Abstract: The present invention relates to rapid, quantitative, specific, high through-put methods for screening test substances for their ability to inhibit activity of an ouabain-resistant Na+-K+-ATPase involved in a variety of biological processes such as regulation of osmotic balance and cell volume, maintenance of the resting membrane potential, establishment of the ionic composition of cerebrospinal fluid and aqueous humor, electrical activity of muscle and nerve, and receptor-mediated endocytosis, cardiac muscle contractility, neurotransmitter metabolism and vascular muscle cell contraction. These methods can be employed to identify compounds for use in therapeutic applications for disease processes in which dysfunction of the Na+-K+-ATPase contributes to a pathological process. The present invention also includes kits which are used in the methods provided herein.

Abstract: The invention involves dimeric forms of the protein known as fibroblast activation protein alpha, or “FAP?” and its uses.

Abstract: A novel human glycosylsulfotransferase expressed in high endothelial cells (GST-3) and polypeptides related thereto, as well as nucleic acid compositions encoding the same, are provided. The subject polypeptides and nucleic acid find use in a variety of applications, including research, diagnostic, and therapeutic agent screening applications.

Abstract: A tumor necrosis factor-? converting enzyme (TACE) is produced, purified, and crystallized. The three-dimensional coordinates of the crystal are obtained by X-ray diffraction. The coordinates can be recorded on a computer readable medium, or are part of a video memory, where they can be used as part of a system for studying for studying TACE. The coordinates are also used in designing, screening, and developing compounds that associate with TACE.

Abstract: DNA is produced by preparing oligomers having partial sequences selected according to a specific scheme based on a target nucleotide sequence, and performing PCR using two of single strand DNAs base-paired at their 3? ends as primers and templates to prepare DNA, in a specific manner.

Abstract: Optical detection techniques for the assessment of the physiological state, health and/or viability of biological materials are provided. Biological materials which may be examined using such techniques include cells, tissues, organs and subcellular components. The inventive techniques may be employed in high throughput screening of potential diagnostic and/or therapeutic agents.

Abstract: The present invention provides vectors and methods which improve the efficiency of nucleic acid insertion into circular vectors, which generally facilitate nucleic acid cloning and specifically facilitate the preparation of DNA libraries. In general, the present invention involves separation of the cloning process into two distinct steps: (a) insertion which is done at a high nucleic acid concentration favoring intermolecular joining, and (b) circularization which is performed at a low nucleic acid concentration favoring intramolecular circularization. The present vectors generally have distinct insertion ends and circularization ends which are blocked from covalent joining during the insertion step. Circularization ends contemplated by the present invention include complementary cohesive ends and topoisomerase-linked ends. The present vectors and methods allow minute amounts of nucleic acid inserts to be efficiently cloned.

Abstract: The present invention provides sensitive methods for detecting the presence or absence of a difference between related nucleic acid sequences. In one aspect of the invention, a method is provided for detecting a difference in the sequence of two nucleic acid molecules. The method includes the steps of: contacting two nucleic acids under conditions that allow the formation of a four-way complex and branch migration; contacting the four-way complex with a tracer molecule and a detection molecule under conditions in which the detection molecule is capable of binding the tracer molecule or the four-way complex; and determining binding of the tracer molecule to the detection molecule before and after exposure to the four-way complex. Competition of the four-way complex with the tracer molecule for binding to the detection molecule indicates a difference between the two nucleic acids.

Abstract: Computer based apparatus and method automates gene prediction in a subject genomic sequence. A plurality of expert systems provide preliminary or intermediate gene predictions. A Bayesian network combiner combines the intermediate gene predictions and forms a final gene prediction. The final gene prediction accounts for dependencies between individual expert systems and dependencies between adjacent parts of the subject genomic sequence.

Abstract: The present invention provides for crystalline cPLA2. The crystal structure of cPLA2 has also been solved using such material. Models based upon such crystal structure are also provided. Methods of identifying inhibitors of cPLA2 activity and membrane binding using such models are also disclosed.

Abstract: The first crystal structure of the androgen receptor ligand binding domain has been determined to 2.0 angstrom resolution. Disclosed are the coordinates for the crystal structure, and methods for determining agonists, partial agonists, antagonists, partial antagonists and selective androgen receptors modulators (SARMs) of the androgen receptor.

Abstract: This invention provides a method, a kit and a reagent for typing of the HLA class I alleles. Explaining concretely, a single HLA class I antigen or allele is determined by combining PCR amplification using a primer pair which can amplify all HLA-A alleles, all HLA-B alleles or all HLA-C alleles, or which is specific to the common sequence to alleles of the specific group consisting of the specific HLA-A alleles or the specific HLA-B alleles, with reverse hybridization analysis using DNA probes capable of specifically hybridizing with the sequence of al least a specific HLA-A allele, at least a specific HLA-B allele or at least a specific HLA-C allele, which are covalently immobilized on wells of microtiter plates.

Abstract: Disclosed is a method for detecting and quantifying clustered damages in DNA. In this method, a first aliquot of the DNA to be tested for clustered damages with one or more lesion-specific cleaving reagents under conditions appropriate for cleavage of the DNA to produce single-strand nicks in the DNA at sites of damage lesions. The number average molecular length (Ln) of double stranded DNA is then quantitatively determined for the treated DNA. The number average molecular length (Ln) of double stranded DNA is also quantitatively determined for a second, untreated aliquot of the DNA. The frequency of clustered damages (&PHgr;c) in the DNA is then calculated.

Abstract: A method of biological assay comprises the steps of providing an enzyme substrate comprising two fluorescence dye groups bound to a flexible peptide, the dye groups being of proximity sufficiently close so as to allow free energy attractions to draw the dyes together to essentially self-quench fluorescence of the dye groups, wherein self quenching of fluorescence of the dye groups is effected by dye dimerization or stacking, and enzymatically cleaving the peptide to release the fluorescence dye groups from dye dimerization or stacking, thereby producing an increase in fluorescence intensity. A protease substrate for use in the method of the invention is also disclosed. This invention finds use in detection and identification of microorganisms, sterilization assurance, pharmaceutical discovery, enzyme assays, immunoassays, and other biological assays.

Abstract: Disclosed is a human Fibroblast growth factor-14 polypeptide and DNA(RNA) encoding such polypeptide. Also provided is a procedure for producing such polypeptide by recombinant techniques. Also disclosed are methods for utilizing such polypeptide for promoting wound healing for example as a result of burns and ulcers, to prevent neuronal damage due to associated with stroke and promote neuronal growth, and to prevent skin aging and hair loss, to stimulate angiogenesis, mesodermal induction in early embryos and limb regeneration. Antagonists against such polypeptides and their use as a therapeutic to prevent abnormal cellular proliferation, hyper-vascular diseases and epithelial lens cell proliferation are also disclosed. Diagnostic methods for detecting mutations in the coding sequence and alterations in the concentration of the polypeptides in a sample derived from a host are also disclosed.

Abstract: The present invention relates to identifying protein epitopes and more particularly to a novel method for identifying, determining the location, optimal length of amino acid residues and immunobiological potency of protein epitopes by fitting a hydrophilicity and/or hydrophobicity plot generated for the amino acid linear sequence of a polypeptide to a mathematically generated continuous curve thereby generating at least one set of potential epitopes which include ranked potential epitopes having a specific number of amino acid residues. The immunobiologically-active linear peptides are deemed the potential epitopes that exhibit the most alternating positioning about an equilibrium position when juxtaposed on the hydrophilicity and/or hydrophobicity plot and their optimal length corresponds to the specific number of amino acid residues in the set of ranked potential epitopes.

Abstract: A method for determining the existence and the amount of soluble fibrin contained in a specimen fluid is provided. The method includes the steps of precipitating soluble fibrin out of the opaque specimen fluid, aggregating the soluble fibrin precipitates in a limited region of a transparent container so as to render the precipitates optically detectable in the opaque specimen fluid, and optically detecting the precipitates. The amount of soluble fibrin may be determined by measuring the time from the addition of the precipitating regent to the detection of the soluble fibrin precipitates. Methods of the present invention allow one to measure soluble fibrin in whole blood, and therefore render the test useful in the operating room under conditions of major surgery and in the presence of severe trauma wherein DIC is likely to supervene.

Abstract: A computer-based method for the identification of binding targets in proteins and other macromolecules is provided. More particularly, the invention includes an algorithm aimed at predicting binding targets in proteins. This algorithm, named Woolford, requires knowledge of the high resolution structure of the protein but no knowledge of the location or identity of natural binding sites or ligands. Binding targets in the protein are identified and classified according to their expected optimal affinities. Binding targets can be located at the protein surface or at internal surfaces that become exposed as a result of partial unfolding, conformational changes, subunit dissociation, or other events. The entire protein is mapped according to the binding potential of its constituent atoms. Once binding targets are identified, optimal ligands are designed and progressively built by the addition of individual atoms or chemical groups that complement structurally and energetically the selected target.

Abstract: A pharmaceutical agent for treating an amyloid disease in a patient, wherein the pharmaceutical agent comprises a glucose monosaccharide containing at least one anionic group, or a pharmaceutically acceptable salt thereof. The agent is directed to amyloid diseases in general and to Alzheimer's disease in particular. Methods of treating an amyloid disease in a patient by administering therapeutically effective amounts of a glucose monosaccharide containing at least one anionic group are also presented.

Abstract: In order to align DNA sequence data traces, an experimental data trace representing the positions of a first species of base within a target polynucleotide and a reference data trace representing the positions of a second species of base (which may be the same as or different from the first species) within a reference polynucleotide are obtained by separating appropriate sequencing fragments generated from the target and reference polynucleotides on an electrophoresis gel. For each reference data trace, a plurality of peaks corresponding to fragments having a size in the range of 40 to 1200 bases are selected. A base number is assigned to each of the selected peaks in the reference data trace, and a numerical “peak file” is created with information about the peak number and migration time (or distance).