Abstract: The present invention relates to methods for screening a polypeptide for desired activity against a target molecule In particular, the present invention relates to methods for screening a polypeptide for desired activity against a target molecule by expressing the polypeptide in a bacterial cell and permeabilising the cell.

Abstract: The present invention relates to methods, compositions and kits concerning resistance to treatment with an anti-cancer agent, specifically an inhibitor of BRAF. In particular embodiments, the invention concerns mutations in a BRAF sequence that confer resistance to a BRAF inhibitor. Identification of such mutations in a BRAF sequence allows the identification and design of second-generation BRAF inhibitors. Methods and kits for detecting the presence of a mutant BRAF sequence in a sample are also provided.

Abstract: The present invention provides a method for detecting nucleic acid cleavage induced by a modified rare-cutting endonuclease derived from an initial rare-cutting endonuclease, said modified rare-cutting endonuclease being able to cleave a DNA target sequence, which may be different from the recognition and cleavage site of the initial rare-cutting endonuclease. In one embodiment of the invention expression of a marker gene is used as an indicator of target DNA cleavage.

Abstract: Methods for the treatment of renal injury include the use of arginase inhibitors in the treatment and prevention of diabetic nephropathy, albuminuria and azotemia amongst others, and methods for identifying agents for the treatment of renal injury.

Abstract: A microfluidic system has a microfluidic mixer and a sample storage component that is in fluid connection with the microfluidic mixer.

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: The invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, ?-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.

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 concerns novel isolated fluorescent proteins, variants thereof, and polynucleotides encoding the same. Methods for making and using the polypeptides and polynucleotides are also provided. For example, methods to detect protein-protein interactions, to develop novel fluorescent reagents, to monitor cellular events, as well as cell-based methods for screening for kinase or phosphatase inhibitors, are set forth. Kits to carry out the methods of the invention are also taught.

Abstract: This disclosure describes a relevant etiology of cancer and a novel anti-cancer therapeutic strategy, based on the discovery that a protein named serine protease inhibitor (SPIK/SPINK/PSTI) was up-regulated by hepatitis B and C virus infections consequently suppressing the cell apoptosis. Accordingly, the present disclosure provides, inter alia, an inhibitor of SPIK and/or a technology of suppression of over-expression of SPIK in cells. The inhibitors include: 1) chemical compounds, which can inhibit SPIK transcripts, protein activity, and gene expression, 2) SPIK siRNA (RNAi gene silence or dsRNA of SPIK, 3) DNA anti-sense and anti-SPIK antibody. Further, this disclosure provides methods of using the inhibitor as an anti-cancer agent to re-instate cancer cell apoptosis (e.g., serine protease dependent cell apoptosis).

Abstract: A method of detecting and quantifying various enzymatic activities using a constructed artificial genetic circuit GESS (genetic enzyme screening system) for sensing phenolic compounds and a method of screening a trace of activities of target enzymes from a metagenome using the artificial genetic circuit, thereby securing target enzyme genes. When the method for screening and quantifying target enzymatic activity is used, useful genes can be screened from various genetic communities, including environmental or metagenomic libraries, at a single cell level in high throughput (million/day). Further, the sensitivity of the genetic circuit to phenol derivatives and the expression thereof can be controlled, and thus the genetic circuit can rapidly sense and quantify various enzymatic activities. Thus, the method can be advantageously used in the protein engineering technology for enzyme modification.

Abstract: The present invention relates to a probe compound that can comprise any substrate or metabolite of an enzymatic reaction in addition to an indicator component, such as, for example, a fluorescence dye, or the like. Moreover, the present invention relates to means for detecting enzymes in form of an array, which comprises any number of probe compounds of the invention which each comprise a different metabolite of interconnected metabolites representing the central pathways in all forms of life. Moreover, the present invention relates to a method for detecting enzymes involving the application of cell extracts or the like to the array of the invention which leads to reproducible enzymatic reactions with the substrates. These specific enzymatic reactions trigger the indicator (e.g. a fluorescence signal) and bind the enzymes to the respective cognate substrates. Moreover, the invention relates to means for isolating enzymes in form of nanoparticles coated with the probe compound of the invention.

Abstract: Disclosed herein are methods, compositions and systems for analyzing and detecting enzyme activity. For examples, methods, compositions and systems for parallel detection and analysis of enzymatic activities of enzymes in complex biological mixtures are provided.

Abstract: The present invention provides a molecular construct capable of fluorescent resonance energy transfer (FRET), comprising a linker peptide, and donor and acceptor fluorophore moieties, where the linker peptide is a substrate of a botulinum neurotoxin selected from the group consisting of synaptobrevin, syntaxin and SNAP-25, or a fragment thereof capable being cleaved by the botulinum neurotoxin, and separates the donor and acceptor fluorophores by a distance of not more than 10 nm, and where emission spectrum of the donor fluorophore moiety overlaps with the excitation spectrum of the acceptor fluorophore moiety; or where the emission spectra of the fluorophores are detectably different. Also provided are isolated nucleic acid expressing the construct, kits comprising said construct and cell lines comprising said nucleic acid. Further provided are methods of detecting a BoNT using the above described construct via FRET, and methods for detecting a BoNT using surface plasmon resonance imaging.

Abstract: The present invention relates generally to hydrogen production for use in fuel cells, foodstuffs and chemical production, and more particularly, to biologically and photosynthetically produced hydrogen. Specifically, disclosed is a method for producing bacteria and green alga that can produce hydrogen in quantities that exceed four hundred percent of the hydrogen produced by green alga in nature; thus, producing organisms which can serve as hydrogen generators for fuel cells, chemical production and numerous other applications.

Abstract: Described herein are compounds that comprise amino acids and their pharmaceutical compositions. Methods used to administer the compounds are described.

Abstract: Methods for isolating and using multi-protein complexes that are biologically active are provided. The complexes contain one or more proteins of interest (e.g. a receptor, ion channel, etc.) and associates scaffolding proteins such as phosphatases, kinases and post synaptic density components. Buffers that do not contain denaturing agents and which may be used to isolate the multi-protein complexes are also provided, as are protein arrays containing the biologically active multi-protein complexes. The protein arrays may be used, for example, for high throughput screening assays.

Abstract: The present invention relates to a method for determining or predicting the response of a patient diagnosed with locally advanced rectal cancer to chemoradiotherapy. The present invention also aims to provide methods and devices for predicting the response of patients diagnosed with rectal cancer to specific medicaments, radiotherapy and/or chemotherapy. More specifically, the present invention provides methods which measure kinase activity by studying phosphorylation levels and profiles in samples of said patients.

Abstract: Methods for analyses of kinase inhibitor specificity and promiscuity using small subsets of kinases including a method comprising providing a set of kinases, ranking the kinases based upon their ability to overcome biases, utilizing a correlation-based feature selection algorithm to select a kinase inferential bases, and screening a kinase inhibitor against the kinase inferential bases.

Abstract: The present invention relates to a method for diagnosing, typing and/or subtyping renal cell carcinoma as well as predicting the response to medication of patients suffering from renal cell carcinoma. More specifically, the present invention provides methods which measure kinase activity by studying phosphorylation levels and profiles in samples of said patients.

Abstract: A method for selecting combinations of drugs for treatment of diseases that arise from deranged signaling pathways is disclosed. The method involves measuring the activity states for signaling proteins in a diseased cell and determining whether the activity states are different from the activity states observed for a reference cell such as a normal cell. Based on the observed differences, combinations of two or more drugs are selected to reduce these differences. Treatment of a subject with the combinations restores the activity states of the signaling proteins of the deranged disease-associated signaling pathways toward the activity states observed in the reference cell. Since the diseased cell and the reference cell can both be obtained from the same subject, combinations of drugs that specifically target patient-specific signaling derangements is possible.

Abstract: A method is described for releasing a soluble or membrane associated intracellular protein of interest (POI) comprising the steps of: providing a cell comprising a soluble or membrane associated intracellular POI; contacting the cell with a membrane extracting composition; and causing the POI to be released from the cell under conditions sufficient for the specific release of the POI and in a soluble form.

Abstract: Compositions, methods, and kits for detecting and monitoring kinase, phosphatase and protein post-translational modification activity are described. The compositions typically include a peptide, a detectable moiety, and a protease cleavage site. Modification of a peptide by a kinase, phosphatase or other protein post-translational modification alters the proteolytic sensitivity of the peptide, resulting in a change of a detectable property of the composition. Panel assays for determining substrates or modulators of kinase, phosphatase or other protein post-translational modification activity are also described.

Abstract: The invention relates to a method for determining if a test compound, or a mix of compounds, modulates the interaction between two proteins of interest. The determination is made possible via the use of two recombinant molecules, one of which contains the first protein a cleavage site for a proteolytic molecules, and an activator of a gene. The second recombinant molecule includes the second protein and the proteolytic molecule. If the test compound binds to the first protein, a reaction is initiated whereby the activator is cleaved, and activates a reporter gene.

Abstract: Disclosed are compositions and methods related to inhibition of PDE1.

Abstract: Prolyl endopeptidase (PE) activity in lung samples is detected by contacting the lung sample with a probe comprising a —P—X— (or —X—P—, —P—X—P—) PE recognition site, wherein P is a prolyl bioisostere, X is a residue that is not a prolyl bioisostere or is a prolyl bioisostere flanked on each side by a residue that is not a prolyl bioisostere, and “-” is an amide bond, under conditions wherein PE activity of the sample specifically hydrolyzes an amide bond of the recognition site to generate an optical signal; and (b) detecting the signal.

Abstract: The present invention is directed to peptide sequences that were identified from combinatorial libraries and could serve as substrates of plague plasminogen activator (Pla). Another aspect of the present invention is drawn to peptides derived from the substrates for Pla as a result of chemical modifications leading to specific inactivation of the proteolytic activity of Pla. Additionally, the present invention is directed to the use of the substrates identified herein in the detection of bacteria expressing omptin family of proteases which includes Y. pestis. Furthermore, the present invention is also directed to the use of the inhibitors identified herein in the prevention and treatment of infection caused by these bacteria.

Abstract: The present invention relates to a method for determining the estrogen receptor status of patients suffering from breast cancer. The present invention also aims to provide methods and devices for predicting the response of patients diagnosed with breast cancer to specific medicaments. More specifically, the present invention provides methods which measure kinase activity by studying phosphorylation levels and profiles in samples obtained from patients diagnosed with breast cancer.

Abstract: An expression vector including two separately inducible converging promoters P1 and P2, and expression system including such an expression vector and an additional regulator vector, a method of protein expression using such an expression system, and a method of investigating (meta)genome libraries using such an expression system.

Abstract: The present disclosure relates to CBH I chimera fusion polypeptides, nucleic acids encoding the polypeptides, and host cells for producing the polypeptides.

Abstract: Synthetic protease substrates and methods which facilitate the identification of substrates of a protease, particularly ubiquitin, ubiquitin-like, or proteasome protein are provided.

Abstract: Compounds of Formulas I-XLIII are identified as direct inhibitors of p97 ATPase or of the degradation of a p97-dependent ubiquitin-proteasome system (UPS) substrate.

Abstract: Disclosed are various forms of an active, isolated ?-secretase enzyme in purified and recombinant form. This enzyme is implicated in the production of amyloid plaque components which accumulate in the brains of individuals afflicted with Alzheimer's disease. Recombinant cells that produce this enzyme either alone or in combination with some of its natural substrates (?-APPwt and ?-APPsw) are also disclosed, as are antibodies directed to such proteins. These compositions are useful for use in methods of selecting compounds that modulate ?-secretase. Inhibitors of ?-secretase are implicated as therapeutics in the treatment of neurodegenerative diseases, such as Alzheimer's disease.

Abstract: Disclosed is a high-throughput analysis apparatus. The high-throughput analysis apparatus comprises a sample introduction unit, a flow control unit, a separation unit, a detection unit, a signal collecting unit and a signal processing unit. Several methods using the same are also provided.

Abstract: Screening assays that allow for the identification of agents that modulate the activity of N-terminal acetylation of a polypeptide and the Doa10 branch of the N-end rule pathway are provided. Also provided are methods of using an agent that modulates the activity of N-terminal acetylation of a polypeptide and the Doa10 branch of the N-end rule pathway to increase or decrease protein degradation in a cell, and to modulate physiologic and pathologic associated with N-terminal acetylation of a polypeptide and the Doa10 branch of the N-end rule pathway.

Abstract: A method for identifying and selecting chemical entities that contributes to a functional effect in the development of new combinatorial drugs. The combinations of two or more chemical compounds show a synergistic effect. The compounds can be e.g. antibodies, antibiotics, anti-cancer agents, anti-AIDS agents, anti-growth factors, antiviral agents, soluble receptors, cytokines, RNAi's, vaccines and mixtures thereof. The method comprises a) providing n samples each comprising a chemical entity, b) mixing 2 or more of the n samples in all possible combinations, c) subjecting this mixture to a functional assay in order to identify entities contributing to the functional effect. The steps a-c are repeated on the chemical entities from step c which contribute to the functional effect.

Abstract: An assay library comprising 14 fluorescently labeled phosphonate esters which act as serine hydrolase inhibitors is provided as an analytical tool enabling activity based identification of serine hydrolases and characterization of enzyme preparations, protein mixtures and complex proteome samples.

Abstract: The present invention relates to high throughput methods of identifying neutral lipid synthases. The invention includes a method of positively selecting yeast cells expressing recombinant neutral lipid synthases, and quantifying the enzyme activities of the recombinant neutral lipid synthases using a fluorescence in situ assay.

Abstract: The invention provides methods of treating a meiotic kinase-associated disease, preferably the meiotic kinase HSET, by administering an inhibitor of the meiotic kinase. Preferably, the disease is associated with the presence of supernumerary centrosomes, such as cancer. Methods of inhibiting the growth of a tumor cell by contacting the cell with an inhibitor of a meiotic kinase, preferably HSET, are also provided. Screening methods for identifying inhibitors of the meiotic kinase HSET are also provided. Methods of selecting subjects for treatment with an inhibitor of a meiotic kinase, such as HSET, are also provided.

Abstract: The invention provides biocatalytic methods for the manufacture of pure single enantiomer compounds. This invention provides methods of screening for enzymes which are highly enantioselective or enzymes that can provide any desired stereoisomer of a compound. The invention provides the use of single enantiomer substrates in performing a growth screen of a clonal library to identify highly stereoselective enzymes. In one aspect, methods for screening and identification of enzymes, e.g., transaminases, nitrilases, aldolases, epoxide hydrolases are provided. Methods for the production and screening of gene libraries generated from nucleic acids isolated from more than one organism for enzyme, e.g., transaminase, activities are also provided.

Abstract: An assay for use in high-throughput screening of chemical libraries to determine whether compounds in such libraries will inhibit CD38 catalytic activity, and CD38 production of ADPR and cADPR.

Abstract: The present inventions relates to methods of discovering or developing novel material or compound. In particular, the methods include the steps of using of general expert knowledge to identify currently available molecules, setting forth desired properties for a target molecule, designing a set of test molecule from the currently available molecule using computational methods (the test molecules having desired properties in the computational models); synthesizing the test molecules, testing the test molecules in real experiments, and identifying the target molecule which is the test molecule that has the desired properties.

Abstract: The invention relates to a device for electrically reading microarrays which can be cleaned and used more than once. The device (1, 1?, 1?) for reading microarrays (6) comprises the following elements: a base (2, 2?, 2?) comprising support means (3, 3?, 3?) for positioning the test surface (7) of the microarray (6) parallel to a reading surface (4) of the base (2, 2?, 2?); a matrix of transducers (5, 5?, 5?) disposed on the reading surface (4) of the base (2, 2?, 2?), transforming a variation of an electrical or chemical value into a variation of an electrical value; and reading means (10) which are connected to the transducers (5, 5?, 5?) and interpret the electrical signals from the transducers (5, 5?, 5?).

Abstract: The invention provides a method for isolating particular members from a library of variant cells in individual microreactors, wherein the phenotype of the biomolecule secreted by the cell is evaluated on the basis of multiple parameters, including substrate specificity and kinetic efficiency.

Abstract: The invention relates to a compositions and methods for generating and using pIX phage display libraries for producing non-antibody peptide or protein proteins or peptides using engineered hybrid phage vectors derived from pIX of M 13 phage.

Abstract: Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.

Abstract: Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.

Abstract: The invention concerns a method which can be used to screen two or more repertoires of molecules against one another and/or to create combinatorial repertoires by combining two or more repertoires. In particular, the invention relates to a method whereby two repertoires of molecules can be screened such that all members of the first repertoire are tested against all members of the second repertoire for functional interactions. Furthermore, the invention relates to the creation and screening of antibody repertoires by combining a repertoire of heavy chains with a repertoire of light chains such that antibodies formed by the all combinations of heavy and light chains can be screened against one or more target ligands.

Abstract: The present invention relates to the use of endogenous protein kinase activity in cerebrospinal fluid for the classification, diagnosis and prognosis of neurological and psychiatric disorders as well as for predicting and monitoring treatment effects. An array of substrates for protein kinases, immobilized on a porous matrix, is used to monitor the protein kinase activity in cerebrospinal fluid. The method of the present invention enables the early diagnosis and discrimination between neurodegenerative disorders.

Abstract: The present invention provides a process for the production of nucleic acid encoding a target protein, which comprises: (a) providing an array of RNA or DNA molecules including one or more encoding the target protein; (b) generating a target protein from the array to form RNA-protein or DNA-protein complexes in which the RNA or DNA molecule is non-covalently or covalently bound to the complex; (c) separating the complexes into compartments wherein most or all of the compartments contain no more than one complex; (d) subjecting the complexes to reaction conditions which allow target protein activity; and (e) selecting nucleic acid encoding the target protein on the basis of the activity associated therewith, wherein when the complex is a DNA-protein complex in which the DNA is non-covalently bound, step b) is performed in the absence of separate compartments for each complex.