Abstract: The present invention provides compositions, kits and methods for rapid identification and quantification of sepsis-causing bacteria by molecular mass and base composition analysis.

Abstract: A method is provided for identifying a compound which affects the formation of AMPA receptors into aggregates. A method is also provided for identifying a compound which affects the formation of synaptic connections. A method is provided for identifying a compound that modulates immediate early gene expression. A method is further provided for increasing the number of excretory synapses of a neuron, including introducing into the neuron a polynucleotide sequence encoding a Narp operatively linked to a promoter, or a Narp polypeptide, thereby increasing the number of excretory synapses of the neuron. A method is provided for treating a subject with a disorder associated with a decrease in a function or expression of Narp, including administering to the subject a therapeutically effective amount of a compound that augments Narp function or expression.

Abstract: The present invention is drawn to methods and compositions for the rapid assessment of fecal indicator bacteria in a sample. Provided herein are novel primer and probe compositions for use in detecting the presence of these organisms in a sample, particularly using quantitative PCR methods. Provided herein are novel oligonucleotide primers and probes, including the primers set forth in SEQ ID NO:1-4, the novel oligonucleotide probe sequences set forth in SEQ ID NO:5-8, and methods for using these primers and probes for the detection and/or quantification of fecal indicator bacteria, particularly E. coli and Enterococcus spp. in a sample.

Abstract: The present invention provides methods of characterizing organ transplant rejection or inflammatory conditions associated with organ transplant rejection using gene expression profiling.

Abstract: The invention pertains to a method for identifying one or more regions within a genome of an organism of interest that mediate the expression of one or more genes of interest. The method comprises identifying a first and a second organism of interest, the first organism of interest is characterized by exhibiting a measurable response to an environmental stimulus, or otherwise, exhibiting a phenotype associated with differential gene expression associated with a process of interest. The second organism of interest is characterized by lacking or not exhibit as strong a response to the stimulus as that observed within the first organism of interest, or it exhibits a different phenotype compared with that of the first organism of interest, wherein the different phenotype is associated with the process of interest, or it exhibits a phenotype of interest that segregates when compared with the first organism of interest, or a combination thereof.

Abstract: The invention provides methods for improving the fidelity of a sequencing-by-synthesis reaction by resequencing at least a portion of a nucleic acid template.

Abstract: In a pre-processing step prior to training a learning machine, pre-processing includes reducing the quantity of features to be processed using feature selection methods selected from the group consisting of recursive feature elimination (RFE), minimizing the number of non-zero parameters of the system (l0-norm minimization), evaluation of cost function to identify a subset of features that are compatible with constraints imposed by the learning set, unbalanced correlation score, transductive feature selection and single feature using margin-based ranking. The features remaining after feature selection are then used to train a learning machine for purposes of pattern classification, regression, clustering and/or novelty detection.

Abstract: The invention relates to a method for producing ligands, in particular aptamers. With this method, a target substance is offered to a set of candidate ligands, and the unbonded ligands are separated out by a cross-flow filtration process. The retentate, which contains ligand-target substance complexes, then undergoes further continuous cross-flow filtration while chemical and/or physical parameters are being varied. After each variation of a parameter, those candidate ligands whose bond with the target substance was dissolved by the parameter variation are collected in separate fractions and separately multiplied.

Abstract: A method for judging the presence or absence of a mutation in a nucleic acid sequence, the method includes utilizing a single-stranded DNA-binding protein; the aforementioned method for judging the presence or absence of a mutation in a nucleic acid sequence, wherein the aforementioned presence or absence of a mutation in a nucleic acid sequence is judged by a product formed by a nucleic acid amplification reaction utilizing the single-stranded DNA-binding protein; and a kit for judging the presence or absence of the aforementioned mutation in a nucleic acid sequence.

Abstract: The present invention relates to a primer set for confirming an increase of mRNA in an ATP-sensitive potassium channel (KATP channel)(Kir6.1) having an effect of protecting heart from hypoxia or an ischemic disease; a kit including the primer set; and a method of identifying an agent for treating an ischemic heart disease.

Abstract: The present invention is related to a transgenic, non-human animal, particularly a transgenic rodent, but especially a transgenic mouse model which allows for the simultaneous, tissue-specific and temporally-controlled regulation of transgene expression and can be used as a tool to investigate the consecutive steps involved in initiation and progression of certain diseases such as cancer, but particularly lung cancer.

Abstract: The present invention provides nucleic acid molecules that encode histone deacetylase, as well as recombinant vectors and host cells that include the subject nucleic acid molecules. Also provided are histone deacetylase polypeptide compositions. The histone deacteylase nucleic acid molecules are useful in a variety of diagnostic and therapeutic applications, which are also provided.

Abstract: The present invention provides SNPs, polymorphic variants, and haplotypes associated with cardiovascular disease. The invention also provides methods for detecting the SNPs, polymorphic variants, and haplotypes. The invention also provides methods for determining an individual's genotype with respect to one or more polymorphisms and/or haplotypes associated with cardiovascular disease. The invention further provides methods of determining whether an individual has or is susceptible to development or occurrence of a cardiovascular disease or event. The methods are useful for providing diagnostic and/or prognostic information, selecting therapeutic regimens, etc. The invention further provides reagents and kits for practicing the methods.

Abstract: The present invention provides methods for predicting the development of and diagnosing preeclampsia, providing a prognosis, and predicting recurrence of the disease using molecular markers that are overexpressed or underexpressed in preeclampia. Also provided are methods to identify compounds that are useful for the treatment or prevention of preeclampsia.

Abstract: The invention relates to compositions and methods for modulating the expression of the MLL-AF4 fusion gene, and more particularly to the downregulation of MLL-AF4 by chemically modified oligonucleotides.

Abstract: The present invention relates to novel marker sequences that are differentially expressed in cancer cells or tissue of a subject with cancerous conditions. The present invention also relates to assays for diagnosis, prognosis, staging, monitoring, therapeutic treatment, and marker sequence related agents including probes, primers, antibodies, and therapeutic compositions.

Abstract: The invention relates to methods for preparing and performing quantitative PCR analyses, a new sealing device and a new use. According to the invention, a sample vessel containing the samples to be analyzed is sealed by placing a planar sealing device on the vessel to cover the samples and applying pressure on the sealing device in order to deform the sealing device so as to form a light-refracting geometry individually for the samples to be analyzed. The invention offers a convenient way of sealing the vessel and forming analysis-improving optical lenses over the samples simultaneously.

Abstract: The present teachings relate to improved methods, kits, and reaction mixtures for amplifying nucleic acids. In some embodiments a novel direct buffer formulation is provided which allows for the direct amplification of the nucleic acids in a crude sample with minimal sample purification.

Abstract: Analytical methods using RNA-containing probes for the detection or analysis of nucleic acid sequences is described. These probes are contacted with a sample suspected of containing the nucleic acid sequence and if they form duplexes, they are hydrolysed. This may be done, for example during an amplification reaction. AMP generated as a result of the hydrolysis is converted to ATP. The ATP may then be detected using bioluminescent reagents. Inclusion of modified adenosine in at least one probe means that the signal arising from one probe will give rise to a different and distinguishable bioluminescent signal thus enabling the use of for example an internal control in bioluminescently-reported nucleic acid tests.

Abstract: The present invention provides heterologous complementation systems and methods of using the systems to detect molecular interactions. In particular, the heterologous complementation systems comprise polypeptide fragments derived from heterologous polypeptides. If a molecular interaction occurs, then the heterologous polypeptide fragments are able to associate and produce a detectable signal.

Abstract: The present invention relates to devices for the analysis of liquid samples, comprising a rotational-symmetric rotor (1) which is insertable into a sample container (11), wherein an annular gap (32) is provided between the sample container (11) and the rotor (1), and the rotor (1) has at least one flow channel (7) for transporting liquids and/or gases into and/or from the interior of the sample container (11), wherein on the rotor (1) and, optionally, on the sample container (11), means for centred mounting of the rotor (1) are provided.

Abstract: The invention relates to a method and test kit for quantitative determination of the amounts or relative proportions of polynucleotides in a mixture. The invention enables assessment of dynamic variations in a mixed population of organisms using affinity aided solution hybridization. The test kit comprises organized pools of polynucleotide probes having approximately the same number of nucleotides, which are distinguishable using resolution enabling tags providing the probes with different sizes. The resolution enabling tags may simultaneously act as tracer, affinity or primer tags. The probes are allowed to hybridize with affinity tagged analyte polynucleotides. The result is hybrids, recoverable on separation aiding tools provided with counterparts of the affinity tag. After the quantitative release of the probes, the individual probes can be amplified and recorded.

Abstract: The present invention relates to methods for detecting, quantifying and high throughput screening of donor-products and the catalytic activities generating the donor-products in group-transfer reactions catalyzed by adenosine triphosphatase (ATPase) or guanine triphosphatase (GTPase). The invention further provides immunoassays, antibodies and kits that may be used to practice the methods of the invention.

Abstract: A pseudo-tissue for quality control is described, which includes a nucleic acid component selected from the group consisting of a nucleic acid and a cell including a nucleic acid, and a gel for holding nucleic acid component.

Abstract: A method for the determination of an analyte which is a) present in a liquid sample 1 suspected of containing the analyte, and b) at least bivalent with respect to simultaneous affinity binding of at least two binding structures BSs. The method comprises formation of an affinity complex that comprises the analyte and an affinity reactant 1 that is immobilized to a solid phase. The method comprises the steps of: (i) providing a microfluidic flow path that comprises a reaction cavity containing a solid phase to which affinity reactant 1 is immobilized, (ii) providing sample 1 upstream of the cavity and flowing it through the cavity for the formation of the affinity complex under flow conditions, (iii) measuring the amount of complex formed in the solid phase by a) incorporating an analytically detectable and soluble affinity reactant 2 that comprises a binding structure BS into the complex subsequent to step (ii), and b) measuring the amount of affinity reactant 2 incorporated.

Abstract: The invention relates to methods for diagnosing conditions characterized by altered expression of a pregnancy related serine protease (PRSP) protein in a mammal. Such conditions include infertility caused by an inability to achieve or sustain embryo implantation, an inability to sustain a pregnancy, early abortion, insufficient placentation, pre-eclampsia, or intrauterine growth restriction. The methods include detecting expression of PRSP, such as SEQ ID NP33. Detection may be accomplished using a PRSP-specific antibody.

Abstract: Newly identified mammalian taste-cell-specific G protein-coupled receptors, and the genes and cDNA encoding said receptors are described. Specifically, T1R G protein-coupled receptors active in taste signaling, and the genes and cDNA encoding the same, are described, along with methods for isolating such genes and for isolating and expressing such receptors. Methods for representing taste perception of a particular tastant in a mammal are also described, as are methods for generating novel molecules or combinations of molecules that elicit a predetermined taste perception in a mammal, and methods for simulating one or more tastes. Further, methods for stimulating or blocking taste perception in a mammal are also disclosed.

Abstract: A method of readily detecting or differentiating rheumatoid arthritis, which has so far been diagnosed in a comprehensive manner based on various tests and clinical symptoms, and a method of readily and objectively estimating the stage of disease and the degree of dysfunction with regard to rheumatoid arthritis are provided. The detection and differentiation of rheumatoid arthritis are performed by measuring the levels of L-PGDS in a sample such as a body fluid such that the measurement value is used as an index. Further, the stage of disease or the degree of dysfunction of a rheumatoid arthritis patient is determined using the measurement value as an index.

Abstract: A novel gene (designated 121P2A3) and its encoded protein, and variants thereof, are described wherein 121P2A3 exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table I. Consequently, 121P2A3 provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 121P2A3 gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 121P2A3 can be used in active or passive immunization.

Abstract: The invention concerns immunogenic glycopeptides derived from pathogenic microorganisms, useful for vaccination and diagnosis of infections caused by said pathogenic microorganisms (bacteria or fungi), and methods for selecting them and preparing them.

Abstract: The present invention is related to accurate detection methods for the measurement only of myelopexidase (MPO) levels or neutrophils, preferably equine neutrophils, in complex biological samples. The present invention is further related to ELISA and SIEFED assays for such detection. SIEFED detection sensitivity of active peroxidase activity was found to be enhanced by the addition of nitrite. Such MPO measurement finds its use in many applications such as the prediction, diagnosis and/or monitoring of pathologies correlated with neutrophil activation and/or destruction; the evaluation of drugs and/or immunomodulators; the assessment of immune responses, either natural and/or after treatment with immunomodulators and/or drugs; and the study of cells and their ability to fight microorganisms and/or to destroy them.

Abstract: Disclosed are compounds having the formula: wherein R1 is selected from the group consisting of hydrogen, C1-C6 alkyl, amino, N-C1-C6-alkylamino, and N,N—C1-C6-dialkylamino; and ring “A” is selected from the group consisting of unsubstituted or substituted C4-C8-cycloalkenyl, unsubstituted or substituted bicyclo [2,2,1]alkenyl, and unsubstituted or substituted bicyclo [2,2,2]alkenyl, unsubstituted phenyl, and phenyl substituted with a moiety selected from the group consisting of C3-C6-alkenyl, acryl, acryl-C1-C6 alkyl, acrylamido, and acrylamido-C1-C6 alkyl; polymers made from these compounds, and ELISAs that use the compounds and polymers as a chemiluminescent detection label.

Abstract: Methods are provided for detecting the formation of complexes of molecules, especially proteins, in a sample, such as a cell or tissue lysate. In one aspect, a cleaving probe specific for a first protein in a complex and one or more binding compounds specific for one or more second proteins in a complex are provided. Upon binding, the cleaving probe is induced to generate an active species, such as singlet oxygen, that cleaves molecular tags attached to the binding compounds only in the local region of the cleaving probe. The released molecular tags are separated from the assay mixture and from one another to provide a readout that is related to the number and types of proteins present in the complex.

Abstract: High-Throughput Screening (HTS) of large compound libraries is the method of drug-lead discovery. It is now well accepted that for a functional assay, quality is more important than quantity. A biochemical NMR method originally proposed by Percival and Withers (Biochemistry, 1992, 31, 498-505) is extended to the screening of Ser/Thr kinases. The method requires the presence of a CF3 (or CF) moiety on the substrate and utilizes 19F NMR spectroscopy for the detection of the starting and enzymatically modified substrates. Experiments can be performed in real time or in an endpoint assay format using protein and substrate concentrations comparable to the ones used by other HTS techniques. Application of this technique to the phosphorylation of a substrate by the protein Ser/Thr kinase AKT1 is presented.

Abstract: Methods for identifying compounds capable of modulating the hydrolase activity of a CLCA protein include screening and computer modelling methods. The compounds, including antibodies, may be useful as therapeutic agents to treat a variety of diseases.

Abstract: The present invention provides a convenient, efficient method for assaying glycated protein, fructosyl peptide, or fructosyl amino acid which can be performed with reduced effect of fructosyl lysine compounds. The invention also provides a reagent for the assay. The invention is directed to a method for reducing the effect of a fructosyl lysine compound in an assay of fructosyl peptide or fructosyl amino acid contained in a sample, characterized by including causing an enzyme for assaying fructosyl peptide or fructosyl amino acid to act specifically on fructosyl peptide or fructosyl amino acid at a pH of 4.0 to 7.0 and measuring the product at a pH of 4.0 to 7.0; and a method for assaying glycated protein through the above method.

Abstract: Provided herein are assays for detecting enzyme activity using Raman Spectroscopy.

Abstract: The invention provides cell culture devices comprising a channel, the channel comprising one or more inlets and one or more outlets, and a cell retention chamber defined by an internal surface of the channel and a plurality of projections extending therefrom. The invention further provides methods of use relating to such cell culture devices.

Abstract: This invention provides proteins and genes thereof involved in the GPI lipid remodeling process and, thereby and constructing a system for screening for useful substances such as anticancer agents and a system for detecting abnormalities in the GPI lipid remodeling process.

Abstract: Spirolactam targeting compounds, related compounds, uses of such compounds, and methods of making such compounds are disclosed.

Abstract: The present invention relates to methods for reprogramming a somatic cell to pluripotency by administering into the somatic cell at least one or a plurality of potency-determining factors. The invention also relates to pluripotent cell populations obtained using a reprogramming method.

Abstract: The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate unnatural amino acids into proteins produced in eubacterial host cells such as E. coli, or in a eukaryotic host such as a yeast cell. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing unnatural amino acids, and translation systems.

Abstract: An isolated mutant Ophiostoma species having enhanced protein excretion capability as compared with its parent strain cultured under similar conditions.

Abstract: The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

Abstract: The present invention provides codon-optimized genes designed to help maximize heterologous protein expression level. The present invention provides codon-optimized recombinant colG and colH collagenase sequences.

Abstract: Stress-related nucleic acid molecules and polypeptides and fragments and variants thereof are disclosed in the current invention. In addition, stress-related fusion proteins, antigenic peptides, and anti-stress-related antibodies are encompassed. The invention also provides recombinant expression vectors containing a nucleic acid molecule of the invention and cells into which the expression vectors have been introduced. Methods for producing the polypeptides and methods of use for the polypeptides of the invention are further disclosed.

Abstract: The present invention relates to the production of variants of a protein in an in vitro evolution method, comprising the steps: (A) provision of an in vitro expression system comprising (i) a nucleic acid sequence S which codes for a protein Y which is to be varied, (ii) a target molecule X which is able to bind to the protein Y and/or at least one variant Y? thereof, (iii) an RNA polymerase (Pol) which is able to transcribe the nucleic acid sequence S, (iv) a reverse transcriptase (RT) which is capable of reverse transcription of transcripts of the nucleic acid sequence S, where either the target molecule X is coupled to Pol and the protein Y is coupled to RT, or the target molecule X is coupled to RT and the protein Y is coupled to Pol, (B)incubation of the in vitro expression system from (A) under conditions which enable transcription, reverse transcription and translation to form variants Y? of the protein Y and nucleic acid sequences S? coding therefor, and which favor the formation of variants Y? with i

Abstract: The present invention relates to increasing the product of aspartate or aspartate-derived metabolites by boosting the activity of the glyoxylate shunt. This is accomplished by increasing the activity of glyoxylate shunt specific enzymes and decreasing the activity of reactions consuming glyoxylate and its precursors.

Abstract: Polypeptides and domains of leptomycin polyketide synthase and the nucleic acids encoding them are provided. Methods to prepare leptomycin, leptomycin analogs, and leptomycin derivatives are described, as are methods to prepare other polyketides using the nucleic acids encoding leptomycin polyketide synthase domains or modifying enzymes.

Abstract: The present invention relates to a process for the enantioselective enzymatic reduction of keto compounds which is carried out in two phases and uses 4-methyl-2-pentanol, 5-methyl-2-hexanol and/or 2-heptanol for coenzyme regeneration.