Abstract: Synthetic protease substrates and methods which facilitate the identification of substrates of a protease, particularly ubiquitin, ubiquitin-like, or proteasome protein are provided.

Abstract: Compositions, kits, and methods for determining plasmin activity using a fluorogenic peptide substrate are provided.

Abstract: Methods of qualitatively and/or quantitatively detecting the presence of mutations, modifications or impurities in a protein sample are provided. The methods utilize isotopically labeled variants of amino acids incorporated into proteins prior to protein digest to enable comparisons of two protein samples in bottom-up liquid chromatography.

Abstract: Compositions for accurately assaying a glycated protein by: 1) avoiding effects of globulin and ascorbic acid components, 2) stabilizing proteases and at least enzymes acting on glycated amino acids; 3) accurately assaying albumin; and 4) assaying glycated albumin while avoiding the effects of glycated hemoglobin, and an assay method are provided. Thus, the contents of a glycated protein and glycated albumin can be more accurately determined.

Abstract: The invention relates to the X-ray crystal structure of PfA-M1 aminopeptidase alone, and in complex with the phosphinate dipeptide analogue hPheP[CH2]Phe. More specifically the present invention provides the structure coordinates of PfA-M1 and PfA-M1 in complex with Co4. The invention also includes the use of the X-ray crystal structures as drug target models for anti-malarial drug design and a method for identifying or designing novel anti-malarial drugs, for example using high-throughput chemical screening and medicinal chemistry methods. The invention further provides anti-malarial drugs identified or designed according to the aforementioned method and their use for obstructing protein metabolism and synthesis in a parasite by blocking the entrance of Hb-derived peptides and/or blocking the exit of released amino acids at the active site of PfA-M1 protease.

Abstract: Stabilizers for colorants used for detection of enzymatic reactions, having a cyclodextrin and a catalase; reagents including stabilizers; and methods of use of such stabilizers and reagents.

Abstract: A device for cell culture, in particular of neuronal cells, including: a substrate defining a first microfluidic chamber to be seeded with a first cell culture, and at least a second microfluidic chamber, a fluidic interconnection system connecting the first and second chambers and enabling cellular extensions, in particular axons, to extend from one chamber to the other, wherein the interconnection system of the device is made so as to promote the progression of at least one first type of cellular extension, the first and second types of extension being different either due to the microfluidic chamber from which they originate, or due to the type of cell of which they constitute an extension.

Abstract: Provided are methods for detecting the presence or absence of a pathogen, disease, or medical condition, or biomarker thereof, using an enzymatic activity assay. In one embodiment, the method provided utilizes competitive inhibition of an enzyme for detecting a pathogen, disease, or medical condition, or biomarker thereof, in a subject. The method comprises providing a biological sample from the subject that may or may not contain an endogenous substrate. A test reaction is provided by contacting the biological sample with an enzyme indicative of the biomarker of a pathogen, disease, or medical condition and a substrate comprising a signaling moiety. The enzyme modifies the endogenous substrate and the substrate comprising the signaling moiety. Modification of the substrate comprising the signaling moiety by the enzyme produces a signal from the signaling moiety. Data from a control reaction comprising the enzyme and the substrate comprising the signaling moiety is further provided.

Abstract: The invention provides assays and methods for determining the substrate specificity of gamma secretase inhibitors and for identifying substrate-selective (and substrate isoform-selective) inhibitors of gamma secretase. The invention provides assays and methods for determining whether a compound inhibits gamma secretase in a site specific or substrate specific manner. The invention provides isolated polypeptide sequences comprising modified gamma secretase substrates, and polynucleotide sequences encoding the polypeptide sequences. The invention also provides compounds that inhibit gamma secretase, pharmaceutical compositions comprising such compounds, and methods of treating Alzheimer's disease using such compounds.

Abstract: The instant invention concerns Francisella bacteria mediated degradation of alkaline phosphatase (AP). Detection of AP degradation may be used to determine the presence of Francisella bacteria in a sample. Furthermore, methods for identifying and treating Francisella infections by detecting AP degradation are described. Methods of the invention also concerns methods for treating Francisella infection by inhibiting AP degradation.

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

Abstract: Fluorescent activatable probes for imaging biological processes and disease detection in vitro and in vivo. There is also described a method for detecting the presence of an enzyme. A sample is contacted with a nanoparticle including a monomer, at least one cleavable spacer comprising at least one fluorescence activation site, and at least two dyes of at least two types. The cleavable spacer is attached at one end to the nanoparticle. The at least two types comprise an energy donor type and an energy acceptor type. At least one dye of one type is embedded in the nanoparticle and the cleavable spacer has at least one dye of the other type attached. The at least two dyes comprise at least one matched pair capable of fluorescence resonance energy transfer. Fluorescence is detected by exposing the sample to a light source, and detecting emitted light with a detector.

Abstract: The present invention provides the enzyme and enzymatic procedures for cleaving the ? secretase cleavage site of the APP protein and associated nucleic acids, peptides, vectors, cells and cell isolates and assays. The invention further provides a modified APP protein and associated nucleic acids, peptides, vectors, cells, and cell isolates, and assays that are particularly useful for identifying candidate therapeutics for treatment or prevention of Alzheimer's disease.

Abstract: The present invention encompasses methods for the simultaneous measurement of the in vivo metabolism of two or more isoforms of a biomolecule. The biomolecule is typically produced in the central nervous system.

Abstract: The present invention provides compositions and methods for detection, diagnosis, treatment and/or prevention of chronic pelvic pain syndrome. In particular, the present invention provides biomarkers of chronic pelvic pain syndrome (e.g., mast cell markers (e.g., tryptase)), and/or inhibition of mast cell function (e g inhibition of MCP-1 and/or MIP-1?) to treat or prevent chronic pelvic pain syndrome.

Abstract: The invention provides agents and vaccines for treating and diagnosing celiac disease. In particular, the present invention provides a combination of three peptides that are useful for treating and diagnosing celiac disease in a large proportion of patients.

Abstract: The current invention is directed to a method for the determination of the glycosylation pattern of a human immunoglobulin of the subclass IgG1 or IgG4 or of a murine immunoglobulin of the subclass Ig-G2a or IgG3 comprising the following steps: a) cleaving said immunoglobulin into fragments by enzymatic digestion with the enzyme IdeS, b) separating the fragments of said immunoglobulin obtained by the enzymatic digestion by reversed phase high performance liquid chromatography, c) subjecting the separated fragments of said immunoglobulin obtained in step b) to a mass spectrometric analysis, and d) determining the glycosylation pattern of said immunoglobulin from the mass spectrometric data obtained in step c).

Abstract: The invention provides a method for the treatment of a subject suffering from a cardiovascular disease using a therapeutically effective amount of at least one enzyme that is capable of inhibiting PAI-1 activity. The invention also provides a method of decreasing the risk of the occurrence of a cardiovascular disease in a subject who presents at least one risk factor that is associated with a cardiovascular disease, by administering to the subject a therapeutically effective amount of at least one enzyme that is capable of inhibiting PAI-1 activity. Additionally, the invention provides a method of inhibiting PAI-1 activity in a subject in need thereof, where the subject is administered an enzyme selected from a protease or peptidase.

Abstract: The present invention relates to acid-stable proteases homologous to those derived from strains of the genus Nocardiopsis, their use in animal feed, feed-additives and feed compositions containing such proteases, and methods for the treatment of vegetable proteins using such proteases.

Abstract: The invention relates to methods of determining a colorectal tumor stage in a patient by gene expression analysis. The method comprises assaying the level of at least one RNA transcript, or its expression product, which is correlated to colorectal tumor stage. The invention may be useful for determining whether a patient has stage II or stage III colorectal cancer.

Abstract: Provided herein is a bioprocessing device, bioprocessing card, and fluidics cartridge for performing automated bioprocessing of a sample. The bioprocessing card may include a plurality of pipette tips; and at least one pump in fluid communication with the plurality of pipette tips. In some embodiments, the pumps and the pipette tips are in fluid communication through a processing channel which may be a microscale channel. Also provided herein is an automated bioprocessing device comprising: at least one bioprocessing card; at least one fluidic cartridge; and an automated control system configured to control automated bioprocessing of a sample. Further provided herein are methods of use of the device, card, and cartridge.

Abstract: The likelihood that a compound will exhibit cardiotoxicity in vivo can be predicted using a model of in vitro assays performed on primary human cardiomyocytes.

Abstract: A means for pre-treatment in glycomic analysis of a glycoprotein is provided by the present invention. A salt of the general formula (I): wherein Z, X, R1, R2, M, m and n are the same as described in DESCRIPTION, is useful as a protein solubilizer, and an oligosaccharide is efficiently released from a sample if reductive alkylation and/or digestion by a proteinase are carried out under the presence of the said solubilizer at the first step in the glycomic analysis of glycoprotein derived from a living body.

Abstract: The subject invention provides novel devices and methods for the detection of the presence and/or activity of proteases in biological samples.

Abstract: The timing of the reaction of moisture-sensitive reagents for detecting the presence of analytes, e.g. leukocytes in urine samples, is used to detect when the reagents have been compromised by excess humidity. The ratio of light reflectance at wavelengths characteristic of the products of reaction between the reagents and the analyte and an infra-red reference dye is measured at two preset times after a urine sample has been applied to a test strip and used to determine whether the reagents have been compromised by excessive humidity. The presence of unusually dark samples is determined from the reflected light at 470 and 625 nm in order to confirm that the test strips are humidity-compromised.

Abstract: Provided herein are a method and system to detect an active protease in a sample, and related methods and systems to diagnose a condition in an individual, the condition being associated to abnormal protease activity in the individual.

Abstract: The present invention provides clostridial toxin substrates useful in assaying for the protease activity of any clostridial toxin, including botulinum toxins of all serotypes as well as tetanus toxins. A clostridial toxin substrate of the invention contains a donor fluorophore; an acceptor having an absorbance spectrum overlapping the emission spectrum of the donor fluorophore; and a clostridial toxin recognition sequence that includes a cleavage site, where the cleavage site intervenes between the donor fluorophore and the acceptor and where, under the appropriate conditions, resonance energy transfer is exhibited between the donor fluorophore and the acceptor.

Abstract: The present invention provides clostridial toxin substrates useful in assaying for the protease activity of any clostridial toxin, including botulinum toxins of all serotypes as well as tetanus toxins. A clostridial toxin substrate of the invention contains a donor fluorophore; an acceptor having an absorbance spectrum overlapping the emission spectrum of the donor fluorophore; and a clostridial toxin recognition sequence that includes a cleavage site, where the cleavage site intervenes between the donor fluorophore and the acceptor and where, under the appropriate conditions, resonance energy transfer is exhibited between the donor fluorophore and the acceptor.

Abstract: Provided herein are methods for the diagnosis, staging, prognosis, or management of liver disease, e.g. chronic liver disease, and other diseases using profiles of the ubiquitin-proteasome system determined from acellular body fluids or cell-containing samples. Further provided are methods of predicting response to therapy in certain populations of patients with liver disease.

Abstract: A presence/absence test for Staphylococcus aureus (S. aureus) involves placing a first generation test sample in a solution that will clot in the presence of S. aureus. The solution contains components that will selectively grow S. aureus and also contains clotting factors that will react with S. aureus, if S. aureus is present in the sample, to clot the solution. Examples of specimen samples that can be tested include nasal swabs and lesion swabs, among others. The test can also be modified to detect the presence or absence of methicillin resistant S. Aureus (MRSA).

Abstract: The present invention provides clostridial toxin substrates useful in assaying for the protease activity of any clostridial toxin, including botulinum toxins of all serotypes as well as tetanus toxins. A clostridial toxin substrate of the invention contains a donor fluorophore; an acceptor having an absorbance spectrum overlapping the emission spectrum of the donor fluorophore; and a clostridial toxin recognition sequence that includes a cleavage site, where the cleavage site intervenes between the donor fluorophore and the acceptor and where, under the appropriate conditions, resonance energy transfer is exhibited between the donor fluorophore and the acceptor.

Abstract: The invention provides methods for quantifying biomolecules, such as polypeptides in mass spectrometric analysis. The methods include use of a biomolecule standard having at least one atomic isotope different than that of the naturally occurring isotopes in the biomolecule of interest. Methods of the present invention also include methods for quantifying biomolecules where the copy biomolecule standard is made by expressing the biomolecule using a recombinant cell. Further included are the biomolecule standards themselves, method for making such standards, kits, systems, reagents, and engineered cells relating to the use of biomolecule standards in mass spectrometric analysis.

Abstract: The present invention provides a method for monitoring of profile changes of components in a dynamic system such as a cell-free in vitro protein synthesis system by using liquid chromatography (LC) combined with mass spectrometry (MS). In an additional aspect, this invention provides a method for enhancing the yield and/or reproducibility in a cell-free protein synthesis system by modulating the level and/or activity of a protein component that has regulatory effects on the system.

Abstract: A method for producing a glycoprotein, which is uniform in terms of functions derived from a sugar chain (e.g., a blood half-life) and physiological activities, i.e., a glycoprotein, which is uniform in terms of the amino acid sequence, the sugar chain structure and the higher-order structure; specifically, a method for producing a glycoprotein, which is uniform in terms of the amino acid sequence, the sugar chain structure, and the higher-order structure, includes the following steps (a) to (c): (a) folding a glycoprotein, which is uniform in terms of the amino acid sequence and the sugar chain structure; (b) fractionating the folded glycoprotein by column chromatography; and (c) collecting a fraction having a specified activity.

Abstract: Polypeptides which are related to the neprilysin enzyme family and have zinc metalloprotease activities and are referred to as IGS5, polynucleotides encoding such polypeptides, vectors containing such polynucleotides, host cells containing such vectors, processes for producing such polypeptides and/or polynucleotides, screening methods for identifying compounds which stimulate or inhibit IGS5 polypeptides and/or polynucleotides, and the use of such polypeptides and/or polynucleotides in therapy of various dysfunctions, disorders or diseases, particularly cardiovascular diseases, metabolic diseases such as diabetes mellitus type II, and neurodegenerative disorders, such as Parkinson's Disease.

Abstract: The present invention provides methods of detecting cancer using biomarkers.

Abstract: The invention relates to an in vitro method for detecting and/or titrating an unconventional transmissible agent (UTA) or a protein of pathological conformation which is a marker for the infectivity of the UTA, in a sample, comprising a step of concentrating the sample before and after digestion with a protease.

Abstract: The present invention provides methods that are useful for the diagnosis of neurodegenerative disease or disorder and for the screening of compounds or therapeutic agents for treating a neurodegenerative disease or disorder. The methods pertain in part to the correlation of a neurodegenerative disease or disorder with abnormal or altered endoplasmic reticulum-mitochondrial-associated membranes (ER-MAM) integrity.

Abstract: The invention pertains to a cyclic peptide comprising the following sequence: -S1-X1-S2-X2- wherein S1 is a first target peptide sequence of a protease enzyme E1, S2 is a second target peptide sequence of a protease enzyme E2, S1 and S2 possibly being the same or different, said first peptide sequence S1 and said second peptide sequence S2 comprising 4 to 14 amino acids, E1 and E2 possibly corresponding to the same protease enzyme or to two different protease enzymes, X1 is a probe carrying a fluorescent donor group and X2 is a probe carrying a fluorescent or non-fluorescent acceptor group. Application of these peptides to determination of the activity of protease enzymes.

Abstract: Described herein are zymogens, methods of use for zymogens, and devices that incorporate zymogens. The zymogens include a substrate and an enzyme. The substrate can inhibit the enzyme and is a target for a protein produced by a microorganism. When the substrate is modified by a protein produced by a microorganism, the enzyme is activated. The zymogens can be used to amplify detection assays.

Abstract: The invention relates to methods and kits for detecting thyroid cancer by detecting differences in the expression of genes that are differentially expressed in thyroid cancer cells.

Abstract: The present invention provides methods for protein engineering. Specifically, the invention provides methods utilizing site evaluation libraries to design libraries that optimize two or more properties of a protein. The present invention also provides variant subtilisins suitable for various uses.

Abstract: The present invention relates to a screening method for identification of a compound suitable for the prevention, treatment or/and diagnosis of an infection with Chlamydiaceae.

Abstract: The instant disclosure describes an electrophoretic procedure capable of resolving and isolating ultra high molecular weight (MW) protein aggregates from nerve tissue. The procedure is based on the use of composite agarose-polyacrylamide gel electrophoresis (CAPAGE) and resolves proteins and protein aggregates over the range of from approximately 225 kDa to approximately 30,000 kDa. Triton X-100 precipitation is used to obtain a cytoskeleton protein fraction that is subsequently resuspended and subjected to gel electrophoresis. This method demonstrates that a protein aggregate of approximately 30,000 kDa is characteristic of normal murine spinal cord tissue and that the amount of said protein aggregate is increased in spinal cord homogenate obtained from transgenic mice bearing copies of a mutant human gene characteristic of familial amyotrophic lateral sclerosis.

Abstract: The present invention relates to polypeptides with a changed amino acid sequence on at least one amino acid position compared to the amino acid sequence according to SEQ ID NO: 1. The present invention further relates to the nucleotide sequences encoding the polypeptide, vectors, comprising the nucleotide sequences and host cells for expression of the polypeptide. The present invention further relates to the use of the polypeptides as a human, veterinary medical or diagnostic substance, in food, in cosmetics, as disinfectant or in the environmental field.

Abstract: Particular genes are aberrantly and consistently expressed in both adenomas and carcinomas of the colon. Products of such genes provide stool and serum markers for colorectal neoplasia. One particular tumor marker, Renal Dipeptidase (RDP), is expressed at high levels in tumors and at greatly reduced levels in normal tissues. The elevated expression of RDP occurs early and remains elevated during the neoplastic process. RDP may therefore be especially useful as a diagnostic tool for the early detection of colorectal neoplasia, even of presymptomatic colorectal neoplasia.

Abstract: Compositions which specifically block cathepsin L function in podocytes, compositions which protect cytoskeletal adaptor protein (CD2AP) for degradation, compositions which modulate expression or function of cytoskeletal adaptor protein (CD2AP), protect against renal diseases or disorders. Methods of treatment in vivo involve use of one or more compositions.

Abstract: Embodiments of an assay for the screening, diagnosis, and differentiation of Alzheimer's disease uses selected sets of serum protein biomarkers. The assay is used to distinguish Alzheimer's disease from Parkinson's disease, other neurodegenerative diseases, and normal controls. Specific sets of serum protein biomarkers are identified for the diagnosis of Alzheimer's disease in drug naïve and drug treated patients.

Abstract: The described invention provides methods and compositions utilizing a NELL1 peptide or nucleic acid encoding a NELL1 peptide for treating or preventing a skin condition. The methods include treating or preventing manifestations of aging in human skin, repairing damage to skin, and preventing skin scarring. Methods are also provided for assaying a test peptide for NELL1 activity.

Abstract: Raised total plasma FVII protein, including activated FVII (FVIIa) in pregnant females, compared with total plasma FVII protein in normal pregnancy, has been found to be an indicator of the pregnancy complication of pre-eclampsia.