Abstract: A computer program product includes a recordable-type signal bearing medium bearing computer usable code configured for causing an automatic evaluation, remotely from a health care facility, of a biological sample acquired from a subject for a presence or an absence of at least one pathogen in the biological sample; computer usable code configured for electronically queuing a first result of the evaluation for transmission to an off-site entity; and computer usable code configured for reporting a second result of the evaluation to the subject after queuing the first result of the evaluation for transmission.

Abstract: The invention is directed to aptamers, methods and kits comprising same for detecting Streptococcus pyogenes. The method of screening a subject for Streptococcus pyogenes involves obtaining a body sample from the subject; contacting the sample or a bacterial culture of the sample with an aptamer or a panel of aptamers specific to S. pyogenes; and detecting the presence or absence of S. pyogenes in the sample or the bacterial culture, wherein binding of the aptamer is indicative of the presence of S. pyogenes.

Abstract: A marker for determining the onset of periodontal disease and a marker far determining the progression stage of periodontal disease, each containing autoinducer-2.

Abstract: Clostridium difficile disease involves a range of clinical presentations ranging from mild to self-limiting diarrhea to life-threatening pseudomembranous colitis and megacolon. Cases of C. difficile are treated differently depending on severity of disease. Mild and moderate cases may be treated with metronidazole while moderate-to-severe and relapsing cases are often treated with vancomycin or fidaxomicin. The presence of C. difficile disease is detected using a biomarker panel that includes C. difficile antigen (GDH), toxins A and B, and fecal lactoferrin. In patients suspected of C. difficile disease, if GDH is detected indicating the presence of C. difficile, and then toxins A and/or B are detected to indicate toxigenic C. difficile and support a diagnosis of C. difficile-associated disease, fecal lactoferrin concentrations are measured to determine severity of the disease by indicating the amount of intestinal inflammation.

Abstract: Presented herein are methods and compositions for generating sequence-specific, secondary amplification products during Loop-mediated Isothermal Amplification (LAMP). Conventional LAMP produces a preponderance of high molecular weight DNA structures concatenated into self-complementary hairpins, which are not amenable to detection by routine probe-based hybridization methods, making multiplex detection of two or more targets or sequence variants in closed-tube formats extremely difficult. Provided herein, for example, are methods for generating secondary LAMP products bearing a fragment of the original target sequence embedded within low-molecular weight products that are devoid of competitive hairpin structures, the lack of which enhances probe-based detection of target sequences. These secondary products can, for example, be produced in real-time, during the LAMP process, and can provide the option of detecting multiple target sequences within a single tube using, e.g.

Abstract: Embodiments disclosed herein relate to a method of detecting specific DNA sequences and the application of this method in the detection of pathogens, viruses, drug-resistant pathogens, genomic variations associated with disease/disorder susceptibility etc. based on specific signature sequences unique to the pathogens, viruses, drug-resistant pathogens or genomic variations. The method can also be used to distinguish a pool of same-sized dsDNA on the basis of sequence differences. The method uses non-optically labeled bis-PNA and/or gamma-PNA probes to tag specific target sequences for identification by solid-state nanopores.

Abstract: Atoxic Clostridium difficile toxin proteins were expressed in an endotoxin-free Bacillus system top develop a vaccine to reduce incidence and severity of C. difficile infection (CDI). Immunogens evaluated as potential vaccine candidates are mutated toxin A (encoded by TcdA) and toxin B (TcdB), and a rationally designed chimeric protein containing full-length TcdB protein except that the receptor binding domain is replaced with that of TcdA (designated as cTxAB). A small deletion (97 amino acids) in the transmembrane domain was used to reduce or eliminate toxicity.

Abstract: A kit for use in a method for detecting live cells, injured cells and dead cells of a microorganism in a test sample by a nucleic acid amplification method is disclosed. The kit includes a cross-linker capable of cross-linking DNA by irradiation with light having a wavelength of 350 nm to 700 nm, medium, and a primer (s) for amplifying a DNA target region in the microorganism by a nucleic acid amplification method. The nucleic acid amplification method may be a PCR, LAMP, SDA, LCR or DNA microarray method. A cross-linker may be included in the kit such as ethidium monoazide, ethidium diazide, psoralen, 4,5?,8-trimethyl psoralen, or 8-methoxy psoralen.

Abstract: The invention relates to systems and methods for analyzing clinically relevant nucleic acid sequences.

Abstract: A marker for determining the onset of periodontal disease and a marker for determining the progression stage of periodontal disease, each containing autoinducer-2.

Abstract: The present invention provides methods and kits that may be used to detect and quantify the presence of Coccidioides species. The methods include quantification PCR assays, and the kits and compositions include oligonucleotides used as primers and probes.

Abstract: The present invention relates to methods for the diagnosis of bacterial vaginosis based on an analysis of a patient sample. For example, patient test samples are analyzed for the presence or absence of one or more lactobacilli and two or more pathogenic organisms. The presence or absence of one or more lactobacilli and two or more pathogenic organisms may be detected using PCR analysis of nucleic acid segments corresponding to each target organism. The quantity of the target organisms can then be used to determine a score which is indicative of a diagnosis of bacterial vaginosis.

Abstract: The invention provides methods for predicting the likelihood that a subject will develop a sterile inflammation or will have an increased propensity to later develop a sterile inflammation, for determining whether a subject with tissue damage should be administered an antimicrobial agent (at full or a reduced dosage) or an anti-inflammatory agent, and for treating a subject with tissue damage. In the methods, an increased ratio of the amount of mitochondrial nucleic acid or peptide to the amount of microbial nucleic acid or peptide indicates a subject that has an increased likelihood of developing a sterile inflammation or an increased propensity to later develop a sterile inflammation, or a subject that should not be administered, or that should be administered at a reduced dosage, an antimicrobial agent or one or more anti-inflammatory agents and not an antimicrobial agent. Kits for detecting mitochondrial and/or microbial nucleic acids or peptides are provided.

Abstract: A rapid, safe method for predicting sepsis, or a condition similar to sepsis, in a mammal is disclosed, which comprises the following steps: I) isolating RNA from a biological sample of a mammal; ii) labeling the isolated RNA of step I) with a detectable marker; iii) hybridizing the labeled isolated RNA of step ii) with at least one DNA of genes Seq.-ID 1 to Seq.-ID 6705 (Table 1), which is spotted onto a microarray and which is a sepsis-specific gene or gene fragment, under the reaction conditions for hybridizations; iv) quantitatively recording labeling signals of the hybridized RNA of step iii) in an expression profile; v) comparing the expression profile of step iv) with a control sample with respect to a stronger or weaker expression of genes or gene fragments which are specific for sepsis; and vi) combining the expression profile of step v) with protein- and metabolite patterns of the biological sample.

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 present invention relates to beacons for fluorescent in-situ hybridisation and chip technology.

Abstract: This invention comprises a multiplex-capable oligonucleotide which is capable of hybridizing to at least one of the C. difficile tcdB, tcdC, or cdtB genes, wherein, wherein said primer consists of a sequence selected from the group consisting of SEQ ID NOS: 1 through 9, or a sequence that exhibits no more than one substitution of a base to a sequence selected from the group consisting of SEQ ID NOS: 1 through 9 and method for polymerase chain reaction (PCR) determining of the presence of a toxigenic strain of C. difficile in a biological sample utilizing said probes.

Abstract: The present invention concerns a method of detection and preferably of quantification of DNA, preferably comprising prokaryotic DNA, extracted from a stool sample of an individual, especially for the molecular determination of the composition of the intestinal flora in the stool. According to the invention, one controls the quality of the DNA extraction by verifying whether one detects a specific DNA of Methanobrevibacter smithii and one performs the quantification of said specific prokaryotic DNA for Archae Methanobrevibacter smithii, for the bacterial genus Lactobacillus, for the phylum Bacteroidetes and for the phylum Firmicutes, respectively, to provide a diagnosis and/or monitoring of the weight status of an individual. The present invention provides a method for carrying out the extraction of prokaryotic DNA in stools.

Abstract: Methods and compositions are provided for performing a set of N DNA sequencing reaction cycles whereby sequence information is obtained for approximately 2*N nucleotide bases.

Abstract: The present invention relates to a method for selectively enriching and/or isolating microbial and optionally additionally viral nucleic acids from samples that contain a mixture of microbial cells, freely circulating nucleic acids and higher eukaryotic cells, and optionally additionally viruses, in a liquid, and to a kit for selectively enriching and/or isolating intracellular and extracellular microbial nucleic acids, and optionally additionally viral nucleic acids, from samples that contain a mixture of microbial and higher eukaryotic cells, freely circulating nucleic acids, in particular extracellular microbial nucleic acids, and optionally additionally viruses in a liquid.

Abstract: Provided herein are methods and systems for the detection of spores in a sample which comprise permeabilizing a protein-based spore coat with a protein degrading agent comprising a non-ionic detergent and in particular with a specific mixture of various protein degrading agents comprising a non-ionic detergent to allow contact of spore nucleic acids with fluorescent reagents suitable for detection.

Abstract: The present disclosure relates generally to the field of nucleic acids and, more particularly, to aptamers capable of binding to toxins produced by Clostridium difficile; diagnostic kits and methods comprising such aptamers; and methods of making and using such aptamers.

Abstract: In one aspect, the invention relates to compounds and methods useful for activating heme sensor systems; for decreasing virulence of bacteria, for example, Staphylococcus aureus; pharmaceutical compositions comprising the compounds; and methods of treating microbial-related disorders. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present invention.

Abstract: The present invention relates to a carbapenemase and methods using said carbapenemase such as screening methods, predictive methods and therapeutic uses.

Abstract: The present invention relates to cultivated tomato plants that are resistant to the pathogenic fungus Botrytis cinerea, which is control led by at least one QTL, particularly by 2 and 3 QTL contributing to said resistance, wherein said QTL are mapping to linkage group 6, and/or linkage group 1b and/or linkage group 9b. The invention further relates to methods for producing said plants, and to the use thereof.

Abstract: The present invention relates to an inhibitor capable of increasing accuracy of the reaction in hybridization, and inhibiting nonspecific hybridization, a clinical diagnostic reagent, and a method of clinical analysis whereby nonspecific hybridization in clinical analysis is inhibited, and a target nucleic substance is detected easily with high accuracy. The inhibitor and the clinical diagnostic reagent contains polymer (H) having a nonspecific hybridization inhibitory action. The polymer has in its molecule at least one of carboxyl and sulfone groups, and phosphorylcholine-like groups, and has a weight average molecular weight of 1000 to 5000000. The method of clinical analysis includes contacting a sample with a test agent capable of hybridizing with a specific nucleic substance in the presence of the inhibitor.

Abstract: A newly isolated lytic bacteriophage specifically against Klebsiella pneumoniae, deposited at DSMZ-Deutsche Sammlung von Mikroorganismen and Zellkulturen with deposit number (DSM 24329), shows broad host ranges and lytic effects on K. pneumoniae isolated from Taiwan under either in vivo or in vitro models.

Abstract: Provided herein are rotation-dependent transcriptional sequencing methods and systems.

Abstract: The invention provides a system of enhancing the expression of transgenes in algae. Transgenes are engineered to have a binding site for certain proteins in proximity to their promoter, for example a LexA binding site. The algae is also engineered to express a nucleosome alteration protein fused to a protein with affinity to the DNA binding site acting in coordination. An example is a LexA-p300 fusion protein, where the p300 is derived from Chlamydomonas. The LexA binding domain guides the p300 to the binding site and the p300 loosens the nucleosome structure by acetylating histones within proximity of the transgene, thus remodeling the local chromatin structure to allow for high-level expression.

Abstract: This disclosure concerns a plant of the genus, Brassica, or parts thereof, which comprise one or more traits selected from the group consisting of high oleic acid content, low linolenic acid content, increased herbicide resistance, restorer of cytoplasmic male sterility, and increased clubroot disease (Plasmodiophora brassicae) resistance, compared to a wild-type plant of the same species. This disclosure further relates to wild-type and mutant alleles of genes involved in these traits, molecular markers linked thereto, and methods of their use.

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 device for collecting and concentrating biological or chemical targets with a view to detecting same, wherein the device comprises a reaction chamber (1) in which functionalized magnetic beads (2) are placed, an ultrasonic agitation system (3), a magnetic field (4) that can be activated (ON position) or inactivated (OFF position), and a fluid movement system (5) for feeding (51) and discharging (52) a portion or the entirety of the contents of the reaction chamber. The present invention also relates to a method for capturing biological or chemical targets using said device.

Abstract: The present application relates to a composition comprising extracellular membrane vesicles derived from indoor air. In addition, the present application provides a method for diagnosing, preventing and/or treating an inflammatory respiratory disease, lung cancer and the like using the extracellular membrane vesicles. In detail, the present application involves injecting extracellular membrane vesicles present in indoor air into an animal in order to prepare an animal respiratory disease model, and enables the search and/or discovery of drug candidates for preventing or treating respiratory diseases using the animal model.

Abstract: The present invention relates to peptide nucleic acid (PNA) probes, PNA probe sets and methods for the analysis of certain Staphylococcus species optionally present in a sample. The invention further relates to diagnostic kits comprising such PNA probes or PNA probe sets.

Abstract: A method of identifying an M17 strain of E. coli in a human biological sample is provided. The method comprises analyzing products of an amplification reaction using DNA extracted from the human biological sample and a primer pair which amplifies an M17 specific nucleic acid sequence of an M17 nucleic acid sequence, wherein the primer pair is selected from the group consisting of SEQ ID NOs: 37 and 38; SEQ ID NO: 39 and 40; and SEQ ID NOs: 45 and 46, wherein a product of the amplification reaction is indicative of an M17 strain of E. coli. Additional primers and kits comprising same are also provided.

Abstract: The present invention is directed to a nucleic acid detection device and method that incorporates bio-nanosensor technology to detect duplex DNA. The device is particularly applicable in detecting the presence or absence of duplex DNA and its correlation to the diagnosis of infectious diseases. In one embodiment, the infectious disease is Lyme disease or a bacterial or viral infection. The device comprises a bio-nanosensor element comprising ssDNA primed nanotubes, either single walled or multi-walled. The method comprises contacting the bio-nanosensor element with a test solution potentially containing DNA of interest. DNA of interest that hybridizes to the ssDNA results in a measurable change in the electrical properties of the bio-nanosensor. Correlations between the results provided by the device and the presence of disease states can result in rapid diagnosis of diseases such as Lyme disease or foodborne infections such as salmonellosis.

Abstract: The invention discloses the use of a protein with an amino acid sequence according to SEQ. ID. NO. 1 or a naturally occurring fragment or variant thereof for identifying infections with S. aureus in a human sample. More specifically, IgE molecules specific for SEQ. ID. NO. 1 are detected in the sample of the patient. Many atopic dermatitis patients have IgE specific for SEQ. ID. NO. 1.

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

Abstract: The present invention relates to methods for detecting the presence or absence of vancomycin resistant enterococci (VRE) in a sample using a multiplex polymerase chain reaction (mtx-PCR) assay. Furthermore, the present invention relates to oligonucleotide primers and kits for the detection of VRE.

Abstract: The present invention relates to methods for characterization of bacterial skin microbiota to provide diagnostic, therapeutic, and preventive measures for alleviating skin conditions. In certain embodiments, the invention relates to characterization of bacterial skin microbiota associated with psoriasis and related diagnostic, therapeutic, and preventive measures for alleviating psoriasis. These methods will be useful for detecting, diagnosing, and monitoring individuals who have or are at risk of certain skin conditions.

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. 84 to 86 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 provides methods of: identifying pathogens in biological samples from humans and animals, resolving a plurality of etiologic agents present in samples obtained from humans and animals, determining detailed genetic information about such pathogens or etiologic agents, and rapid detection and identification of bioagents from environmental, clinical or other samples.

Abstract: Described herein are primers and probes useful for the detection, screening, isolation and sequencing of MRSA, MSSA, Staphylococci markers, and the antibiotic resistance gene mecA.

Abstract: The present invention provides a method of specifically detecting the presence of one or more Mycobacteria of the M. tuberculosis complex, said method comprising detecting ilvC nucleic acid of one or more Mycobacteria of the M. tuberculosis complex in a sample under conditions that do not detect ilvC nucleic acid of the M. avium complex. The invention also provides methods of diagnosis and treatment of tuberculosis in a subject employing the specific detection ilvC nucleic acid of one or more Mycobacteria of the M. tuberculosis complex.

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 oligonucleotides useful in methods for determining whether a sample contains Borrelia afzelii, a spirochete which is a causative agent of Lyme disease in humans. These oligonucleotides, which have nucleotide sequences derived from a coding segment of the gene encoding the p24 gene for the outer surface protein of Borrelia afzelii, are useful as forward and reverse primers for a polymerase chain reaction using nucleic acids from a biological sample as templates, and as probes for detecting any resultant amplicon. Detection of an amplicon indicates the sample contains Borrelia afzelii. Real-time PCR and detection using florescence resonance energy transfer is disclosed.

Abstract: The present invention makes known an array of nucleotidic sequences for rapidly and simultaneously identifying the presence of certain genes that codify proteins with relevant activities in biotechnology present in a microbiological sample, and the method with which this array is used in the identification of the above mentioned genes. Specifically speaking, genes that codify for proteins relevant in the biofilm formation, in CO2 fixation, in energetic metabolism, for chemiotaxis and mobility, in iron oxidizing, in nitrogen metabolism, in sulfur assimilation, and in oxidation/reduction of sulphide compounds, are identified. This array of nucleotidic sequences is presented as a useful tool in biotechnology whenever evaluating the quality of a microbiological community is required.

Abstract: The invention provides an improved method for sensitive and specific detection of target molecules, cells, or viruses. The inventive method uses large area imaging to detect individual labeled targets complexed with a target-specific selection moiety. The invention eliminates wash steps through the use of target-specific selection through one or more liquid layers that can contain optical dye and density agents. By eliminating washes the invention simplifies instrumentation engineering and minimizes user steps and costs. The invention uses sensitive image analysis to enumerate individual targets in a large area, is scalable, and can be deployed in systems ranging in complexity from manual to highly automated.

Abstract: Methods and systems are provided for creating molecular barcodes or indicia for cellular constituents within single cells and for resolving such barcodes or indicia with super resolution technologies such as super resolution microscopy. By this approach, numerous molecular species that can be measured simultaneously in single cells. It has been demonstrated that multiple mRNA transcripts can be labeled with a spatially ordered sequence of fluorophores, and that barcode can be resolved. The methods and systems can be used for genome-wide transcriptional profiling in individual cells by super-resolution barcoding and suggest a general strategy to bring large-scale-omics approach into single cells.

Abstract: The present invention relates generally to detection of antibiotic-resistant bacteria in a sample. In particular, the invention provides methods, compositions and kits for detecting and analyzing methicillin-resistant Staphylococcus aureus (MRSA) and other methicillin-resistant bacteria in a sample.