Abstract: The present invention provides a nucleic acid synthesis method which involves the step of incubating a double-stranded nucleic acid template under conditions that ensure a complementary strand synthesis reaction using a primer as an origin. This method involves the step of placing a region, to which a primer capable of isothermally amplifying the template nucleic acid will anneal, in a condition that ensures base pairing, using an arbitrary primer. The arbitrary primer initiates the complementary strand synthesis reaction, using the double-stranded nucleic acid as a template and DNA polymerases catalyzing the complementary strand synthesis reaction which comprises the destabilization of the double-stranded nucleic acid and strand displacement, thereby providing a region that can undergo base pairing.

Abstract: Cryptic-like polypeptides and polynucleotides and methods for producing such polypeptides by recombinant techniques are disclosed. Also disclosed are methods for utilizing cryptic-like polypeptides and polynucleotides in diagnostic assays.

Abstract: The present invention relates to a method for analysing the phenotypic characteristics shown by certain virus strains, particularly human immunodeficiency viruses, involving the construction of a recombinant virus obtained by homologous recombination.

Abstract: The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.

Abstract: The invention provides methods of detecting a nucleic acid. The methods comprise contacting the nucleic acid with one or more types of particles having oligonucleotides attached thereto. In one embodiment of the method, the oligonucleotides are attached to nanoparticles and have sequences complementary to portions of the sequence of the nucleic acid. A detectable change (preferably a color change) is brought about as a result of the hybridization of the oligonucleotides on the nanoparticles to the nucleic acid. The invention also provides compositions and kits comprising particles. The invention further provides methods of synthesizing unique nanoparticle-oligonucleotide conjugates, the conjugates produced by the methods, and methods of using the conjugates. In addition, the invention provides nanomaterials and nanostructures comprising nanoparticles and methods of nanofabrication utilizing nanoparticles. Finally, the invention provides a method of separating a selected nucleic acid from other nucleic acids.

Abstract: A method for discovery of a polymorphism in a population is provided. The method includes the steps of obtaining samples of body tissue or fluid from a plurality of organisms; isolating a biopolymer from each sample; pooling each isolated biopolymer; optionally amplifying the amount of biopolymer; cleaving the pooled biopolymers to produce fragments thereof; obtaining a mass spectrum of the resulting fragments; and comparing the frequency of each fragment to identify fragments present in amounts lower than the average frequency, thereby identifying any polymorphisms.

Abstract: A method for detecting species in a target plant genus comprises the steps of conducting PCR using at least one member selected from the group consisting of primers (A) and (B), which can hybridize under stringent conditions to a nucleic acid molecule having a common nucleotide sequence for all species in. the target plant genus in 45S rRNA precursor gene sequence thereof, wherein 3′ end of primer (A) can complementarily bind to a base in ITS-1 sequence of the target plant genus when the primer hybridizes to the nucleic acid molecule while 3′ end of primer (B) can complementarily bind to a base in ITS-2 sequence of the target plant genus when the primer hybridizes to the nucleic acid molecule, and identifying the presence of the resulting amplification product from PCR containing at least a part of ITS-1 or ITS-2 sequence of the target plant genus.

Abstract: The invention provides human human kinases (PKIN) and polynucleotides which identify and encode PKIN. 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 aberrant expression of PKIN.

Abstract: Compositions and methods are disclosed for detecting multiple target analytes, particularly polynucleotide target analytes. In accordance with one aspect of the invention, a template-dependent extension reaction is performed to generate detection probes, such that each detection probe has (i) at least one molecular tag attached by a cleavable linkage and (ii) either a capture moiety or a cleavage-inducing moiety attached. The template-dependent extension reaction may be carried out directly on a polynucleotide analyte to generate molecular tags, wherein the polynucleotide analyte serves as a template in the template-dependent extension reaction, or it may be carried out indirectly on an oligonucleotide label that, in turn, is attached to a binding moiety specific for an analyte of interest. In either case, a plurality of molecular tags are generated, after which they are separated and identified to determine the presence or absence or the quantity of the target analytes in a sample.

Abstract: A reporter construct contains mammalian INGAP 5′-regulatory region or a fragment thereof, a minimal promoter element from mammalian INGAP or a heterologous promoter, and a reporter gene. The reporter construct can be used to screen for agents which alone or in combination up-regulate or down-regulate reporter gene expression. Alternatively, the reporter construct can be used to screen for agents that bind to the hamster INGAP 5′-regulatory region or a fragment thereof.

Abstract: A method for detecting a target nucleic acid in a sample, which method comprises: (a) providing a primer air comprising a first primer having a target specific sequence complementary to the sequence of the first strand of said target nucleic acid and an overhang sequence unrelated to said target nucleic acid sequence and a second primer having a target specific sequence complementary to the sequence of the second strand of said target nucleic acid and an attachment means; (b) contacting a nucleic acid sample with said first and second primers; (c) carrying out a polymerase chain reaction (PCR) under conditions suitable for the formation of a product having said attachment means and a sequence comprising the sequence of said target nucleic acid and the sequence of said overhang; (j) separating the first strand of said product comprising said first primer from the second strand of said product comprising said second primer using said attachment means; and (k) detecting said first strand or said second strand th

Abstract: The present invention is within the fields of human origins, medicine and evolutionary biology. More precisely, the invention relates to a method and kit for determining the geographic or population origin of a human based on mitochondrial DNA sequences and specifically to the use of mitochondrial DNA variants (polymorphisms) from the complete human mitochondrial genome. This information is employed in the comparison of biological samples with samples of known origin or with a database of mitochondrial genome sequences.

Abstract: The present invention provides a polyol-doped aerogel material with improved properties for trapping biological particles and facilitating analysis and identification thereof. The polyol-doped aerogel material can be used in combination with a substrate by coating or otherwise depositing the material thereon. The present invention provides a method for detecting a biological particle involving use of a polyol-doped aerogel material.

Abstract: The invention provides an asymmetric cyanine dye compound having the structure 1

Abstract: Disclosed is a method of detecting specific nucleic acids using an oligonucleotide linked to a cleavable tag. The presence of a specific nucleic acid in a population of nucleic acids is determined by hybridizing an oligonucleotide containing the tag to a population of nucleic acids, separating hybridizing bound oligonucleotides, and then removing and identifying the tag. Also provided are compositions and kits comprising oligonucleotides linked to a cleavable tag.

Abstract: Methods for determining the inventory of small process and control molecules (The Metabolome) and the interaction of the Metabolome with the Genome and Proteome (Metabolomic databases). Methods for evaluating Metabolomic databases for biochemical markers that correlate with outcome of a disease, allow monitoring of therapy and direct therapy. Methods for evaluating Metabolomic databases for lead therapeutic molecules and target systems for therapeutic manipulation. Methods of evaluating all relationships in a Metabolomic database for outcome of disease or therapy. The methods of Metabolomic database evaluation have application to stroke. Outcome predicting and therapy directing or monitoring markers of Methylation and oxidative processes in stroke have been determined. Methylation processes have been identified as targets for therapeutic development. A novel class of potential therapeutic agents that bind to DNA have been identified in stroke.

Abstract: The invention provides methods and devices for detecting the presence of one or more target analytes in a sample employing a channel having affixed therein one or more binding partners for each target analyte. Assays are carried out by transporting the sample through the channel to each successive binding partner so that target analyte present in said sample binds to the corresponding binding partner. The sample is then transported beyond the binding partner(s), followed by detection of any target analyte bound to each binding partner. In one embodiment, binding efficiency is increased by the use of segmented transport, wherein a first bolus or bubble of a fluid that is immiscible with the sample precedes the sample during transport and a second bolus or bubble of a fluid that is immiscible with the sample follows the sample. Many configurations are possible for the device of the invention.

Abstract: The invention relates to methods for treating, preventing and diagnosing macular degeneration-related disorders.

Abstract: An electrophoretic separation system configured to determine a size of each of a plurality of sample polynucleotides includes a plurality of sample separation lanes, such as capillaries. Each separation lane is configured to subject a number plurality of respective sample polynucleotides and a respective internal standard polynucleotide (ISP) to electrophoresis. The system also includes a ladder separation lane for subjecting at least two members of polynucleotide ladder to electrophoresis. A processor of the system is configured to determine migration coordinates of (1) the ISP and sample polynucleotides subjected to electrophoresis within each separation lane and (2) at least two of the PLMs. The processor also transforms the migration coordinates of the sample polynucleotides of each separation lane from a migration dimension of their respective separation lane to a migration dimension of the polynucleotide ladder.

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

Abstract: cDNA microarrays are provided for increasing the accuracy and reliability of expression profiling techniques and for identifying new genes. An array comprises a plurality of nucleic acid members, each member having a unique position and stably associated with a solid support. Each nucleic acid member comprises a noncoding sequence present at either the 3′-end or the 5′-end of an RNA transcript (e.g., such as an untranslated region or UTR). In one embodiment, each nucleic acid member is less than 1000 nucleotides. In another embodiment, each nucleic acid member is less than 600 nucleotides. In a further embodiment of the invention, each nucleic acid member comprises substantially noncoding sequences.

Abstract: The present invention relates to oligonucleotides of probes or primers for detection or identification of Mycobacterium. In the claimed invention, oligonucleotide sequences of ITS (Internal Transcribed Spacer Region) from M. fortuitum, M. chelonae, M. abscessus, M. vaccae, M. flavescens, M. asiaticum, M. porcinum, M. acapulcensis and M. diernhoferi have been identified. Using these ITS sequences, PCR primers or hybridization probes for detection or identification of Mycobacterium have been developed and presented as seq ID: 10 to seq ID: 241.

Abstract: A method is provided for determining the probable surname of a male from a sample of his tissue or DNA, wherein the haplotype of his sample is compared with a database, the database containing information which correlates Y chromosome haplotypes to given surnames.

Abstract: This invention relates to the discovery of nucleic acids and proteins associated with aging processes. The identification of these aging-associated nucleic acids and proteins have diagnostic uses in detecting the aging status of a cell population as well as application for treating or delaying cellular and physiological changes that occur with aging or the onset of diseases typically associated with aging.

Abstract: The present invention provides a TADG-12 protein and a DNA fragment encoding such protein. Also provided is a vector/host cell capable of expressing the DNA. The present invention further provides various methods of early detection of associated ovarian and other malignancies, and of interactive therapies for cancer treatment by utilizing the DNA and/or protein disclosed herein.

Abstract: The present invention relates to nucleic acids isolated from Tetrahymena which code for a ciliate-specific triterpenoid cyclase. The inventive nucleotide sequences and the polypeptide sequences derived therefrom demonstrate a surprisingly minimal sequence identity to known isoprenoid cyclases. The invention also relates to the use of nucleic acids for the regulation of triterpenoid cyclase expression in a host organism, as well as the targeted knockout or repriming of the triterpenoid cyclase gene. As a result of the altered expression of the triterpenoid cyclase, it is possible to modify and enrich the levels of multiple unsaturated fatty acids in the host organism.

Abstract: The invention provides a human kinesin-like motor protein (KLIMP) and polynucleotides which identify and encode KLIMP. 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 KLIMP.

Abstract: Novel human polynucleotide and polypeptide sequences are disclosed that can be used in therapeutic, diagnostic, and pharmacogenomic applications.

Abstract: Unique bacterial strains and identifying 16S rDNA sequences have been isolated from activated wastewater sludge. The 16S rDNA sequences are diagnostic for organisms which are key to the health of activated sludge wastewater systems.

Abstract: Unique bacterial strains and identifying 16S rDNA sequences have been isolated from activated wastewater sludge. The 16S rDNA sequences are diagnostic for organisms which are key to the health of activated sludge wastewater systems.

Abstract: Bacterial strains transformed with the pcu genes are useful for the production of para-hydroxybenzoate (PHBA). Applicant has provided the p-cresol utilizing (pcu) and tmoX gene sequences from Pseudomonas mendocina KR-1, the proteins encoded by these sequences, recombinant plasmids containing such sequences, and bacterial host cells containing such plasmids or integrated sequences. Method for the use of these materials to produce PHBA are also disclosed.

Abstract: The present invention provides a novel method for ligation of oligonucleotides containing 5′-phosphorothioates on complementary templates by the action of DNA ligases. This reaction is readily applied to the synthesis of a single stranded circular DNA containing a phosphorothioate linkage at the site of ligation junction. The efficiency of 5′-phosphorothioate directed ligation reaction by ATP dependent DNA ligase reaction is similar to conventional 5′-phosphate ligation. The utility of enzymatic ligation in probing specific sequences of DNA is also described. The present invention also provides a novel non-enzymatic ligation of 5′-phosphorothioates that has been applied to the synthesis of single strand phosphorothioate and phosphate circular DNA.

Abstract: Disclosed is a class of compounds referred to herein as effector compounds. Effector compounds are useful in connection with the modulation of an immune response. Modulation refers to the ability of the effector compounds of the present invention to either enhance (antigen supercharging) or inhibit (immunosuppressant activities) antigen presentation, depending upon the nature of the particular effector compound and the therapeutic context. Effector compounds include peptides, modified peptides and peptidomimetics. Also disclosed are methods for modulating presentation of an MHC class II restricted antigenic peptide to a T cell. Also disclosed are effector compounds demonstrated to act specifically on a human MHC class II allele. Also disclosed is a second class of compounds, referred to herein as immunomodulatory organic compounds.

Abstract: Methods of identifying agents which alter the NAD-dependent acetylation status and mono-ADP-ribosylation of nuclear proteins are disclosed. The methods further include identifying agents which alter the life span or aging of a cell or an organism by determining the level of NAD-dependent acetylation and/or ADP ribosylation of a nuclear protein. The invention also relates to a mammalian Sir2 protein which acetylates or deacetylates nuclear proteins in a NAD-dependent manner and has mono-ADP-ribosyltransferase activity. Host cells producing the Sir2 protein and antibodies to the Sir2 protein are also provided.

Abstract: The methods and apparatus 100, disclosed herein are of use for sequencing 150 and/or identifying 160 proteins 230, 310, polypeptides 230, 310 or peptides 230, 310. Proteins 230, 310 containing labeled amino acid residues may be synthesized and passed through nanopores 255, 330. A detector 257, 345 operably coupled to a nanopore 255, 330 may detect labeled amino acid residues as they pass through the nanopore 255, 330. Distance maps 140 for each type of labeled amino acid residue may be compiled. The distance maps 140 may be used to sequence 150 and/or identify 160 the protein 230, 310. In different embodiments of the invention, amino acid residues labeled with luminescent labels 235, 245 or nanoparticles 315 may be detected using photodetectors 257 or electrical detectors 345. Apparatus 100 of use for protein 230, 310 sequencing 150 and/or identification 160 are also disclosed herein.

Abstract: Collections of cultured eukaryotic cells, particularly human cells, in which the cells are coisogenic at a common target locus, are provided. Particularly provided are collections of coisogenic cells that differ in genomic sequence by no more than 0.05%, excluding changes at the target locus, collections in which the coisogenic cells differ in genomic sequence by no more than 0.005%, excluding changes at the target locus, and collections in which the cells lack heterologous genetic elements within 10 kilobases of the coisogenic target locus. Kits comprising the cell collections, methods of making the collections, kits for making the collections, and methods of using the collections to facilitate pharmacogenomic analyses are presented. Preferred target loci at which the cells are coisogenic include genes that affect drug resistance, drug sensitivity, and/or drug metabolism.

Abstract: Method for specific detection of one or more analytes in a sample. The method includes specifically associating any one or more analytes in the sample with a scattered-light detectable particle, illuminating any particle associated with the analytes with light under conditions which produce scattered light from the particle and in which light scattered from one or more particles can be detected by a human eye with less than 500 times magnification and without electronic amplification. The method also includes detecting the light scattered by any such particles under those conditions as a measure of the presence of the analytes.

Abstract: A 1,2-dioxetane derivative of the formula (I): 1

Abstract: Compositions comprising non-naturally occurring fibrinogen binding moieties are described, together with methods of use thereof, e.g., for detecting or isolating fibrinogen molecules in a solution, for blood circulation imaging, and for linking therapeutics or other molecules to fibrinogen. Preferred binding peptides having a high affinity for fibrinogen are particularly disclosed.

Abstract: This invention relates to encoding methods using up-converting phosphors for high-throughput screening of catalysts. In particular, the invention relates to polymerization catalysts. In one embodiment of the invention, a monomer is combined with at least one labeled catalyst particle. The labeled catalyst particle comprises an up-converting phosphor label and a catalyst. The up-converting phosphor label identifies a particular catalyst. The monomer is polymerized to form a polymer bead surrounding the labeled catalyst particle. According to the invention, it is possible to combine two or more labeled catalyst particles in a commercially relevant large scale reactor to obtain direct comparison of different catalysts, and to avoid reactor effects that may occur when performed on the microscale. After the reaction, the resulting polymer beads are sorted, based on their size and/or phosphor labels.

Abstract: The immunoassay element for quantitatively analyzing an antigen by determining the change in enzymatic activity of an enzyme-labelled antigen or antibody caused by an immunological reaction. The immunoassay element comprises a substrate layer containing a non-diffusible substrate which forms a diffusible material in the presence of the labelling enzyme, and a reagent layer containing a fragmenting enzyme for further fragmenting the diffusible material into a lower molecular weight product. As the non-diffusible substrate, a substrate capable of reacting solely with the lebelling enzyme and incapable of reacting the fragmenting enzyme is utilized. When an endo-active glucosidase is used as the labelling enzyme, and an exo-active glucosidase is used the fragmenting enzyme in the reagent layer, the non-diffusible substrate of the substrate layer is preferred to be an endo type selectively reactive substrate, which means a substrate having a reactivity specific to endo-active glucosidase.

Abstract: A novel form of lipase, namely feline pancreatic lipase (also termed feline classical pancreatic lipase) has an N-terminal amino acid sequence as shown in SEQ ID NO. 1. A method of purifying this lipase includes collecting pancreatic tissue from cats, delipidating the pancreatic tissue to produce a delipidated pancreatic extract, extracting pancreatic lipase from the delipidated pancreatic extract, and eluting the extracted pancreatic lipase through various columns. This lipase can be used for measuring pancreatic lipase immunoreactivity in serum thereby diagnosing pancreatitis in cats. To do so, antiserum against feline pancreatic lipase is prepared, and immunoassays are then performed in serum samples using this antiserum. In the event that increased concentration of pancreatic lipase immunoreactivity above the control range is detected in the serum, the cat might have pancreatitis.

Abstract: The present invention relates to a newly identified human agmatinase-like arginase, designated “25312”. The invention also relates to polynucleotides encoding the agmatinase-like arginase. The invention further relates to methods using the agmatinase-like polypeptides and polynucleotides as a target for diagnosis and treatment in disorders mediated by or related to the agmatinase-like arginase. The invention further relates to drug-screening methods using the polypeptides and polynucleotides to identify agonists and antagonists for diagnosis and treatment. The invention further encompasses agonists and antagonists based on the polypeptides and polynucleotides. The invention further relates to agonists and antagonists identified by drug screening methods with the polypeptides and polynucleotides as a target.

Abstract: The present invention relates to a process for preparing monolayers and microarrays of biomolecules by reacting functionalized dendrimers on a solid surface with biomolecules such as proteins, antigens, antibodies, enzymes, ligands, receptors, and the like. The present invention can be widely applied to the areas including preparation of kits and biosensors for disease diagnosis and compound analyses using the ascribed biomolecules as target substances, and more recently, integrated high-throughput analyzing system such as development of protein chips.

Abstract: Humanized anti-CD11a antibodies and various uses therefor are disclosed. The humanized anti-CD11a antibody may bind specifically to human CD11a I-domain, have an IC50(nM) value of no more than about 1 nM for preventing adhesion of Jurkat cells to normal human epidermal keratinocytes expressing ICAM-1, and/or an IC50 (nM) value of no more than about 1 nM in the mixed lymphocyte response assay.

Abstract: A subgenus of olfactory receptors (ORs) that are activated by isovaleric acid (IVA) are identified as well as assays that utilize one or more of these ORs. These assays are useful for identifying potential anti-odorants which may be used in deodorants, air and carpet fresheners, fabric deodorizers, and other compositions for camouflaging odor attributable to IVA and related carboxylic acids.

Abstract: The present invention provides methods and apparatus for mixing samples in-line in a microfluidic system, comprising methods of and means for introducing a first fluid sample into a flow-tube at a first end at a first velocity via a first conduit; methods of and means for introducing a second fluid sample into the flow-tube at the first end at a second velocity, the second velocity different from the first velocity, via a second conduit, wherein the first fluid sample and the second fluid sample converge in the flow tube to form an interface; whereby the first fluid sample and the second fluid sample mix at the interface within the flow-tube, wherein fluid flow at the first end of the flow-tube is laminar and fluid flow at a second end of the flow-tube is laminar, and wherein the flow-tube has a constant diameter between the first end and the second end of the flow-tube.

Abstract: The present invention provides a cancer marker protein, PCAM-1, and polynucleotides which identify and encode this protein. Detection of this marker is useful in diagnosing and prognosticating cancer in a patient. Also provided are expression vectors and host cells for expression of PCAM-1 as well as antibodies raised against the PCAM-1 protein. In addition, a Monte Carlo-like screening assay for identification of specific 8 mer sequences which selectively bind proteins in a crude extrract of tissues, cells or other biological fluids is provided.

Abstract: The present disclosure provides the nucleotide sequence encoding a cell surface NADH oxidase/protein disulfide-thiol interchange protein (tNOX) characteristic of neoplastic and virus-infected cells. Also provided are recombinant DNA molecules comprising a sequence portion encoding full length or truncated tNOX, recombinant host cell which express full length or truncated tNOX, methods for recombinant production of tNOX or truncated tNOX, and diagnostic methods which employ either nucleotide sequences of the neoplastic cell-specific tNOX or antibodies specific for the rNOX protein.

Abstract: This invention provides a method for determining whether a compound is capable of suppressing ras functions comprising: (a) contacting an effective amount of the compound with Ha-ras transformed cloned rat embryo fibroblast cells under conditions permitting the compound to suppress ras functions in the cells; and (b) determining the expression or inhibition of certain indicator gene or genes, thereby determining whether the compound is capable of suppressing ras function. This invention further provides the determined compound and a pharmaceutical composition comprising the compound and a pharmaceutically acceptable carrier. This invention also provides methods for generating transcriptional switched Ha-ras transformed cloned rat embryo fibroblast cells. This invention also provides the generated cells and different uses of the cells.