Abstract: The present invention relates to a method aiding in the assessment of cancer. It discloses the use of the human fibroblast activation protein (FAP/seprase) as a universal marker of different cancer types. Seprase aids in the assessment of pulmonary or lung cancer (LC) or of colon cancer, e.g., of non-small cell lung carcinoma (NSCLC) or colorectal cancer (CRC), but also likely of other specific types of cancer. Such specific cancer types are, e.g., esophagus, head and neck cancer, stomach cancer, bile duct cancer, pancreas cancer, kidney cancer, cervix cancer, ovary cancer, breast cancer, bladder cancer, endometrium cancer or prostate cancer. Furthermore, it especially relates to a method for assessing cancer from a liquid sample, derived from an individual by measuring seprase in said sample. Measurement of seprase can, e.g., be used in the early detection of cancer or in the surveillance of patients who undergo surgery.

Abstract: Embodiments described herein relate to compositions, methods and uses for alpha-1 antitrypsin (AAT) or derivatives or analogs or peptides or mutants thereof for treating a subject exposed to radiation. In certain embodiments, AAT or derivatives thereof or analogs thereof can be used to modulate adverse effects of radiation therapy on subjects undergoing treatment for cancer. In other embodiments, compositions disclosed herein can be used for treating a subject having been exposed to non-therapeutic or accidental radiation. Some embodiments reported herein concern compositions and methods for enhancing radiotherapy. Certain embodiments relate to methods and compositions for preventing or reducing radiation exposure-induced cellular damage in a subject.

Abstract: The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins that are particularly advantageous for quantifying the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Abstract: Methods for assessing the condition of keratinized structures, including hair, in particular methods to determine the condition of keratinized structures in relation to suitability for analysis of analytes of interest in a test sample, are presented. The methods comprise contacting the keratinized structure with a non-proteolytic reducing agent and an optional proteolytic agent. The methods further include inspection of the hair sample, or measurement of free protein eluted from the keratinized structure, after reduction and optional proteolysis to determine condition prior to analyte identification and quantitation by known techniques such as immunoassays.

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: The present invention provides a method for screening a therapeutic and/or prophylactic agent for Alzheimer's disease using at least one index selected from the group consisting of the levels of A? oligomers, BiP, cleaved caspase 4, PRDX4 and ROS in nerve cells or the like whose differentiation has been induced from iPS cells derived from somatic cells of a patient with Alzheimer's disease.

Abstract: Methods for liquid-liquid extraction, as can be effected using polymeric reverse micelles, such methods as can be used in conjunction with various mass spectrometric techniques.

Abstract: The present application relates to extracellular vesicles (EVs) derived from gram-positive bacteria. In detail, the present application provides animal models of disease using extracellular vesicles derived from gram-positive bacteria, provides a method for screening an active candidate substance which is capable of preventing or treating diseases through the animal models of disease, provides vaccines for preventing or treating diseases caused by extracellular vesicles derived from gram-positive bacteria, and provides a method for diagnosing the causative factors of diseases caused by gram-positive bacteria using extracellular vesicles.

Abstract: Methods and systems for using fibrosis biomarkers associated with a prolonged period of physical inactivity are provided. Also provided is a method of reducing the effect of prolonged physical inactivity on the development of fibrosis in a subject who is experiencing or is expected to experience prolonged physical inactivity in the near future by administering a therapeutically effective amount of a leucine metabolite (e.g., ?-hydroxy-?-methylbutyric acid (HMB)) to the subject.

Abstract: Sirt5, a mitochondrial Sirtuin, has been identified herein as an efficient demalonylase and desuccinylase. Disclosed herein are assays to identify Sirt5 modulators based on this robust enzymatic activity. Sirt5-specific modulators can be used study the biological function of Sirt5 and to target Sirt5 activities in treating human diseases.

Abstract: A novel reagent for clarification of an emulsion containing a salt and first and second surfactants is used in a method of clarifying emulsions which may contain inorganic, organic or biological particles to be measured. The reagent may be proved as kit of parts for in situ preparation thereof.

Abstract: The invention provides methods and compositions for simultaneously detecting the activation state of a plurality of proteins in single cells using flow cytometry. The invention further provides methods and compositions of screening for bioactive agents capable of coordinately modulating the activity of a plurality of proteins in single cells. The methods and compositions can be used to determine the protein activation profile of a cell for predicting or diagnosing a disease state, and for monitoring treatment of a disease state.

Abstract: A biological tissue processing substrate for fixing proteins in a biological tissue or degradation products of the proteins, the substrate comprising: a porous body that forms a contact surface with the biological tissue, the porous body holding in pores an enzyme for obtaining the proteins or the degradation products of the proteins from the biological tissue, wherein the proteins or the degradation products obtained by the action of the enzyme are brought into contact with a member consisting of a metal.

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: Providing is a new enzyme assay method for enzymes having a water-insoluble or substantially water-insoluble substrate. In the method for measuring enzymatic activity, a prescribed amount of an enzyme is disposed on a part of the surface of a gel comprising dispersoids, at least some of which are the substrate of the enzyme. Recesses formed in the surface of the gel by the action of the enzyme are measured, and the enzyme activity is calculated on the basis of the measurement results and the amount of the enzyme. The measurement of the recesses formed in the surface of the gel is performed using a method for measuring the shape and the volume of the recesses, a method for measuring changes in the optical transmittance of the gel due to the formation of the recesses, or a method for measuring changes in the optical reflectance of the gel surface due to the formation of the recesses.

Abstract: Disclosed herein are methods and compositions for treating autism. Disclosed herein are methods and compositions for treating an autism spectrum disorder.

Abstract: Disclosed is a method which enables semiquantitative or quantitative determination of the ratio between cysteine and formylglycine residues in a protein. The method includes (a) a step of labeling the protein (i) with a halogen-substituted carboxylic acid, (ii) with a halogen-substituted carboxylic acid amide, and (iii) with a halogen-substituted carboxylic acid and then with hydrazine, or with a halogen-substituted carboxylic acid and then by oximation, (b) a step of digesting each labeled protein to provide a corresponding mixture of peptide fragments, (c) a step of subjecting each mixture to reverse phase chromatography to separate the peptide fragments from each other to produce a chromatogram, (d) a step of comparing the produced chromatograms with each other to identify the peak corresponding to the peptide fragment that contained a cysteine residue and the peak corresponding to the peptide fragment that contained a formylglycine residue.

Abstract: Aspects of the disclosure include methods for analyzing an analyte composition by mass spectrometry employing a macroporous metal organic polymer matrix. In practicing methods according to certain embodiments an analyte composition is applied to a macroporous metal organic polymer matrix, a voltage is applied to the macroporous metal organic polymer matrix sufficient to produce and expel analyte ions from the macroporous metal organic polymer matrix and the analyte ions are analyzed by mass spectrometry. In other embodiments, a composition having biological macromolecules is applied onto a surface-modified macroporous metal organic polymer matrix and analytes produced by reaction (e.g., enzymatic cleavage of the biological macromolecules) at or near the surface of the macroporous metal organic polymer matrix are measured by mass spectrometry.

Abstract: The present invention provides small molecules useful to affect cancer cells, along with related methods. The present compounds, formulations, kits and methods are useful for a variety of research, diagnostic and therapeutic purposes. STAT3 inhibitors, particularly LLL12, are disclosed. The STAT3 inhibitors are useful to treat breast cancer in general and breast cancer initiating cells in particular.

Abstract: Stromal stem cells are prospectively isolated from human bone marrow then expanded into clonal populations and cultured and used, the isolation being on the basis of expression of a cell surface marker, wherein the cell surface marker binds an antibody and wherein said antibody cross reacts with a cell surface marker found on mouse stromal stem cells or rat stromal stem cells, and optionally also on a cell of at least one other mammalian species selected from mouse, rat, horse, rabbit and pig cells. Useful stromal stem cell populations are positive for SDC2.

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: 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 relates to a method for measuring the activity of enzymes in a sample which contains at least one enzyme and at least one enzyme inhibitor corresponding to said enzyme, whereby after de-inhibition the activity of the released enzyme is measured in such a way that a substrate is added to the sample and the time course of the concentration of at least one reaction product (cleavage product) is recorded and the enzyme specific substrate has a fluorogenic part which is cleaved in the enzymatic reaction and the fluorescence (measuring parameter) of which can be detected in a wavelength range where the measuring parameter can be assigned unambiguously to the enzyme activity to be measured, whereby the de-inhibition is carried out by immersing a rigid carrier, to which the inhibitor binding substance is bound, into the sample. The present invention relates also to a corresponding device for measuring the activity on enzymes in a sample.

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 carbapenem, and said resistance markers are proteins or peptides. Preferably, said proteins or peptides are proteins from said microorganism.

Abstract: Method for the determination of the renal function wherein the amount of at least one agrin fragment derived by neurotrypsin cleavage of agrin is measured in a sample taken from a patient and the measured amount of the agrin-fragment in the sample is used as indicator for renal function.

Abstract: The purpose of the present invention is to provide a method for screening anticancer drugs that use novel treatment mechanisms, and an anticancer drug that induces cell death and uses a substance that increases the activity of granzyme M as an active ingredient. This method for screening anticancer drugs comprises: a step for administering test substances to cancer cells; a step for detecting the activity of granzyme M in which cancer cells are expressed, and selecting test substances for which an increase in activity has been verified; and/or a step for detecting the presence or absence of cancer cell death induced by the activation of granzyme M in which cancer cells are expressed, and selecting test substances for which cell death has been verified.

Abstract: The present invention provides methods 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. The present invention also provides 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., malignant versus benign, SCLC versus NSCLC).

Abstract: Materials and Methods for identifying and measuring pharmacodynamic biomarkers of neuropsychiatric disease (e.g., major depressive disorder), stratifying disease severity, and monitoring a subject's response to treatment are provided.

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: The present application relates to a composition including gut flora-derived extracellular vesicles, and to an animal disease model using same. In addition, the present application relates to a method for using the gut flora-derived extracellular vesicles to efficiently search for a candidate drug which may prevent or treat diseases that occur due to gut flora-derived extracellular vesicles, and to a vaccine which can efficiently prevent or treat infections caused by gut flora or diseases that occur due to gut flora-derived extracellular vesicles. Further, the development of diagnostic technology to discover, using the gut flora-derived extracellular vesicles of the present application, the etiology of diseases that occur due to gut flora-derived extracellular vesicles, can be achieved.

Abstract: The present invention relates to a chromogenic method for simultaneously determining the activity of multiple coagulation proteases or for simultaneously determining the inhibition of multiple coagulation proteases in a single test reaction. For this purpose, use is made of two chromogenic substrates which have different absorption maxima and whose color signals can be separated spectrally.

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

Abstract: A cell based assay for detection for protease activity is disclosed. In the assay a cell is engineered to express a protease substrate with at least one label, preferably on its C-terminus. Cleavage of the substrate by the protease that recognizes it results in a C-terminal fragment and a N-terminal fragment, where the fragment having the label is subject to ubiquitin proteasome degradation. The assay measures the disappearance of the label due to degradation of the fragment to which it is attached. A cell free assay is also described for detection of protease activity. In the cell free assay, the protease substrate is expressed in a solution that includes the elements of the ubiquitin proteasome pathway for degradation of the fragment. The assay measures the disappearance of the label attached to the fragment that results from cleavage by the protease.

Abstract: A method for measuring expression of autoregulatory molecules within living cells is provided. An autoregulatory molecule and marker construct is expressed in vivo, where the marker is cleaved from the construct during translation. The method comprises the expression of a construct having an autoregulatory molecule bound to a measurable expression marker by a cleavable linker. The cleavable linker is the substrate of a protease, which acts on its substrate in vivo during translation. Cleavage during translation, allows the autoregulatory molecule to fold normally as it would in its native form. The measurable marker is released and available for detection upon cleavage by the protease. As a result, the concentration of the measurable marker is directly related to the level of expression of the autoregulatory molecule.

Abstract: The invention relates to recombinant nucleic acid and polypeptides encoding collagenase I and collagenase II, methods for the preparation thereof and methods for the use thereof. The invention also encompasses methods related to releasing a composition comprising collagenase prior to therapeutic administration.

Abstract: Embodiments of the present disclosure relate to amino acid, modified amino acid, peptide and protein identification and sequencing, by means of, for example, electronic detection of individual amino acids or small peptides.

Abstract: A protein used as a biomarker for diagnosing IgA nephropathy and TGBM (thin-glomerular-basement-membrane) using urine through a target proteomics method. A diagnosis biomarker protein and a kit for diagnosing IgA nephropathy and TGBM and predicting progress of the nephropathy in advance using the protein are provided. The degree of the progression of the disease can be grasped by detecting IgA nephropathy and TGBM, enabling early diagnosis and confirming progress from the patient's urine. In addition, a monoclonal antibody produced based on the diagnosis biomarker protein can be used for an immunoassay kit (ELISA, antibody coated tube test, lateral-flow test, potable biosensor). The monoclonal antibody is used in early diagnosis and progression detection of IgA nephropathy and development of a novel drug for the purpose of treatment.

Abstract: Provided herein are compositions comprising native and denatured human leukocyte antigens (HLA) and methods of making said compositions. Also provided herein are methods and kits for the detection of antibodies to native HLAs.

Abstract: This patent application discloses and describes proteins found to be differentially expressed between primary tumor breast cancer cells histologicaly defined as early stage (stage 0) breast cancer and primary breast cancer cells histologicaly defined as late stage (stage 3) breast cancer. These proteins can be used either individually or in specific combinations in diagnostic and prognostic protein assays on various biological samples from breast cancer patients to indicate the that a breast cancer patient's cancer is in an early, non-aggressive stage or in a late, aggressive stage. Determination of differential expression of these proteins can also be useful for indicating additional therapies to combat the aggressiveness of late stage breast cancer. The full length intact proteins can be assayed or peptides derived from these proteins can be assayed as reporters for these proteins.

Abstract: This patent application discloses and describes proteins found to be differentially expressed between primary tumor breast cancer cells that did not give rise to recurrent breast cancer disease after initial diagnosis and primary breast cancer cells that did give rise to recurrent breast cancer disease after initial diagnosis. These proteins can be used either individually or in specific combinations in diagnostic and prognostic protein assays on various biological samples from breast cancer patients to indicate the likelihood that a breast cancer patient's cancer will recur after initial diagnosis and treatment. Determination of differential expression of these proteins can also be useful for indicating additional therapies to combat the likelihood of recurrent breast cancer. The full length intact proteins can be assayed or peptides derived from these proteins can be assayed as reporters for these proteins.

Abstract: Disclosed herein are “equipment-free” flow-through assay devices based on patterned porous media, methods of making same, and methods of using same. The porous, hydrophilic media are patterned with hydrophobic barriers for performing assays on liquids.

Abstract: Provided herein are methods for detecting endotoxin or Gram negative bacteria in a sample. Kits for detecting endotoxin or Gram negative bacteria in a sample are provided.

Abstract: Rational design of immunotherapeutics relies on clear knowledge of the immunodominant epitopes of antigens. Current methods for identifying kinetically stable peptide-MHC complexes are in many cases inadequate for a number of reasons. Disclosed herein is a reductionistic system incorporating known participants of MHC class II antigen processing in solution to generate peptide pools from antigens, including those for which no immunodominant epitope has yet been identified, that are highly enriched for proteolytic fragments containing their immunodominant epitopes. HLA-DM-mediated editing contributes significantly to immunodominance and is exploited in discovering immunodominant epitopes from novel or previously uncharacterized antigens, particularly antigens associated with pathogens, tumors or autoimmune diseases.

Abstract: Methods for identifying a compound capable of interacting with a Receptor Tyrosine Kinase (RTK) including providing a device capable of measuring cell-substrate impedance, adding test cells expressing a RTK to the device, measuring first impedances, adding a compound to at least one compound well and adding a vehicle control to at least one control well, measuring second impedances of the compound well and the control well, determining the change in the impedance for the compound well and the one control well, comparing the change in impedance between the compound well and the control well, and identifying the compound interacts with the RTK if the comparison demonstrates a significant difference between the change in impedance.

Abstract: A sterility indicating composition comprising a plurality of sterilization process resistant spores which contain an active protease during germination and initial outgrowth of the spores; and a germination medium comprising at least one labeled protease substrate and at least one nutrient for germination of the spores; wherein the medium is essentially free of a) any active protease other than the active protease contained by the plurality of spores and b) any protease substrate other than the at least one labeled protease substrate, other than any protease substrate originating from the plurality of spores, and other than any protease substrate which does not compete with the labeled protease substrate for the active protease; and wherein the at least one labeled protease substrate comprises a peptide which can be cleaved by the active protease and which is labeled with one or more dye groups, at least one of which undergoes a detectable change when the peptide is cleaved by the active protease, and wherein

Abstract: Injectable compositions for the MRI detection of an analyte selected from the group consisting of reactive oxygen species, proteases and enzymes, comprising a) a matrix material based on a responsive hydrophobic polymer capable of undergoing a chemical reaction with the analyte to be detected, such reaction leading to a disruption of the polymer chain of the responsive polymer, b) a contrast agent suitable for use in magnetic resonance imaging, embedded in or encapsulated in the polymer a), c) optionally, a functionality capable of binding a marker or probe or a probe for creating a second detection signal, and d) optionally, a non-responsive polymer not undergoing a chemical reaction with the analyte under the conditions where polymer a) undergoes a reaction leading to chain breakage

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: The present invention provides methods for continuous measurement of protein and/or triglyceride digestibility during a meal. Stable isotope of 15N-spirulina protein and 2H5-phenylalanine was added to the nutritional supplement. Protein digestibility is calculated by measuring the ratio [15N]PHE to [2H5]PHE in plasma and the nutrition. In another embodiment, [1,1,1-13C3]tripalmitin and [2,2-2H2]palmitic acid were added to the meal. The ratio between [1-13C]palmitic acid/[2,2-2H2]palmitic acid will represent the percentage digestion of triglycerides by lipase from the pancreas.

Abstract: A method for analyzing the polypeptide content of animal tissue is described. The method includes the steps of (a) providing an animal tissue specimen; (b) depositing one or more portions of a hydrogel mixture including a protease on spatially discrete portions of the animal tissue specimen; (c) allowing sufficient time to pass for animal tissue under the hydrogel mixture to be form a digested mixture of animal tissue and hydrogel mixture; (d) removing the digested mixture from the animal tissue and extracting the polypeptides from the digested mixture to provide an extract; and (e) analyzing the polypeptide content of the extract by mass spectrometry.