Abstract: A method for predicting a property of a sample molecule involves, for each of a multitude of reference molecules, obtaining a multitude of fingerprints and at least one property, and obtaining the multitude of fingerprints of the sample molecule. The method further involves for each of the multitude of reference molecules, using each of the multitude of fingerprints, calculating distances to the sample molecule, and for each of the multitude of reference molecules, determining a relative predictive dominance, based on the distances to the sample molecule. The method also involves, for each of the multitude of reference molecules, determining a fitness value based on the relative predictive dominance, and predicting the at least one property of the sample molecule based on the at least one property of the multitude of reference molecules and the fitness values obtained for the reference molecules.

Abstract: Methods and devices for identifying agents that block binding or activation of peripheral membrane proteins are disclosed.

Abstract: Novel therapeutic immunotherapy compositions comprising at least two vectors, each vector encoding a functional CAR, whereby the combination of vectors results in the expression of two or more non-identical binding domains, wherein each vector encoded binding domain(s) are covalently linked to a transmembrane domain and one or more non-identical intracellular signaling motifs are provided herein as well as are methods of use of same in a patient-specific immunotherapy that can be used to treat cancers and other diseases and conditions.

Abstract: Provided are methods and systems useful for screening large libraries of effector molecules. Such methods and systems are particularly useful in microfluidic systems and devices. The methods and systems provided herein utilize encoded effectors to screen large libraries of effectors.

Abstract: A chemical sensor including at least one resonant detection structure, the detection structure including at least one layer based on a porous material, the pores of which are covered with at least one functionalization layer that can adsorb or absorb at least one chemical species.

Abstract: Disclosed is a cyclin-dependent kinase substrate including a polypeptide that contains an amino acid sequence represented by formula (1): R1—P (wherein R1 represents a serine residue or a threonine residue, P represents a proline residue, “—” represents a single bond, and the left side represents the N-terminal side), and satisfies the following (a1) and/or (b1): (a1) the second amino acid residue counting from the proline residue toward the N-terminal side in the formula (1) is an aromatic amino acid residue, and/or (b1) at least two amino acid residues from the proline residue toward the C-terminal side in the formula (1) are acidic amino acid residues.

Abstract: Systems and methods that enable the rapid identification of target molecules present in a sample at low concentrations is provided. The system includes a sample volume, and a detection structure that is connected to the sample volume by a conduit. The detection structure includes a microfluidic chip that defines a plurality of fluid channels. The walls of the fluid channels are formed from or covered with a metal oxide to which target molecules attach. After the sample volume has been passed through the detection structure, and in particular through the channels, visible microparticles are passed through the detection structure. The visible microparticles are configured to have an affinity for the target molecules. The microfluidic chip is then imaged to detect visible microparticles, and to thereby obtain information regarding the presence of the target molecules.

Abstract: Provided is a method of producing L-amino acids by using a recombinant coryneform microorganism in which the expression of a target gene is weakened by using a gene transcription inhibition method.

Abstract: A method for the prediction, prognosis and/or diagnosis of bladder cancer or bladder cancer recurrence in a subject, the method includes: providing a test sample from the subject; measuring DNA methylation levels of at least a portion of two or more polynucleotides selected from the group consisting of HOXA9, SOXI, NPY, IRAK3, L1-MET, and Z02 in the test sample; calculating a risk score based on the measured DNA methylation levels, comparing the calculated risk score to a cut-off value derived from a reference DNA methylation profile based on DNA methylation levels of the one or more biomarkers derived from a control group, members of which had bladder cancer; and based on the comparison calculated risk score to the cut-off value, determining at least one of: (1) whether bladder cancer has recurred; (2) whether there is likelihood that the bladder cancer will recur; and (3) whether the patient has bladder cancer.

Abstract: An object of the present invention to discover a short peptide having an anti-aging effect and to provide a novel anti-aging agent comprising the peptide as an active ingredient. The inventors have discovered that a peptide consisting of an amino acid sequence ELKLIFLHRLKRLRKRLKRK (SEQ ID NO: 1) or a partial sequence thereof and having one or more effects selected from the group consisting of promoting fibroblast growth, promoting hyaluronic acid production and contracting a collagen gel, or a derivative or salt of the peptide is useful as an active ingredient of an anti-aging agent.

Abstract: A diagnostic device 10 for screening for a target analyte in a sample is provided. The diagnostic device 10 comprises a substrate 12 and a hydrophobic material 20 disposed on the substrate. The hydrophobic material 20 is selected to be converted from the hydrophobic material 20 to a hydrophilic material 22 upon contact with a conversion component within or derived from a sample introduced to the device 10.

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 present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.

Abstract: The present disclosure provides systems, compositions and methods for regulating expression of a target polynucleotide in a cell. The systems, compositions and methods comprise a chimeric receptor polypeptide comprising a G-protein coupled receptor (GPCR) or a fragment thereof, a chimeric adaptor polypeptide, at least one actuator moiety and a cleavage moiety.

Abstract: Provided is a method of producing L-amino acids by using a recombinant coryneform microorganism in which the expression of a target gene is weakened by using a gene transcription inhibition method.

Abstract: A method for determining a biological response of a target (41, 42) to a soluble candidate substance includes the steps: introducing a soluble candidate substance into a laminar flow of a buffer liquid (2) to form a candidate substance solute (3) having an initial concentration profile (31); dispersing the initial concentration profile (31) to form a dispersed concentration profile (32); directing the dispersed concentration profile (32) into a detection channel (12) to form a final symmetrical concentration profile (33) therein; introducing a target into the detection channel (12) to obtain a combined concentration profile including a constant target concentration profile overlying the final symmetrical concentration profile (33); holding in the detection channel (12) at least one half of the combined concentration profile; and optically scanning the combined concentration profile to detect an optical signal representative of the biological response of the target to the soluble candidate substance.

Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.

Abstract: The present invention relates to variants with improved activity in an amide-bond reaction. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

Abstract: A process for enzymatically converting a furanoside substrate in a product of interest, includes contacting the substrate with an enzyme in presence of an alcohol acceptor, wherein the enzyme is preferably Araf51, and wherein the product is preferably an alkyl furanoside. The mutant Araf51 enzyme showing improved transglycosylation activity in comparison with the native wild-type (wt) Araf51 enzyme, and a method for screening the mutants are also described.

Abstract: The disclosure relates to methods of detecting a neural injury biomarker in a biological sample. The method includes subjecting a biological sample to an assay disclosed that produces a measurable signal and detecting the measurable signal. The presence or absence of the measurable signal indicates the presence or absence of the neural injury biomarker in the sample, and thereby diagnosing a subject as having a neural injury. The disclosure further relates to methods of determining the state of a subject's neural injury. Further disclosed are systems and devices useful in carrying out the methods disclosed.

Abstract: Disclosed is a microcapsule encoded depending on the kind of a target substance included therein. The encoded microcapsule has a hydrophilic liquid core including the target substance and a hydrophobic shell surrounding the liquid core. The encoded microcapsule includes graphical codes introduced on the surface of the shell.

Abstract: Methods for the evolution of NADPH specific ketol-acid reductoisomerase enzymes to acquire NADH specificity are provided. Specific mutant ketol-acid reductoisomerase enzymes isolated from Pseudomonas that have undergone co-factor switching to utilize NADH are described.

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 provides.

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: Provided are a method for measuring histone methyltransferase activity, a method for screening for compounds that inhibit histone methyltransferase activity, a reagent kit for measuring histone methyltransferase activity, and a kit for screening for compounds that inhibit histone methyltransferase activity. A substrate compound represented by general formula (I): R1-X-K-R2 (I), or a salt thereof, wherein R1 represents a hydrogen atom or a protecting group for an amino terminus; X represents a peptide consisting of 0 or 1 or more amino acid residues; K represents a lysine residue; and R2 represents a dye label linked via an amide bond to the carbonyl terminus of a lysine residue, wherein the cleavage of the amide bond by peptidase changes the fluorescence property or chromogenic property of the dye label, and the methylation of the ? amino group of the lysine residue by the histone methyltransferase decreases susceptibility to peptidase, is used.

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: The invention provides a fluorescence polarization (FP)-based assay to identify inhibitors of resolvase's DNA cleavage activity. The invention also provides resolvase inhibitors identified by the assay, as well as derivatives and analogs thereof. In certain embodiments, the compounds of the invention are useful to treat a poxvirus infection in an infected subject.

Abstract: The present invention concerns a method for the screening of antibacterial substances comprising a step of determining the ability of a candidate substance to inhibit the activity of a purified enzyme selected from the group consisting of: (i) a D-aspartate ligase comprising a polypeptide having an amino acid sequence possessing at least 50% amino acid identity with an amino acid sequence selected from the group consisting of SEQ ID No 1 to SEQ ID No 10, or a biologically active fragment thereof; and (ii) a L,D-transpeptidase comprising a polypeptide having an amino acid sequence possessing at least 50% amino acid identity with the amino acid sequence of SEQ ID No 11, or a biologically active fragment thereof.

Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.

Abstract: In one aspect, the invention relates to a method for identifying a compound which modulates the activity of a voltage-gated protein. In certain embodiments, the voltage gate protein is a voltage-gated ion channel. In certain embodiments, the voltage-gated protein is a voltage sensitive phosphatase. In certain embodiments, the voltage-gated protein used in conjunction with the methods of the invention is modified to altered permeability or voltage sensitivity.

Abstract: A luminescence detecting apparatus and method for analyzing luminescent samples is disclosed. Luminescent samples are placed in a plurality of sample wells in a tray, and the tray is placed in a visible-light impervious chamber containing a charge coupled device camera. The samples may be injected in the wells, and the samples may be injected with buffers and reagents, by an injector. In the chamber, light from the luminescent samples pass through a collimator, a Fresnel field lens, a filter, and a camera lens, whereupon a focused image is created by the optics on the charge-coupled device (CCD) camera. The use of a Fresnel field lens, in combination with a collimator and filter, reduces crosstalk between samples below the level attainable by the prior art. Preferred embodiments of the luminescence detecting apparatus and method disclosed include central processing control of all operations, multiple wavelength filter wheel, and robot handling of samples and reagents.

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: Disclosed herein are methods of treating a patient at risk of developing or having a neurofibromatosis or a sporadic schwannoma. In exemplary embodiments, the method involves administering to a subject in need an effective amount of a modulator of a target related to neurofibromatosis. Also disclosed are screening assays involving the implementation of Merlin-null Schwann cells, and to compounds identified using same.

Abstract: Carbon monoxide (CO) is a member of the gasotransmitter family that includes NO and H2S and is implicated in a variety of pathological and physiological conditions. Whereas exogenous therapeutic additions of CO to tissues and whole animals have been well studied, the real-time spatial and temporal tracking of CO at the cellular level remains an open challenge. We now report a new type of turn-on fluorescent probe for selective CO detection by exploiting palladium-mediated carbonylation reactivity. The compounds of the invention are capable of detecting CO both in aqueous buffer and in live cells with high selectivity over a range of biologically relevant reactive small molecules, providing a potentially powerful approach for interrogating its chemistry in biological systems.

Abstract: Provided herein are compositions and methods for identifying and detecting modulators of Ras protein conformational states through the use of second harmonic generation (SHG) technology. Also provided herein are methods for detecting a conformational changes in the three dimensional structure of a protein bound to a supported lipid bilayer.

Abstract: The present invention relates to modulators, in particular inhibitors, of the expression and/or the function of NADPH Oxidase 4 (Nox4) for use in the prevention and/or treatment of nerve injury, in particular pain, more particularly neuropathic pain. Further disclosed is a method for the identification of Nox4 modulators, a pharmaceutical composition comprising a Nox4 inhibitor and a method for preventing and treating pain, in particular neuropathic pain, in a subject in need of such a treatment. Also, the invention relates to modulators, in particular inhibitors, of the expression and/or the function of NADPH Oxidase 4 (Nox4) for use in the prevention and/or treatment of nerve injury associated with dysmyelination and methods for preventing and treating dysmyelination and diseases associated with dysmyelination.

Abstract: Methods of screening for candidate compounds capable of inhibiting activity of fyn in phosphorylating tau protein at Y394 or binding to fyn to inhibit interaction with tau protein at Y394, including determining whether, and optionally the extent, the candidate compounds have these capabilities under conditions where fyn has these capabilities in the absence of the candidate compound. Methods of screening for substances capable of promoting dephosphorylation of tau protein by a phosphatase at a site of tau protein including contacting a candidate substance, the tau protein and a phosphatase capable of dephosphorylating the tau protein under conditions where the phosphatase is capable of dephosphorylating the site in absence of the candidate substance, where the kinase is fyn; determining whether, and optionally the extent, the candidate substance promotes dephosphorylation of the tau protein at the site; and selecting the candidate substance which promotes dephosphorylation of the tau protein the sites.

Abstract: Means of determining the condition of the oral cavity in a subject is provided. The condition of the oral cavity in the subject is determined by using an analytical tool comprising the following (A), (B), and (C): (A) a reagent for measuring one or more parameters that reflect the dental caries risk for a test sample obtained from the oral cavity, (B) a reagent for measuring one or more parameters that reflect the periodontal disease risk for the test sample obtained from the oral cavity, and (C) a reagent for measuring one or more parameters that reflect the degree of oral cleanliness for the test sample obtained from the oral cavity.

Abstract: Embodiments of the present invention provide methods, microfluidic devices, and systems for the detection of an active target agent in a fluid sample. A substrate molecule is used that contains a sequence which may cleave in the presence of an active target agent. A SNAP25 sequence is described, for example, that may be cleaved in the presence of Botulinum Neurotoxin. The substrate molecule includes a reporter moiety. The substrate molecule is exposed to the sample, and resulting reaction products separated using electrophoretic separation. The elution time of the reporter moiety may be utilized to identify the presence or absence of the active target agent.

Abstract: The invention relates to a method for selecting a sequence set from a library of expressed nucleic acid sequences, wherein cells are provided, each cell comprises an expressed nucleic acid sequence expressed as a target protein. The cells are encapsulated by treating them with a cationic polysaccharide and subsequently treating them with an anionic polysaccharide, yielding encapsulated cells, perforating the membrane of the encapsulated cells, yielding solubilized compartments, contacting them with a ligand to said target protein, the ligand bearing a detectable label, and selecting a subset of solubilized compartments as a function of detectable label and isolating the expressed nucleic acid sequences from the selection as a selected sequence set.

Abstract: An electrochemical method for measuring the activity of enzymes using nanoelectrode arrays fabricated with vertically aligned carbon nanofibers. Short peptide substrates specific to disease-related enzymes are covalently attached to the exposed nanofiber tips. A redox moiety, such as ferrocene, can be linked at the distal end of the nanofibers. Contact of the arrays with a biological sample containing one or more target enzymes results in cleavage of the peptides and changes the redox signal of the redox moiety indicating the presence of the target enzymes.

Abstract: Methods and kits for enzymes involved in post-translational modifications are provided. The methods employ elemental analysis, including ICP-MS.

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 in some embodiments is a non-naturally occurring variant of a wild type restriction enzyme defined by SEQ ID NO: 20, wherein the variant has at least a 2 fold increase in cleavage at 5-? glucosylhydroxymethylcytosine (5?ghmC) compared with methylcytosine relative to the wild type enzyme. Methods for examining hydroxymethylation of a DNA sample using the variant enzyme are also provided.

Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.

Abstract: There is provided a method for quantifying a subject substance, of which typical examples are amino acids. The method of the present invention comprises the following steps: the step of allowing an enzyme that can generate pyrophosphate by using adenosine triphosphate (ATP) as a substrate with converting the subject substance to act on the subject substance to generate pyrophosphate; the step of allowing pyruvate pyrophosphate dikinase (PPDK) to act on the generated pyrophosphate in the presence of adenosine monophosphate (AMP) and phosphoenolpyruvate (PEP) to generate ATP, phosphoric acid, and pyruvate; and the step of quantifying the generated pyruvate, and amount of the subject substance is determined on the basis of the obtained amount of pyruvate. According to the present invention, an amino acid in a biological sample containing a lot of various kinds of contaminants such as inorganic phosphoric acid and urea can be conveniently and quickly quantified without being influenced by the contaminants.

Abstract: Provided are compositions comprising a cocaine esterase (CocE) and a compound that thermostabilizes the CocE. Also provided are methods of thermostabilizing a cocaine esterase. Additionally provided are methods of treating a mammal undergoing a cocaine-induced condition. Methods of determining whether a compound is a thermostabilizing agent for a protein are also provided. Uses of the above-described compositions for the treatment of a cocaine-induced condition is additionally provided. Additionally provided is an isolated nucleic acid encoding a CocE polypeptide having the substitutions L169K and G173Q, and the CocE polypeptide encoded by that nucleic acid, and pharmaceutical compositions thereof. Further provided is the use of that composition for the manufacture of a medicament for the treatment of a cocaine-induced condition and for the treatment of a cocaine-induced condition.

Abstract: This invention relates to therapeutic compounds which are inhibitors of serine proteases, to pharmaceutical compositions thereof and to their use in the treatment of the human or animal body. More specifically, the present invention relates to a method for the treatment, diagnosis or prognosis of skin diseases comprising the administration to a subject in need thereof of a therapeutically effective amount of a Serine protease inhibitor.

Abstract: Provided in certain embodiments are new methods for forming azido modified nucleic acid conjugates of reporter molecules, carrier molecules or solid support. In other embodiments are provided methods for enzymatically labeling nucleic acids with an azide group.

Abstract: Novel ALK and NTRK1 fusion molecules and uses are disclosed.