Abstract: The invention relates to a method for detecting Kingella microorganisms through PCR of a chaperonin gene.

Abstract: The present invention provides a method, a kit and composition for determining MRSA and other Staphylococcus strain resistance to one or more antibiotic agents through detecting the presence of the respective antibiotic resistance gene. The methods include real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes.

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: The present invention provides systems, methods, and compositions for identifying a subject as infected with a parasite by detecting nucleic acid from an endosymbiont of the parasite in a sample from the subject. In certain embodiments, the parasite is a nematode that infects humans or dogs (e.g., D. immitis, O. volvulus, W. bancrofti, B. timori, or B. malayi) and the endosymbiont is Wolbachia.

Abstract: A primer pair and probe for the large subunit ribosomal RNA gene of enterococci for use in a real-time nucleic acid sequence based amplification (NASBA) assay.

Abstract: The present invention relates to an isolated nucleic acid sequence coding for a PntR transcription factor comprising a nucleotide sequence that is the same as, or is complementary to, or contains any suitable codon substitutions for any of those of SEQ ID NOs: 1, 3 or 5 or comprises a sequence which has at least 60% sequence homology with any of SEQ ID NOs: 1, 3 or 5, as well as corresponding polypeptides, vector systems and host cells comprising the same. In particular, the invention relates to sequences which are obtained from an Aspergillus, Trichoderma or Penicillium cell. The invention further relates to methods for disrupting PntR expression in a cell as well as methods for expression or production of a POI in a host cell in which PntR expression has been disrupted.

Abstract: Compositions and methods are provided for enhanced expression of light emitting reporters. Such reporters are used in methods for monitoring cultures for production of target compounds. Additionally, methods are provided for the use of light emitting reporter systems and other reporter systems for selecting desired traits in an organism and for identifying or optimizing culture conditions.

Abstract: In various embodiments, the present disclosure describes methods and systems for detecting microbes in a sample. The methods are generally applicable to quantifying the number of target bacteria in a sample counted from a detection region of a flow cytometer histogram. The detection methods can be employed in the presence of other microorganisms and other non-target microbe components to selectively quantify the amount of a target microbe. The methods are advantageous over those presently existing for testing of foodstuffs and diagnostic evaluation in their speed, accuracy and ease of use. Various swab collection devices and kits useful for practicing the present disclosure are also described herein.

Abstract: The present invention pertains to a molecular biology-based method and kit for measuring the specific growth rate (or cell doubling time) of distinct microbial populations. The method and kit can be used to analyze mixed culture samples that have been exposed to chloramphenicol or other protein synthesis inhibitors for defined times. In a preferred embodiment, the method of the invention (also referred to herein as FISH-RiboSyn) is an in situ method that utilizes fluorescence in situ hybridization (FISH) with probes that target: (1) the 5? or 3? end of precursor 16S rRNA; or (2) the interior region of both precursor 16S rRNA and mature 16S rRNA. Images can be captured for a defined exposure time and the average fluorescent intensity for individual cells can be determined. The rate of increase of the whole cell fluorescent intensity is used to determine the specific growth rate.

Abstract: The present invention relates to methods and compositions for improved detection of infectious agents and microbes. In particular, the present invention provides novel methods for detecting infectious agents, providing information about the viability status of such infectious agents and for determining drug susceptibility. In certain embodiments, the present invention employs techniques involving nucleic acid amplification-based microbial identification together with phage-based biological detection of drug resistance. The methods of the invention are suitable for all microbes and infectious agents, including bacterial agents such as Mycobacteria.

Abstract: The invention provides biosynthetic routes to xylitol production that do not require pure D-xylose for synthesis and that can utilize inexpensive substrates such as hemicellulose hydrolysates.

Abstract: A process for analysing a biological sample, comprising the steps of: (a) identifying a micro-organism present within the sample; and (b) determining the effect of one or more antimicrobial(s) on a micro-organism from the sample, wherein steps (a) and (b) are performed by analysing the micro-organism's nucleic acid. Steps (a) and (b) will generally occur in that order, but they may take place concurrently. The steps may advantageously be performed within a single apparatus. Conveniently, the nucleic acid analyte used for step (a) is the same as that used in step (b) e.g. the same PCR amplicon. A micro-organism's nucleic acids can thus be used both to identify the presence of the micro-organism within a sample and then to assess the effect of antimicrobials on its growth.

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: The present invention is a method of extracting infectious pathogens from a volume of blood including the steps of creating a fibrin aggregate confining the pathogens and introducing a fibrin lysis reagent to expose the pathogens for analysis. The fibrin lysis reagent is preferably composed of plasminogen and streptokinase frozen in coincident relation until the fibrin lysis reagent is needed whereby streptokinase enzymatically reacts with plasminogen to form plasmin upon thawing. The plasminogen is suspended in an aqueous salt solution prior to freezing including NaCl and Na3PO4.

Abstract: Systems and methods for diagnosing parasite infections. According to at least one embodiment of a stabilizing system of the present disclosure, a stabilizing system comprises a stabilizing agent useful to completely or substantially prevent degradation or inactivation of a diagnostic marker for a parasite infection in a body fluid comprising the diagnostic marker and a detection agent capable of detecting the diagnostic marker.

Abstract: Systems and methods of analyzing biomarker levels. In at least one embodiment of a method of analyzing biomarker levels, the method comprises the steps of combining a body fluid comprising a diagnostic marker with a stabilization agent for an incubation period, introducing the stabilized body fluid into a detection platform, combining a detection agent with the stabilized body fluid, determining an interaction characteristic of the detection agent and the diagnostic marker of the stabilized body fluid using a detection device in communication with a processor, comparing the interaction characteristic with a plurality of indexed interaction records contained on a database in communication with the processor to determine an identity and concentration of the detection marker, generating a report of the identity and concentration of the detection marker in the body fluid, and delivering the report to a recipient.

Abstract: Rinse composition for the stabilization of diagnostic biomarkers. In at least one embodiment of a rinse useful to stabilize a diagnostic marker, the rinse comprises a stabilizing agent useful to completely or substantially prevent degradation or inactivation of a diagnostic marker in saliva, and a liquid.

Abstract: Systems and methods for diagnosing bacterial infections. According to at least one embodiment of a system of the present disclosure, the system a stabilizing agent useful to completely or substantially prevent degradation or inactivation of a diagnostic marker for a bacterial infection in a body fluid comprising the diagnostic marker and a detection agent capable of detecting the diagnostic marker.

Abstract: Chewable compositions for the stabilization of diagnostic biomarkers. In at least one embodiment of a chewing gum composition useful to stabilize a diagnostic marker, the a chewing gum composition comprises a stabilizing agent useful to completely or substantially prevent degradation or inactivation of a diagnostic marker in saliva, and a liquid.

Abstract: Drink mixture for the stabilization of diagnostic biomarkers. In at least one embodiment of an ingestible beverage useful to stabilize a diagnostic marker, the rinse comprises a stabilizing agent useful to completely or substantially prevent degradation or inactivation of a diagnostic marker in saliva, and a liquid.

Abstract: Systems and methods for diagnosing fungal infections. According to at least one embodiment of a stabilizing system of the present disclosure, the system comprises a stabilizing agent useful to completely or substantially prevent degradation or inactivation of a diagnostic marker for a fungal infection in a body fluid comprising the diagnostic marker and a detection agent capable of detecting the diagnostic marker.

Abstract: The present invention is a method of extracting infectious pathogens from a volume of blood including the steps of creating a fibrin aggregate confining the pathogens and introducing a fibrin lysis reagent to expose the pathogens for analysis. The fibrin lysis reagent is preferably composed of plasminogen and streptokinase frozen in coincident relation until the fibrin lysis reagent is needed whereby streptokinase enzymatically reacts with plasminogen to form plasmin upon thawing. The plasminogen is suspended in an aqueous salt solution prior to freezing including NaCl and Na3PO4.

Abstract: The present invention relates generally to identification of fungi pathogens, and provides methods, compositions, systems and kits useful for this purpose when combined, for example, with molecular mass or base composition analysis.

Abstract: The present invention provides live, attenuated Mycoplasma gallisepticum bacteria that exhibit reduced expression of a protein identified as MGA_0621. In certain embodiments, the attenuated bacteria may additionally exhibit reduced expression of one or more proteins selected from the group consisting of pyruvate dehydrogenase, phosphopyruvate hydratase, 2-deoxyribose-5-phosphate aldolase, and ribosomal protein L35, relative to a wild-type M. gallisepticum bacterium. Also provided are vaccines and vaccination methods involving the use of the live, attenuated M. gallisepticum bacteria, and methods for making live attenuated M. gallisepticum bacteria. An exemplary live, attenuated strain of M. gallisepticum is provided, designated MGx+47, which was shown by proteomics analysis to exhibit significantly reduced expression of MGA_0621, and was shown to be safe and effective when administered as a vaccine against M. gallisepticum infection in chickens.

Abstract: The present invention relates generally to identification of antibiotic-resistant bacteria and provides methods, compositions and kits useful for this purpose when combined, for example, with molecular mass or base composition analysis.

Abstract: The present invention relates generally to identification of members of the bacterial class Mollicutes or the bacterial genus Mycoplasma and provides methods, compositions and kits useful for this purpose when combined, for example, with molecular mass or base composition analysis.

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

Abstract: The present invention relates generally to identification of members of the bacterial class Alphaproteobacter and provides methods, compositions and kits useful for this purpose when combined, for example, with molecular mass or base composition analysis.

Abstract: The present invention relates generally to the identification of Streptococcus pneumoniae, such as antibiotic resistant Streptococcus pneumoniae, and provides methods, compositions, kits and systems useful for this purpose when combined, for example, with molecular mass or base composition analysis.

Abstract: Certain embodiments disclosed relate to compositions, including therapeutic compositions, methods, devices, and systems that include modified microorganisms including at least one genetic element encoding at least one therapeutic agent or environmental treatment agent.

Abstract: Certain embodiments disclosed relate to compositions, including therapeutic compositions, methods, devices, and systems that include modified microorganisms including at least one genetic element encoding at least one therapeutic agent or environmental treatment agent.

Abstract: The invention relates to methods and compositions for identifying and selecting maize plants with enhanced resistance to Fusarium ear mold. Maize plants generated by the methods of the invention are also a feature of the invention.

Abstract: Methods for detecting an infection with Mycobacterium tuberculosis (Mtb) in a subject are disclosed, wherein the subject is a child, a subject with a latent Mycobacterium tuberculosis infection. Method are also disclose for detecting an extra-pulmonary Mycobacterium tuberculosis infection in a subject. The methods include detecting the presence of CD8+ T cells that specifically recognize an Mtb polypeptide. The methods include in vitro assays for detecting the presence of CD8+ T cells in a biological sample.

Abstract: The present invention relates generally to the detection and identification of Neisseria, Chlamydia, and/or Chlamydophila bacterial bioagents, and provides methods, compositions and kits useful for this purpose when combined, for example, with molecular mass or base composition analysis.

Abstract: Certain embodiments disclosed relate to compositions, including therapeutic compositions, methods, devices, and systems that include modified microorganisms including at least one genetic element encoding at least one therapeutic agent or environmental treatment agent.

Abstract: The invention generally relates to methods and kits for isolating nucleic acids from an organism. In certain embodiments, methods of the invention involve contacting a plurality of lytic enzymes to an organism, thereby lysing a cell wall of the organism to release the nucleic acid, and introducing at least one agent to separate the nucleic acid from the lysed cells, thereby isolating the nucleic acid.

Abstract: The present invention provides oligonucleotide primers, compositions, and kits containing the same for rapid identification of bacteria which are members of the Francisella genus by amplification of a segment of bacterial nucleic acid followed by molecular mass analysis.

Abstract: A modified vector comprising a reporter gene having a STOP codon upstream of the multiple cloning site of the vector which is characterized in that the recombinant clones show fluoresce or show color in presence of inducer. A method for identification and selection of recombinant clones comprising the modified vector wherein the recombinant clones florescence or show color in a suitable suppressor strain of the STOP codon associated with the gene of interest.

Abstract: The invention provides methods of screening a microbial host cell for a property of interest in a microfluidic device, the method comprising the steps of: a) transforming a d-alanine racemase-deficient microbial host cell with a polynucleotide construct comprising: i) one or more polynucleotide region providing the property of interest when present in the host cell, and ii) at least one polynucleotide region complementing the d-alanine racemase deficiency when present in the host cell; and b) screening the transformed host cell for the property of interest in the microfluidic device in the absence of externally provided d-alanine.

Abstract: The present invention relates to identification of centromeric sequences of Candida dubliniensis and localization of CdCse4p centromeric histone to the identified region. Also the present invention relates to distinguishing Candida dubliniensis from other members of genus Candida.

Abstract: The subject invention concerns materials and methods for evaluating the susceptibility of bacterial cells to an antibiotic or other antimicrobial compound or agent. In one embodiment, a sample comprising a microbial population is exposed to an antibiotic of interest. The sample is then processed using FISH-RiboSyn methods to determine the specific growth rate of the antibiotic-exposed microbes as compared to an untreated control. The subject invention also concerns materials and methods for determining the most suitable and/or effective antibacterial treatment for a person or animal having a bacterial infection.

Abstract: The present invention relates to methods of detection, as well as assays, reagents and kits for the specific detection of clinically important bacterial and fungal species. The present invention allows for the specific detection of nucleic acids of each of these pathogens in a single assay.

Abstract: The invention provides a method for generating and selecting drug-sensitizing antisense DNA fragments. In one embodiment, the method includes identifying a gene of interest using knowledge of bacterial physiology, biochemistry, genetics, genomics, and other means. The method includes PCR amplification of a gene of interest using genomic DNA as a template; fragmentation of the DNA by sonication or other means; selecting DNA fragments no longer than 400 base pairs; ligating the DNA fragments into a suitable expression plasmid with a selectable marker; transforming the plasmids containing the DNA fragments into the organism from which the gene of interest originated; and selecting clones from transformed cells that show a phenotypic difference of the clone grown in the presence of the inducer relative to the phenotype in the absence of inducer.

Abstract: A method of detecting a heat-resistant fungus, which has a step of identifying the heat-resistant fungus using the following nucleic acid (I) or (II): (I) a nucleic acid including a nucleotide sequence set forth in any one of SEQ ID NOS: 24 to 35 and 83 to 86, or a complementary sequence thereof; or (II) a nucleic acid including a nucleotide sequence resulting from a deletion, substitution, or addition of one to several nucleotides in the nucleotide sequence set forth in any one of SEQ ID NOS: 24 to 35 and 83 to 86 and being capable of detecting the heat-resistant fungus, or a complementary sequence thereof.

Abstract: A method for detecting a microorganism comprising reducing the complexity of a microbial genome or microbial nucleic acid by generating a simplified form of the microbial genome or microbial nucleic acid in which substantially all of the positions naturally occupied by cytosines are occupied by uracil or thymine; and assaying for a microbial specific nucleic acid in the simplified form of the microbial genome or microbial nucleic acid, wherein presence of the microbial specific nucleic acid is indicative of the microorganism.

Abstract: Assays for detecting anti-streptococcal antibodies in biological samples using one or more streptococcal antigens are described herein. Various combinations of antigens may be used in the assays. For example, one or more of Ply, PhtD, PhtE, LytB and PcpA may be utilized. Additional streptococcal antigens may also be used. The assays may also be used in combination with assays that detect streptococcal nucleic acids.

Abstract: A method for evaluating relative bacterial virulence of a biphasic bacteria in environmental systems includes measuring the concentration of DNA in the bacteria, measuring the concentration of RNA in the bacteria, determining a ratio of the concentration of RNA to the concentration of DNA and correlating the concentration ratio with a level of relative pathogenicity, wherein the bacteria is preferentially Legionella pneumophila, Mycobacterium tuberculosis and Listeria.

Abstract: A method of collecting, detecting and enumerating microorganisms in a fluid comprising subjecting a sample of the fluid to dielectrophoresis and collecting the microorganisms onto a microelectrode, scanning the microelectrode using a scanning laser and determining the number of microorganisms present on the microelectrode. Alternatively, the microorganisms may be spun onto a substrate which has been pre-treated with a polycationic electrolyte.