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.

Abstract: The invention herein generally relates to kits and methods for detecting the presence of a bacterium in a subject, for example, methicillin resistant S. aureus.

Abstract: The in vivo and in vitro use of Invaplex to transport materials, including functional proteins and biologically active nucleic acids, across eukaryotic cell membranes. The eukaryotic cells include a variety of cell types, e.g. insect, reptile, fish, mammal and tumor cells. The suitable materials for transport include biochemicals such as reporter molecules, antibiotics, biopharmaceuticals and carbohydrates including polysaccharides, lipopolysaccharides, polynucleotides, such as DNA and RNA, and glycoproteins and proteins including antigens, enzymes, antibodies, receptors and hormones. In addition, Invaplex enhances the immune response to DNA vaccines and also can function by itself as a vaccine against shigellosis.

Abstract: A method of producing a low molecular weight organic compound (e.g. a plant or bacteria secondary metabolite) in increased yields involving use of a microorganism cell, which comprises a gene involved in the biosynthesis pathway leading to a low molecular weight organic aglycon compound and a glycosyltransferase gene capable of glycosylating the produced aglycon.

Abstract: Provided is a microbial composition which is tailored based on the spectrum of microbes found more frequently from the intestine of non-secretor individuals than from the intestine of secretor individuals. Further provided is a method of tailoring a microbial composition based on the spectrum of microbes found more frequently from the intestine of non-secretor individuals than from that of secretor blood group status. Further provided is a use of the secretor status of an individual as a criterion for microbial supplementation tailored based on the differences in the spectra of microbes found between secretor and non-secretor individuals.

Abstract: Disclosed are methods for monitoring the gastrointestinal tract of the human gastrointestinal system. The method includes: 1) grouping microbes into specific operational taxonomic units (OTU); 2) using oligonucleotide probes and PCR primers to detect and quantify specific microbes (bacteria, fungi/yeast, protozoans and parasitic worms) in human fecal material. The inventions also discloses a kit that includes: a DNA isolation step; 2) accumulation of specific operational taxonomic units (OTU); 3) identification and quantifying of sequences internal to the OTU; 4) reporting changes the indigenous population of the human gastrointestinal system.

Abstract: The invention provides methods to detect C. difficile in biological samples using real-time PCR. Primers and probes for the detection of C. difficile are provided by the invention. Articles of manufacture containing such primers and probes for detecting C. difficile are further provided by the invention.

Abstract: A method for cloning and expressing a target gene by homologous recombination, and more particularly a method for cloning and expressing a target gene by homologous recombination, wherein a host cell transformed with a recombinant vector and a plasmid containing a recombinase system is introduced with a linear DNA fragment comprising a target gene and a sequence having homology to the recombinant vector. Because complicated genetic engineering steps, such as the restriction enzyme treatment and ligation of a vector and a target gene, are not required, the cloning of a gene can be performed without needing a high degree of skill, and enzyme cost can be reduced. The inventive method can be effectively used for the massive, high-speed cloning and protein expression of genes, and the disclosed pRMT-iTGR system can be used as an analytical means for improving high-efficiency recombinase.

Abstract: The invention relates to oligonucleotides that are specific for the fungi belonging to Aspergillus genus, and which are able to hybridize to facC gene homologues present in those fungi and show homology with the facC gene of Streptomyces griseus 45H, the sequence of said homologous gene is identical with any sequences of SEQ ID NO: 118 to 120. These oligonucleotides make possible the detection and identification the members of the Aspergillus genus, specifically the Aspergillus fumigatus or Aspergillus terreus.

Abstract: A recombinant adenovirus target-oriented co-expressing human p53 variant and p53AIP1 is disclosed, which is inserted an expression cassette co-expressing human p53 variant and p53AIP1 in E1 deletion region of the adenovirus. The expression cassette consists of tumor specific promoter, human p53 variant, internal ribosome entry site (IRES), human p53AIP1, and SV40.

Abstract: The present invention provides methods to concentrate cells onto microparticles, to concentrate the microparticles, and to detect the cells. The present invention also includes unitary sample preparation and detection devices to be used in accordance with the methods.

Abstract: The present application describes compositions, methods and kits for rapid detection and identification of various microorganisms using inducible RNA. Methods for rapidly detecting microorganisms by detecting expression of inducible RNA of target genes following induction of a target gene using an inducer are described. Some embodiments describe methods and workflows for rapidly detecting microbes such as, but not limited to, Salmonella spp, Listeria spp. and Vibrio spp. Compositions and kits comprise primer nucleic acid sequences having hybridization specificity for priming amplification of genes of microorganisms (or gene fragments) that are responsive to one or more RNA-inducing agents. In some embodiments, kits and compositions further comprise probe nucleic acid sequences having hybridization specificity for genes responsive to RNA-inducing agents or fragments thereof.

Abstract: Methods and devices are provided for the rapid and specific detection of target microorganisms, cells, and the like. In one embodiment, the methods involve contacting a target microorganism (e.g., in a sample) with a permeabilization reagent that selectively permeabilizes or lyses the microorganism; contacting the selectively permeabilized microorganism with a detection reagent that is taken into the selectively permeabilized organism or that contacts metabolites or enzymes released by the selectively permeabilized microorganism, where the detection reagent produces a signal in the presence of said metabolites or enzymes; and detecting a signal produced by the detection reagent in the presence of the metabolites or enzymes wherein the strength of the signal indicates the presence and/or amount of the target microorganism in the sample.

Abstract: The present invention provides nucleic acid amplification methods that desirably reduce or eliminate false positive amplification signals resulting from contaminating biological material, e.g., nucleic acid, that may be present in one or more reagents used in an amplification reaction and/or that may be present in the environment in which an amplification reaction is performed. The invention offers the further advantage of requiring less stringent purification and/or sterility efforts than conventionally needed in order to ensure that enzymes and other reagents used in amplification reactions, and the environment in which an amplification reaction is performed, are free of bacterial or other nucleic acid contamination that may yield false positive results.

Abstract: The present invention provides methods and kits for determining the presence, absence, or level of an infectious agent in a sample. Specifically, the present invention provides methods and kits for detecting or quantifying certain target polynucleotides of the infectious agent. In certain embodiments, the present invention provides for such detection without the need for amplification (e.g., replication) of the target molecule and/or without the need for labor intensive purification procedures. In certain embodiments, the present invention provides positive control and housekeeping gene for normalization and quantatively detection of the copy numbers of infectious agent in a sample. In these or other embodiments, the invention allows for such detection with the desired sensitivity and/or specificity, even where the polynucleotide is present in the sample at low copy number.

Abstract: Essential genes coding for the metabolic pathway of solventogenic autotrophic Clostridia were sequenced, and functionality was confirmed. The present invention utilizes a comparative inter-species approach to develop the minimum set of essential genes for metabolic function and estimate productivity in species of suspected solventogenic capability.

Abstract: Methods and systems for detecting viable bacterial endospores in a sample and related methods to quantify viable bacterial endospores in a sample.

Abstract: The present invention relates to a method for detecting a quantitative trait locus (QTL) associated with resistance to Botrytis cinerea in tomato, including the steps of crossing a Botrytis-resistant donor tomato plant with a non-resistant, or Botrytis-susceptible, recipient tomato plant, contacting one or more offspring plants with an infective amount of Botrytis, quantitatively determining the disease incidence and/or the rate of lesion growth in the one or more offspring plants, establishing a genetic linkage map that links the observed disease incidence and/or rate of lesion growth to the presence of chromosomal markers of the donor tomato plant in the one or more offspring plants, and assigning to a QTL the contiguous markers on the map that are linked to a reduced disease incidence and/or a reduced lesion growth rate.

Abstract: The present invention relates to a method for the specific detection on a filter of one or more microorganisms present in a fluid, characterized in that it comprises the following steps: a) contacting the microorganisms present in the fluid or on the surface with the filter; b) amplifying specifically the nucleic acids from the microorganism or microorganisms present on the filter, in an isothermal manner, in order to obtain amplification products, c) detecting the amplification products. The invention also relates to a device, a kit and oligonucleotides suitable for the implementation of this method.

Abstract: Fluid handling devices, systems, methods and kits are disclosed. Fluid handling devices according to the disclosure comprise: an inlet for receiving a sample; a reagent layer comprising, a substrate having a first surface and an opposing second surface, at least one reagent storage compartment configured to hold a reagent, and a seal in communication with the at least one reagent storage compartment; and a reaction layer having a first surface and an opposing second surface comprising, a reaction area, and an outlet in communication with the reaction area, wherein the reagent layer and reaction layer are adapted and configured to permit movement of at least one of the reagent layer and the reaction layer in a plane relative to the other layer.

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

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

Abstract: An apparatus for detecting the presence of a microorganism in a sample includes a housing that includes a base fixed with a first DNA primer having a nucleotide sequence that is complementary to a DNA sequence of the microorganism of interest, a fibrinogen-splitting agent that is bound with a second DNA primer having a nucleotide sequence that is also complementary to a DNA sequence of the microorganism of interest, a rinsing unit configured to rinse the housing; and a fibrinogen adding unit configured to add fibrinogen to the housing so that the fibrinogen chemically reacts with the fibrinogen-splitting agent to produce a viscous substance, an ultrasonic emitter configured to emit ultrasonic signal to the housing, and an ultrasonic receiver configured to receive ultrasonic signal from the housing and transmit the received ultrasonic signal to an ultrasonic analyzer, wherein the ultrasonic analyzer determines whether the microorganism of interest exists.

Abstract: A method for identifying A. baumannii with OXA-131-like drug resistance in diabetic patients includes the steps of obtaining a sample from a patient; identifying an isolate as A. baumannii; screening the isolate for genes encoding an OXA-51-like enzyme; sequencing any of the genes encoding an OXA-51-like enzyme; and identifying the isolate as OXA-131-like when the sequence matches the sequence for OXA-90 (SEQ ID NO: 1), OXA-130 (SEQ ID NO: 2), OXA-131 (SEQ ID NO: 3), or OXA-132 (SEQ ID NO: 4). The method may further include the step of identifying the ISAba1 sequence upstream from the gene encoding the OXA-131-like enzyme.

Abstract: The present invention relates to a recombinant E. coli exhibiting a complex phenotype, comprising three or more heterologous DNA fragments integrated into a chromosome of the recombinant E. coli bacterium. Also provided are methods for screening such a recombinant E. coli.

Abstract: Nucleic acid sequences are provided which in an embodiment provide a primer pair. The primers are capable of amplifying a nucleic acid molecule that indicates the presence of a propane-oxidizing and/or butane-oxidizing microorganism. A method is provided which employs such primers in a process that indicates the presence of such organisms. The method is useful in detecting the presence of petroleum-like products.

Abstract: The present invention is based on the discovery that drug resistance in microorganisms can be rapidly and accurately determined using mass spectrometry. A mass spectrum of an intact microorganism or one or more isolated biomarkers from the microorganism grown in drug containing, isotopically-labeled media is compared with a mass spectrum of the intact microorganism or one or more isolated biomarkers from the microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting and detecting a characteristic mass shift of one or more biomarkers using algorithms. The characteristic mass shift is indicative that the microorganism is growing in the presence of the drug and incorporating the isotopic label into the one or more biomarkers, resulting in change in mass.

Abstract: The invention relates to CRISPR sequences found in bifidobacteria and their uses.

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

Abstract: 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 methods and compositions useful for the detection and quantitation of analytes. The present invention has particular applicability to the detection and quantitation of analytes in samples of biological origin or that interact with biological systems.

Abstract: The present invention relates to a method for isolating microorganisms and/or microorganisms nucleic acids from a bodily fluid that may comprise or may be suspected to comprise microorganisms and/or host cells and/or host cells debris. Microorganisms nucleic acids may further be isolated by lysing the isolated microorganisms. The present invention also relates to a method for detecting microorganisms in a bodily fluid. The present invention further relates to a saponin formulation and its use.

Abstract: Methods of decreasing non-specific binding in solid phase assays for an analyte are disclosed. In the methods, the solid phase apparatus (lateral flow solid phase apparatus or capillary flow solid phase apparatus) is subjected to elevated heat. The elevated heat can be applied subsequent to application of a test sample to the solid phase apparatus.

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

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

Abstract: The present invention provides a lysis buffer comprising a chaotropic agent and a reducing agent suitable for liquefaction of a highly viscous liquid biological sample, such as sputum, a use of said lysis buffer for the processing of a highly viscous liquid biological sample, methods for processing or analyzing a highly viscous liquid biological sample, or a method for detecting a pathogen within a highly viscous liquid biological sample. Furthermore, the present invention relates to a lysate comprising a highly viscous liquid biological sample and the lysis buffer according to the present invention, a ready-to-use reaction tube and a kit comprising the lysis buffer according to the present invention.

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

Abstract: A self-contained, fully automated, biological assay-performing apparatus includes a housing; a dispensing platform including a controllably-movable reagent dispensing system, disposed in the housing; a reagent supply component disposed in the housing; a pneumatic manifold removably disposed in the housing in a space shared by the dispensing platform, removably coupled to a fluidic transport layer and a plurality of reservoirs, wherein the fluidic transport layer, the reservoirs, and a test sample to be introduced therein are disposed in the housing in the space separate from the dispensing platform; a pneumatic supply system removably coupled to the pneumatic manifold in the housing in a space separate from the dispensing platform; and a control system coupled to at least one of the dispensing platform and the pneumatic supply system, disposed in the housing.

Abstract: A process for detecting the presence or absence of gram-positive bacteria in a biological sample. The biological sample can be obtained from any mammal and contains, at a minimum, cellular components. The sample is combined with an enzymatic lysing agent such as achromopeptidase, and lysed at room temperature. Ferric oxide is then added to the sample containing achromopeptidase. A magnetic field is applied to the sample and nucleic acids are extracted from the cellular components. Target nucleic acids, if present, are amplified using techniques such as Polymerase Chain Reaction (PCR) and then used to detect the presence or absence of gram-positive bacteria. Staphylococcus aureus and Streptococcus agalactiae are examples of target bacteria detected by the methods of the present invention.

Abstract: Fast and highly accurate mass spectrometry-based processes for detecting particular nucleic acid molecules and mutations in the molecules are provided.

Abstract: The present invention relates, inter alia, to a method for detecting methicillin-resistant Staphylococcus aureus (MRSA) strains, wherein one of the following method variants is carried out: variant A a) chromosomal DNA of S. aureus is isolated from the sample by means of a genome probe, and b) a nucleotide sequence which is specific for MRSA is detected in the isolated DNA; or variant B a) DNA is isolated from the sample, wherein the isolation makes use of a genome probe which is specific for an MRSA nucleotide sequence, preferably an MRSA resistance gene, and b) the DNA isolated in step a) is tested for specific sequences of S. aureus. In addition, suitable kits for carrying out the corresponding methods are provided.

Abstract: Method for producing multiple modifications in the chromosome of Gram-negative bacteria and Salmonella strains which are deficient in c-di-GMP synthesis obtained by said method. The method can be used to make multiple modifications in the genome of Gram-negative bacteria, simply and efficiently, using the plasmids of the invention, which comprise a marker gene under the control of a constitutive promoter, a replication origin specific for Gram-negative bacteria, a gene which encodes a heat-sensitive protein essential for initiating replication of the plasmid, making the replication origin heat-sensitive, and a counter-selection gene.

Abstract: The invention generally relates to using magnetic particles and alternating magnet fields to separate a target analyte from a sample. In certain embodiments, methods of the invention involve contacting a sample with magnetic particles including first moieties specific for a target analyte, thereby forming target/particle complexes in the sample, flowing the sample through a channel including second moieties attached to at least one surface of the channel, applying alternating magnetic fields to the flowing sample to result in target/particle complexes being brought into proximity of the surface to bind the second moieties and unbound particles remaining free in the sample, binding the target/particle complexes to the second moieties, and washing away unbound particles and unbound analytes of the sample.

Abstract: The invention generally relates to conducting an assay on a sample that isolates a bacterium from the sample, in which the assay isolates as low as about 1 CFU/ml of bacteria in the sample.

Abstract: The invention generally relates to conducting an assay on a sample that isolates a pathogen from the sample and allows for analysis of the pathogen with minimal (i.e., at most 24 hrs of culturing) or no culturing of the pathogen. In certain embodiments, the invention provides methods for identifying a pathogen from a sample that involve obtaining a sample including a pathogen, conducting an assay that isolates the pathogen from the sample, culturing the isolated pathogen for at most about 24 hrs, and analyzing the pathogen.

Abstract: The present invention allows a screening method for identifying novel drugs for the treatment of tuberculosis as well as a diagnostic method for identifying clinical strains that are resistant to these novel drugs. In particular, the present invention relates to a method for screening in vitro drug candidates for the treatment of tuberculosis by interfering with the arabinogalactan biosynthesis, the said method comprising a step of putting into contact a Mycobacterium tuberculosis cell culture overexpressing a protein that performs the transformation of decaprenyl-P-ribose to decaprenyl-P-arabinose and that can be encoded by rv3790 gene or homologues thereof or any open-reading artificial frame whose gene product is identical or homologue to Rv3790 protein, with a drug candidate and then evaluating the percentage of inhibition caused by the drug candidate against a control in an assay test, such as an antibacterial test or an enzymatic test.

Abstract: The invention generally relates to methods of using compositions that include sets of magnetic particles, members of each set being conjugated to an antibody specific for a pathogen, and magnets to isolate a pathogen from a body fluid sample.

Abstract: The invention features compositions and methods that are useful for the detection of a target analyte, such as a pathogen, in a sample.