Abstract: The disclosure provides a method of identifying a subject as having B-cell non-Hodgkin lymphoma (NHL) such as testing a sample from a subject for a mutation in one or more biomarkers. Also described are methods for classifying or monitoring a subject having, or suspected of having, B-cell non-Hodgkin lymphoma comprising testing the sample for a mutation in one or more biomarkers.

Abstract: Methods for detecting urogenital conditions or urogenital status in a subject are described comprising measuring urogenital markers or polynucleotides encoding the markers in a sample from the subject. The invention also provides localization or imaging methods for urogenital conditions, and kits for carrying out the methods of the invention. The invention also contemplates therapeutic applications for urogenital conditions employing urogenital markers, polynucleotides encoding the markers, and/or binding agents for the markers.

Abstract: A high-throughput flow system includes an array of wells and a separate mechanical tip positioned within each well. Each mechanical tip is separately actuated to impart a shear stress pattern. A separate sleeve may be associated with each tip for maintaining a predetermined distance between the tip and a floor of the tip's corresponding well, with each tip being rotatable within its corresponding sleeve. Alternatively, a separate post may be associated with each tip for maintaining a predetermined distance between the tip and a floor of the tip's corresponding well, with each tip being rotatable about its corresponding post.

Abstract: A system, a composition, a method and a kit for identifying anti-bacterial agents are provided. The invention described herein is useful in identifying inhibitors of any bacterial stress response. Moreover, the invention can be applied to any sRNA and its target, any transcription factor and its target, and any transcription factor/sRNA pair (i.e., a transcription factor that regulates a sRNA). In particular, the present invention provides a system, a composition, a method and a kit for the identification of cyclic peptides that block the ?E pathway in Escherichia coli.

Abstract: An in situ gel-forming composition is disclosed. The in situ gel-forming composition comprises one or more absorbable polymers, solvents such as N-methyl-2-pyrrolidone, polyethylene glycol or DMSO, and optionally one or more bioactive agent. The composition forms a hydrogel or semi-solid mass on contact with an aqueous environment. The method of using in situ gel-forming composition for various applications is also disclosed.

Abstract: The present invention provides a method and a reagent for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient by analyzing genes with expression levels (in peripheral blood) that vary in association with digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer cases, compared with normal healthy subjects. Specifically, the method for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient based on expression profiles comprises obtaining the expression profile of at least one gene selected from the group consisting of probes corresponding to genes with expression levels (in peripheral blood) that vary in digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, and biliary tract cancer cases, compared with normal healthy subjects.

Abstract: Analysis of a system and/or sample involves the use of absorption-encoded micro beads. Each type of micro bead is encoded with amounts of the k dyes in a proportional relationship that is different from proportional relationships of the k dyes of others of the n types of absorption-encoded micro beads. A system and/or a sample can be analyzed using information obtained from detecting the one or more types of absorption-encoded micro beads.

Abstract: Methods of isolating cells or generating cell lines comprising the step of exposing the cells to signaling probes that produce a signal upon hybridization to a target sequence, as well as methods of quantifying the level of expression of an RNA of interest, methods for identifying genetic recombinational events in living cells and methods of generating a transgenic animal using the isolated cells. Methods for isolating a plurality of cells encoding a plurality of different RNAs associated with a same nucleic acid tag sequence, comprising the step of exposing the cells to a same signaling probe that produces a detectable signal upon hybridization to the same nucleic acid tag sequence, are also provided. Signaling probes and protease probes that form stem-loop structures, three-arm junction structures, and dumbbell structures may be used in the above methods.

Abstract: The invention relates to a method for generating a gene mosaic by somatic in vivo recombination, comprising: e) in a single step procedure (vii) transforming a cell with at least one gene A having a sequence homology of less than 99.5% to another gene to be recombined that is an integral part of the cell genome or presented in the framework of a genetic construct, (viii) recombining said genes, (ix) generating a gene mosaic of the genes at an integration site of a target genome, wherein said at least one gene A has a single flanking target sequence either at the 5? end or 3? end anchoring to the 5? or 3? end of said integration site, and f) selecting clones comprising the gene mosaic, as well as a method of producing a diversity of gene mosaics and gene assembly.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Abstract: The invention relates to methods of identifying a binding partner of a target molecule within a plurality of analyte molecules, including a plurality of peptides and/or proteins. The target molecule is physically combined with a target labeling nucleic acid molecule. Each member of the plurality of analyte molecules is physically linked to an analyte labeling nucleic acid molecule, each analyte labeling nucleic acid molecule comprising a selected nucleotide sequence. This specific nucleotide sequence may include a sequence encoding a peptide/protein combined therewith. The target molecule is contacted with the analyte molecules and a complex between the target molecule and an analyte molecule forms. The mixture is subdivided into compartments. The target labeling nucleic acid molecule and the analyte labeling nucleic acid molecule are linked and the plurality of compartments allowed to disintegrate. The linked nucleic acid molecule is retrieved and the sequence determined.

Abstract: Some embodiments of the invention are directed to a microarray of binary nucleic acid probes for the detection of one or a plurality of nucleic acid analytes in a complex sample in a single high throughput assay with extraordinary specificity under physiologic conditions. Any binary nucleic acid probes that generate a detectable signal when bound to analyte are suitable for use in the microarrays, including binary deoxyribozyme or ribozyme probes; nonenzymatic binary probes for fluorescent detection, nonenzymatic binary dye-binding probes, and binary split enzyme peroxidase probes for visual detection of nucleic acids. The invention is also directed to new non nonenzymatic binary probes that bind to reporter oligonucleotides.

Abstract: A method of evaluating the effect of a xenobiotic on biomarkers, such as drug transporters and drug-metabolizing enzymes in hepatocytes is provided. The method comprises the formation of a xenobiotic-stimulated biological sample, such as whole blood, which contains a plurality of cytokines. A portion of xenobiotic-stimulated biological sample is cultured with hepatocytes. The hepatocytes are then analyzed to evaluate the activity of drug transporters and/or drug-metabolizing enzymes, or other biomarkers to determine the effect of the xenobiotic on drug metabolism in the hepatocytes.

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: A method for identifying persons with increased risk of developing type 1 diabetes mellitus, or having type I diabetes mellitus, utilizing selected biomarkers described herein either alone or in combination. The present disclosure allows for broad based, reliable, screening of large population bases. Also provided are arrays and kits that can be used to perform such methods.

Abstract: Disclosed are methods, compositions and kits related to making double-tagged DNA libraries from RNA/DNA samples. A double-tagged oligonucleotide (DTO) is employed to efficiently add two different tags to ends of DNAs to make a double-tagged DNA libraries. Also disclosed are methods to make mate pair libraries using the double-tagged oligonucleotide, and methods to make double-tagged single stranded DNA. The double-tagged DNA libraries of the invention are ready to be used on next generation sequencing machines.

Abstract: This invention provides methods of detecting and quantifying target nucleic acids in samples in multiplexed single chamber reactions. Consumables incorporating chambers optimized to reduce signal background proximal to high efficiency arrays are provided, as well as methods of use. Devices and systems configured to use the consumables to practice the methods are a feature of the invention.

Abstract: The present invention provides a method for detecting or enriching for a target deoxyribonucleic acid (DNA) present in a nucleic acid sample, said method comprising: (a) fragmenting a nucleic acid sample to generate nucleic acid fragments including a target fragment containing said target DNA and non-specifically ligating an adaptor sequence to an end of said fragments; (b) rendering said fragments at least partially single-stranded; (c) contacting the at least partially single-stranded fragments of step (b) with oligonucleotides A and B of a single target-specific nucleic acid probe; (d) ligating oligonucleotide B of said probe to the part of the single-stranded portion of said target fragment which is hybridised to oligonucleotide A of said probe to produce a probe-target fragment hybrid; and (e) detecting or enriching for said probe-target fragment hybrid.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.