Abstract: The invention relates to a method and system for the specific detection of a Mycobacterium tuberculosis (M. tuberculosis) in a biological sample, a difference being made, in particular between M. tuberculosis and other elements of M. tuberculosis complex, i.e., Mycobacterium bovis (M. bovis), Mycobacterium bovis BCG (M. bovis BCG), Mycobacterium africanum (M. africanum) and Mycobacterium microti (M. microti) based on a SNP in a narGHJI promoter.

Abstract: The present invention relates to nucleic acid probes specific to E. coli, which is useful for detecting and identifying E. coli in a biological sample. More particularly, the present invention relates to a DNA chip for detecting and identifying E. coli, on which nucleic acid probes derived from 23 S rRNA gene of E. coli are immobilized. The application of the DNA chip according to the present invention allows time-saving and accurate diagnosis of bacterial infection compared with the conventional of bacterial culture methods. In addition, it is not affected by antibiotics addition in clinical practice, thus leading to more accurate diagnosis.

Abstract: The present invention relates to nucleic acid probes specific to Staphylococcus aureus, which is useful for detecting and identifying S. aureus in a biological sample. More particularly, the present invention relates to a DNA chip for detecting and identifying S. aureus, on which nucleic acid probes derived from 23 S rRNA gene of S. aureus are immobilized. The application of the DNA chips according to the present invention allows time-saving and accurate diagnosis of bacterial infection compared with the conventional bacterial culture methods.

Abstract: Sequences of nucleic acid oligonucleotides for amplifying different portions of gag and pol genes of HIV-1 and for detecting such amplified nucleic acid sequences are disclosed. Methods of amplifying and detecting HIV-1 nucleic acid in a biological sample using the amplification oligonucleotides specific for gag and pol target sequences are disclosed.

Abstract: Provided are an oligonucleotide primer set for amplifying at least one target sequence of the genomic RNA of norovirus, an oligonucleotide probe or probe set specifically hybridizing with at least one target sequence of the genomic RNA of norovirus, a microarray immobilized with the probe or probe set, and a method of detecting norovirus using the probe or probe set.

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: Specific reagents for quantitative assay of HDV and more specifically to follow HDV viral load in chronically infected patients and such a quantitative assay.

Abstract: This invention relates to the use of genetic probes for detection of the presence of the SCCmec cassette in Staphylococcus aureus. In one aspect, the invention allows specific detection and identification of methicillin-resistant S. aureus (MRSA) in a clinical sample without interference from the presence of other non-S. aureus methicillin-resistant staphylococci. In another aspect, the invention allows specific detection and identification of methicillin-resistant coagulase negative staphylococci (MRCNS) originating from a clinical sample without interference from the presence of methicillin-resistant S. aureus.

Abstract: The present invention relates to methods and compositions for selecting a subject for treatment with an agonist or antagonist of macrophage migration inhibitory factor (MIF), identifying a subject at risk for developing a disease associated with high or low MIF expression, predicting the severity of a disease associated with high or low MIF expression in a subject, and for predicting whether a subject is susceptible to a disease associated with high or low MIF expression. The invention also provides novel methods of diagnosing a patient for a disease associated with high or low MIF expression. Also provided are methods for treating a subject having a disease or disorder associated with high or low MIF expression.

Abstract: The present invention relates to a pair of primers specific to mycobacterial species, a polynucleotide of an hsp 65 gene fragment, and a method for the identification of mycobacterial species by using the same. More specifically, the 604-bp hsp 65 gene fragment can be applied to identification methods of mycobacteria such as the comparative sequence analysis method, the probe hybridization method, and PCR-RFLP, which can resolve the problems of a conventional identification method based on bio-chemical characteristics, where the genus mycobacterium covers various species and has a low growth rate, and of the problems of 16s rDNA. Thus, according to the identification method of the present invention, the mycobacterial species can be identified simply, economically, and accurately.

Abstract: In one aspect, the invention provides methods and compositions for the expression of small RNA molecules within a cell using a retroviral vector (FIG. 1A). The methods can be used to express double stranded RNA complexes. Small interfering RNA (siRNA) can be expressed using the methods of the invention within a cell, that interfere with a viral life cycle by down regulating either the viral genome, a viral genome transcript, or a host cell that. In another aspect the invention provides methods for treating patients having suffering from infection, particularly infection with HIV. In a further aspect, the invention provides methods for producing siRNA encoding lentivirus where the siRNA activity may interfere with the lentiviral life cycle.

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 NOS. 62 to 64 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 an internal control nucleic acid molecule including at least one forward primer binding site, at least one reverse primer binding site, and at least one amplifiable region, wherein the forward primer binding site, the reverse primer binding site, and the amplifiable region are all randomly generated. The invention also provides a kit that includes at least one internal control nucleic acid molecule of the invention, at least one forward primer, configured to be complementary to the forward primer binding site of the internal control nucleic acid molecule, and at least one reverse primer, configured to be complementary to the reverse primer binding site of the internal control nucleic acid molecule. The invention also provides methods of using the internal control nucleic acid molecules and kits of the invention.

Abstract: This invention relates to a method of monitoring a fermentation process. In particular, the invention relates to a method of monitoring a fermentation process comprising the step of measuring the expression level of one or more zinc regulated nucleic acid molecules from a microorganism, preferably selected from the group consisting of Escherichia Bacillus, Cyanobacter, Streptomyces, Corynebacteria, Zymomonas, Saccharomyces, Zygosaccharomyces, and Schizosaccharomyces cells, present in the fermentation and comparing the expression level to a reference level of expression for the nucleic acid molecules, wherein the expression level is indicative of sub-optimal fermentation. Preferably the fermentation process is a beer brewing process.

Abstract: The present invention is directed to a method for analyzing the presence of a bacterial pathogen in a clinical sample comprising the steps of (i) at least partially isolating nucleic acid from said sample, characterized in that said nucleic acid is selected from a group consisting of either total nucleic acid, total DNA or total RNA, (ii) quantifying the amount of nucleic acid comprising a preselected sequence which is specific for said bacterial pathogen, and (iii) determining whether said amount of nucleic acid comprising a preselected sequence which is specific for said bacterial pathogen exceeds a first predetermined cut off value.

Abstract: The invention relates to a process for genotyping any HCV isolate present in a biological sample, previously identified as being HCV positive, and for classifying said isolate according to the percentage of homology with other HCV isolates, comprising the steps of: contacting said sample in which the ribonucleotides or deoxyribonucleotides have been made accessible, if need be, under suitable denaturation, with at least one probe from about 10 to about 40 nucleotides, with said probe being liable to hybridize to a region being in the domain extending from nucleotide at position ?291 to nucleotide at position ?66 of the 5? untranslated region of one of the HCV isolates represented by their cDNA sequences, with said numbering of position beginning with the first ATG codon of the open reading frame encoding the HCV polyprotein, or with said probe being complementary to the above-defined probes, detecting the complexes possibly formed between said probe and the nucleotide sequence of the HCV isolate to be iden

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 NOS. 40 to 42 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 proteins from Neisseria meningitidis (strains A & B), including amino acid sequences, the corresponding nucleotide sequences, expression data, and serological data. The proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics.

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: This invention provides polynucleotides encoding Helicobacter pylori cytotoxin associated immunodominant antigen. The polynucleotides can be used as probes to identify the presence of complementary target nucleotide sequences. The invention also provides kits and vectors containing the polynucleotides of the invention.

Abstract: To identify a domain in HIF-1? protein, which participates in stabilization of a fused protein, DNA encoding the following polypeptide (A) or (B) is provided: (A) a polypeptide having the amino acid sequence of SEQ ID NO: 1 (B) a polypeptide having an amino acid sequence comprising at least 16 amino acid residues in the amino acid sequence of SEQ ID NO: 1, and imparting stability dependent on an oxygen concentration to other protein in a cell harboring a fused protein, when the polypeptide is fused with a nuclear localization signal and the other protein to form the fused protein.

Abstract: The present invention provides a simple high-throughput assay for detecting bcr/abl translocations. The method includes qualitative PCR methods for identifying the particular amplified translocation (e1a2 or b2a3/b3a2) and real time PCR for quantifying an amount of bcr/abl transcript (e1a2, b2a3 and b3a2). Quantitative measurement of bcr/abl transcript in accordance with the methods of the invention is useful for monitoring response to therapy.

Abstract: Compositions and methods for sequencing a template polynucleotide comprising a sequence of interest are provided herein. The compositions and methods employ at least one blocking probe that is designed to bind in a sequence-specific manner to a blocking sequence such that primer extension beyond the site where the blocking probe binds is reduced or prevented.

Abstract: A novel gene of Bifidobacteria and the polypeptides encoded thereby. In particular, a gene belonging to the Serpin superfamily and its use in the production of bacterial Serpins is provided. Also provided are vectors, host cells, and methods for producing bacterial Serpin polynucleotides and/or polypeptides.

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 primers, probes, primer sets, primer and probe sets, methods and kits for detecting human papillomaviruses, human beta globin sequences and human papillomaviruses and human beta globin sequences in a test sample.

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 NOS. 46 to 48 or a combination of at least two of them is used for detecting the gene of an infectious disease pathogenic bacterium.

Abstract: The invention relates to the field of diagnosis of and vaccination against Streptococcal infections and to the detection of virulence markers of Streptococci. The invention discloses a method for modulating virulence of a Streptococcus, the method comprising modifying a genomic fragment of Streptococcus wherein the genomic fragment comprises at least a functional part of a fragment identifiable by hybridization in Streptococcus suis to a nucleic acid or fragment thereof as shown in FIG. 5.

Abstract: The invention relates to recombinant polyketide synthase enzymes, polyketide modifying proteins, and other proteins involved in polyketide biosynthesis or function. The invention provides domains of geldanamycin and herbimycin polyketide synthases, polynucleotides that encode such enzymes, and to host cells in which such encoding polynucleotides can be advantageously expressed.

Abstract: Compositions are disclosed as nucleic acid sequences that may be used as amplification oligomers, including primers, capture probes for sample preparation, and detection probes specific for Candida albicans 26S rRNA sequences or DNA encoding 26S rRNA. Methods are disclosed for detecting the presence of C. albicans in samples by using the disclosed compositions in methods that include in vitro nucleic acid amplification of a 26S rRNA sequence or DNA encoding the 26S rRNA sequence to produce a detectable amplification product.

Abstract: We have developed a novel TaqMan quantitative PCR (Q-PCR) based DNA test for detecting annual and/or intermediate ryegrass types in perennial ryegrass. This DNA test was designed using an insertion/deletion (InDel) site in the LpVRN2_2 gene. The new DNA test is more reliable, accurate, and cost effective in detecting annual and intermediate type contamination in perennial ryegrass, having a sensitivity of 0.04% in a sample size of 5000 seeds. Use of a higher sample size (12.5-fold higher compared to the SRF test) provides additional accuracy in detecting the level of contamination A forward and reverse set of primers also identified an approximately 450 bp fragment in or near the LpVRN1 promoter, the fragment being present for all perennial, but not annual, varieties tested.

Abstract: The invention provides methods to detect herpes simplex virus (HSV) in biological samples and further to distinguish between HSV-1 and HSV-2. Primers and probes for the differential detection of HSV-1 and HSV-2 are provided by the invention. Articles of manufacture containing such primers and probes for detecting HSV are further provided by the invention.

Abstract: The invention provides BASB082, BASB083, BASB091, BASB092 and BASB101 polypeptides and polynucleotides encoding BASB082, BASB083, BASB091, BASB092 and BASB101 polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are diagnostic, prophylactic and therapeutic uses.

Abstract: Compositions, methods and kits for detecting the nucleic acids of HIV-1, HIV-2, or the combination of HIV-1 and HIV-2. Particularly described are oligonucleotides that are useful as hybridization probes and amplification primers, including cross-reacting hybridization probes and cross-reacting amplification primers, for detecting very low levels of viral nucleic acids.

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 provides BASB047, BASB054, BASB068 and BASB069 polypeptides, and polynucleotides encoding BASB047, BASB054, BASB068 and BASB069 polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are diagnostic, prophylactic and therapeutic uses.

Abstract: The present invention relates to a nucleic acid molecule or molecules and to a process for the detection of bacteria of the Salmonella genus. The invention relates also to a test kit or test kits for carrying out the mentioned detection processes.

Abstract: A fragment of a nucleic acid specific to mycobacteria of M. tuberculosis complex having a nucleotide sequence of SEQ ID No: 1 and SEQ ID No: 2 and their complimentary sequences.

Abstract: Disclosed are methods of detecting penicillin tolerance in Group B Streptococcus by detecting at least one of two single nucleotide polymorphisms (SNP) in penicillin binding protein 4. Also disclosed are primers and hybridization probes that may be used in such methods.

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

Abstract: The present invention relates to a high sensitivity assay for molecular typing of a biological sample using surface-enhanced Raman scattering (SERS) including resonance scattering (SERRS); capture probes for capturing nucleic acid; a detector probe to detect captured nucleic acid; a kit for molecular typing of biological sample using surface-enhanced Raman scattering (SERS) including resonance scattering (SERRS); and lastly a method of manufacturing said kit.

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: This invention provides isolated nucleic acids encoding polypeptides comprising amino acid sequences of streptococcal matrix adhesion (Ema) polypeptides. The invention provides nucleic acids encoding Group B streptococcal Ema polypeptides EmaA, EmaB, EmaC, EmaD and EmaE. The present invention provides isolated polypeptides comprising amino acid sequences of Group B streptococcal polypeptides EmaA, EmaB, EmaC, EmaD and EmaE, including analogs, variants, mutants, derivatives and fragments thereof. Ema homologous polypeptides from additional bacterial species, including S. pneumoniae, S. pyogenes, E. faecalis and C. diptheriae are also provided. Antibodies to the Ema polypeptides and immunogenic fragments thereof are also provided. The present invention relates to the identification and prevention of infections by virulent forms of streptococci.

Abstract: The present invention relates a fluorescent multiplex PCR assay for detecting the presence of an HPV type in a sample using multiple fluorophores to simultaneously detect a plurality of HPV genes of the same HPV type, wherein the HPV type is selected from the group consisting of: HPV33, HPV35, HPV39, HPV51, HPV56, and HPV59. The present invention also relates to oligonucleotide primers and probes specific to said HPV types for use in the methods of the present invention.

Abstract: The present invention describes novel oligonucleotides targeted to nucleic acid sequences derived from Cryptosporidium organisms, and Cryptosporidium parvum organisms in particular, which are useful for determining the presence of Cryptosporidium organisms in a test sample. The oligonucleotides of the present invention include hybridization assay probes, helper probes and amplification primers. The present invention further describes a novel method for obtaining purified ribonucleic acid from viable oocysts.

Abstract: The present invention relates to an assay system, kits and methods for detecting microorgansims (especially for M. tuberculosis) of a suspected patient. The present invention also relates to an apparatus for performing the integration of thermal and magnetic control in the same apparatus to largely reduce the whole process of M. tuberculosis detection to less than 5 hours.

Abstract: The present invention relates to detection of pathogenic mycobacteria in clinical specimens such as sputum, cerebrospinal fluid, gastric lavage and tissue biopsies etc., wherein the novel stretch of DNA that lies in the intergenic region between methyl mycolic acid synthase genes mmaA1 and mmaA2 and the flanking region in mmaA1 and mmaA2 genes and is the invention uses a pair of designed oligonucleotide primers that specifically amplifies the target DNA from the clinical specimens.

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 NOS. 52 to 54 or a combination of at least two of them is used for detecting the gene of an infectious disease pathogenic bacterium.

Abstract: The present invention provides oligonucleotide primers specifically hybridizing to an arbitrary nucleotide sequence designed from the nucleotide sequence of hemagglutinin of an H5 or H7 avian influenza virus, a nucleic acid amplification method using the primers, a method for diagnosis of infection with an H5 or H7 avian influenza virus by detection of nucleic acid amplification, and a kit for influenza diagnosis.

Abstract: Templates that are engineered to contain a predetermined sequence and a hairpin structure are provided by a nested oligonucleotide extension reaction. The engineered template allows Single Primer Amplification (SPA) to amplify a target sequence within the engineered template. In particularly useful embodiments, the target sequences from the engineered templates are cloned into expression vehicles to provide a library of polypeptides or proteins, such as, for example, an antibody library.