Abstract: The current disclosure provides for specific peptides from the Insulin Receptor Substrate 1 (IRS1) protein and the derived ionization characteristics of those peptides that are advantageous for quantifying IRS1 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. IRS1 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 IRS1 peptides include those bearing phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.

Abstract: A novel enhanced surface area conico-cylindrical flask (ES-CCF) providing increased surface area by virtue of its' inner arrangement and useful in routine small-scale studies of bioactives production by any biofilm-forming marine as well as terrestrial microorganisms. Compared to corresponding Erlenmeyer flask of similar volume the ES-CCF provides more than 80% additional surface for biofilm attachment and growth. The ES-CCF does not require steam sterilization and is durable as the device is constructed of polymethyl methacrylate or any other such hydrophobic material and offers possibility of altering the nature of the growth surface (hydrophilic and hydrophobic). The ES-CCF also provides external aeration like a bioreactor, thus increasing the versatility of applications. Further, the device can be operated as a cylindrical flask, that is without the inner arrangement.

Abstract: A method is provided of diagnosing and monitoring acute renal injury leading to acute renal failure in a human or mammalian subject by determining the ratio of the concentration of neutrophil gelatinase-associated lipocalin (NGAL) in urine to that in plasma or serum.

Abstract: In accordance with the present invention, it has been discovered that compounds which modulate the ?-secretase enzyme to make more of the shorter, less toxic and less aggregation-prone A? peptides (such as A?37 and A?38), while making less of the longer and more toxic and aggregation-prone AB peptides (such as AB40 and AB42) are useful as gamma-secretase modulators. In addition, these GSM compounds have further been discovered to have the selective property of modulating the formation of various AB peptides, while not inhibiting the overall activity of the ?-secretase enzyme. Thus, such compounds do not impede other critical functions of the ?-secretase enzyme, such as generating fragments from Notch that appear to control gene expression and cell differentiation. Therefore, in accordance with the present invention, there are provided screening assays useful for determining whether test compounds have GSM activity; accordingly, invention assays facilitate the identification of new gamma-secretase modulators.

Abstract: This invention relates to a probe reagent comprising, in order from the N-terminus to the C-terminus, the amino acid sequences of a fluorescent protein I, a peptide capable of terminating protein degradation (i.e., a degradation-terminating peptide), a spacer peptide, a fluorescent protein II, and a protein to be degraded, wherein the protein to be degraded is a protein degraded by the ubiquitin-proteasome system, and the probe reagent is degraded from the C-terminus, but that the degradation of the probe reagent is terminated at the degradation-terminating peptide, a nucleic acid encoding the probe reagent, and use of the probe reagent or the nucleic acid.

Abstract: The disclosure includes assays and methods for screening for risk of Down syndrome and/or trisomy 21 in a fetus. The assays and methods comprise determining the level of at least one biomarker selected from mucin 13 (MUC13), bile salt-activated lipase (CEL), dipeptidyl peptidase 4 (DPP4), carboxypeptidase A1 (CPA1), amyloid precursor protein (APP) and tenascin-C (TNC-C) polypeptides in a test biological sample from a pregnant subject, wherein a decreased level of MUC13, CEL, DPP4, and/or CPA1 polypeptide and/or an increased level of APP and/or TNC-C polypeptide in the test biological sample compared to a corresponding reference biomarker polypeptide level indicates an increased risk of Down syndrome or trisomy 21 in the fetus. The disclosure also includes assays, compositions, immunoassays, and kits for performing the methods disclosed herein.

Abstract: The present invention provides an approach for the simultaneous determination of the activation states of a plurality of proteins in single cells. This approach permits the rapid detection of heterogeneity in a complex cell population based on activation states, and the identification of cellular subsets that exhibit correlated changes in activation within the cell population. Moreover, this approach allows the correlation of cellular activities or properties. In addition, the use of potentiators of cellular activation allows for characterization of such pathways and cell populations.

Abstract: A method for identifying a protease secretion deficient strain of a microorganism involves producing a mutant of the microorganism, followed by adding the mutant to gel-filled wells of a microtitration plate, incubating the mutant in the gel-filled wells under conditions call sing the mutant to secrete proteins, separating the mutant from the gel, and measuring activity of a secretion protease of the microorganism in the gel, wherein either (i) the gel is a substrate for the secretion protease or (ii) the gel contains a substrate for the secretion protease.

Abstract: A reactive mass label for labelling a biological molecule for detection by mass spectrometry, which label comprises a reactive functionality for labelling thiol groups or carbonyl groups. Also provided is a reactive mass label for labelling a biological molecule for detection by mass spectrometry, wherein the mass label comprises the following structure: X-L-M-S-Re wherein X is a mass marker moiety, L is a cleavable linker, M is a mass normalization moiety, S is a mass series modifying group comprising the following group: wherein J is C?O, K is NH, and n is 2 or J and K are both CH2 and n is 1, and wherein m is at least 1; and Re is a reactive functionality for attaching the mass label to a biological molecule.

Abstract: The present invention relates to methods of diagnosing, monitoring, and assessing treatment effects for neurological and neurodegenerative diseases and disorders, such as Alzheimer's Disease, early in the course of clinical disease or prior to the onset of brain damage and clinical symptoms. Methods of measuring the in vivo metabolism of biomolecules produced in the CNS in a subject are provided.

Abstract: The present invention relates to development, validation and application of new sets of biomarkers for diagnosis of Alzheimer's disease (AD) and related disorders including early diagnosis of MCI and early prodrome of AD, identification of disease sub types, prediction of their response to disease management procedures, drugs and their combinations and for monitoring response for these treatment, including validation of biomarkers for clinical trials.

Abstract: Methods of identifying polypeptides have been developed using a de novo sequencing technique. Methods use photodissociation and low-energy fragmentation and the spectra of peptide ions obtained therefrom, such as obtained by post-source decay (PSD), have been developed. The methods include photodissociation and the spectra therefrom obtainable from treating ions with predetermined wavelengths of radiation in the vacuum ultraviolet range of the electromagnetic spectrum. The confidence of amino acid assignments based on x-type ions is evaluated by observing complementary y-, v- and w-type ions that provide additional constraints to sequence identification.

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

Abstract: A method of identifying and classifying non-small-cell lung carcinoma in a biological sample includes a first test wherein the expression level of at least one biomarker is measured in a sample, the at least one=biomarker is selected from a first group consisting of chaperonin, 2,3-bisphosphoglycerate mutase, thymidine phosphorylase, and minichromosome maintenance deficient protein 5, and comparing the measured expression levels against a normal expression level, wherein a significant difference diagnoses or aids in the diagnosis of non-small cell lung carcinoma; and a second test wherein the expression level of at least one biomarker is measured in the sample, the at least one biomarker is selected from a second group consisting of selenium binding protein and Napsin A, and comparing the measured expression level against a normal expression level, wherein a significant difference confirms or aids in confirmation of Non-Small Cell Carcinoma.

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: This invention provides methods of measuring the viability of cultured cells by detecting one or more cell death-stable proteins or enzyme activities. Methods provided by the invention correlate viability to relative levels of enzyme activity in cell-containing and non-cell-containing fractions of a cell culture.

Abstract: An object of the present invention is to provide a biosensor and a method for immobilizing a physiologically active substance, by which preconcentration effects can be obtained at a pH that is equivalent to or higher than the isoelectric point of the physiologically active substance and the physiologically active substance can be covalently bound to the surface. The present invention provides a biosensor comprising a solid substrate to which a polymer having a primary or secondary amino group is bound, by which a physiologically active substance can be chemically immobilized following preconcentration of the substance at a pH that is equivalent to or higher than the isoelectric point of the substance.

Abstract: A method of identifying a biofilm that includes non-typeable Haemophilus influenza (NTHi) including a step of screening a sample for the presence of one or more biofilm-specific proteins that are expressed by NTHi. In some cases, an NTHi biofilm-related disease in a subject is diagnosed. Also disclosed are protein microarrays for screening biofilm-specific proteins in a sample, formulations comprising one or more biofilm-specific proteins or fragments thereof, and methods for inducing an immune response in a patient against a biofilm-related infection.

Abstract: The present invention relates to a novel enzyme composition comprising a prolyl protease and tripeptidyl proteases having unique catalytic properties. The present invention further relates to methods for producing the enzyme composition as well as a pharmaceutical composition and a food supplement containing the enzyme composition and its use in the degradation of polypeptides.

Abstract: The present invention relates, e.g., to a method for pre-processing a sample for mass spectral analysis, comprising cleaving proteins in the sample to peptides and immunodepleting highly abundant and/or well-ionizing and/or proteotypic peptides from the sample. Also described are methods for identifying well-ionizing peptides for use in this and other methods; analytic (diagnostic) methods using antibodies against highly ionizable peptides from a protein target of interest; and compositions, kits and devices comprising antibodies of the invention.

Abstract: A method for analyzing secretome, a biomarker for lung cancer metastasis, and a siRNA compound for inhibiting lung cancer metastasis are disclosed. The method for analyzing secretome of the present invention comprises the following steps: (A) collecting proteome secreted from a cell; (B) providing a purification gel, wherein the purification gel comprises a low-density layer, and a high-density layer, and the low-density layer is stacked on the high-density layer; (C) adding the proteome on the low-density layer, and separating the proteome through the low-density layer and the high-density layer of the purification gel; (D) collecting the separated proteome on the interface between the low-density layer and high-density layer, and tagging the separated proteome with a reagent after digestion; and (E) analyzing the separated proteome tagged with the reagent, and comparing an analysis result with a proteomic database.

Abstract: The disclosure relates to the development of improved methods for quantifying antigen in a vaccine composition in the absence of available antigen standards. More specifically, the disclosure provides fast and robust methods of separating antigens from vaccine compositions, comprising the steps of solubilizing antigen without detergent and without alkylation, using acidification to prevent antigen subtypes from binding again, isolating antigen subtypes with chromatography, and quantifying the eluted antigen with amino acid analysis. The methods of the disclosure are applicable for use with a variety of antigens, thereby providing an improved method in the art of vaccine manufacturing to date.

Abstract: At least one embodiment of a stabilizing system includes a stabilizing agent present in an amount or concentration sufficient to completely or substantially prevent or reduce degradation or inactivation of a glycosylated hemoglobin (HbA1c) in a body fluid and a detection agent capable of detecting the HbA1c.

Abstract: The present invention relates to an analytical method for quantitation of selected multiple recombinant proteins in a complex matrix such as recombinant polyclonal antibodies in serum or recombinant polyclonal antibodies expressed in a culture supernatant.

Abstract: The present invention relates to a method for characterizing at least one microorganism from a sample, said method including identifying said at least one microorganism and determining the properties of typing, potential resistance to at least one antimicrobial, and virulence factor, characterized in that determining the properties of typing, resistance to at least one antimicrobial, and virulence factor for said at least one microorganism is implemented by means of mass spectrometry through the use of proteins, peptides and/or metabolites as markers of said properties of typing, resistance to at least one antimicrobial, and virulence factor.

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: The invention generally relates to methods for quantifying an amount of enzyme molecules. Systems and methods of the invention are provided for measuring an amount of target by forming a plurality of fluid partitions, a subset of which include the target, performing an enzyme-catalyzed reaction in the subset, and detecting the number of partitions in the subset. The amount of target can be determined based on the detected number.

Abstract: The present invention provides ZPA polypeptides, antibodies, nucleic acid molecules, antagonists, agonists, potentiators and compositions relating to ZPA polypeptides, and methods of identifying, making and using the same, that are useful for treating and preventing diseases and for medical diagnosis and research. The present invention also provides model systems for the intrinsic apoptotic pathway.

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: The present invention relates to a method that allows comprehensive quantitation of one or a plurality biomolecules, including the entire complement of biomolecules in a sample by comparing their quantity to the quantity of reference biomolecules in a standard mixture obtained via extraction from at least two different cell populations. The invention further relates to said standard mixture itself, its preparation and use.

Abstract: The invention relates to a method for identifying and quantifying by mass spectrometry at least one target molecule in a sample, comprising the following steps: a) depositing the sample to be analyzed on a support; b) analyzing the sample by mass spectrometry, so as to obtain the mass spectrum of the target molecule in said sample; c) weighting a signal associated with the mass spectrum of the target molecule in said sample by a extinction coefficient (TEC) specific to the target molecule and to the sample; and d) using the weighted signal of the target molecule to determine the quantity of target molecule in the sample.

Abstract: The present invention relates to a method for detecting a wound infection comprising the steps of: contacting a sample obtained from a wound with at least two substrates for at least two enzymes selected from the group consisting of lysozyme, elastase, cathepsin G and myeloperoxidase, and detecting a wound infection when a conversion of the at least two substrates with said at least two enzymes are determined.

Abstract: The present invention relates to a method for diagnosing cancer using information on the aberrant glycosylation of a glycoprotein. More precisely, the present invention relates to a cancer diagnosis peptide marker, which is screened by: a step of separating, using a lectin, a glycoprotein which is aberrantly glycosylated in accordance with the occurrence of cancer; and a step of selecting a hydrolyzed peptide marker derived from the aberrantly glycosylated glycoprotein by observing the quantitative changes in the separated glycoprotein. The present invention also relates to a method for diagnosing cancer using the peptide marker as an agent.

Abstract: The present invention provides compositions and methods useful for regulating fertilization and for use as a contraceptive based on the discovery herein of an oocyte specific protein, SAS1R (Sperm Acrosomal SLLP1 Receptor), which is a sperm protein receptor. Six SAS1R variants, including the full length SAS1R, were identified. mSLLP1 and SAS1R co-localized to oocytes and to acrosomes of acrosome-reacted sperm. Interactions between mSLLP1 and SAS1R were demonstrated by far-western analysis, in a yeast two-hybrid system under stringent selection conditions, and by immunoprecipitation of SAS1R by anti-mSLLP1 as well as the converse. Purified recombinant SAS1R was found to have protease activity, to inhibit fertilization in-vitro, and to induce an immune response in females.

Abstract: Methods for detecting proteases by contacting a sample to be assayed with a substrate at least partially coated with a film of a synthetic polymeric matrix, and measuring a signal output of the substrate is provided herein.

Abstract: A biomarker is provided for an allergic disease caused by an allergic reaction that is caused not exclusively by histamine release, such as pruritus, and use of the same. Use of Granzyme A as a biomarker makes it possible to provide an indication for chronic itching skin disease, for which existing antiallergic drugs have little effect, and easily and adequately allow diagnosis of the disease. It is possible to, for example, make a diagnosis of an allergic disease with an IV type allergy-like reaction not depending on the antigen-antibody reaction system. Screening with the use of Granzyme A enables the development of novel remedies for allergic diseases. Moreover, a drug capable of specifically controlling the action of a granzyme enables treatment of allergic disease with little side effect.

Abstract: Provided are methods of determining whether a cell in a tissue site is viable or nonviable. Also provided are methods of debriding tissue from a tissue site. Further provided are kits comprising a compound that distinguishes between viable and nonviable cells and instructions for using the compound on a tissue site. Additionally, the use of a compound that distinguishes between viable and nonviable cells is provided, where the use is to determine whether a cell in a tissue site is viable or nonviable. Also provided is a use of a compound that distinguishes between viable and nonviable cells, where the use is for the manufacture of the above-described kit.

Abstract: The application discloses MCAM as a new biomarker for fluid homeostatic imbalance; methods for predicting, diagnosing, prognosticating and/or monitoring fluid homeostatic imbalance based on measuring said biomarker; and kits and devices for measuring said biomarker and/or performing said methods.

Abstract: Provided are a method of stabilizing a leuco dye storable as a liquid for a long time, a method of reducing nonspecific color development thereof at a time of a color development reaction, and a stable liquid reagent composition using the methods. The inventors of the present invention found that coexistence of the leuco dye with a specific reducing agent resulted in suppression of self color development and its remarkably improved stability in a solution, and that when a color development reaction of the leuco dye with hydrogen peroxide was performed, coexistence of the leuco dye, in a reaction solution, with another dye which had an absorption spectrum not influencing a measurement wavelength of the leuco dye and did not react with hydrogen peroxide suppressed nonspecific color development and lowered a reagent blank value, which was applied to an analytical reagent.

Abstract: A method of utilizing the chymotrypsin level of an individual as a measure of the success of secretin, other neuropeptides, and peptides or digestive enzyme administration to such individuals, and in particular, as a prognosticative of potential secretin, other neuropeptides, peptides, and digestive enzyme administration for persons having ADD, ADHD, Autism and other PDD related disorders.

Abstract: A method of providing a patient with controlled release of ketone-containing opioid using a prodrug capable, upon enzymatic activation and intramolecular cyclization, of releasing the ketone-containing opioid is disclosed. The disclosure also provides such prodrug compounds and pharmaceutical compositions comprising such compounds. Such pharmaceutical compositions can optionally include an enzyme inhibitor that interacts with the enzyme(s) to mediate the enzymatically-controlled release of the ketone-containing opioid from the prodrug so as to modify enzymatic cleavage of the prodrug. Also included are methods to use such compounds and pharmaceutical compositions.

Abstract: Apparatus and methods to perform hydrogen/deuterium exchange using semipermeable membranes are described. The system has two channels separated by a semipermeable membrane. One channel comprises a flow carrying the analyte of interest, and the second channel comprises a solution comprising a deuterated solvent (e.g. deuterium oxide). The system does not require an external electric field gradient across the membrane to perform the hydrogen-deuterium exchange procedure. The present invention facilitates sample and reagent handling as well as simplifies manufacture of devices and/or instrumentation related to deuterium exchange. Further described is a chemical analysation device for analysing chemical compositions and/or compounds, and a method for analysing chemical compounds and a computer program product for inducing a computer to perform steps in the method.

Abstract: A method of screening for compounds that enhance or depress contractile function, based on measuring the formation of heterodimers of contractile fibers (e.g. Tm and actin, myosin heavy and myosin light chains), for example through disulfide bond formation. Diagnostic and prognostic methods and kits are also provided.

Abstract: This disclosure is directed to methods and compositions to inhibit MASP protein activity using small molecule inhibitors. In one aspect, the disclosure is directed to methods for identifying inhibitors of MASP protein activity, including methods of screening capable of inhibiting MASP protein activity.

Abstract: The disclosure includes a method of screening for, diagnosing or detecting non-small cell lung carcinoma or an increased likelihood of developing non-small cell lung carcinoma in a subject. The method comprises: (a) determining the level of at least one biomarker in a test sample from the subject wherein the at least one biomarker is selected from the biomarkers set out in Table 2, 4A, 4B, 6 and/or 7; and (b) comparing the level of the at least one biomarker in the test sample with a control; wherein detecting a difference in the level of the at least one biomarker in the test sample compared to the control is indicative of whether the subject has or does not have non-small cell lung carcinoma or an increased likelihood of developing non-small cell lung carcinoma.

Abstract: Elevated levels of cathepsin E (catE) are demonstrated to be diagnostic of intestinal forms of cancer, such as colorectal cancer. Elevated levels of cathepsin E (catE, monomeric forms) are demonstrated to be detectable in the urine of animals having colorectal cancer, and a diagnostic/screening method for identifying and/or detecting colorectal cancer in an animal from a urine sample is provided. Specific tissue immunohistochemcial staining for catE (monomeric forms) in dysplastic tissue is also disclosed, and is shown to correlate with the level of dysplastic lesion severity. Hence, a method for identifying and determining the level of dysplastic lesion severity is provided. Cathepsin E mRNA transcription and expression levels are also demonstrated to be upregulated in dysplastic tissue, relative to non-dysplastic tissue. Hence, a method for transcriptionally profiling an animal to monitor the progression of colorectal disease is provided.

Abstract: A method of detecting hepatocellular carcinoma includes using an isolated protein including an amino acid sequence represented by SEQ ID NO: 1.

Abstract: A method for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each include portions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS-provided intensity data. A set of precursor-ions that has substantially similar intensity ratios in both sample portions is determined to be associated with the same polypeptide.

Abstract: Methods for detecting BoNT/A activity in a sample, methods for screening molecules able to compete with BoNT/A receptor binding, methods for reducing BoNT/A activity in a human and methods of marketing a neurotoxin capable of selectively binding to FGFR3 to a governmental or regional regulatory authority.

Abstract: The present invention provides a method of pretreating a sample containing a glycated amine as an analyte, thereby enabling highly reliable measurement of a glycated amine. A glycated amino acid in the sample is degraded by causing a fructosyl amino acid oxidase (FAOD) to act thereon, and thereafter, a FAOD further is caused to act on the glycated amine as the analyte in the sample to cause a redox reaction. The amount of the glycated amine is determined by measuring the redox reaction. The substrate specificity of the FAOD caused to act on the glycated amino acid may be either the same as or different from that of the FAOD caused to act on the glycated amine. When using the same FAOD, a FAOD is caused to act on the glycated amino acid to degrade it, and thereafter, the sample is treated with a protease to inactivate the FAOD and also to degrade the glycated amine.