Abstract: Provided are compositions, methods and kits for quantifying the expression and/or activity of MMP-14 and other biomarkers of cancer, which may be used diagnostically and prognostically, e.g., in patient stratification and evaluation of appropriate therapeutic regimens.

Abstract: Provided is a method of detecting infection in a wound caused by an infecting organism at a wound site. Also provided is a system for detecting an infection in a wound at a wound site. Additionally, a porous pad comprising luciferase is provided.

Abstract: A transformed diatom includes a nucleic acid sequence operatively linked to a promoter, wherein the nucleic acid sequence encodes an amino acid sequence including (i) an heterologous signal peptide and (ii) a polypeptide, the heterologous signal peptide leading to the secretion of the polypeptide in the extracellular medium of the transformed diatom; a method for producing a polypeptide which is secreted in the extracellular medium, the method including the steps of (i) culturing a transformed diatom, (ii) harvesting the extracellular medium of the culture and (iii) purifying the secreted polypeptide in the extracellular medium; and use of the transformed diatom for the secretion of a polypeptide in the extracellular medium.

Abstract: Methods and kits provide for diagnosis and prognosis of ischemia by using biomarkers comprising albumin-bound protein/peptide complex (ABPPC).

Abstract: A process of quantifying proteins in a complex mixture is provided. The invention has utility in quantifying proteins in a complex preparation of uni- or multivalent commercial or research vaccine preparations.

Abstract: The present invention provides a method of screening for compounds which affect the cleavage of EphA7 by ?-secretase. The method includes the following steps: (i) contacting a first biological composition containing ?-secretase or a biologically active fragment thereof with a second biological composition containing EphA7 in the presence and absence of a candidate compound; (ii) measuring the cleavage of the EphA7 in the presence and absence of the candidate compound; (iii) selecting those candidate compounds which affect the cleavage of the EphA7 by ?-secretase; and (iv) identifying the candidate compounds selected in step (iii) as compounds which affect the cleavage of EphA7 by ?-secretase.

Abstract: Specific nitroprotein biomarkers may be used as prognostic and diagnostic tools for COPD. Identification of certain specific nitroprotein biomarkers allows the development of targeted therapies aimed at prevention and treatment of COPD.

Abstract: The present invention provides methods for assessing efficacy of a methotrexate (MTX) dosing regimen in a patient.

Abstract: There is provided an optical analysis technique enabling identification of a kind of light-emitting particle corresponding to a signal on a time series light intensity data or identification of a signal corresponding to light-emitting particles other than a particle to be observed in an optical measurement using a confocal microscope or a multiphoton microscope. The inventive optical analysis technique measures simultaneously and separately intensities of lights of two or more wavelength bands from a light detection region in a sample solution containing light-emitting particles of two or more kinds to generate time series light intensity data of the respective wavelength bands; detects signals simultaneously generated on the time series light intensity data of at least two wavelength bands; and identifies the simultaneously generated signals as signals of a light-emitting particle of at least one specific kind.

Abstract: Methods are provided for identifying biomarker proteins that exhibit differential expression in subjects with a first lung condition versus healthy subjects or subjects with a second lung condition. Also provided are compositions comprising these biomarker proteins and methods of using these biomarker proteins or panels thereof to diagnose, classify, and monitor various lung conditions. The methods and compositions provided herein may be used to diagnose or classify a subject as having lung cancer or a non-cancerous condition, and to distinguish between different types of cancer (e.g.

Abstract: The invention relates to methods and products for modulating glycosylation of proteins. The invention is useful for identifying therapeutic compounds to treat glycosylation-associated disorders such as neurodegeneration, diabetes, including complications of diabetes such as insulin resistance, nephropathy, microvascular damage, and endothelial dysfunction. The invention is also useful for identifying therapeutic compounds to treat de-glycosylation-associated disorders such as ischemic damage and traumatic injury. The invention also relates in part to assays that are useful for identifying and testing candidate compounds for modulating glycosylation of proteins and also relates in part to compounds to treat glycosylation-associated diseases and disorders.

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 present invention provides markers of endothelial progenitor cells (EPCs) and use of those markers and reagents that bind thereto to detect EPC cells or diagnose, prognose, treat or prevent EPC-associated conditions.

Abstract: Methods and devices for assaying the effectiveness of a cleaning composition in removing a protein or a biofilm from a surface are disclosed. Such methods include the steps of providing one or more proteins at an interface between an aqueous phase and a liquid crystal phase or at the surface of a liquid crystal, contacting the interface or liquid crystal surface with a cleaning composition, and observing the orientational ordering of the liquid crystal at the interface or liquid crystal surface. A continuous change in the orientational ordering of the liquid crystal at the interface or liquid crystal surface indicates that the proteins are being removed from the interface, and the rate of change in orientational ordering, the extent of the change in orientational ordering, or both, are correlated with the effectiveness of the cleaning composition.

Abstract: Methods for detection of the activity of proteolytic enzymes, particularly isopeptidases, are disclosed.

Abstract: Methods are described for monitoring the amounts of PTH variants in a biological sample by digesting the sample to produce surrogate peptides specific to the targeted PTH variants, and detecting and quantifying the surrogate peptides by selective reaction monitoring (SRM) mass spectrometry, using a set of precursor-to-product ion transitions optimized for sensitivity and selectivity. The PTH variants, or a portion thereof, may be concentrated in the sample by means of immunoaffinity capture or other suitable technique. The mass spectrometric method described herein enables the concurrent measurement of peptides representative of a plurality of targeted PTH variants in a single assay.

Abstract: Methods are provided for identifying biomarker proteins that exhibit differential expression in subjects with a first lung condition versus healthy subjects or subjects with a second lung condition. Also provided are compositions comprising these biomarker proteins and methods of using these biomarker proteins or panels thereof to diagnose, classify, and monitor various lung conditions. The methods and compositions provided herein may be used to diagnose or classify a subject as having lung cancer or a non-cancerous condition, and to distinguish between different types of cancer (e.g.

Abstract: Quantitation of analytes, including but not limited to peptides, polypeptides, and proteins, in mass spectrometry using a labeled peptide coupled to a reporter, and a universal reporter.

Abstract: Pharmaceutical compositions and their methods of use are provided, where the pharmaceutical compositions comprise an opioid prodrug that provides enzymatically-controlled release of an opioid, and an enzyme inhibitor that interacts with the enzyme(s) that mediates the enzymatically-controlled release of the opioid from the opioid prodrug so as to attenuate enzymatic cleavage of the opioid prodrug.

Abstract: Provided herein is technology relating to proteases and proteomics and particularly, but not exclusively, to compositions comprising OmpT, methods of using OmpT, and methods of manufacturing OmpT for proteomics.

Abstract: The present invention relates to a screening system for modulators of GPCRs. Further it relates to recombinant vector systems for the heterologous expression of heterodimeric G-protein coupled receptors (GPCRs) in eukaryotic host cells. Preferably the functional expression of engineered GPCRs for the perception of sweet and L-amino acid taste or more preferably the use of these receptors for the identification of functional ligands is also encompassed.

Abstract: Pharmaceutical compositions and their methods of use are provided, where the pharmaceutical compositions comprise a phenol-modified opioid prodrug that provides enzymatically-controlled release of a phenolic opioid, and an enzyme inhibitor that interacts with the enzyme(s) that mediates the enzymatically-controlled release of the phenolic opioid from the phenol-modified opioid prodrug so as to modify enzymatic cleavage of the phenol-modified opioid prodrug.

Abstract: The present disclosure provides pharmaceutical compositions, and their methods of use, where the pharmaceutical compositions comprise a prodrug that provides enzymatically-controlled release of a drug and an enzyme inhibitor that interacts with the enzyme(s) that mediates the enzymatically-controlled release of the drug from the prodrug so as to attenuate enzymatic cleavage of the prodrug. The disclosure provides pharmaceutical compositions which comprise an enzyme inhibitor and a prodrug that contains an enzyme-cleavable moiety that, when cleaved, facilitates release of the drug.

Abstract: Provided herein are methods useful in detecting degradative enzymes in bodily fluid samples.

Abstract: The present invention relates to a novel cell based sensor useful for drug discovery that comprises a cell line with professional regulated exocytosis of secretory granules transfected with a protease as a reporter polypeptide stored in the regulated secretory granules of the cell line with professional regulated exocytosis and having either an endogenous or a heterologous molecule as a modulator of regulated secretory granules exocytosis, such said granule stored protease reporter having at least: a high resistance to conditions already present inside the granules such as low pH and proteolysis by other proteases; enzymatic activity after exocytosis; a highly specific cleavage sequence; a very low level of secretion under unstimulated or basal conditions; and a high signal to background activity in a media compatible with cell culture viability and granule exocytosis for a high throughput robust and sensitive detection.

Abstract: The present disclosure includes the use of an R—(X)n-Fluo-Rep-(Gly)m-Z—NH2 peptide for detecting and assaying the activity of the major surface protease of Legionella pneumophilia. This disclosure also includes a method for detecting and quantifying Legionella pneumophilia in any medium likely to be contaminated with the bacterium, for example a domestic hot water supply and cooling tower circuits.

Abstract: Embodiments of the present disclosure provide for enzyme sensors, protease sensors, methods for producing and using the enzyme and protease sensors, methods of detecting and/or measuring protease activity, methods for characterizing protease cellular activity, fusion proteins, polynucleotides, and vectors corresponding to the enzyme and protease sensors, kits, and the like.

Abstract: Provided herein are methods for developing selected reaction monitoring mass spectrometry (LC-SRM-MS) assays.

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 describes a method for assaying HCV NS3 protease activity using an NS3•4A protease molecule. The invention also provides a method for screening and identifying modulators of NS3 protease.

Abstract: The present invention provides for a method of characterizing and classifying a sample of peptide or polypeptide mixtures or a biomolecule comprising a polypeptide component by using mass spectrometry and statistic methods for analyzing the mass spectrometry results.

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

Abstract: Disclosed herein are novel methods, assays and kits useful for the diagnosis and monitoring of subjects with mucopolysaccharidoses (MPS), The methods, assays and kits are particularly useful for detecting the presence of one or more glycosaminoglycans which correlate to MPS and its severity in a variety of biological samples.

Abstract: An enzyme detection product (1) for detecting the presence of an enzyme in a sample. The product (1) comprises: a reaction zone (16) for receiving the sample; a visualization zone (10) for presenting a signal in response to the detection of the activity of the enzyme; and a membrane (11). The membrane (11) is interposable between the reaction zone (16) and the visualization zone (10) and prevents passage from the reaction zone (16) to the visualization zone (10) the components having a size greater than a threshold size. The reaction zone (16) comprises a reactant capable of reacting with the enzyme in order to generate a reaction product having a size less than a threshold size.

Abstract: This invention pertains to methods, mixtures, kits and compositions pertaining to analyte determination by mass spectrometry using labeling reagents that comprise a nucleophilic reactive group that reacts with a functional group of an analyte to produce a labeled analyte. The labeling reagents can be used as isobaric sets, mass differential labeling sets or in a combination of isobaric and mass differential labeling sets.

Abstract: Biomarkers that can be used for the diagnosis and prognosis of multiple sclerosis in pediatric patients presenting with clinically isolated syndrome or acquired demyelination syndrome are described.

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

Abstract: The present invention provides a compound that can utilize hydrogen isotope and, at the same time, can quantify multiplexed samples at one time, as well as decreasing the cost for synthesis of the labeling agent. In addition, the present invention provides a novel method for quantitatively analyzing protein and peptide analytes having different quantities form each other using the labeling agent, wherein y-type fragment ions having a high mass which comprises the analyte remained after coupling the labeling agent with the analyte and then removing a part of the labeling agent through tandem mass spectrometry are utilized to conduct the quantitative analysis.

Abstract: The present invention provides methods for identifying tumor-specific polypeptides, polypeptides so identified, and methods for their use.

Abstract: Supramolecular assemblies for delivering active agents to cancerous or precancerous tissues in a subject are provided. These supramolecular assemblies are also useful in assays for detecting and imaging of cancerous and precancerous cells. The assemblies are protease-sensitive and comprise a peptide linkage containing a protease consensus sequence. The assemblies can be selectively targeted to cancerous tissue where the protease enzymes degrade the peptide linkage thereby releasing the active agents which were physically or mechanically contained in or retained by the supramolecular assembly.

Abstract: An antibody comprising an antigen recognition region which comprises CDR amino acid sequences set forth in SEQ ID NO: 7, 8, 9, 10, 11 and 12.

Abstract: Biomarkers for pre-Diabetes, Diabetes and/or a Diabetes related conditions, and methods of their use, including the biomarkers in Tables 1 and 2 such as peroxiredoxin-2, complement C1q subcomponent subunit B, sulfhydryl oxidase 1 and apolipoprotein A-IV.

Abstract: Methods and compositions for identification of candidate antigen-specific variable regions as well as generation of antibodies or antigen-binding fragments that could have desired antigen specificity are provided. For example, in certain aspects, methods for determining amino acid sequences of serum antibody CDR3 and abundancy levels are described. In some aspects, methods for determining nucleic acid sequences of antibody variable region sequences and the frequency thereof in biological samples are provided. Furthermore, the invention provides methods for identification and generation of antibodies or antigen-binding fragments that comprise highly-represented CDR domains.

Abstract: It is to provide a method for measuring glycated hemoglobin in a hemoglobin-containing sample, comprising reacting the hemoglobin-containing sample with a proteolytic enzyme in the presence of a surfactant, and then reacting the obtained reaction product with fructosyl peptide oxidase, wherein at least one of the former reaction and the latter reaction is performed in the presence of an isothiazolinone derivative; and measuring the generated hydrogen peroxide. The present invention provides a method for accurately and highly sensitively measuring glycated hemoglobin in a hemoglobin-containing sample without being influenced by hemoglobin.

Abstract: A method for assessing the effect of a test compound on LRRK2 in a cell-based system, the method comprising the steps of a) assessing the effect of exposing the cell-based system comprising LRRK2 to the test compound on the phosphorylation state of Ser910 and/or Ser935 of the LRRK2; and/or b) assessing the effect of exposing the cell-based system comprising LRRK2 to the test compound on the binding of the LRRK2 to a 14-3-3 polypeptide. The method may comprise or further comprise the step of assessing the effect of exposing the cell-based system comprising LRRK2 to the test compound on the subcellular location of LRRK2. The method is considered to be useful in assessing the effect of putative LRRK2 inhibitors in cell based systems, including in vivo systems.

Abstract: The present disclosure provides a method of suppressing oomycete infection, such as a Phytophthora infection, or triggering programmed cell death in Solanaceae plants comprising administering at least one modulator, wherein the at least one modulator modulates at least one of the genes listed in Table 1 or variants or homologs thereof. The present disclosure also provides compositions useful in suppressing oomycete infection, such as Phytophthora infection and triggering programmed cell death and screening assays for identifying substances useful in suppressing oomycete infection, such as Phytophthora infection and triggering programmed cell death.

Abstract: Novel fluorescent phycobiliprotein fusion proteins and methods of use are described. The novel phycobiliproteins can be produced in a cell comprising two or more heterodimeric lyases, an apoprotein and a bilin reductase, which components react to form the phycobiliprotein fusion protein. Also described are phycobiliprotein based transcription reporter cells and assays, which cells conditionally express a heterologous, fluorescent, phycobiliprotein domain even in anoxic conditions.

Abstract: The invention relates to a method of diagnosing or monitoring major depressive disorder using MMP-3 as a biomarker.

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

Abstract: Devices and methods use an integrated microfluidic system that has the capability of realizing a wide range of accurate dilutions in a logarithmic way through semi-direct dilution of samples inside a chip. The device for dose response analysis is able to contain a first fluid source on a microfluidic chip, wherein the first fluid source comprises a drug, a second fluid source on the microfluidic chip, a mixing area on the microfluidic chip fluidically coupling with the first and the second fluidic source, and a detection area coupling with the mixing area for drug information detection using a detection system.