

Abstract: Disclosed is a novel type II restriction endonuclease. Such enzyme recognizes a particular non-palindromic sequence of 5 oligonucleotides and cleaves DNA downstream of the DNA recognition sequence of nucleotides at the fourth base in the upper strand and the fifth base in the lower strand, and forms a one-base protruding end in the 5?-end after cleavage. The recognition and cleavage site of HpyC1I is identical to the known restriction endonuclease BccI respectively, but the nucleotide sequence and the amino acid sequence are different from any other know restriction enzymes.

Abstract: The present invention features substantially pure HDAC9, HDAC9a, HDAC9(?NLS), HDAC9a(?NLS), an HDRP(?NLS) polypeptides, and isolated nucleic acid molecules encoding those polypeptides. The present invention also features vectors containing HDAC9, HDAC9a, HDAC9(?NLS), HDAC9a(?NLS), and HDRP(?NLS) nucleic acid sequences, and cells containing those vectors.