Abstract: The present invention relates to a method for the detection of essentially intact encapsulated or non-encapsulated parasites in meat, comprising the maceration of the meat with an alkaline digestion solution which contains a digestive enzyme that is active in an alkaline environment. Further, uses of a serine endopeptidase in a method for the detection of essentially intact encapsulated or non-encapsulated parasites in meat are described. The present invention also describes serine endopeptidases for use in a diagnostic method for the detection of essentially intact encapsulated or non-encapsulated parasites in meat. Finally, a kit is disclosed which comprises the enzymes and alkaline digestion solutions of the present invention.

Abstract: The disclosure provides for methods to determine prognosis, aggressiveness, and progression of prostate cancer with the ability to differentiate between aggressive and non-aggressive prostate cancer. The method utilizes the differential enzymatic activity in patient samples, for example of enzymatically active prostate specific antigen (PSA) activity, in order to determine the aggressiveness and prognosis of prostate cancer, and monitor the progression of prostate cancer therapy. The invention also encompasses assay platforms (e.g., optical or electrochemical) that specifically detect PSA-triggered peptide cleavage events.

Abstract: In one embodiment, the present invention provides methods of modulating the deacetylase activity of SIRT1 in one or more cell by modifying the binding affinity of lamin A to SIRT1 via one or more interaction modifying compound. In another embodiment, the present invention provides methods of screening SIRT1-activating/inhibiting compounds based on the interaction between lamin A and SIRT1 proteins and SIRT1-activating property of lamin A. In another embodiment, the present invention provides uses of SIRT1-activating compounds to treat patient(s) suffering from metabolic and/or aging-related degenerative diseases, and uses of SIRT1-inhibiting compounds to treat human malignancies.

Abstract: Embodiments of the present invention relate to compositions and methods of treating patients for type 1 diabetes mellitus (T1D) by administering a therapeutically effective dose of recombinant human KLK1, variants of KLK1, or active fragments thereof. Such patients may be increase risk patients for developing T1D or T1D patients in the Honeymoon Phase. Such treatment may be expected to prevent or delay the onset of T1D, to ameliorate the symptoms of T1D, or to ameliorate the extent to which the T1D manifests.

Abstract: The invention relates to the field of parasitology. Methods and peptidic substrate for screening and identifying inhibitors of Plasmodium are described. Also described are compounds identified by these screening methods, including more particularly inhibitors of Plasmodium subtilisin-like proteases. The invention also concerns anti-malaria compounds, anti-malaria compositions, and uses thereof for preventing, treating, improving, and/or alleviating a Plasmodium infection in a subject, and more Plasmodium vivax and/or by Plasmodium falciparum human infections.

Abstract: The invention relates to the discovery and characterization of mannan binding lectin-associated serine protease-2 (MASP-2), a new serine protease that acts in the MBLectin complement fixation pathway.

Abstract: Apparatus and methods are provided for detecting and monitoring proteolysis of protein matrices such as fibrin clots, extracellular matrix and collagen matrix. The apparatus and methods involve in general the measurement of diffusion-limited electrochemical currents generated by an electroactive species or elactomer in a synthetic protein matrix. The apparatus and methods are applied in various embodiments to detect and monitor the proteolytic activities of a sample, and more specifically fibrinolytic activities and collagenase activities of a sample. The apparatus and methods are utilized generally in the monitoring and diagnostics of cardiovascular, cerebralvascular, and oncology conditions.

Abstract: Methods and kits for diagnosis and staging of non-septic shock are presented in which one or more trypsin protease activities are measured from a biological sample to so identify and/or stage non-septic shock.

Abstract: Latent fluorescent tags, including compounds of Formula I, methods of making latent fluorescent tags, and methods of fluorescently labeling living cells are provided. The compounds of Formula I have the structure: wherein each of the variables are as defined herein.

Abstract: In one form, a fructosyl peptidyl oxidase derived from a budding yeast Phaeosphaeria nodorum for assaying a glycated protein in a sample is provided. The fructosyl peptidyl oxidase has higher activity toward fructosyl valine as well as fructosyl valyl histidine, and may be useful in assaying HbA1c with higher sensitivity and specificity. Still, other forms include unique methods, techniques, systems and devices involving a fructosyl peptidyl oxidase.

Abstract: A method of measuring acidic species generated by degradation of a Fab or Fab? component of a Fab-PEG or a Fab?-PEG is provided. The method involves: a) cleaving PEG and a linker from the Fab-PEG or Fab?-PEG with an enzyme; b) optionally separating the PEG and linker from the Fab or Fab? to provide isolated Fab or Fab?; and c) quantitatively analyzing acidic species associated with the cleaved Fab or Fab? and/or the cleaved PEG.

Abstract: The present disclosure provides nuclear magnetic resonance (NMR) methods for characterizing mixtures of N-linked glycans. Without limitation, methods of the present disclosure may be useful in characterizing monosaccharide composition, branching, fucosylation, sulfation, phosphorylation, sialylation linkages, presence of impurities and/or efficiency of a labeling procedure (e.g., labeling with a fluorophore such as 2-AB). In certain embodiments, the methods can be used quantitatively. In certain embodiments, the methods can be combined with enzymatic digestion to further characterize glycan mixtures.

Abstract: The present invention pertains to a method of detection, by mass spectrometry, of at least one marker of at least one mechanism of resistance to at least one antimicrobial, resistance of at least one microorganism contained in a sample, characterised in that the antimicrobial is a cephalosporin, and said resistance markers are proteins or peptides. Preferably, said proteins or peptides are proteins from said microorganism.

Abstract: The present invention provides a test device for indicating the presence, concentration and effectiveness of chemical and biological agents. The test device interacts with the target agent producing a detectable signal indicating the presence, concentration and effectiveness of the agent. The test device includes a first carrier which changes color consequent to interaction with the target agent in proportion to the concentration of the target agent. The test device includes a second carrier which remains unreacted and unchanged in color in the presence of the target agent. The second carrier serves as an integrated reference to which the color change of the first carrier is compared.

Abstract: Systems and methods for culturing and monitoring, ex vivo, pharmacologic and metabolic response in a biological sample, including receiving at a fluidic apparatus the biological sample retrieved from the patient, retaining the biological sample within a channel of the fluidic apparatus, providing for the culture of the biological sample within the channel of the fluidic apparatus, flowing a fluid past the biological sample, retrieving and analyzing the fluid to determine a pharmacologic and/or metabolic response of the sample.

Abstract: Methods and kits to detect the presence or amount of at least one molecule for an enzyme-mediated reaction in a multiplex luminogenic/nonluminogenic assay are provided.

Abstract: Alkyl amines act to release formaldehyde cross-linking that occurs in biological samples. Thus, contacting alkyl amines to formaldehyde fixed samples is a useful way to render biological components of the samples, including nucleic acids or proteins, more accessible to detection and characterization.

Abstract: The invention provides mass spectrometry methods, compositions and systems which enable a unique platform for analyte quantitation accessing very high degrees of multiplexing and accurate quantification, particularly well-suited for a range of quantitative analysis for proteomics applications. Embodiments of the present methods and systems combine isotopic coding agents characterized by very small differences in molecular mass with mass spectrometry methods providing large resolving power to provide relative or absolute analyte quantification in a large number of samples.

Abstract: The invention relates to methods and biomarker for evaluating cancer metastasis, pharmaceutical composition for inhibiting cancer metastasis, and method for analyzing secretome. By combining a hollow fiber cartridge (HFC) culture system with quantitative proteomics technology, cancer metastasis-related secrectomes can be found. Furthermore, this is the first time to use PARK7 as a biomarker for judging the process of non-small cell lung cancer.

Abstract: The present invention is directed to methods of identifying biomarkers in liquid biological samples obtained from cancer patients or patients exhibiting a disease state. Such methods may include the use of electrospray ionization-time of flight mass spectrometry (ESI-TOF MS).

Abstract: Disclosed herein are novel nanobeacon imaging agents having the following formula: wherein: D is 1 to 4 fluorophores; L is 1 to 4 enzymatically cleavable peptide linkers; PEP is a hydrophilic cell penetrating peptide sequence; A is a side chain moiety of an amino acid of PEP; and Q is a fluorescence quencher molecule. The present invention provides a generic design of a new type of supramolecular nanobeacon imaging agents with a well-defined size and surface chemistry for protease detection. In contrast to soluble molecular beacons, the imaging agent molecules are specifically designed to self-assemble into core-shell micellar structures, with the enzyme-sensitive design feature being deeply embedded within the micellar core and thus inaccessible to the enzyme. Only in the monomeric form can these nanobeacon imaging agent molecules be cleaved by the target enzyme to generate fluorescence signals.

Abstract: The invention relates to proteins for use as a marker for the efficacy of sublingual immunotherapy. In particular, the proteins may be used to predict the responsiveness of a patient to immunotherapy. The invention may find use in selecting patients as suitable candidates for immunotherapy.

Abstract: Drug affinity responsive target stability (DARTS) is a 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 disclosure provides devices and rapid methods to acquire a wound sample to detect and measure NOx, and optionally, one or more other analytes that are indicative of the status of a wound.

Abstract: A liquid processing system to process liquid biological material includes: a trunk provided turnable on an axis, set within a predetermined work space; a first arm provided to the trunk and having at least three degrees of freedom or higher degrees of freedom; a second arm provided to the trunk and having at least three degrees of freedom or higher degrees of freedom; a driving mechanism configured to drive each of the trunk, the first arm, and the second arm; and physiochemical equipment situated within the work space and within the range of movement of at least one of the first and the second arm. The driving mechanism is operated by teaching playback based on the positions and shapes of the physiochemical equipment, and the biological material is processed using the physiochemical equipment.

Abstract: The present invention relates to the field of biomarkers and, more specifically, to biomarkers useful in diagnosing aggressive prostate cancer. In specific embodiments, a method for diagnosing aggressive prostate cancer in a patient comprises (a) measuring the levels of one or more biomarkers in a sample collected from the patient; and (b) comparing the levels of the one or more biomarkers with predefined levels of the same biomarkers that correlate to a patient having aggressive prostate cancer and predefined levels of the same biomarkers that correlate to a patient not having aggressive prostate cancer, wherein a correlation to one of the predefined levels provides the diagnosis.

Abstract: The present invention relates to methods of diagnosing the presence of a non-specific disease or disorder in a subject, wherein a determined level of YKL-40 above a reference level indicates the presence of a non-specific disease or disorder. The subject may suffer from a variety of diseases or disorders. The reference level may be a reference level obtained from healthy individuals or it may be a previous measurement obtained from the same subject. The present invention furthermore relates to a method for classifying the severity of a non-specific disease or disorder in a subject, wherein a determined level of YKL-40 above or below one or more reference levels gives the severity of said non-specific disease or disorder. The present invention further relates to a kit and a device that may be used in the method of the present invention comprising means for measuring the level of YKL-40 in a sample; and means for comparing the measured level of YKL-40 with at least one reference level of YKL-40.

Abstract: A method of screening an agent for ability to interfere with collagen synthesis includes the steps of reacting a polypeptide having an amino acid sequence comprising SEQ ID NO: 1 with collagen mRNAs in the presence of the agent and detecting if the agent has interfered with binding of the polypeptide to the mRNAs. Another method includes the steps of reacting the polypeptide with nonmuscle myosin filaments in the presence of the agent and detecting if the agent has interfered with binding of the polypeptide to the nonmuscle myosin filaments.

Abstract: Disclosed herein are methods of detecting blood disorders, such as diabetes. In particular examples the method includes contacting a blood sample with an amine reagent, blocking an excess of the amine reagent with a blocking reagent, digesting the modified blood sample with trypsin to produce a digested blood sample containing a plurality of glycated N-terminal peptides and non-glycated N-terminal peptides, then analyzing the digested blood sample with MALDI MS. Also provided are reagents for use in such methods.

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.

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: A method of enhancing an enzymatic activity of a disintegrin-like domain, and metalloprotease, with an isolated human thrombospondin type 1 motif, member 13 (ADAMTS-13) by substituting on or more positions in the isolated human ADAMTS-13.

Abstract: Provided herein are a novel class of oligopeptides and prodrugs that include amino acid sequences containing cleavage sites for fibroblast activation protein (FAP). Also provided herein are methods of treating FAP related disorders, including cancer.

Abstract: The present invention relates to an information acquisition method of acquiring information of distribution of a protein or peptide in a sample based on mass information obtained by mass spectrometry of the protein or peptide. The method includes mass spectrometry of a definite region of the sample after limited proteolysis of the protein or peptide and acquisition of information relating to distribution using an ion peak that has a two-dimensional intensity distribution having a Pearson product-moment correlation coefficient of 0.5 to more and 1.0 or less in the definite region against the two-dimensional intensity distribution of the parent ion of the protein or the peptide subjected to the limited proteolysis and has a peak intensity ratio of larger than 1.0 against the peak intensity of the integrated spectrum of the parent ion in the definite region, wherein the m/z of the ion peak is greater than 500.

Abstract: This invention provides general methods for selective labeling of proteins on their N-termini with synthetic peptides. The methods of this invention can be applied to the global proteomic profiling of complex mixtures of proteins and polypeptides.

Abstract: A method for the detection of an early biomarker for assessing a change in renal status in a mammalian subject following a renal event. The method typically includes the steps of (a) providing a body fluid sample obtained from a mammalian subject; (b) analyzing the molecular weight of the proteins in the sample using proteome analysis; and (c) identifying the presence of a protein in the sample selected from the group consisting of a 6.4 kDa protein, a 28.5 kDa protein, a 33 kDa protein, a 44 kDa protein, a 67 kDa protein, and combinations thereof. The presence of one of these proteins can serve as an early biomarker for assessing a change in renal status. The levels of these proteins can be compared to predetermined levels, and thus provide a determination of the subject's renal status. The invention also includes a method of assessing the administration of aprotinin during cardio-pulmonary bypass surgery and provides for methods where the level of the 6.

Abstract: The invention is concerned with methods of assaying the activity of enzymes based on measurement of fluorescence lifetime (FLT). In particular, the invention relates to assays for enzymes which are capable of modifying the structure of peptide substrates, including for example enzymes catalysing methylation, demethylation, acetylation, deacetylation or deimination of peptide substrates.

Abstract: The present invention provides a method of determining the absolute amount of a target polypeptide in a sample, said method comprising the following steps: (a) adding (aa) a fusion polypeptide to said sample, said fusion polypeptide comprising (i) at least one tag sequence and (ii) a subsequence of the target polypeptide; and (ab) a known absolute amount of a tag polypeptide comprising or consisting of said tag sequence according to (aa) to said sample, wherein said fusion polypeptide on the one hand is mass-altered as compared to said target polypeptide and said tag polypeptide on the other hand, for example, said fusion polypeptide on the one hand and said target polypeptide and said tag polypeptide on the other hand are differently isotope labeled; (b) performing proteolytic digestion of the mixture obtained in step (a); (c) subjecting the result of proteolytic digestion of step (b), optionally after chromatography, to mass spectrometric analysis; and (d) determining the absolute amount of said target poly

Abstract: Method and test kit for quantitative determination of Vitamin D metabolites in blood, wherein a predetermined amount of blood is pre-analytically immobilised on a solid sorption material. Thereby, hemolysis of the blood has no effect on the analysis of vitamin D metabolites. For quantitative analysis the dried blood spot on the sorption material is dissolved with an aqueous solvent buffer containing detergent, pH 7.0 to 10.0, and the vitamin D metabolites are eluted with a protic organic solution having a permittivity of less than 35. The eluate is analysed for vitamin D metabolites using conventional methods.

Abstract: The invention provides a method detecting and quantifying proteins by mass spectrophotometric analysis using peptide internal standards and provides a highly sensitive way of detecting protein modifications. In one aspect, the invention provides a method for determining a site of ubiquitination in a polypeptide and for evaluating ubiquitination targets in a population of polypeptides. In this way, a proteome ubiquitination map can be obtained which comprises information relating to the ubiquitination states of a plurality of cellular polypeptides. Maps can be obtained for a variety of different types of cells and cell states. For example, ubiquitination targets in normal and diseased cells can be evaluated. Preferably, the map is stored as data files in a database. Individual ubiquitinated polypeptides identified can be used to generate molecular probes diagnostic of a cell state and/or can serve as targets for agents that modulate one or more cellular processes.

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 methods for enhancing chemical reactions of molecules, e.g., biomolecules, with destructible surfactants. The chemical reactions may involve and/or be associate with analysis, e.g., solubilizing, separating, purifying and/or characterizing the molecules. In one aspect, the anionic surfactants of the present invention may be selectively broken up at relatively low pH. The resulting breakdown products of the surfactants may be removed from the molecule/sample with relative ease. The invention has applicability in a variety of analytical techniques.

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: An embodiment of the present invention is a method for measuring activity of cell pathways, such as the cell cycle pathway and correlating the resulting profile to phenotypes. The resulting correlations are useful in diagnosis, prognosis, selection and development of drug treatment regimens, and drug screening applications.

Abstract: In order to provide a composition for treating, improving, or preventing pain, it has been found out that a metallothionein protein is expressed in a normal peripheral nerve, and that the expression is not observed in a peripheral nerve producing pain. Moreover, it has been found out that administering metallothionein to rats having neuropathic pain suppresses the pain in the rats.

Abstract: The present invention relates to the field of recombinant toxin protein production in bacterial hosts. In particular, the present invention relates to production processes for obtaining high levels of a recombinant CRM197, Diphtheria Toxin, Pertussis Toxin, Tetanus Toxoid Fragment C, Cholera Toxin B, Cholera holotoxin, and Pseudomonas Exotoxin A, from a bacterial host.

Abstract: Described herein are methods of detecting a wound 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: Altered protein products resulting from somatic mutations are directly identified and quantified by mass spectrometry. The peptides expressed from normal and mutant alleles are detected by Selected Reaction Monitoring (SRM) of their productions using a triple quadrupole mass spectrometer. As a prototypical example of this approach, we quantify the number and fraction of mutant Ras protein present in cancer cell lines. There were an average of 1.3 million molecules of Ras protein per cell and the ratio of mutant to normal Ras proteins ranged from 0.49 to 5.6. Similarly, we detected and quantified mutant Ras proteins in clinical specimens such as colorectal and pancreatic tumor tissues as well as in pre-malignant pancreatic cyst fluids. These methods are useful for diagnostic applications.

Abstract: The present invention relates to a method for the measurement of active alpha1-proteinase inhibitor (A1PI) in a sample, comprising the steps of binding elastase to a solid support, letting the A1PI contained in the sample bind to the solid phase-bound elastase, and detecting solid phase-bound A1PI with a detection reagent.

Abstract: The invention relates to a method for the diagnostic investigation of biological samples from a person for inflammation of the liver, in particular hepatic fibrosis and/or cirrhosis of the liver, where the sample is investigated for one or more proteins as markers of inflammation of the liver, in particular hepatic fibrosis and/or cirrhosis of the liver, where a concentration of the proteins which is elevated or decreased by comparison with the healthy state indicates the presence of an inflammation of the liver, in particular a hepatic fibrosis and/or cirrhosis of the liver.