Abstract: Objective of the present invention is to provide a method for keeping of directional information in double-stranded DNA. We suggest to convert polynucleotide into a hybrid double-stranded DNA. One particular strand of this hybrid double-stranded DNA should be synthesised using at least one modified nucleotide. Thus, this particular strand would contain modified nucleotides along the whole length. Density of directional markers would not depend on the length of polynucleotides. Any internal fragments of the hybrid double-stranded DNA would have directional information. When it is necessary the modified strand may be easily degraded or separated from the other strand. It was found that such hybrid double-stranded DNA may be easily generated in a number of molecular biology tasks and may be used for molecular cloning, library preparation and strand separation.

Abstract: According to an aspect of the present invention, a pair of oligonucleotide strands are anchored onto the surface of a substrate by immobilizing one of the ends thereof onto the substrate. Each of the immobilized oligonucleotide strands is bound to a target nucleic acid sequence (single-stranded) having complementary sequences thereto to form a cross-linked structure on the substrate, thereby forming a finely reticulated space. Ligands are captured by this reticulated space through physical adsorption and caused to color with active substances reactive to the ligands. As a result of this, the present invention is capable of highly sensitively detecting even an exceedingly small concentration of a particular target nucleic acid sequence to be detected, at low cost and for a short time.

Abstract: The invention relates to a method of identifying an individual nucleotide, comprising (a) contacting the nucleotide with a transmembrane protein pore so that the nucleotide interacts with the pore and (b) measuring the current passing through the pore during the interaction and thereby determining the identity of the nucleotide. The invention also relates to a method of sequencing nucleic acid sequences and kits related thereto.

Abstract: The disclosure provides a field-effect transistor (FET)-based biosensor and uses thereof. In particular, to FET-based biosensors using thermally reduced graphene-based sheets as a conducting channel decorated with nanoparticle-biomolecule conjugates. The present disclosure also relates to FET-based biosensors using metal nitride/graphene hybrid sheets. The disclosure provides a method for detecting a target biomolecule in a sample using the FET-based biosensor described herein.

Abstract: The present invention provides novel microfluidic devices and methods for performing pulsed field mobility shift assays in microfluidic devices. In particular the devices and methods of the invention utilize differences between electrophoretic mobilities (e.g., as between reactants and products, especially in non-fluorogenic reactions) in order to separate the species and thus analyze the reaction.

Abstract: Here, we describe a sensitive and specific assay and kit for the detection of chemokines having activity that is upregulated by Th-1 cytokines (such IFN-?) and chemokines that upregulate the activity of Th-1 cytokines (such as IFN-?). In a typical embodiment, detection of the chemokine monokine induced by gamma interferon (MIG) provides a measure of the biological effect of IFN-? rather than direct quantitation of IFN-? or IFN-? secreting cells per se. Upregulation of MIG expression was observed following in vitro activation of PBMC with defined CD8+ T cell epitopes derived from influenza virus, CMV, or EBV, and in all cases this was antigen-specific, genetically restricted and dependent on both CD8+ T cells and IFN-?. Responses as assessed by the MIG assay paralleled those detected by conventional IFN-? ELISPOT, but the magnitude of response and sensitivity of the MIG assay were superior.

Abstract: Fusarium root rot, cyst nematode and soybean sudden death syndrome resistance genes; Fusarium root rot, cyst nematode and soybean sudden death syndrome resistance proteins; Fusarium root rot, cyst nematode and soybean sudden death syndrome resistant plant lines, and methods of breeding and engineering same.

Abstract: The invention provides nucleotide sequences that mediate one or more functions of IKK?, kits and methods for using these sequences to identify therapeutic compounds that alter IKK? related pathology.

Abstract: According to an aspect of the present invention, a pair of oligonucleotide strands are anchored onto the surface of a substrate by immobilizing one of the ends thereof onto the substrate. Each of the immobilized oligonucleotide strands is bound to a target nucleic acid sequence (single-stranded) having complementary sequences thereto to form a cross-linked structure on the substrate, thereby forming a finely reticulated space. Ligands are captured by this reticulated space through physical adsorption and caused to color with active substances reactive to the ligands. As a result of this, the present invention is capable of highly sensitively detecting even an exceedingly small concentration of a particular target nucleic acid sequence to be detected, at low cost and for a short time.

Abstract: Methods of isolating weakly interacting molecules in a fluidic sample using an immiscible phase filtration technique are disclosed. A complex is formed between a solid phase substrate, a molecule immobilized on the solid phase substrate, and at least one target molecule present in the fluidic sample. The complex is transferred into an immiscible phase by applying an external force to the solid phase substrate. The methods eliminate the need for complex and time consuming washing steps.

Abstract: The present invention provides methods, compositions and kits for the characterization of cellular pathways in cells containing genetic alterations.

Abstract: The present invention discloses methods and agents for diagnosing the presence or risk of development of ankylosing spondylitis (AS) in mammals, which are based on the detection of polymorphisms within any one or more of the ARTS-1 gene, the IL-23R gene, the TNFR1 gene locus, the TRADD gene locus, the IL-1R1 gene locus, the IL-1R2 gene locus, the CD74 gene locus and the chromosome loci 2P15, 2Q31.3 and 4Q13.1. The present invention also features methods for the treatment or prevention of AS based on the diagnostic methods.

Abstract: Cell-based and cell-free assays are disclosed that detect compounds that promote aggregation of proteins, glycoproteins, and protein-nucleic acid complexes. Also disclosed are pharmaceutical formulations useful for treating or preventing viral infections, bacterial infections, cancer, and diseases involving hyper-proliferative cells.

Abstract: To efficiently identify and select a clone from clones of induced pluripotent stem cells (iPS cell) having low tumor formation rate in vivo when allowed to differentiate and transplanted in a living body, iPS cells of the clones are induced to differentiate, undifferentiated cells among the cells after the induction of differentiation are detected, and a clone having the content of the undifferentiated cell below a control is selected.

Abstract: The present invention is directed to methods of centromere discovery using centromere-associated proteins in a variety of experimental formats. The methods of the invention can be used on any organism, and include using Cal1, Cbf1, Cbf3, Cbf5, CenH3 (Cenp-A), Cenp-B, Cenp-C, Cenp-D, Cenp-E, Cenp-F, Cenp-G, Cenp-H, Cenp-I, Cenp-K, Cenp-L, Cenp-M, Cenp-N, Cenp-O, Cenp-P, Cenp-Q, Cenp-R, Cenp-S, Cenp-T, Cenp-U, Cenp-V, Cenp-W, Chd1, Chp1, cohesin, condensin, Dnmt3b, Fact, Gcn5p, H2A.Z, Haspin, Hjurp, HP1, Hst4, Ima1, Incep, Ino80, Kms2, Knl-2, Mif2, Mis6, Np95, Pich, Sad1, Scm3, Shugoshin, Sim3, Skp1, Sororin, Survivin, Tas3, ZW10, and homologs thereof to identify centromere sequences. The invention is also directed to artificial chromosomes comprising centromeres made according to the methods of the invention, as well as to cells comprising such artificial chromosomes.

Abstract: The present invention provides a blood analyzer and a blood analyzing method capable of obtaining information regarding B lymphocytes and T lymphocytes without using a fluorescence-labeled antibody. The blood analyzer of the present invention includes a blood specimen supplying portion, a sample preparation portion that prepares a measurement sample without using a fluorescence-labeled antibody by mixing a blood specimen supplied from the blood specimen supplying portion, a hemolyzing agent, and a fluorescent dye that stains nucleic acid, a light source, a first detector that detects fluorescence, a second detector that detects scattered light, and information processing portion that classifies lymphocytes based on the intensity of fluorescence and scattered light, and based on the fluorescence intensity of the classified lymphocytes, obtains information regarding B-lymphocytes and T-lymphocytes.

Abstract: The present invention generally relates to subpopulations of mammalian cells with distinctive ribosome translational profiles, i.e. translational activities. The present invention further relates to methods for identifying and isolating such cells, kits comprising the same, or methods which utilize different translational activities of these subpopulations of mammalian cells.

Abstract: This invention provides a method for the detection of hydroxymethylation patterns in a DNA sample, especially in genetic regions. A test sample containing hydroxymethylated DNA is hybridized to capture oligonucleotides immobilized on a solid phase. The hydroxymethylated DNA in hybrid is detected using an antibody which specifically recognizes hydroxymethylcytosine structure the marker of DNA hydroxymethylation-followed by immuno-signal amplification. The present invention provides a method to detect gene-specific hydroxymethylation in a simple, rapid and high throughput format with high specificity and sensitivity.

Abstract: A method for selecting combinations of drugs for treatment of diseases that arise from deranged signaling pathways is disclosed. The method involves measuring the activity states for signaling proteins in a diseased cell and determining whether the activity states are different from the activity states observed for a reference cell such as a normal cell. Based on the observed differences, combinations of two or more drugs are selected to reduce these differences. Treatment of a subject with the combinations restores the activity states of the signaling proteins of the deranged disease-associated signaling pathways toward the activity states observed in the reference cell. Since the diseased cell and the reference cell can both be obtained from the same subject, combinations of drugs that specifically target patient-specific signaling derangements is possible.

Abstract: Methods for identification of successful transformation without a need for in vitro selection are provided. Direct detection of nucleotide sequences of interest is described which eliminate the need for use of ancillary nucleotide sequences.

Abstract: An extensible RNA-based framework for engineering ligand-controlled gene regulatory systems, called ribozyme switches, that exhibit tunable regulation, design modularity, and target specificity is provided. These switch platforms typically contain a sensor domain, comprised of an aptamer sequence, and an actuator domain, comprised of a hammerhead ribozyme sequence. A variety of modes of standardized information transmission between these domains can be employed, and this application demonstrates a mechanism that allows for the reliable and modular assembly of functioning synthetic hammerhead ribozyme switches and regulation of ribozyme activity in response to various effectors. In some embodiments aptamer-regulated cis-acting hammerhead ribozymes are provided.

Abstract: The present invention relates to a method for producing Cypridina luciferase labeled with hydrophilic biotin, characterized in that a biotin reagent containing a polyalkylene glycol structure as a spacer is reacted with Cypridina luciferase, and biotin-labeled Cypridina luciferase wherein a sugar chain in Cypridina luciferase has been biotinylated.

Abstract: Methods and products for detecting in vitro the presence of damage on DNA or the presence of a biological response to damage on DNA at the molecular level. Molecular Combing or other nucleic acid stretching methods are employed together with compounds reacting with DNA, probes binding DNA, or nucleic acid monomers, especially labeled nucleic acid monomers.

Abstract: The present invention relates to methods of detecting renal transplant rejection and other forms of renal damage. Protein markers or renal damage are provided, along with assays for detecting said markers. Also provided are methods for identifying markers of renal damage.

Abstract: A kit including a target sequence-binding protein and a method of detecting a target nucleic acid by using the kit that may ensure efficient detection of the target nucleic acid in a biological sample are disclosed.

Abstract: The invention relates to a microfabricated device for the rapid detection of DNA, proteins or other molecules associated with a particular disease. The devices and methods of the invention can be used for the simultaneous diagnosis of multiple diseases by detecting molecules (e.g. amounts of molecules), such as polynucleotides (e.g., DNA) or proteins (e.g., antibodies), by measuring the signal of a detectable reporter associated with hybridized polynucleotides or antigen/antibody complex. In the microfabricated device according to the invention, detection of the presence of molecules (i.e., polynucleotides, proteins, or antigen/antibody complexes) are correlated to a hybridization signal from an optically-detectable (e.g. fluorescent) reporter associated with the bound molecules. These hybridization signals can be detected by any suitable means, for example optical, and can be stored for example in a computer as a representation of the presence of a particular gene.

Abstract: The present invention relates a method for assessing in vivo hematotoxicity. The method utilizes differential staining of nucleated and non-nucleated blood cells, and also differential labeling of cells with functional versus dysfunctional mitochondrial membrane potential. Quantitative analyses can be conducted on stained whole blood specimens, and is based on blood cells' fluorescent emission and light scatter properties following exposure to an excitatory light source. The ratio of certain cell populations can be readily measured. Furthermore, it is also possible to express cell population values in terms of number per unit volume. This invention can be used to evaluate the hematotoxicity of drugs, chemicals, radiation, and other exogenous agents, or the effects that a suspected protective agent may have on induced hematotoxicity. Furthermore, the matrix of measurements provided by this invention is useful in estimating radiation dose, i.e., retrospectively.

Abstract: Provided herein are isolated genomic polynucleotide fragments from the from the p15 region of chromosome 11 encoding human and tumor suppressing subtransferable candidate 4 (TSSC4) and methods of use.

Abstract: Disclosed are methods and compositions related to the regulation of goblet cell differentiation, mucus production and mucus secretion. In some embodiments, methods for the treatment of mucus hyperproduction, methods for the treatment of pulmonary inflammation, methods of screening compounds, compositions for the treatment of mucus hyperproduction, or compositions for the treatment of pulmonary inflammation are provided.

Abstract: Provided herein are assays useful, for example, for determining the activity of a protein involved in a cellular process. In some embodiments, the activity of the protein is assessed using a nucleic acid tag, and in particular, by detecting the presence of a nucleic acid tag. Such assays can be used, for example, to study the effects of test compounds as modulators, e.g., inhibitors, agonists and antagonists, of protein activity.

Abstract: A nucleic acid includes at least 15 nucleotides with a length specifically binding with the human factor VII/VIIa.

Abstract: Using gene expression analysis, specific biomarker genes and gene products have been identified which are activated in transformed cells, but suppressed in nontransformed cells; or suppressed in transformed cells, but activated in transformed cells affected by Contact Normalization. Thus, the present invention features compositions and methods for detecting, diagnosing, treating and prognosing cancer.

Abstract: Methods, compositions and articles of manufacture for assaying a sample for a target polynucleotide are provided. A sample suspected of containing the target polynucleotide is contacted with a polycationic multichromophore and a sensor PNA complementary to the target polynucleotide. A signaling chromophore absorbs energy from the excited multichromophore and emits light in the presence of the target polynucleotide. The methods can be used in multiplex form. Kits having reagents for performing such methods are also provided.

Abstract: The present invention generally relates to sub-diffraction limit image resolution and other imaging techniques. In one aspect, the invention is directed to determining and/or imaging light from two or more entities separated by a distance less than the diffraction limit of the incident light. For example, the entities may be separated by a distance of less than about 1000 nm, or less than about 300 nm for visible light. In one set of embodiments, the entities may be selectively activatable, i.e., one entity can be activated to produce light, without activating other entities. A first entity may be activated and determined (e.g., by determining light emitted by the entity), then a second entity may be activated and determined. The entities may be immobilized relative to each other and/or to a common entity.

Abstract: This invention provides methods, primers and kits for restoration of nucleic acid from tissue, in particular degraded tissue and formalin-fixed and paraffin-embedded (FFPE) tissue, where the methods involve complementary-template reverse-transcription (CT-RT) where short single-stranded DNA sequences reverse-transcribed from mRNA are used for reverse-transcription of complementary sense-RNA templates. The methods can be used to determine patterns of gene expression and chromosomal alterations in archived tissue samples, and may be used to identify expression of disease-related genes.

Abstract: This invention is related to a method for rapidly quantifying hydroxymethylated DNA by binding DNA to a plastic carrier followed by immunodetection of 5-hydroxymethylcytosine or a hydroxymethylcytosine structure that is marker of DNA hydroxymethylation.

Abstract: The present invention to a nucleotide sequence encoding one or more Arc DNA binding domains, one or more Arc DNA binding sites and at least one polypeptide domain.

Abstract: Compositions and methods for multiplex immunodetection of analytes in single cells or cell populations are described. The invention utilizes analytical nanotags (ANTs) each specific for a different target analyte (TA) species. Analytical nanotags typically comprise biocompatible composite organic-inorganic nanoparticles (bCOINs) that include probe molecules specific for a particular TA species. A plurality of ANTs each specific for a different TA species can be used in a single multiplex assay, including assays for analyzing intracellular analytes in living cells.

Abstract: Embodiments of the invention relate to a branched or multichain nucleic acid switch adapted to switch from a first conformation to a second conformation upon ligand binding. The switch includes a probe strand, P, which includes the ligand binding domain; a switching framework which includes a cover strand (C), and a tether that holds P and C together and a signaling apparatus. Some embodiments include a toggle strand (T) where now the tether holds P, C, T, and the signaling apparatus together. As the switch changes between the first and second conformations; the signaling apparatus reports the state of the switch. The signaling entity is typically a lumiphore and a quencher located along the switching framework. Nucleic acid switches have applications in real time assays for diverse agents including infectious agents, environmental toxins, and terrorist agents, as well as screening methods for such agents. Further applications are found for nanoelectronics, nanofabrication and nanomachines.

Abstract: The presence of mycotoxins in agricultural products necessitates large scale testing of a wide range of sample material to ensure the safety of food and feed. The mycotoxin ochratoxin A represents an enablement for all mycotoxins as the level of sensitivity necessary for regulatory requirements for this compound at the part per billion level are as low or lower than any other mycotoxin. This invention describes the identification of a set of DNA ligands with sufficiently high binding affinity and specificity for ochratoxin A to enable an improvement over existing methods for the separation, concentration and quantitative determination of ochratoxin A in sample material.

Abstract: This invention provides nucleic acid molecules that catalyze their own replication and undergo exponential amplification at a constant temperature and in the absence of proteins or other biological components, such as those employed in other amplification reactions, e.g., proteins including DNA or RNA polymerase and a method of detect a selected molecule using said nucleic acid.

Abstract: A nucleic acid sequencing device includes at least one nanochannel, a first electrode and a second electrode disposed at opposite ends of the nanochannel for applying a voltage in the lengthwise direction of the nanochannel, and a first detector that detects a location signal of a target nucleic acid passing through the nanochannel and a second detector that detects a signal from a detectable label bound to the target nucleic acid.

Abstract: This document relates to methods and materials involved in assessing samples for enzyme-nucleic acid complexes. For example, methods and materials for using antibodies to determine the presence, absence, or amount of enzyme-nucleic acid complexes (e.g., human topoisomerase I-DNA complexes) in a sample (e.g., a biological sample such as a tissue biopsy) are provided.

Abstract: Disclosed are methods and systems for determining the three-dimensional structure of chromatin in eukaryotic cells. More specifically, disclosed are methods and systems for obtaining chromatin structural information by surface immobilization, i.e tethering crosslinked protein:DNA complexes and/or ligated DNA complexes to media such as beads, gels, and or matrices during the conformation capture assay. In general, the method includes contacting a cell with a cross-linking reagent to cross-link DNA and protein in the cell; lysing the cell, producing cross-linked protein:DNA complexes by cutting the chromatin using a chemical, physical or enzymatic method, substantially immobilizing the cross-linked protein:DNA complexes, ligating the cross-linked protein:DNA complexes intramolecularly such that the ligated protein:DNA complexes represent structural organization of the chromatin; characterizing the ligated DNA by sequencing or other methods; and identifying any structural organization of the chromatin.

Abstract: The invention features methods for identifying compounds that inhibit binding between iron response elements (IREs) and iron response proteins (IRPs). These compounds are potentially useful for treating or preventing diseases, in particular cancer, but also including anemia, neurodegenerative diseases, inflammation and iron overload. The methods are based on contacting a candidate compound in an in vitro system and monitoring the binding of an IRE to an IRP. In addition, the invention features methods of treating or preventing a proliferative disease, such as cancer, using the compounds of the invention.

Abstract: A method of diagnosing Alzheimer's disease (AD) and Mild Cognitive Impairment (MCI) is disclosed which was identified by the fact that an increased level of iron regulating protein-2 (IRP-2) was identified in Alzheimer's patients. Further, diseases of increased cellular metabolism such as cancer showed high levels of both IRP-2 and transferrin receptor. This suggests that, in diseases of increased cellular metabolism, both aspects of iron accumulation are highly expressed, while in Alzheimer's disease only IRP-2 is highly expressed. From these results, a non-invasive test for Alzheimer's disease may be produced using patient samples containing peripheral blood cells and identifying the level of expression of IRP-2 and Transferrin receptor. Those patients which: 1. over-express IRP-2 as compared with normal controls, and 2. have comparable levels of Transferrin receptor expression to normal controls, can be identified as having or prone to AD and MCI.

Abstract: This invention relates to detection of specific extracellular nucleic acid in plasma or serum fractions of human or animal blood associated with neoplastic or proliferative disease. Specifically, the invention relates to detection of nucleic acid derived from mutant oncogenes or other tumor-associated DNA, and to those methods of detecting and monitoring extracellular mutant oncogenes or tumor-associated DNA found in the plasma or serum fraction of blood by using rapid DNA extraction followed by nucleic acid amplification with or without enrichment for mutant DNA. In particular, the invention relates to the detection, identification, or monitoring of the existence, progression or clinical status of benign, premalignant, or malignant neoplasms in humans or other animals that contain a mutation that is associated with the neoplasm through detection of the mutated nucleic acid of the neoplasm in plasma or serum fractions.

Abstract: There is described a method for identifying an interaction between an RNA and an RNA binding protein in a biological sample, comprising the steps of: a) contacting the biological sample with an agent that creates a covalent bond between the RNA and the RNA binding protein; b) fragmenting said RNA; c) ligating a first adapter to the fragmented RNA; d) hybridising a reverse transcription primer to said first adapter and reverse transcribing said cross-linked RNA; e) circularising the transcribed cDNA; f) linearising the circularised cDNA; and g) determining the sequence of one or more of the cDNAs.

Abstract: We describe herein a cell-based multiplexing technique called detectable cell barcoding (DCB). In DCB, each individual sample is labeled with a different DCB signature that distinguishes each sample by one or both of detected intensity or type of detection characteristic. The samples are then combined and analyzed for a detectable characteristic of interest (e.g., presence of an analyte). By employing multiple distinct DCB labels at varying concentrations, one can perform multiplex analyses on up to hundreds or thousands (or more) of cell samples in a single reaction tube. DCB reduces reagent consumption by factors of 100-fold or more, significantly reduces data acquisition times and allows for stringent control sample analysis.

Abstract: The present invention relates to compositions and methods for diagnosing, monitoring and/or treating disease (e.g., autoimmune or chronic inflammatory disease, heart disease and/or stroke). In particular, the present invention provides methods for diagnosing, monitoring and treating disease based upon detecting or altering (e.g., altering expression or methylation status of) disease proteins (e.g., CD70, CD40L, and/or KIR). The present invention also provides kits for detecting methylation status of disease proteins (e.g., CD70, CD40L, and/or KIR) and for diagnosing, monitoring and/or treating diseases (e.g., autoimmune or chronic inflammatory disease, heart disease and/or stroke).