Abstract: Mass spectrometry-based methods are described for the detection or quantification of targeted proteins in biological samples e.g., plants, animals, and microorganisms, parts (e.g., tissue or cells) thereof, and products derived from plants, animals or microorganisms.

Abstract: The inventor discovered that ?-GTP (?-glutamyl transpeptidase) was scarcely contained in the gingival crevicular fluid of patients with gingivitis, but was contained in the gingival crevicular fluid of patients with periodontitis. Thus, the inventor provides a determination method of development of periodontitis by detecting or measuring ?-GTP contained in the gingival crevicular fluid. Also, this method can be applied to the determination of the development of peri-implant inflammation.

Abstract: This invention relates to a soluble form of PHEX, PHEX being a type II integral membrane glycoprotein. This enzyme is the gene product of a phosphate-regulating gene with homologies to endopeptidases on the X chromosome. To produce a soluble form of PHEX, the transmembrane anchor domain has been modified to encode a signal peptidase coding sequence. The soluble PHEX therefore comprises the active ectodomain. An inactive mutant of PHEX is also an object of this invention. Both soluble and inactive mutant forms of PHEX can be used to screen ligands to PHEX. These ligands can also be used as substrates or inhibitors of PHEX. PHEX being phosphaturic, an inhibitor thereof will be used to treat phosphaturia and/or hypophosphatemia. On the opposite, a substrate for PHEX or PHEX itself can be used to treat hyperphosphatemia.

Abstract: This invention is directed towards methods of destabilizing proteins in living cells, and their use for the development of novel assays. In one embodiment, the invention comprises the use of non-cleavable multimerized ubiquitin fusion proteins to destabilize a target protein, such as a reporter moiety. In one aspect of this method the constructs also comprises a linker that operatively couples the reporter moiety to the multimerized ubiquitin fusion protein. In this embodiment, enzymatic modification of the linker results in a modulation of the coupling of the reporter protein to the multimerized ubiquitin domains resulting in a change in the stability of the reporter moiety. The level of the reporter moiety in the cell can then be used as a measure of the enzymatic activity in the cell. In another embodiment the invention provides for a generalized way of coordinately regulating the cellular concentration of a plurality of target proteins.

Abstract: A method involves the detection of enzyme-catalyzed cleavage reactions using modular chemical compounds as substrates for the enzymes involved, and detection is effected by use of molecular-weight-sensitive methods.

Abstract: A reagent is provided for the detection of an exotoxin protein produced by a beta-hemolytic streptococcus bacteria suspected of being present in a host biological fluid collected from a subject. An enzyme inhibitor is present to inhibit rogue protein modification of the substrate to prevent a false positive result of the color change. A kit is provided that is readily usable by an untrained user and merely requires that an element of the kit be contacted with a biological sample and thereafter no further actions are required by the user before a discernable color change is observed with visible or UV light and a positive/negative results reference card.

Abstract: The present provides compounds capable of modulating IL-4 receptor-mediated IgE production, as well as IL-4 induced processes associated therewith, methods and kits for identifying such compounds that utilize a CLLD8 protein as a surrogate analyte and methods of using the compounds in a variety of in vitro, in vitro and ex vivo contexts.

Abstract: The cellular response to cosmetic products has been characterized on the molecular level through the use of gene and protein expression technologies. Nucleic acid and protein molecules, the expression of which are induced or repressed in response to exposure to cosmetics, are identified according to a temporal pattern of altered expression post exposure. Methods are disclosed that utilized these cosmetics-regulated molecules as markers for effectiveness of cosmetics. Other screening methods of the invention are designed for the identification of compounds that modulate the response of a cell to exposure to cosmetics. The invention also provides compositions useful for drug screening or pharmaceutical purposes.

Abstract: The present invention provides for novel reagents whose fluorescence increases in the presence of particular proteases. The reagents comprise a characteristically folded peptide backbone conjugated to two fluorophores such that the fluorophores are located opposite sides of a cleavage site. When the folded peptide is cleaved, as by digestion with a protease, the fluorophores provide a high intensity fluorescent signal at a visible wavelength. Because of their high specificity and their high fluorescence signal in the visible wavelengths, these protease indicators are particularly well suited for detection of protease activity in biological samples, in particular in frozen tissue sections. Thus this invention also provides for methods of detecting protease activity in situ in frozen sections.

Abstract: A method treats urogenital and/or intestinal tract cancer and includes administering a therapeutically effective amount of at least one annexion protein, annexin of A3, to a mammal.

Abstract: The present invention relates to inhibitors of insulin-regulated aminopeptidase (IRAP) and methods for inhibiting same, as well as compositions comprising said inhibitors. In particular, the inhibitors of the present invention may be useful in therapeutic applications including enhancing memory and learning functions, regulating cellular glucose uptake and homeostasis, inducing labour and lactation, and other disorders or conditions wherein excessive or undesirable IRAP activity is implicated.

Abstract: The invention relates to chromogenic compounds and the use thereof for the determination of enzymes of the family of carboxypeptidases N and carboxypeptidases U. The above is more specifically a compound of formula (I) in which A=(1), (2), (3), (4) or (5), R1, R2=H, —CH3, —CH(CH3)2, —OCH3, —Cl,—CF3,—OCF3,—SCH3, R3=an amino acid group which may be hydrolysed by a carboxypeptidase A and R4=a basic amino acid group.

Abstract: Methods are provided for determining the position of a post-translationally modified (PTM) amino acid residue such as a phosphorylated amino acid residue or an O-glycosylated amino acid residue in a peptide. Also provided are methods for determining the identity of a PTM amino acid residue in a peptide. In addition, kits for practicing such methods are provided.

Abstract: An apparatus for detecting pepsin comprising a solid support, and a peptide chain wherein the peptide chain is operatively configured to be cleaved by pepsin, and the peptide chain is disposed on a surface of the solid support.

Abstract: The present invention provides methods, systems, and code for accurately classifying whether a sample from an individual is associated with irritable bowel syndrome (IBS). In particular, the present invention is useful for classifying a sample from an individual as an IBS sample using a statistical algorithm and/or empirical data. The present invention is also useful for ruling out one or more diseases or disorders that present with IBS-like symptoms and ruling in IBS using a combination of statistical algorithms and/or empirical data. Thus, the present invention provides an accurate diagnostic prediction of IBS and prognostic information useful for guiding treatment decisions.

Abstract: The present invention provides methods of detecting and treating cancer.

Abstract: There are provided polypeptides which bind to caspase-8. Production and use of such polypeptides is also provided, as well as DNA encoding them, and vectors and host cells having such DNA.

Abstract: A sensitive bioluminescent assay to detect proteases, including caspases and proteases that specifically cleave a peptide substrate having aspartate, is provided. In one embodiment, the assay employs an aminoluciferin or a carboxy-terminal protected derivative thereof covalently linked via a peptide bond to a substrate for a caspase or an aminoluciferin or a carboxy-terminal protected derivative thereof covalently linked via a peptide bond to a peptide substrate comprising aspartate that is specifically cleaved by a protease specific for the substrate.

Abstract: A method for providing a personalized skin-care composition for an individual includes sampling the skin of an individual for whom a personalized skin-care composition is to be provided, testing for a predetermined set of biomarkers so as to produce an individual biomarker profile, analyzing the biomarker profile using a biomarker profile database, and producing a personalized skin-care composition based on the results. The personalized skin-care composition is adapted for treating one or more skin conditions which the individual has, and can be adapted according to the preferences of the individual.

Abstract: Provided herein are methods for the diagnosis, prognosis, or management of hematological disorders and other diseases using the proteasome activity levels determined in acellular body fluids or cell-containing samples. Also provided are methods of monitoring treatment with proteasome inhibitors through assaying proteasome activity in acellular body fluids. Further provided are methods of predicting response to therapy in certain populations of leukemia patients.

Abstract: Kits and peptide substrates for detecting transferase activity of a sample are provided. The kits include a substrate including a reporter compound, at least one of a phosphate group donor and a phosphate group acceptor, a buffer that supports enzymatic activity of the transferase, and a peptidase that cleaves a non-phosphorylated peptide substrate at a first rate and a phosphorylated peptide substrate at a second rate. The peptide substrates include a reporter compound and a first transferase substrate linked to the reporter compound on a first side of the reporter compound.

Abstract: The present invention is directed to novel peptides and compositions capable of modulating apoptosis in cells, and to methods of modulating apoptosis employing the novel peptides and compositions of the invention. In one aspect, the invention is directed to a novel peptide designated the “GD domain,” which is essential both to Bak's interaction with Bcl-xL, and to Bak's cell killing function. Methods of identifying agonists or antagonists of GD domain function are provided. The GD domain is responsible for mediating key protein/protein interactions of significance to the actions of multiple cell death regulatory molecules.

Abstract: We disclose methods of sorting or separating mixtures of living cells (e.g., eukaryotic, prokaryotic, mammalian, pathogenic, bacterial, viral, etc.). We perform our methods by activating cell-selective photophoric labels, which photosensitize and chemically reduce a photosensitive metal compound to form metal grains, particles or crystals. The metal adheres to the cells and forms the basis for sorting or separating different cell types. Photophoric labels may include chemiluminescent agents such as peroxidase enzymes activated with peroxidase substrates capable of luminescence. Photosensitive metal compounds may be present in a light-sensitive matrix or emulsion containing photosensitizable metal compounds, which form metal grains, particles or crystals upon exposure to a developer solution. Developer solutions are formulated to substantially allow living cells to remain viable after exposure to the developing solution.

Abstract: Provided are crystals relating to DPPIV and its various uses.

Abstract: Method for determining the biological activity of defibrotide by a) bringing into contact defibrotide, plasmin and a substrate specific for the plasmin which, by reaction with the plasmin, provides a measurable product; and b) measuring the amount of product formed at successive times, to thereby determine the biological activity of the defibrotide.

Abstract: The invention provides methods for quantifying enzymatic activity of an enzyme with a known substrate. The methods employ SELDI-TOF mass spectrometry, and are suitable, in particular, for assaying aspects of the renin-angiotensin system. The methods may be utilized to assess and/or monitor biological conditions associated with the renin-angiotensin system prior to the manifestation of known physiological and biomarkers for such conditions. The methods are suitable for analysis of pharmacological effectors of the renin-angiotensin system, and are particularly suitable for automation and high-throughput screening assay design.

Abstract: The compounds of the invention are modified forms of therapeutic agents. A typical prodrug compound of the invention comprises a therapeutic agent, an oligopeptide having an isoleucine residue, a stabilizing group and, optionally, a linker group. The prodrug is cleavable by an enzyme associated with the target cell. Methods of making and using the compounds are also disclosed.

Abstract: The present invention relates to compositions and an apparatuses for determining protease activity. The compositions of the invention contain a reporter protein fused to at least one protease cleavage sequence, and a linker for attaching the protease cleavage sequence to a solid support. Methods for determining protease activity and characterizing proteases are also provided.

Abstract: The present invention concerns a further development and use of biological assays to determine the amount or concentration of an active ingredient present in a sample. The enzyme assay of the present invention determines the amount or concentration of protease inhibitors, including retroviral protease inhibitors such as HIV inhibitors.

Abstract: The present invention provides for novel reagents whose fluorescence increases in the presence of particular proteases. The reagents comprise a characteristically folded peptide backbone conjugated to two fluorophores such that the fluorophores are located opposite sides of a cleavage site. When the folded peptide is cleaved, as by digestion with a protease, the fluorophores provide a high intensity fluorescent signal at a visible wavelength. Because of their high specificity and their high fluorescence signal in the visible wavelengths, these protease indicators are particularly well suited for detection of protease activity in biological samples, in particular in frozen tissue sections. Thus this invention also provides for methods of detecting protease activity in situ in frozen sections.

Abstract: The present invention provides a method of treating or preventing a chronic obstructive pulmonary disease in a subject, comprising administering to said subject an amount of an agent affective to inhibit apoptosis of the subject's lung cells and thus treat or prevent chronic obstructive pulmonary disease in the subject. The present invention provides for a method of diagnosing the disease.

Abstract: The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS—MS), and/or MS3 analysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide.

Abstract: The present invention is based on the discovery that a polypeptide containing the JAB subunit or the JAM domain has peptidase activity, e.g., isopeptidase activity. The present invention provides polypeptides and crystalline polypeptides containing the JAM domain and methods of using such polypeptides to screen for agents capable of affecting the peptidase activity of the polypeptides. The present invention also provides methods of using the JAM domain for rational drug design or identifying agents capable of affecting the peptidase activity of the JAM domain.

Abstract: Methods for identifying agents that can increase or decrease the isopeptidase activity of a COP9 signalsome (CSN) are provided, as are agent identified using such screening assays. In addition, methods of ameliorating a pathologic condition such as a cancer or an autoimmune disease in a subject by modulating the CSN isopeptidase activity are provided, as are medicaments useful for treating a subject having such a condition.

Abstract: The acetylation level of a peptide is determined utilizing the fact that the changes in the acetylation level are reflected in the sensitivity of the substrate peptide to a peptidase. This method can be used for measuring activities of deacetylase and acetylase, and also enables screening for substances that influence the activity of these enzymes. The deacetylase activity can be measured by a simple procedure according to the present invention.

Abstract: The present invention relates to a novel human orphan nuclear receptor that binds to a cytochrome P-450 monooxygenase (CYP) promoter and that is activated by compounds that induce CYP gene expression. The invention further relates to nucleic acid sequences encoding such a receptor, to methods of making the receptor and to methods of using the receptor and nucleic acid sequences encoding same. The invention also relates to non-human animals transformed to express the human receptor and to methods of using such animals to screen compounds for drug interactions and toxicities.

Abstract: This invention has as its object a method for detecting catalytic activity of a sample, characterized in that it comprises: the incubation of a substrate (S) with the sample that may have the catalytic activity that it is desired to detect, the addition of a reagent (X) that can react either with a chemical group of unconsumed substrate (S) or with a chemical group of product (P) that is formed after an incubation period with the sample, the addition of a developer (R) that can react with reagent (X), and the detection of the transformation of developer (R).

Abstract: The present invention relates to novel chromogenic substrates which are used to detect aminopeptidase activity in microorganisms or to determine whether at least one bacterium belongs to the Gram-positive group or to the Gram-negative group according to the color thereof. The invention also relates to culture media containing such substrates, to the use of the substrates or media for the detection of aminopeptidase activities and/or the differentiation of Gram-positive bacteria from Gram-negative bacteria and to methods of use. The aforementioned novel substrates have the formula below: in which: R1 is nothing or an alkyl, allyl or aryl group, R2 consists of at least one amino acid, preferably alanine, R3, R4, R5 and R6 consist, independently of one another, of H— or —O-alkyl, preferably —O—CH3, R7 consists of H, O—CH3, alkyl or halogen, R8 consists of H or Cl, and n is an integer corresponding to 0 or 1. The invention is particularly suitable for use in the field of diagnostics.

Abstract: The present provides compounds capable of modulating IL-4 receptor-mediated IgE production, as well as IL-4 induced processes associated therewith, methods and kits for identifying such compounds that utilize a CLLD8 protein as a surrogate analyte and methods of using the compounds in a variety of in vitro, in vitro and ex vivo contexts.

Abstract: Described herein are methods which identify candidate agents as binding to a protein or as a modulator of the binding characteristics or biological activity of a protein. Generally, the methods involve the use of ADP or phosphate. The assays can be used in a high throughput system to obviate the cumbersome steps of using gels or radioactive materials.

Abstract: The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS—MS), and/or MS3 analysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide.

Abstract: A method for detecting transferase activity of a sample includes contacting the sample with a substrate and at least one of a phosphate group donor and a phosphate group acceptor. The substrate includes a reporter compound and amino acids. A peptidase is added that cleaves a non-phosphorylated substrate at a first rate and a phosphorylated substrate and a second rate. The output of the reporter compound is detected. In a preferred embodiment, the transferase activity detected is a kinase activity. In another preferred embodiment, the transferase activity detected is a phosphatase activity. Also provided is a method of screening for alterations in a transferase reaction. Kits and peptide substrate are also provided for carrying out at least one of the methods of the invention.

Abstract: The present invention is based on the findings that BACE2, a homolog of ?-secretase BACE, is able to stimulate processing of APP in a non-amyloidogenic pathway, thereby suppressing the level of A?. Accordingly, the present invention provides methods and means for the identification and use of modulators of this unique activity of BACE2 to suppress A? production. The compounds identified using the methods and means provided herein may be used as potential candidates for the treatment of Alzheimer's disease and other neurological diseases by reducing ?-amyloid deposit formation.

Abstract: The invention concerns the use of a PyA-(Z)x-pNF group in a substrate for detecting, identifying and/or analyzing by fluorometry peptidases or proteases capable of cleaving the or a bond between a PyA and pNF and/or compounds with inhibiting or activating activity with respect to enzymes capable of cleaving said bond.

Abstract: Provided is a method for characterizing a polypeptide, which method comprises the steps of: (a) optionally reducing cysteine disulphide bridges in the polypeptide to form free thiols, and capping the free thiols; (b) cleaving the polypeptide with a sequence specific cleavage reagent to form peptide fragments; (c) optionally deactivating the cleavage reagent; (d) capping one or more ?-amino groups that are present with a lysine reactive agent; (e) analyzing peptide fragments by mass spectrometry to form a mass fingerprint for the polypeptide; and (f) determining the identity of the polypeptide from the mass fingerprint.

Abstract: Novel proteins or polypeptides having significant sequence homology to DPPIV, nucleic acids coding therefor, cells which have been modified with such nucleic acid so as to express these proteins, antibodies to these proteins, screening methods for the discovery of new therapeutic agents which are inhibitors of the activity of these proteins or of related proteins, and therapeutic agents discovered by such screening methods, as well as new therapeutic treatments, are all provided.

Abstract: A novel arterial thrombosis risk factor comprising one or more of the identified mutants of coagulation factor VII-activating protease (FSAP) is described. In addition, diagnostic determination methods for detecting these mutants which are identified as risk factors are described.

Abstract: This invention relates generally to the field of glycated protein detection. In particular, the invention provides chimeric proteins, nucleic acids encoding the chimeric proteins, methods and kits for assaying for a glycated protein in a sample, using inter alia, an amadoriase.

Abstract: A sensitive bioluminescent assay to detect proteases including caspases, trypsin and tryptase is provided.

Abstract: A method for detecting or measuring homocysteine in a sample includes the steps of (a) reacting a D-amino acid present in a sample with a D-amino acid converting enzyme to convert the D-amino acid into a substance that does not serve as a substrate of D-amino acid oxidase or D-amino acid acetyltransferase; (b) reducing homocysteine in the sample with a thiol compound; (c) reacting the reduced homocysteine with a methyltransferase and a methyl donor to newly produce D-amino acid; and (d) reacting the produced D-amino acid with the D-amino acid oxidase or the D-amino acid acetyltransferase in the presence of an SH reagent to produce hydrogen peroxide, and color-developing the produced hydrogen peroxide by using an oxidative color-developing agent.