Abstract: Target-specific hybrid capture (TSHC) provides a nucleic acid detection method that is not only rapid and sensitive, but is also highly specific and capable of discriminating highly homologous nucleic acid target sequences. The method produces DNA:RNA hybrids which can be detected by a variety of methods.

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 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: 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: The invention provides a method of detecting a nucleic acid analyte. The method consists of (a) contacting a mixture of nucleic acid analytes under conditions sufficient for hybridization with a plurality of target specific nucleic acid probes each having a different specifier; (b) contacting the mixture under conditions sufficient for hybridization with a corresponding plurality of antigenedigits each having a unique label, the plurality of anti-genedigits having a diversity sufficient to uniquely hybridize to genedigits within the specifiers, and (c) uniquely detecting a hybridized complex between one or more analytes in the mixture, a target specific probe, and an anti-genedigit.

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: 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 present invention relates to new nucleic acid sequences derived from the ITS (Internal Transcribed Spacer) region, between the 16S and 23S rRNA genes, to be used for the specific detection and/or identification of Serratia species, in particular of Serratia marcescens, Serratia ficaria and/or Serratia fonticola, in a biological sample. The present invention relates also to a method for the specific detection and/or identification of Serratia species, in particular Serratia marcescens, Serratia ficaria and/or Serratia fonticola, using said new nucleic acid sequences derived from the ITS region. It relates also to nucleic acid primers to be used for the amplification of said spacer region of Serratia species in a sample.

Abstract: Compositions and methods for the rapid and sensitive detection of a carbapenemase in a sample are provided. The compositions include novel primer and probe compositions for use in detecting the presence of this enzyme in a sample, particularly using PCR methods. These primers and probe sets can be used in amplification methods (such as PCR, particularly quantitative PCR) and packaged into kits for use in amplification methods for the purpose of detecting carbapenemase in a test sample, particularly a patient sample, particularly a direct sample. Thus, in one embodiment, the present invention provides for novel oligonucleotide primers set forth in SEQ ID NOs:1, 2, 4, 5, 7, 8, 14, 15, 17, 18, and 20, and the novel oligonucleotide probe sequences set forth in SEQ ID NOs:3, 6, 9, 16, and 19. These sequences can be used in a method of detecting carbapenemase in a sample.

Abstract: The invention is directed to a Feline Picorna Virus, an isolated nucleic acid and amino acid sequences therefrom, and uses thereof.

Abstract: The invention concerns the isolation of nucleotide and peptide sequences in particular for differentiating, in diagnostic terms, an immunisation resulting from BCG vaccination of an infection by M. tuberculosis. Said sequences are either M. bovis BCG/M. bovis specific or M. tuberculosis specific. The invention also concerns a method for detecting said sequences, a method for detecting antibodies generated by the products expressing said sequences as well as kits for implementing said methods. Finally, the invention concerns novel vaccines.

Abstract: The invention provides a method for rapidly detecting a pathogen in fish comprising conducting loop-mediated isothermal amplification with a specific primer set and a nucleic acid in a test sample. If at least one amplification is carried out, the test sample comprises the pathogen in fish. The invention also provides a primer set, probe and kit for detecting a pathogen in fish.

Abstract: The invention pertains to novel proteins corresponding to Chrysosporium glycosyl hydrolases of families 7 and 10, exhibiting a minimum aminoacid identity of 70 and 75%, respectively, with the amino acid sequence of SEQ ID No's 2 and 4, and to a protein corresponding to a Chrysosporium glyceraldehyde phosphate dehydrogenase, exhibiting at least 86% amino acid identity with the partial amino acid sequence of SEQ ID No. 6. The invention further relates to nucleic acid sequences encoding these proteins, and especially to promoter sequences regulating the expression of the corresponding genes. The preferred host for expressing these genes is a fungus, especially a Chrysosporium strain.

Abstract: This novel form of multiplexing allows the user to probe for multiple targets and simultaneously identify a specific target. An example of solutions provided here comprises: providing one or more assay mixes for a number of targets (the number of assay mixes is less than the number of targets); providing a number of reference patterns (each of the reference patterns is associated with one of the targets); contacting each of a number of aliquots with one of the assay mixes; generating a result pattern, based on positive or negative results; and selecting the reference pattern most similar to the result pattern, to thereby detect the target. Differential multiplexing with pattern recognition may involve molecular or immunological techniques to identify one of many indicators of drug use, illness, disease, or medical condition.

Abstract: The present invention relates to a group of novel viral RNA regulatory genes, here identified as “viral genomic address messenger genes” or “VGAM genes”, and as “genomic address genes” or “GR” genes. VGAM genes selectively inhibit translation of known host target genes, and are believed to represent a novel pervasive viral attack mechanism. GR genes encode an operon-like cluster of VGAM genes. VGAM and viral GR genes may therefore be useful in diagnosing, preventing and treating viral disease. Several nucleic acid molecules are provided respectively encoding several VGAM genes, as are vectors and probes both comprising the nucleic acid molecules, and methods and systems for detecting VGAM genes, and for counteracting their activity.

Abstract: The present disclosure gives description of a method used for the detection and quantification of dengue viral infection caused by dengue virus using nucleic acids isolated from blood, plasma or serum samples by employing Oligonucleotide probes. The method employed here for detection is by Real time PCR. The instant disclosure also provides for primers, probes, PCR Reaction mixture and kit thereof.

Abstract: The present invention relates to a method for the specific detection and/or identification of Enterococcus species, in particular Enterococcus faecalis and/or Enterococcus faecium, using new nucleic acid sequences derived from the ITS (Internal Transcribed Spacer) region. The present invention relates also to said new nucleic acid sequences derived from the ITS region, between the 16S and 23S ribosomal ribonucleic acid (rRNA) or rRNA genes, to be used for the specific detection and/or identification of Enterococcus species, in particular of Enterococcus faecalis and/or Enterococcus faecium, in a biological sample. It relates also to nucleic acid primers to be used for the amplification of said spacer region of Enterococcus species in a sample.

Abstract: Disclosed is an isolated strain of a previously unknown Staphylococcus, Staphylococcus pseudolugdunensis. Also disclosed are the sequences of the S. pseudolugdunensis tuf gene and 16s rRNA and methods for distinguishing S. pseudolugdunensis from other staphylococcal species.

Abstract: This invention relates to novel nucleic acid-based probes and methods for detecting Plasmodium parasites in biological samples as well as detecting different Plasmodium parasites selectively from one another.

Abstract: RpoB gene sequences of various species of Acinetobacter bacteria, and a method of detection by molecular identification of various species of Acinetobacter bacteria using rpoB gene sequences.

Abstract: This invention relates to a rapid method for detection of Salmonella in a sample based on the presence of nucleic acid sequences, in particular, to a PCR-based method for detection, and to oligonucleotide molecules and reagents and kits useful therefore. In certain embodiments, the method is employed to detect Salmonella in a food or water sample. The present invention further relates to isolated polynucleotides, replication compositions, and kits for carrying out the method of the present invention.

Abstract: The invention provided Mucorales CotH polypeptides and encoding nucleic acid molecules. The Mucorales CotH polypeptides and encoding nucleic acids can be advantageously used to diagnose, treat or prevent fungal conditions, in particular mucormycosis.

Abstract: The present invention refers to the development of a Peptide Nucleic acid (PNA) probe for the detection of the Salmonella genus in different types of samples. PNA is a synthetic molecule analogue to DNA that, due to its physicochemical properties, allows a faster analysis with higher sensitivity than the DNA probes. These probes are combined with fluorescence in situ hybridization (FISH), a molecular biology technique that allows the direct visualization of the microorganism in the sample. The combination of these two technologies rendered the FISH procedure faster, simpler and more efficient. This probe can be applied to a great variety of samples such as blood, food, biopsies, feces, water and other clinical, environmental or agriculture and food industry samples. The present invention also includes the development of the kit of detection and respective procedure for the identification of Salmonella spp. using the above referred sample types.

Abstract: Compositions and methods for the detection of vancomycin-resistant pathogens using primers and/or probes to the vanA and vanB genes.

Abstract: The present invention relates, in general, to probes, methods, and kits used to determine the presence or absence of a microorganism in a sample. The probes, methods, and kits comprise at least one capture probe and/or at least one detector probe.

Abstract: The invention relates to a method of detecting pathogenic Legionella pneumophila strains by hybridizing genomic DNA of a sample suspected to contain Legionella to two or five specific sequence markers, as identified by MARKER NO. 1 through MARKER NO. 5 or homologues thereof. The invention further relates to a kit of parts comprising an array and reference materials for performing a method of the invention.

Abstract: The invention concerns a method for the extraction of nucleic acids from biological samples e.g. tissue material or sputum derived from human or animal species and the quantitative detection thereafter of said nucleic acids e.g. in terms of viral load, more specifically RSV viral load detection.

Abstract: This invention features systems and methods for the detection of analytes, and their use in the treatment and diagnosis of disease.

Abstract: This invention relates to a rapid method for detection and characterization of STEC bacteria based on the presence of nucleic acid sequences, in particular, to a PCR-based method for detection, and to oligonucleotide molecules and reagents and kits useful therefore. This method is preferably employed to detect STEC bacteria in a food or water sample, such as a beef enrichment. The present invention further relates to isolated polynucleotides, replication compositions, kits, and reagent tablets for carrying out the method of the present invention.

Abstract: The present invention relates to a probe for diagnosing HPV genotype and to a method of analyzing the same.

Abstract: Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

Abstract: A nucleic acid probe for classification of pathogenic bacterial species is capable of collectively detecting bacterial strains of the same species and differentially detecting them from other bacterial species. Any one of the base sequences of SEQ ID NO. 55 or a combination of at least two of them is used for detecting the gene of an infectious disease pathogenic bacterium.

Abstract: The invention provides methods and means for distinguishing FECV and FIPV, and methods and means for determining whether FIPV is present in a sample. Further provided are primers and probes for detecting FIPV specific nucleic acid sequences encoding a spike protein, antibodies for detecting a FIPV, and an immunogenic composition and use thereof for eliciting an immune response against a feline coronavirus, preferably a FIPV.

Abstract: The present invention relates to peptide nucleic acid (PNA) probes, PNA probe sets and methods for the analysis of certain Staphylococcus species optionally present in a sample. The invention further relates to diagnostic kits comprising such PNA probes or PNA probe sets.

Abstract: Isolated a Turkey Viral Hepatitis picomavirus-like viruses associated with Turkey viral hepatitis, and isolated nucleic acid sequences and polypeptides are disclosed. Antibodies against antigens from Turkey Viral Hepatitis picornavirus-like viruses, iRNAs which target nucleic acid sequences of the Turkey Viral Hepatitis picornavirus-like virus, methods for detecting the presence or absence of Turkey Viral Hepatitis picomavirus-like viruses in an animal, and immunogenic compositions for inducing an immune response against Turkey Viral Hepatitis picomavirus-like viruses in an animal are also disclosed.

Abstract: The present invention provides compositions, kits and methods for rapid identification and quantification of bacteria by molecular mass and base composition analysis.

Abstract: Disclosed are methods and compositions for conducting assays of samples utilizing polymerase chain reactions (“PCRs”) in the detection of serotypes of Chlamydia trachomatis capable of causing lymphogranuloma venereum (“LGV”). These assays take advantage of a deletion occurring in the cytotoxin gene locus specific to the L I, L II, and L serotypes. Each of these assays employs a first primer having a nucleotide sequence flanking one side of the deletion point and a second primer having a nucleotide sequence flanking the other side of the deletion point, wherein the first primer and the second primer are capable of hybridizing respectively to the plus strand and the minus strand of the genome of Chlamydia trachomatis during the PCR. Synthesis during the PCR of a sequence-specific amplicon containing this deletion point indicates that the sample contains nucleic acid specific to an LGV-causing serotype of Chlamydia trachomatis.

Abstract: The present invention relates to an oligonucleotide which is designed on the basis of a nucleotide sequence shown in SEQ ID NO: 1 or SEQ ID NO: 2 and hybridizes with the endogenous plasmid gene of Chlamydia trachomatis, oligonucleotide primer and probe for detecting Chlamydia trachomatis, the detection method of Chlamydia trachomatis using said primer and probe, and a primer for detecting Chlamydia trachomatis of said oligonucleotide or the use to a probe design.

Abstract: Described herein are primers and probes useful for the binding, detecting, differentiating, isolating, and sequencing of influenza A, influenza B and RSV viruses.

Abstract: The invention relates to a method of identifying a specific fungal species in patient tissue or body fluid. The method comprises the steps of extracting and recovering DNA of the fungal species from the patient tissue or body fluid, amplifying the DNA, hybridizing a probe to the DNA to specifically identify the fungal species, and specifically identifying the fungal species. The invention also relates to a method of identifying a mycotoxin in patient tissue or body fluid. The method comprises the steps of extracting and recovering the mycotoxin from the patient tissue or body fluid, contacting the mycotoxin with an antibody directed against the mycotoxin, and identifying the myocotoxin. Both of these methods can be used to determine if a patient is at risk for or has developed a disease state related to a fungal infection, and to develop an effective treatment regimen for the patient.

Abstract: Target-specific hybrid capture (TSHC) provides a nucleic acid detection method that is not only rapid and sensitive, but also highly specific and capable of discriminating highly homologous nucleic acid sequences. The method produces DNA/RNA hybrids which can be detected by a variety of methods.

Abstract: A method of genome analysis is provided. In certain embodiments, the method comprises: a) contacting a double-stranded genomic DNA with a site-specific nicking endonuclease that recognizes a sequence comprising a single nucleotide polymorphism (SNP), in which the endonuclease nicks the genomic DNA at a nick site only if a first allele of the SNP is present; b) denaturing the genomic sample; c) contacting the denatured genomic sample with an array comprising a first probe and a second probe, in which nicking results in less binding of the denatured sample to the first probe relative to a sample that is not nicked; and d) comparing the amount of hybridization to the first probe to the amount of hybridization to said second probe, in which decreased binding of the denatured genomic samples to the first probe relative to the second probe indicates that the first allele of the SNP is present.

Abstract: The present invention relates to methods for diagnosis or monitoring of viral infection by detecting the presence of transrenal viral nucleic acids or nucleic acids of viral origin in urine sample, with or without isolation of nucleic acids from a urine sample. The analysis of the nucleic acids is performed through hybridization of the nucleic acids with specific probes, or through a chain amplification reaction with specific primers. The methods are applicable to all viral pathogenic agents, including RNA, DNA, episomal, or integrated viruses.

Abstract: Disclosed are oligonucleotides useful in methods for determining whether a sample contains Cryptococcus neoformans, a causative agent for human cryptococcosis. These oligonucleotides, which have nucleotide sequences derived from a coding segment of the gene encoding the fungal specific transcription factor gene in Cryptococcus neoformans, are useful as forward and reverse primers for a polymerase chain reaction using nucleic acids from a biological sample as templates, and as probes for detecting any resultant amplicon. Detection of an amplicon indicates the sample contains Cryptococcus neoformans. Real-time PCR and detection using florescence resonance energy transfer is disclosed.

Abstract: Hybrid luminescent probes emit light of distinct wavelength ranges and intensities upon energy transfer from an in-common, acridinium ester chemiluminophore to a coupled luminophore. The probes include: (1) a target binding region with a base sequence that is substantially complementary to a portion of the target nucleic acid sequence; (2) an acridinium ester (AE) moiety attached to a first region flanking the target binding region; (3) a luminophore coupled to the AE moiety to allow energy transfer from an acridone moiety, produced by a chemical triggering of the AE moiety, to the luminophore; and (4) a quencher moiety attached to a second region flanking the target binding region, such that the first and second flanking regions are on the opposite sides of the target binding region. The probes are particularly useful in homogeneous assays for sensitive, multiplex quantification of nucleic acid target sequences without prior enzymatic amplification.

Abstract: Nucleic sequences of plasmid origin are isolated from bacteria of the enterohaemorrhagic Escherichia coli group (EHEC) and used for the identification of EHEC(s), especially those possessing the genes encoding the virulence factors enterohaemolysin and intimin, and more particularly the specific detection of serotype O157:H7, and in detection kits.

Abstract: A multiplex PCR assay for simultaneously detecting biological threat agents whose genome is DNA or RNA, by using computational tools to identify a specific target sequence which is unique to a specific genus or species of organism and is also a conserved sequence within that group, selecting specific primer sets, creating a probe to label the target nucleic acid, extracting the target nucleic acid from a sample, amplifying the targeted nucleic acid to detectible levels and reading the presence or absence of the target nucleic acid simultaneously from all threat agents.

Abstract: The invention provides methods to detect C. difficile in biological samples using real-time PCR. Primers and probes for the detection of C. difficile are provided by the invention. Articles of manufacture containing such primers and probes for detecting C. difficile are further provided by the invention.

Abstract: The present invention relates to an isolated novel virus causing Severe Acute Respiratory Syndrome (SARS) in humans (“hSARS virus”). The hSARS virus is identified to be morphologically and phylogenetically similar to known member of Coronaviridae. The present invention provides the complete genomic sequence of the hSARS virus. Furthermore, the invention provides the nucleic acids and peptides encoded by and/or derived from the hSARS virus and their use in diagnostic methods and therapeutic methods, including vaccines. In addition, the invention provides chimeric or recombinant viruses encoded by said nucleotide sequences and antibodies immunospecific to the polypeptides encoded by the nucleotide sequences.

Abstract: The invention concerns the isolation of nucleotide and peptide sequences in particular for differentiating, in diagnostic terms, an immunization resulting from BCG vaccination of an infection by M. tuberculosis. Said sequences are either M. bovis BCG/M. bovis specific or M. tuberculosis specific. The invention also concerns a method for detecting said sequences, a method for detecting antibodies generated by the products expressing said sequences as well as kits for implementing said methods. Finally, the invention concerns novel vaccines.