Abstract: The invention provides novel mutations, mutation combinations or mutational profiles of HIV-1 reverse transcriptase and/or protease genes correlated with phenotypic resistance to HIV drugs. More particularly, the present invention relates to the use of genotypic characterization of a target population of HIV and the subsequent correlation of this information to phenotypic interpretation in order to correlate virus mutational profiles with drug resistance. The invention also relates to methods of utilizing the mutational profiles of the invention in databases, drug development, i.e., drug design, and drug modification, therapy and treatment design, clinical management and diagnostic analysis.

Abstract: The invention provides novel mutations, mutation combinations or mutational profiles of HIV-1 reverse transcriptase and/or protease genes correlated with phenotypic resistance to HIV drugs. More particularly, the present invention relates to the use of genotypic characterization of a target population of HIV and the subsequent correlation of this information to phenotypic interpretation in order to correlate virus mutational profiles with drug resistance. The invention also relates to methods of utilizing the mutational profiles of the invention in databases, drug development, i.e., drug design, and drug modification, therapy and treatment design, clinical management and diagnostic analysis.

Abstract: The present invention provides non-invasive methods for detecting, monitoring, staging, and diagnosing malignant melanoma in a skin sample of a subject. The methods include analyzing expression in skin sample of one or more melanoma skin markers. The melanoma skin markers include IL-1 RI, endothelin-2, ephrin-A5, IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (?A subunit), TNF RII, SPC4, and CNTF R?. The skin sample can include nucleic acids, and can be a human skin sample from a lesion suspected of being melanoma.

Abstract: Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

Abstract: Methods and compositions are provided for objectively identifying: i) bovine animals having the genetic potential to produce beef that is marbled or tender, and ii) bovine carcasses whose beef is marbled or tender. The methods comprise extracting DNA from a sample obtained from a bovine animal or carcass, assaying for the presence of a DNA comprising a sequence, referred to hereinafter as a “genetic marker”, in the DNA sample. In one aspect, the genetic marker is a marker of marbling, and comprises the sequence set forth in SEQ ID NO. 1. In another aspect, the genetic marker is a marker of tenderness, and comprises the sequence set forth in SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4 or combinations thereof. The compositions include primers that amplify markers of marbled or tender beef present in bovine animal or carcass genomes and hybridization probes to detect marbling or tenderness markers.

Abstract: The kits and methods of the present invention relate to the diagnosis of cardiovascular disorders. In one aspect, the invention discloses a method and a kit for determining whether a subject has a fragile plaque disorder. In one aspect, the invention discloses a method and a kit for determining whether the subject has an occlusive disorder. In one aspect, the invention discloses a method and a kit for determining whether the subject has a restenosis disorder. Other methods of the present invention relate to the selection of therapeutics for a patient with a cardiovascular disease.

Abstract: An immunoassay method including reacting a sample from a patient with a bispecific antibody, wherein the bispecific antibody includes one antibody specific for a compound to be detected and a second antibody specific for a compound foreign to said patient sample, and subsequently reacting the patient sample with a polymer probe, wherein the polymer probe includes a compound recognized by the second antibody in the bispecific antibody complex and further includes at least two detectable signals; the bispecific antibody; and the polymer probe of the immunoassay method are disclosed.

Abstract: A method for measuring the presence of polynucleotide in a sample, comprising the steps of: (1) preparing a sample, an agglutinative agent and an agglutination promoter capable of binding to polynucleotide; (2) mixing said sample, said agent and said promoter; and (3) measuring the degree of agglutination of the agent.

Abstract: The discriminating capability of hybridization assays is increased by a combination of labelled primers which produce amplificates of one strand of a nucleic acid with a capture probe which is complementary to the same strand of the nucleic acid.

Abstract: An auto allele caller executed in a computer system for identifying alleles from a trace is described. The auto allele caller applies a typical shape of an allele for a marker to the trace to identify potential allele calls that match to the typical shape of the allele at the marker and assigns a quality factor to the allele calls.

Abstract: In order to make possible to preserve promptly and efficiently a DNA and to distribute the same without taking much labor and much time, a DNA solution is allowed to adhere to a sheet-like support having a prescribed thickness, and the DNA solution which has been allowed to adhere to the support is dried to fix the DNA onto the support.

Abstract: Disclosed herein is a process for liquid cultivating Schizophyllum commune Fr. for isolation of &bgr;-1,6-branched-&bgr;-1,3-glucan and a composition for external application containing &bgr;-1,6-branched-&bgr;-1,3-glucan as an active ingredient, which can defer skin aging, impart skin whitening effect and cure skin damage effectively.

Abstract: This invention provides reagents, libraries and sets of the reagents, and assay methods using the reagents, the reagents comprising an analyte moiety and a tag moiety, wherein the tag moiety contains information defining the identify and location of the analyte residues of the analyte moiety which is detectable by mass spectrometry.

Abstract: The present invention is directed to a method for detection, characterization and isolation of nucleic acids encoding proteins of a desired property, such as a particular cellular localization. The invention further provides for rapid expression of such proteins or glycoproteins in mammalian cells and for facilitated purification of the novel secreted proteins or glycoproteins. Further, the invention provides for radioactive labelling of the novel proteins or glycoproteins, for rapid identification of sites of binding including animals and for rapid production of infective viral vectors for use in gene transfer.

Abstract: Methods of detecting the presence of a plasmid DNA sequence integrated in a chromosomal DNA molecule of a eukaryotic cell in a sample that contains chromosomal DNA molecules of eukaryotic cells and free plasmid DNA molecules are disclosed. According to the invention, chromosomal DNA of eukaryotic cells which are free of deoxyadenosine methyltransferase, and free plasmid DNA molecules which are produced in cells that contain deoxyadenosine methyltransferase and which have a DpnI site, are digested with one or more restriction enzymes that cleave plasmid DNA sequences integrated in the chromosomal DNA and plasmid DNA molecules to produce DNA digestion segments that are then fractionated to produce a plurality of fractions. The DNA digestion segments in each fraction is digested with DpnI and plasmid DNA sequences are amplified using sets of primers that flank a DpnI site in the plasmid DNA sequence.

Abstract: The invention provides devices and methods for use in detecting nucleic acid analytes in samples. The devices each include a solid support to which is bound a two-dimensional distribution or field of nucleic acid probes that each bind to a nucleic acid analyte, which is detected by use of amplification methods.

Abstract: Amplification primers and methods for specific amplification and detection of a Campylobacter jejuni and C. coli target are disclosed. The primer-target binding sequences are useful for amplification and detection of C jejuni and C. coli target in a variety of amplification and detection reactions.

Abstract: Methods for diagnosing multiple myeloma are disclosed. These methods are based upon the observation that tumor rejection antigen precursors are expressed in multiple myeloma. By assaying bone marrow samples, one can diagnose multiple myeloma, and also monitor the disease's progress. Therapeutic approaches of multiple myeloma are also disclosed.

Abstract: The invention relates to genetical modification of DNA polymerase to reduce its innate selective sequence-related discrimination against incorporation of fluorescent dye-labeled ddCTP and ddATP in the enzymatic reaction for preparation of samples for automated florescent dye-labeled terminator DNA sequencing. The modified DNA polymerases are more resistant to heat inactivation and are more effective in dideoxynucleotide incorporation than current DNA polymerases.

Abstract: Genomic sequences of human mismatch repair genes are described, as are methods of detecting mutations and/or polymorphisms in those genes. Also described are methods of diagnosing cancer susceptibility in a subject, and methods of identifying and classifying mismatch-repair-defective tumors. In particular, sequences and methods relating to human mutL homologs, hMLH1 and hPMS1 genes are provided.

Abstract: The object of the present invention is to provide a simple, rapid and highly sensitive method of examining EHEC or VTEC in the examination of food poisoning and diarrhea. In the present invention, the oligonucleotides of SEQ ID NOS: 1-9 hybridizing selectively with a Vero toxin gene from EHEC (or VTEC) or with an O antigen-synthesizing region gene from pathogenic E. coli O157 are prepared and used as primers for gene amplification. By this method, bacteria producing O157 as one of the pathogenic factors in these bacteria and E. coli capable of producing Vero toxin can be selectively detected.

Abstract: The association of the molecular variant G-6A of the angiotensinogen gene with human hypertension is disclosed. The determination of this association enables the screening of persons to identify those who have a predisposition to high blood presure.

Abstract: Amplification primers and methods for specific amplification and detection of a Salmonella spp. target are disclosed. The primer-target binding sequences are useful for amplification and detection of Salmonella target in a variety of amplification and detection reactions.

Abstract: The invention provides a human pinin splice variant (PNIN) and polynucleotides which identify and encode PNIN. The invention also provides expression vectors, host cells, agonists, antibodies and antagonists. The invention also provides methods for treating disorders associated with expression of PNIN.

Abstract: Amplification primers and methods for specific amplification and detection of a Shiga-like toxin I (SLT-I) target are disclosed. The primer-target binding sequences are useful for amplification and detection of SLT-I target in a variety of amplification and detection reactions.

Abstract: Genetic markers associated with programmed cell death were characterized and their extent of polymorphism in normal populations was determined allowing for a method for determining genetic predisposition to SLE and other autoimmune diseases by genotyping. The allelic distribution of these gene markers in a large Mexican American SLE cohort and ethnically matched controls was determined. The results were that bcl-2, Fas-L, and IL-10 loci showed significantly different allelic distribution in SLE patients compared with controls, indicating an association between these gens and SLE. The method allows for determining the presence of these alleles. Alone, the presence of each of these alleles is associated with a moderate increase in SLE risk, while the occurrence of these alles together increases the odds of developing SLE by more than 40-fold.

Abstract: Methodology is provided for developing probes for identifying sequence differences between two related DNA populations, sets of DNA fragments or collections of restriction-endonuclease-cleaved DNA or cDNA. The method employs an initial stage to obtain a representation of both DNA populations, namely using the PCR to produce relatively short fragments, referred to as amplicons. Tester amplicons containing target DNA, sequences of interest, are ligated to adaptors and mixed with excess driver amplicons under melting and annealing conditions, followed by PCR amplification. The process may be repeated so as to greatly enrich the target DNA. Optionally, the target DNA may then be cloned and the DNA used as probes.

Abstract: A method for in vitro construction of a library of recombined homologous polynucleotides from a number of different starting DNA templates and primers by induced template shifts during an polynucleotide synthesis is described, wherebyA. extended primers are synthesized bya) denaturing the DNA templatesb) annealing primers to the templates,c) extending the said primers by use of a polymerase,d) stop the synthesis, ande) separate the extended primers from the templates,B. a template shift is induced bya) isolating the extended primers from the templates and repeating steps A.b) to A.e) using the extended primers as both primers and templates, orb) repeating steps A.b) to A.e),C. this process is terminated after an appropriate number of cycles of process steps A. and B.a), A. and B.b), or combinations thereof.Optionally the polynucleotides are amplified in a standard PCR reaction with specific primers to selectively amplify homologous polynucleotides of interest.

Abstract: The present invention relates to a method for in vitro evolution of protein function. In particular, the method relates to the shuffling of nucleotide segments obtained from exonuclease digestion. The present inventors have shown that polynucleotide fragments derived from a parent polynucleotide sequence digested with an exonuclease can be combined to generate a polynucleotide sequence which encodes for a polypeptide having desired characteristics. This method may be usefully applied to the generation of new antibodies or parts thereof having modified characteristics as compared to the parent antibody.

Abstract: Disclosed are new methods comprising the use of in situ hybridization to detect abnormal nucleic acid sequence copy numbers in one or more genomes wherein repetitive sequences that bind to multiple loci in a reference chromosome spread are either substantially removed and/or their hybridization signals suppressed. The invention termed Comparative Genomic Hybridization (CGH) provides for methods of determining the relative number of copies of nucleic acid sequences in one or more subject genomes or portions thereof (for example, a tumor cell) as a function of the location of those sequences in a reference genome (for example, a normal human genome). The intensity(ies) of the signals from each labeled subject nucleic acid and/or the differences in the ratios between different signals from the labeled subject nucleic acid sequences are compared to determine the relative copy numbers of the nucleic acid sequences in the one or more subject genomes as a function of position along the reference chromosome spread.

Abstract: Oligonucleotides and other biomolecules are immobilized in high density on solid substrates through covalent forces using either a permanent thioether bond, or a chemoselectively reversible disulfide bond to a surface thiol. Substrates which have hydroxyl groups on their surfaces can be first silanized with a trichlorosilane containing 2-20 carbon atoms in its hydrocarbon backbone, terminating in a protected thiol group. The oligonucleotides or other biomolecules are first connected to a tether consisting of a hydrocarbon or polyether chain of 2-20 units in length which terminates in a thiol group. This thiol may be further modified with a halobenzylic-bifunctional water soluble reagent which allows the conjugate to be immobilized onto the surface thiol group by a permanent thioether bond. Alternatively, the oligonucleotide-tether-thiol group can be converted to a pyridyldisulfide functionality which attaches to the surface thiol by a chemoselectively reversible disulfide bond.

Abstract: Hybridization chambers suitable for use in binding, e.g. hybridization, assays are provided. The subject chambers comprise an elongate container, a block element and a cap, where each of the components is preferably injection molded. Also provided are methods of using the subject chambers and kits that include the subject chambers. The subject chambers find use in a variety of applications, particularly in hybridization assays in which small sample volumes are employed.

Abstract: A method for the construction of a library of recombined polynucleotides from a number of different starting single or double stranded parental DNA templates is disclosed, wherein the starting single or double stranded parental DNA templates represent discrete points in a population of genes encoding evolutionary or synthetic homologues of a peptide having homologies ranging over a broad spectrum from less than 15% to more than 80%, said population exhibiting at least one identification sequence, and whereby said genes are subjected to a gene shuffling procedure to generate shuffled mutants of said population of genes representing additional discrete points between those of said starting templates.

Abstract: A method of diagnosis of a disease, Syndrome X in one embodiment, in an individual comprises determining the genotype of a microsatellite region of a glucocorticoid receptor gene in said individual. A method of identifying an individual predisposed or susceptible to the disease comprises determining the genotype of a microsatellite region of a glucocorticoid receptor gene in said individual. Methods of treatment and therapy for diseased or predisposed or susceptible individuals are provided, together with apparatus for carrying out the diagnosis.

Abstract: The present invention provides a novel method for identifying individuals who are likely to have negative responses to regular administration of .beta.-agonists. The invention also provides kits useful for this purpose.

Abstract: Disclosed are nucleic acid and amino acid sequences encoded by a novel, prostate specific gene (UC41) and diagnostic techniques for the detection of human prostate cancer utilizing such nucleic acid and amino acid sequences. Genetic probes and methods useful in monitoring the progression and diagnosis of prostate cancer are described. Methods of treatment for prostate cancer utilizing antisense constructs or antibodies specific for UC41 gene products are also described.

Abstract: A novel gene encoding a 37 kDa outer membrane protein from Campylobacter coli M275 has been cloned and sequenced. This protein has been named CadF and is expressed in a large number of clinical isolates of Campylobacter species. The invention also provides assays for detecting the presence of pathogenic Campylobacter species based on the antibody-based detection of CadF, or the polymerase chain reaction (PCR)-based amplification of a segment of the C. coli cadF gene.

Abstract: Disclosed is a specific identification method of an MRSA and MRC-NS, which is speedy, simple and reliable. Specifically, the present invention provides a diagnostic method of an MRSA or MRC-NS, which comprises performing a reaction with a sample by making combined use of a part of a mecDNA, which is an integrated adventitious DNA existing on a chromosome of the MRSA or MRC-NS and carrying an mecA gene thereon, and a part of a nucleotide sequence of a chromosomal DNA surrounding the integrated DNA; and also a diagnostic method of an MRSA or MRC-NS by PCR, LCR or hybridization, which comprises performing a reaction with a sample by using a nucleotide sequence of a chromosomal DNA surrounding an integrated site of a mecDNA in a chromosome of an MSSA or MSC-NS, wherein said method makes use of an occurrence of a negative reaction when said sample contains a mecDNA integrated therein.

Abstract: Allelic ladders of short tandem repeat (STR) loci selected from the group consisting of D16S539, D7S820, D13S317, and D5S818; methods for their use in analyzing STR polymorphisms, and kits containing the allelic ladders are disclosed.

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 methods of detecting and monitoring extracellular mutant oncogenes or tumor-associated DNA found in the plasma or serum fraction of blood, using DNA extraction followed by nucleic acid amplification with or without enrichment for mutant DNA. In particular, the invention relates to detection, identification, or monitoring of the existence, progression or clinical status of benign, premalignant, or malignant neoplasms in humans or animals that contain a mutation associated with the neoplasm through detection of the mutated nucleic acid of the neoplasm in plasma or serum fractions.

Abstract: The present invention provides primers which can be used for M. tuberculosis complex-specific detection of .alpha.-antigen DNA in a diagnostic assay performed on clinical specimens or in a culture-confirmation assay following growth of the organism in vitro. These primers and probes can also be employed in a reverse transcriptase-mediated amplification system for M. tuberculosis complex .alpha.-antigen mRNA. Such an assay provides a means by which to determine the viability of M. tuberculosis complex organisms either in clinical specimens or when grown in culture. The specific DNA or mRNA target region can be amplified using SDA, PCR, LCR, Nucleic Acid Sequence Based Amplification (NASBA), Self-sustained Sequence Replication (3SR) or Q.beta. Replicase-mediated systems. Also described are methods for the detection of the products of amplification with a radiolabeled probe by chemiluminescent assay or fluorescence polarization analysis.

Abstract: The present invention provides a method of arbitrary sequence oligonucleotide fingerprinting (ASOF), a novel technology which eliminates gel electrophoresis as a step in polymorphic marker analysis, species identification and transcriptional profiling. ASOF greatly increases the speed and throughput of analysis, with aconcomitant decrease in cost. Furthermore, the miniaturization and automation of ASOF analysis leads to an exceedingly increased throughput of nucleic acid analysis.

Abstract: A method for in vitro mutagenesis and recombination of polynucleotide sequences based on polymerase-catalyzed extension of primer oligonucleotides is disclosed. The method involves priming template polynucleotide(s) with random-sequences or defined-sequence primers to generate a pool of short DNA fragments with a low level of point mutations. The DNA fragments are subjected to denaturization followed by annealing and further enzyme-catalyzed DNA polymerization. This procedure is repeated a sufficient number of times to produce full-length genes which comprise mutants of the original template polynucleotides. These genes can be further amplified by the polymerase chain reaction and cloned into a vector for expression of the encoded proteins.

Abstract: Screening assays for identifying ligase activity modulators are provided, in both solid phase and liquid phase formats. Solid phase formats detect ligase activity by ligating a labelled nucleic acid to a capture nucleic acid in the presence of the ligase modulator and detection of the labelled nucleic acid. Liquid phase assays detect ligation-dependent changes in interactive labels between nucleic acids such as proximity quenching of fluorescent labels. Compositions, apparatus and integrated systems for assays are also provided.

Abstract: The present invention relates to a process for quantitatively determining CD95 ligand, comprising the following processing steps:(a) isolation of total RNA from cells,(b) transcription the total RNA from (a) into cDNA by reverse transcription, and(c) amplification of the cDNA from (b) and a CD95 ligand competitor fragment by CD95 ligand-specific primers in a PCR reaction.The process is suitable for determining the extent and/or course of apoptosis.

Abstract: The invention relates to methods and kits for the sensitive, specific, and, preferably, quantitative detection of C. parvum oocysts in aqueous samples using immunomagnetic separation and amplification.

Abstract: The present invention is directed to a mechanism for marking biological samples (blood, semen, saliva, etc.) that are to be used for subsequent nucleic acid analysis. The method involves adding a nucleic acid (DNA) molecule of known sequence to the biological sample at the time of sample collection. The method further utilizes primers specific to the complementary strands of the added DNA, such that they will direct the synthesis of another DNA molecule of known length when used in a standard or multiplex polymerase chain reaction (PCR). This provides an unambiguous identifying label for the collected forensic or medical samples, including blood, semen, saliva, urine, tissue, and mixtures of bodily fluids. When used with the supplied primers or DNA probe(s), PCR or nucleic acid hybridization techniques will produce or recognize DNA fragments of predetermined size(s), preventing errant confusion of said samples with other forensic or medical samples that do not contain the aforementioned DNA additive.

Abstract: The association of the molecular variant A-20C of the angiotensinogen gene with the prognosis of human hypertension as determined by the G-6A molecular variant is disclosed. The determination of this association enables the screening of persons to identify the severity of hypertension or the severity of the risk of a predisposition to high blood pressure.

Abstract: The invention concerns novel compounds having defined structural formulae and methods of mutating a nucleic acid sequence, the method comprising replicating a template sequence in the presence of a nucleoside triphosphate analogue in accordance with the invention, so as to form non-identical copies of the template sequence comprising one or more nucleoside triphosphate analogue residues, and a kit for use in performing the method of the invention.

Abstract: A highly sensitive method to detect melanoma micrometastasis by examining lymph nodes for the presence of tyrosinase messenger RNA. In a preferred mode, this is accomplished using the combination of reverse transcription and double round polymerase chain reaction (RT-PCR). The amplified samples are examined on a 2% agarose gel and tyrosinase is seen as a 207 base pair fragment. The lymph nodes examined are determined using pre- and intra- operative node mapping.