Abstract: The invention provides a universal method to detect the presence of chromosomal abnormalities by using paralogous genes as internal controls in an amplification reaction. The method is rapid, high throughput, and amenable to semi-automated or fully automated analyses. In one aspect, the method comprises providing a pair of primers which can specifically hybridize to each of a set of paralogous genes under conditions used in amplification reactions, such as PCR. Paralogous genes are preferably on different chromosomes but may also be on the same chromosome (e.g., to detect loss or gain of different chromosome arms). By comparing the amount of amplified products generated, the relative dose of each gene can be determined and correlated with the relative dose of each chromosomal region and/or each chromosome, on which the gene is located.

Abstract: Many genes are identified as being metastasis associated. Identifying and profiling of these genes expression can be used to evaluate a sample, to diagnose tumor invasive potential or metastatic development in a sample, or screen for a test compound useful in the prevention or treatment of tumor metastasis.

Abstract: An apparatus and method for comparative genomic mapping of a sample and a reference is disclosed that includes an array of oligonucleotides having a surface derived from a selected portion of a genome. A reader capable of producing a signal disposed to detect events that occur at the surface of the array of oligonucleotides and a computer attached to the reader, wherein the computer processes a signal from the reader to determine the relative intensity produced at the array surface and capable of comparing the intensity of the signal from the array to provide map with a resolution of about 20, 30, 50, 100, 200, 500, 1,000, 2,000, 5,000, 20,000, 50,000, 100,000, 200,000, 500,000, 1,000,000, 2,000,000 basepairs.

Abstract: The present invention is directed to methods for performing negative selection assays leading to the identification of cytostatic or cytotoxic agents that cause a lethal phenotype. The invention is useful also for evaluation of conditional cytotoxicity and cell-specific cytotoxicity.

Abstract: Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.

Abstract: A composition and method for killing fire ants is disclosed that includes the purified and activated Cry toxin from a novel strain of Bacillus thuringiensis, wherein the water soluble, partially purified, activated toxin is provided along with an attractant to kill the imported fire ant using a biodegradable, environmentally sound glycoprotein without a need for toxic chemicals.

Abstract: The invention concerns an expressible nucleic acid construct, which contains only the sequence information necessary for expressing a gene for RNA or protein synthesis. Expression constructs of this type can be used in gene therapy and genetic vaccination and avoid many of the risks associated with constructs today. The invention further concerns the possibility of improving the conveying of the construct into cells or tissue by covalent linkage of the construct, for example to particles of peptides.

Abstract: The invention provides methods of using probe arrays for polymorphism identification and profiling. Such methods entail constructing a first array of probes that span and are complementary to one or more known DNA sequences. This array is hybridized with nucleic acid samples from different individuals to identify a collection of polymorphisms. A second array is then constructed to determine a polymorphic profile of an individual at the collection of polymorphic sites. The polymorphic profile is useful for, e.g., genetic mapping, epidemiology, diagnosis and forensics.

Abstract: Techniques for facilitating the identification of candidate genes from a plurality of DNA sequences. According to an embodiment of the present invention, techniques are provided for extracting and integrating information from various information sources and results of various analyses, and storing the integrated information in a form which is conducive to identification of candidate genes. The stored information may include results of a homology search for the plurality of DNA sequences, annotative information for the plurality of DNA sequences indicating the biochemical functions and physiological roles of the plurality of DNA sequences, gene expression profile data for the plurality of DNA sequences describing behavioral patterns of the plurality of DNA sequences, results from clustering the plurality of DNA sequences based on time course data as described by the gene expression profile data, and other information.

Abstract: A method for extracting nucleic acids from a biological material such as blood comprises contacting the mixture with a material at a pH such that the material is positively charged and will bind negatively charged nucleic acids and then eluting the nucleic acids at a pH when the said materials possess a neutral or negative charge to release the nucleic acids The nucleic acids can be removed under mildly alkaline conditions to the maintain integrity of the nucleic acids and to allow retrieval of the nucleic acids in reagents that are immediately compatible with either storage or analytical testing.

Abstract: Reversibly labeled nucleotides and methods involving the nucleotides are disclosed. The methods included methods of determining a sequence of a nucleic acid.

Abstract: The present invention relates to an in vitro method for the diagnosis of multiple sclerosis and/or the susceptibility to multiple sclerosis comprising the steps of a) obtaining a biological sample; and b) detecting and/or measuring the increase, decrease and/or absence of (a) specific marker gene(s) as disclosed herein.

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

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

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: The present invention makes available a rapid, effective assay for screening and identifying pharmaceutically effective compounds that specifically interact with and modulate the activity of a cellular receptor or ion channel. The subject assay enables rapid screening of large numbers of polypeptides in a library to identifying those polypeptides which induce or antagonize receptor bioactivity. The subject assay is particularly amenable for identifying surrogate ligands for orphan receptors.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: Methods and systems are provided for constructing recombinant antibody libraries based on three-dimensional structures of antibodies from various species including human. In one aspect, a library of antibodies with diverse sequences is efficiently constructed in silico to represent the structural repertoire of the vertebrate antibodies. Such a functionally representative library provides a structurally diverse and yet functionally more relevant source of antibody candidates which can then be screened for high affinity binding to a wide variety of target molecules, including but not limited to biomacromolecules such as protein, peptide, and nucleic acids, and small molecules.

Abstract: A method for identifying a protein including cleaving the protein with a proteolytic agent to produce peptide fragments, providing an array comprising a solution set of binding reagents, contacting the peptide fragments with the array to promote specific interactions between the fragments and the array, detecting the binding pattern of the peptide fragments on the array, and comparing the binding pattern of the peptide fragments to a reference set. A solution set refers to a set of binding reagents, or epitopes associated with such binding reagents, that can identify members of a given protein mixture or protein catalog using a minimal number of binding reagents (or epitopes corresponding to the binding reagents) based on certain constraints. The solution set can be determined using a randomized greedy algorithm. The solution set can be refined using a local search algorithm.

Abstract: The invention relates to a complex of specifically complex-forming proteins which are not naturally occurring, comprising the following components: a) at least one ligand specific for a target structure, b) at least one protein comprising a mutated dimerization domain, the mutated dimerization domain having been derived by mutation of a naturally occurring dimerization domain, it being possible for this mutated dimerization domain to interact specifically with component c) and the component b) being connected covalently to the component a), c) at least one protein comprising a mutated dimerization domain, the mutated dimerization domain having been derived by mutation of a naturally occurring dimerization domain, it being possible for this mutated dimerization domain to interact specifically with component b) and the component c) is linked covalently to the component d), and d) at least one effector.

Abstract: In general, the invention features the use of novel protection schemes and solid phase synthesis reactions to generate molecules of core structure M, which have a plurality of moieties, each of which can be individually deprotected or subsequently derivatized. In a preferred process, M is a multifunctional low molecular weight compound, such as a saccharide, aminosugar, deoxysugar, nucleoside, nucleotide, coenzyme, amino acid, lipid, steroid, vitamin, hormone, alkaloid, or small molecule drug. In a particularly preferred process, M is an oligomeric compound (e.g. a oligosaccharide, oligonucleotide, peptide or protein).

Abstract: The present invention provides a polypeptide of less than 600 amino acids comprising the sequence set forth as SEQ ID NO:1. SEQ ID NO: 1 is an example of a GPR motif. The invention also provides a polypeptide consisting of the sequence set forth as SEQ ID NO:1. Also provided is a method of inhibiting G protein mediated signal transduction comprising administering to a subject a GPR motif or mimetic of a GPR motif.

Abstract: A method is described for the early detection of stroke which uses a reagent which includes a fluorescently modified fatty acid binding protein. A fluorescence difference is noted between the bound and unbound condition. Elevated levels of unbound free fatty acids from blood are used as indicators of stroke.

Abstract: A bioconjugate comprising a fluorescer (P) linked to a quencher (Q) by a tether (T) is provided. The tether (T) includes a segment that can recognize and interact with a target biomolecule. In the absence of a specific interaction of the bioconjugate with an enzyme or other target biomolecule recognizing the bioconjugate, the fluorescence of the polymer (P) is attenuated or modified by the relatively close proximity thereto of the quencher (Q). As a consequence of the association of the bioconjugate with the target biomolecule, a reaction can occur which results in a cleavage of the bioconjugate tether and a release of the fluorescent polymer and/or quencher. This sequence of events can be followed by an enhancement or amplification of the polymer fluorescence.

Abstract: This invention relates to the treatment and diagnosis of Type-1 Diabetes (T1D); particularly to the use of glial fibrillary acidic protein (GFAP) as a mediator of the disease; and most particularly to GFAP binding proteins useful for prediabetes screening and/or staging.

Abstract: Monoclonal antibodies which bind specifically to the extracellular domain of the SIRP cell surface glycoproteins, and which, in some cases, block the interaction of SIRP with the surface molecule CD47, are described.

Abstract: This invention provides means of measuring oxidative response of cells without recourse to preparation of cell culture.

Abstract: Nucleic acid molecule and polypeptide sequences encoding a novel tumor suppressor protein, EPLIN, are provided. Also included is a method for detecting a cell proliferative disorder associated with EPLIN. EPLIN is a marker that can be used diagnostically, prognostically and therapeutically over the course of cell proliferative disorders associated with EPLIN.

Abstract: The present invention relates to the discovery of gene and its sequence variation associated with lipid disorder and cancer. The present invention also relates to the study of metabolic pathways and cellular mechanisms to identify other genes, receptors, and relationships that contribute to lipid disorder and cancer. The present invention also relates to germline or somatic sequence variation and its use in the diagnosis and prognosis of predisposition to lipid disorder and cancer. The present invention also provides primers or probes specific for the detection and analysis of such sequence variation. The present invention also relates to methods to screen drugs for inhibition or restoration of gene function as an anti-lipid disorder or anti-cancer therapy. Finally, the present invention relates to other anti-lipid disorder or anti-cancer therapies, such as gene therapy, protein replacement therapy, etc.

Abstract: A method for prognosis of patients with prostate cancer, e.g., clinically localized prostate cancer, is provided.

Abstract: The present invention relates to novel colorectal cancer related polynucleotides and the polypeptides encoded by these polynucleotides herein collectively known as “colorectal cancer antigens,” and the use of such colorectal cancer antigens for detecting disorders of the colon and/or rectum, particularly the presence of colorectal cancer and colorectal cancer metastases. More specifically, isolated colorectal cancer associated nucleic acid molecules are provided encoding novel colorectal cancer associated polypeptides. Novel colorectal cancer polypeptides and antibodies that bind to these polypeptides are provided. Also provided are vectors, host cells, and recombinant and synthetic methods for producing human colorectal cancer associated polynucleotides and/or polypeptides.

Abstract: The present invention relates to novel ovarian cancer and/or breast cancer related polynucleotides, the polypeptides encoded by these polynucleotides herein collectively referred to as “ovarian and/or breast antigens,” and antibodies that immunospecifically bind these polypeptides, and the use of such ovarian and/or breast polynucleotides, antigens, and antibodies for detecting, treating, preventing and/or prognosing disorders of the reproductive system, particularly disorders of the ovaries and/or breast, including, but not limited to, the presence of ovarian and/or breast cancer and ovarian and/or breast cancer metastases. More specifically, isolated ovarian and/or breast nucleic acid molecules are provided encoding novel ovarian and/or breast polypeptides. Novel ovarian and/or breast polypeptides and antibodies that bind to these polypeptides are provided.

Abstract: An immunoassay for detecting lipopolysaccharides, and a device for conducting the same, the immunoassay comprising the steps of:

Abstract: A recombinant protein that is a fusion protein containing a protein binding domain and a domain that is post-translationally modified to become lipid-tagged. This molecule has both a domain with highly specific binding capabilities and a domain which is very hydrophobic in nature. This type of molecule can be used to coat hydrophobic surfaces such as polystyrene easily and effectively for use in solid phase binding assays.

Abstract: Immunoassay methods and standards are provided for determining the presence of polychlorinated biphenyl compounds, in a sample of interest:

Abstract: The present invention provides novel microfluidic devices and methods that are useful for performing high-throughput screening assays. In particular, the devices and methods of the invention are useful in screening large numbers of different compounds for their effects on a variety of chemical, and preferably, biochemical systems.

Abstract: A method for identifying and quantifying peptides resulting from enzyme cleavage of collagen type II by mass spectrometric analysis to detect characteristic peptide fragments of a carboxy-terminus having known mass to charge ratios to identify the peptide having that carboxy-terminus. Identification and quantification of the peptides in a biological sample is used to assess activity of proteolytic enzymes in diseases or physiological conditions such as osteoarthritis and rheumatoid arthritis and to assess the efficacy of enzyme blocking agents.

Abstract: A method for determining the presence of an analyte in a fluid is described along with various components of an apparatus specifically designed to carry out the method. The method involves taking a reflectance reading from one surface of an inert porous matrix impregnated with a reagent that will interact with the analyte to produce a light-absorbing reaction product when the fluid being analyzed is applied to another surface and migrates through the matrix to the surface being read. Reflectance measurements are made at two separate wavelengths in order to eliminate interferences, and a timing circuit is triggered by an initial decrease in reflectance by the wetting of the surface whose reflectance is being measured by the fluid which passes through the inert matrix. The method and apparatus are particularly suitable for the measurement of glucose levels in blood without requiring separation of red blood cells from serum or plasma.

Abstract: A method of screening for disorders of glucose metabolism such as impaired glucose tolerance and diabetes allows prevention, or early detection and treatment of diabetic complications such as cardiovascular disease, retinopathy, and other disorders of the major organs and systems. A mathematical algorithm evaluates the shape of a subject's glucose profile and classifies the profile into one of several predefined clusters, each cluster corresponding either to a normal condition or one of several abnormal conditions. The series of blood glucose values making up the glucose tolerance curve may be measured using any glucose analyzer including: invasive, minimally invasive and noninvasive types. The method is executed on a processing device programmed to perform the steps of the method. Depending on the outcome of the screening, a subject may be provided with additional information concerning their condition and/or counseled to consult further with their health care provider.

Abstract: A dry analytical element for immunoassay that is not affected by maltose internally caused by a test sample and has high accuracy is provided. In the analytical element, either (1) fragmentation speed of the maltose to glucose is made larger (a first aspect) or (2) the maltose is removed before it reaches a reagent layer (a second aspect).

Abstract: Systems and method are provided for modeling substrate molecules so that the various pathway reaction rates, and thus their overall reaction rates and metabolic properties, can be predicted. The current invention provides various systems and methods for stoichiometrically measuring the pathway reaction rates, both directly and indirectly. By repeating this for a class or several classes of substrate molecules, a general model of pathway reaction rates can be developed by correlating observed pathway reaction rates to the actual structural descriptors of the molecules, in particular, features around the reactive sites. The model can then be used to predict and design substrates according to desired metabolic characteristics. The systems and methods are particularly applicable to metabolism of substrate molecules by the cytochrome P450 enzymes.

Abstract: Electrode membrane combinations for use in biosensors to detect analytes in a sample and methods for making and storing same are disclosed.

Abstract: A reagent containing a purified horseshoe crab Factor C, particularly a recombinantly produced Factor C, and a surfactant can be used in a sensitive, rapid, and reproducible assay to detect endotoxin.

Abstract: The invention relates to methods for detecting a soluble guanylate cyclase whose heme iron is in the trivalent oxidation state, and to methods for finding chemical substances which stimulate the activity of a soluble guanylate cyclase when the heme iron of at least part of this soluble guanylate cyclase is oxidized to the trivalent state and also to diagnostic aids or kits for detecting a soluble guanylate cyclase with trivalent heme iron. Further, the invention relates methods for detecting a soluble guanylate cyclase lacking a heme group, and to methods for finding chemical substances which stimulate the activity of a soluble guanylate cyclase lacking a heme group.

Abstract: The invention discloses a method for preparing an active slide, including introducing a monomer containing an aldehyde group, or a mixture of a monomer containing an aldehyde group and an acidic functional group provider into a plasma chamber; and depositing the aldehyde group and acidic functional group onto the surface of an organic or inorganic matrix using plasma deposition to form a slide comprising a layer of polymerized actively functional groups thereon. The aldehyde groups and negatively charged groups are deposited on the surface of the active slide, such that the bio-molecules bound thereto possess the properties of an inducible orientation and thus form a mono-layer.

Abstract: The present invention is summarized in that a cell extract suitable for recovery and analysis of a cellular component (a protein or a nucleic acid, for example) can be made by lysing the cells directly in the culture medium. The extract obtained can be used for subsequent applications such as protein recovery that were conventionally done with cell extracts of harvested cells. The elimination of the cell-harvest step makes these applications more amenable to high throughput adaptation.