Abstract: The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

Abstract: The invention relates to a method for the isolation of hepatitis C virus. The method comprises the separation of particles termed exosomes from the blood plasma of an individual infected with hepatitis C virus (HCV) and the extraction or RNA from these exosome particles.

Abstract: A non-symmetric polymerase chain reaction (PCR) amplification method employing a limiting primer in low concentration whose concentration-adjusted melting point at least equals, and preferably exceeds, that of the excess primer, the latter in turn not being more than 25° C. below the melting temperature of the amplicon. Assays employing such amplification and labeled hybridization probes, including assays that include a detection step following primer extension or a low-temperature probe, or both. Kits for performing such assays and primer or primer-and-probe sets for performing the foregoing amplifications and assays.

Abstract: A primer set used to screen a polynucleotide sample to detect and identify variants in the Cytochrome P450 isoenzyme 2D6 (CYP2D6) gene. A method of screening a polynucleotide sample to detect and identify the presence of one or more than one variant in the CYP2D6 gene in the sample. A method of predicting the potential for altered metabolism of a substance, including one or more than one pharmaceutical drug, by a first individual compared to a second control individual, where the substance is metabolized by the CYP2D6 isoenzyme, and where the second control individual is homozygous for the wild type allele of the CYP2D6*1, SEQ ID NO:1. A method of screening a population to detect and identify the presence of one or more than one variant in the CYP2D6 gene. A purified or isolated variant of SEQ ID NO:1. A purified or isolated variant of SEQ ID NO:3.

Abstract: The invention provides caspase recruitment domain (CARD)-containing polypeptides, CARD, NB-ARC, ANGIO-R, LRR and SAM domains therefrom, as well as encoding nucleic acid molecules and specific antibodies. The invention also provides related screening, diagnostic and therapeutic methods.

Abstract: The present invention relates to PG1, a gene associated with prostate cancer. The invention provides polynucleotides including biallelic markers derived from PG1 and from flanking genomic regions. Primers hybridizing to these biallelic markers and regions flanking are also provided. This invention provides polynucleotides and methods suitable for genotyping a nucleic acid containing sample for one or more biallelic markers of the invention. Further, the invention provides methods to detect a statistical correlation between a biallelic marker allele and prostate cancer and between a haplotype and prostate cancer. The invention also relates to diagnostic methods of determining whether an individual is at risk for developing prostate cancer, and whether an individual suffers from prostate cancer as a result of a mutation in the PG1 gene.

Abstract: The present invention provides methods and kits for detecting chromosome translocations. The present invention further provides methods for diagnosing cancer.

Abstract: A class of asymmetric monobenzoxanthene compounds useful as fluorescent dyes are disclosed having the structure wherein Y1 and Y2 are individually hydroxyl, amino, imminium, or oxygen, R1–R8 are hydrogen, fluorine, chlorine, alkyl, alkene, alkyne, sulfonate, amino, amido, nitrile, alkoxy, linking group, and combinations thereof, and R9 is acetylene, alkane, alkene, cyano, substituted phenyl, and combinations thereof. The invention further includes novel intermediate compounds useful for the synthesis of asymmetric benzoxanthene compounds having the general structure where substituents R3–R7 correspond to like-referenced substituents in the structure of described above, and Y2 is hydroxyl or amine. In another aspect, the invention includes methods for synthesizing the above dye compounds and intermediates.

Abstract: This document describes a method of detecting DNA variation by monitoring the formation or dissociation of a complex consisting of: (a) a single strand of a DNA sequence containing the locus of a variation, (b) an oligonucleotide or DNA analogue probe specific for one allele of the variation and capable of hybridizing to the single strand (a) to form a duplex, a marker specific for the duplex structure of (a) plus (b) which forms a complex with the said duplex and reacts uniquely when interacting within the duplex, which comprises continually measuring an output signal indicative of interaction of the marker with duplex formed from the strand (a) and probe (b) and recording the conditions at which a change in reaction output signal occurs which is attributable to formation or dissociation of the complex and is thereby correlated with the strength with which the probe (b) has hybridized to the single strand (a).

Abstract: An integrated microfabricated instrument for manipulation, reaction and detection of microliter to picoliter samples. The instrument is suited for biochemical reactions, particularly DNA-based reactions such as the polymerase chain reaction, that require thermal cycling since the inherently small size of the instrument facilitates rapid cycle times. The integrated nature of the instrument provides accurate, contamination-free processing. The instrument may include reagent reservoirs, agitators and mixers, heaters, pumps, and optical or electromechanical sensors. Ultrasonic Lamb-wave devices may be used as sensors, pumps and agitators.

Abstract: The invention provides a unique set of nucleic acid sequences which is appropriate for use for a wide variety of applications requiring nucleic acid tags. As such, the sequence tags of the presently claimed invention may be used, for example, to label biological and nonbiological materials, in genotyping applications and in a variety of other analyses.

Abstract: An apparatus, compositions and related methods for sequencing a target nucleic acid are described. In certain embodiments, the apparatus is a microfluidic apparatus comprising an input chamber, microchannel, output chamber and a detection unit that is operatively connected to the microchannel. In preferred embodiments, the methods include hybridizing a target nucleic acid to one or more probe libraries, moving the hybridized target nucleic acid past the detector, and detecting bound probes. Probe libraries may comprise oligonucleotides or oligonucleotide analogs, preferably with each probe uniquely labeled. A linear order of labeled probes hybridized to the target nucleic acid can be detected and the target nucleic acid sequence deduced. In preferred embodiments, probe labels are detected by analysis of electron-induced fluorescence of probes labeled with conductive polymers.

Abstract: Fluorescent energy transfer dyes capable of moving between a more stacked configuration to exhibit fluorescent quenching and a more spaced configuration to exhibit fluorescence can be conjugated to a peptide epitope or nucleic acid for use in the detection of an unknown antibody in bulk solution. The resulting labeled peptide reagent can be used in an immunoassay procedure by placing it in bulk solution along with the unknown antibody to be detected. When the antibody binds to the peptide epitope, the pair of dyes carried by the peptide epitope will have their configuration altered from a stacked to an unstacked configuration and will exhibit a fluorescent increase in response thereto.

Abstract: The cloning of a novel PCVII viral genome is described as is expression of proteins derived from the PCVII genome. These proteins can be used in vaccine compositions for the prevention and treatment of PCVII infections, as well as in diagnostic methods for determining the presence of PCVII infections in a vertebrate subject. Polynucleotides derived from the viral genome can be used as diagnostic primers and probes.

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 present invention provides compositions and methods for detecting mutations associated with polycystic kidney disease in the cat.

Abstract: The invention provides novel universal primers that can amplify the fragment of cytochrome b gene of any animal species in polymerase chain reaction (PCR) and reveal the identity of the biological material of any unknown animal origin and a method for identification of the specific animal from a given biological sample.

Abstract: This invention relates to novel nucleic acid sequences encoding three novel human phosphodiesterase (hPDE IV) isozymes. It also relates to polypeptides encoded by such sequences. This invention also relates to an assay method for detecting the presence of such novel isozymes in human cells, and to a method of identifying compounds or other substances that inhibit or modify the activity of such isozymes.

Abstract: A method is provided for genotyping a target sequence at at least two allelic sites by a 5? nuclease amplification reaction.

Abstract: The present invention provides a method, referred to as CpG retrieval, to overcome incomplete bisulfite modification of DNA recovered from formalin-fixed tissue samples. The method involves boiling deparaffinized tissue samples in citrate buffer, followed by DNA extraction for promoter methylation analysis. In general, the extracted DNA is further modified by sodium bisulfite and then subjected to a method of promoter methylation analysis. The present invention also reports that hypermethylation of ataxia-telangiectasia-mutated gene promoter is correlated with decreased overall survival in patient with head and neck squamous cell carcinoma.