Abstract: A method of detecting and recovering of exosomes in a sample, as well as a method of determining the recovery rate of exosomal recovery, and a method of screening for a material that induces secretion of the exosomes in a sample, which methods employ the use of a protease.

Abstract: Cigarette smoking is a primary determinant of chronic obstructive pulmonary disease (COPD), which is the fourth leading cause of morbidity and mortality in the United States. Unique proteins associated with COPD capable of differentiating subjects likely to experience rapid (RPD) or slow (SLW) decline in lung function have been identified using comprehensive high-throughput proteomic approaches. Thirty peptides, which mapped to 21 unique proteins, were linearly associated with annualized rates of lung function decline among smokers with COPD characterized as having rapid or slow decline and smokers without COPD. Using three different statistical approaches to assess the data, the RPD and SLW groups are differentiated by 55 peptides, which mapped to 33 unique proteins. A number of the identified peptides are proteolytic fragments of proteins that are involved in the complement and/or coagulation systems, have anti-protease activity, or metabolic functions.

Abstract: A first aspect of the invention relates to a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, complex or pro-drug thereof, wherein: one of R3 and R4 is H, and the other is selected from C1-6-alkyl, C1-6-haloalkyl, C1-6-alkoxy, and C6-12-aralkyl; or R3 and R4 are each independently selected from C1-6-alkyl and halo; R9 is a substituted 5 or 6-membered aryl or heteroaryl group or a 6,5- or 6,6-fused biaryl or heterobiaryl group. Compounds of formula (I) exhibit surprisingly high efficacies for human cathepsin S, excellent selectivity verses other mammalian cathepsins and are useful for treatment of diseases such as rheumatoid arthritis, multiple sclerosis, myasthenia gravis, transplant rejection, diabetes, Sjogrens syndrome, Grave's disease, systemic lupus erythematosis, osteoarthritis, psoriasis, idiopathic thrombocytopenic purpura, allergic rhinitis, asthma, atherosclerosis, obesity, chronic obstructive pulmonary disease and chronic pain.

Abstract: Methods for the use of keratinocyte chemoattractant (KC)/human growth-regulated oncogene (GRO) (KC/GRO), apolipoprotein A2 (APOA2), angiotensinogen r (AGT), thyroglobulin (TG), disintegrin and metalloproteinase domain-containing protein 17 (ADAM17), anionic trypsin-1 (PRSS1), complement C4 (C4A), zona pellucida sperm-binding protein 1 (ZP1), neuropilin-2 (NRP2), solute carrier family 13 member 2 (SLC13A2), glucagon-like peptide 2 receptor (GLP2R), lipoma high mobility group protein isoform I-C (HMGIC) fusion partner-like protein 4 (LHFPL4), and claudin-3 (CLDN3) as biomarkers for diagnosis and prognosis, and for monitoring the efficacy of treatment, in hemorrhagic shock (HS).

Abstract: The present invention relates to the visualization of acidic organelles based upon organelle enzyme activity. The organelle substrates of the invention are specific for enzyme activity of the organelle and label these organelles, such as lysosomes, rendering them visible and easily observed. Substrates of the present invention include substrates that produce a fluorescent signal. The fluorogenic acidic organelle enzyme substrates of this invention are designed to provide high fluorescence at low pH values and are derivatized to permit membrane permeation through both outer and organelle membranes of intact cells and can be used for staining cells at very low concentrations. They can be used for monitoring enzyme activity in cells at very low concentrations and are not toxic to living cells or tissues.

Abstract: The disclosed subject matter relates to a force-clamp spectrometer that enables operation in constant force mode and allows for automated data acquisition and analysis, using feedback electronics and software. The disclosed subject matter also relates to methods of using the force-clamp spectrometer for the measurement of the dynamics of chemical reactions. The methods may include, but are not limited to, the measurement of the dynamics of substrate folding and unfolding, as well as bond cleavage and bond formation.

Abstract: Novel cross-linking compounds that can be used in mass spectrometry, tandem mass spectrometry, and multi-stage tandem mass spectrometry to facilitate structural analysis of proteins and protein complexes are provided and have the formula: where X is an N-hydroxy-succinimidyl or similar heterocyclic group. Also provided is a method of mapping protein-protein interactions of protein complexes using various mass spectrometry techniques.

Abstract: Disclosed herein are methods of detecting and/or prognosing myocardial infarction by detecting a proteolytic fragment of caspase-3 such as the p17 fragment or the p12 fragment. The myocardial infarction can be STEMI or NSTEMI.

Abstract: Certain embodiments of the present invention relate to methods for detecting kidney disease, in particular early stage kidney disease.

Abstract: The current invention provides a method for directly converting histopathologically processed biological samples, tissues, and cells into a multi-use biomolecule lysate. This method allows for simultaneous extraction, isolation, solubilization, and storage of all biomolecules contained within the histopathologically processed biological sample, thereby forming a representative library of said sample. This multi-use biomolecule lysate is dilutable, soluble, capable of being fractionated, and used in any number of subsequent experiments.

Abstract: A diagnostic test kit for detecting the presence or quantity of an enzyme or enzyme inhibitor is provided. The diagnostic kit utilizes reactive complexes to facilitate the detection of the enzyme or enzyme inhibitor. The reactive complexes include a substrate joined (e.g., covalently bonded, physically adsorbed, etc.) to a reporter and specific binding member. In one embodiment, for example, a peptide, protein, or glycoprotein substrate is joined to a reporter (e.g., dyed latex particle) and specific binding member (e.g., biotinylated compound). In this embodiment, the substrate provides a cleavage target for a proteolytic enzyme. Specifically, upon contacting the reactive complexes, the proteolytic enzyme cleaves the substrate and releases the reporter and/or specific binding member. The signal exhibited by the released reporters may then be used to indicate the presence or quantity of an enzyme or enzyme inhibitor within the test sample.

Abstract: Provided are methods for determining the amount of thyroglobulin in a sample using various purification steps followed by mass spectrometry. The methods generally involve purifying thyroglobulin in a test sample, digesting thyroglobulin to form peptide T129, purifying peptide T129, ionizing peptide T129, detecting the amount of peptide T129 ion generated, and relating the amount of peptide T129 ion to the amount of thyroglobulin originally present in the sample.

Abstract: The invention relates to a one-step chemical composition that preserves animal tissue, cells, and biomolecules, such as human tissue, human cells, and biomolecules therein. It improves the fidelity and morphologic structure of cells, organelles, and nuclear chromatin, and maintains and enhances the cellular antigenicity for immunohistochemistry and flow cytometry, while preserving proteins, post-translational modifications of proteins, and nucleic acids. In one embodiment, the composition comprises a) a non-aldehyde precipitating fixative at a concentration below 25% (volume/volume), b) a reversible/cleavable protein cross-linker that targets lipid-associated molecules, and c) a c reversible/cleavable protein cross-linker that targets water soluble molecules. In another embodiment, the composition further includes a kinase inhibitor, a phosphatase inhibitor, and a permeation enhancer.

Abstract: A method and kit for detecting the early onset of renal tubular cell injury, utilizing NGAL as an early urinary biomarker. NGAL is a small secreted polypeptide that is protease resistant and consequently readily detected in the urine following renal tubule cell injury. NGAL protein expression is detected predominantly in proximal tubule cells, in a punctate cytoplasmic distribution reminiscent of a secreted protein. The appearance of NGAL in the urine is related to the dose and duration of renal ischemia and nephrotoxemia, and is diagnostic of renal tubule cell injury and renal failure. NGAL detection is also a useful marker for monitoring the nephrotoxic side effects of drugs or other therapeutic agents.

Abstract: A biomarker, method, test kit, and diagnostic system for detecting the presence of lymphoma in a person are disclosed. The lymphoma may be Hodgkin's lymphoma or non-Hodgkin's lymphoma. The person may be a high-risk subject. In one embodiment, a plasma sample from a person is obtained. The level of at least one protein listed in Table S3 in the plasma sample is measured. The level of at least one protein in the plasma sample is compared with the level in a normal or healthy subject. The lymphoma is diagnosed based upon the level of the at least one protein in the plasma sample in comparison to the normal or healthy level.

Abstract: The invention relates to a novel method for characterizing and multi-dimensionally representing the folding process of proteins (FIG. 9). Said method comprises, in a methodically novel combination, kinetically arranging the hydrodynamic size of the refolding and thus modified protein, associating the proteolytically fragmented intermediates on the basis of the bioinformatic detection patterns, classifying the folding pathway association of the intermediates, characterizing the folding sequences, and multi-dimensionally visualizing the characterized folding process in a computer-aided manner. Said method is characterized in that all intermediates modified during the refolding and thus structurally blocked are identified and digitalized according to the four individual characteristics of said intermediates, namely the hydrodynamic size, the formation time, the folding pathway association, and amount.

Abstract: A method for detecting the absence or presence of cells of interest in a liquid sample, wherein: (a) the sample: (i) comprises an extracellular medium containing an enzyme with a measurable activity; and (ii) is suspected of containing cells of interest that contain an enzyme with said measurable activity; and (b) the method comprises the steps of: (i) treating the liquid sample with a reagent that inactivates said measurable activity in the extracellular medium, but does not inactivate the measurable activity in said cells of interest; (ii) lysing the cells of interest to release the intracellular enzyme; and (iii) measuring said measurable activity. Thus the intracellular enzyme can be measured without interference from the extracellular enzyme. The invention is particularly useful for treatment of bacterially-infected blood using a detection assay based on adenylate kinase activity.

Abstract: Anionic acid-labile surfactants may generally comprise compounds represented by the formula: wherein R1 is independently selected from —(CH2)0-9CH3, R2 is selected from the group consisting of —H and —(CH2)0-5CH3, Y is an anion, X is a cation, and n is an integer from 1 to 8. Methods of making and using the anionic acid-labile surfactants are also described. The anionic acid-labile surfactants may be used to facilitate the solubilization of proteins and other molecules in an aqueous environment.

Abstract: Disclosed herein are methods of detecting or predicting diastolic heart failure in a subject, comprising identifying a profile of matrix metalloproteinases (MMPs) and tissue inhibitors of matrix metalloproteinases (TIMPs) from a body fluid of the subject that is associated herein with the existence of likely development of left ventricular dilation (LVD).

Abstract: The present invention discloses strains of Lactobacillus and Streptococcus which have a capacity to degrade gliadin peptides involved in coeliac disease and which peptide degrading activity is stable under low pH and in the presence of mammalian digestive enzymes. These strains are suitable in a product for use in prevention and/or treatment of celiac disease.

Abstract: The application discloses a new tool for predicting, diagnosing and prognosing hypertensive disorders of pregnancy and particularly preeclampsia; methods for the diagnosis, prediction, prognosis and/or monitoring said disorders; and kits and devices for measuring said biomarker and/or performing said methods.

Abstract: It is to provide a method for measuring glycated hemoglobin in a hemoglobin-containing sample, comprising: reacting glycated hemoglobin in the hemoglobin-containing sample with a proteolytic enzyme in the presence of at least one salt selected from the group consisting of a pyridinium salt, a phosphonium salt, an imidazolium salt, and an isoquinolinium salt; reacting the obtained reaction product with fructosyl peptide oxidase; and measuring the generated hydrogen peroxide. The present invention provides a method for accurately measuring glycated hemoglobin in a hemoglobin-containing sample.

Abstract: The present: invention reveals a strong correlation between FGL-2 prothrombinase activity levels and the presence of a malignant proliferative disorder in a subject. Thus, the present invention provides FGL-2 prothrombinase activity as a diagnostic tool for malignancy.

Abstract: An information acquisition method for acquiring information on a target object, that includes a step of promoting ionization of the target object using a substance for promoting ionization of the target object to cause the target object to emit, and a step of acquiring information on the mass of the flew target object using time-of-flight secondary ion mass spectrometry.

Abstract: Anionic acid-labile surfactants may generally comprise compounds represented by the formula: wherein R1 is independently selected from —(CH2)0-9CH3, R2 is selected from the group consisting of —H and —(CH2)0-5CH3, Y is an anion, X is a cation, and n is an integer from 1 to 8. Methods of making and using the anionic acid-labile surfactants are also described. The anionic acid-labile surfactants may be used to facilitate the solubilization of proteins and other molecules in an aqueous environment.

Abstract: As a result of collecting blood from pancreatic cancer patients, esophageal cancer patients, and stomach cancer patients, and conducting mass spectrometry on N-linked sugar chains in the plasmas, sugar chains whose abundances are significantly different from those of healthy subjects have been successfully identified from the blood samples of the cancer patients.

Abstract: Sample container for holding and transferring a liquid sample and method thereof. The sample container includes an inlet configured to allow a liquid sample to enter a sample container, and an outlet configured to allow one or more droplets of the liquid sample to exit the sample container by one or more acoustic ejections respectively. The inlet and the outlet are in different locations.

Abstract: According to the microchemical chip of the present invention, the sample introducing port 11 is formed as a hole penetrating a face and a back of the first substrate 10, the sample flow path 21 is formed as a slit penetrating a face and a back of the second substrate 20, the sample discharging port 31 is formed as a hole penetrating a face and a back of the third substrate 30, the second substrate 20 is disposed between the first substrate 10 and the third substrate 30, the sample introducing port 11 and the sample discharging port 31 are in communication with each other through the sample flow path 21, and one of ends of the sample flow path 21 is an opening port, and thus, a square hollow groove including an angle having one piece of about 100 microns can be produced as the sample flow path 21.

Abstract: Diagnostic tests for characterizing a test subject's risk of developing or having cancer, based on determining the level of LRG1 and/or CD13 in a bodily sample obtained from a test subject are described. Levels of LRG1 and/or CD13 are then compared to a predetermined value that is derived from measurements of the levels of LRG1 and/or CD13 in comparable bodily samples obtained from control subjects. Such comparison characterizes the test subject's risk of developing or having cancer.

Abstract: The application relates to a substrate for measuring the activity of a deubiquitinating enzyme (DUB), comprising a diubiquitin molecule, wherein an ubiquitin monomer is labeled with a fluorescent label, as well as an assay for DUB enzymes using such substrates.

Abstract: Novel substrates for detection of activity of amyloid beta degrading enzyme, such as Neprilysin (NEP) and insulin degrading enzyme (IDE), associated with Alzheimer's disease, are provided. A quenched fluorogenic peptide substrate containing the first seven residues of the A?peptide plus a C-terminal Cys residue to detect neprilysin activity with a fluorophore attached to the C-terminal Cys and a quencher linked to the N-terminus of the peptide is disclosed. An assay system sensitive to endopeptidase activity of NEP and IDE, but insensitive to other A?-degrading enzymes is disclosed. Active compounds are identified by a cell-based assay system for high-throughput screening.

Abstract: A complex protein mixture is analyzed by jointly digesting the mixture, separating the digest peptides chromatographically or electrophoretically, and ionizing the digest peptides eluting from the separation device by an ionizing method that generates multiply charged ions. Digest peptide ions within a pre-selected range of m/z-values are isolated in an RF ion trap and subsequently reduced in their charge state. The charge-reduced ions can be measured with very high sensitivity. By repeating this process with adjacent isolation mass windows within the time duration of each separation peak, it is possible to determine the masses m, the prevalent charge states z, the retention times t, and the intensities i of a huge number of digest peptides of the complex protein mixture in a single separation run.

Abstract: A therapeutic composition for the treatment of the symptoms of complex regional pain syndrome and a method for preparing the therapeutic composition is disclosed. The therapeutic composition is a stable pharmaceutical composition comprising one or more digestive and/or pancreatic enzymes. The therapeutic composition may be manufactured by a variety of encapsulation technologies. Delivery of the therapeutic composition may be made orally, through injection, by adherence of a medicated patch or by other methods. Further, a method of using fecal chymotrypsin level as a biomarker for the presence of complex regional pain syndrome, or the likelihood of an individual to develop complex regional pain syndrome is disclosed.

Abstract: The present invention provides pregnancy associated plasma protein A2 (PAPP-A2), its nucleotide and amino acid sequences, antisense molecules to the nucleotide sequences which encode PAPP-A2, expression vectors for the production of purified PAPP-A2, antibodies capable of binding specifically to PAPP-A2, hybridization probes or oligonucleotides for the detection of PAPP-A2-encoding nucleotide sequences, genetically engineered host cells for the expression of PAPP-A2, and methods for screening for pathologies in pregnant and non-pregnant patients. Methods for screening for altered focal proliferation states in pregnant and/or non-pregnant patients, which include detecting levels of PAPP-A2, are also described.

Abstract: The present invention is related to a method for preparing an internal peptide standard, comprising a) providing a first tag, and b) coupling of a first peptide to the first tag, whereby the first peptide comprises an amino acid sequence, or a) providing a first tag and b) coupling to the first tag the amino acids forming the first peptide comprising an amino acid sequence, whereby the C-terminal end of the amino acid sequence of the first peptide corresponds to the C-terminal end generated by a sequence-specific hydrolysis of an amide bond, ester bond or thioester bond preferably of an amide bond of a peptide.

Abstract: A molecular construct comprises a donor label, an acceptor label, a linker peptide disposed between the donor and the acceptor, the linker having a cleavage site sequence, and a spacer between at least one of (a) the donor and the cleavage site sequence and (b) the acceptor and the cleavage site sequence. Preferably, the construct is selected from the group consisting of CFP-(SGLRSRA)-SNAP-25-(SNS)-YFP, and CFP-(SGLRSRA)-synaptobrevin-(SNS)-YFP. In preferred embodiments, the linker peptide is a substrate of a botulinum neurotoxin selected from the group consisting of synaptobrevin (VAMP), syntaxin and SNAP-25, or a fragment thereof that can be recognized and cleaved by the botulinum neurotoxin. Advantageously, the spacer increases the electronic coupling between the donor label and the acceptor label relative to a corresponding construct without the spacer.

Abstract: The present invention relates to a method for identifying at least two groups of microorganisms expressing the same enzymatic activity, comprising the following steps: a) incubating said groups of microorganisms in a reaction medium comprising a first enzyme substrate and a second enzyme substrate, said first and second enzyme substrates being metabolized by the same enzymatic activity; b) identifying said groups of microorganisms.

Abstract: Methods and kits for diagnosis and staging of non-septic shock are presented in which one or more protease activities are measured from a biological sample to so identify and/or stage non-septic shock. Most preferably, at least two protease activities are correlated, however, additional or alternative markers may also be measured.

Abstract: The present invention relates to a GCP II (glutamate carboxypeptidase II) mutant (K699S) having the activity of inhibiting glutamate production and the activity of cleavaging ?-amyloid, and to a pharmaceutical composition for the prevention and treatment of a disease selected from the group consisting of amyloidosis, Alzheimer's disease, Down syndrome accompanying Alzheimer's disease, stroke, dementia, Huntington's disease, Pick's disease, and Creutzfeldt-Jakob disease comprising the GCP II mutant (K699S) as an active ingredient. The GCP II (glutamate carboxypeptidase II) mutant (K699S) demonstrates not only excellent A? cleavage activity compared with the wild type GCP II but also excellent activity of inhibiting glutamate production, unlike the wild type GCP II, so that the mutant has been confirmed to have higher effect and stability than the wild type, suggesting that the GCP II mutant can be effectively used for the prevention or treatment of neurodegenerative diseases.

Abstract: A procedure for the identification of a functional disorder of the pancreas by the use of parts of all iso-enzymes of the pancreas elastase and of synthetic amino-acid sequences as antigens for obtaining specific antibodies, as well as their use in immuno-chemical test procedures.

Abstract: Described herein are method(s), kit(s), reagent(s) and the like for determining von Willebrand factor (VWF) activity in a sample in the absence of ristocetin.

Abstract: The invention relates to a method of diagnosing or monitoring schizophrenia or other psychotic disorder. The biomarkers used are selected from cyclophilin A, cytosalic non-specific dipepditase, Caoctosin-like protein, Glucose-6-phosphate isomerase, uncharacterized protein KIAA0423, myosin 14, myosin 15, nicotinamide phosphoribosyltransferase, pyruvate kinase isozyme R/L, phosphoglyterate mutase 4.

Abstract: Methods and assays examining expression of one or more biomarkers in a mammalian tissue or cell sample are provided. According to the disclosed methods and assays, detection of the expression of GalNac-T related molecules, such as GalNac-T14 or GalNac-T3, is predictive or indicative that the tissue or cell sample will be sensitive to apoptosis-inducing agents such as Apo2L/TRAIL and anti-DR5 agonist antibodies. Kits and articles of manufacture are also provided.

Abstract: A set of biomarkers indicative of early gastric cancer and method of diagnosing gastric cancer at an early stage by directing the these biomarkers in a blood sample. Detection of over-expression of one or more protein biomarks in the group consisting albumin, T-kininogen I, ?-2-HS glycoprotein, ?-1-antitrypsin, afamin and ?-actin and/or detection of under-expression of one or more protein biomarks in the group consisting stress 70 protein, apolipoprotein A-I, apolipoprotein A-IV, transthyretin and murinoglobulin is indicative of the presence of gastric cancer.

Abstract: The invention feature devices and methods for preserving and processing samples comprising a fluid having deuterated compounds. The device of the present invention comprises a housing defining a first chamber and a second chamber. The first chamber is heated to an elevated temperature and receives the sample and performs a digestion process on the sample at the elevated temperature. The second chamber is cooled to a low temperature and receives the deuterated digested sample from the first chamber and performs one or more separation steps to isolate an analyte. The device of further comprises conduit means for containing and moving the sample into the first chamber to form a digested sample. The conduit means moves the digested sample from the first chamber to the second chamber to separate the sample to form at least one analyte. The analyte is maintained at the low temperature to preserve its deuterated form.

Abstract: The current disclosure provides for specific peptides from the Secreted Protein Acidic and Rich in Cysteine (SPARC) protein and the derived ionization characteristics of those peptides that are advantageous for quantifying SPARC directly in formalin fixed biological samples by the method of Selected Reaction Monitoring (SRM) mass spectrometry. Such fixed biological samples include: formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and formalin fixed and paraffin embedded tissue culture cells. SPARC protein is quantitated in biological samples by the method of SRM/MRM mass spectrometry by quantitating one or more of the peptides described herein. The peptides can be quantitated if they reside in a modified or an unmodified form. Examples of potentially modified forms of SPARC peptides include those bearing phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.

Abstract: Disclosed is a method of diagnosing graft-versus-host disease, comprising measuring the level of CCL8 protein in a sample obtained from a subject as an indicator for the diagnosis or course of graft-versus-host disease. Also a diagnostic reagent for graft-versus-host disease comprising an anti-CCL8 antibody is disclosed. The method of the present invention enables diagnosis of the onset of graft-versus-host disease and monitoring of the progress, in particular, differential diagnosis between graft-versus-host disease and an infectious disease. The present invention also provides a method for treating graft-versus-host disease utilizing the anti-CCL8 antibody.

Abstract: The present invention provides a method comprising allowing a reaction of a sample, a reagent containing Factor C, which can be activated by binding with endotoxin, and a synthetic luminescent substrate comprising a luminescent substrate bound to a peptide, for release of the luminescent substrate from the synthetic luminescent substrate, allowing a luminescent enzyme to act on the luminescent substrate released in the luminescent substrate release step, for measurement of the luminescence intensity, and quantifying the level of endotoxin in the sample based on a measured value obtained in the luminescence measuring step, the method enabling endotoxin to be simply and quickly measured at a level that cannot be detected in conventional methods for endotoxin measurement, without use of any dedicated measuring device.

Abstract: A method of measuring the degradation of intact proteins includes a step of providing a protein substrate having one or more free or exposed carboxyl groups and then reductively attaching 7-amino-4-methylcoumarin (AMC) to the protein substrate with a reducing agent. The protein substrate is contacted in a test solution with one or more proteolytic enzymes that degrade the protein substrate. The amount of AMC attached to the protein substrate is then determined by monitoring the fluorescence of free 7-amino-4-methylcoumarin that is formed during degradation of the protein substrate to protein fragments.

Abstract: The present invention provides novel mitochondrial fusion transcripts, the parent mutated mtDNA molecules, and the resulting translation products (proteins) for predicting, diagnosing and/or monitoring cancer. Hybridization probes complementary thereto for use in the methods of the invention are also provided.