Abstract: Members of the Amyloid Precursor Protein family (APP molecules) and their neurotoxic cleavage product A? are key players in the development of Alzheimer's disease (AD). Proteolytic processing of APP molecules is influenced by metal ions, protein ligands and its oligomerization state. X-ray structures of the metal bound molecule at 2.6-2.0 ? resolution are presented, providing structural and functional bases for the regulation of APP molecules using conformational information. A metal-dependent molecular switch located within the E2 domain of APP coinciding with a high affinity copper and zinc binding site within the monomeric E2 domain was evaluated. The metal specific coordination spheres of this E2 domain comprise four evolutionary conserved histidine residues. Metal binding induces large conformational changes relative to the metal free protein. This conformational change provides a basis for influencing APP molecule processing and thus trafficking and the production of A?.

Abstract: The present invention provides particular anti-inflammatory factors, compositions containing them, methods of making, identifying, and/or characterizing them, and methods of using them. In some embodiments, provided factors are expressed by human bone marrow stromal cells (MSC). In some embodiments, provided factors are characterized by an ability, when contacted with mammalian leukocytes in culture, to alter production of at least one inflammatory or anti-inflammatory agent by the mammalian leukocytes. In some embodiments, provided factors include GALNT1 polypeptides, LGALS3BP polypeptides, MFAP5 polypeptides, PENK polypeptides and/or HAPLN1 polypeptides. In some embodiments, provided factors are useful in the inhibition of inflammatory agents, in the promotion of anti-inflammatory agents, and/or for the treatment of subjects suffering from or susceptible to a disease, disorder or condition characterized by inflammation.

Abstract: The present invention relates to mast cell cultures that are derived from hematopoietic progenitors and the use thereof. The invention describes a method for generating in-vitro cultures of human mast cells with functional phenotype of connective tissue-type mast cells. By monitoring the levels of chemokines released into the medium, such mast cell cultures can be used as a cell-based assay to assess regulation of mast cell functions and pharmacological activities of tryptase inhibitors.

Abstract: Provided are modified factor IX (FIX) polypeptides and methods of generating modified FIX polypeptides. Also provided are pharmaceutical compositions, including compositions formulation for oral administration, that contain the modified FIX polypeptides, and methods of treatment using modified FIX polypeptides.

Abstract: It is disclosed herein that isolated lymphocytes, such as human B-cells and CD4+ T-cell can be used to determine an amount of lymphocyte-associated anthrax lethal toxin activity present. Methods of using isolated lymphocytes to identify anthrax therapeutic agents and to determine the efficacy of a potential anthrax therapeutic are disclosed. Methods are also provided for diagnosing and treating anthrax infections.

Abstract: The present invention is directed to topical enzymatic wound debriding compositions with enhanced enzymatic activity. These compositions comprise a dispersed phase comprising at least one proteolytic enzyme and at least one hydrophilic polyol; and a continuous phase comprising a hydrophobic base.

Abstract: The invention relates to methods and kits for determining the toxicity of an agent on a population of eukaryotic cells, particularly human cells. The cells may comprise a nucleic acid construct comprising a DNA damage induced response element operably linked to a sequence encoding a reporter gene. The multiplex methods and kits provide means for distinguishing between genotoxic and cytotoxic agents.

Abstract: The present invention relates to methods of determining enzyme activity in a fluid, wherein the activity over time provides a viscosity-change in the fluid, by the use of a device (FIG. 1) equipped with at least one pressure sensor (FIG. 1 (4)) to determine the change in the fluid viscosity over time as a measure of the enzyme activity.

Abstract: The application discloses new biomarkers for hypertensive disorders of pregnancy and particularly preeclampsia; methods for the diagnosis, prediction, prognosis and/or monitoring said disorders based on measuring said biomarkers; and kits and devices for measuring said biomarker and/or performing said methods.

Abstract: A method for identifying persons with increased risk of developing type 1 diabetes mellitus, or having type I diabetes mellitus, utilizing selected biomarkers described herein either alone or in combination. The present disclosure allows for broad based, reliable, screening of large population bases. Also provided are arrays and kits that can be used to perform such methods.

Abstract: Described herein are methods of detecting an infection and for detecting the presence or absence of microorganisms, for example, wound pathogens in a sample, by contacting a sample with an enzyme produced and/or secreted by the bacteria, and detecting modification or the absence of modification of the substrate, as an indicator of the presence or absence of the enzyme in the sample. The present invention also features a biosensor for detecting the presence or absence of bacteria in a sample.

Abstract: Methods for interpretation of mass spectrometric tests for clinical biomarkers in which the amounts of internal standards are set to equal clinical evaluation thresholds, and preparations for adding stable isotope labeled peptide species to sample digests while minimizing losses and alterations in peptide stoichiometry.

Abstract: The application discloses LTBP2 as a new biomarker for renal dysfunction; methods for predicting, diagnosing, prognosticating and/or monitoring said dysfunction based on measuring said biomarker; and kits and devices for measuring said biomarker and/or performing said methods. LTBP2 is also involved in glomerular filtration rate, dyspnea, acute heart failure, left ventricular hypertrophy, cardiac fibrosis, preeclampsia, pregnancy- associated proteinuria.

Abstract: The present invention relates to a method for identifying compounds that modulate the activity of telomerase. Compounds of the invention are identified by designing or screening for a compound which binds to at least one amino acid residue of the TRBD, “thumb,” “finger,” and/or “palm” domain of telomerase and testing the compound for its ability to modulate the activity of telomerase.

Abstract: The present invention provides novel markers for diagnosing pancreatic cancer, and methods for determining if a subject has pancreatic cancer utilizing the markers, etc. The methods involve comparing mass-spectrometric peaks of certain sugar chains, obtained from patients' blood and determining if there is a significant decrease in peak intensity, compared with corresponding peaks from patients without pancreatic cancer.

Abstract: Methods for producing an isotope-labeled mammalian, including a human, biomolecule, such as polypeptides and proteins, in a cell-free protein synthesis system. A biomolecule standard is produced having at least one isotope different in abundance than that of the naturally occurring isotopes in the biomolecule. Methods for quantifying biomolecules standards expressed using mammalian cell-free extracts are disclosed. Methods for producing such standards, kits, systems and reagents, relating to the use of isotope-labeled biomolecule as quantification standards in mass spectrometric and nuclear magnetic resonance analysis.

Abstract: The present invention provides a method for detecting onset of, or the risk of development of, a protein misfolding disease, and a method for predicting the age of onset of a protein misfolding disease using nerve cells derived from iPS cells. The present invention also provides a kit to be used in these methods.

Abstract: It is intended to provide a method for determining a carbohydrate which enables more accurate determination of a carbohydrate. The invention for achieving this object is directed to a method for determining a carbohydrate using a digestive enzyme, characterized in that as the digestive enzyme, an animal-derived low-molecular-weight carbohydrate digestive enzyme is used. More specifically, the invention is directed to a method for determining a carbohydrate using a digestive enzyme, characterized by comprising a first reaction step using thermostable ?-amylase; a second reaction step using protease and amyloglucosidase; and a third reaction step using an animal-derived low-molecular-weight carbohydrate digestive enzyme.

Abstract: The present invention provides compositions and processes for preparing the same wherein the compositions are useful for monitoring breast cancer treatment.

Abstract: Provided are methods for measuring renin activity in a plasma sample using mass spectrometry. The methods generally involve ionizing purified angiotensin 1 from the sample and detecting the amount of angiotensin 1 ions generated. The amount of detected angiotensin 1 ions are then related to the amount of angiotensin 1 generated in the sample, which in turn is related to renin activity in the sample.

Abstract: A method and kit are provided for enhancing the tolerance of an assay reagent to compounds in an assay sample, the assay reagent including a luciferase enzyme. The method includes contacting the luciferase with a tolerance enhancement agent in an amount sufficient to substantially protect luciferase enzyme activity from interference of the compound and minimize interference by at least about 10% relative to an assay not having tolerance enhancement agent.

Abstract: Methods and kits for identifying and/or monitoring neurological conditions in a patient using ratios of biomarkers are disclosed. The neurological conditions may include, for example, Alzheimer's disease or mild cognitive impairment. The particular biomarkers that may be useful in identifying and/or monitoring neurological conditions may include, for example, biliverdin reductase, biliverdin reductase, estrogen receptor alpha, superoxide dismutase, S100A7, hemeoxygenase 1, matrix metalloproteinase 9 and platelet derived growth factor receptor. In particular, ratios of these biomarkers are useful.

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

Abstract: An apparatus to separate and analyze components of a liquid sample include a high performance liquid chromatograph with a mass spectrometer utilizing desorption electrospray ionization. This permits separation and evaluation of different components in a liquid sample. Further, this can be combined with online derivation via reactive DESI and, further, can be used with further electrochemistry.

Abstract: Disclosed are fluorogenic substrates for measuring ADAMTS13 activity or ADAMTS13 inhibitor activity. Substrates can comprise an oligopeptide which can consist of up to 80 amino acids of sequence of von Willebrand Factor (VWF). The oligopeptide can include modifications of sequence of VWF, including an amino-terminal glycine, a scissile Y-M peptide, and a cysteine substitution located from 1 to 12 amino acids from the scissile Y-M in the carboxy terminal direction. A substrate can further comprise a fluorophore and a fluorescence quencher bound to the oligopeptide on opposite sides of the scissile Y-M peptide, wherein the fluorescence quencher is not identical to the fluorophore. An oligopeptide can be encoded by a nucleic acid sequence which can also encode a His tag. An oligopeptide can be expressed in a cell or microorganism. Also disclosed are methods of using a fluorogenic substrate to measure ADAMTS13 activity or ADAMTS13 inhibitor activity.

Abstract: A bladder cancer biomarker and a test method using the same are provided. The biomarker contains serum amyloid A-4 protein (SAA4), which exist in the urine specimen of a testee. The expression intensity of the biomarker can facilitate diagnosis of bladder cancer and evaluation of aggressiveness and malignancy of bladder cancer. Thereby, the physician can arrange an optimized treatment to achieve the best therapeutic effect.

Abstract: The invention discloses identification and therapeutic use of matrix metalloproteinase oligopeptides, SEQID 5-SEQID 21. These oligopeptides are bound to antibodies to create an immune response in the subject mammal against the matrix metalloproteinases of various diseases. This is a means of therapeutic intervention against the disease spread created by the matrix metalloproteinases. Further use of these oligopeptide-antibody responses can be extended to any and all diseases that use the matrix metalloproteinases to aid in their pathogenicity.

Abstract: A method for testing efficacy of a protease enzyme assay, the method comprising providing an enzyme which acts as a surrogate enzyme control for the protease enzyme; combining the surrogate enzyme control with an assay substrate for the protease enzyme; and determining a change in the assay substrate resulting from the surrogate enzyme control acting on the assay substrate; wherein the protease enzyme is selected from the group consisting of metalloproteinases, serine proteases, and cysteine proteases; a method for conducting a protease enzyme assay using the method for testing efficacy; a kit including an enzyme which acts as a surrogate enzyme control for a protease enzyme in testing efficacy of a protease enzyme assay; and a method of releasing the kit are provided.

Abstract: Provided are differential antibodies recognizing the cleaved and non-cleaved forms of matrix metalloproteinases (MMPs), and methods of using the antibodies as surrogate diagnostic markers for the presence of active MMPs in cancer, such as growing breast cancers.

Abstract: A method for detecting the absence or presence of cells of interest in a liquid sample is provided. The method comprises providing a sample suspected of containing cells of interest that contain an intracellular enzyme with a measurable activity. The sample further comprises an extracellular medium that also includes an extracellular enzyme with the measurable activity. The method further comprises the steps of treating the liquid sample with a reagent that inactivates the measurable activity in the extracellular medium but does not inactivate the measurable activity in the cells of interest, lysing the cells of interest to release the intracellular enzyme, and measuring the measurable activity. Thus, the measurable activity of 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: 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: 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: Compositions and methods for analyzing intracellular BoNT protease activity, and especially BoNT/B, BoNT/G, BoNT/D, and/or BoNT/F protease activity are provided. Most preferably, cells express one or more recombinant hybrid proteins that include one or more fluorescent proteins and at least one BoNT protease recognition and cleavage sequence, and analysis is performed using FRET analysis.

Abstract: The current invention is directed to a method for determining amino acid sequence mutations in a produced polypeptide, comprising the following steps of a) providing a sample of a produced polypeptide, b) incubating the polypeptide in the sample with a protease, c) performing a two dimensional analysis using reversed phase chromatography coupled with a high resolution mass spectroscopy (FT-ICR/FT-orbitrap) and MS/MS analysis of the amino acid sequence fragments of the peptides, d) data evaluation by comparing the LC-MS data sets obtained for the samples side by side with the data set of a reference sample, by searching for differences in the signal intensities at given retention times and by evaluation of differential signals with respect to amino acid sequence mutations. The reference sample for data evaluation (d) can be either a well characterized standard or one of the samples to be analyzed.

Abstract: Methods are disclosed to detect, characterize, measure, and quantitate human and humanized antibodies, and their conjugates, present in pre-clinical animal biological samples, including plasma/serum and tissue samples.

Abstract: In accordance with the invention, the development and use of antibodies within the digestive tract is provided. Antibodies are described that are used to treat disorders associated with altered permeability of the digestive tract. Antibodies are described with increased stability within the environment of the digestive tract. Antibodies are described with enhanced permeability to a compromised digestive tract.

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. In some cases, the methods entail treating the co-polymer with pyro-glutamate aminopeptidase to cleave N-terminal pyro-glutamate residues.

Abstract: The present invention relates to a method of predicting the risk of a subject developing a cardiovascular event, comprising determining the presence of a biomarker that is indicative of the risk of developing a cardiovascular event in exosomes from the subject. The exosomes are suitably isolated from a body fluid selected from serum, plasma, blood, urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, breast milk, saliva, in particular serum. The biomarker is selected from the proteins Vitronectin, Serpin F2, CD14, Cystatin C, Plasminogen, Nidogen 2 or any combination of two or more of these proteins.

Abstract: Methods for identifying modified proteases with modified substrate specificity or other properties are provided. The methods screen candidate and modified proteases by contacting them with a substrate, such as a serpin, an alpha macroglobulins or a p35 family protein or modified serpins and modified p35 family members or modified alpha macroglobulins, that, upon cleavage of the substrate, traps the protease by forming a stable complex. Also provided are modified proteases.

Abstract: A composition includes an artificial construct having (a) a reporter-containing portion chemically coupled to (b) a cleavage site. The cleavage site interacts with an investigational substance in a manner that cleaves the reporter-containing portion from a remainder of the construct. The cleaved portion is destroyed or otherwise degraded by the local environment, and presence of an investigational substance is evidenced by reduction in signal from the reporter. The investigational substance is preferably a Botulinum toxin (BoTN), and the cleavage sequence is all or part of a SNARE protein. The cleavable reporter-containing portion is preferably Yellow Fluorescent Protein (YFP), Citrine, Venus, or a YPet protein.

Abstract: Some embodiments of the present invention relate to methods and compositions for assessing the absence, presence, progression, or stage of cancer. In particular, methods and compositions for detecting endometrial cancer or ovarian cancer are provided.

Abstract: The invention relates to an arrangement, comprising a solid carrier and a matrix arranged on the solid carrier, said matrix comprising at least one enzymatically convertible or modifiable molecule and comprising at least one enzyme that can be released by the conversion or modification of the molecule, said enzyme being capable of converting at least one color-changing substrate located in the matrix and/or on the solid carrier.

Abstract: Described herein are devices and methods for identifying the existence of an oral condition in a subject.

Abstract: A diagnostic method for determining the absence or presence of a disease is provided. The method generally includes assaying the amount and/or types of oxidized peptides in a sample from a subject, and comparing these to the amount and types of reference oxidized polypeptides. The method may include the use of stable isotope label, affinity selection, to identify and quantify changes in oxidized peptides or oxidized proteins associated with diseases such as type II diabetes mellitus, breast cancer, and Parkinson's disease, to monitor a patient's response to a therapeutic agent (e.g., an antioxidant), and/or to monitor disease recurrence.

Abstract: The invention provides biomarkers and combinations of biomarkers useful in diagnosing lung diseases such as non-small cell lung cancer or reactive airway disease. The invention also provides methods of differentiating lung disease, methods of monitoring therapy, and methods of predicting a subjects response to therapeutic intervention based on the extent of expression of the biomarkers and combinations of biomarkers. Kits comprising agents for detecting the biomarkers and combination of biomarkers are also provided.

Abstract: This invention relates to novel phosphorylation sites in the desmin protein that are associated with the onset of heart failure. The phosphorylation sites, i.e., Ser-27 and Ser-31, can be used as biomarkers for (i) identifying subjects at risk for the development of heart failure, (ii) treating subjects having a higher than normal level of the biomarker, and (iii) monitoring therapy of a subject at risk for the development of heart failure. Also described are antibodies, reagents, and kits for carrying out a method of the present invention.

Abstract: The disclosure relates to the identification of an essential Clostridium difficile gene that encodes a polypeptide with protease activity and its use in the identification of anti-microbial agents and as antigen in subunit vaccines.

Abstract: The current disclosure provides for specific peptides from the Insulin-Like Growth Factor 1 Receptor (IGF-1R) protein and the derived ionization characteristics of those peptides that are advantageous for quantifying the IGF-1R 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. IGF-1R 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 an IGF-1R peptides include those bearing phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.

Abstract: The present invention provides a particle aggregate comprising particles linked to other particles via linkers that are capable of being cleaved by an enzyme. The particles may be linked directly to other particles by the linkers or may be linked indirectly by means of a binding moiety. The invention also provides a particle coupled to a binding moiety via a linker that can be cleaved by an enzyme. The present invention may be used in diagnosing a disease or condition associated with the enzyme, or may be used to treat such a disease or condition whereby the drug is retained in the particle aggregate until the linkers are cleaved by the enzyme.

Abstract: An improved method is described for the synthesis of aspartame using a condensation reaction between the alpha-carboxyl group of the L-aspartic acid and the amino group of the methyl L-phenylalaninate catalyzed by an enzyme. The method allowed efficient and cost effective production of aspartame. A method of identifying an enzyme useful for preparing aspartame is also described.