Abstract: Described are single-stranded new sequences of TT viruses, rearranged TTV sequences and hybrid molecules of a specific TT virus sequence and host cell DNA that are capable of replicating autonomously for use in diagnosis, prevention and treatment of diseases like cancer and autoimmunity. In addition, it relates to the use of such molecules as gene vectors and artificial chromosomes.

Abstract: Disclosed is a method for determining the presence of Mycobacterium avium complex nucleic acids in a biological sample. In particular, the IS1245 gene of M. avium and the DT1 gene of M. intracellulare are detected, preferably following amplification. In addition, the method distinguishes between species of M. avium and M. intracellulare. Also described are oligonucleotides that can be used as primers to amplify target genes such as IS1245 and DT1 genes and as probes as well as kits containing the oligonucleotides.

Abstract: The use of the Ayg1 gene or an RNA transcript of the Ayg1 gene or fragments thereof as target regions in a diagnostic assay for the eukaryotic organism Aspergillus fumigatus species is described. The unique sequence of the Ayg1 gene in Aspergillus fumigatus provides the basis of nucleic acid diagnostic test for the identification of the pathogen at a the molecular level.

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: An infectious etiologic agent detection probe set which detects an infectious etiologic agent gene, includes a plurality of kinds of probes including oligonucleotide having base sequences selected from each of a plurality of groups selected from a first group including base sequences of SEQ ID Nos. 1 to 14 and complementary sequences thereof, a second group including base sequences of SEQ ID Nos. 15 to 24 and complementary sequences thereof, a third group including base sequences of SEQ ID Nos. 25 to 36 and complementary sequences thereof, a fourth group including base sequences of SEQ ID Nos. 37 to 47 and complementary sequences thereof, a fifth group including base sequences of SEQ ID Nos. 48 to 57 and complementary sequences thereof, a sixth group including base sequences of SEQ ID Nos. 58 to 68 and complementary sequences thereof, a seventh group including base sequences of SEQ ID Nos. 69 to 77 and complementary sequences thereof, an eighth group including base sequences of SEQ ID Nos.

Abstract: The present disclosure gives description of a method used for the detection and quantification of malarial infection caused either by Plasmodium falciparum or Plasmodium vivax using nucleic acids isolated from blood samples by employing Oligonucleotide probes. The method employed here for detection is by Real time PCR.

Abstract: The present disclosure provides a method for the detection and quantification of Hepatitis B Virus. It discloses oligonucleotide probes set forth in SEQ ID Nos. 1 and 2 for detection of Hepatitis B Virus along with respective primers [sense and antisense] set forth in SEQ ID Nos. 3, 4, 5 and 6. It also provides a PCR reaction mixture for detection of Hepatitis B Virus and a kit for detection of HBV comprising said mixture along with an instruction package.

Abstract: The invention relates to identification of novel sequences associated with cervical cancer, probes and kits for the identification of said sequences, and vaccines suitable for vaccination against new cancer causing HPV types.

Abstract: The present invention provides compositions and methods for the detection and characterization of HCV sequences. More particularly, the present invention provides compositions, methods and kits for using invasive cleavage structure assays (e.g. the INVADER assay) to screen nucleic acid samples, e.g., from patients, to determine HCV genotype.

Abstract: Provided herein are sequences of the genomes and encoded proteins of a new human parvovirus, Bocavirus-2, and variants thereof. Also provided are methods of detecting the Bocavirus-2 and diagnosing Bocavirus-2 infection, methods of treating or preventing Bocavirus-2 infection, and methods for identifying anti-Bocavirus-2 compounds.

Abstract: The present invention relates to oligonucleotide primers and primer sets that can be used to identify the bacterial pathogen Acidovorax avenae subsp. citrulli in a test sample.

Abstract: The invention relates to a method of determining the strain or strains of yeast in a sample, comprising: obtaining and screening nucleic acid from yeast for target sequences comprises all or part of a gene, or a flanking region associated with a gene, in the yeast mitochondrial DNA; and determining from the results of the screen the yeast strain or strains in the sample. Also provided is a method of determining the genetic stability of a yeast strain in a sample, wherein one target sequences in the nucleic acid comprises all or part of a gene, or a flanking region associated with a gene, in the yeast mitochondrial DNA or all or part of a gene, or a flanking region associated with a gene, located in the subtelomeric region of a chromosome; and determining from the results of the screen if the yeast strain is genetically stable.

Abstract: Binary probe and clamp compositions conduct methods for target hybridization detection. Where the probe is a substrate for exonuclease cleavage, the composition provides quantitation and detection of PCR products, by real-time and end-point measurements. Where the probe is an amplification primer, the composition provides an improved method for labelling and detection of PCR products. Probes and clamps may be labelled with fluorescent dyes, quenchers, hybridization-stabilizing moieties, chemiluminescent dyes, and affinity ligands. Clamps may be nucleic acid analogs, such as 2-aminoethylglycine PNA.

Abstract: Methods for detecting strains of Clostridium difficile (e.g. toxigenic and non-toxigenic) in a specimen are disclosed. Oligonucleotide primer pairs based on the sequences of multiple loci of the bacteria are disclosed. In one application, up to five loci in the genomic DNA sequences of Clostridium difficile were amplified. Two fragments of C. difficile were amplified from each locus, wherein a second fragment was an internal fragment of the first fragment.

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

Abstract: A method for determining whether a human individual is or has been infected with Neisseria gonorrhoeae, is provided. The method detects a Neisseria gonorrhoeae, porA nucleic acid fragment obtained from a biological sample. The method includes subjecting the biological sample to nucleic acid sequence amplification using primers having respective nucleotide sequences according to SEQ ID NO:1 and SEQ ID NO:2, to thereby produce a porA Neisseria gonorrhoeae, amplification product. The amplification product is detected by fluorescence resonance energy transfer using oligonucleotides having respective nucleotide sequences according to SEQ ID NO:3 which has a donor fluorophore and SEQ ID NO:4, which has an acceptor fluorophore.

Abstract: Compositions and methods are provided that relate to the bioremediation of chlorinated ethenes, particularly the bioremediation of vinyl chloride by Dehalococcoides-like organisms. An isolated strain of bacteria, Dehalococcoides sp. strain VS, that metabolizes vinyl chloride is provided; the genetic sequence of the enzyme responsible for vinyl chloride dehalogenation; methods of assessing the capability of endogenous organisms at an environmental site to metabolize vinyl chloride; and a method of using the strains of the invention for bioremediation.

Abstract: The present invention relates to Human Immunodeficiency Virus-1 (HIV-1) Group P of the strain designated 06CMU14788 and fragments thereof, primers which are derived from HIV-1 Group P, immunogenic regions thereof, immunoassays and nucleic acid based assays for the detection of Human Immunodeficiency Virus (HIV) that employ said HIV-1 Group P or fragments thereof and therapeutic compositions containing said HIV-1 Group P or fragments thereof.

Abstract: Provided herein are vaccine compositions for control of Trypanosoma cruzi infection and Chagas disease. The compositions comprise plasmids encoding o GPI-anchored genes ASP-2, TcG-1, TcG2 and TcG4 from Trypanosoma cruzi; plasmids encoding cytokines IL12 and GM-CSF; and plasmids encoding a gene expression system. Certain vaccine compositions comprise recombinant proteins, selected from TcG-1, TcG2 and TcG4 from Trypanosoma cruzi. In another vaccination strategy, the recombinant proteins are replaced by lysates comprising Trypanosoma rangeli cells. Further provided herein are diagnosis compositions comprising 1) recombinant proteins, selected from TcG-1, TcG2 and TcG4 from Trypanosoma cruzi; 2) antibodies that specifically binds the TcG-1, TcG2 and TcG4 proteins; 3) sense and antisense polynucleotide sequences that encode the TcG-1, TcG2 and TcG4 proteins. Said compositions can be used in diagnosing and/or evaluating efficacy of treatments against Trypanosoma cruzi infection.

Abstract: This invention provides compositions and methods for detecting HPV in a sample. This invention also provides related kits, systems, and computers.

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: Stabilized forms of gp120 polypeptide, nucleic acids encoding these stabilized forms, vectors comprising these nucleic acids, and methods of using these polypeptides, nucleic acids, vectors and host cells are disclosed. Crystal structures and computer systems including atomic coordinates for stabilized forms of gp120, and gp120 with an extended V3 loop, and methods of using these structures and computer systems are also disclosed.

Abstract: Described herein are oligonucleotides useful for detecting, isolating, amplifying, quantitating, monitoring, screening and sequencing the C. Difficile genes encoding toxin B, and/or toxin A, and/or binary toxin, and methods of using the described oligonucleotides.

Abstract: Methods for identifying forensic samples using panels of markers and gene expression profiling, including without limitation, mRNA profiling, miRNA profiling, or both, are disclosed. Panels of markers for identifying certain tissue samples and certain body fluid samples are also disclosed. Kits for expediting performance of certain of the disclosed methods are provided.

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 2 and mutated sequences thereof.

Abstract: Disclosed is are methods for identifying a nucleic acid in a sample. In one example, the method includes: (a) contacting the nucleic acid in the sample with an oligonucleotide that is specific for the nucleic acid in the sample and that is labeled with at least a first fluorescent dye; (b) contacting the nucleic acid in the sample with a second fluorescent dye that is different from the first fluorescent dye, such that the second fluorescent dye interacts with the nucleic acid; (c) amplifying the nucleic acid if present in the sample; and (d) detecting the nucleic acid if present in the sample by observing fluorescence from the first fluorescent dye after the oligonucleotide hybridizes to the amplified nucleic acid and determining the melting temperature of the amplified nucleic acid by measuring the fluorescence of the second fluorescent dye. The second fluorescent dye may include a fluorescent intercalating agent.

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 2 and mutated sequences thereof.

Abstract: This invention relates to methods for molecular detection, particularly to methods utilizing target-specific molecular probes. In exemplary embodiments, target-specific molecular probes include single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) aptamers. In general, the molecular probe may bind with relatively high specificity to a given target. In one aspect, a method for molecular detection comprises a molecular probe paired to a reporter molecule wherein the molecular probe impairs the amplification of the reporter molecule in the absence of the target molecule.

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: There is provided a method and reagents for detecting S. enterica subsp. IIIa and/or IIIb in a sample, the method comprising: (a) contacting the sample with a pair of forward and reverse oligonucleotide primers, wherein said forward and reverse primers hybridise to target nucleic acid sequences located within the lacZ gene of S. enterica subsp. III, or the complement thereof; (b) extending said forward and reverse primers to generate an amplification product; and (c) detecting the amplification product. There is also provided a method a reagents for detecting S. enterica subsp. I in a sample, the method comprising: (a) contacting the sample with a pair of forward and reverse oligonucleotide primers, wherein said forward and reverse primers hybridise to target nucleic acid sequences located within the hilA gene of S. enterica subsp. I, or the complement thereof; (b) extending said forward and reverse primers to generate an amplification product; and (c) detecting the amplification product.

Abstract: The present invention relates to a method and a kit for detecting Mycobacterium tuberculosis (MTB) or Nontuberculous mycobacteria (NTM) of patients. The present invention also relates to primers and probes used to detect Mycobacterium tuberculosis (MTB) or Nontuberculous mycobacteria (NTM) by performing PCR.

Abstract: Disclosed are oligonucleotides useful in methods for determining whether a sample contains Borrelia afzelii, a spirochete which is a causative agent of Lyme disease in humans. These oligonucleotides, which have nucleotide sequences derived from a coding segment of the gene encoding the p24 gene for the outer surface protein of Borrelia afzelii, 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 Borrelia afzelii. Real-time PCR and detection using florescence resonance energy transfer is disclosed.

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 3 and mutated sequences thereof.

Abstract: The invention relates to a method for determining the resistance status of fungi and yeasts in a body sample of a patient suspected of having an invasive infection, comprising the steps of isolating DNA from a body sample of the patient, identifying mutations in a gene of the fungus or yeast, and correlating the resistance status of the fungus or yeast to the mutations found, wherein the body sample is blood or a blood derivative or a sample of an organ, and is in particular serum. Suitably, the method is performed in closed-tube format. The method of the invention is particularly suitable when the fungus of which the resistance status is to be determined is Aspergillus fumigatus.

Abstract: There is disclosed a method for determining azole resistance in Candida glabrata. A biological sample containing Candida glabrata is obtained and a normalized mRNA level of CDR1 gene is determined using qRT-PCR. Using a microbroth dilution assay conducted at azole concentrations of about 2-8 ?g/mL, a susceptible isolate of Candida glabrata is obtained. A qRT-PCR assay is employed on the susceptible isolate and an average mRNA level of CDR1 is obtained. A fold-change value for CDR1 is obtained by comparing the CDR1 mRNA level of the biological sample with that of the average mRNA level. A ?2-fold change value is indicative of an azole resistance in Candida glabrata. The present method provides a qRT-PCR assay for azole resistance that has a sensitivity of ?90% and a specificity of ?90%.

Abstract: The current invention relates to a diagnostic kit for a bacterial species and/or fungal and/or yeast species comprising at least one oligonucleotide probe capable of binding to at least a portion of the LepA and/or Guf1 genes or its corresponding mRNA.

Abstract: The current invention relates to a diagnostic kit for a yeast or fungal species comprising at least one oligonucleotide probe capable of binding to at least a portion of the eIF2y gene or its corresponding mRNA.

Abstract: The present invention relates to nucleic acid primers and probes to detect one or more fungal and yeast species. More specifically the invention relates to the P2, P2A and P2B gene sequences (also known as 60S acidic ribosomal protein P2, RLA-2-ASPFU, Allergen ASP f8 or Afp2), the corresponding RNA, specific probes, primers and oligonucleotides related thereto and their use in diagnostic assays to detect and/or discriminate fungal and yeast species.

Abstract: The invention relates to the SWI5 gene, the corresponding RNA, specific probes, primers and oligonucleotides related thereto and their use in diagnostic assays to detect and/or discriminate between fungal and yeast species.

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 3 and mutated sequences thereof.

Abstract: The invention concerns a method for identifying and/or cloning nucleic acid regions representing qualitative differences associated with alternative splicing events and/or with insertions, deletions located in RNA transcribed genome regions, between two physiological situations, comprising either hybridization of RNA derived from the test situation with cDNA's derived from the reference situation and/or reciprocally, or double-strand hybridization of cDNA derived from the test situation with cDNA's derived from the reference situation; and identifying and/or cloning nucleic acids representing qualitative differences. The invention also concerns compositions or banks of nucleic acids representing qualitative differences between two physiological situations, obtainable by the above method, and their use as probe, for identifying genes or molecules of interest, or still for example in methods of pharmacogenomics, and profiling of molecules relative to their therapeutic and/or toxic effects.

Abstract: The invention relates generally to methods and materials concerning diseases caused by Streptococcus equi, and in particular relating to the detection of this pathogen by assessing the presence or absence of the S. equi eqbE gene sequence.

Abstract: Methods for detecting cancer that include hybridizing a set of chromosomal probes to a biological sample obtained from a patient, and identifying if aneusomic cells are present in a selected subset of cells obtained from the biological sample are described. A set of chromosomal probes and kits for detecting cancer that include sets of chromosomal probes, are also described.

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 2 and mutated sequences thereof.

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 3 and mutated sequences thereof.

Abstract: A method for detecting pathogens, particularly organisms associated with sexually transmitted diseases, especially Human papilloma virus genotypes is described. The method involves the use of real-time PCR using specially designed probes. The probes, kits for carrying out the method, and methods for designing primers suitable for use in the method of the invention are also described.

Abstract: The invention provides compositions and methods for producing androstenedione (4-androstenedione), of improved purity and for modulating its production, for example by deletion or inactivation of ksdA, cxgA, cxgB, cxgC, or cxgD. The invention also provides methods and compositions, including nucleic acids that encode enzymes, for producing 1,4-androstadiene-3,17-dione (ADD) and related pathway compounds, including 20-(hydroxymethyl)pregna-4-en-3-one and 20-(hydroxymethyl)pregna-1,4-dien-3-one. The compositions of the invention include nucleic acids, probes, vectors, cells, transgenic plants and seeds, transgenic animals, kits and arrays.

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

Abstract: The inventors have found a novel fungal lipoxygenase from Manaporthe salvinii and determined its sequence. They have sequenced the gene and cloned it into E. coli and deposited the clone. Oligonucleotides probes based on the sequence information are useful for screening a eukaryotic library to obtain a lipoxygenase. The lipoxygenase is useful in baking and in a detergent.

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 2 and mutated sequences thereof.