Abstract: The invention provides a method and related kits and reagents for producing, purifying, isolating, or enriching desired nucleic acids from a library. The desired nucleic acids are produced from polymerase enzyme extension products, generated from specific primers or sets of primers, in a form that is immediately replicable in a host cell. The invention can be practiced in solution phase, thus eliminating the need for solid phase filter hybridizations, column hybridizations, or gel electrophoresis purification when enriching for or isolating a target sequence or vector from one or more libraries.

Abstract: The invention provides mechanisms for the co-localization in a living cell of a target molecule and of an inhibitor for the target molecule. The invention also provides novel chimeric tRNALys-ribozyme molecules that compete effectively with tRNALys for HIV-1 reverse transcriptase binding sites. The chimeric human tRNALys-ribozymes inhibit HIV reverse transcription by delivering inhibitors such as ribozymes of HIV-1 reverse transcriptase directly to the virion particle and render it non-functional. The chimeric molecules of the invention thus serve as highly specific non-toxic therapeutic agents and vaccines for viral, including lentiviral, infections. These chimeric molecules also reveal a novel, site specific RNA cleaving activity of HIV-1.

Abstract: Genes and polymorphisms associated with cardiovascular disease, methods that use the polymorphism to detect a predisposition to developing high cholesterol, low HDL or cardiovascular disease, to profile the response of subjects to therapeutic drugs and to develop therapeutic drugs are provided.

Abstract: The present invention concerns oligonucleotides containing one or more modified nucleotides which increase the binding affinity of the oligonucleotides to target nucleic acids having a complementary nucleotide base sequence. These modified oligonucleotides hybridize to the target sequence at a faster rate than unmodified oligonucleotides having an identical nucleotide base sequence. Such modified oligonucleotides include oligonucleotides containing at least one 2′-O-methylribofuranosyl moiety joined to a nitrogenous base. Oligonucleotides can be modified in accordance with the present invention to preferentially bind RNA targets. The present invention also concerns methods of using these modified oligonucleotides and kits containing the same.

Abstract: This invention is directed to methods, kits and compositions pertaining to PNA Molecular Beacons. PNA Molecular Beacons comprise self-complementary arm segments and flexible linkages which promote intramolecular or intermolecular interactions. In the absence of a target sequence, PNA Molecular Beacons facilitate efficient energy transfer between the linked donor and acceptor moieties of the probe. Upon hybridization of the probe to a target sequence, there is a measurable change in at least one property of at least one donor or acceptor moiety of the probe which can be used to detect, identify or quantitate the target sequence in a sample.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: A method of treating a substrate for immobilizing a biomolecule and substrates produced by the method are disclosed. The method includes contacting at least a portion of a substrate with a reducing agent such as a hydride. Treatment with an appropriate reducing agent substantially eliminates autofluorescence on substrates.

Abstract: A method for making polymerized molecules is provided whereby a solution containing monomer is contacted to a solid substrate so as to form discrete accumulations of the monomer on the substrate; and the accumulations are contacted with a polymerizing agent, wherein the agent is dispersed in a vehicle which prevents cross contamination of the accumulations.

Abstract: The present invention relates to detection or genotyping (or other sample analysis) of target nucleic acids following immobilization of the target nucleic acids onto a surface. The target nucleic acids can be re-used multiple times, thus conserving sample materials and simplifying sample preparation.

Abstract: A method and system for signal generation and signal amplification from an array containing bound, unlabeled target molecules. Following exposure of the array to a sample solution containing unlabaled target RNA molecules, blunt ends are generated on each probe/target double-stranded hybrid labeled primer oligonucleotide linker is then bound to the blunt ends. Next, in an iterative, inner process, additional layers of labeled oligonucleotide, linkers are added, shell-by-shell, to form a dendrimer-like molecular complex bound through the oligonucleotide linker to the probe/target hybrid.

Abstract: A novel approach for combining the ease of cleavage of carboxylic acid linker arms with the single phosphoramidite coupling chemistry of the universal supports useful in oligonucleotide synthesis. There is disclosed a new class of phosphoramidite reagents, linker phosphoramidites, which contain a bifunctional linker arm with a protected nucleoside linked through a 3′-ester bond on one end and a reactive phosphoramidite group or other phosphate precursor group on the other end—see FIGS. 2 and 3. The phosphoramidite group on the linker phosphoramidite may be activated under the same conditions and has similar reactivity as conventional nucleoside-3′-phosphoramidite reagents lacking the intermediate linker arm. The 3′-ester linkage contained within the linker phosphoramidite has similar properties to the linkages on prederivatized supports.

Abstract: A method for observing and determining the size of individual molecules and for determining the weight distribution of a sample containing molecules of varying size, which involves placing a deformable or nondeformable molecule in a medium, subjecting the molecule to an external force, thereby causing conformational and/or positional changes, and then measuring these changes. Preferred ways to measure conformational and positional changes include: (1) determining the rate at which a deformable molecule returns to a relaxed state after termination of the external force, (2) determining the rate at which a molecule becomes oriented in a new direction when the direction of the perturbing force is changed, (3) determining the rate at which a molecule rotates, (4) measuring the length of a molecule, particularly when it is at least partially stretched, or (5) measuring at least one diameter of a spherical or ellipsoidal molecule.

Abstract: The methods of the invention detect epidermal growth factor RNA, epidermal growth factor receptor RNA, her-2/neu RNA, c-myc RNA, heterogeneous nuclear ribonucleoprotein A2/B1 RNA or any combination thereof in blood plasma, serum, and other bodily fluids. The inventive methods are useful for detection, diagnosis, monitoring, treatment, or evaluation of neoplastic disease.

Abstract: The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

Abstract: The present invention relates to methods for identifying and/or classifying patients with inflammatory bowel diseases (IBD), particularly patients with Crohn's disease or ulcerative colitis. Gene expression profiling shows broad and fundamental differences in the pathogenic mechanism of UC and CD. The subject method is based on the findings that certain genes are differentially expressed in intestinal tissue of IBD patients compared with related normal cells, such as normal colon cells. That change can be used to identify or classify IBD cells by the upregulation and/or downregulation of expression of particular genes, alterations in protein levels or modification, or changes at the genomic level (such as mutation, methylation, etc), e.g., an event which is implicated in the pathology of inflammatory bowel diseases.

Abstract: A computational method designed to extract information about gene regulatory network from raw gene expression data sets that are comprised of a time course of expression levels is disclosed. At a first step in this method, genes with similar temporal expression profiles are clustered into modules characterizing by distinct expression signatures. These fundamental patterns of gene expression are analyzed using the assumption that temporal profiles are shaped by interactions between genes belonging to different modules. The underlying genetic connectivity is retrieved using an optimization procedure developed in computational neurobiology for extracting information about neural circuitry. The objective is to find an optimal regulatory structure making calculated temporal patterns as close as possible to experimental data. A set of algorithms was used to evaluate statistical significance of putative regulatory connections derived from gene expression patterns.

Abstract: A method for detecting a target nucleic acid sequence in a sample, by subjecting it to an amplification reaction and taking continuous electrochemical measurements on it during the reaction. The method can be used to determine whether an amplification reaction has taken place, to quantitate the amount of target in the sample or to determine sequence characteristics. Also disclosed is apparatus for use in the method, comprising (i) an amplification reaction vessel which comprises an electrochemical cell, (ii) means for taking continuous electrochemical measurements on a sample contained in the vessel and (iii) temperature control and measurement means, wherein the electrochemical cell comprises an element formed from an electrically conducting plastics material such as a polymer loaded with an electrically conducting material. Further disclosed is a reaction vessel for use in the apparatus, a probe for use in the method and a kit for effecting the method.

Abstract: Disclosed herein are materials and processes for a novel method of polynucleotide sequence analysis termed Matrix Sequencing. The invention utilizes a set of distinct probes, each distinct probe comprising a common first section (registering sequence) which specifically hybridizes to a target, and an adjoining second section consisting of universal nucleotides the number of which is distinct for each distinct probe. Microarrays of these novel probes, unlike those used in Sequencing by Hybridization (SBH), allow serial reading of the target sequence in a fashion similar to electrophoretic gels.

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

Abstract: The invention provides isolated nucleic acid and amino acid sequences of KinI-3, antibodies to KinI-3, methods of screening for KinI-3 modulators using biologically active KinI-3, and kits for screening for KinI-3 modulators.

Abstract: Human CAD genes are identified as modulators of the p53 pathway, and thus are therapeutic targets for disorders associated with defective p53 function. Methods for identifying modulators of p53, comprising screening for agents that modulate the activity of CAD are provided.

Abstract: Methods for generating an mRNA expression profile are provided. In the subject methods, a population of nucleic acid targets is first generated from an acellular blood sample that contains a plurality of distinct mRNAs, i.e., a disease specific particular blood fraction. The resultant nucleic acid targets are hybridized to an array of nucleic acid probes to obtain an mRNA expression profile. The subject mRNA expression profiles are useful in the identification of disease specific markers. In such applications, the mRNA expression profiles are compared to a control expression profile to identify disease specific markers, where the identified markers subsequently find use in diagnostic applications. The subject methods also find use in diagnostic applications, where the mRNA expression profile is compared to a reference in making a diagnosis of the presence of a disease condition. Finally, kits for use in practicing the various methods are provided.

Abstract: Human P5CR genes are identified as modulators of the p53 pathway, and thus are therapeutic targets for disorders associated with defective p53 function. Methods for identifying modulators of p53, comprising screening for agents that modulate the activity of P5CR are provided.

Abstract: A method of measuring the relative metabolic state of a multicellular organism is disclosed.

Abstract: A method is provided for identifying components of a mixture by labeling the individual components with fluorescent agents having different fluorescence lifetimes. The components are subsequently separated, fluorescent labels detected and their lifetimes measured. Based on the measured fluorescent lifetimes, the components of mixtures of small organic molecules, polymers, peptides, saccharides and nucleic acids can be identified.

Abstract: This invention concerns systems for collecting and storing epigenetic and phenotypic information about samples in order to measure and analyse tissue samples and/or cell lines, where the epigenetic parameter is DNA methylation and the phenotypic parameters describe an individual. The method includes parameters such as the diagnosis of diseases and/or drug resistance, wherein the correlation of the epigenetic with the phenotypic parameters is done substantially without human intervention.

Abstract: The present invention relates to the use of diacylglycerol kinase delta (DGK&dgr;) in methods for the identification of pharmaceutically useful agents, in particular agents useful for increasing insulin-stimulated glucose uptake in a mammalian cell and for the treatment or prophylaxis of diabetes.

Abstract: In a human or animal organ or other region of interest, specific objects, such as liver metastases and brain lesions, serve as indicators, or biomarkers, of disease. In a three-dimensional image of the organ, the biomarkers are identified and quantified. Multiple three-dimensional images can be taken over time, in which the biomarkers can be tracked over time. Statistical segmentation techniques are used to identify the biomarker in a first image and to carry the identification over to the remaining images.

Abstract: The invention relates to oligonucleotide probes attached to discrete particles wherein the particles can be grouped into a plurality of sets based on a physical property. A different probe is attached to the discrete particles of each set, and the identity of the probe is determined by identifying the discrete particles from their physical property. The physical property includes any that can be used to differentiate the discrete particles, and includes, for example, relative or absolute location, size, flourescence, radioactivity, electromagnetic charge, or absorbance, or label(s) may be attached to the particle such as a dye, a radionuclide, or an EML. The invention also relates to methods using the probes complexed with the discrete particles to analyze target nucleic acids.

Abstract: Disclosed are smooth surfaced porous membranes having one or more advantages such as low autofluorescence, thermal-cyclability, especially under humid conditions, and three-dimensional binding capacity. The membrane can be free-standing or, preferably in combination with a support as in a composite membrane. The present invention provides a composite membrane comprising a porous polymer layer disposed on a support. The present invention further provides devices such as microarray devices comprising the composite for the analysis of biomaterials such as nucleic acids.

Abstract: A system for holding a multiple welled plate during processing comprised of a multiple welled plate, typically containing 96, 384 or more individual wells, each having an open bottom closed by a membrane and a holder for such a plate. The holder is formed with a filter support portion that supports the lower surface of the filter during processing. The holder may optionally be thermally conductive or if not thermally conductive, may include an additional thermally conductive layer between the lowermost surface of the filter and the filter support portion to provide for thermal cycling applications.

Abstract: A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data, The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

Abstract: The invention relates to a process for separating viruses of different sizes, with the virus-containing solution preferably being filtered through one or more filter membranes.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the Human genome, the GPCR peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the GPCR peptides and methods of identifying modulators of the GPCR peptides.

Abstract: Articles, such as high density arrays, on heat-relaxable substrates that can be relaxed by exposure to thermal energy are disclosed, along with methods of manufacturing the arrays, and systems/apparatus for relaxing arrays using electromagnetic energy. The arrays may themselves include electromagnetic energy sensitive material in their construction, in which case exposure of the arrays to suitable electromagnetic energy can provide the thermal energy required to cause the arrays to relax. In other embodiments, the arrays may not include an electromagnetic energy sensitive material in their construction, in which case the arrays may be heated indirectly, i.e., by locating the arrays within a system or apparatus that includes an electromagnetic energy sensitive material and transferring the thermal energy from the electromagnetic energy sensitive material to the array by, e.g., conduction.

Abstract: The present invention provides crystalline LuxS, machine readable media embedded with the three-dimensional atomic structure coordinates of LuxS, and subsets thereof, and methods of using them.

Abstract: The invention relates to methods of selecting proteins, out of large libraries, having desirable characteristics. Exemplified are methods of expressing enzymes and antibodies on the surface of host cells and selecting for desired activities. These methods have the advantage of speed and ease of operation when compared with current methods. They also provide, without additional cloning, a source of significant quantities of the protein of interest.

Abstract: The present invention provides a novel four stage ab initio approach for predicting the tertiary structure of polypeptides. The methods of the invention combine the classical and modem views of protein folding, while using free energy calculations and integer linear optimization to predict helical and &bgr;-sheet structures. Derivation of restraints, detailed atomistic modeling, and a deterministic global optimization method, &agr;BB, coupled with torsion angle dynamics, form the basis for the final tertiary structure prediction. The performance of the methods of the invention is illustrated using several different polypeptides.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: Methods of determining whether a sample includes one or more analytes, particularly proteinaceous analytes, of interest are provided. In the subject methods, an array of binding agents, where each binding agent includes an epitope binding domain of an antibody, is contacted with the sample. In many embodiments, contact occurs in the presence of a metal ion chelating polysaccharide, e.g., a pectin. Following contact, the presence of binding complexes on the array surface are detected and the resultant data is employed to determine whether the sample includes the one or more analytes of interest. Also provided are kits, systems and other compositions of matter for practicing the subject methods. The subject methods and compositions find use in a variety of applications, including proteomic applications such as protein expression analysis, e.g., differential protein expression profiling.

Abstract: A method for multiplexed detection and quantification of analytes by reacting them with probe molecules attached to specific and identifiable carriers. These carriers can be of different size, shape, color, and composition. Different probe molecules are attached to different types of carriers prior to analysis. After the reaction takes place, the carriers can be automatically analyzed. This invention obviates cumbersome instruments used for the deposition of probe molecules in geometrically defined arrays. In the present invention the analytes are identified by their association with the defined carrier, and not (or not only) by their position. Moreover, the use of carriers provides a more homogenous and reproducible representation for probe molecules and reaction products than two-dimensional imprinted arrays or DNA chips.

Abstract: A protein solubilization reagent made in two parts, of which one part is a dry urea-agent and the second part is a diluent for re-hydration of the dry urea-agent. The urea-agent comprises of urea and one or more agents selected from a group consisting of dry thiourea, detergents, sufobetaines, sulfonates, buffer agents, and dyes. The diluent contain pure water and other agents.

Abstract: A method of using elongate multicellular organisms in conjunction with a specialized flow cytometer for drug discovery and compound screening. A stable, optically detectable linear marker pattern on each organism is used to construct a longitudinal map of each organism as it passes through the analysis region of the flow cytometer. This pattern is used to limit complex data analysis to particular regions of each organism thereby simplifying and speeding analysis. The longitudinal marker pattern can be used to alter signal detection modes at known regions of the organism to enhance sensitivity and overall detection effectiveness. A repeating pattern can also be used to add a synchronous element to data analysis. The marker patterns are established using known methods of molecular biology to express various indicator molecules. Inherent features of the organism can be rendered detectable to serve as marker patterns.

Abstract: A method to recover receptors without removing microenvironmental components associated with them is described. The membranes containing the receptors are first associated with ligand-coupled solid supports to achieve association of the membranes through a receptor/ligand complex which includes the microenvironment to the solid support and then removing the membrane from the receptor and its microenvironment by shear forces. The thus isolated receptors and their microenvironments can then be analyzed for their role in cellular differentiation, apoptosis, transformation and the like.

Abstract: The invention provides antibody which can bind to an antigen present in a heme-containing cell and to which a fluorophore with an emission wavelength of between 420 nm and 500 nm is bound. The antibody of the invention can bind to an antigen of interest in a heme-containing cell and, due to the fluorophore, the binding interaction can be visualized. This facilitates the use of fluorescent labels for immunophenotyping of red blood cells and, in particular, fetal red blood cells within a blood sample from a pregnant female. It also facilitates simultaneous use of immunophenotyping and fluorescence-based nucleic acid analytical techniques such as FISH. Genotype and phenotype can be detected at the same time.

Abstract: The invention relates, inter alia, to the use of neuregulin-&bgr; as a target in a screening method for active compounds, in particular for exerting an influence on changes in calcium concentration which are mediated by glutamate receptors.

Abstract: The invention is a new human cathepsin (LCAP), the cDNAs that encode LCAP, and antibodies that specifically bind LCAP that are used in methods for diagnosing and treating disorders of cell proliferation, particularly lung cancer, as associated with expression of LCAP. The invention provides expression vectors, host cells, and methods for making LCAP and agonists, antibodies and antagonists that specifically bind the protein.

Abstract: The present invention is directed to methods and compositions for the diagnosis and treatment of vascular conditions, particularly diabetes and atherosclerosis. The present invention comprises methods and compositions for determining the expression or activity of enzymes effecting HSPG, preferably, heparanase. The invention also comprises methods and compositions for treatment of vasculophathic diseases comprising administration of therapeutic compounds that are effective in inhibiting the expression or activity of heparanase.

Abstract: The present invention is directed to methods and compositions for the detection of infection and disease due to members of the genus Mycobacterium. In particular, the present invention is well-suited to the detection and identification of patients with disease or infection due to M. tuberculosis or MAC.