Abstract: The present invention provides isolated polypeptides comprising a fragment of the amino acid sequence of SEQ ID NO:1, or a variant, derivative or fusion thereof, which is capable of binding specifically to and lysing cells of Clostridium difficile, wherein the polypeptide exhibits greater lytic activity on cells of Clostridium difficile than the polypeptide of SEQ ID NO: 1. The invention further provides means for producing the same, methods for killing bacterial cells such as cells of Clostridium difficile, as well as methods for diagnosing, treating and preventing diseases and conditions associated with infection of the same.

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. 65 to 67 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 discloses an oligonucleotide which comprises a part or the entire sequence of the nucleotide sequence shown in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8, or a part or the entire sequence of a sequence complementary to the nucleotide sequence shown in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8, wherein the oligonucleotide is capable of hybridizing with a nucleotide sequence of Mycobacterium intracellulare gene; a primer or a probe for the detection of M. intracellulare, which comprises the aforementioned oligonucleotide; and a method for detection of M. intracellulare using the aforementioned primer and/or the probe. According to the detection method of the present invention, any false-positive result in diagnosis can be eliminated and detection or diagnosis of M.

Abstract: The present invention provides methods, compositions and kits for detecting the presence or absence of an integrated insertion polynucleotide.

Abstract: The present invention provides a novel mycovirus that suppresses phytopathogenic fungi and a novel method for controlling plant diseases. A novel mycovirus that is present endogenously in a predetermined rice blast fungus, has four types of double-stranded RNAs of 2.8 to 3.6 kb, and suppresses a phytopathogenic fungus has been found. This virus suppresses phytopathogenic fungi such as rice blast fungus.

Abstract: The invention provides methods, devices and kits for rapid detection and identification of one or more live target microorganisms in a liquid sample or grown on plates containing nutrient media. The invention includes mixing one or more target microorganisms with one or more aptamers and/or one or more antibodies, each conjugated to a reporter compound and specific for a first site on one or more target microorganisms to form a mixture. The mixture is placed on a permeable membrane having immobilized thereon one or more aptamers linked to an amine compound, and/or one or more antibodies, each specific for a second site on one or more target microorganisms or a site on the aptamer conjugate and/or antibody conjugate. A detection solution is added to the membrane and detection and identification of one or more target microorganisms is achieved in about one hour or less.

Abstract: Microbial ecology of a specimen is evaluated using an approach (Level I) that utilizes nucleic acid amplification with specific gene primers that will identify panels of microorganisms and antibiotic-resistance factors generating a diagnostic report (optionally with quantification of each microorganism or antibiotic-resistance factor) and an approach (Level II) that utilizes universal or semi-universal primers to amplify conserved genes at a general or specific taxonomic level that are tagged specimen specifically using a genetic or chemical marker that is specific to the specimen from which it was derived, then sequencing the amplified products with highly-parallel, high-throughput technology to provide comprehensive sequences of the microbial population in the specimen followed by analysis of this sequence information and specific targeted information from Level I and/or Level II to generate a comprehensive analysis, interpretation, and/or diagnostic report.

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: An isolated human Apolipoprotein L-I corresponding to a wild type human Apolipoprotein sequence is modified by a deletion at its C-terminal end.

Abstract: Four highly conserved genes, encoding translation elongation factor Tu, translation elongation factor G, the catalytic subunit of proton-translocating ATPase and the RecA recombinase, are used to generate species-specific, genus-specific, family-specific, group-specific and universal nucleic acid probes and amplification primers to rapidly detect and identify algal, archaeal, bacterial, fungal and parasitical pathogens from clinical specimens for diagnosis. The detection of associated antimicrobial agents resistance and toxin genes are also under the scope of the present invention.

Abstract: The present invention includes novel compounds and pharmaceutically acceptable formulations of said compounds which exhibit antibiotic activity against microorganisms bearing a guanine riboswitch that controls the expression of the guaA gene, including organisms which are resistant to certain antibiotic families, and which are useful as antibacterial agents for treatment or prophylaxis of bacterial infections in animals or in humans, in particular but not limited to infections of the mammary gland, or their use as antiseptics, agents for sterilization or disinfection.

Abstract: Disclosed are methods and kits for identifying a virulent bacteria in a sample, which may include virulent bacteria belonging to the Bacillus genus (e.g., Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis). Typically, the methods include (a) reacting a mixture that includes, in addition to nucleic acid isolated from the sample, (i) at least one oligonucleotide capable of specifically hybridizing to nucleic acid of plasmid pX01; and (ii) at least one oligonucleotide capable of specifically hybridizing to nucleic acid of plasmid pX02. In addition, the mixture may include control nucleic acid. In the methods, nucleic acid of plasmid pX01 and nucleic acid of plasmid pX02 are detected, and optionally control nucleic acid is detected, thereby identifying the virulent bacteria.

Abstract: The present invention relates to a human monoclonal antibody specific for the serotype IATS 01 of P. aeruginosa, and a hybridoma producing said monoclonal antibody. In addition, the present invention relates to pharmaceutical compositions comprising at least one antibody or at least one nucleic acid encoding said antibody.

Abstract: The present invention is a method for screening drugs for antibiotic activity by screening a drug for activity to disrupt a toxin-antitoxin complex in a bacterial cell.

Abstract: Accordingly, the invention provides constructs in which the nucleic acids encoding Plasmodium falciparum MSP4 and MSP5, and the resulting polypeptides, have been modified. More particularly, this invention provides constructs encoding recombinant MSP4 and MSP5 polypeptides, which are expressed as soluble, secreted polypeptides in a baculovirus-insect cell expression system. It was surprisingly found that the recombinant polypeptides contain an EGF-like domain at the C-terminus that is properly folded in the polypeptide.

Abstract: Methods for identifying bacterial strains by using sets of distributed genes that are present in some but not all strains of a given species, associated methods for treating bacterial infections are disclosed. The methods may include examining a sample of a bacterial species, selecting a strain of interest based on possession of a unique genetic characteristic that is present in only the strain of interest and not in the other strains, examining the distributed genes possessed by the strain of interest, and detecting gene-possession variation in the distributed genes of the sample strains as compared to genes of known strains.

Abstract: A method of quickly producing a vaccine for a biotype of pathogenic microorganism is described, where a nucleic acid molecule or fragment thereof is obtained from a biological sample from an animal exposed to the microorganism, a protective molecule is prepared based on the nucleic acid molecule of interest or fragment thereof, and administered to an animal which has been or is as risk of being exposed to the microorganism. A protective response to the biotype of the microorganism is obtained in the animal.

Abstract: The present invention relates to a method for simultaneously detecting DNA of Histoplasma capsulatum and Paracoccidioides brasiliensis by means of the real-time quantitative multiplex PCR technique, based on specific probes marked with different fluorophores. This technique is applicable both in biological samples and microbiological cultures and environmental samples. Furthermore, another aspect of the invention is that a kit has been developed enabling the two micro-organisms to be detected simultaneously.

Abstract: The present invention is generally related to products and methods that facilitate the use of Venezuelan equine encephalitis (VEE) virus TC-83 (TC-83) as a non-hazardous simulant, or surrogate, for viable pathogenic viruses. Specifically, TC-83 nucleic sequences are used in a method of detecting VEE or TC-83 in a sample thought to contain a biological threat agent. TC-83 and its nucleic acid sequence may therefore be used in the research, development, testing, evaluation, and training for technologies that enable the detection of biological threat agents. More particularly, specific primers and probes may be used to verify that instruments and systems using PCR detection methods are functioning properly.

Abstract: This invention includes a fluorophore-tagged antimalarial represented by the following structural formula (1) or a salt thereof. This invention relates to the synthesis of fluorophore-tagged antimalarials and describes the synthesis of a fluorophore-tagged antimalarial. These fluorophore-tagged antimalarials can be used to image live cells to determine the location of the antimalarial in the cell, identify drug resistance and growth related pathways in Plasmodium isolates, identify new drug targets and chemo-sensitizers to reverse drug resistance.

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

Abstract: Disclosed are compositions and methods for detecting the presence of viable cells in a sample. Included are compositions and methods for increasing the sensitivity of a nucleic acid amplification test for determining the presence of at least one target microorganism in a sample. Also disclosed are compositions and methods for detecting ribosomal RNA precursors (pre-rRNA) as dynamic indicators of viable microorganisms in a sample.

Abstract: Methods are described for the production and use of fluorescence resonance energy transfer (FRET)-based competitive displacement aptamer assay formats. The assay schemes involve FRET in which the analyte (target) is quencher (Q)-labeled and previously bound by a fluorophore (F)-labeled aptamer such that when unlabeled analyte is added to the system and excited by specific wavelengths of light, the fluorescence intensity of the system changes in proportion to the amount of unlabeled analyte added. Alternatively, the aptamer can be Q-labeled and previously bound to an F-labeled analyte so that when unlabeled analyte enters the system, the fluorescence intensity also changes in proportion to the amount of unlabeled analyte.

Abstract: The invention provides a method for isolating and culturing a previously unculturable microorganism, which comprises: (i) collecting a sample from an environmental source; (ii) counting/estimating the number of microorganisms in the sample; (iii) diluting the sample in an appropriate medium; (iv) adding a gelating agent such as to entrap one or more microorganisms within a sphere of the gelating agent; (v) coating the spheres containing the entrapped microorganism(s) with a natural or synthetic polymer to form a polymeric membrane; (vi) incubating the coated spheres in the original environment for an appropriate time; (vii) cutting the spheres and scanning for microorganisms colonies; and (viii) isolating the microorganisms, and repeating steps (iii) to (vii) until a pure clone of said previously unculturable microorganism is obtained.

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. 76 to 77 and complementary or modified sequences thereof 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 relates to nucleic acids, vectors and polypeptides that are suitable markers for detecting Streptococcus strains of the anginosus group, preferably for detecting Streptococcus anginosus and/or Streptococcus constellatus as well as for discriminating Streptococcus anginosus and/or Streptococcus constellatus from other streptococci. The present invention furthermore relates to these nucleic acids and polypeptides for use in the diagnosis and/or prognosis of infections with Streptococcus strains of the anginosus group. The present invention furthermore relates to methods utilizing these nucleic acids and polypeptides as well as to arrays and antibodies.

Abstract: Provided herein is a method for detecting the presence or absence of at least one of Clostridium botulinum toxin gene A, B, E, and F in a biological sample by means of PCR amplification using toxin specific primers and labeled probes in connection with real time or delayed detection. Also provided are specific primer and probe sequences, a diagnostic method and a kit comprising primers and probes for detection of toxin genes A, B, E, or F in a biological sample.

Abstract: Methods of detecting Chlamydophila, including differentiating between species of Chlamydophila and/or strains of Chlamydophila psittaci are disclosed, for example to detect and genotype a Chlamydophila psittaci infection. A sample suspected of containing a nucleic acid of a Chlamydophila, is screened for the presence of that nucleic acid. The presence of the Chlamydophila nucleic acid indicates the presence of the Chlamydophila bacterium. Determining whether a Chlamydophila nucleic acid is present in a sample can be accomplished by detecting hybridization between a Chlamydophila specific primer, a Chlamydophila psittaci specific primer, and/or a Chlamydophila psittaci genotype-specific primer and the Chlamydophila nucleic acid containing sample. Thus, primers for the detection, species-specific and/or genotype-specific identification of Chlamydophila psittaci are disclosed. Kits that contain the disclosed primers also are disclosed.

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 provides novel binding pair compositions of defined and limited stability comprising nucleic acid detection markers useful for the homogeneous, sensitive detection of analytes. Also provided are methods for the sensitive homogenous detection of analytes, particularly analytes of clinical relevance. Kits for preparing binding pairs of the invention and for performing the methods of the invention are also provided.

Abstract: A composition of matter which comprises a non-gaseous nitrogen containing compound; and a spore of a micro-organism. A method of determining a source of a material the material being an explosive or a substance used in the preparation of the explosive, the material comprises a spore of a micro-organism uniquely associated with the material, the method comprises inducing the spore to transform into a vegetative micro-organism and identifying the micro-organism as being associated with the material, thereby determining the source of the material.

Abstract: Provided are methods for identifying lpf genes in pathogenic serotypes of the Enterobacteriaceae family and for differentiating Escherichia coli (E. coli) O157:H7 strains in an isolate using primer pairs specific to lpf gene variants, particularly IpfA1 and/or lpfA 2 genes and amplicon size of the PCR product to identify prototypic Enterobacteriaceae serotypes or more specifically, to differentiate strains of E. coli serotype O157:1-17. Differentiation further requires identifying the E. coli isolate's eae gene variant type which in combination with the IpfA1 and/or lpfA2 variant identification provides unique markers. Also provided are the primer pairs and a kit comprising the same.

Abstract: The present invention relates to a method using a composition for permeabilizing microorganism walls for counting and detecting in a targeted manner the microorganisms on a membrane. The invention also relates to a kit and to probes that are suitable for carrying out the method.

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. 68 to 69 and complementary or modified sequences thereof or a combination of at least two of them is used for detecting the gene of an infectious disease pathogenic bacterium.

Abstract: Methods for identifying fungal infection, assays for identifying genomic and protein markers of fungal infection, and methods for diagnosing the fungal infection. In one aspect, the method of identifying fungal infection by proteomic assay involves measuring the protein levels of proteins listed in Table 2A in a peripheral blood cell sample and comparing the determined protein levels to standard protein levels. In another aspect, subjects identified as being infected with fungal infection are treated with anti-fungals.

Abstract: The invention is a herd management schema based upon the inventor's analysis of the natural history of bovine infection due to Mycobacterium avium subspecies paratuberculosis (Map) and related genomic variants and upon the ability of two distinct Map ELISA tests to sequentially or in parallel determine prior and current Map infection and evidence of active mycobacterium replication. Interpretation of the test results are integrated into sequential directives designed to enhance productive retention of infected animals as well as identify animals not previously infected. The sequential utilization of the data guidelines is developed to minimize the adverse economic impact.

Abstract: A nucleic acid encoding an acetolactate synthase (ALS) protein that provides resistance to ALS inhibitors, e.g., sulphonylurea and imidazolinone compounds, is provided. The nucleic acid may be used as a selectable marker for expression of a protein of interest in host cells.

Abstract: The present invention relates to engineered Clostridium difficile type IV pilin (tfp) genes, type IV pilin proteins which can serve as a diagnostic marker for identification of patients infected with C. difficile, and vaccines comprising type IV pilin proteins, antigenic fragments and variants thereof for therapeutic interventions.

Abstract: The present invention relates to portable systems and devices, and corresponding methods, for detecting bioagents. In particular, the present invention provides systems, devices, and methods that utilize one or more of a sample preparation component, sample analysis component employing broad range primers, and sample detection component.

Abstract: Four highly conserved genes, encoding translation elongation factor Tu, translation elongation factor G, the catalytic subunit of proton-translocating ATPase and the RecA recombinase, are used to generate species-specific, genus-specific, family-specific, group-specific and universal nucleic acid probes and amplification primers to rapidly detect and identify algal, archaeal, bacterial, fungal and parasitical pathogens from clinical specimens for diagnosis. The detection of associated antimicrobial agents resistance and toxin genes are also under the scope of the present invention.

Abstract: A kit for detecting Neisseria gonorrhoeae in a test sample is disclosed. In addition a method is described for the real-time detection of Neisseria gonorrhoeae in a test sample using the kit. According to method of detection, the results of the detection can be rapidly identified with a reduced number of copies of a sample in real-time.

Abstract: Compositions and methods for detecting Toll-like receptor binding to ligands and test compounds are disclosed herein.

Abstract: This application pertains to methods for the whole-cell analysis of gram-positive bacteria. The methods are capable of making a determination of whether or not a sample (e.g. a clinical sample) comprises one or more select gram-positive bacteria as well as, for example, whether or not none, some or all of said select gram-positive bacteria in said sample, or possibly other bacteria in said sample, possess a select trait or traits of interest. In some embodiments, the methods can be used to determine methicillin-resistant (the select trait) staphylococcus aureus (the select gram-positive bacteria), coagulase-negative staphylococci (another select gram-positive bacteria) and/or methicillin-sensitive staphylococcus aureus (MSSA) in said sample. The whole-cell analysis can be performed, for example, by in-situ hybridization (ISH), fluorescence in-situ hybridization (FISH), immunocytochemistry (ICC), or any combination of two or more of the foregoing.

Abstract: The present invention discloses novel isolates of Neorickettsia risticii, compositions comprising such isolates, vaccines and methods for using such vaccines against Potomac Horse Fever.

Abstract: The invention relates to a method for isolation of target molecules from a nucleic acid population.

Abstract: The invention provides methods for certification of carcasses, and for detecting a contaminated carcass and preventing its movement into or across a production area. The inventive methods comprise obtaining, early in the production process (pre-fabrication), a test sample from at least one test location of at least one split-portion of each carcass, wherein the test samples are obtained prior to or during chilling of the respective split portions, before entry thereof in the production chain. Composite test samples are assayed for pathogens or microbes, whereby certification is afforded, or whereby entry of the chilled split-carcass-Lot into the production area is precluded if the corresponding composite-Lot test sample is contaminated. Methods for remedial reconditioning of contaminated split-carcasses are provided, wherein essentially 100% of the carcasses are targeted to the production line. The inventive methods provide substantial public health benefit, and are efficient and economical to implement.

Abstract: The present invention relates to an assay including a surface having silver colloids or islands attached thereto. Attached to the surface and/or silver colloids/islands are polynucleotides which are complimentary to a target polynucleotide sequence. The assay is performed by adding the target polynucleotide sequence to the assay surface and allowed to hybridize with the capture polynucleotides. Fluorophore-labeled capture polynucleotides are added and hybridize to the target polynucleotide. Bound target polynucleotides are detected by metal enhanced fluorescence.

Abstract: Four highly conserved genes, encoding translation elongation factor Tu, translation elongation factor G, the catalytic subunit of proton-translocating ATPase and the RecA recombinase, are used to generate species-specific, genus-specific, family-specific, group-specific and universal nucleic acid probes and amplification primers to rapidly detect and identify algal, archaeal, bacterial, fungal and parasitical pathogens from clinical specimens for diagnosis. The detection of associated antimicrobial agents resistance and toxin genes are also under the scope of the present invention.

Abstract: Based on detection of Treponema bacteria or Campylobacter bacteria present in a sample derived from the tonsil of a subject who has a positive result on at least one of a urinary protein test and a urinary occult blood test, or of a patient diagnosed with possible IgA nephropathy, presumed IgA nephropathy can be detected with a high accuracy, in a simple and quick manner without physical burden on subjects. Also, an IgA nephropathy patient for whom tonsillectomy is effective in therapy of IgA nephropathy can be selected with a high accuracy, in a simple and quick manner without physical burden on subjects.

Abstract: The invention provides improved nucleic acids for anti-HIV therapy. The invention further provides selection methods which are capable of predicting already at an early stage of development whether promising anti-pathogenic candidate compounds will be suitable for therapeutic use in vivo.