Abstract: The present invention relates to a method for detection and/or genetic analysis of HBV in a biological sample, comprising hybridizing the polynucleic acids of the sample with a combination of at least two nucleotide probes, with said combination hybridizing specifically to a mutant target sequence chosen from the HBV RT pol gene region and/or to a mutant target sequence chosen from the HBV preCore region and/or to a mutant target sequence chosen from the HBsAg region of HBV and/or to a HBV genotype-specific target sequence, with said target sequences being chosen from FIG.

Abstract: The invention relates to human endogenous retrovirus env (HERV-WL) polypeptides, nucleotide sequences, HERV-WL antibodies, methods to detect cancer, and methods to determine the effectiveness of the treatment of cancer.

Abstract: The present invention is directed to devices, systems and methods that enable the detection of low copy numbers of bacterial polynucleotides in a sample without having to use multiple species specific primer sequences.

Abstract: The invention provides a novel strain of HIV-2 capable of causing immunodeficiency. The invention also provides compositions comprising the nucleic acids and polypeptides characteristic of this HIV-2 virus, antibodies specific for this HIV-2 virus, methods of using these compositions, and methods of detecting HIV-2 virus.

Abstract: The present invention relates to a genetically modified bacterium of the species Listeria monocytogenes, wherein the genomic locus of the transcriptional factor PrfA has been deleted, characterized in that it comprises on genomic level an artificial sequence that acts as internal amplification control, the use of this bacterium as well as a method for detecting and determining qualitatively and/or quantitatively the occurrence of wild type Listeria monocytogenes in a sample suspected to be contaminated with said micro-organism and a kit.

Abstract: The invention relates to a method of detecting Legionella pneumophila strains by hybridizing genomic DNA of a sample suspected to contain Legionella to one or morespecific sequence markers, as identified by SEQ ID NO:1 through SEQ ID NO:10 or homologues thereof or in an immunoassay with antibodies specifically recognizing the amino acid sequence of SEQ ID NO: 11 and/or 12. The invention further relates to a kit of parts comprising an array and reference materials for performing a method of the invention.

Abstract: Method for the detection of a target sequence comprising ligating two probes when annealed adjacent to the target sequence, hybridization of a compound primer to the ligated probes and after elongation of the compound primer, amplifying the elongated compound primer from primers annealing to primer binding sites provided in the compound primer and one of the probes to produce detectably amplicons.

Abstract: Probes and methods are described for detecting polymorphisms, including short tandem repeats, in a target nucleotide sequence. The probes include first and second regions separated by a linker sequence, with the first and second regions having discrete melting temperatures with their respective target sequences. In a first embodiment, the first and second regions are both reporter sequences; in a second embodiment, one region is an anchor sequence while the other is a reporter sequence.

Abstract: Disclosed herein are methods and materials for facilitating the detection of nucleic acid analytes of interest. Specifically exemplified herein are methods for detecting mycobacterial microorganisms, namely Mycobacterium avium spp. paratuberculosis. Also disclosed is new hybridizing magnetic relaxation nanosensor (hMRS) particularly adapted to detect a target nucleic acid analyte of interest.

Abstract: The invention relates to a method of identifying an Aspergillus terreus or an Aspergillus niger fungal species in patient tissue or body fluid and to primers and probes for use in such a method.

Abstract: Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several Listeria species in a sample, particularly in a food or environmental sample. Embodiments of the disclosure may also be used to detect one or more species or strains of Listeria from each other, for example L. grayi may be detected independently of other Listeria spp. Some embodiments also describe a duplexed assay that can detect L. monocytogenes, L. innocua, L. welshimeri, L. seelgeri, L. marthii (formerly incertae-sedis), L. ivanovii, and L. grayi. Kits for detection of Listeria are also described. In some embodiments, methods and kits of the disclosure may comprise a TAQMAN® assay. In some embodiments, 0.2-2 cfu of Listeria spp. are detected using the compositions, methods and kits after a 24-28 hour enrichment period.

Abstract: Provided are an oligonucleotide which realizes specific and highly sensitive detection of toxigenic C. difficile, and a method for detecting toxigenic C. difficile, the method employing the oligonucleotide. 1) A primer pair containing an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 1, and an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 2; or a primer pair having complementary sequences to the nucleotide sequences. 2) A primer pair containing an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 4, and an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 5; or a primer pair having complementary sequences to the nucleotide sequences.

Abstract: Oligonucleotides useful for determining the presence of Trichomonas vaginalis in a test sample.

Abstract: The various embodiments of the present disclosure relate generally to single molecule sensitive probes for detecting RNA, and more particularly to multivalent fluorescent probes for detecting a single molecule of RNA in a cell. The present invention includes a RNA imaging probe comprising: a multivalent core comprising a plurality of attachment sites; a plurality of RNA/DNA chimeric oligonucleotides having a specificity for a target RNA, wherein a RNA/DNA chimeric oligonucleotide is bound to an attachment site of the multivalent core; and a plurality of fluorophores, wherein a fluorophore is bound to the RNA/DNA chimeric oligonucleotide.

Abstract: The present invention relates to a rapid detection of microbial-associated nuclease activity with chemically modified nuclease (e.g., ribonuclease) substrates, and probes and compositions useful in detection assays. Accordingly, in certain embodiments, the present invention provides a probe for detecting a microbial endonuclease comprising a substrate oligonucleotide of 2-30 nucleotides in length, a fluorescence-reporter group operably linked to the oligonucleotide, and a fluorescence-quencher group operably linked to the oligonucleotide. The fluorescence-reporter group and the fluorescence-quencher group are separated by at least one RNAse-cleavable residue, e.g., RNA base.

Abstract: Methods and compositions are disclosed for detection of probiotic bacteria strains intentionally provided to animals comprising: providing an animal with a known amount or number of probiotic bacteria; following a pre-determined time, obtaining a biological sample suspected of comprising the inoculated probiotic bacteria from the animal; and quantitatively detecting the amount of probiotic bacteria in the biological sample.

Abstract: The invention provides a group of nucleic acid fragments, shown in the sequence listing, for prevention of HIV infection or AIDS and the usage thereof. In the invention, a series of RNA fragments, which are highly homogenous to all the published HIV gene sequences, were obtained by homology compare. The double-stranded RNA (dsRNA) derived from these fragments can effectively inhibit the expression of the HIV genes. The RNA transcribed by plasmid, also can suppress the expression of the HIV in the cell. After the adenovirus or associated virus which carry DNA corresponding above RNA infect the cell, the transcription dsRNA can inhibit the expression of the HIV genes.

Abstract: There is provided a method for detecting M. genitalium nucleic acid in a sample, comprising: (i) amplifying a nucleic acid sequence comprising a fragment of SEQ ID NO: 1 (Mg219 gene); and (ii) detecting said amplified nucleic acid sequence.

Abstract: The present invention relates to compositions, methods, and kits for determining the presence or absence of HAV in a sample.

Abstract: A process for detecting Neisseria meningitidis nucleic acid in a sample is provided including producing an amplification product by amplifying Neisseria meningitidis nucleotide sequence of the sodC gene or mRNA using a forward primer of SEQ ID NO: 1, and a reverse primer of SEQ ID NO: 2, and detecting the amplification product to detect Neisseria meningitidis in the sample. Also provided are reagents and methods for detecting and distinguishing Neisseria meningitidis from other infectious agents. A kit is provided for detecting and quantifying Neisseria meningitidis in a sample.

Abstract: Provided is a novel lactic acid bacterium strain which is capable of suppressing production of volatile sulfur compounds by oral bacteria, has no cariogenicity and no causative role in infective endocarditis, and is safe in an oral cavity, and provided is an agent for preventing, improving and/or treating oral diseases and discomforts by use of the bacterial strain.

Abstract: A method of detecting a fungus belonging to genus Geosmithia, including identifying a fungus belonging to genus Geosmithia using a nucleic acid represented by the nucleotide sequence defined in the following (a) or (b): (a) a partial nucleotide sequence of ?-tubulin gene shown in any one of SEQ ID NOS: 1 to 3, or a complementary sequence thereof; (b) a nucleotide sequence including deletion, substitution, insertion or addition of one or several nucleotide(s) in the nucleotide sequence shown in any one of SEQ ID NOS: 1 to 3, or a complementary sequence thereof.

Abstract: The present invention is directed to the discovery of single nucleotide polymorphisms (SNPs) in the presence of metronidazole-resistant Trichomonas vaginalis. The presence of G76C, C213G, or C318A (SNP) in tvntr 4 or the presence of A238T, G427C, or T476C (SNP) in tvntr6 provides a reliable biomarker for the presence of metronidazole-resistant Trichomonas vaginalis. The present invention further provides reagents used for detecting the SNPs to screen subjects for metronidazole resistance in Trichomonas vaginalis.

Abstract: The invention relates to methods for the identification of HIV-1 infected subjects capable of controlling viral load based on the determination of the expression levels of several miRNAs. In addition, the invention also relates to methods for controlling HIV infection by using some of the differentially expressed miRNAs or polynucleotides encoding said miRNAs, as well as to compositions comprising a miRNA or a polynucleotide encoding said miRNA and an anti-HIV agent.

Abstract: The present invention relates to polynucleotides enabling the rapid, simple and specific detection of Group B Streptococcus highly-virulent ST-17 clones. The present invention also relates to the polypeptides encoded by the polynucleotides, as well as to antibodies directed or raised against the polypeptides. The present invention also relates to kits and methods for the specific detection of Group B Streptococcus highly-virulent ST-17 clones, using the polynucleotides, the polypeptides or the antibodies according to the invention.

Abstract: A probe, a set of probes, and a probe carrier on which the probe or the set of probes is immobilized, are provided for classification of fungus species. The probe or the set of probes is capable of collectively detecting fungus of the same species and distinguishingly detecting those fungus from fungus of other species. The probe is an oligonucleotide probe for detecting a pathogenic fungus DNA and includes at least one of base sequences of SEQ ID NOS. 1 to 4 and mutated sequences thereof.

Abstract: The invention relates to an aptamer that binds to protein A, G or L, protein A-, G- or L-containing substances, and also to protein A-, G- or L-containing microorganisms, in particular Staphylococcus aureus, Streptococcus or Peptostreptococcus, methods for detection and enrichment of protein A, G or L, protein A-, G- or L-containing substances or protein A-, G- or L-containing microorganisms in which the aptamer is used, and also a kit, a biosensor, a lateral flow assay device and a measuring instrument which contain such an aptamer and can be used in said methods.

Abstract: Replicons of genotype 6 hepatitis C virus (HCV) are provided. These replicons contain adaptive mutations giving rise to the HCV's capability to replicate in vitro. Methods of preparing genotype 6 replicons and methods of using these replicons to screen antiviral agents are also provided.

Abstract: Methods of detecting influenza, including differentiating between type and subtype are disclosed, for example to detect, type, and/or subtype an influenza infection. A sample suspected of containing a nucleic acid of an influenza virus, is screened for the presence or absence of that nucleic acid. The presence of the influenza virus nucleic acid indicates the presence of influenza virus. Determining whether the influenza virus nucleic acid is present in the sample can be accomplished by detecting hybridization between an influenza specific probe, influenza type specific probe, and/or subtype specific probe and an influenza nucleic acid. Probes and primers for the detection, typing and/or subtyping of influenza virus are also disclosed. Kits and arrays that contain the disclosed probes and/or primers also are disclosed.

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 present invention provides a standardized method and a kit for an accurate quantification of HAV in clinical and food samples. The general approach is based on the use of several controls to measure the efficiency of those critical steps of the quantification: the nucleic acids extraction and the RT-PCR reactions. The kit comprises: a Mengo virus mutant strain with the same growth properties than those of the wild-type Mengo virus and with no pathogenic capacity; a single stranded RNA molecule corresponding to a fragment of the HAV genome; primers that specifically bind to regions of the 5? non coding region of the HAV genome; a detectable labeled probe that specifically binds to the amplimer resulting from the RT-PCR; and an appropriate molecule to generate an standard curve for the quantification of HAV.

Abstract: The present teachings provide methods, compositions, and kits for synthesizing and sequencing nucleic acids. In some embodiments, reversible di-nucleotide compounds are employed along with cleaving reactions that remove a label and a blocking moiety. Improved sequencing efficiency is achieved by the rapid polymerase-mediated incorporation of reversible di-nucleotide compounds. In some embodiments, the di-nucleotides do not contain conventional nucleotide triphosphates, but rather employ amino acid phosphoramidate nucleotides (AAPNs).

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

Abstract: The present invention relates to compositions, methods, and kits for determining the presence or absence of HIV in a sample, in particular for determining HIV-1 group M, HIV-1 group O, and/or HIV-2, in particular for simultaneous determining of HIV-1 group M, HIV-1 group O, and HIV-2.

Abstract: Polynucleotides useful for detecting Chlamydia trachomatis and/or Neisseria gonorrhoeae in a test sample, kits, a nucleic acid amplification method and detection method including the same.

Abstract: The characterization of a new strain of human rhinovirus of genetic group C (HRV-C) as well as methods and kits for detecting the presence of HRV-C by PCR amplification are provided.

Abstract: Disclosed herein are PNA probes, or PNA probe sets and their use as well as kits useful for the analysis of certain Oxalobacter species and/or strain(s) present in a sample of interest. Probe sequences may sequence that are at least about 86% identical to the nucleobase sequence or complement thereof selected from the following sequences: GACAATGTAGAGTTGACT (SED ID NO. 1); caggatggtcagaagttc (SEQ ID NO. 2); CCGGTTACATCGAAGGA (SEQ ID NO. 3); and AATGTAGAGTTG ACT (SEQ ID NO. 4).

Abstract: The current disclosure generally relates to the field of saxitoxins and the identification of microorganisms capable of producing them. In particular, the saxitoxin A (sxtA) gene comprising catalytic domain sequences saxitoxin A1 (sxtA1) and saxitoxin A4 (sxtA4) is identified in a number of dinoflagellate species. The disclosure relates to methods of detection of saxitoxin-producing dinoflagellates by amplification and detection of the sxtA gene (in particular by PCR) and kits and primers for use in the method are also disclosed. Saxitoxin-producing dinoflagellate genera detected by the method include Alexandrium, Pyrodinium or Gymnodinium.

Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.

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 generally relates to a molecular test of Influenza A, Influenza B, Respiratory Syncytial Virus A, and Respiratory Syncytial Virus B in order to identify patients with a viral infection. Accordingly methods and compositions are disclosed to determine the presence or absence of a viral pathogen in a sample containing one or more target nucleic acids from the M gene of Influenza A, Influenza B, Respiratory Syncytial Virus A, and/or Respiratory Syncytial Virus B.

Abstract: The invention provides siRNA compositions that interfere with viral replication in respiratory viral infections, including respiratory syncytial virus and avian influenza A, including the H5N1 strain. The invention further provides uses of the siRNA compositions to inhibit expression of viral genes in respiratory virus-infected cells, and to uses in the treatment of respiratory virus infections in a subject. Generally the invention provides polynucleotide that includes a first nucleotide sequence of 15 to 30 bases that targets the genome of a respiratory syncytial virus or an influenza A virus, a complement thereof, a double stranded polynucleotide or a hairpin polynucleotide. Additionally the invention provides vectors, cells and pharmaceutical compositions containing siRNA sequences.

Abstract: New polymorphisms in the nucleic acid sequences of the DNA polymerase/reverse transcriptase open reading frame and viral surface antigen open reading frame of the hepatitis B virus are reported. In particular, the present invention relates to the mutation YMDD?YSDD in the HBV reverse transcriptase domain and to the W196V mutation in the small HBV viral surface antigen. Said polymorphisms are affecting the detection of drug resistance mutations by genotypic methods and diagnostic kits based thereon. The present invention relates to methods and diagnostic kits for detection of a HBV virus comprising said nucleic acid polymorphisms. In particular, those methods utilizing oligonucleotides capable of hybridizing to said HBV nucleic acid polymorphisms are envisaged.

Abstract: Methods for the rapid detection of the presence or absence of Clostridium difficile in a biological or nonbiological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes, and kits are provided that are designed for the detection of Clostridium difficile.

Abstract: Disclosed herein is a hairpin probe for detecting a target pathogenic microorganism in a sample. The hairpin probe includes a microbead and an oligonucleotide having its 3?-end coupled to the microbead. The oligonucleotide includes, from 5? to 3?, a Tag sequence hybridizable to a specific identification sequence of the pathogenic microorganism, an internal control sequence having at least four words each having 4 nucleotides with a 75% AT-content, an anti-Tag sequence being a reverse complement of the Tag sequence, and a tail having at least two consecutive thymidine residues. The Tag and anti-Tag sequences are operable to form a stem of the hairpin probe with the internal control sequence being a loop. Also disclosed herein are, a kit including the hairpin probe and a method for using the kit in the detection of a target pathogenic microorganism.

Abstract: Described are compositions, methods and kits for detection and/or differential detection of serovars of Salmonella enterica subsp. enterica serovar such as S. Heidelberg and S. Hadar in samples. Some embodiments relate to multiplex amplification based molecular assays.

Abstract: The present invention discloses a method for the treatment of Flaviviridae infection that includes the administration of a 2?-branched nucleoside, or a pharmaceutically acceptable prodrug and/or salt thereof, to a human in need of therapy in combination or alternation with a drug that directly or indirectly induces a mutation in the viral genome at a location other than a mutation of a nucleotide that results in a change from serine to a different amino acid in the highly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA polymerase region, or is associated with such a mutation. The invention also includes a method to detect a mutant strain of Flaviviridae and a method for its treatment.

Abstract: A method for detecting the bacteria Staphylococcus epidermidis includes isolating DNA from a biological sample suspected of containing the bacteria. The method further includes subjecting the DNA to a Polymerase Chain Reaction (PCR) amplification method utilizing at least one primer derived from a cell division gene. The method may further include characterizing an indicator of a Staphylococcus epidermidis phenotype of interest. The method additionally includes detecting the bacterium Staphylococcus epidermidis by visualizing the product of the polymerase chain reaction. Amplification products of cell division genes and virulence genes are also provided.

Abstract: The invention is directed to novel reductive dehalogenase genes encoding for reductive dehalogenases, which are capable of dehalogenating halogenated organic compounds and may be useful for environmental assessment and monitoring, and in the bioremediation of pollutants. In particular, the invention provides isolated polynucleotides of novel reductive dehalogenase genes dcpA and dcpB and fragments thereof as well as isolated polypeptides encoding the DcpA and DcpB proteins or fragments thereof. The invention is also directed to methods of identifying and/or quantifying dechlorinating bacterial organisms or polynucleotides encoding a reductive dehalogenase, such as the dcpA or dcpB polynucleotides or fragments thereof, in a sample.

Abstract: The invention provides isolated polynucleotide molecules that comprise a DNA sequence encoding an infectious RNA sequence encoding a genetically-modified North American PRRS virus, methods to make it and related polypeptides, polynucleotides, and various components. Vaccines comprising the genetically modified virus and polynucleotides and a diagnostic kit to distinguish between naturally infected and vaccinated animals are also provided.