Abstract: The present invention provides a DNA chip including: a solid support having a surface; a DNA fragment immobilized on the surface; and a graft polymer bonded to the surface, wherein the DNA fragment is immobilized on the surface via the graft polymer. The invention also provides a DNA chip including: a solid support made of a resinous material and having a surface; a DNA fragment immobilized on the surface; and a graft polymer bonded to the surface, wherein the DNA fragment is immobilized on the surface via the graft polymer.

Abstract: The invention concerns a method for quantitative measuring of gene expression by obtaining marked probes of pre-selected homogeneous size, after reverse transcription and amplification. The invention also concerns the method for preparing marked probes, and implementing kits using microarrays and macroarrays.

Abstract: Fluorescent labels having at least one donor and at least one acceptor fluorophore bonded to a polymeric backbone in energy transfer relationship, as well as methods for their use, are provided. Of particular interest are the subject labels wherein the polymeric backbone is a nucleic acid and the donor fluorophore is bonded to the 5′ terminus of said nucleic acid. Such labels find use as primers in applications involving nucleic acid chain extension, such as sequencing, PCR and the like.

Abstract: The present invention concerns the discovery of a new family of hedgehog binding proteins, refered to herein as “hedgehog interacting proteins” or “HIPs”, which are demonstrated to bind to hedgehog polypeptides with high affinity. As described herein, the vertebrate HIP proteins exhibit spatially and temporally restricted expression domains indicative of important roles in hedgehog-mediated induction.

Abstract: The present invention is directed to branched reactive water-soluble polymers comprising at least two polymer arms, such as poly(ethylene glycol), attached to a central aliphatic hydrocarbon core molecule through heteroatom linkages. The branched polymers bear at least one functional group for reacting with a biologically active agent to form a biologically active conjugate. The functional group of the branched polymer can be directly attached to the aliphatic hydrocarbon core or via an intervening linkage, such as a heteroatom, -alkylene-, —O-alkylene-O—, -alkylene-O-alkylene-, -aryl-O—, —O— aryl-, (—O-alkylene-)m, or (-alkylene-O—)m linkage, wherein m is 1-10.

Abstract: A method for high-throughput genomics analysis, to identify the therapeutic or diagnostic utility of genes, entails the use of a construct to disrupt a gene or alleles of a gene in cells of interest. Arrays of such cells can be used to monitor such disrupted cells phenotypically in the context, for example, of testing drug candidates. Polynucleotides that comprise part of the disrupted genes can be recovered from such “knockout” cells, by virtue of an origin of replication or a host cell selection marker sequence that is part of the construct. The recovered polynucleotides can be used to identify the disrupted genes or to make homologous recombination vectors, which in turn can be employed to make multi-allele knockout cells. Double-stranded RNA molecules designed to target the recovered polynucleotide are used to down regulate the polynucleotide in vitro and in vivo, following determination of a therapeutically effective dosage of the RNAi molecule.

Abstract: The invention provides nanoparticle-bioconjugate probes that are useful for detecting target analytes such as nucleic acids. The probes of the invention are stable towards heat and resistant to displacement by thiol containing compounds such as DTT (dithiothreitol).

Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3′ end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.

Abstract: This invention relates to detection of specific extracellular nucleic acid in plasma or serum fractions of human or animal blood associated with neoplastic or proliferative disease. Specifically, the invention relates to detection of nucleic acid derived from mutant oncogenes or other tumor-associated DNA, and to those methods of detecting and monitoring extracellular mutant oncogenes or tumor-associated DNA found in the plasma or serum fraction of blood by using rapid DNA extraction followed by nucleic acid amplification with or without enrichment for mutant DNA. In particular, the invention relates to the detection, identification, or monitoring of the existence, progression or clinical status of benign, premalignant, or malignant neoplasms in humans or other animals that contain a mutation that is associated with the neoplasm through detection of the mutated nucleic acid of the neoplasm in plasma or serum fractions.

Abstract: Provided herein are two 1-8 family gene interferon tau inducible genes, bovine 1-8U and bovine Leu-13, and methods of detecting the same to determine bovine pregnancy.

Abstract: Oligonucleotides in which one or more purine residues are substituted by pyrazolo[3,4-d]pyrimidines exhibit improved hybridization properties. Oligonucleotides containing pyrazolo[3,4-d]pyrimidine base analogues have higher melting temperatures than unsubstituted oligonucleotides of identical sequence. Thus, in assays involving hybridization of an oligonucleotide probe to a target polynucleotide sequence, higher signals are obtained. In addition, mismatch discrimination is enhanced when pyrazolo[3,4-d]pyrimidine-containing oligonucleotides are used as hybridization probes, making them useful as probes and primers for hybridization, amplification and sequencing procedures, particularly those in which single- or multiple-nucleotide mismatch discrimination is required.

Abstract: The present invention relates to at least one novel anti-TNF antibodies, including isolated nucleic acids that encode at least one anti-TNF antibody, TNF, vectors, host cells, transgenic animals or plants, and methods of making and using thereof, including therapeutic compositions, methods and devices.

Abstract: The present invention relates to the use of nanoparticle detection probes to monitor amplification reactions, especially polymerase chain reactions (“PCR”). More specifically, the present invention involves the use of nanoparticles oligonucleotide conjugates treated with a protective agent such as bovine serum albumin in an homogeneous assay format in order to quantitatively and qualitatively detect a target polynucleotide.

Abstract: The accurate synthesis of nucleic acid molecules is important for use of amplified nucleic acid molecules as hybridization probes, in the regulation of gene expression, as templates for the production of recombinant proteins, as diagnostic probes, and in forensic analyses. Methods are provided to separate nucleic acid molecules that are free of mutations from a population of nucleic acid molecules that contain unwanted nucleotide alternations.

Abstract: The present invention relates to chemically modified genomic sequences of genes associated with the immune system, to oligonucleotides and/or PNA-oligomers directed against the sequence, for the detection of the methylation status of genes, associated with the immune system as well as to a method for ascertaining genetic and/or epigentic parametres of genes, associated with the immune system.

Abstract: Highly hydrophilic non-nucleosidic tags with multiple labels are provided for use in nucleic acid probes. The tags are branched structures having a phosphodiester backbone, which have the advantages of a small dimensional size and high hydrophilicity. After the tag is labeled, its high negative charge and minimal size help to keep the carriers away from DNA or RNA molecules, due to repulsion between negative charges. Non-specific intercalation and steric hindrance are therefore minimized, and the hydrophobicity, if any of reporter molecules is reduced. The probes are used in place of conventionally labeled oligonucleotides for a variety of hybridization reactions.

Abstract: Methods of using a genetic polymorphic variation in the human beta-1 adrenergic receptor gene as a drug response marker are presented. Determining the presence or absence of the A145G genetic variation in the human beta-1 adrenergic receptor gene is useful in predicting an individual's relative response to different antihypertensive drugs; optimizing antihypertensive treatment for an individual; selecting candidate human subjects for participation in clinical trials involving antihypertensive drugs; and, predicting the relative responses among a plurality of individuals to an antihypertensive drug.

Abstract: The present invention provides a method of identifying a gene product. The method comprises providing a multiplicity of cells comprising a first gene product. Preferably, the first gene product is produced in the multiplicity of cells by expressing a first exogenous nucleic acid sequence encoding the first gene product. A library of second nucleic acid sequences encoding second gene products is then introduced into the multiplicity of cells. The second nucleic acid sequences are expressed in the multiplicity of cells to produce the second gene products such that the first gene product and at least one of the second gene products contact. The method further comprises causing a complex to form between the first gene product, an affinity molecule that binds the first gene product, and at least one of the second gene products, and subsequently retrieving the complex. At least one second gene product of the complex then is identified.

Abstract: The invention relates to methods and compositions for the diagnosis and treatment of metabolic disorders, including, but not limited to, obesity, diabetes, overweight, insulin resistance, anorexia, and cachexia. The invention further provides methods for identifying a compound capable of treating a metabolic disorder. The invention also provides methods for identifying a compound capable of modulating a metabolic activity. Yet further, the invention provides a method for modulating a metabolic activity. In addition, the invention provides a method for treating a subject having a metabolic disorder characterized by aberrant SARP3 polypeptide activity or aberrant SARP3 nucleic acid expression. In another aspect, the invention provides methods for modulating lipogenesis in a subject and methods for modulating lipolysis in a subject.

Abstract: The present invention relates to the isolation, purification and characterization of proteins mediating switch recombination. It further relates to recombinant SRTA-70 proteins, DNA sequences encoding these proteins, vectors containing these DNA sequences and hosts containing these vectors. The use of these proteins for identifying agonists or antagonists and other proteins involved in class switch recombination is also provided.

Abstract: Provided herein are addressable collections of anti-tag capture agents, such as antibodies, that are used as tools for sorting proteins containing polypeptide tags for which the capture agents are specific. Also provided are methods of nested sorting using the collections. The methods include the steps of creating tagged collections of molecules by introducing a set of nucleic acid molecules that encode unique preselected polypeptides to create a library of tagged molecules; either before or after introducing the tags, dividing the library into N divisions; translating each division and reacting each with one of N capture agent collections, identifying the capture agents bound to the polypeptide tags linked to molecules of interest, and thereby identifying the one of the divided collections that contains the molecules of interest.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.

Abstract: Novel solution-based methods and materials, including apparatus, for sequence analysis by hybridization are provided.

Abstract: Disclosed and claimed is the CaESS1 gene, portions thereof such as primers or probes, expression products therefrom, and methods for using the gene, and expression products; for instance, for diagnostic, therapeutic or preventive compositions.

Abstract: Disclosed herein are arrays of nucleic acid-protein fusions which are immobilized to a solid surface through capture probes which include a non-nucleosidic spacer group and an oligonucleotide sequence to which the fusion (such as an RNA-protein fusion) is bound. Also disclosed herein are solid supports on which these arrays are immobilized as well as methods for their preparation and use (for example, for screening for protein-compound interactions such as protein-therapeutic compound interactions).

Abstract: The present invention provides two ATP synthase subunits (designated individually as Asy-1 and collectively as Asy) and polynucleotides which identify and encode Asy. The invention also provides genetically engineered expression vectors and host cells comprising the nucleic acid sequences encoding Asy and a method for producing Asy. The invention also provides for use of Asy and agonists, antibodies, or antagonists specifically binding Asy, in the prevention and treatment of diseases associated with expression of Asy. Additionally, the invention provides for the use of antisense molecules to polynucleotides encoding Asy for the treatment of diseases associated with the expression of Asy. The invention also provides diagnostic assays which utilize the polynucleotide, or fragments or the complement thereof, and antibodies specifically binding Asy.

Abstract: The invention provides a method that allows the construction of a chimeric and/or modified and/or reconstructed DNA molecule from two DNA fragments in a defined order and orientation, and to clone the molecule one step in a suitable vector using site specific recombination. No initial step of classical cloning via restriction enzymes is needed, in contrast to the classical recombination systems. This method allows the reliability of the recombination method for cloning with the flexibility of PCR to introduce modifications in the insert sequence. Moreover, this method allows the construction of chimerical DNA molecules associating two different elements, such as promoter-gene association or fusion proteins.

Abstract: A method is described for determining the sequence of nucleic acids. The method employs small solid phase particles having transponders, with a primary layer of an oligonucleotide of known sequence attached to the outer surface of the particle. A read/write scanner device is used to encode and decode data on the transponder. The stored data includes the sequence of the oligonucleotide immobilized on the transponder. The sequence of sample nucleic acids is determined by detecting annealing to an oligonucleotide bound to a particle, followed by decoding the transponder to determine the sequence of the oligonucleotide.

Abstract: The present invention provides a substantially purified carbohydrate ligand that specifically binds to a leczyme. The invention also provides methods to identify a carbohydrate ligand that specifically binds to a leczyme or a leczyme that specifically binds to a carbohydrate ligand. The invention further provides methods to identify a peptide that binds to the carbohydrate ligand binding site of a leczyme.

Abstract: Nuclear matrix proteins (NMP) which are characterized by a defined expression in tissue are provided. These NMPs are useful markers in diagnosing and monitoring the stage of malignancy of a cell and treating cell proliferative disorders associated with the NMP. Also provided are substantially purified polypeptides and nucleotide sequences encoding the NMPs of the invention.

Abstract: The invention provides human RNA binding proteins (RNABP) and polynucleotides which identify and encode RNABP. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. The invention also provides methods for diagnosing, treating or preventing disorders associated with expression of RNABP.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the transporter peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the transporter peptides, and methods of identifying modulators of the transporter peptides.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the enzyme peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the enzyme peptides, and methods of identifying modulators of the enzyme peptides.

Abstract: The present invention relates to a procedure for the qualitative and/or quantitative analysis of biological substances, which are preferably biological substances, that are present in a conductive liquid medium, with the aid of at least one affinity sensor that includes at least one structure that includes at least one semiconductor material, which is coated on one of its surface with at least one layer of an isolating material, which in turn is affixed adhesively to at least one sensitive membrane, which is in contact with the conductive medium and which includes ligands that are complementary to the biological substances in question and which are capable of, and suitable for, forming pairs specifically with the latter biological substances, with the said procedure being characterized by the fact that it consists essentially of applying a voltage between the semiconductor and the conductive medium; of gathering the variations in the electrical signals induced by a charge-effect phenomenon directly and essent

Abstract: Disclosed are processes for specifically modulating the properties of a target molecule T, and/or of a component C, which interacts directly or indirectly with T. Also disclosed are processes for the production of a targeted effector having the capacity to specifically modulate the properties of an intracellular target molecule and/or a cellular component C which interacts directly or indirectly in the cell with the molecule. Also disclosed are effector molecules, nucleic acids encoding same and constructs e.g., vectors and host cells, containing the nucleic acids, as well as pharmaceutical compositions, and uses of the effector molecules. Further disclosed are intracellular recognition molecules containing proteinaceous recognition domains, as well as processes for identifying dimeric recognition moieties having the capacity to force an interaction between two target molecules T1 and T2, and/or a cellular component C which interacts directly or indirectly in a cell with T1 and T2.

Abstract: A method for determining the presence of food allergy or food intolerance and their cross-reactive tissue antigens is disclosed. The method includes determining a level of antibodies against a dietary antigen in a mucosal sample from the patient and comparing the level with normal levels of the antibodies. Dietary antigens that were tested include milk and milk products; eggs and egg products; meat and meat products; fish, mollusks, and crustaceans and their products; oils, fats, and their products; grains and grain products; pulses, seed, kernels, nuts, and their products; vegetable and vegetable products; fruit and fruit products; sugar, sugar product, chocolate products, and confectionary; and spices.

Abstract: A method and apparatus for predicting a protein tertiary structure or designing a protein sequence using potential profiles calculated by using multidimensional singleton potentials dependent only on a residue type of one of residues of a residue pair and on a multidimensional relative structural relationship (including direction and orientation) between residues of each residue pair. Existing dynamic programming is used in predicting a protein tertiary structure.

Abstract: The present invention concerns compositions, methods of production and methods of use of polydiazoaminotyrosine (DAT), a novel organic semiconductor. In preferred embodiments, the DAT is oxidized (O-DAT). In certain embodiments, recognition complexes comprising DAT operably coupled to a binding moiety are provided. The recognition complexes are of use for detection, identification and/or neutralization of various analytes. In alternative embodiments, DAT in combination with a source of activating radiation may be used to neutralize various analytes, such as anthrax spores.

Abstract: An apparatus and method for synthesizing a combinatorial library comprising a plurality of chemical compounds such that the chemical composition of each compound is easily tracked. The library compounds are synthesized on solid-phase supports, which are spatially arranged in frames during synthesis according to a predetermined protocol, such that each solid-phase support passes through a series of unique spatial 2D or 3D addresses by which the chemical composition of each compound may be determined at any point during synthesis. Solid-phase supports include hollow tubular-shaped lanterns and gears.

Abstract: A method for measuring the activity of creatine kinase MB (CK-MB) isozyme which is accurate, high in specificity, convenient, by inhibiting the activity of a mitochondria-localized creatine kinase (mCK) isozyme to avoid the influence of mCK and a measurement reagent therefor are provided.

Abstract: The invention relates to Tango-73, Tango-74, Tango-76, Tango-78, and Tango-83 polypeptides, nucleic acid molecules encoding Tango-73, Tango-74, Tango-76, Tango-78, and Tango-83, and uses thereof. The invention provides isolated nucleic acids encoding a variety of proteins having diagnostic, preventive, therapeutic, and other uses. These nucleic and proteins are useful for diagnosis, prevention, and therapy of a number of human and other animal disorders. The invention also provides antisense nucleic acid molecules, expression vectors containing the nucleic acid molecules of the invention, host cells into which the expression vectors have been introduced, and non-human transgenic animals in which a nucleic acid molecule of the invention has been introduced or disrupted. The invention still further provides isolated polypeptides, fusion polypeptides, antigenic peptides and antibodies. Diagnostic, screening, and therapeutic methods using compositions of the invention are also provided.

Abstract: The present invention provides a novel protein that regulates degranulation of mast cells (degranulation regulator), a gene encoding it, a protein (conjugate factor) that interacts with the regulator, a gene encoding it, a screening method of an inhibitor of the degranulation, which uses this degranulation regulator and the conjugate factor, an inhibitor obtained by the screening method and the like.

Abstract: The present invention relates to a 3-part hybrid system for detection protein interactions in live mammalian cells and screening for compounds modulating such interactions. The method is fully compatible with HTS. The three hybrids are a first heterologous conjugate comprising an anchor protein that specifically binds to an internal structure within the cell conjugated to an interactor protein of type A, a second heterologous conjugate comprising an interactor protein of type B conjugated to the first protein of interest, a third heterologous conjugate comprising a second protein of interest conjugated to a detectable group. When applying a dimerizer compound, interactor proteins A and B bind to each other and if the two proteins of interest interact, the distribution of the detectable group will mimic the distribution of the anchor protein. However, if there is no interaction, the distribution of the detectable group will mimic the distribution of the second protein of interest.

Abstract: The invention provides methods for assaying the activity of the translocase enzyme and/or transferase enzyme involved in peptidoglycan biosynthesis in bacteria using scintillation proximity assay methodology. The methods are suitable for high throughput screening of potential anti-bacterial drugs.

Abstract: An assay method and kit for detecting the presence of a predesignated, target IgG antibody in a sample selected from one or more patient bodily fluids. The method comprises the following steps: (a) contacting the sample of one or more patient bodily fluids with a membrane-bound recombinant protective antigen to bind to the target IgG antibody in the sample; (b) previously, simultaneously or subsequently to step (a), binding the protective antigen (PA) with a conjugated label producing a detectable signal; and (c) detecting the signal whereby the presence of the target IgG antibody is determined in the sample by the intensity of the signal. The method can further comprise the step of evaluating immunization status of the patient from whom the sample came by comparing the signal or lack thereof with immunizations previously received by the patient. In a preferred embodiment, the recombinant protective antigen (PA) specifically binds to anthrax protective antigen-specific IgG antibodies.

Abstract: A clinical diagnostic assay is performed on an optical bio disc and is read with a disc drive. More specifically this invention relates to capture layer assemblies for cellular assays using optical bio-discs. The current invention includes methods for determining the quality and quantity of a specific type of cell in a biological sample. These methods includes binding capture agents to a capture zone on the disc, providing a sample to the capture zone, remove portions of the sample that are not bound in the capture zone, and counting bound cells. The current invention also includes methods and apparatus for performing a cluster designation marker assay using an optical disc and disc drive and method for making optical analysis discs for performing such cluster designation assays.

Abstract: An antibody/carrier complex which makes it possible to easily control the reactivity in an antigen-antibody reaction without producing a new antibody. This antibody/carrier complex is a complex containing at least one antibody and has a polymer structure wherein each antigen-binding site of the antibody is allowed to be arranged so as to react with the antigen.

Abstract: The present invention is an analytical device which comprises a porous piece assembly consisting of a liquid reagent-receiving porous piece (1), a labeled substance-retaining piece (2), a test piece (3) comprising a detection site (4) and a reference site (5), and a sample-absorbing porous material piece (6); and a sample-receiving porous material piece (7) disposed independently therefrom and partially communicated therewith through a connection. The analytical device of the present invention exhibits extremely high sensitivity and can accurately perform various types of analysis.

Abstract: A method for conducting a receptor-ligand association reaction includes the steps of dipping a biochemical analysis unit including a substrate formed with a plurality of absorptive regions which contain receptors or ligands and are formed to be spaced apart from each other in a reaction solution containing a ligand or receptor labeled with a labeling substance, simultaneously inserting a plurality of electrodes into all of the plurality of absorptive regions containing the receptors or ligands and sequentially applying a positive voltage to one of the electrodes at a time while other electrodes are grounded, thereby conducting a receptor-ligand association reaction. According to the this method, it is possible to efficiently react a ligand or receptor with receptors or ligands fixed in the plurality of absorptive regions of the biochemical analysis unit and produce biochemical analysis data having an excellent quantitative characteristic with good repeatability.

Abstract: Here, we describe a sensitive and specific assay and kit for the detection of chemokines having activity that is upregulated by Th−1 cytokines (such IFN-&ggr;) and chemokines that upregulate the activity of Th−1 cytokines (such as IFN-&ggr;). In a typical embodiment, detection of the chemokine monokine induced by gamma interferon (MIG) provides a measure of the biological effect of IFN-&ggr; rather than direct quantitation of IFN-&ggr; or IFN-&ggr; secreting cells per se. Upregulation of MIG expression was observed following in vitro activation of PBMC with defined CD8+ T cell epitopes derived from influenza virus, CMV, or EBV, and in all cases this was antigen-specific, genetically restricted and dependent on both CD8+ T cells and IFN-&ggr;. Responses as assessed by the MIG assay paralleled those detected by conventional IFN-&ggr; ELISPOT, but the magnitude of response and sensitivity of the MIG assay were superior.