Abstract: The present invention describes compositions for both diagnostic and therapeutic applications. In one embodiment, the present invention contemplates a method of identifying an active M. tuberculosis infection. In another embodiment, the present invention contemplates a method of monitoring a M. tuberculosis infection. In yet another embodiment, the present invention contemplates a method of monitoring a patient's response to treatment for an active M. tuberculosis infection. In a further embodiment, the present invention contemplates a method of monitoring a patient's response to treatment for an active M. tuberculosis infection.

Abstract: The present invention concerns a new competence stimulating peptide identified in Firmicutes, in particular Streptococcus, and more preferably S. thermophilus and methods of producing transformation competent Firmicutes, in particular Streptococcus, and more preferably S. thermophilus bacteria.

Abstract: The invention provides a method of identifying an antigen from a pathogen or a disease antigen comprising the use of an adenoviral vector array comprising two or more different adenoviral vectors, wherein each adenoviral vector comprises a nucleic acid sequence encoding a different antigen of a pathogen. The adenoviral vectors are administered to antigen presenting cells (APCs) in vitro or to an animal in vivo. The immunogenicity of the antigen is measured by screening for an immune response from effector T lymphocytes in vitro and by screening for the absence of pathogen-induced disease onset in vivo.

Abstract: An aptamer-based SERS detection technique that directly monitors an aptamer-analyte capture event by generating spectroscopic information regarding the identity of the analyte that has been bound to the aptamer from a complex biological sample. A reproducible SERS spectrum is measured for an aptamer-analyte complex formed on a metal surface and this spectral information is used directly to identify the specific aptamer-analyte complex and optionally also to quantify the analyte in the sample, thus enabling discrimination between true and false positives in quantitative analyte assays on complex biological samples. In one embodiment the aptamer is attached directly to the metal surface and surrounded by a self-assembled monolayer (SAM) of amphiphilic molecules. In an alternative embodiment the metal surface is coated with a SAM and the aptamer is attached to the amphiphilic molecules of the SAM.

Abstract: The present invention relates to a slide chip for a sensor for detection of food-borne bacteria and a fabrication method thereof. More particularly, the invention relates to a slide chip for a sensor for detection of food-borne bacteria and a fabrication method thereof, the slide chip comprising: a substrate coated with a metal; a linker having a substituent which may be bonded to the metal and is located at the 5? end of deoxythymidine (dT); and a food-borne bacterium-derived RNA aptamer that is bound to the linker by the 3?-end poly A tail. The slide chip makes it possible to detect food-borne bacteria in a rapid and accurate manner.

Abstract: The present invention claims an isolated nucleotide sequence characterized by encoding the PFR1 protein of Leishmania infantum or a fragment thereof. This PFR1 protein or a fragment thereof comprises at least a selected immunodominant epitope between the following group: 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 and SEQ ID No: 8, where the immunodominant epitope is able to induce an antigen-specific T cell cytotoxic immune response in an animal, against the kinetoplastids causing the leishmaniasis disease. The immunodominant epitopes are cytotoxic T-lymphocyte activators and they present a high binding affinity for A2 type MHC Class I molecule.

Abstract: Devices, systems and methods including a sonicator for sample preparation are provided. A sonicator may be used to mix, resuspend, aerosolize, disperse, disintegrate, or de-gas a solution. A sonicator may be used to disrupt a cell, such as a pathogen cell in a sample. Sample preparation may include exposing pathogen-identifying material by sonication to detect, identify, or measure pathogens. A sonicator may transfer ultrasonic energy to the sample solution by contacting its tip to an exterior wall of a vessel containing the sample. Multipurpose devices including a sonicator also include further components for additional actions and assays. Devices, and systems comprising such devices, may communicate with a laboratory or other devices in a system for sample assay and analysis. Methods utilizing such devices and systems are provided. The improved sample preparation devices, systems and methods are useful for analyzing samples, e.g. for diagnosing patients suffering from infection by pathogens.

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: Provided herein are methods and systems for rapid identification and quantification of the taxonomic composition of a microbial metagenome in a sample, based on compositional spectra analysis. The methods and systems are useful in diagnostic and analytic methods in the clinic and in the field.

Abstract: The invention encompasses method of using quantitative PCR to detect fungal organisms in clinical and environmental samples to generate standards that allow the quantification of fungal organisms in the samples.

Abstract: Methods of identifying geological materials of interest comprising (i) providing a nanoprobe composition comprising one or more nanoprobes; wherein the nanoprobe includes (a) at least one tag; and (b) at least one signal generator; (ii) introducing the nanoprobes to a geological material; and (iii) detecting the presence of a signal generated by the signal generator on association of the tag with a target. Nanoprobe compositions identify geological materials, systems include such nanoprobe compositions, and methods use such nanoprobe compositions for the evaluation of geological materials.

Abstract: The embodiments herein provide a dipstick nano-biosensor for diagnosing Plasmodium vivax and Plasmodium falciparum. The dipstick biosensor comprises a backing plate coated with a cellulose membrane, nitrocellulose membrane and fibreglass. Gold nanoparticles coated with antidigoxigenin are immobilized on the dipstick along with probes comprising strptavidin, texas red, biotin and fluorescein. The dipstick biosensor has three regions comprising a wicking pad, conjugate pad having two control lines and two test lines and an absorbent pad. The first Control line comprises nitrocellulose membrane coated with antifluorescein. The second control line comprises nitrocellulose membrane coated with anti anti-sheep. The first test line comprises nitrocellulose membrane coated with streptavidin conjugated to biotin. The second test line comprises nitrocellulose membrane coated with anti texas red. The two test lines help to confirm the diagnostic results.

Abstract: Particular aspects provide a method of sampling, testing and validating test lots (e.g., single-unit production lots), comprising: assembling a plurality of product portions from each of a plurality of test lots and combining the collected product portions to provide a corresponding set of test lot samples (wherein each test lot sample is attributed to a particular corresponding test lot); enriching the set of test lot samples; removing equal portions of each enriched sample, and combining the removed portions to provide a modular composite sample; and testing of the modular composite sample for the target agent/organism, wherein where such testing is positive, individual test lots may nonetheless yet be validated by further testing of a respective enriched test lot sample and obtaining a negative test result. The methods have broad utility for monitoring all sorts of test lots (e.g., environmental lots, production lots, pharmaceutical lots, etc.

Abstract: Calcium-binding photoproteins showing the luminescence pattern with a slow decay of are desired. The invention provides a mutant apoprotein comprising an amino acid sequence wherein the 23rd to 34th amino acids in the amino acid sequence of SEQ ID NO: 2 are substituted with an amino acid represented by formula I below: Xaa23-Xaa24-Xaa25-Xaa26-Xaa27-Xaa28-Xaa29-Xaa30-Xaa31-Xaa32-Xaa33-Xaa 34; having a function to bind to the peroxide of coelenterazine or the peroxide of a coelenterazine analogue to form a photoprotein capable of emitting light under the action of calcium ions; and, having a half decay time of the luminescence emitted by binding of the photoprotein to calcium ions being not less than 2 seconds.

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: The present invention describes compositions for both diagnostic and therapeutic applications. In one embodiment, the present invention contemplates a method of identifying an active M. tuberculosis infection. In another embodiment, the present invention contemplates a method of monitoring a M. tuberculosis infection. In yet another embodiment, the present invention contemplates a method of monitoring a patient's response to treatment for an active M. tuberculosis infection. In a further embodiment, the present invention contemplates a method of monitoring a patient's response to treatment for an active M. tuberculosis infection.

Abstract: The present invention relates to kits and methods for efficiently generating 5? capped RNA having a modified cap nucleotide and for use of such modified-nucleotide-capped RNA molecules. In particular, the present invention provides kits and methods for capping RNA using a modified cap nucleotide and a capping enzyme system, such as poxvirus capping enzyme. The present invention finds use for in vitro production of 5?-capped RNA having a modified cap nucleotide and for in vitro or in vivo production of polypeptides by in vitro or in vivo translation of such modified-nucleotide-capped RNA. The invention also provides methods and kits for capturing or isolating uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate, and methods and kits for using a capping enzyme system and modified cap nucleotides for labeling uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate with detectable dye or enzyme moieties.

Abstract: A vector that allows for easy accomplishment of a variety of cloning, and use of the vector for measurement of the transcription-inducing activity of a promoter or production of a desired gene product in Corynebacterium.

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

Abstract: The present invention relates to a method for evaluating the integrity of the cell wall of the bacteria present in a culture in the presence of an antibiotic acting on the bacterial cell wall which, from a practical point of view, allows quickly determining if a bacterium is sensitive or resistant to an antibiotic acting on the bacterial cell wall. Likewise, the present invention also relates to a lysis solution applicable in the preceding method, specifically affecting bacteria having the cell wall damaged by the action of an antibiotic acting on the bacterial cell wall, which allows distinguishing bacteria sensitive to said antibiotic from those resistant to said antibiotic.

Abstract: The invention aims at providing an adsorbent for bacterial toxins, a method for removal of such toxins by adsorption, and an adsorber packed with said adsorbent. Provided are an adsorbent for bacterial toxins, which comprises a water-insoluble porous material having a mode of pore radius of 20 angstroms to 1,000 angstroms, a method for removal of bacterial toxins using said adsorbent, and an adsorber packed with said adsorbent.

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 present invention relates to a method for detecting resistant microorganisms to a therapeutic agent in a biological sample, comprising the following steps: a. inoculate the said sample, uncultured, on a first tube with, and on a second tube without, at least one therapeutic agent; preferentially further including at least one lysing agent and/or a buffer, and/or a suitable culture medium, or put the sample on a separation serum tube; and incubated it; b. add to both tubes a fluorescent marker; c. perform a fluorescence analysis for obtaining one or more fluorescence or growth parameters for each of the two tubes; wherein the microorganisms resistant phenotype of the biological sample to said therapeutic agent is obtained by comparing the one or more fluorescence parameters between the two tubes.

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: 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: Disclosed are compositions, kits, and methods for detecting, extracting, visualizing, and identifying a pathogenic protozoan. Quantitative real time polymerase chain reaction in connection with specifically designed oligonucleotide probes are used to detect a variety of pathogenic protozoans in patient samples.

Abstract: The present invention relates to an isolated truncated form of the secretory aspartyl proteinase 2, as well as to nucleic acid molecules encoding same. The present invention also relates to a composition comprising an isolated truncated form of the secretory aspartyl proteinase 2, as well as to nucleic acid molecules encoding same.

Abstract: The present invention relates to an in vitro method, for predicting a risk of onset of type 2 diabetes in a subject, which method comprises the steps of: a) measuring the concentration of bacterial 16S rDNA in a biological sample of said subject; and b) comparing said measured concentration of bacterial 16S rDNA to a threshold level; wherein a measured concentration of bacterial 16S rDNA higher than the threshold level is indicative of an increased risk of onset of type 2 diabetes in the subject, and a measured concentration of bacterial 16S rDNA lower than the threshold level is indicative of a decreased risk of onset of type 2 diabetes in the subject.

Abstract: System and method for detecting and measuring chemical perturbations in a sample. The system and method are useful for non-invasive pH monitoring of blood or blood products sealed in storage bags.

Abstract: A method of assessing an intracellular pathogen infection and/or monitoring an intracellular pathogen infection in an individual comprises determining whether the individual has (a) T-cells that secrete IFN-? only, (b) T-cells that secrete IL-2 only or (c) T-cells that secrete both IFN-? and IL-2 in response to an intracellular pathogen antigen and optionally determining any change in this cytokine profile.

Abstract: An affinity ligand-matrix conjugate of the structure Z-Spacer-[NX-A]m-NY-A-NK2 is useful for the isolation, separation, purification, characterization, identification or quantification of endotoxins in an aqueous system, wherein m is an integer of at least one; each A independently represents an optionally substituted linear, branched or cyclic saturated hydrocarbon chain containing 1 to 6 carbon atoms; each X independently represents hydrogen or alkyl; Y is X or A-NX2; and Z is a support matrix attached to the ligand through an optional spacer arm (Spacer).

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: The present invention relates to compositions and methods for the reduction of atherosclerotic plaques and the decrease in the level of total serum cholesterol, triglycerides, serum LDL cholesterol, and serum HDL cholesterol. The present invention also relates to methods for the diagnosis, prevention and treatment of atherosclerosis and mycoplasma associated diseases, cardiotoxicity related to cancer treatment, and Chagas disease related cardiomyopathies.

Abstract: The invention provides compositions (e.g., peptide compositions) useful for the detection of antibodies that bind to Borrelia antigens. The peptide compositions comprise polypeptide sequences comprising variants in the IR6 domain of the Borrelia VlsE protein. The invention also provides devices, methods, and kits comprising such peptide compositions and useful for the detection of antibodies that bind to Borrelia antigens and the diagnosis of Lyme disease.

Abstract: The invention generally relates to devices for target detection and methods of use thereof.

Abstract: The invention generally relates to a system for isolating or separating a target from a sample. In certain aspects, processes performed by the target capture system include introducing a plurality of magnetic particles, in which a plurality of the particles include at least one binding moiety specific to a target, into a sample to form at least one target/particle complex and applying a magnetic field to isolate the magnetic particle/target complexes from the sample. The process starts at inputting a sample into the system and ends at delivering a capture target or nucleic acids of the target into a container for further analysis.

Abstract: The present invention generally relates to methods of generating antibodies against a species of pathogen that involve identifying the pathogen that is most genetically representative of member of pathogen species and using the identified pathogen to generate an antibody.

Abstract: The invention relates to a method for isolating a microorganism containing a known genetic element. The method employs several rounds of 1) dilution of a mixed culture containing the selected microorganism in several replicates, 2) growing the replicates, 3) detecting the organism in at least one of the replicates and repeating steps 1) through 3) until the organism can be isolated by standard procedures.

Abstract: This invention is a process for improving the production levels of recombinant proteins or peptides or improving the level of active recombinant proteins or peptides expressed in host cells. The invention is a process of comparing two genetic profiles of a cell that expresses a recombinant protein and modifying the cell to change the expression of a gene product that is upregulated in response to the recombinant protein expression. The process can improve protein production or can improve protein quality, for example, by increasing solubility of a recombinant protein.

Abstract: Described herein are improved diagnostic tools for veterinary and human use which can be used for serodiagnosing A. platys in mammals, particularly in members of the Canidae family and in humans. The diagnostic tools are a group of outer membrane proteins of A. platys and variants thereof, referred to hereinafter as the “OMP proteins”, a group of outer membrane proteins of A. platys and variants thereof referred to hereinafter as the “P44 proteins”, and antibodies to the OMP proteins and the P44 proteins.

Abstract: Methods and compositions for preparation of a sample, including a sample to be analyzed for the presence of one or more pathogens. Transport of a non-diluted sample from an individual suspected of having the pathogen and transfer of the sample directly into a nucleic acid extraction buffer occurs in a single step. The process is an improvement over known methods because it provides accurate, rapid analysis that utilizes fewer steps and/or reagents from methods used in the art. In specific embodiments, it has one or more of the following characteristics: 1) it is a one-step process; 2) it eliminates dilution of the sample; 3) smaller sample sizes are employed; 4) fewer reagents are utilized; 5) transport media is not required; 6) less than 1 colony forming unit is required for detection; 7) fast; and 8) economic.

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: Methods for the identification of microorganisms or infectious disorders are disclosed, comprising obtaining a suitable sample from sources such as persons, animals, plants, food, water or soil. The methods also comprise providing tailored nucleic acid substrate(s) designed to react with a type 1 topoisomerase from one or more microorganism(s) or infectious agent(s), and incubating said substrate with said sample, or extracts or preparations from the sample, so that the substrate is processed by said topoisomerase if said microorganism(s) or infectious agent(s) is present in the sample. Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are also provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted by that enzyme.

Abstract: A method of identifying a subject at risk of developing or having a neurodegenerative disorder is provided. The method includes obtaining a biological sample from the subject and assaying a level of a marker of intestinal permeability in the sample. The method further includes comparing the subject's level to a control level for the marker of intestinal integrity and identifying the subject having an increased intestinal permeability relative to the control intestinal permeability as having an increased risk of developing or having a neurodegenerative disorder. A method of monitoring the efficacy of a treatment for a neurodegenerative disorder is also provided.

Abstract: The present invention relates to methods of producing a polypeptide, comprising: (a) cultivating a mutant of a parent Fusarium venenatum strain in a medium for the production of the polypeptide, wherein the mutant strain comprises a polynucleotide encoding the polypeptide and one or more (several) genes selected from the group consisting of pyrG, amyA, and alpA, wherein the one or more (several) genes are modified rendering the mutant strain deficient in the production of one or more (several) enzymes selected from the group consisting of orotidine-5?-monophosphate decarboxylase, alpha-amylase, and alkaline protease, respectively, compared to the parent Fusarium venenatum strain when cultivated under identical conditions; and (b) recovering the polypeptide from the cultivation medium. The present invention also relates to enzyme-deficient mutants of Fusarium venenatum strains and methods for producing such mutants.

Abstract: Schistosomiasis mansoni is caused by flukes called Schistosoma(es) that enters the human body through the skin in Schistosoma infested waters. The Schistosomes travel from the skin into human blood vessels where they mate, produce antigen containing eggs that travel from the blood vessels into the small intestines, where they are released in the human feces. Male and female Schistosome mates in human blood vessels, male Schistosomes secrete a protein called TGR ? protein to the Trk receptor sites on the females Schistosomes membranes. The process stimulates the formation of chemical SmInAct in female Schistosomes, a chemical necessary for the female Schistosomes to produce eggs. This novel technique describes new methods to inhibit Trk receptor sites on female Schistosome membranes using Trk inhibitor agent to prevent TGR ? proteins from binding to the Trk receptor sites. Thus, preventing SmInAct from being created in female Schistosomes, preventing production of eggs and Schistosomiasis.

Abstract: The present invention concerns compositions and methods of extracting infectious pathogens from a volume of blood. In one embodiment, the method includes the steps of creating a fibrin aggregate confining the pathogens and introducing a fibrin lysis reagent to expose the pathogens for analysis. The present invention also concerns materials and methods for removing aurintricarboxylic acid (ATA) from a sample.

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: 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: A recombinant marker gene encoding an orotate transporter polypeptide comprising an amino acid sequence at least 60% identical to SEQ ID NO: 2, a polynucleotide construct comprising at least one copy of the recombinant marker gene, a cell comprising at least one exogenous copy of the marker gene, and a method of selecting or identifying a cell comprising at least one copy of the recombinant marker gene, and/or selecting or identifying a cell which has been cured of the recombinant marker gene.