Abstract: The present invention is directed to compositions and methods relating to a G-protein coupled receptor kinase-5 polymorphism. The methods include, for example: detecting enhanced desensitization of the beta adrenergic receptor signaling pathway in an individual, assessing partial protection against heart failure progression in an individual, and assessing an individual's response to beta-blocker therapy. The compositions include polynucleotides or fragments thereof of a nucleotide sequence encoding for a G-protein receptor kinase-5 molecule with a thymine at amino acid position 122 and oligonucleotide primers that hybridize thereto.

Abstract: The present invention relates to the use of molecular markers and related signaling mechanisms for the preclinical and clinical profiling of inhibitors of enzymes having histone deacetylase activity. The invention also relates to the use of such markers as diagnostic and/or prognostic tools for the treatment of tumor patients with such inhibitors.

Abstract: A method is described for the real-time detection of Salmonella species in foods and on surfaces. Salmonella are enriched in media to increase their cell density prior to analysis. DNA is recovered by lysis in the presence of azide, proteinase K, and detergent. Real-time detection of Salmonella species is performed in a PCR reaction using gene specific primers and a cleavable chimeric fluorescent probe. The method also describes an internal control to confirm the efficiency of nucleic acid amplification and detection. The method is amenable to medium and high throughput analysis.

Abstract: A method for detecting and isolating AAV sequences in a sample of DNA obtained from tissue or cells is provided, which sample contains DNA and proviral AAV. The method involves subjecting the sample containing DNA to amplification via polymerase chain reaction (PCR) using a first set of primers which specifically amplify a first AAV region. The first AAV region is characterized by having at least 250 nucleotides of AAV capsid nucleic acid sequence, a variable sequence flanked by a sequence of at least 18 nucleotides at the 5? end of the first AAV region and a sequence of at least 18 nucleotides at the 3? end of the first AAV region. Each of the 5? and 3? at least 18 nucleotides is the same over at least 9 consecutive nucleotides relative to corresponding sequences in an alignment of at least two AAV serotypes. Each of the sets of primers consist of a 5? primer and a 3? primer. The method is further useful for identifying AAV sequences in the sample by the presence of amplified proviral AAV sequences.

Abstract: The present invention relates to a method, kit and use of various nucleic acid sequences for deleting and/or quantifying one or more nucleic acids of a genome in a sample. Wherein the nucleic acid is amplified and the locus that is amplified is a multi copy locus within the genome, the multicopy locus has copies on at least two different chromosomes and the amplification product is detected and/or quantified.

Abstract: Assays using non-natural bases are described. In one embodiment, the method involves contacting a sample suspected of containing the target nucleic acid with a polymerase and first and second primers; amplifying the target nucleic acid by PCR using the first and second primers to generate an amplification product having a double-stranded region and a single-stranded region that comprises the non-natural base; contacting the sample with a reporter comprising a label and a non-natural base that is complementary to the non-natural base of the single-stranded region; annealing at least a portion of the reporter to the single-stranded region of the amplification product; and correlating a signal of the label with the presence of the target nucleic acid in the sample. The invention also provides corresponding kits for use in detecting target nucleic acids in a sample.

Abstract: Provided are a method of analyzing a sequence of a first probe nucleic acid using a substrate on which a second probe nucleic acid is immobilized, and a microarray and a kit for the same.

Abstract: Solid support assays using non-standard bases are described. A capture oligonucleotide comprising a molecular recognition sequence is attached to a solid support and hybridized with a target. In some instances, the molecular recognition sequence includes one or more non-standard bases and hybridizes to a complementary tagging sequence of the target oligonucleotide. In other instances, incorporation of a non-standard base (e.g., via PCR or ligation) is used in the assay.

Abstract: The present invention relates to a method for predicting a clinical response of a patient suffering from or at risk of developing cancer, preferably colorectal cancer, towards a given mode of treatment, the method including the steps of: a) obtaining a biological sample from the patient; b) determining the expression level of at least SPON-2, and optionally determining the expression level of SPON-1, in the sample; c) comparing the expression level or expression levels determined in (b) with one or several reference expression levels; and d) predicting therapeutic success for the given mode of treatment in the patient or implementing therapeutic regimen in the patient from the outcome of the comparison in step (c).

Abstract: Aspects of the present invention relate to methods and compositions for the detection and/or quantification of S. aureus from a sample, as well as methods and compositions useful for the detection and/or quantification of S. aureus and MRSA in a single assay. Embodiments include nucleic acids that hybridize to S. aureus-specific nuc sequences and MREJ sequences.

Abstract: The present invention relates to amplification primers and detection probes, which are useful for the detection of human papillomaviruses (HPV), and more particularly of HPV, which can be oncogenic for the mucosal epithelia. The amplification and detection systems provided by the present invention are group-targeted systems, namely A5-, A6- A7-, and A9-targeted systems. The amplification and detection systems of the invention allow for an amplification of HPV in multiplex as well as for a real-time detection, whereby at least the thirteen HR HPV can be detected in a single-tube assay. The invention further allows for a reliable quantitation of HPV viral loads in real-time multiplex amplification.

Abstract: A primer for the amplification of a DNA template comprising a protelomerase target sequence, particularly for production of closed linear DNA, which primer is capable of specifically binding to a palindromic sequence within a protelomerase target sequence and priming amplification in both directions.

Abstract: The present invention relates to the use of at least one nucleic acid comprising or consisting of: (i) (SEQ?ID?NO:?1) CATCGATGAAGAACGCWGCRAAHTGCGATAMGTARTGYGAATTGCAGR ATTCAGTGARTCATCGAAWYTTTGAACGCAYMTTGCRC, wherein: R represents A or G Y represents C or T M represents A or C W represents A or T H represents A or C or T (ii) a portion of SEQ ID NO: 1, provided said nucleic acid binds under stringent conditions to a nucleic acid comprising or consisting of the complementary sequence of SEQ ID NO: 1, or (iii) complementary sequences of (i) and (ii);for the detection of nucleic acids from one or more fungi in a sample.

Abstract: A novel transgenic corn event designated MZDT09Y is disclosed. The invention relates to nucleic acids that are unique to event MZDT09Y and to methods of detecting the presence of event MZDT09Y based on DNA sequences of the recombinant constructs inserted into the corn genome that resulted in the MZDT09Y event and of genomic sequences flanking the insertion site. The invention further relates to corn plants comprising the transgenic genotype of event MZDT09Y and to methods for producing a corn plant by crossing a corn plant comprising the MZDT09Y genotype with itself or another corn variety. Seeds of corn plants comprising the MZDT09Y genotype are also objects of the invention.

Abstract: A method for sequencing a nucleic acid is described that comprises the steps of: coupling an adaptor to at least one end of a template nucleic acid molecule; circularizing the adaptor coupled nucleic acid molecule; amplifying the adaptor coupled nucleic acid molecule to form a linear amplified concatamer molecule comprising a plurality of copies of the template nucleic acid molecule; compacting the linear amplified concatamer molecule with a branched polyelectrolyte species to form a branched polyelectrolyte compacted amplified concatamer molecule; and sequencing the branched polyelectrolyte compacted amplified concatamer molecule to produce a sequence composition of the template nucleic acid molecule.

Abstract: The present invention relates generally to detection of antibiotic-resistant bacteria in a sample. In particular, the invention provides methods, compositions and kits for detecting and analyzing methicillin-resistant Staphylococcus aureus (MRSA) and other methicillin-resistant bacteria in a sample.

Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.

Abstract: The present invention relates to primers for PCR amplification comprising abasic parts within the primer sequences and a method for PCR amplification using the same. More precisely, the present invention relates to primers capable of amplifying different templates and having abasic parts complementary to mutated site or polymorphic site of template DNA and a method for PCR amplification comprising the steps of mixing the composition for PCR amplification comprising the primers with nucleic acid template; and performing PCR with the mixture. The primers for PCR amplification of the present invention contain abasic parts not having specific coding information in their nucleotide sequences, so that they can amplify different templates having mutated sites at the same time.

Abstract: The present invention aims to provide a novel reagent for tumor testing and a novel pharmaceutical composition for tumor prevention. The present invention provides a reagent for tumor detection, which comprises a probe for the FEAT gene or amplification primers for the FEAT gene, or an antibody against the FEAT protein or a fragment of the antibody. Moreover, the present invention also provides a pharmaceutical composition for tumor prevention, which is configured to use the FEAT gene or the FEAT protein as a tumor marker to thereby recognize tumor cells.

Abstract: Processes for the serotype specific detection and identification of one or more Salmonella serotypes are provided. A family of specific primers and probes are provided that allow screening of biological or environmental samples for robust, rapid, and reproducible detection and identification of one or more Salmonella serotypes in the sample.

Abstract: The invention relates to the exponential amplification of specific target nucleic acids. The invention provides methods, reagents and kits for carrying out such exponential amplification via the autoligation chain reaction (ACR).

Abstract: Oligonucleotide primer useful for synthesizing a cDNA copy of HIV-1 nucleic acids from a broad range of HIV-1 subtypes, including M group and O group variants.

Abstract: Two genes, ARID1A (AT-rich interactive domain-containing protein 1A) and PPP2R1A (protein-phosphatase 2, regulatory subunit 1, alpha), can be used in methods which are useful for detecting cancer, diagnosing cancer, contributing to a diagnosis of cancer, confirming a diagnosis of cancer, identifying appropriate treatments for cancer, monitoring treatment of cancer, and evaluating treatment protocols for cancer, including ovarian clear cell carcinoma, breast cancer, colon cancer, gastric cancer, lung cancer, medulloblastoma, pancreatic cancer, and prostate cancer.

Abstract: Disclosed are methods and kits for detecting high risk HPV genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68, that are known to cause abnormal cell growth and cancer. The disclosed methods and kits allow a rapid and quantitative real-time PCR detection of all high risk strains of HPV in a single PCR reaction. The procedure promises to facilitate the rapid high throughput detection of high risk strains of HPV in a cost effective and reliable manner.

Abstract: A method of detecting genetic material deriving from Chlamydia trachomatis comprising detection of a specified nucleic acid sequence, optionally using specific primers and probes and optionally in combination with the detection of genetic material deriving from Pectobacterium atrosepticum as an internal control; and related products and kits.

Abstract: Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers revealed an average of nine rearranged sequences (range 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints were able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients.

Abstract: In a method for synthesizing a pool of nucleic acid molecules, a first nucleic acid has a first 5? region and a first 3? region and a second nucleic acid has a second 5? region and a second 3? region. The second 3? region and the first 5? region have identical nucleic acid sequences. The first 3? region is hybridized with an oligonucleotide, extending the hybridized oligonucleotide and producing a first extension product having a 3? region complementary to the first 5? region. The second nucleic acid is hybridized with the first extension product to hybridize the 3? region of the first extension product to the second 3? region, extending the 3? region of the first extension product and producing a second extension product having a 3? region complementary to the second 5? region. Error-containing molecules are separated from error-free molecules by a component that selects for a sequence error.

Abstract: In one embodiment of the invention a method for detecting low frequency occurrence of one or more HIV sequence variants associated with drug resistance is describe that comprises generating cDNA species from RNA molecules in an HIV sample population; amplifying first amplicons from the cDNA species, wherein each amplicon comprises amplified copies and is amplified with a pair of nucleic acid primers that define a locus; clonally amplifying the amplified copies of the first amplicons to produce second amplicons that comprise an immobilized population of substantially identical copies from one of the amplified copies of first amplicons; determining a nucleic acid sequence composition from at least 100 of the immobilized populations in parallel on a single instrument; detecting one or more sequence variants that occur at a frequency of 5% or less in the nucleic acid sequence composition of the at least 100 immobilized populations; and correlating the detected sequence variants with variation associated with HIV

Abstract: The invention relates to the use of particles comprising binding ligands and electron transfer moieties (ETMs). Upon binding of a target analyte, a particle and a reporter composition are associated and transported to an electrode surface. The ETMs are then detected, allowing the presence or absence of the target analyte to be determined.

Abstract: Oligonucleotides targeted to HPV Type 16 and/or Type 18 nucleic acid sequences which are particularly useful to aid in detecting HPV type 16 and or 18 are described. The oligonucleotides can aid in detecting HPV Type 16 and/or Type 18 in different ways such as by acting as hybridization assay probes, helper probes, and/or amplification primers.

Abstract: High-throughput detection for the interesting base or the mutation site in the nucleic acid sample can be achieved by means of the linear test probe pairs P1 and P2. The test probe pairs P1 and P2 respectively comprise either of the flanking complementary sequences which are adjacent to the interesting base or the mutation site in the nucleic acid sample. The invention can be applied to the re-sequencing the target nucleic acid sequence, the detection and analysis for the mutation, insertion, or deletion sites of a known nucleic acid sequence, and the genotyping of the pathogenic microorganism.

Abstract: The invention relates to a method for detecting bacterial contaminations preferably in physiological samples as well as sequences of synthetic oligonucleotides used therefor. The method comprises the steps of i) extracting the nucleic acid, particularly bacterial DNA, ii) amplification by means of primers and detection by means of oligonucleotides, particularly fluorescence-marked oligonucleotides as hybridization probes, containing a sequence that is selected from among a group encompassing SEQ ID NO:5 to SEQ ID NO:35, preferably in real-time PCR, and iii) evaluation by means of fusion curve analysis.

Abstract: The present invention provides a method of selection of a patient, who is a candidate for treatment with an NMDA antagonist drug, such as (S)-1-phenyl-2-(pyridin-2-yl)ethanamine or ketamine, whereby to predict an increased or decreased likelihood of response to the NMDA antagonist. The invention provides a method for determining the sequence of GABR-A2 at any of four single nucleotide polymorphism (SNP) sites known as rs3756007, rs11503016, rs17537359 or rs1372472. The method also provides ARMS primers optimised for determining the sequence at these GABR-A2 SNPs and diagnostic kits comprising suitable primers or probes for determining the particular SNPs.

Abstract: The present invention relates to a method of identifying a target antigen of T cells comprising (a) contacting (aa) cells expressing (i) a functional T cell receptor complex comprising predefined matching T cell receptor ? and ? chains; and (ii) a read-out system for T cell activation; with (ab) antigen-presenting cells carrying (iii) peptide libraries encoded by randomised nucleic acid sequences; and (iv) MHC molecules recognised by the T cell receptor of (i); (b) assessing T cell activation using said read-out system; (c) isolating antigen-presenting cells that are in contact with the cells in which the read-out system indicates T cell activation; (d) identifying the target antigen or the nucleic acid molecule encoding said target antigen.

Abstract: The invention provides a method for determining the presence, species, and/or quantity of Leishmania in a sample.

Abstract: This invention provides methods, primers and kits for restoration of nucleic acid from tissue, in particular degraded tissue and formalin-fixed and paraffin-embedded (FFPE) tissue, where the methods involve complementary-template reverse-transcription (CT-RT) where short single-stranded DNA sequences reverse-transcribed from mRNA are used for reverse-transcription of complementary sense-RNA templates. The methods can be used to determine patterns of gene expression and chromosomal alterations in archived tissue samples, and may be used to identify expression of disease-related genes.

Abstract: The present invention relates to primers for the universal amplification and detection of Archaea, which primers are designed based on a multiple sequence alignment of Archaea Type II chaperonin (thermo-some) genes. For detection of Archaea having templates with a GC content of below 60%, primers are designed so that inosine residues are found at degenerate positions. For amplification of higher GC content templates, degenerate positions are replaced with specific nucleotide bases found in the high GC organism. The primers are useful for detecting, identifying and quantifying Archaea in a sample and for determining a phylogenetic relationship of a test Archaea organism.

Abstract: The present invention concerns the V617F variant of the protein-tyrosine kinase JAK2, said variant being responsible for Vaquez Polyglobulia. The invention also relates to a first intention diagnostic method for erythrocytosis and thrombocytosis allowing their association with myeloproliferative disorders, or to the detection of the JAK2 V617F variant in myeloproliferative disorders allowing their reclassification in a new nosological group.

Abstract: The present invention relates to a single nucleotide polymorphism (SNP) for predicting the sensitivity to an anticancer targeted therapeutic formulation, a polynucleotide containing the same, and a method for predicting the sensitivity to an anticancer targeted therapeutic formulation. According to the present invention, it is possible to predict the sensitivity of each individual to a certain anticancer targeted therapeutic formulation, using a small amount of a sample taken from a patient and thus to select a most suitable targeted therapeutic formulation over the entire duration of treatment for the patient.

Abstract: A region of the Chlamydia trachomatis pmpA gene has been identified which is useful for performing amplification assays to determine specifically whether C. trachomatis is present in the sample being tested. Oligonucleotides useful for performing thermal Strand Displacement Assay (tSDA) reactions on this gene are disclosed. The disclosed oligonucleotides can be used in an assay which is specific for multiple strains of C. trachomatis and which does not show cross reactivity with the genomes of other microorganisms or with human DNA.

Abstract: There is provided an in vitro method of detecting human papillomavirus nucleic acid in a sample, comprising: (a) contacting said sample with forward and reverse oligonucleotide primers, wherein said primers bind to target sites in the human papillomavirus L1 gene, or the complement thereof, under conditions suitable to promote amplification of a portion of said human papillomavirus L1 gene or complement, thereby generating an amplicon; (b) contacting said amplicon with a probe, wherein the probe binds to a target site within said amplicon; and (c) detecting binding of said probe to said amplicon; wherein said forward primer binds to a target site having the sequence SEQ ID NO: 1; and wherein said reverse primer binds to a target site having the sequence SEQ ID NO: 2.

Abstract: The present invention discloses a method to identify and quantify environmental microorganisms useful in biomining processes. These microorganisms are basically 10, belonging to Bacteria: Acidiphilium sp., Leptospirillum sp., Sulfobacillus sp., Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans; and Archaea: Acidianus sp., Ferroplasma sp., Metallosphaera sp., Sulfolobus sp. and Thermoplasma sp. The method comprises performing a PCR with specific primers designed in our laboratories for different taxons SEQ ID No. 4 to SEQ ID No.: 407. With qPCR results and other data obtained from the analyzed sample, the microorganism concentration of each analyzed taxon present in the sample is calculated using a mathematical formula.

Abstract: Therapeutic agents which target heat shock protein (hsp) 27 in vivo are used to provide treatment to individuals, particularly human individuals, suffering from prostate cancer and other cancers that overexpress hsp27. A therapeutic agent, for example an antisense oligonucleotide or RNAi nucleotide inhibitor with sequence specificity for hsp27 mRNA, for example human hsp27 mRNA, is administered to an individual suffering from prostate cancer or some other cancer expressing elevated levels of hsp 27 in a therapeutically effective amount. The therapeutic agent is suitably formulated into a pharmaceutical composition which includes a pharmaceutically acceptable carrier, and packaged in dosage unit form. A preferred dosage unit form is an injectable dosage unit form.

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 amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified 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: Means for determining the presence of the risk of drug-induced granulocytopenia in a human is provided. A method for assessing the risk of drug-induced granulocytopenia, including detecting a polymorphism of the human insulin receptor substrate-2 gene of a subject, and determining the presence of the risk of drug-induced granulocytopenia of the subject by use of the genetic polymorphism as an index.

Abstract: Mutations located within the gene encoding the homeobox transcription factor, ENGRAILED 2 (EN2), have now been identified as molecular markers associated with susceptibility for autism and related disorders. Thus, the present invention relates to compositions in the form of diagnostic kits, primers and target sequences, for use in methods for determining the predisposition, the onset or the presence of autism spectrum disorder in a mammal. Moreover, therapeutic methods for treating a person inflicted with, or predisposed to, an autism spectrum disorder based upon modulating the level or activity of EN2 are also provided.

Abstract: Provided herein are novel methods for diagnosing ovarian and breast cancer risk in a Latin American/Hispanic population based on the presence of specific BRCA1 and/or BRCA2 mutations.

Abstract: Methods of amplifying nucleic acid are described. Primers on solid support, e.g. a population of beads, are employed. A population of nucleic acid template molecules, wherein the nucleic acid template molecules have been treated with bisulfite, is amplified so as to create loaded beads comprising amplified nucleic acid.

Abstract: The invention relates to an in vitro method for the detection of bacteria of the Salmonella spp. genus by means of a quantitative polymerase chain reaction using specific primers for the pathogen from DNA and RNA samples from the microorganism. The method is useful in the detection of viable and non-viable microorganisms of Salmonella spp. in environmental, clinical and food samples. Likewise, the invention also relates to a kit used for putting the method into practice.

Abstract: The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-) dominant genotypes of the genetic markers.