Abstract: This invention pertains to the in vitro detection of proteases using a single peptide-conjugate nanocrescent surface enhanced Raman scattering (SERS) probes with at least nanomolar sensitivity. The probe enables detection of proteolytic activity in extremely small volume and at low concentration. In certain embodiments the probes comprise an indicator for the detection of an active protease, where the indicator comprises a nanocrescent attached to a peptide, where said peptide comprises a recognition site for the protease and a Raman tag attached to the peptide.

Abstract: The disclosure relates to a method of generating catalytic nucleic acid probes useful for detecting microorganisms such as bacterial pathogens. In one embodiment, the catalytic nucleic acid probes are fluorogenic DNAzymes. The disclosure also relates to catalytic nucleic acid probes and methods of using the probes for detecting microorganisms.

Abstract: The present invention relates to compounds, compositions, and methods, for treating subjects suspected of needing treatment for a Nidovirales virus infection. In certain embodiments, the compounds comprise Nidovirales helicase inhibitors that do not significantly affect helicase ATPase enzymatic activity or nucleic acid binding activity of the helicase.

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: The present invention relates to methods for identifying compounds that modulate untranslated region-dependent expression of a target gene. The invention particularly relates to using untranslated regions of a target gene or fragments thereof linked to a reporter gene to identify compounds that modulate untranslated region-dependent expression of a target gene. The methods of the present invention provide a simple, sensitive assay for high-throughput screening of libraries of compounds to identify pharmaceutical leads.

Abstract: A LAGLIDADG homing endonuclease variant, having mutations in two separate subdomains, each binding a distinct part of a modified DNA target half-site, said LAGLIDADG homing endonuclease variant being able to cleave a chimeric DNA target sequence comprising the nucleotides bound by each subdomain. Use of said herodimeric meganuclease and derived products for genetic engineering, genome therapy and antiviral therapy.

Abstract: Methods and devices are provided for preparing a protein array having a plurality of proteins. In one embodiment, the method includes providing a plurality of nucleic acids each having a predefined sequence and expressing in vitro a plurality of proteins from the plurality of nucleic acids. In another embodiment, protein arrays having a solid surface and a microvolume are also provided. The solid surface can have a plurality of anchor oligonucleotides capable of hybridizing with a plurality of nucleic acids. The microvolume can cover each of the plurality of anchor oligonucleotides and can be configured to produce a polypeptide from each of the plurality of nucleic acids.

Abstract: Disclosed herein are methods and related compositions for identifying compounds that stabilize natively folded tetrameric ?-synuclein. These methods and compositions are useful for the treatment and diagnosis of ?-synuclein-associated diseases and disorders.

Abstract: A method for the production of nucleic acid encoding a target protein. The method 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.

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: Serine hydrolases are implicated in malconditions such as cancer, central nervous system disorders, cardiovascular disorders, obesity, and metabolic disorders. Many serine hydrolases expressed in proteomic libraries are of unknown function in vivo. Compounds identified through library versus library screening can be used for treatment of malconditions associated with the specific serine hydrolase KIAA1363 (also known as AADACL1). A library of inhibitors of KIAA1363 was prepared and candidate compounds were identified as a potent inhibitors having submicromolar IC50 values. An exemplary compound of the invention was shown to be an effective inhibitor of prostate cancer pathogenesis. Other inhibitory compounds of the invention comprising fluorophore groups are shown to be effective in spatial and temporal localization of the serine hydrolase in cells and tissues.

Abstract: A high throughput method and apparatus for rapidly screening a plurality of genotoxicants to determine the degree and type of genotoxicity are provided.

Abstract: Provided is a device that can detect cells or bacteria in units of a single cell or bacterium, and can further measure the amounts of activity of cells or bacteria or responses of the cells or bacteria to drugs in units of a single cell or bacterium. A plurality of partitioned regions each having about the same size as a cell or a bacterium is provided, and a plurality of types of electrical sensors 201 and 202 are arranged in each partitioned region.

Abstract: Described are methods and means for enhancing enzyme activity toward insoluble substrates. This is achieved by means of in vitro compartmentalization in which an insoluble microparticle functions both as the enzyme substrate and as a structure for negative selection. Enhanced enzymes expressed from a microparticle-linked polynucleotide library preferentially degrade the microparticle releasing specific gene variants into solution. Gene variants encoding less active enzyme variants remain linked to the microparticle and may be removed through centrifugation, thus enriching the polynucleotide library for more active enzyme variants. These methods may be used to enhance cellulase and ligninase activity toward insoluble cellulosic biomass.

Abstract: The invention relates to methods and compositions for identifying a candidate nucleic acid (CNA) comprising a polynucleotide sequence encoding at least a part of a natural product gene cluster (NPGC), a secondary metabolite biosynthesis cluster (SMBC), a non ribosomal peptide (NRP), a polyketide (PK) biosynthesis cluster, a protein involved in NRP and/or PK biosynthesis, a protein involved in other secondary metabolite biosynthesis, and/or a phosphopantetheinyl transferase (PPTase), by expressing the candidate nucleic acid (CNA) to form at least one PPTase, incubating the PPTase with a non ribosomal peptide synthetase (NRPS), and detecting activation of the NRPS, wherein activation indicates that said CNA comprises a polynucleotide sequence encoding at least one of the above.

Abstract: Disclosed are methods, compositions and devices for screening a protein library for proteins having a desired activity, such as capable of catalyzing the formation of a bond between two reactants. In an exemplary embodiments, a plurality of proteins are expressed in vitro from a plurality of nucleic acids, the plurality of proteins are exposed with two single stranded oligonucleotides having complementary sequences, each oligonucleotide having a reactant and a fluorophore, the fluorescence of the protein-reactant-oligonucleotide-fluorophore complexes is detected and the complexes showing detectable fluorescence energy transfer are isolated, thereby isolating proteins having the desired enzymatic activity.

Abstract: The invention relates to a variant of a parent Termamyl-like alpha-amylase, comprising mutations in two, three, four, five or six regions/positions. The variants have increased stability at high temperatures (relative to the parent). The invention also relates to a DNA construct comprising a DNA sequence encoding an alpha-amylase variant of the invention, a recombinant expression vector which carries a DNA construct of the invention, a cell which is transformed with a DNA construct of the invention, the use of an alpha-amylase variant of the invention for washing and/or dishwashing, textile desizing, starch liquefaction, a detergent additive comprising an alpha-amylase variant of the invention, a manual or automatic dishwashing detergent composition comprising an alpha-amylase variant of the invention, a method for generating a variant of a parent Termamyl-like alpha-amylase, which variant exhibits increased.

Abstract: The present invention relates to an aptazyme comprising an aptamer for hepatitis C virus (HCV) RNA-encoding component; a hammerhead ribozyme comprising an antisense sequence to microRNA at the site released by self-cleavage; and a communication module sequence that connects the aptamer and hammerhead ribozyme and triggers a self-cleavage activity of the hammerhead ribozyme upon binding of the aptamer with the HCV RNA-encoding component. The present aptazyme inhibits microRNA activity specifically in HCV proliferating cells and thus a composition of the present invention comprising the aptazyme can be effectively used for treatment of HCV-related diseases.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Abstract: Disclosed are compositions and methods for measuring tyrosine kinase activity.

Abstract: A method and engineered proteins for use therewith suitable for studying SERCA that are capable of being used in vivo and do not require protein purification or chemical labeling of SERCA, or reconstitution into artificial membranes. The engineered protein for calcium handling within human cells includes a two-color SERCA construct having three component proteins fused together. The three component proteins include a blue fluorescent protein (cerulean), SERCA2a and a yellow fluorescent protein (YFP), or a red fluorescent protein (tagRFP acceptor), SERCA and a green fluorescent protein (GFP). The method of determining SERCA activity for optimization of cardiac function includes resolving structure changes of the two-color SERCA construct. The two-color SERCA constructs are catalytically active and able to pump calcium following the step of resolving structure changes.

Abstract: The present disclosure provides DDAH modulators. Thus, the present disclosure provides a method of treating a patient suffering from a disorder characterized by excessive NO production and/or elevated DDAH activity, the method comprising administering to said patient an effective amount of a compound of one of formulae I-X. The present disclosure also provides a pharmaceutical composition comprising a compound of one of formulae I-X.

Abstract: The present invention relates to a method for the identification of modulators of catechol O-methyltransferase enzyme activity (COMT).

Abstract: A method for engineering I-CreI homing endonuclease variants able to cleave mutant I-CreI sites having variation in positions ±8 to ±10. A I-CreI homing endonuclease variant obtainable by said method, a vector encoding said variant, a cell, an animal or a plant modified by said vector. Use of said I-CreI endonuclease variant and derived products for genetic engineering, genome therapy and antiviral therapy.

Abstract: The present invention relates to an apparatus to detect biological parameters in the analysis of a sample, specimen, or assay. The system includes a device for determining one or more values for one or more measurable characteristics of a sample. In an aspect, the device can be configured to operate on any of a mobile device, tablet computer, laptop computer, desktop computer, digital pen, medical testing tool or electronic device. In another aspect, the device can comprise a synchronization component that synchronizes the device to a network system.

Abstract: The present invention relates to methods, compositions, and diagnostic tests for treating and diagnosing cancer and other related diseases that result in dysregulation of malic enzyme 2. In particular, the methods and compositions include combination therapy, such as with a combination of two or more ME2 inhibitors or a combination of an ME2 inhibitor and an anticancer agent.

Abstract: Human PFK genes are identified as modulators of the IGFR pathway, and thus are therapeutic targets for disorders associated with defective IGFR function. Methods for identifying modulators of IGFR, comprising screening for agents that modulate the activity of PFK are provided.

Abstract: The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising of the steps of: (a) compartmentalising genetic elements into microcapsules; (b) expressing the genetic elements to produce their respective gene products within the microcapsules; (c) sorting the genetic elements which produce the gene product having a desired activity. The invention enables the in vitro evolution of nucleic acids by repeated mutagenesis and iterative applications of the method of the invention.

Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: The present disclosure relates to compositions and methods for screening a plurality of polypeptide variants.

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: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: The present invention relates to a method of identifying a compound having an antiarrhythmic effect and to a use of adenosine-diphospho-ribose cyclase (cardiac ADPRC) for the identification of a compound having said effect.

Abstract: The present invention provides compositions including peptide display scaffolds that present at least one candidate peptide and at least one detectable moiety in at least one of the N-terminal and C-terminal candidate peptide presenting domains that when expressed in a cell are accessible at a surface of the cell outermembrane. In addition, the present invention also provides kits and methods for screening a library of cells presenting the candidate peptides in peptide display scaffolds to identify a ligand for an enzyme.

Abstract: The invention discloses cellulase enzymes with optimized properties for processing of cellulose- and lignocellulose-containing substrates. In particular, cellobiohydrolase enzymes with preferred characteristics are disclosed. The present invention provides fusion, insertion, deletion and/or substitution variants of such enzymes. Enzyme variants have enhanced thermostability, proteolytic stability, specific activity and/or stability at extreme pH. Nucleic acid molecules encoding said enzymes, a composition comprising said enzymes, a method for preparation, and the use for cellulose processing and/or for the production of biofuels are disclosed.

Abstract: The present invention provides a composition for preventing or treating diabetes, comprising an NAD glycohydrolase (NADase) inhibitor as an active ingredient. The NAD glycohydrolase (NADase) inhibitor according to the present invention has the effect of reducing blood glucose levels and promoting insulin secretion and thus can be effectively used as a therapeutic agent for diabetes, particularly type II diabetes.

Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: The present application relates to a method of assaying ubiquitination in a sample by combining ubiquitin together with a substrate in a sample containing UBE1, UbcH3, Skp2-isoform 1, Skp1, Cul1, Rbx1, Cks1, CDK2 and Cyclin E1 under conditions suitable for ubiquitination to take place, exposing the sample to a labelled binding partner which is specific for the ubiquitin, and measuring the amount of ubiquitin bound to the substrate.

Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: The present invention generally relates to systems and methods to create stable emulsions with low rates of exchange of molecules between microdroplets.

Abstract: Novel substrates for detection of activity of amyloid beta degrading enzyme, such as Neprilysin (NEP) and insulin degrading enzyme (IDE), associated with Alzheimer's disease, are provided. A quenched fluorogenic peptide substrate containing the first seven residues of the A?peptide plus a C-terminal Cys residue to detect neprilysin activity with a fluorophore attached to the C-terminal Cys and a quencher linked to the N-terminus of the peptide is disclosed. An assay system sensitive to endopeptidase activity of NEP and IDE, but insensitive to other A?-degrading enzymes is disclosed. Active compounds are identified by a cell-based assay system for high-throughput screening.

Abstract: An object is to provide a means which is useful for the development of an anti-malaria agent. It was found that a mitochondrial DNA polymerase of falciparum malaria shows a bivalent iron ion requirement. Thus, disclosed is a method for measuring the activity of a DNA polymerase, including the steps of: (1) incubating a solution containing a bivalent iron ion, a mitochondrial DNA polymerase of falciparum malaria, template DNA, and at least one deoxyribonucleoside triphosphate or deoxyribonucleoside triphosphate derivative; (2) detecting the synthesized double-stranded DNA; and (3) calculating the activity of the DNA polymerase from the result of the detection carried out in step (2).

Abstract: A bacillus composition characterized by fast germination and outgrowth in bile salts (simulated gut environment) and by high-level secretion of phytase. The bacillus composition may be used as supplement in animal feed where it has a probiotic (health promoting) effect and increases the digestion and availability of nutrients from animal feeds.

Abstract: The present invention relates to systems and methods for generating microdroplets with varying concentrations of a particular solute from a solution at fixed concentration.

Abstract: Proteinopathies result from the proteasome not acting efficiently enough to eliminate harmful proteins and prevent the formation of the pathogenic aggregates. As described herein, inhibition of proteasome-associated deubiquitinase Usp 14 results in increased proteasome efficiency. The present invention therefore provides novel compositions and methods for inhibition of Usp14, enhancement of proteasome activity and treatment of proteinopathies.

Abstract: The disclosure relates to a method of forming a pattern having pattern elements with a plurality of sizes on a substrate surface with a tilted pen array that includes choosing a tilt geometry for a pen array with respect to a substrate, inducing the tilt geometry between the pen array and the substrate surface, and forming a pattern having pattern elements on the substrate surface with the titled pen array, whereby the size of the formed pattern elements varies across the substrate surface along the tilted axis or axes. For example, the tilt geometry is in reference to the substrate surface and comprises a first angle with respect to a first axis of the substrate and a second angle with respect to a second axis of the substrate, the second axis being perpendicular to the first axis, and at least one of the first and second angles being non-zero.

Abstract: Methods of isolating at least one cell of interest, methods of making fixed arrays, arrays comprising a glass substrate bonded to a patterned siloxane structure having inlets, outlets and microchannels, array kits, and methods of making microfluidic apparati are provided in the present application.

Abstract: The invention generally relates to methods and apparatuses for optimizing conditions for optical mapping. In certain embodiments, methods of the invention involve providing a substrate including a gradient of silanes in a first direction, introducing to the substrate, a gradient of enzyme activity in a second direction, contacting a plurality of enzymes and a plurality of nucleic acids to the substrate, and analyzing enzymatic activity and interaction of the nucleic acids with the substrate, thereby determining the optimal conditions for optical mapping of the nucleic acid.