Abstract: The present invention provides methods to characterize the structure, stability, and intersubunit interfaces between the matrix, capsid, and nucleocapsid domains of the Gag polyprotein during HIV capsid assembly and maturation. A method of screening for compounds that promote or inhibit viral assembly and maturation is disclosed. A novel mass spectrometry based approach to measure hydrogen/deuterium exchange profiles is also disclosed. Quantitative data resulted from these studies may lead to well defined capsid assembly assays that can be adapted for rapid antiviral drug screening.

Abstract: Methods and compositions for identifying or detecting viral nucleic acids in a host cell are described. DNA fragments are bound to DNA-binding protein in a host cell and enriched using immunoprecipitation. The enriched fragments are then hybridized to a microarray containing sequences complementary to proviral DNA and genomic DNA.

Abstract: Disclosed are methods and compositions for creating a DNA, RNA or protein molecule with two or more nucleic acid or polypeptide domains, respectively, joined by a linker region. These methods are used to generate random linker libraries of nucleic acids that encode dual-domain or multi-domain polypeptides. The linker regions are characterized by both length and sequence variability.

Abstract: This invention is an oligomer-based analog neural network (ANN) comprising weight and saturation oligomers, the concentrations of which are selected such that activation of the ANN by a set of input oligomers generates a set of output oligomers, the sequences and relative concentrations of which are dependent on the sequences and relative concentrations of the input oligomers. The invention further includes methods for using such an ANN for solving any problems amenable to solution by a trained neural network. A preferred embodiment of the claimed invention is a DNA-based ANN that accepts cDNA molecules as inputs and analyzes the gene expression profile of the cells from which the cDNA is derived. The DNA-based ANN is typically trained with a computer to identify the weights giving accurate mapping of the inputs to the outputs; and the concentrations of weight oligomers of the DNA-based ANN are then selected accordingly.

Abstract: The present invention provides non-invasive methods for detecting, monitoring, staging, and diagnosing malignant melanoma in a skin sample of a subject. The methods include analyzing expression in skin sample of one or more melanoma skin markers. The melanoma skin markers include IL-1 RI, endothelin-2, ephrin-A5, IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (?A subunit), TNF RII, SPC4, and CNTF R?. The skin sample can include nucleic acids, and can be a human skin sample from a lesion suspected of being melanoma.

Abstract: The health condition of a living organism is detected by electrochemically analyzing samples from selected areas of the body of said living organism for elevated free levels of nucleotide excision products resulting from DNA or RNA damage.

Abstract: The invention relates to the use of scaffold proteins, particularly green fluorescent protein (GFP), in fusion constructs with random and defined peptides and peptide libraries, to increase the cellular expression levels, decrease the cellular catabolism, increase the conformational stability relative to linear peptides, and to increase the steady state concentrations of the library peptides and peptide library members expressed in cells for the purpose of detecting the presence of the peptides and screening peptide libraries. N-terminal, C-terminal, dual N- and C-terminal and one or more internal fusions are all contemplated. Novel fusions utilizing self-binding peptides to create a conformationally stabilized fusion domain are also contemplated.

Abstract: This invention relates to an isolated nucleic acid molecule which is a) a nucleic acid molecule comprising SEQ ID No. 3, or b) a nucleic acid molecule which exhibits at least 90% sequence identity to the nucleic acid molecule of SEQ ID No. 3, and the claimed nucleic acid molecule encodes luciferase. It also relates to an expression vector and to a transformed host cell.

Abstract: A novel method for characterizing nucleic acids. A nucleic acid is combined with a double stranded nucleic acid-specific dye to form a detectable complex between the dye and one or more double stranded structures within the nucleic acid. The combination is then exposed to varying temperatures and the fluorescence emission of the dye is measured to determine the melting temperature(s) for the double stranded structures. In some embodiments that melting temperature profile is then compared to melting temperature profiles generated for other nucleic acid(s) to discern differences between the compared nucleic acids.

Abstract: Disclosed are compositions and methods for amplification of nucleic acid sequences of interest. It has been discovered that amplification reactions can produce amplification products of high quality, such as low amplification bias, if performed on an amount of nucleic acid at or over a threshold amount and/or on nucleic acids at or below a threshold concentration. The threshold amount and concentration can vary depending on the nature and source of the nucleic acids to be amplified and the type of amplification reaction employed. Disclosed is a method of determining the threshold amount and/or threshold concentration of nucleic acids that can be used with nucleic acid samples of interest in amplification reactions of interest. Because amplification reactions can produce high quality amplification products, such as low bias amplification products, below the threshold amount and/or concentration of nucleic acid, such below-threshold amounts and/or concentrations can be used in amplification reactions.

Abstract: The subject invention pertains to a method for the production of an array of molecules immobilised on a substrate, comprising the deposition of the molecules from a micropipette containing them, onto the substrate, in a liquid environment, wherein the distance of the micropipette from the substrate is controlled in response to the ion current in the liquid. This method is particularly suitable for the deposition of biological molecules. The subject invention also pertains to an array of biological molecules deposited on a substrate.

Abstract: The present invention is intended to elucidate the cause of severe cardiomyopathy in subline (T) not manifesting the macroscopic cardiac hypertrophy, which has been separated from a hamster (B) with hypertrophic cardiomyopathy and clarify the pathogenic cause of dilated cardiomyopathy, thereby establishing a method of detecting and identifying dilated cardiomyopathy and a method of preventing and treating the same. The present invention relates to a desmin gene having a point mutation at the site corresponding to the 571-position of the base sequence in the cDNA translation region of Syrian hamster; a polypeptide thereof; and an oligonucleotide consisting of 5 to 250 bases including the point mutation site or an oligonucleotide having a sequence complementary thereto.

Abstract: This disclosure provides TRT antisense oligonucleotides, methods of detecting TRT, methods of diagnosing telomerase-related conditions, methods of diagnosing and providing a prognosis for cancer, and methods of treating telomerase-related conditions, including cancer.

Abstract: The invention relates to the determination of the genomic structure of HERG which is a gene associated with long QT syndrome. The sequences of the 15 intron/exon junctions has been determined and this information is useful in devising primers for amplifying and sequencing across all of the exons of the gene. This is useful for determining the presence or absence of mutations which are known to cause long QT syndrome. Also disclosed are many new mutations in HERG which have been found to be associated with long QT syndrome.

Abstract: Provided are a method for preparing an array for authenticating biological samples and a method for authenticating the biological samples based on analysis of variable sequences of ribosomal RNA genes as well as a kit for authentication of the biological samples. The hybridization of probes of the samples to the array of overlapping fragments of authentic variable ribosomal RNA gene regions is quantified. The test enables distinction of species or prokaryotic strains and is unaffected by intra-species or strain polymorphism. The method disclosed is illustrated by authentication of traditional Chinese medicinal materials.

Abstract: The present invention provides methods and compositions for interaction trap assays for detecting protein-protein, protein-DNA, or protein-RNA interactions. The methods and compositions of the invention may also be used to identify agents which may agonize or antagonize a protein-protein, protein-DNA, or protein-RNA interactions. In certain embodiments, the interaction trap system of the invention is useful for screening libraries with greater than 107 members. In other embodiments, the interaction trap system of the invention is used in conjunction with flow cytometry. The invention further provides a means for simultaneously screening a target protein or nucleic acid sequence for the ability to interact with two or more test proteins or nucleic acids.

Abstract: Disclosed herein are point mutations in the LMNA gene that cause HGPS. These mutations activate a cryptic splice site within the LMNA gene, which leads to deletion of part of exon 11 and generation of a mutant Lamin A protein product that is 50 amino acids shorter than the normal protein. In addition to the novel Lamin A variant protein and nucleic acids encoding this variant, methods of using these molecules in detecting biological conditions associated with a LMNA mutation in a subject (e.g., HGPS, arteriosclerosis, and other age-related diseases), methods of treating such conditions, methods of selecting treatments, methods of screening for compounds that influence Lamin A activity, and methods of influencing the expression of LMNA or LMNA variants are also described.

Abstract: A novel gene designated as FRAG1 from and its encoded protein is disclosed. A fusion protein called FGFR2-ROS, which is formed by chromosomal rearrangement of rat FRAG1 with FGFR2 is also disclosed. Methods of producing FRAG1 protein, related fusion proteins, and antibodies against FRAG1 are disclosed, as are related pharmaceuticals and methods of using such nucleic acids, polypeptides, and antibodies are also disclosed.

Abstract: Probes for detecting a target polynucleotide are provided. One aspect provides a molecular beacon probe set wherein the donor molecular beacon comprises a quantum dot and an acceptor molecular beacon comprises at least one reporter. The probes optionally comprise a protein transduction domain, targeting signal, or a combination thereof. Methods for detecting target polynucleotides using the disclosed probes are also provided.

Abstract: Compositions and methods for fluorescent detection of nucleic acids are provided. The compositions can be detected by fluorescence when hybridized to a nucleic acid containing a target sequence, but are non-fluorescent in the non-hybridized state. Alternatively, the fluorescence properties of the compositions change in a detectable manner upon hybridization to a nucleic acid containing a target sequence. Methods for synthesis and methods of use of the compositions are also provided.

Abstract: An object of the present invention is to provide an allele specific primer which is accompanied by less possibility of the false positive and enables definite discrimination when a base immediately adjacent to on the 3? side of a target SNP base is A, while a base adjacent with one base spaced apart is T. According to the present invention, the 3? end base is designed to be the base corresponding to SNP; the second base from the 3? end to be C; the third base from the 3? end to be any one of T, C or G; and the base sequence of from the fourth from the 3? end to the 5? end base to be complementary to the sequence of from a base three bases away from the target SNP base on the 3? side to a desired base.

Abstract: An immobilizing device for biological material comprises a rigid support (12) carrying a substrate layer (20, 20?) of polymer having biological immobilizing properties, e.g. for amino and nucleic acids. Substantially solid ultra-thin substrate layers (20?) having a thickness less than about 5 micron, preferably between about 0.1 and 0.5 micron, and micro-porous, ultra-thin substrate layers (20?) having a thickness less than about 5 micron, preferably less than 3 micron, 2 or 1 micron are shown, which may be segmented by isolating moats M. The substrate layer is on a microscope slide (302), round disc (122), bio-cassette, at the bottom of a well of a multiwell plate, and as a coating inside a tube. Fluorescence or luminescence intensity and geometric calibration spots (420) are shown. Reading is enhanced by the intensity calibration spots. (420) to enable normalization of readings under uneven illumination conditions, as when reading by dark field, side illumination mode.

Abstract: An object of the present invention is to provide an allele specific primer which is accompanied by less possibility of the false positive and enables definite discrimination when a base immediately adjacent to on the 3? side of a target SNP base is C, while a base adjacent with one base spaced apart is C. According to the present invention, the 3? end base is designed to be the base corresponding to SNP; the second and the third bases from the 3? end to be 5?-AT-3?, 5?-TA-3?, 5?-TT-3? or 5?-CT-3?; and the base sequence of from the fourth from the 3? end to the 5? end base to be completely complementary to the sequence of from a base three bases away from the target SNP base on the 3? side to a desired base.

Abstract: An object of the present invention is to provide an allele specific primer which is accompanied by less possibility of the false positive and enables definite discrimination when a base immediately adjacent to on the 3? side of a target SNP base is C, while a base adjacent with one base spaced apart is T. According to the present invention, the 3? end base is designed to be the base corresponding to SNP; the second base from the 3? end to be T; the third base from the 3? end to be any one of T, G or C; and the base sequence of from the fourth from the 3? end to the 5? end base to be completely complementary to the sequence of from a base three bases away from the target SNP base on the 3? side to a desired base.

Abstract: Monoclonal antibodies are provided which bind to heat-treated proteins of meats. The antibodies are useful in detecting the presence of an exogenous meat in a cooked or raw meat sample. Furthermore, the antibodies can be used to determine the end point temperature of a meat sample.

Abstract: A peptide or protein microassay method and apparatus in which a wide variety of chromogenic or fluorogenic peptide or protein substrates of interest are individually suspended or dissolved in a hydrophilic carrier, with aliquots of each substrate being deposited in an array or microarray of reaction loci, or “dots.” Each dot, therefore, provides an individual reaction vessel containing the peptide or protein of interest, to which a biological sample may be applied for assay purposes. The sample is applied to the array or microarray of dots by one of a variety of focused sample application techniques, including aerosolizing or misting of the sample, or target application of the sample, onto each dot without creating fluid channels between the dots which would cause cross-contamination. In additional aspects, the present invention provides methods of transferring samples from an electrophoretic gel to a target plate for subsequent MALDI MS analysis.

Abstract: The present invention provides devices, methods and kits for detecting the presence of an analyte in a liquid sample. The invention provides devices having a positive control area covered with an opaque, movable material, such as an ink, dye, or other material, that is moved on the device by the flow of liquid sample, thereby exposing the positive control area underneath. Using the interaction of colored signals from the positive control area and the analyte binding area, a recognizable symbol is revealed on the device that correlates with the test results, and appears as the test is conducted.

Abstract: Described herein are methods of identifying a transmembrane receptor (TMR) agonist and compounds identified by this method. The TMR agonist (TMRA) is capable of activating TMR signaling while exhibiting reduced TMR internalization over a control compound.

Abstract: Sequences and partial sequences for three types of mammalian (human and rat) sequences identified) T-type calcium channel subunits which we have labeled as the ?1G, ?1H and ?1I subunits are provided. Knowledge of the sequence of these calcium channel permits the localization and recovery of the complete sequence from human cells, and the development of cell lines which express the novel calcium channels of the invention. These cells may be used for identifying compounds capable of acting as agonists or antagonists to the calcium channels.

Abstract: A new method of evaluating the ability of drug molecules to penetrate the cornea is described. The permeation rate of the drug molecules in MDCK cells is utilized to predict the ability of the molecules to penetrate the cornea. The method is useful for in vitro screening of potential new ophthalmic drugs, as well as in the design of new drug molecules for topical ocular administration.

Abstract: Nucleoside diphosphates (NDPs) are detected or measured by following the dephosphorylation of the phosphoenzyme form of nucleoside diphosphate kinase (NDPK), and nucleoside triphosphates (NTPs) are detected or measured by following the phosphorylation of NDPK to its phosphoenozyme form. A typical process involves (a) causing NDP in sample to bind to NDPK phosphoenzyme, or causing NTP in sample to phosphorylate NDPK and (b) detecting a change in a characteristic of the enzyme which differs between its phosphorylated and unphosphorylated forms. This may be aided by labelling the enzyme. Quantitative data can be obtained. Both in vivo and in vitro measurements can be made.

Abstract: Provided are crystals relating to FAP? and its various uses.

Abstract: The invention provides a protein in a form that is functional for the enzymatic conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate to 1-hydroxy-2-methyl-2-butenyl 4-diphosphate notably in its (E)-form of the non-mevalonate biosynthetic pathway to isoprenoids. The invention also provides a protein in a form that is functional for the enzymatic conversion of 1-hydroxy-2-methyl-2-butenyl 4-diphosphate, notably in its (E)-form, to isopentenyl diphosphate and/or dimethylallyl diphosphate. Further, screening methods for inhibitors of these proteins are provided. Further, 1-hydroxy-2-methyl-2-butenyl 4-diphosphate is provided and chemical and enzymatic methods of its preparation.

Abstract: Disclosed are a method of adhering active enzymes to an inert support, the product produced thereby, and a method of using the enzyme-coated support in enzyme-catalyzed reactions such as the glucose isomerase-catalyzed conversion of glucose to fructose. The method includes the steps of coating an inert support with a cationic copolymer, preferably a polyamine, and most preferably a di-C1-C6-alkylamino-epichlorohydrin copolymer, and then adhering enzyme to the coated support in the absence of any intervening cross-linking agent.

Abstract: The invention includes a multitude of methods and compositions for remodeling a peptide molecule, including the addition or deletion of one or more glycosyl groups to a peptide, and/or the addition of a modifying group to a peptide.

Abstract: From fish egg skin produced by utilization of roe grains of various fish, constituent proteins thereof are enzymatically degraded to obtain peptides and amino acids, of which effective utilization is achieved. The invention provides a method for producing amino acids and peptides (useful as nutrient enhancers for foods) from fish egg skins which comprises treating cold water-washed fish egg skins with ozonized water at room temperature or below, subsequently, degrading the resultant product with a proteolytic enzyme produced by Bacillus subtilis, or further treating with a proteolytic enzyme produced by Aspergillus oryzae, to degrade myogenic fiber proteins (contractile proteins: myosins) in the fish egg skin, and then concentrating/drying the degraded solution.

Abstract: A gene encoding glutathione synthetase from Candida utilis is provided and food containing ?-glutamylcysteine cysteine or cystenylglycine is produced by cultivating Candida utilis modified by means of a gene encoding glutathione synthetase under a suitable condition and mixing the obtained culture or a fraction thereof or the culture or a fraction thereof subjected to heat treatment with a raw material of food or drink to process food or drink.

Abstract: A method of reducing superoxide damage to a cell is disclosed. In one embodiment, this method comprises the step of engineering the cell to produce more than a native amount of the YggX protein or its homolog, wherein the cells are rendered more resistant to superoxide damage.

Abstract: Novel zinc finger proteins and nucleic acids encoding the proteins are provided. The zinc finger proteins interact with ZNF202, a zinc finger protein that regulates the expression of a variety of genes involved in lipid metabolism and transportation. Modulation of the novel zinc finger proteins and their interactions with ZNF202 can be useful in the treatment of coronary heart diseases, dyslipidemia, dyscholesterolemia and obesity.

Abstract: Use of a polypeptide or protein with amino acid sequence corresponding substantially to AFP-type III HPLC 12 as additive in a product for improvement of said product, said improvement residing in improved properties of modification of ice crystal growth processes influencing size and shape characteristics of ice in particular in regrowth thereby e.g. minimising potential freezing damage e.g. by preventing or inhibiting ice recrystallisation of the product upon freezing, said use occurring in a manner known per se for anti freeze peptides to obtain higher specific modification activity in particular antifreeze activity than obtainable with the same amount of Winter Flounder AFP.

Abstract: An oligonucleotide for cleavage, detection or amplification of the mecA gene, a gene element of methicillin-resistant Staphylococcus aureus (MRSA), or RNA derived from said gene is provided. Further, a method for detecting the mecA gene is provided.

Abstract: The invention provides methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension. Some applications of the invention utilize total internal reflection fluorescence microscopy to image polynucleotide molecules at single molecule resolution.

Abstract: The invention provides compositions containing a mixture of (a) an enzyme that possesses substantial 3?-5? exonuclease activity (b) a DNA polymerase with less 3?-5? exonuclease activity than the enzyme with substantial 3?-5? exonuclease activity. Preferably, the DNA polymerase for inclusion in the compositions are DNA polymerases that substantially lack 3?-5? exonuclease activity. A preferred embodiment of the invention is a composition comprising Taq DNA polymerase (isolated from Thermus aquaticus) and Pfu DNA polymerase (isolated from Pvrococcus furiosus). Another aspect of the invention is to provide methods for synthesizing polynucleotides using compositions comprising an enzyme that possesses substantial 3?-5? exonuclease activity and a DNA polymerase with less 3?-5? exonuclease activity than the enzymes possessing substantial 3?-5? exonuclease activity, preferably a DNA polymerase that substantially lacks 3?-5? exonuclease activity.

Abstract: Large circular (LC)-sense molecules in an array is disclosed. The LC-sense molecules array is combined with cDNA hybridization to detect differences in expression profile between different cells. LC-sense molecules were purified from nonredundant clones with recombinant phagemid and arrayed onto silanized slide glasses. By hybridization of LC-sense array with Cy3 or Cy5-labelled cDNA preparations at 60° C., 29 up-regulated and 6 down-regulated genes in cancerous liver tissue were detected.

Abstract: A DNA fragment which encodes a polypeptide defined in the following (a) or (b), and a polypeptide defined in the following (c) or (d): (a) a polypeptide which has at least the amino acid sequence of the amino acid numbers 50 to 393 in SEQ ID NO: 2 shown in Sequence Listing, (b) a polypeptide which has at least the amino acid sequence of the amino acid numbers 50 to 393 in SEQ ID NO: 2 shown in Sequence Listing including substitution, deletion, insertion, addition, or inversion of one or several amino acids, and can constitute a protein having a carbamoyl-phosphate synthetase activity with a large subunit of carbamoyl-phosphate synthetase having the amino acid sequence of SEQ ID NO: 3, (c) a polypeptide which has the amino acid sequence of SEQ ID NO: 3 shown in Sequence Listing, (d) a polypeptide which has the amino acid sequence of SEQ ID NO: 3 shown in Sequence Listing including substitution, deletion, insertion, addition, or inversion of one or several amino acids, and can constitute a protein having a car

Abstract: Compositions comprising a plurality of yeast cells, wherein said plurality of yeast cells have been cultured in the presence of an alternating electric field having a specific frequency and a specific field strength for a period of time sufficient to increase the capability of said plurality of yeast cells to treat epilepsy. Also included are methods of making such compositions and methods of treating epilepsy.

Abstract: The present invention relates to elongase genes, their polypeptides and their control regions, and the use of such genes, polypeptides and control regions in determining compositions for use in the treatment of disease. The identified compositions regulate the expression of the elongase genes or modulate the activity of their protein products. The nucleotide and amino acid sequences are taught for ELG4, ELG6 and ELG7. The control sequences and function are taught for ELG1, ELG2, ELG3, ELG4, ELG5, ELG6 and ELG7.

Abstract: This invention provides genes and their encoded proteins, involved in the biosynthesis of farnesyl dibenzodiazepinones, including ECO-04601. The invention relates to expression vectors comprising the genes and to host cell transformed with these vectors. The invention further relates to methods of producing farnesyl dibenzodiazepinone compounds using the genes and proteins of the invention, for example, involving expression of biosynthetic pathway genes in transformed host cells.

Abstract: This invention provides compositions, organisms and methodologies employing a novel human protein kinase, MCRK1. The novel human kinase has sequence homology to rat myotonic dystrophy kinase-related Cdc42 binding kinase (MRCK) alpha. The gene encoding the novel kinase is localized in locus 11q13 of human chromosome 11. The novel protein kinase comprises multiple functional/structural domains that include a kinase domain, a pkinase_C domain, a DAG-PE binding domain, and a CNH domain. The sequence and structure similarity between the novel human protein and rat MRCK alpha indicates that the novel human protein may function as a downstream effector of Cdc42 in cytoskeleton reorganization.

Abstract: DNA isolates coding for human DNase and methods of obtaining such DNA are provided, together with expression systems for recombinant production of human DNase useful in therapeutic or diagnostic compositions.