Abstract: The present invention relates to prognostic methods which are useful in medicine, particularly cancer chemotherapy. The object of the invention to provide a method for assessing Dihydropyrimidine dehydrogenase (DPD) expression levels in tissues and prognosticate the probable resistance of a patient's tumor to treatment with 5-FU based therapies by examination of the amount of DPD mRNA in a patient's tumor cells and comparing it to a predetermined threshold expression level. More specifically, the invention provides to oligonucleotide primer pairs DPD3A and DPD3B and methods comprising their use for detecting levels of Dihydropyrimidine dehydrogenase (DPD) mRNA.

Abstract: A method for enrichment of natural antisense mRNA which involves hybridization of cDNA obtained from sense RNA with cDNA obtained from antisense RNA, followed by DNA polymerase treatment of the sense-antisense hybrid DNA molecule. A natural antisense library can be generated by cloning of sense-antisense hybrid DNA molecules in a vector.

Abstract: The invention provides methods and compositions for normalizing and amplifying RNA populations. The methods generally comprise the steps of copying message RNA (mRNA) to form first single-stranded (ss) cDNA; converting the first ss-cDNA to first double-stranded (ds) cDNA; linearly amplifying the first ds-cDNA to form first amplified RNA (aRNA); tagging the 3? end of the first aRNA with a known sequence to form 3?-tagged first aRNA; copying the 3?-tagged first aRNA to form second ss-cDNA; and normalizing the mRNA and/or the first aRNA.

Abstract: Disclosed herein is the discovery of a novel hepatitis C virus (HCV) isolated from a human patient. Embodiments of the inevntion include HCV peptides, nucleic acids encoding said HCV peptides, antibodies directed to said peptides, compositions containing said nucleic acids and peptides, as well as, methods of making and using the aforementioned compositions including, but not limited to, diagnostics and medicaments for the treatment and prevention of HCV infection.

Abstract: Methods and products for the evaluation of HIV treatment are provided. The methods are based on evaluating molecular events at the HIV integrase resulting in altered therapeutic efficacy of tho investigated compounds. The methods rely on providing an integrase gene and evaluating either through integrase gene genotyping or phenotyping.

Abstract: Described is an improved multiplex ligation-dependent amplification method for detecting the presence and quantification of at least one specific single stranded target nucleic acid sequence in a sample using a plurality of probe sets of at least two probes, each of which includes a target specific region and a non-complementary region comprising a primer binding site. The probes belonging to the same set are ligated together when hybridised to the target nucleic acid sequence and amplified by a suitable primer set. By using a femtomolar amount of the probes a large number of different probe sets can be used to simultaneously detect and quantify a corresponding large number of target sequences with high specificity.

Abstract: A method for synthesizing cDNA characterized by performing a reverse transcription reaction in the presence of an enzyme having a reverse transcriptional activity and another enzyme different from the former one which as a 3?-5? exonuclease activity.

Abstract: The present invention relates to carcinogenesis biomarkers produced by phenobarbital-treated rat hepatocytes, nucleic acid molecules that encode carcinogenesis biomarkers or a fragment thereof and nucleic acid molecules that are useful as probes or primers for detecting or inducing carcinogenesis, respectively. The invention also relates to applications of the factor or fragment such as forming antibodies capable of binding the carcinogenesis biomarkers or fragments thereof.

Abstract: A primer design system in which DNA nucleotide sequences are obtained from a database comprising a plurality of different DNA nucleotide sequences, and the nucleotide sequences of primers capable of hybridizing specifically to the DNA thus obtained are determined. A plurality of primers capable of hybridizing specifically to mutually different DNAs can be efficiently designed.

Abstract: This invention relates to an improved process for detecting and quantifying a desired nucleic acid sequence. The process involves synthesizing single stranded RNA, single stranded DNA, double-stranded DNA followed by detection using an electrochemiluminescent labeled binding species.

Abstract: Oligonucleotides useful in the detection of a nucleic acid target sequence in a sample.

Abstract: The present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immuno-deficiency Virus (HIV). With the present invention nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid. The oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained. The benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity.

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: Disclosed are compositions and a method for detection of nucleic acid sequences. The disclosed method uses a structured probe to distinguish between sequences. Structured probes are bifunctional molecules where one function is as a probe to a target nucleic acid sequence and the other function is as a detection sequence to facilitate detection of the probe. Structured probes include a detection sequence, sequence complementary to a target sequence, and sequences that form duplex regions (higher order structures). The duplex region is stable unless the probe hybridizes to the target sequence. The disclosed method involves hybridizing the structured probe to a target sequence and detecting the detection sequence on the structured probe. The detection sequence is available for detection only if the duplex region of the structured probe is disrupted. This links detection of the structured probe with the hybridization of the structured probe to the target sequence.

Abstract: Compositions and methods for enhancing the effect of vaccines in animals, such as domestic, sport, or pet species, and humans are disclosed. More particularly, vaccine compositions comprising ribavirin and an antigen, preferably an antigen that has an epitope present in Hepatitis C virus (HCV), are disclosed for use in treating and preventing disease, preferably HCV infection.

Abstract: The present invention relates to the cloning and characterization of a human serine/threonine kinase (h-sgk: serum and glucocorticoid dependent kinase). The invention furthermore relates to reagents for diagnosing conditions associated with a change in cell volume and/or in “macromolecular crowding” in the body, such as, for example, hypernatremia, hyponatremia, diabetes mellitus, renal failure, hypercatabolism, hepatic encephalopathy, inflammation and microbial or viral infections. The present invention additionally relates to pharmaceuticals comprising the h-sgk, nucleic acids which code for the h-sgk, or receptors, in particular antibodies, which specifically bind to the h-sgk.

Abstract: PCR-based monitoring of microorganisms in systems for the biological treatment of wastewater. In particular, measuring both the abundance and expression of indicator/effector genes or gene combinations, where expression of an “effector” gene correlates with the degradative activity of a particular microbial sample, and where the abundance of an “indicator” gene correlates with the abundance of microbe. Effector gene expression is measured by competitive quantitative RT-PCR, and indicator gene abundance is measured by competitive quantitative PCR. The indicator and effector genes may be the same or different genes. In one embodiment, the indicator and effector gene are sequences from the glyphosate oxidoreductase (gox) gene and the quantitative techniques employed are competitive quantitative PCR and competitive quantitative RT-PCR.

Abstract: Recombinant hepatitis C virus (HCV) capsid proteins that self-assemble into large spherical virus-like particles structures and viral capsids that include conformational antigenic epitopes are provided. The large spherical virus-like particles structures and viral capsids, including capsid proteins that are expression products of a viral particle coding sequence protein, may be prepared as vaccines to induce a cellular or humoral immune response. The self assembling capsid proteins may also be used as elements of diagnostic immunoassay procedures for HCV infection.

Abstract: The present invention relates to a process for amplifying DNA of an organism. More particularly, the present invention is directed to a process for amplifying DNA of an organism through Polymerase Chain Reaction(PCR) without any information regarding a primer needed for amplifying DNA of an organism.

Abstract: A method for rapidly identifying porcine estrogen receptor (ESR) marker comprises using published primers to amplify the target DNA fragment by polymerase chain reaction (PCR). The DNA fragment is cloned and then sequenced. The key positions of the sequence are modified to generate three primers which are used to amplify different DNA fragments with different genotypes by PCR to eliminate extra restriction cut reaction. A long one of the primers is to specifically amplify non-prolific allele, a short one of the primers is to specifically amplify prolific allele, and the remaining one is mutual and complimentary to the sequence. After PCR and electrophoresis, the sample with 90 bp band is identified as prolific genotype, the sample with 110 bp band is identified as non-prolific genotype, and the sample with 90 bp and 110 bp bands is identified as hetero-genotype.

Abstract: The invention provides a process for preparing capped mRNAs from an RNA mixture, e.g. whole RNA isolated from a cell or tissue extract, that includes combining in a reaction mixture RNA comprising capped mRNA with a separable affinity matrix having high-affinity eIF4E bound thereto, under conditions sufficient for binding to occur between the high-affinity eIF4E and the capped mRNA, whereby capped mRNA is bound to the affinity matrix, separating the affinity matrix from the reaction mixture, then separating the capped mRNA from the affinity matrix. High affinity eIF4E mutants previously described are employed in the process as well as a novel mutant disclosed and claimed herein. The mRNA preparation process is based on isolation of 5?-capped mRNA. The mRNA molecules thus isolated have intact sequences encoding the NH2-terminal ends of the proteins they encode, unlike those isolated by prior methods.

Abstract: Oligonucleotide molecules labeled with a plurality of fluorophores of one or more types embedded in the backbone of said oligonucleotide, wherein at least one of said fluorophores is not located at either the 3? or 5? terminus of said oligonucleotide. The invention further provide methods for using the subject labeled oligonucleotides in detecting biological molecules, sequencing DNA molecules and particularly generating cDNA molecules for characterizing the differential expression of genes.

Abstract: Disclosed is a process for transcribing RNA using a nucleotide reagent as the promoter. Such a reagent enables any type of RNA to be transcribed without sequence specification and without protein cofactors, by means of an RNA polymerase that is known to be DNA-dependent such as the RNA polymerase of the phage T7, or by means of new, mutated RNA polymerase with the ability to synthesize a transcription product of a polynucleotide matrix with a higher yield when the matrix is RNA than when said matrix is DNA. This type of RNA polymerase can be obtained by effecting mutations on a coding gene for a wild-type RNA polymerase, and then by selecting the mutated RNA polymerase with said ability. The invention can be applied notably to the detection, synthesis or quantification of RNA.

Abstract: A nucleic acid having a first nucleotide sequence encoding an infectious hepatitis C virus, a second nucleotide sequence encoding a ribozyme, and an inducible promoter operably linked to the first and second nucleotide sequences, the ribozyme being configured to remove a 3′ sequence unnecessary for replication of the infectious hepatitis C virus from a transcript initiated by the inducible, is described. A cell containing the nucleic acid and methods of using the cell are also described.

Abstract: A method for examining nucleotide sequences of a sample includes adding a group of primers of multiple species to a solution containing the sample and simultaneously synthesizing complementary strands at each of the multiple regions containing the nucleotide sequences; designing the DNA probes with specific sequences elongate the complementary strands by the presence or absence of mutations in the nucleotide sequences, wherein the same number of such DNA probes and the nucleotide sequences are used for complementary strand synthesis; using the nucleotide sequences or their complementary sequences as a template to convert pyrophosphate produced during the elongation reaction to ATP which then reacts with chemiluminescent substrates to develop luminescence to be detected. According to the method, sensitivity is greatly increased by amplification of the amount of pyrophosphate produced in synthesis of the complementary strands without amplifying the copies of nucleotide sequences.

Abstract: There is disclosed a cancer diagnostic method based upon DNA methylation differences at specific CpG sites. Specifically, the inventive method provides for a bisulfite treatment of DNA, followed by methylation-sensitive single nucleotide primer extension (Ms-SNuPE), for determination of strand-specific methylation status at cytosine residues.

Abstract: The invention provides a wide range of methods and compositions for detecting and treating cervical cancer in an individual. Specifically, the invention provides target cervical cancer-associated proteins, which permit a rapid detection, preferably before metastases occur, of cervical cancer. The target cervical cancer-associated protein, may be detected, for example, by reacting the sample with a labeled binding moiety, for example, a labeled antibody capable of binding specifically to the protein. The invention also provides kits useful in the detection of cervical cancer in an individual. In addition, the invention provides methods utilizing the cervical cancer-associated proteins either as targets for treating cervical cancer or as indicators for monitoring of the efficacy of such a treatment.

Abstract: The present invention is a general method for irreversibly inactivating ribonucleases. Ribonucleases are completely inactivated by treating them with a reducing agent and heat. RNA samples contaminated with ribonuclease may be treated with this method to protect them from degradation. The RNA may then be used directly in a variety of enzymatic reactions and molecular biology techniques. This method may also be applied to a variety of molecular biology reagents which may be contaminated with ribonuclease to protect an RNA from being degraded when incubated with the reagent.

Abstract: The present invention provides methods and compositions for detecting and analyzing clonal T-cell receptor (TCR) gene rearrangement using temporal temperature gradient gel electrophoresis (TTGE), which employs a gradual and uniform increase in the temperature of a constant denaturing gel to resolve different DNA molecules based on base pair composition. The present invention also provides methods and compositions for providing appropriate DNA migration markers for TTGE analysis.

Abstract: An adaptation of the real-time PCR assay allows for highly sensitive detection of any eubacterial species with simultaneous speciation. The assay relies on a ‘multiprobe’ design in which a single set of highly conserved sequences encoded by the 16S rRNA gene serves as the primer pair, and it is used in combination with both an internal highly conserved sequence, the universal probe, and an internal variable region, the species-specific probe. A pre-PCR ultrafiltration step can be used to effectively decontaminate or remove background DNA. The real-time system reliably identifies 14 common bacterial species with a detection limit of 50 fg.

Abstract: Embodiments of the present invention are directed to the detection of fetal or maternal RNA in a blood sample from a pregnant subject, and may involve subjecting the sample to a test for fetal or maternal analysis indicative of a fetal or maternal condition or characteristics. For instance, the RNA analysis may involve the assessment of the gene expression pattern of an unborn fetus by analyzing a blood sample from the mother. The prenatal monitoring technology allows, for the first time, the detection of genes which are expressed by the fetus, just by analysis of a sample of maternal blood. In specific embodiments, the prenatal monitoring technology is based on the discovery of circulating RNA of fetal origin in the plasma of pregnant women. In general, the detection method performed on a maternal serum or plasma sample from a pregnant female comprises detecting the presence of RNA of fetal or maternal original in the sample.

Abstract: The disclosed nucleic acid primer sets, used in combination with quantitative amplification (PCR) of tissue cDNA, can indicate the presence of specific proteases in a tissue sample. The detected proteases are themselves specifically overexpressed in certain cancers, and their presence may serve for early detection of associated ovarian and other malignancies, and for the design of interactive therapies for cancer treatment. More specifically, the present invention relates to the uses of stratum corneum chymotrytic enzyme as a marker for ovarian tumor cells.

Abstract: Compositions and methods for the therapy and diagnosis of cancer, such as ovarian cancer, are disclosed. Compositions may comprise one or more ovarian carcinoma proteins, portions thereof, polynucleotides that encode such portions or antibodies or immune system cells specific for such proteins. Such compositions may be used, for example, for the prevention and treatment of diseases such as ovarian cancer. Polypeptides and polynucleotides as provided herein may further be used for the detection and monitoring of ovarian cancer.

Abstract: The present invention pertains to methods, reagents, compositions, kits, and instruments for use in simultaneously amplifying multiple targets. In particular, this invention is based on the discovery of a two-step multiplex amplification reaction wherein the first step truncates the standard initial multiplex amplification round to “boost” the sample copy number by only a 100-1000 fold increase in the target. Following the first step the product is divided into optimized secondary single amplification reactions, each containing one of the primer sets that were used previously in the first or multiplexed booster step. The booster step can occur using an aqueous target nucleic acid or using a solid phase archived nucleic acid.

Abstract: The present invention relates to prognostic methods which are useful in medicine, particularly cancer chemotherapy. The object of the invention to provide a method for assessing ERCC1 expression levels in fixed or fixed and paraffin embedded tissues and determine a platinum-based chemotherapy by examination of the amount of ERCC1 mRNA in a patient's tumor cells and comparing it to a predetermined threshold expression level. More specifically, the invention provides to oligonucleotide primer pair ERCC1 and methods comprising their use for detecting levels of ERCC1 mRNA.

Abstract: The present invention related to oligonucleotides for use in amplifying and detecting HIV nucleic acid in a sample.

Abstract: Primers and probes derived from the 5′ untranslated region of the HCV genome which facilitate detection and/or quantification of all presently known genotypes of HCV. Disclosed sequences may be used in a variety of primer and probe constructs for amplification and/or detection of HCV nucleic acids.

Abstract: The present invention relates to the amplification of nucleic acids, preferably from mRNA. A primer and promoter are added to a target sequence to be amplified and then the target is amplified in an in vitro transcription reaction.

Abstract: The present invention describes a methodology for generating high fidelity PCR products, and also cloning of such high fidelity PCR products in a suitable vector. Generation of polymerase-induced mutant fraction of target sequences during PCR amplification is linearly proportional to the number of doublings of the target sequences. Thus the high fidelity PCR products are generated by minimizing the number of doublings of the target nucleic acid sequences during PCR amplification. Minimization of number of doublings of the target sequences is achieved by reducing the number of cycles of PCR amplification of the target sequences. The high fidelity PCR products thus obtained are then cloned into a suitable vector. As an example, a 960 bp target sequence from E. coli DNA was PCR-amplified only for 3 cycles, and it was then directly cloned into a positive selection cloning vector pRGR2Ap.

Abstract: The present invention provides an alternative PCR amplification which does not draw upon the use of thermostable DNA polymerases. It provides means for the controlled manipulation of denaturing conditions which do not demand the use of high denaturing temperature. More particularly, it provides means for the controlled oscillation of divalent metal ions, preferably of divalent metal ions such as Cu2+, Zn2+, Mn2+ and Cd2+, which are known to destabilize the DNA helix and thereby decrease the melting temperature of the DNA helix. The invention also provides methods for the automatization of this process. For instance, by means of cathodic reduction of the divalent metal species the concentration can be decreased to levels that allows for reannealing of separated strands with the primers; while oxidation of deposited metals or oxidation of monovalent metal ions, can restore the initially high concentration that allows for separation of both strands that make up the DNA helix.

Abstract: Disclosed is a method of detecting the presence of a nucleic acid target sequence of interest in a sample, comprising the steps of: (a) reacting the sample containing the target sequence of interest with a first nucleic acid probe, so as to cause hybridization between complementary portions of the target and the probe, wherein the first probe comprises 5′ and 3′ portions complementary to respective, substantially adjacent portions of the target sequence and an intervening non-complementary portion which does not become hybridized to the target, thereby creating a loop region looped out from a complex formed between the first probe and the target, such that non-contiguous portions of the first probe are brought into close proximity; (b) hybridizing a second nucleic acid probe to the non-contiguous portions of the first probe, (c) initiating nucleic acid synthesis, using the first probe as template, in a manner dependent upon hybridization of the second probe to the first probe; and (d) detecting th

Abstract: Methods for identifying differentially expressed mRNA molecules are described, as well as methods for amplifying nucleic acid sequences.

Abstract: This invention provides methods for constructing a normalized cDNA library, constructing a low copy gene library, preparing a probe from a biological sample and a kit for constructing a normalized cDNA library.

Abstract: A method for assaying a target nucleic acid, comprising: providing an RNA amplification system comprising producing a double-stranded DNA using, as a template, a target RNA containing a specific nucleotide sequence in a sample, said double-stranded DNA having a promoter sequence and being capable of transcribing an RNA comprising the specific nucleotide sequence or a sequence complementary to the specific nucleotide sequence, producing an RNA transcription product comprising the specific nucleotide sequence or a sequence complementary to the specific nucleotide sequence in the presence of an RNA polymerase, and producing the double-stranded DNA using the RNA transcription product as a template, in the presence of a probe labeled with an intercalating fluorochrome having a sequence complementary to the RNA transcription product; measuring the fluorescence intensity in the RNA amplification system with time; calculating a time when the fluorescence intensity satisfies a prescribed criterion based on the measure

Abstract: The present invention relates to an improved and efficient method for simultaneous monitoring of abundance of individual mutants of a microbe in mixed populations where insertion of a known transposon in the genome of a microbe such that each mutant caries a single transposon insertion, isolating the genomic DNA of the mixed population of mutants, fragmenting the same with a frequently cutting restriction enzyme, ligating a double standard adapter to the genomic DNA fragments, amplifying the DNA fragments adjoining transposon insertions thereby generating a set of DNA fragments corresponding only to mutated genes resolving the said amplified DNA fragments followed by comparing the intensity of DNA fragments obtained from population of mutants before selection with that obtained from the population subjected to selection and finally sequencing the DNA fragments that change in abundance to identify the mutated genes.

Abstract: The disclosed nucleic acid primer sets, used in combination with quantitative amplification (PCR) of tissue cDNA, can indicate the presence of specific proteases in a tissue sample. The detected proteases are themselves specifically overexpressed in certain cancers, and the presence of their genetic precursors may serve for early detection of associated ovarian and other malignancies, and for the design of interactive therapies for cancer treatment.

Abstract: Described herein are methods and reagents for the selection of protein molecules that make use of RNA-protein fusions.

Abstract: A kit is provided for preferentially amplifying target RNA in a sample of tester RNA relative to non-target RNA in the sample, the kit driver sequences complementary to the non-target tester RNA under conditions where the driver sequences hybridize to the non-target RNA, a nucleic acid primer capable of hybridizing to the target RNA under conditions suitable for extension of the nucleic acid primer; and a promoter template capable of hybridizing to a DNA that is complementary to the target RNA under conditions suitable for extension of the complementary DNA such that a functional double promoter is formed.

Abstract: Methods and compositions for synthesizing cDNA in vivo are disclosed, wherein a synthetic polynucleotide molecule which anneals in vivo to an RNA template molecule is utilized as a primer for reverse transcriptase in vivo.

Abstract: An RNA amplification method is particularly useful for diagnosing bacterial or viral infections or genetic disorders and for cell typing. The method includes the steps of denaturing a solution containing RNA, synthesizing a first cDNA strand from a suitable primer in the presence of reverse transcriptase, denaturing the heteroduplex formed, synthesizing a second cDNA strand from a second primer in the presence of DNA polymerase and then subjecting the cDNA formed to a sufficient number of amplification cycles. All the reactants and solvents are first placed in the same container to provide a single manipulation step that avoids the risk of contamination.