Abstract: A method of identifying nucleic acid samples comprising:

Abstract: The invention provides methods of distinguishing benign growths arising from congenital melanocytic nevi from malignant melanoma. The methods comprise detecting a change in chromosome number that is specifically associated with benign growths. These changes include a gain of chromosome 10, a gain of chromosome 11, and a loss of chromosome 7.

Abstract: The present invention is based at least in part on the discovery of polymorphisms within the endothelin-1 (EDN1) gene. Accordingly, the invention provides nucleic acid molecules having a nucleotide sequence of an allelic variant of an EDN1 gene. The invention also provides methods for identifying specific alleles of polymorphic regions of an EDN1 gene, methods for determining whether a subject has or is at risk of developing a disease which is associated with a specific allele of a polymorphic region of an EDN1 gene, e.g., a vascular disease, based on detection of one or more polymorphisms within the EDN1 gene, and kits for performing such methods. The invention further provides methods for identifying a subject who has, or is at risk for developing, a vascular disease or disorder as a candidate for a particular clinical course of therapy or a particular diagnostic evaluation.

Abstract: The laminin &ggr;2 subunit of equine laminin-5 gene has been cloned and the nucleic acid and corresponding protein amino acid sequence is provided. A method of diagnosing junctional epidermolysis bullosa in horses is also provided based on the determination that a mutation in the laminin &ggr;2 gene in which a cytosine is inserted at position 1368 is associated with the disease.

Abstract: The present invention relates to all facets of novel polynucleotides, the polypeptides they encode, antibodies and specific binding partners thereto, and their applications to research, diagnosis, drug discovery, therapy, clinical medicine, forensic science and medicine, etc. The polynucleotides, Urb-ctf, are expressed in breast cancer and are therefore useful in variety of ways, including, but not limited to, as molecular markers, as drug targets, and for detecting, diagnosing, staging, monitoring, prognosticating, preventing or treating, determining predisposition to, etc., diseases and conditions especially related to breast cancer.

Abstract: A method is provided for identifying multiple different activated transcription factors in a cell sample. The method comprises transducing or transfecting a cell sample to comprise a library of constructs. Each construct comprises a cis element sequence including one or more copies of a cis element to which a transcription factor is capable of binding. The cis element sequence varies within the library of constructs and include a promoter sequence 3′ relative to the cis element sequence, and a reporter sequence 3′ relative to the promoter sequence that comprises a variable sequence that varies within the library wherein a same cis element sequence is employed with a given reporter sequence within the library of constructs.

Abstract: Methods to predict a patient's responsiveness to 5-HT3 receptor antagonists are disclosed. The methods allow a clinician to predict a patient's responsiveness to 5-HT3 receptor antagonists by determining the correlation that exists between a genotype in the promoter region of the gene encoding a serotonin transporter protein and patient response to 5-HT3 receptor antagonist therapy. In addition, methods to treat patients suffering from diarrhea-predominant irritable bowel syndrome and methods to identify a patient population for inclusion in a 5-HT3 receptor antagonist clinical trial are disclosed.

Abstract: A method for single molecule identification of a target DNA molecule in a random coil state having the following steps: a) attaching an optically distinguishable material to a DNA sequence recognition unit; b) hybridizing the DNA sequence recognition unit to the target DNA molecule in a random coil state to form a hybridized DNA complex in a random coil state; c) stretching the hybridized DNA complex in a random coil state to form a hybridized DNA complex in a substantially linear configuration; and d) detecting the optically distinguishable material in a sequential manner along the substantially linear hybridized DNA complex, thereby identifying the target DNA molecule.

Abstract: The present invention provides an apparatus and a method for the synthesis of arrays of oligomers that have tight illumination intensity requirement. The apparatus and the method contains a mechanism to correct for illumination nonuniformity during the oligomer array synthesis process. To correct for illumination nonuniformity, the illumination intensity of different oligomer synthesis positions across an area in which oligomers are synthesized are determined first. Then, the difference in illumination intensity among the positions are evaluated mathematically. Next, any nonuniformity in illumination intensity is corrected by either reducing the intensity of the light for the brighter positions before the light reaches the illumination area or reducing the illumination time of the brighter positions during one protection group deprotection period.

Abstract: A method, apparatus and computer program products relating to the reading of chemical arrays and extracting feature characteristics therefrom. In a method multiple chemical arrays each having a plurality of features, are read to obtain array signal data. The array signal data for the multiple arrays is saved in a memory. The saved signal data for chemical arrays is retrieved from the memory and feature characteristics extracted therefrom, wherein the saved signal data for a chemical array is extracted while another chemical array is being read.

Abstract: The present invention is directed to the identification of markers that can be used to determine whether tumors are sensitive or resistant to a therapeutic agent. The present invention is also directed to the identification of therapeutic targets. The invention features a number of sensitivity and resistance markers. These are markers that are expressed in most or all cell lines that are sensitive to treatment with an agent and which are not expressed (or are expressed at a rather low level) in cells that are resistant to treatment with that agent. The invention also features a number of “resistance markers.” These are markers that are expressed in most or all cell lines that are resistant to treatment with an agent and which are not expressed (or are expressed at a rather low level) in cells that are sensitive to treatment with that agent. The invention also features marker sets that can predict patients that are likely to respond or not to respond to an agent.

Abstract: This invention provides methods of amplifying a sequence of interest present within a nucleic acid molecule. In addition, this invention provides a method of determining the nucleotide sequence of a sequence of interest present within a nucleic acid molecule (e.g. GAWTS and RAWTS) which can be used to sequence tissue specific genes (e.g. tsRAWTS) and genes accross species (e.g. zooRAWTS).

Abstract: The majority of PCR-based fingerprinting technologies generate dominant genetic markers; homozygote present and heterozygote genotypes cannot be distinguished using conventional detection methods. In contrast, codominant genetic markers provide an unambiguous distinction among each genotype. A genotyping method is described that includes procedures implemented in software. This method quantifies allele copy number and enables recovery of codominant genotypes from markers expressing ostensibly dominant phenotypes. These procedures are designed and implemented to (1) greatly reduce variability attributable to sample assay and detector noise, (2) accurately estimate allele size and copy number, (3) provide normalization criteria for intra- and inter-marker comparisons, and (4) scale the resulting data to determine the genotype of individual markers.

Abstract: The invention relates to a method for labeling and fragmenting a single- or double-stranded deoxyribonucleic acid (DNA) comprising the following steps:

Abstract: The present invention is directed to methods and compositions for the use of electron transfer moieties with different redox potentials to electronically detect nucleic acids, particularly for the electrochemical sequencing of DNA.

Abstract: The invention relates, in part, to methods useful in identifying molecules, that bind TRPM4b, which modulate TRPM4b ion channel activity, and/or which alter expression of TRPM4b within cells. The TRPM4b channels as described herein comprise TRPM4b polypeptides, which are in turn encoded by TRPM4b nucleic acids. The ion channels described herein are preferably formed in HEK-293 cells and comprise one or more novel TRPM4b polypeptides, which exhibit one or more of the unique TRPM4b properties described herein.

Abstract: The present invention provides methods of putatively identifying, based on presence of rare codon usage, cellular components involved in virulence. Also included are methods of verifying putative virulence genes and methods of attenuating such virulence, e.g., through identification and modification of genes/gene products that modulate translation of gene subsets involved in pathogen virulence. The methods include examining the codon usage and frequency employed in the organism, and identifying and structurally characterizing, e.g., tRNA molecules associated with over-represented or under-represented codons. By targeting the cell's ability to decode specific sets of genes, the virulence of a pathogen can be modulated.

Abstract: Mutants of steroid receptor ligand binding domains and synthetic ligands which have specific binding affinities for these receptors are provided. The use of these LBD-ligand combinations for construction of selective “molecular gene switches” is disclosed. Methods of regulating gene function using these switches are provided.

Abstract: The present invention relates to a mutant DNA sequence encoding peroxisome proliferator-activated receptor-&ggr; coactivator-1 (PGC-1), a method of detecting a mutation in the gene encoding peroxisome proliferator-activated receptor-&ggr; coactivator-1, as well as a diagnostic composition and a test kit for use in the method.

Abstract: Nucleoside derivatives as building blocks for templated libraries are described.

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: A method for identifying a nucleic acid which codes for a polypeptide factor affecting the covalent bonding of polypeptides to the surface of Gram-positive bacteria, comprising the following steps:

Abstract: The invention provides isolated nucleic acids molecules, designated collagen XXII nucleic acid molecules, which encode a novel collagen. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing collagen XXII nucleic acid molecules, host cells into which the expression vectors have been introduced, and nonhuman transgenic animals in which a collagen XXII gene has been introduced or disrupted. The invention still further provides isolated collagen XXII proteins, fusion proteins, antigenic peptides and anti-collagen XXII antibodies. Diagnostic methods utilizing compositions of the invention are also provided.

Abstract: The invention relates to an analytical measuring and evaluation method for determining the interaction parameters between an analyte and a ligand, preferably in a biosensor. According to the inventive method, the concentration of the analyte is gradually changed at defined intervals ti and the initial association or dissociation rates or association and dissociation constants are determined. The invention further relates to a device for carrying out the inventive method.

Abstract: The present invention relates to a receptacle for receiving samples, containing a nucleic-acid-stabilizing solution and a nucleic-acid-binding solid phase.

Abstract: This invention provides methods for practical enzymatic conversion of GDP-mannose to GDP-fucose. These methods are useful for efficient synthesis of reactants used in the synthesis of fucosylated oligosaccharides.

Abstract: The disclosure provided herein identifies and characterizes the domain in HER3 receptor that interacts with heregulin ligand. Typical embodiments of the invention disclosed herein include HER3 variant polypeptides having amino acid sequences which differ from the native HER3 polypeptide sequence and which have altered affinities for heregulin. Also disclosed herein are methods and materials for identifying compounds that bind to the heregulin binding domain in HER3 as well as methods and materials for modulating the interaction between HER3 and heregulin.

Abstract: A method is provided for immobilizing a ligand, e.g., a nucleic acid, on a solid support. The method includes providing a solid support containing an immobilized latent thiol group, activating the thiol group, contacting the activated thiol group with a nucleic acid comprising an acrylamide functional group, and forming a covalent bond between the two groups, thereby immobilizing the nucleic acid to the solid support. Kits containing the solid supports and method of utilizing the solid supports are also provided.

Abstract: A method is provided for immobilizing a ligand, e.g., a nucleic acid, on a solid support. The method includes providing a solid support containing an immobilized latent thiol group, activating the thiol group, contacting the activated thiol group with a nucleic acid comprising an acrylamide functional group, and forming a covalent bond between the two groups, thereby immobilizing the nucleic acid to the solid support. Kits containing the solid supports and method of utilizing the solid supports are also provided.

Abstract: A method for detecting one or more pathogens in a subject. The method includes the steps of: (a) procuring a biological sample, wherein the biological sample comprises nucleic acid material; (b) amplifying the nucleic acid material using random primers to produce a set of random amplicons; (c) providing one or more pathogen-specific probes or probe sets; (d) hybridizing the set of random amplicons with the one or more pathogen-specific probes or probe sets; and (e) determining selective hybridization between a random amplicon and a pathogen-specific probe or probe set, whereby the presence of a pathogen in a biological sample is detected.

Abstract: A computerized decision support system and method for predicting which of one or more drugs suitable to treat a cancerous condition in a patient are the optimum drug(s), where such selection is based upon the particular patient's genotype. A PCR kit and/or a gene chip detects multiple genes, expressions and/or mutations associated with a particular cancer using a sample of the patient's tissue or blood. A detector accepts the gene chip and analyzes the patient's genotype; and a computerized system using a database which associates patient genotypes and the efficacy and toxicity of various anti-cancer drugs used in treating patients with a particular cancerous condition connected to the detector correlates the output of the detector to the database to provide a recommendation as to which drugs are optimum for treating the patient's cancer.

Abstract: The present invention relates to a method of detecting whether a target animal is Bovine Viral Diarrhea Virus (BVDV) positive or negative by determining whether a gp48 protein-specific reagent binds to a gp48 Bovine Viral Diarrhea Virus protein or protein fragment, which retains antigenic specificity, from a target animal's tissue sample.

Abstract: A method of analysing the length of a particular region within a nucleic acid, said method comprising a) subjecting a sample of said nucleic acid to a plurality of amplification reactions in which said region is amplified, wherein the time of the extension phase in each of said reactions is varied; b) monitoring the progress of said amplification reactions; c) determining the minimum time during which extension phase of the amplification is completed within each reaction mixture and relating that to the length of the sequence undergoing extension. The method, combined with melting point analysis will allow percentage GC content of a sequence to be determined. Length analysis of this type can be used in diagnosis or analysis as well as in recombinant DNA technology to check for the presence of concatamers, and in taxonomic classification or forensics. Apparatus for use in the method is also described and claimed.

Abstract: The method is used for detecting a position of several hybridization sites on a support (2001) containing probes (3002) having hybridized targets (3003) remaining attached thereto after a washing step. It comprises the steps of: emitting a radiation (3004) from a source (3001) towards the support (2001); receiving the radiation coming from the support on a microelectrode detector (1002) sensitive to the radiation; and quantifying the targets in different sites of the support at the same time.

Abstract: A method for presenting a target protein or an array of target proteins for analysis is disclosed. The method includes the steps of forming a coding sequence; placing the coding sequence and protein-synthesis components capable of expressing the target protein under selected protein-synthesis conditions in a well on a substrate, the well having a surface which has been functionalized with the second coil-forming peptide; expressing said coding sequence under such conditions, wherein the target protein so synthesized binds to the well through coil-coil heterodimer formation, and is thus presented for analysis in the well in captured form; and washing said well to remove unbound components.

Abstract: The subject invention relates to compositions comprising an enzyme mixture which comprises a first enzyme and a second enzyme, where the first enzyme comprises a DNA polymerization activity and the second enzyme comprises an 3′-5′ exonuclease activity and a reduced DNA polymerization activity. The invention also relates to the above compositions in kit format and methods for high fidelity DNA synthesis using the subject compositions of the invention.

Abstract: The present invention provides a method for rapid identification of sites of insertion of DNA in to a cellular chromosome. The present invention also provides a gene trap vector. In one embodiment, the method of the present invention comprises the steps of stably transfecting a population of cells with a gene-trap vector, identifying cells with a trapped gene, distributing sorted cells into a matrix format, pooling cells from the matrix into discrete pools, producing cDNA sequence tags from the trapped genes in the pooled cells, making concatamers for each pool, cloning and sequencing the concatamers, defining the sequence tag of each well in the matrix.

Abstract: The invention provides methods and compositions relating to novel human cellular inhibitor of apoptosis proteins (c-IAP1/2) comprising a series of defined structural domain repeats and/or a RING finger domain; in particular, at least two of: a particular first domain repeat, a particular second domain repeat, and a particular third domain repeat, and/or a particular RING finger domain. The proteins provide a c-IAP specific function, with preferred proteins being capable of modulating the induction of apoptosis; for example, by binding a human tumor necrosis factor receptor associated factor (TRAF). The compositions include nucleic acids which encode the subject c-IAP and hybridization probes and primers capable of hybridizing with the disclosed c-IAP genes.

Abstract: The invention features methods for rapidly and sensitively identifying molecular targets in medical, industrial, and environmental samples. The invention labels target molecules and then images them using large area imaging. Diagnostic tests based on the invention can be rapid, ultrasensitive, quantitative, multiplexed, and automated. A broad range of infectious agents (e.g., bacteria, viruses, fungi, and parasites) and molecules (e.g., proteins, DNA, RNA, hormones, and drugs) can be detected by the methods. The invention enables rapid, ultra-sensitive, cost-effective, and portable assays. The ability of the invention to detect low levels of target molecules rapidly and cost-effectively results from the combination of high intensity labeling, formats that facilitate rapid reaction kinetics, and large area imaging based using either instrumentation made from off-the-shelf commercial components or no instrumentation at all.

Abstract: A method of detecting the presence of an analyte, such as a target nucleic acid sequence, protein sequence or small molecule, which can also be employed to detect the formation of duplex structures, is disclosed. The method can comprise nucleic acids, proteins and small molecules, employing photoelectrochemically active nanoparticles, branched polymers or other structures that carry photoelectrochemically active molecules capable of generating a photocurrent when excited by light in the presence of an electric field is disclosed. The method can be employed to detect hybridization on an array and can be employed in sequencing, mutational analysis (for example, single nucleotide polymorphisms and other variations in a population) and for monitoring gene expression by analysis of the level of expression of messenger RNA extracted from a cell. The method is applicable to the detection of antibody binding or other protein binding for analyte detection in an array format.

Abstract: The present invention provides compositions including polypeptides useful for regulating the cell cycle, proliferation, tumorigenesis, and genomic stability, mutants of such polypeptides useful in identifying abnormal cells and diagnosing disease, antibodies useful for identifying the polypeptides, and polynucleotides that encode the polypeptides.

Abstract: The present invention is directed to a novel Afx response element comprising the nucleotide sequence AACATGTT, said nucleotide sequence having a DNA binding site for the human fork head transkription factor Afx. The invention also relates to the use of the Afx response element in the screening for genes as diabetes drug targets and in the bioinformatic analysis of the human genome, said genes in turn being useful in other screening methods for compounds modifying the insulin receptor signaling pathway. A further aspect of the invention is a vector construct comprising the novel nucleotide sequence, a host cell transformed with said vector construct as well as the fusion protein expressed by said host cell.

Abstract: Methods for detecting low frequency nuclear mutations in a target sequence from a genomic DNA sequence are disclosed.

Abstract: The present invention relates to systems, compositions, and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for attaching nucleic acids to solid supports and modifying nucleic acids. For example, in some embodiments, the 5′ nuclease activity of a cleavage agent is used to cleave a cleavage structure formed on the solid support, the occurrence of the cleavage event indicating the presence of specific nucleic acid sequences.

Abstract: The invention provides methods for identifying polymorphic markers for herbicide resistance in weeds and for generating herbicide susceptible and herbicide resistant weeds by mutagenizing weeds and comparing genetic differences between herbicide resistant and herbicide susceptible weeds. The methods may involve the inhibition of mismatch repair in the weeds through the introduction of dominant negative alleles of mismatch repair genes, through T-DNA insertional mutations, or the use of chemical inhibitors of mismatch repair. The invention also provides polymorphic markers of herbicide resistance and methods and kits to screen for herbicide resistant weeds, such as horseweed, goosegrass and rye grass.

Abstract: Disclosed are compositions and a method for amplification of nucleic acid sequences of interest. The disclosed method generally involves replication of a target sequence such that, during replication, the replicated strands are displaced from the target sequence by strand displacement replication of another replicated strand. In one form of the disclosed method, the target sample is not subjected to denaturing conditions. It was discovered that the target nucleic acids, genomic DNA, for example, need not be denatured for efficient multiple displacement amplification. The primers used can be hexamer primers. The primers can also each contain at least one modified nucleotide such that the primers are nuclease resistant. The primers can also each contain at least one modified nucleotide such that the melting temperature of the primer is altered relative to a primer of the same sequence without the modified nucleotide(s). The DNA polymerase can be &phgr;29 DNA polymerase.

Abstract: The invention provides human phosphodiesterases (HPDE) and polynucleotides which identify and encode HPDE. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. The invention also provides methods for diagnosing, treating, or preventing disorders associated with aberrant expression of HPDE.

Abstract: The invention provides human drug metabolizing enzymes (DME) and polynucleotides which identify and encode DME. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. The invention also provides methods for diagnosing, treating, or preventing disorders associated with aberrant expression of DME.

Abstract: Reagents which regulate human dopamine-like G protein-coupled receptor (DA-like GPCR) and reagents which bind to human DA-like GPCR gene products can play a role in preventing, ameliorating, or correcting dysfunctions or diseases including, but not limited to, obesity and diseases related to obesity, cancer, diabetes, osteoporosis, anxiety, depression, hypertension, migraine, compulsive disorders, schizophrenia, autism, neurodegenerative disorders, such as Alzheimer's disease, Parkinsonism, and Huntington's chorea, and cancer chemotherapy-induced vomiting.

Abstract: The invention comprises novel methods and strategies to detect and/or quantify nucleic acid analytes. The methods involve nucleic acid probes with covalently conjugated dyes, which are attached either at adjacent nucleotides or at the same nucleotide of the probe and novel linker molecules to attach the dyes to the probes. The nucleic acid probes generate a fluorescent signal upon hybridization to complementary nucleic acids based on the interaction of one of the attached dyes, which is either an intercalator or a DNA groove binder, with the formed double stranded DNA. The methods can be applied to a variety of applications including homogeneous assays, real-time PCR monitoring, transcription assays, expression analysis on nucleic acid microarrays and other microarray applications such as genotyping (SNP analysis). The methods further include pH-sensitive nucleic acid probes that provide switchable fluorescence signals that are triggered by a change in the pH of the medium.