Abstract: Disclosed herein are methods and compositions for rapidly identifying active nucleases and cells having nuclease-mediated genomic modifications.

Abstract: The present invention relates to the providing of a method for preparing a stool sample that enables a nucleic acid in a stool to be stably preserved without requiring a complex procedure, a solution for preparing a stool sample, a stool collection kit used in that method, and a method for recovering and analyzing a nucleic acid in a stool using a stool sample prepared using the preparation method of the present invention. A method for preparing a stool sample according to the present invention is a method for preparing a stool sample being used for analyzing a nucleic acid contained in the stool, and is characterized in that a collected stool is mixed with a solution having a protease inhibitor as an active ingredient.

Abstract: Methods and kits for predicting the efficacy of antifolate (e.g., methotrexate) treatment of rheumatoid arthritis by detecting polymorphisms, particularly single nucleotide polymorphisms, in adenosine pathway genes.

Abstract: The present invention relates to the providing of a method for preparing a sample from a nucleic acid-containing sample such as biological samples, where inhibitory substance's action against a enzyme reaction using a nucleic acid as substrate are decreased, a solution for preparing a sample used for the method, a stool collection kit used in that method, and a method for recovering and analyzing a nucleic acid in a nucleic acid-containing sample using a sample prepared using the preparation method of the present invention. A method for preparing a sample according to the present invention is a method for preparing a sample being used for analyzing a nucleic acid, and is characterized in that a nucleic acid-containing sample is mixed with a solution having one or more members selected from the group consisting of a polycation and a chelating agent as an active ingredient.

Abstract: The present invention relates to the identification of genetic markers patients with leukemia, especially including acute lymphoblastic leukemia (ALL) at high risk for relapse, especially high risk B-precursor acute lymphoblastic leukemia (B-ALL) and associated methods and their relationship to therapeutic outcome. The present invention also relates to diagnostic, prognostic and related methods using these genetic markers, as well as kits which provide microchips and/or immunoreagents for performing analysis on leukemia patients.

Abstract: This invention relates to antiviral drug susceptibility and resistance tests to be used in identifying effective drug regimens for the treatment of human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS), particularly treatment regimens including a protease inhibitor. The invention further relates to the means and methods of monitoring the clinical progression of HIV infection and its response to antiretroviral therapy using phenotypic or genotypic susceptibility assays.

Abstract: A method for measuring human CYP3A inducibility upon administration of a test drug, characterized in that anon-human animal to which a test drug is administered or a population of human cells cultured in a medium containing a test drug is infected with viruses (A) and (B); virus (A) being an adenovirus which is used as a vector and engineered by incorporating thereto a detectable reporter gene and at least 3 human PXR binding regions falling within an untranslated region of a human CYP3A gene, and virus (B) being an adenovirus which is used as a vector and engineered by incorporating thereto a human PXR cDNA; and subsequently expression level of the reporter gene is determined in the non-human animal or the cultured human cells.

Abstract: We found mutations of the R132 residue of isocitrate dehydrogenase 1 (IDH1) in the majority of grade II and III astrocytomas and oligodendrogliomas as well as in glioblastomas that develop from these lower grade lesions. Those tumors without mutations in IDH1 often had mutations at the analogous R172 residue of the closely related IDH2 gene. These findings have important implications for the pathogenesis and diagnosis of malignant gliomas.

Abstract: The present invention provides methods and compositions for detecting a predisposition to an inflammation-mediated cardiovascular disease in a human subject by detecting a level of leukotriene C4 synthase (LTC4S) gene product in a sample from a human subject indicative of a predisposition to an inflammation-mediated cardiovascular disease or detecting the presence or absence of an allele of LTC4S indicative of a predisposition to an inflammation-mediated cardiovascular disease. In addition, the present invention also provides kits for practicing the methods.

Abstract: In accordance with the invention, novel gene deletions and translocations involving chromosome 2 resulting in fusion proteins combining part of Anaplastic Lymphoma Kinase (ALK) kinase with part of a secondary protein have now been identified in human solid tumors, e.g. non-small cell lung carcinoma (NSCLC). Secondary proteins include Echinoderm Microtubule-Associated Protein-Like 4 (EML-4) and TRK-Fusion Gene (TFG). The EML4-ALK fusion protein, which retains ALK tyrosine kinase activity, was confirmed to drive the proliferation and survival of NSCLC characterized by this mutation. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant ALK kinase polypeptides, probes for detecting it, isolated mutant polypeptides, recombinant polypeptides, and reagents for detecting the fusion and truncated polypeptides.

Abstract: The present invention is one gene construct or a combination of two gene constructs or expression vectors incorporating a Cypridina luciferase gene and a copepod luciferase under the control of distinct promoters. These gene constructs and expression vectors are useful for making a mammalian cell incorporating the Cypridina luciferase gene and the copepod luciferase to be capable of stably expressed and extracellularly secreted under the control of the distinct promoters.

Abstract: The present invention relates generally to methods and compositions for expression of polypeptides or delivery of interfering RNA's in various cell types.

Abstract: Nucleic acid encoding a novel bacterial polypeptide ykuR, the isolated ykuR polypeptide, its expression from host cells, and its use in screening for potential antibacterial agents. Inhibition of ykuR activity results in inhibition of bacterial growth.

Abstract: Methods and compositions according to embodiments of the present invention are provided that specifically and sensitively detect alcohol consumption and whether alcohol consumption is moderate or high in a subject. Aspects of the present invention relate to assays of panels of proteins for detecting non-consumption, moderate consumption and high consumption of ethanol by a subject.

Abstract: A method for detection of susceptibility to nitrous oxide neurologic syndrome in a subject is disclosed. In one embodiment, the method comprises: (a) providing a sample from a subject, wherein said subject is a candidate for nitrous oxide anesthesia; and (b) detecting the presence or absence of folate, cobalamin, methionine and homocysteine pathway genetic polymorphisms in said sample, wherein the presence of a polymorphism indicates that the subject is susceptible to nitrous oxide neurologic syndrome.

Abstract: The invention relates to a method of screening a subject for at least one risk factor associated with a neurodegenerative disease such as Alzheimer's disease comprising detecting the presence or absence of at least one risk marker in the HtrA1 gene (PRSS11). Furthermore, diagnostic kits as well as therapeutic approaches are provided.

Abstract: Described herein are methods of predicting the likelihood of survival in a subject. Additionally, described herein are methods of modulating survival in a subject.

Abstract: This invention pertains to chemometric methods for the analysis of chemical, biochemical, and biological data, for example, spectral data, for example, nuclear magnetic resonance (NMR) spectra, and their applications, including, e.g., classification, diagnosis, prognosis, etc., especially in the context of bone disorders, e.g., conditions associated with low bone mineral density, e.g., osteoporosis.

Abstract: Methods are provided for determining whether a subject has a graft tolerant phenotype. In practicing the subject methods, the expression of at least 5 genes in a sample from the subject, e.g., a blood sample, is assayed to obtain a gene expression result for the at least 5 genes. The obtained gene expression result for the at least 5 genes is then employed to determine whether the subject has a graft tolerant phenotype. Also provided are compositions, systems and kits that find use in practicing the subject methods. The methods and compositions find use in a variety of applications, including the determination of an immunosuppressive therapy regimen.

Abstract: The invention provides novel uses of sequence-specific or sequence-directed endonucleases for molecular plant breeding. The invention also provides novel plant transformation vectors and expression cassettes, which include novel combinations of an endonuclease with plant expression and transformation elements. Plants and derivatives thereof produced by such methods are also provided.

Abstract: This invention provides antibodies immunologically specific for human ARL-1 (also referred to AKR1B10), a species of the aldo-keto reductase superfamily of proteins. The invention also provides methods of making and methods of using said antibodies.

Abstract: The present invention is partly based on the discovery that adverse factors can prevent an effective extraction of nucleic acids from a biological sample and that novel and unexpected agents and steps may be used to mitigate or remove the adverse factors, thereby dramatically improving the quality of the extracted nucleic acids. As such, one aspect of this invention is a novel method for extracting high quality nucleic acids from a biological sample. The high quality extractions obtained by the novel methods described herein are characterized by high yield and high integrity, making the extracted nucleic acids useful for various applications in which high quality nucleic acid extractions are preferred, e.g., a diagnosis, prognosis or therapy evaluation for a medical condition.

Abstract: Host nucleic acids and host proteins that participate in viral infection, such as human immunodeficiency virus (HIV), influenza A, and Ebola virus, have been identified. Interfering with or disrupting the interaction between a host nucleic acid or host protein and a virus or viral protein confers an inhibition of or resistance to infection. Thus, interfering with such an interaction in a host subject can confer a therapeutic or prophylactic effect against a virus. The sequences identified can be used to identify agents that reduce or inhibit viral infection.

Abstract: The invention provides methods of treating a meiotic kinase-associated disease, preferably the meiotic kinase HSET, by administering an inhibitor of the meiotic kinase. Preferably, the disease is associated with the presence of supernumerary centrosomes, such as cancer. Methods of inhibiting the growth of a tumor cell by contacting the cell with an inhibitor of a meiotic kinase, preferably HSET, are also provided. Screening methods for identifying inhibitors of the meiotic kinase HSET are also provided. Methods of selecting subjects for treatment with an inhibitor of a meiotic kinase, such as HSET, are also provided.

Abstract: The present invention is directed to a scraping instrument for collection of a biological sample, and a non-invasive method for obtaining nucleic acid from buccal mucosa epithelial cells using the scraping instrument. Such nucleic acid can be used for example for gene expression profiling, including to assess lung disease risk associated with airway pollutants.

Abstract: Use of the large form of human 2?,5?-Oligoadenylate Synthetase (OAS3) for diagnosis, prevention and treatment of infection with positive-sense single-stranded RNA viruses and for prediction of human genetic susceptibility to positive-sense single-stranded RNA virus-related diseases.

Abstract: The current invention provides a method for aiding in the assessment of prostate cancer (including metastatic prostate cancer) and/or benign prostate hyperplasia in a patient, wherein the method comprises the step of determining the level of Glycine N-methyltransferase (GNMT) nucleic acid and/or protein in a sample from the patient. The invention also provides compounds that target Glycine N-methyltransferase (GNMT) protein and/or nucleic acid for use in treating prostate cancer. Also provided are screening methods for selecting a compound considered to be useful in treating prostate cancer, comprising the steps of determining the ability of a test compound to reduce GNMT activity and selecting a compound that reduces GNMT activity. The invention also provides methods for aiding in the diagnosis of prostate cancer in a patient comprising obtaining a sample from the patient and assessing said sample for a marker of GNMT activity.

Abstract: The invention relates to mutations in B-Raf gene products. The mutations described are identified in human tumours of natural origin. These mutations are associated with cancerous phenotypes and can be used as a basis for the diagnosis of cancer, cancerous cells or a predisposition to cancer in human subjects, and the development of anti-cancer therapeutics.

Abstract: The present invention features methods for classifying, determining severity, and predicting clinical endpoints of scleroderma based upon the expression of selected biomarker genes.

Abstract: The present invention relates to methods to identify factors associated with muscle growth, angiogenesis, obesity, insulin sensitivity body weight, fat mass, muscle mass and cardiovascular function. In particular, the methods of the present invention relates to assays to identify such factors using a transgenic animal model and/or a cell-based assay.

Abstract: The present invention relates to methods of diagnosing chronic rejection of a cardiac allograft using genomic expression profiling, proteomic expression profiling, or a combination of genomic and proteomic expression profiling.

Abstract: The present invention relates to a marker gene for screening of drug candidates inducing pulmonary toxicity and a screening method using the same, more precisely a marker gene up- or down regulated by amiodarone which is a drug inducing pulmonary toxicity and a method for screening drug candidates inducing pulmonary toxicity using the same. The marker gene of the present invention can be effectively used for monitoring and identifying drugs or chemical having high risk of inducing pulmonary toxicity and can be used as an effective tool for examining the mechanism of amiodarone which causes pulmonary toxicity and side effects.

Abstract: Methods and compositions for the identification of breast cancer grade signatures are provided. The signature profiles are identified based upon multiple sampling of reference breast tissue samples from independent cases of breast cancer and provide a reliable set of molecular criteria for identification of cells as being in one or more particular stages and/or grades of breast cancer.

Abstract: This invention relates generally to methods for detecting cell damage as a consequence of pathophysiological or traumatic insults such as in a nuclear accident, bioterror attack, tumorigenesis, infections or in individuals with cardiovascular disease.

Abstract: In order to provide a therapeutic agent for nerve injury which contains iPS-derived neural stem cells and has low or no risk of side effects, as well as a method for treating a nerve injury using the iPS cells, by efficiently establishing in vivo the iPS-derived neural stem having low or no risk of tumor formation, neurospheres are formed following formation of embryoid bodies from the iPS cells, and a clone whose ratio of cells in which the promoter of Nanog gene is activated is 0.01% or less is selected, and the clone is administered to a patient suffering from the nerve injury.

Abstract: The present invention provides a method for diagnosis or prognosis of IgA nephropathy in a subject based on detection of the expression level of one or more biomarker genes selected from the group consisting of thymosin ?4 (Tmsb4), serine or cysteine proteinase inhibitor clade E member 2 (Serpine2), secreted phosphoprotein 1 (OPN), butyrophilin-like-2 (BTNL2), S100 calcium binding protein A8 (S100A8), Cystatin C (CysC), and any combination thereof.

Abstract: This invention relates to an isolated nucleic acid fragment encoding a 1-deoxy-D-xylulose 5-phosphate reductoisomerase. The invention also relates to the construction of a chimeric gene encoding all or a portion of the 1-deoxy-D-xylulose 5-phosphate reductoisomerase, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the 1-deoxy-D-xylulose 5-phosphate reductoisomerase in a transformed host cell.

Abstract: The present invention concerns a method to determine the gene expression profile on a sample previously obtained from a patient diagnosed for a liver tumor, comprising assaying the expression of a set of genes in this sample and determining the gene expression profile (signature). In a particular embodiment, said method enables to determine the grade of the liver tumor, such as hepatoblastoma (HB) or a hepatocellular carcinoma (HCC). The invention is also directed to kits comprising a plurality of pairs of primers or a plurality of probes specific for a set of genes, as well as to solid support or composition comprising a set of probes specific for a set of genes. These methods are useful to determine the grade of a liver tumor in a sample obtained from a patient, to determine the risk of developing metastasis and/or to define the therapeutic regimen to apply to a patient.

Abstract: The present invention provides an in vitro method for determining the resistance or sensitivity of a cell line or patient sample to a deoxyribonucleoside kinase-dependent drug, wherein the method comprises the steps of: (i) treating a patient sample or cell line, or a portion thereof, with a deoxyribonucleoside kinase-dependent drug; (ii) lysing the cells of the patient sample or cell line from step (i); (iii) optionally, mixing a portion of the cell lysate from step (ii) with a bioluminescent reporter bacteria incorporating a gene coding for deoxyribonucleoside kinase; (iv) mixing a portion of the cell lysate from (ii) with a bioluminescent reporter bacteria incorporating a gene coding for a deoxyribonucleoside kinase and a deoxyribonucleoside kinase transcription promoter; (v) mixing a portion of the cell lysate from step (ii) with a bioluminescent reporter bacteria incorporating a gene coding for a deoxyribonucleoside kinase, a deoxyribonucleoside kinase transcription promoter and a dephosphorylating agent

Abstract: A quantification of the expression levels of a number of specific genes and their corresponding proteins can be utilized in accurately determining, using samples from faeces or blood, whether the patient is suffering from irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD), and in a follow up analysis using a biopsy, determine if the same patient is afflicted with ulcerative colitis (UC) or Crohn's disease (CD). The method also has utility in determining the severity of the disease, as well as observing a patient's response to treatment.

Abstract: A gene profiling signature is disclosed herein. The gene signature can predict whether a subject with ovarian cancer will be chemorefractory, chemoresistant or chemosensitive. Thus, methods are disclosed for determining whether a subject with ovarian cancer is sensitive to treatment with a chemotherapeutic agent. Methods are also provided for increasing sensitivity to the chemotherapeutic agent if the presence of differential expression indicates that the ovarian cancer has a decreased sensitivity to chemotherapeutic agent.

Abstract: An individual at risk for necrotizing enterocolitis and related disorders can be identified by measuring the level of at least one secretor antigen in a biological sample from the individual and comparing the measured level of the at least one secretor antigen to a predetermined value or a predetermined range of values. Among the secretor antigens which can be measured are: the H-1, H-2, Lewisb and Lewisy antigens and derivatives thereof (e.g., a sialylated form of Lewis a, Lewis x, Lewis b, Lewis y; H-1, H-2, Lewis a, Lewis x, Lewis b or Lewis y).

Abstract: The invention is directed to materials and methods associated with polymorphic variants in two enzymes involved in folate-dependent and one-carbon metabolic pathways: MTHFD1 (5,10-methylenetetrahydrofolate dehydrogenase, 5,10-methenyltetrahydrofolate cyclohydrolase, 10-formyltetrahydrofolate synthetase) and methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like (MTHFD1L). Diagnostic and therapeutic methods are provided involving the correlation of polymorphic variants in MTHFD1, MTHFD1, and other genes with relative susceptibility for various pregnancy-related and other complications.

Abstract: Human GFAT genes are identified as modulators of the Axin pathway, and thus are therapeutic targets for disorders associated with defective Axin function. Methods for identifying modulators of Axin, comprising screening for agents that modulate the activity of GFAT are provided.

Abstract: Polynucleotides encoding a mutant human carboxylesterase enzyme and polypeptides encoded by the polynucleotides which are capable of metabolizing a prodrug and inactive metabolites thereof to active drug are provided. Compositions and methods for sensitizing cells to a prodrug agent, inhibiting cell growth, treating drug addiction, and facilitating the metabolism of an organophosphate with this enzyme are also provided. In addition, a screening assay for identification of drugs activated by this enzyme is described.

Abstract: The present invention relates to polynucleotide sequences which enable a polynucleotide control sequence, such as a promoter, to direct expression in a wide range of industrially relevant species, both prokaryotes and eukaryotes.

Abstract: An in vitro or in vivo method for screening for candidate compounds for the preventive or curative treatment of acne, of seborrhoeic dermatitis or of skin disorders associated with hyperseborrhoea, includes determining the ability of a compound to modulate the expression or the activity of carnitine octanoyltransferase (CROT), and also utilizes modulators of the expression or of the activity of this enzyme, for the treatment of acne, of seborrhoeic dermatitis or of skin disorders associated with hyperseborrhoea; methods for the in vitro diagnosis of or in vitro prognosis for these pathologies are also featured.

Abstract: An in vitro or in vivo method for screening for candidate compounds for the preventive or curative treatment of acne, of seborrhoeic dermatitis or of skin disorders associated with hyperseborrhoea, includes determining the ability of a compound to modulate the expression or the activity of the carboxylesterase 1 (CES1) and/or carboxylesterase 3 (CES3) proteins.

Abstract: The present invention relates to various in vitro methods of diagnosing a vasoregulation disorder or a predisposition thereto in a subject being suspected of having developed or of having a predisposition to develop a vasoregulation disorder or in a subject being suspected of being a carrier for a vasoregulation disorder, wherein the vasoregulation disorder is selected from hypertension, migraine, pre-eclampsia and recurrent pregnancy loss. Moreover, the present invention also relates to methods for identifying compounds capable of modulating coagulation factor XII activity, suitable as medicaments or as lead compound for a medicament for the treatment and/or prevention of a vasoregulation disorder. Furthermore, the present invention relates to gene therapy methods and to a kit for diagnosing a vasoregulation disorder.

Abstract: A method of estimating a risk of the expression of an adverse drug reaction caused by the administration of irinotecan, and a method of reducing the adverse drug reaction caused by the administration of irinotecan. A polymorphism on the basis of a difference in the repeating numbers of TA repetitive sequences in the promoter region of UGT1 gene and two types of polymorphisms (bases at the 211- and 686-positions) on the basis of single nucleotide polymorphisms in the exon 1 are analyzed. Based on the analytical data, the risk of the expression of an adverse drug reaction caused by the administration of irinotecan is estimated. Further, the administration doses of irinotecan is designed for individual patients depending on the risk of the expression of the adverse drub reaction, thereby reducing the adverse drug reaction caused by the administration of irinotecan.