Abstract: The present invention provides a diagnostic reagent or assay for assessing the activity of a protease in vivo or in vitro and methods of detecting the presence of a cancerous or precancerous cell. The assays are comprised of two particles linked via an oligopeptide linkage that comprises a consensus sequence specific for the target protease. Cleavage of the sequence by the target protease can be detected visually or using various sensors, and the diagnostic results can be correlated with cancer prognosis.

Abstract: Uses of recombinant procalcitonin 3-116 in the diagnosis and therapy of septic diseases and the measurement of prohormones other than procalcitonin, and of dipeptidyl peptidase IV, as biomarkers in the diagnosis of sepsis.

Abstract: Provided herein is a method of inhibiting optic nerve damage in an individual in need thereof, comprising administering to the individual an agent that inhibits peptidyl arginine deiminase 2 (PAD2). In a particular embodiment, the present invention is directed to a method of inhibiting glaucomatous optic nerve damage in an individual in need thereof, comprising administering to the individual an agent that inhibits peptidyl arginine deiminase 2 (PAD2). The present invention is also directed to a method of treating glaucoma (e.g., primary open angle glaucoma) in an individual in need thereof, comprising administering to the individual an agent that inhibits (e.g., specifically inhibits) peptidyl arginine deiminase 2 (PAD2).

Abstract: Methods for analyzing, selecting, characterizing or classifying compositions of a co-polymer, e.g., glatiramer acetate are described. The methods entail analysis of pyro-glutamate in the composition, and, in some methods, comparing the amount of pyro-glutamate present in a composition to a reference standard.

Abstract: Provided is a method of separating and measuring highly active HMW adiponectin in adiponectin multimers. A method of measuring high-molecular-weight adiponectin in a sample, wherein adiponectin multimers are separated by use of a protease and measured immunologically, the method comprising reacting a sample containing adiponectin multimers with chymotrypsin.

Abstract: A method of controllably changing an intrinsic property of a quantum dot by using a biological entity, either attached or in close proximity to the quantum dot, and changing the state of biological entity with a controllable mechanism. The change in state of the biological entity controllably changes the intrinsic property of the quantum dot. The photoluminescence emission of quantum dots can be controlled by the present method. The methods disclosed include controlling the magnitude of QD photoluminescence as well as turning the photoluminescence on/off. The methods disclosed include using the same biological control architecture to control other intrinsic QD properties such as charge state, magnetic or other property.

Abstract: A method for identifying a subject being at risk for or having a chronic inflammatory disease, fibrillinopathy, atherosclerosis, or coronary artery disease is provided. The method may include determining the concentration of GrA and/or GrB in a blood or serum sample from said subject; and comparing the concentrations to the corresponding concentration in a control sample, wherein an elevated concentration of GrA and/or GrB may be indicative of a chronic inflammatory disease, fibrillinopathy, atherosclerosis, or coronary artery disease. The method may further include identifying concentrations of fibrinogen, elastin and/or fibrillin.

Abstract: The invention provides methods and kits for characterizing the activity of an acetyl transferase or deacetylase. The method involves enzymatically acetylating or deacetylating in vitro a substrate that is a peptide fragment of a full-length polypeptide, and then non-enzymatically acylating the peptide substrate with acyl groups that differ in molecular weight from the enzymatically added or removed acetyl groups. Typically, deuterated acetic anhydride is used to non-enzymatically acylate the substrate. The fully acylated substrate is then characterized by mass spectrometry to determine the amino acid positions of the substrate that are enzymatically acetylated or deacetylated.

Abstract: Provided are methods and devices for detecting methicillin-resistant Staphylcoccus aureus.

Abstract: Methods and kits for assessing proteolytic enzyme activity and a modulator's effect thereof employ a Ubiquitin or Ubiquitin-like Protein and a signal producing structure. The corresponding fusion polynucleotide is employed for production of transgenic cells, plants and animals that may be produced by stably transfection, optionally transforming the cell, plant or animal with a Ubiquitin-, UBL- or their C-terminal binding functional fragment-Reporter fusion polynucleotide. A method of diagnosing a disease or condition, comprises contacting or administering a sample obtained from a subject suspected of being afflicted with the disease or condition with the cell, plant or animal, detecting any signal produced by the reporter in the presence of the sample and comparing the signal to controls for 0% and 100% signals.

Abstract: Mixing structures for use on sample processing devices are disclosed. The mixing structures include one or more mixing chambers in fluid communication with a process chamber, such that changing the rotational speed of the sample processing device forces sample material into and out of the mixing chamber to achieve mixing of the sample material. The mixing chambers are in fluid communication with the process chambers through mixing ports that are located on the distal sides of the process chambers with respect to the axis about which the sample processing device is rotated.

Abstract: A gene profiling signature for predicting ovarian cancer patient survival is disclosed herein. The gene signature can be used to diagnosis or prognosis ovarian cancer, identify agents to treat an ovarian tumor, to predict the metastatic potential of an ovarian tumor and to determine the effectiveness of ovarian tumor treatments. Thus, methods are provided for diagnosing and prognosing an ovarian tumor, such as ovarian cancer, in a subject. Methods are also provided for identifying agents that can be used to treat an ovarian tumor, for determining the effectiveness of an ovarian tumor treatment, or to predict the metastatic potential of an ovarian tumor. Methods of treatment are also disclosed which include administering a composition that includes a specific binding agent that specifically binds to one of the disclosed ovarian survival factor-associated molecules and ovarian tumor in the subject.

Abstract: An object of the present invention is to provide a method capable of detecting and quantifying endotoxin in a sample in which endotoxin derived from gram-negative bacteria cannot be accurately detected or quantified by the method described in Commentary of the Japanese Pharmacopoeia Fourteenth Edition, Hirokawa Publishing Co. 2001 B-63. It has been found that the above object can be achieved by performing an endotoxin test using a lysate reagent in which the lysate reagent is added into a sample in the presence of albumin and/or globulin.

Abstract: The invention relates to an ex vivo animal or challenge model as a method to identify protective (recombinant) proteins and rapidly measure protective immunity in intestinal segments directed against parasites and vaccines directed against parasitic infections. The invention further relates to vaccines directed against infection with parasites, such as Fasciola hepatica, which vaccines contain protective (recombinant) proteins identified and shown to be protective in studies using the ex vivo model. The invention further relates to protective (recombinant) proteins obtained from newly excysted juveniles (NEJ) of Fasciola hepatica. The protective (recombinant) protein corresponding to an NEJ protein has an apparent molecular weight of 32 kD and an N-terminal amino acid sequence comprising the sequence XXDVSWPFWDRMYNY (SEQ ID NO:1).

Abstract: A method of diagnosing Alzheimer's disease in a patient comprises determining whether the phosphorylation level of an indicator protein in cells of the patient after stimulus with an activator compound is abnormally elevated as compared to a basal phosphorylation level, the indicator protein being e.g. Erk1/2 and the activator compound being e.g. bradykinin.

Abstract: The present invention provides assays for detecting ADP, GDP and inorganic phosphate. These assays can be used directly to detect the presence of ADP, GDP and inorganic phosphate or can be used as part of a number of methods for identifying candidate agents that bind to a target protein or serve as modulators of the biological activity of a target protein.

Abstract: The invention provides a synthetic phytase polypeptide which encodes an enzymatically susceptible phytase. Also provided are feed or food products comprising an enzymatically susceptible phytase, and transgenic plants which express the enzymatically susceptible phytase. Further provided are methods for making and using enzymatically susceptible phytases, e.g., a method of using an enzymatically susceptible phytase in feed and food processing.

Abstract: Particular aspects of the present invention relate to methods for detecting glycated hemoglobin in, for example, human whole blood, that are not affected by the presence of variation in amino acid sequence that can exist in hemoglobin ? chains. The methods detect all glycated hemoglobin in a sample, regardless of the form of the hemoglobin that has been glycated, and thus detect glycated human Hemoglobin A, Hemoglobin S, and Hemoglobin C.

Abstract: The invention relates to a method for aiding the diagnosis of a disorder in a subject, said method comprising; providing a sample from said subject wherein the sample comprises blood; assaying at least two characteristics of said sample, said characteristics selected from: the structural composition of a polypeptide comprised by said sample; a metabolite comprised by said sample; and a catalytic activity comprised by said sample, wherein each of said at least two characteristics is determined from a multiplexed analysis of the same sample. The invention also relates to certain compositions.

Abstract: Antibodies are biological macromolecules which may be subject to modification and degradation processes. A new LC/MS-based method for separating and characterizing antibody-specific degradation products is described in the present application which comprises an enzymatic digestion step to cleave the heavy chain using the enzyme IdeS.

Abstract: An 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: A method for identifying, diagnosing, and monitoring cancerous lung tissues in a subject may include measuring the expression of at least one biomarker in a biological sample in the subject, and comparing the expression against a normal value. When a differential expression of the at least one biomarker between the biological sample and the normal value is more than 1.5-fold, the lung tissue sample is cancerous.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: Method for the detection of the in-vivo activity of neurotrypsin wherein the amount of the 22-kDa-fragment of agrin is measured in a sample taken from a patient and the measured amount of the 22-kDa-fragment of agrin in the sample is used to calculate the activity of neurotrypsin, use of the method for diagnosis and monitoring of neurotrypsin-related disturbances and use of the 22-kDa-fragment of agrin as biomarker for neurotrypsin-related disturbances.

Abstract: Provided are methods to identify modulators and in particular inhibitors of body malodour formation employing peptidase enzymes, the peptidase enzymes and corresponding nucleotide sequences, expression vectors, transfected host cells, methods of forming the peptidase enzymes and methods to prevent body malodour.

Abstract: A biomarker is provided for an allergic disease caused by an allergic reaction that is caused not exclusively by histamine release, such as pruritus, and use of the same. Use of Granzyme A as a biomarker makes it possible to provide an indication for chronic itching skin disease, for which existing antiallergic drugs have little effect, and easily and adequately allow diagnosis of the disease. It is possible to, for example, make a diagnosis of an allergic disease with an IV type allergy-like reaction not depending on the antigen-antibody reaction system. Screening with the use of Granzyme A enables the development of novel remedies for allergic diseases. Moreover, a drug capable of specifically controlling the action of a granzyme enables treatment of allergic disease with little side effect.

Abstract: The present invention provides methods for detecting protein in plasma comprising contacting said plasma with a protease capable of digesting said protein into at least one detectable fragment and detecting said at least one detectable fragment using high performance liquid chromatography and mass spectroscopy.

Abstract: The present invention relates to methods, systems, and kits for intoxicating cells, neuronal and non-neuronal cells, with a toxin or fragment thereof. This is done by subjecting toxin substrate and a lipid or polymeric carrier (e.g., DNA uptake facilitating agent) to one or more cells for use in cell based assays. In an aspect, the methods of the present invention allow for high throughput assays and, as such, for the evaluation of drug candidates.

Abstract: The invention provides methods and compositions for modulating hepsin activity and the HGF/c-met signaling pathway, in particular by regulating pro-HGF activation by hepsin.

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, a stabilizing group and, optionally, a linker group. The prodrug is cleavable by the CD10 enzyme. Methods of treatment using the prodrug and methods of designing the prodrug are also disclosed.

Abstract: Novel methods of regulating cellular apoptosis by affecting the interaction of hepatitis B X-interacting protein (HBXIP) with Survivin are described. More specifically, these novel methods of enhancing apoptosis of neoplastic cells comprises inhibiting interaction of hepatitis B X-interacting protein (HBXIP) with Survivin using siRNA or antisense compounds.

Abstract: The invention relates to fluorescence methods for measuring enzyme activity, in particular enzyme cleaving and joining activities. The invention also relates to fluorogenic substrates which are useful for measuring enzyme activity and as in vitro and in vivo imaging probes.

Abstract: The present invention relates to markers for kidney disease.

Abstract: Drug affinity responsive target stability (DARTS) is a novel method of drug target ID with several significant advantages over current techniques. In certain embodiments the method involves contacting a sample comprising one or more protein target(s) with a test agent to form a sample/test agent mixture; contacting the mixture with a protease; and identifying a protein or protein fragment that is protected from proteolysis, wherein the protection from proteolysis is an indicator that the protein or protein fragment binds to or interacts with the test agent.

Abstract: The present invention relates to a crystal. In particular the present invention relates to a crystal of the N-domain of ACE protein. The present invention also relates to methods, processes, domain specific modulators, pharmaceutical compositions and uses of the N-domain crystal and the structure co-ordinates thereof.

Abstract: Compositions, apparatus, systems, kits, and methods for obfuscating the nucleic acid and/or protein content of an environment.

Abstract: The present invention provides isolated and purified polynucleotides, polypeptides, and antibodies related to mammalian (e.g., mouse and human) legumain and the novel legumain splice variant, ZB-1. The invention further relates to the use of these isolated and purified polynucleotides, polypeptides, and antibodies, as well as other legumain and ZB-1 agonists and antagonists, in modulating legumain and/or ZB-1 activity, expression, and/or secretion in a cell or cell population, e.g., monocytes, macrophages, foam cells, vascular endothelial cells, kidney proximal tubule cells, arterial endothelial cells, sites of inflammatory cell invasion into a vessel intima, and neointimal lesional areas of an artery. The invention also provides legumain and ZB-1 antagonists, e.g., antagonistic small molecules, antibodies and antibody fragments to legumain and ZB-1, legumain and ZB-1 inhibitory polypeptides, and legumain and ZB-1 inhibitory polynucleotides.

Abstract: The present invention relates to a method for differentiating in a subject suffering from chronic shortness of breath (dyspnea) between (i) a pulmonary disease, (ii) a cardiovascular complication, (iii) a cardiovascular complication accompanied by a pulmonary disease and (iv) dyspnea without cardiovascular or pulmonary causes. The method comprises the steps of determining an amount of a pulmonary surfactant protein in a sample of a subject, determining an amount of a natriuretic peptide in a sample of said subject, and differentiating between (i) a pulmonary disease, (ii) a cardiovascular complication, (iii) a cardiovascular complication accompanied by a pulmonary disease and (iv) chronic dyspnea without cardiovascular or pulmonary causes by comparing the amount determined in a) and the amount determined in b) with a reference amount for each. The present invention further provides a device and a kit for carrying out the inventive methods.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with a linker moiety that facilitates their conjugation to other species. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Abstract: A method of screening a compound which modulates dipeptidyl peptidase I (DPPI) activities comprises the steps of adding a peptide substrate of DPPI to a reaction mixture which comprises DPPI and a compound, wherein the peptide substrate of DPPI has at least 3 amino acids and binds to a binding site of DPPI in addition to the S1-S2 site; and measuring the molecular weight of the substrate, wherein a change in the molecular weight of the substrate is indicative of the presence of DPPI activity.

Abstract: The present invention is directed to a method for separating, characterizing and/or identifying microorganisms in a test sample. The method of the invention comprises an optional lysis step for lysing non-microorganism cells that may be present in a test sample, followed by a subsequent separation step. The method may be useful for the separation, characterization and/or identification of microorganisms from complex samples such as blood-containing culture media. The invention further provides for the use of one or more identifier agents and interrogating the microorganism sample and/or said one or more identifier agents to produce measurements which characterizing and/or identifying the microorganism based on the produced measurements and/or the presence or absence of the identifier agent or a metabolized form of the identifier agent in the microorganism sample.

Abstract: A method for the in vitro diagnosis of colorectal cancer by determining the presence of Aminoacylase 1 tumor marker in a biological sample taken from a patient suspected of having colorectal cancer. Said method can be used for early diagnosis, screening, therapeutic follow-up and prognosis, and also for relapse diagnosis in relation to colorectal cancer.

Abstract: Disclosed is a method of selectively inhibiting for growth of non-target cells in a mixed population of target and non-target cells, the method comprising the steps of: (a) contacting the mixed population with a selective agent which comprises a carrier moiety linked by a scissile linkage to a toxic moiety; wherein the selective agent is able to enter non-target cells in which the scissile linkage is cleaved, releasing the toxic moiety to exert a toxic effect on the non-target cells causing inhibition of the growth of the non-target cells, whereas the selective agent is unable to enter target cells and/or the scissile linkage is not cleaved in target cells and/or toxic moiety, if released from the selective agent, does not exert a toxic effect on the target cell; and (b) culturing the cells in conditions which allow for growth of non-inhibited cells.

Abstract: The present invention relates to an enzyme substrate for detecting peptidase activity in microorganisms, of formula (I) below: in which X is S; NX1; O; or NX1-CO; R1 is nothing or one of the following substituents: Cl, Br, F, I, OH, or an alkyl, aryl or carboxyl group; R2 is nothing or one of the following substituents: Cl; O—CH2—O; O—CH3; F, diethylenediamine-CH3, NR3R4, Br, I, OH, an alkyl, aryl or carboxyl group, NO2, or X1 is selected from: H, C2H4Ph, OH, an alkyl group and an aryl group; R3 and R4 are independently H or an alkyl group containing from 1 to 4 carbon atoms and P is a peptide.

Abstract: Provided herein is are polypeptides that include the protease domain of a type II transmembrane serine protease (MTSP) as a single chain. Methods using the polypeptides to identify compounds that modulate the protease activity of an MTSP are provided. Also provided are MTSPs designated MTSP3 and MTSP4 and a form of an MTSP designated MTSP6.

Abstract: The present invention relates to methods for the detection, identification and/or quantification of microorganisms with peptidase activity using enzymatic substrates with the following general formula:

Abstract: The invention relates to a method for detecting and/or identifying Escherichia coli (E. coli) in a biological sample, that comprises inoculating the biological sample liable to contain E. coli on a detection medium that comprises tryptophan and a substrate for an enzyme A, expressed by the majority of E. coli, in order to obtain bacterial colonies; detecting the colonies expressing the activity of the enzyme A and identifying them as being E. coli; and detecting the colonies that do not express the activity of the enzyme A, carrying out an indole test, and identifying the colonies having a positive indole test as being E. coli.

Abstract: The invention provides methods and kits for characterizing the activity of an acetyl transferase or deacetylase. The method involves enzymatically acetylating or deacetylating in vitro a substrate that is a peptide fragment of a full-length polypeptide, and then non-enzymatically acylating the peptide substrate with acyl groups that differ in molecular weight from the enzymatically added or removed acetyl groups. Typically, deuterated acetic anhydride is used to non-enzymatically acylate the substrate. The fully acylated substrate is then characterized by mass spectrometry to determine the amino acid positions of the substrate that are enzymatically acetylated or deacetylated.

Abstract: Provided herein are methods for detecting gram negative bacteria or lipopolysaccharide in a sample. Kits for detecting gram negative bacteria or lipopolysaccharide in a sample are provided.

Abstract: The present invention provides methods for reducing the level of amyloid beta protein in a cell or tissue, the methods generally involving contacting the cell or tissue with an agent that reduces cystatin C levels and/or activity. The present invention provides methods for treating Alzheimer's disease (AD), and methods for treating cerebral angiopathy, in an individual, the methods generally involving administering to an individual having AD a therapeutically effective amount of an agent that reduces cystatin C levels and/or activity. The present invention further provides methods for identifying an agent that reduces cystatin C levels and/or activity.