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: The invention relates generally to the fields of making biological unit lysates or admixtures of body fluids and of RNA analysis. More specifically, it relates to direct methods for the detection of a specific sequence of RNA in a biological unit, for example a virus, cell or tissue sample, or a body fluid, for example saliva, sputum, blood plasma, etc. More generally, the invention may be used to enzymatically manipulate and protect the RNA in lysate or bodily fluids for a number of applications.

Abstract: The present invention relates to methods and reagents for modifying the emission of light from labeled nucleic acids for the purpose of real time detection, analysis, and quantitation of nucleic acid sequences, e.g., using singly labeled probes. These methods and reagents exploit advantageous properties of thiazine dyes and diazine dyes. Furthermore, the use of these light emission modifiers in background reduction, nucleic acid duplex stabilization and other uses is also described. Related kits, reaction mixtures and integrated systems are described.

Abstract: The described method provides, methods, and kits to produce, identify, catalog and classify a comprehensive collection of nucleic acid targets produced from a nucleic acid sample. The method, referred to as Cataloging and Classification of Sequence Tags, involves generating a set of target nucleic acid fragments; coupling the target nucleic acid fragments to a nucleic acid bridge comprising, for example, two or more primer binding sites and two recognition sites for cleavage at a site offset from the recognition site to the fragment's end; and cleaving the fragments to generate chimeric nucleic acids of known length. The nucleic acid bridge is thus disposed between the two nucleic acid fragments in the chimeric nucleic acid. The resulting duplex nucleic acids comprise a set of sequence tags (i.e., by amplification using universal primers), comprising an addressable portion, a target nucleic portion and a portion of the nucleic acid bridge.

Abstract: The present invention is directed to detection and measurement of gene transcripts in blood. Specifically provided is a RT-PCR analysis performed on a drop of blood for detecting, diagnosing and monitoring diseases using tissue-specific primers. The present invention also describes methods by which delineation of the sequence and/or quantitation of the expression levels of disease-associated genes allows for an immediate and accurate diagnostic/prognostic test for disease or to assess the effect of a particular treatment regimen.

Abstract: The present invention relates to an assay including a surface having silver colloids or islands attached thereto. Attached to the surface and/or silver colloids/islands are polynucleotides which are complimentary to a target polynucleotide sequence. The assay is performed by adding the target polynucleotide sequence to the assay surface and allowed to hybridize with the capture polynucleotides. Fluorophore-labeled capture polynucleotides are added and hybridize to the target polynucleotide. Bound target polynucleotides are detected by metal enhanced fluorescence.

Abstract: The present invention provides compositions and methods for performing free-solution conjugate analysis of nucleic acid molecules. For example, the present invention provides multiplexed single-base extension assays for genotyping. In particular, the present invention provides a series of disperse polyamide “drag tags” for use in achieving high-resolution separation of nucleic acid reaction products.

Abstract: This document provides methods and materials related to genetic markers of schizophrenia (SZ), schizotypal personality disorder (SPD), and/or schizoaffective disorder (SD), (collectively referred to herein as “schizophrenia spectrum disorders” or SSDs). For example, methods for using such genetic markers to identify an SSD (e.g., SZ) endophenotype are provided.

Abstract: Four highly conserved genes, encoding translation elongation factor Tu, translation elongation factor G, the catalytic subunit of proton-translocating ATPase and the RecA recombinase, are used to generate species-specific, genus-specific, family-specific, group-specific and universal nucleic acid probes and amplification primers to rapidly detect and identify algal, archaeal, bacterial, fungal and parasitical pathogens from clinical specimens for diagnosis. The detection of associated antimicrobial agents resistance and toxin genes are also under the scope of the present invention.

Abstract: A method and assay are described for measuring the interaction between a ligand and an analyte. The assay can include a suspension of colloidal particles that are associated with a ligand of interest. The colloidal particles are maintained in the suspension at or near a phase transition state from a condensed phase to a dispersed phase. An analyte to be tested is then added to the suspension. If the analyte binds to the ligand, a phase change occurs to indicate that the binding was successful.

Abstract: The present invention relates to a soluble receptor variant of TREM-1. More particularly, present invention relates to methods of modulating an immune response by administering variants of TREM-1.

Abstract: A method of determining the immune response of a mammal to circulating tumour marker proteins is described in which a sample of bodily fluid, for example plasma or serum, is contacted with a panel of two or more distinct tumour marker antigen. The presence of complexes between the tumour marker antigens and any autoantibodies to the antigens present in the sample are detected and provide an indication of an immune response to a circulating tumour marker protein. The method is useful for the diagnosis of cancer, particularly for identifying new or recurrent cancer in an otherwise assymptomatic patient.

Abstract: Disclosed are major allergenic proteins in cashew nut, which are legumin-like proteins and 2S albumins. Also disclosed is a polypeptide allergen in the 7S superfamily, which includes vicilin-like and sucrose binding proteins. Several linear epitopes of the cashew nut are identified and characterized. The invention further discloses the sequence of cDNA encoding the allergenic polypeptide, the allergen being designated Ana o 1, and also describes the characterization of the expressed recombinant polypeptide and associated methods employing the polypeptide.

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: A type IV collagen-like immunoreactive peptide and an antibody thereof which are useful for detecting nephritis, a method for selecting a type IV collagen-like immunoreactive peptide, a method for screening an immunoreactive antibody and an immunoreactive peptide, a nephritis model, a method for detecting chronic nephritis, a vaccine, and a therapeutic agent for nephritis are provided. A type IV collagen-like immunoreactive peptide immunologically reacts with an isolated, chronic nephritis-derived biological sample. Preferably, the type IV collagen-like immunoreactive peptide includes at least one member selected from the group consisting of at least one chain selected from alpha 1 to alpha 6 chains as a constituent alpha chain, at least one region selected from 7S, the central helical domain, and NC1 as a constituent region, and a peptide having 3 to 35 amino acids as a constituent peptide.

Abstract: The present invention provides compositions and methods for diagnosing and treating fibrotic lung disease.

Abstract: The present invention provides a method, an assay and a kit for providing an indication of abnormal cell function. It was surprisingly found that the change in the serum ADAM12 concentration in individuals was useful as a prognostic tool to predict the clinical outcome, complications and mortality following an abnormal cell function. The present inventors describes ADAM12 as a overall general marker for abnormal cell function, and the present inventor for the first time demonstrate that ADAM12 is an important indicator of fetal chromosomal disease and placenta function. Specifically ADAM12 is a good marker for e.g. Downs's syndrome, trisomy 18, preeclampsia, Turner syndrome in both first and second trimester. The present inventors developed an enzyme-linked immunosorbent assay (ELISA) and a time-resolved immunofluorometric assay for the quantification of ADAM12 in serum.

Abstract: The present invention relates to a diagnostic method for the detection of small quantities of amniotic fluid in the vagina. More specifically, the invention relates to the detection of PAMG-1 in the vagina using anti-PAMG-1 antibodies.

Abstract: The invention provides methods of coupling protein ligands to a solid support. The invention also provides affinity chromatography matrices and methods of using affinity chromatography matrices to purify a target molecule.

Abstract: Assay systems and specialized antibodies for the detection and quantitation of troponin I and troponin T in body fluids as an indicator of myocardial infarction are disclosed. Troponin I and T exist in various conformations and the ratios of monomeric troponin I and T and the binary and ternary complexes, as well as which form of troponin present in the blood, may be related to the metabolic state of the heart. Disclosed are systems to determine the presence of a troponin form or a group of troponin forms in whole blood, serum or plasma samples. Disclosed is a method for improving the recovery of troponin I or T from a surface used in immunoassays. Also disclosed are antibodies which recognize unbound troponin forms, the forms of troponin in binary complexes, the ternary complex of troponin I, T and C, and the conformations of troponin I having intramolecularly oxidized and reduced cysteines.

Abstract: Methods are provided for the detection and quantitation of proteins generally and apolipoprotein A-I and oxidized derivatives thereof in particular. Further provided are methods for the assessment of the risk cardiovascular disease in a subject, wherein the assessment is based on the amount of oxidized and unoxidized apolipoprotein A-I in a biological sample obtained from a subject.

Abstract: Contemplated compositions, devices, and methods are drawn to various antigens from the pathogen M. tuberculosis and their use in vaccines, therapeutic agents, and various diagnostic tests. In particularly preferred aspects, the antigens are immunodominant and have quantified and known relative reactivities with respect to sera of a population infected with the pathogen, and/or have a known association with a disease parameter.

Abstract: The invention provides an improved method for identifying and interpreting tissue specimens and/or cells derived from tissue specimens. A panel of cell-based reagents provides a number of readouts of cellular states or biomarkers that together define a profile of a diversity of cellular states or biomarkers in a tissue specimen representing the “systems” nature of biology. This cellular profile is interpreted using informatics tools, to identify similarities between specimens, in vivo medical conditions, and suggest options for treating medical conditions.

Abstract: The invention provides an ELISA assay for the determination of serum mast cell ?-tryptase levels using rabbit anti-tryptase as the capture antibody and alkaline phosphatase conjugated G3 as the detecting antibody. Luminescent substrate CPSD was used to enhance the assay sensitivity. Also provided are methods for aiding in the diagnosis of irritable bowel syndrome by detecting the serum level of ?-tryptase, histamine and/or prostaglandin E2.

Abstract: The invention involves a method for measuring phosphorylation of proteins at specific sites and, as such, is an indicator of the protein kinase activity of enzymes capable of phosphorylating those sites. The method involves the in vitro or in vivo phosphorylation of a target protein at a specific serine, threonine or tyrosine residue, subjecting that protein (non-phosphorylated) to reaction mixture containing all reagents, including phosphokinase which allow the creation of a phosphorylated form of protein. The phosphorylated protein is measured by contacting it with an antibody specific for the phosphorylation site(s). The invention includes antibodies useful in practicing the methods of the invention. The invention particularly relates to all proteins modified by phosphorylation and dephosphorylation as illustrated by Tau, Rb and EGFR proteins and antibodies specific for the site of phosphorylation of the Tau, Rb or EGFR proteins.

Abstract: The present invention relates to the field of immunology and hyperproliferative diseases. More specifically, the present invention relates to a method of detecting and monitoring therapeutic antibody:antigen complex, soluble antigen and soluble therapeutic antibody, wherein a patient has undergone at least one course of immunotherapy. Yet further, levels of therapeutic antibody:antigen complexes, soluble antigens or soluble therapeutic antibodies may be measured and used to stage or monitor a hyperproliferative disease.

Abstract: Biological markers for multiple sclerosis, and their use in the diagnosis and prognosis of the disease, are described. Also described are methods for treating multiple sclerosis by administering an inhibitor of cathepsin B activity or a neuroprotective composition comprising a modified terpenoid compound. Also described are isolated polypeptide biomarkers, polynucleotides encoding the polypeptide biomarkers, and antibodies that bind specifically to the polypeptide biomarkers. Further described are kits that include the above-mentioned isolated polypeptide biomarkers, the polynucleotides encoding them, or specific antibodies against the polypeptide biomarkers.

Abstract: The present invention discloses a dysregulation of a PRKX gene and the protein products thereof in Alzheimer's disease patients and individuals being at risk of developing Alzheimer's disease. Based on this finding, the invention provides methods for diagnosing and prognosticating Alzheimer's disease in a subject, and for determining whether a subject is at increased risk of developing Alzheimer's disease. Furthermore, this invention provides therapeutic and prophylactic methods for treating and preventing Alzheimer's disease and related neurodegenerative disorders using a PRKX gene and its corresponding gene products. Screening methods for modulating agents of neurodegenerative diseases are also disclosed.

Abstract: Novel conjugates and immunogens derived from lenalidomide and antibodies generated by these immunogens are useful in immunoassays for the quantification and monitoring of thalidomide and lenalidomide in biological fluids.

Abstract: Novel reporter bacteriophages are provided. Provided are compositions and methods that allow bacteriophages that are used for specific detection or killing of E. coli 0157:H7 to be propagated in nonpathogenic E. coli, thereby eliminating the safety and security risks of propagation in E. coli 0157:H7. Provided are compositions and methods for attaching active bacteriophages to the surface of a polymer in order to kill target bacteria with which the phage comes into contact. Provided are modified bacteriophages immobilized to a surface, which capture E. coli 0157:H7 and cause the captured cells to emit light or fluorescence, allowing detection of the bacteria in a sample.

Abstract: The invention relates to a method and a device for determining the glucose concentration in tissue fluid whereby test values for glucose and for an endogenous reference substance are detected in a sample liquid obtained by microdialysis, microperfusion or ultrafiltration, and the glucose value is corrected in accordance with the test value for the reference substance. The recovery rate for glucose is determined from a non-linear relationship with the recovery rate for the ionic reference substance, and the test value for glucose is corrected therewith. In addition, the concentration of lactate and/or pyruvate is used as a further reference substance in the sample liquid to make further corrections.

Abstract: The present invention pertains to the domain of brain diseases, and provides novel markers and methods for diagnosing a brain alteration in an individual, especially in patients suffering from neurodegenerative diseases such as Alzheimer's disease. The present invention also provides tools for evaluating the probability, for an individual, of developing the disease, as well as a target for identifying new drugs for treating neurodegenerative diseases such as Alzheimer's disease. In particular, the invention provides a genetic marker based on combination of two single nucleotide polymorphism, at positions ?389 and ?241 of the ornithine transcarbamylase (OTC) gene.

Abstract: The invention describes a method for cell analysis in which the cells to be analyzed are adhesively applied to a slide and stained with a first stain. A first digital image is then taken and stored of the cells applied to the slide and stained. After the first digital image is taken, these same cells are treated with a second stain while on the same slide in such a way that their optically measurable properties change. A second digital image is then taken of the cells applied to the slide and stored. According to the invention, a group of preparations with cells to be analyzed is first stained with a stain of a highly sensitive analysis method, and only the preparations with positive findings are further processed.

Abstract: The present invention embraces a fungal strain deficient in nicotinamide riboside import and salvage and use thereof for producing nicotinamide riboside. Methods for producing nicotinamide riboside and a nicotinamide riboside-supplemented food product using the strain of the invention are also provided.

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

Abstract: This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

Abstract: Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

Abstract: Modified interferon beta polypeptides and uses thereof are provided.

Abstract: Nucleic acids encoding spider glue proteins and methods of use thereof are disclosed.

Abstract: The present invention relates to a method of producing a biologically active polypeptide having insulinotropic activity, the method comprising steps of: (a) transforming a genetically modified host cell that has protease gene knockout, with a polynucleotide vector encoding the polypeptide; and (b) growing the transformed host cell to produce the biologically active polypeptide; and a method of producing a biologically active polypeptide having an N-terminal recognition site His-Gly with insulinotropic activity, the method comprising steps of: (a) transforming a genetically modified Pichia pastoris that has protease gene STE13 knockout, with a polynucleotide vector encoding the polypeptide; and (b) growing the transformed Pichia pastoris to produce the biologically active polypeptide.

Abstract: The present invention relates, in general, to methods for detecting and quantitating plasma-derived protein and recombinant protein in a sample based on the difference in protein glycosylation, when the plasma protein and the recombinant protein are essentially the same protein.

Abstract: The instant invention provides methods, systems and reagents for immunodetection involving novel epitope tags and antibodies which recognize these new epitope tags as well as the antibodies which detect the FLAG epitope tag. Fusion proteins comprising the epitope tags, as well as methods of purifying these proteins and kits detecting these proteins are also provided.

Abstract: The present invention relates to microbial trypsin variants having chymotrypsin-like activity, comprising: (a) a one or more substitutions corresponding to positions 144, 193, 198, 201, 218, 223, 227, 228, 229, 230, and 231 of amino acids 25 to 248 of SEQ ID NO: 2, (b) one or more deletions corresponding to positions 192, 197, and 226 of amino acids 25 to 248 of SEQ ID NO: 2; and (c) an insertion between positions corresponding to positions 224 and 225 of amino acids 25 to 248 of SEQ ID NO: 2. The present invention further relates to nucleotide sequences encoding microbial trypsin variants having chymotrypsin-like activity; nucleic acid constructs, expression vectors, and recombinant host cells comprising such nucleotide sequences; and methods of producing microbial trypsin variants having chymotrypsin-like activity or a precursor thereof.

Abstract: Provided in certain embodiments are new methods for forming azido modified nucleic acid conjugates of reporter molecules, carrier molecules or solid support. In other embodiments are provided methods for enzymatically labeling nucleic acids with an azide group.

Abstract: In the absence of substantial sequence overlap between a recombinant adenoviral vector and the genome of a packaging cell, helper-dependent E1-containing particles (HDEP) can be formed at low frequency. Provided are means and methods for reducing or preventing the generation of HDEP. To this purpose, novel packaging cells and methods of making these are provided.

Abstract: Stable and active arabinitol dehydrogenases (LAD) from Neurospora crassa and mutants thereof are disclosed. Arabinitol dehydrogenases are useful in the production of xylitol and ethanol from an arabinose containing substrate. Recombinant and heterologously expressed arabinitol dehydrogenases are useful in converting biomass into biofuels and other industrial food products.

Abstract: The present invention provides a method for producing an L-amino acid using a bacterium of the Enterobacteriaceae family, particularly a bacterium belonging to genus Escherichia or Pantoea, which has been modified to attenuate expression of the sfmACDFH-fimZ cluster and/or the fimZ gene.

Abstract: A method of preparing macrocycles using solid support chemistry and thioesterases is disclosed. Also disclosed are novel macrocycles.

Abstract: This invention describes genes, metabolic pathways, microbial strains and methods to produce methyl butanol and other compounds of interest from renewable feedstocks.

Abstract: A method for producing vitamin K2 comprising: culturing Bacillus natto in a liquid medium to obtain a Bacillus natto culture or culture supernatant thereof, wherein the culture or culture supernatant contains vitamin K2; treating the culture or culture supernatant with at least one coagulant selected from the group consisting of an inorganic coagulant and a cationic polymer coagulant, with the proviso that the coagulant excludes chitosan, so as to obtain a treated coagulant to which vitamin K2 is absorbed or aggregated; separating the treated coagulant from the treated culture or culture supernatant, and obtaining an oily product that contains vitamin K2 from the separated coagulant.