Abstract: The invention provides methods and materials for determining cancer diagnosis and prognosis based on examining the levels of CRISP-3 RNA and polypeptides in biological samples from a patient. The invention also provides kits that can be used to determine a cancer diagnosis or prognosis. The kits contain CRISP-3 antibodies, CRISP-3 nucleic acids, PSA antibodies, PSA nucleic acids, or any combinations of these.

Abstract: External control reagents for nucleic acid amplification are provided that verify the absence or presence of specific target sequences, and correct primers and probes. A single-stranded, external control polynucleotide is amplified with primers of the same sequence as target primers. Probes with detectable labels and sequences specific for target and external control polynucleotides allow for detection and measurement. The primers and the detectable probe are adjacent or substantially adjacent when hybridized to the external control polynucleotide. Target and control amplicons may be detected by increased fluorescence induced by polymerase-mediated 5′ nuclease cleavage or hybridization of a self-quenching probe complementary to both target and external control polynucleotides. A kit of PCR reagents can be dispensed into vessels for rapid and accurate nucleic acid amplification assay, with real-time or end-point measurements.

Abstract: Disclosed is a method of altering a nucleic acid. The method includes fragmenting a parent nucleic acid strand to generate nucleic acid fragments. At least a subset of the fragments are ligated to generate shuffled nucleic acid strands. A selected strand is identified from the shuffled nucleic acid strands for a criterion.

Abstract: The disclosed nucleic acid primer sets, used in combination with quantitative amplification (PCR) of tissue cDNA, can indicate the presence of specific proteases in a tissue sample. Specifically, the present invention relates to expression of hepsin protease. The detected proteases are themselves specifically over-expressed in certain cancers, and the presence of their genetic precursors may serve for early detection of associated ovarian and other malignancies, and for the design of interactive therapies for cancer treatment.

Abstract: The present invention provides a method of compiling a plant functional gene profile, a method of changing the phenotype or biochemistry of a plant, a method of determining a change in phenotype or biochemistry of a plant, and a method of determining the presence of a trait in plant. The methods comprise expressing transiently a nucleic acid sequence of a plant into a host plant to affect phenotypic or biochemical changes in the host plant. A viral vector functional genomic screen has been developed to identify nucleotide sequences in transfected plants by systemically knocking out endogenous gene expression in an antisense mechanism. Once the presence of a trait in a plant is identified by phenotypic or biochemical changes in the host plant, the nucleic acid insert in the cDNA clone or in the vector that results in the changes is then sequenced. The present invention exemplifies that genes encoding GTP binding proteins in one plant can silence endogenous gene expression in a different plant.

Abstract: The present invention provides a method of compiling a plant functional gene profile, a method of changing the phenotype or biochemistry of a plant, a method of determining a change in phenotype or biochemistry of a plant, and a method of determining the presence of a trait in plant. The methods comprise expressing transiently a nucleic acid sequence of a plant into a host plant to affect phenotypic or biochemical changes in the host plant. A viral vector functional genomic screen has been developed to identify nucleotide sequences in transfected plants by systemically knocking out endogenous gene expression in an antisense mechanism. Once the presence of a trait in a plant is identified by phenotypic or biochemical changes in the host plant, the nucleic acid insert in the cDNA clone or in the vector that results in the changes is then sequenced. The present invention exemplifies that genes encoding GTP binding proteins in one plant can silence endogenous gene expression in a different plant.

Abstract: A random combinatorial selection method is disclosed for the construction of oligonucleotide aptamers in which nuclease resistance is conferred by the inclusion of modified nucleotides. The modified nucleotides are incorporated during PCR amplification to form achiral modified oligonucleotides. Thio-substituted aptamers are provided that bind tightly to the nuclear factor for human IL6 (NF-IL6).

Abstract: The present invention relates to a method and kit for diagnosing GH (growth hormone) deficiency, in particular isolated growth hormone deficiency II (IGHD II). The method comprises the steps of analysing the missense mutation G6191 to T in exon 4 of GH-1 which changes valine 110 to phenylalanine.

Abstract: The present invention relates to the process of selectively exposing matter to a specific wavelength of electromagnetic energy in sufficient flux density per wavelength to cause or promote a desired effect. The process includes, but is not limited to, destroying, disinfecting, denaturing, disinfesting, disrupting, or dehydration of one or more of the substances present. More specifically, present invention relates to subjecting matter, which may contain a mixture of substances, to electromagnetic energy, in concurrence with its spectral properties to exploit the spectral differences within the substance or within a mixture of substances. Energies are applied to cause wavelength-dependent reactions resulting from differential absorption; this additional applied energy manifests itself in changes, or quantum transitions, in the vibrational, rotational, magnetic, and electronic states of the molecules.

Abstract: Apparatus for the manipulating and testing of molecules and in particular of DNA comprising

Abstract: Human SLC7 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 SLC7 are provided.

Abstract: The present invention provides luminescent lanthanide metal chelates comprising a metal ion of the lanthanide series and a complexing agent comprising at least one salicylamidyl moiety. Also provided are probes incorporating the salicylamidyl ligands of the invention and methods utilizing the ligands of the invention and probes comprising the ligands of the invention.

Abstract: A method of amplification of one or more DNA sequences in a DNA containing sample, and methods of investigating such samples are provided in which an improved amplification cycling regime is used. The regime features a first phase and a second phase, the first phase including a denaturation temperature step, followed by an annealing temperature step, followed by a corrected annealed primer extension temperature step, these steps being followed by an annealing temperature step, corrected annealed primer extension temperature step prior to any further denaturation temperature steps being applied. Increased amplification from a given number of amplification cycles and maximised sensitivity for the DNA amplification process is achieved as a result.

Abstract: The instant invention provides nucleic acid molecules encoding insect ethanolamine kinase, as well as ethanolamine kinase encoded thereby. The invention further provides methods of identifying agents that modulate a level of ethanolamine kinase mRNA, polypeptide, or enzyme activity. Such agents are candidate insecticidal compounds.

Abstract: An isolated DNA molecule which includes a promoter-effective region of a Tetrahymena metallothionein gene, as well as a chimeric gene, expression vectors, and host cells containing the same. Also disclosed is a method of expressing an RNA or a polypeptide of interest using a chimeric gene of the invention.

Abstract: A method, kit, and assay for measuring levels of a therapeutic compound in a sample by providing a reaction vessel containing a sample, the sample includes a therapeutic compound having a biological activity and biological substance. A probe coated with a substrate for the biological substance is provided, the substrate having a detectable label. The probe is inserted into the reaction vessel such that the therapeutic compound and the substrate contact the biological substance and interact within the biological substance resulting in the label being released. The probe is removed from the reaction vessel and the quantity of detectable label is measured, thereby measuring the level of therapeutic compound. The concentration of therapeutic compound is calculated based upon a standard curve or by calculating the percentage of inhibition and expressing the results in arbitrary units.

Abstract: Described herein are methods and reagents for generating nucleic acid-protein fusion multimers, and methods for using such fusion molecule multimers to select an interaction between a protein or a peptide and a compound.

Abstract: The invention relates to a process for the metallisation of nucleic acids, comprising providing tris(hydroxymethyl)phosphine-Au (THP-Au) particles or derivatives thereof, binding said THP-Au particles to a nucleic acid to produce a metal nanoparticle-nucleic acid composite, and treatment of the metal nanoparticle-nucleic acid composite with an electroless plating solution. The invention further relates to a metallized nucleic acid obtainable according to such a method and a nanowire including a method for the manufacture of a nanowire.

Abstract: The present invention provides methods of performing enzymatic reactions which require the use of magnesium dependent enzymes, including restriction endonucleases, ligases, and reverse transcriptases. The method is based on sequestration of magnesium ions in the form of a precipitate which renders a magnesium dependent enzyme inactive until the appropriate time in the reaction when a certain temperature is reached and the magnesium ions are released from the precipitate. Also provided are kits comprising reagents and instructions for DNA digestion and ligation, and for reverse transcription of RNA into cDNA. Furthermore, the kits and reagents of the present invention can be utilized in other reactions requiring magnesium dependent enzymes.

Abstract: Technical field: analysis of mixtures, predominantly of biologic origin, for the contents of biological and/or chemical components, and analysis of mixtures, which parameters determine vital functions of biologic objects.

Abstract: The present invention provides methods of identifying cellular genes necessary for viral growth and cellular genes that function as tumor suppressors. Thus, the present invention provides nucleic acids related to and methods of reducing or preventing viral infection or cancer. The invention also provides methods of producing substantially virus-free cell cultures and methods for screening for additional such genes.

Abstract: The object of the present invention is to provide a method for easily immobilizing a physiologically active substance to a metal surface wherein the processes are simple and highly safe.

Abstract: The object of the present invention is to provide a method for easily immobilizing a physiologically active substance to a metal surface wherein the processes are simple and highly safe.

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 invention provides a method of screening a compound for bioactivity, comprising contacting a candidate bioactive compound with an organized tissue, and measuring in at least a cell of the organized tissue a biological parameter that is associated with bioactivity, wherein a change in the biological parameter that occurs as a result of the contacting step is indicative of bioactivity of the candidate compound.

Abstract: A process and apparatus for isolating and purifying nucleic acids and other target molecules directly from blood, plasma, urine, cell cultures and the like by totally automated means, without centrifugation, aspiration or vacuum. After mixing a sample containing target molecules with a test reagent in an environmentally isolated compartment, target molecules are adsorbed onto a binding material and eluted in a small volume using an elution reagent. A preferred embodiment purifies nucleic acids and automatically detects target sequences from a sample of fresh blood.

Abstract: A method and apparatus for mass producing biochips quickly and easily, wherein a plurality of DNA molecules are amplified using a PCR (polymerase chain reaction) method and transcribing the amplified DNA molecule to other substrates by contact.

Abstract: Methods and compositions comprising immunoassays for the detection of antigens and antibodies in a sample are described. In particular, the present invention provides assays that are useful for the rapid and simultaneous detection of multiple different antigens and antibodies. In preferred embodiments, the assays include fluorescent labels of multiple wavelengths or intensities, which are used to label the antigens and antibodies directly and to label beads coated with molecules specific for the antigen or antibody. The detection of a fluorescence shift indicates the presence or identity of the antigen or antibody in the sample.

Abstract: An automated analyzer for performing multiple diagnostic assays simultaneously includes multiple stations, or modules, in which discrete aspects of the assay are performed on fluid samples contained in reaction receptacles. The analyzer includes stations for automatically preparing a specimen sample, incubating the sample at prescribed temperatures for prescribed periods, preforming an analyte isolation procedure, and ascertaining the presence of a target analyte. An automated receptacle transporting system moves the reaction receptacles from one station to the next.

Abstract: The invention provides for anti-platelet binding proteins, and corresponding nucleic acids encoding the binding proteins, that are isolated, for example, from a phage display library by an in vitro selection process. The in vitro selection process involves screening a diverse human antibody variable domain expression library against at least one human platelet antigen to identify clones expressing single-chain antigen-binding proteins useful for inhibiting platelet aggegation and thrombosis, both in vitro and in vivo, as well as in both in vitro and in vivo assays and diagnostic procedures. Anti-platelet binding proteins conjugated to substantially non-antigenic polymers are also provided.

Abstract: Disclosed are expression profiles of genes that are regulated by progesterone receptors, and particularly by progesterone receptor isoforms PR-A and PR-B. Methods for using such genes to identifying progesterone receptor agonist and antagonist ligands are described. Also described are methods for identifying isoform-specific progesterone receptor ligands, for identifying tissue-specific progesterone receptor ligands, and for determining the profile of genes regulated by progesterone receptors in a breast tumor sample. In addition, pluralities of polynucleotides from genes that are regulated by progesterone receptors are disclosed, as are pluralities of antibodies that selectively bind to proteins encoded by such genes.

Abstract: The invention provides a binding polypeptide, or functional fragment thereof, comprising a kon of at least about 9×107 M−1s−1 for associating with a ligand and having therapeutic potency. The invention also provides a method of determining the therapeutic potency of a binding polypeptide. The methods consist of (a) contacting a binding polypeptide with a ligand; (b) measuring association rate for binding between the binding polypeptide and the ligand, and (c) comparing the association rate for the binding polypeptide to an association rate for a therapeutic control, the relative association rate for the binding polypeptide compared to the association rate for the therapeutic control indicating that the binding polypeptide will exhibit a difference in therapeutic potency correlative with the difference between the association rates.

Abstract: The present invention provides methods to measure alpha synuclein aggregation in vitro. The methods of the present invention are useful to determine the anti-aggregation potential of compounds or to screen for drugs with anti-aggregation or dis-aggregation properties.

Abstract: This invention provides methods of inhibiting calcification of a soft tissue (e.g., an artery, a heart valve, an atherosclerotic plaque, a cancer, a kidney, a prostate, skin, muscle, cartilage, viscera, and heart muscle) in a mammal. These methods involve inhibiting osteoclastic bone resorption in said mammal (e.g., a mammal diagnosed as having or at risk for a pathology characterized by calcification of a soft tissue). The inhibition is preferably by administration of a bisphosphonate to the mammal in a concentration sufficient to inhibit bone resorption without inhibiting bone mineralization. The methods of this invention can also be used to mitigate a symptom of atherosclerosis in a mammal. Such methods involve inhibiting osteoclastic bone resorption in the mammal.

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: Compostions, kits and methods are provided for generating highly diverse libraries of proteins such as antibodies via homologous recombination in vivo, and screening these libraries against protein, peptide and nucleic acid targets using a two-hybrid method in yeast.

Abstract: Provided by the present invention are novel methods of detecting substrate-ligand interactions, and more specifically relates to methods for detecting and characterizing polypeptide-ligand interactions. By practice of this invention, protein interaction maps may be generated for humans or for other organisms.

Abstract: Methods and apparatus for the evaluation of interactions between substances using inverse chromatography are disclosed. Preferably, interactions are evaluated between a liquid test sample and a solid phase comprising a receptor in the presence of a liquid carrier. Preferably, one of the modifying agent or receptor are members of a combinatorial library.

Abstract: Presented herein are methods, devices and kits for the mass spectrometric immunoassay (MSIA) of proteins present in complex biological fluids or extracts Pipettor tips containing porous solid supports that are covalently derivatized with affinity ligand and used to extract specific proteins and their variants from various biological fluids Nonspecifically bound compounds are rinsed from the extraction devices using a series of buffer and water rinses, after which the wild type protein (and/or its variants) are eluted directly onto a target in preparation for analysis such as matrix-assisted laser desorption/ionization time-of-light mass spectrometry (MALDI-TOF MS). Mass spectrometry of the eluted sample then follows with the retained proteins identified via accurate molecular mass determination.

Abstract: The present invention relates to the identification of diarylsulfonylurea binding proteins (DBPs) as therapeutic targets for agents that suppress the release of inflammatory mediators such as interleukin IL-1 and IL-1&bgr;.

Abstract: Provided are peptides having an activity to promote the release of active TGF-&bgr; from latent TGF-&bgr; or an activity to promote the binding of latent TGF-&bgr; to a cell membrane which are represented by general formula (I):

Abstract: Methods for efficiently depositing small quantities of a protein containing fluid onto the surface of a substrate are provided. A feature of the subject methods is that the deposition process does not substantially modulate the protein activity/functionality of the deposited fluid. In practicing the subject methods, a small volume of fluid containing the protein(s) of interest is front loaded into a thermal inkjet device. Next, a small quantity of the front loaded fluid is expelled onto the surface of a substrate. The subject methods find use in a variety of different applications where the deposition of small volumes of a fluid containing a protein of interest is desired.

Abstract: The invention provides an isolated polypeptide, or a fragment thereof, comprising a coiled-coil and an engineered site sufficient for the addition of a “moiety”, i.e., a group, that is one or more of a phosphate, ubiquitin, glycosyl or ADP-ribosyl moiety, wherein the polypeptide binds to a binding partner in a phosphorylation-, ubiquitination-, glycosylation- or ADP-ribosylation-dependent manner. The invention also relates to methods and kits utilizing an isolated polypeptide and its binding partner, which methods and kits permit monitoring of addition or removal of the one or more moieties.

Abstract: Candidates for biological activity are screened in capsules, each capsule containing a candidate, a target (which may be a molecular species or a biological cell or multiple copies of such a species or cell), and an intelligent substance. The target is one with which a successful candidate will interact to evoke a particular response in the target, and the intelligent substance is one that undergoes a transformation as a result of the response, the transformation being detectable by observation of the capsule itself. The candidate and the target are isolated from each other in the capsule until a designated point in time thereby enabling the operator to control the time interval between exposure of the target to the candidate and the observation of the capsule to determine whether or not a successful interaction has occurred and the transformation has taken place.

Abstract: A test device (20) for detecting human blood includes a strip (22) having an introduction station (24), a test station (26), and a control station (28) disposed in spaced apart relationship. The test sample introduction station (24) has labeled antihuman Hb antibodies, the test station (26) has immobilized antihuman Hb antibodies, and the control station has immobilized polyclonal antibodies. A test sample (500) is deposited at the introduction station (24). If human hemoglobin is present in the test sample (500), a colored line will appear at the test station (26) and at the control station (28). If no human hemoglobin is present in the test sample (500), a colored line will only appear at the control station (28).

Abstract: The invention relates to a method and system for identifying and evaluating the physiological responses of an organism to a condition, such as a disease or other pathological condition, a drug or agent, an environmental condition, and the like, by evaluating the expression of one or more GPCR pathway biomolecules in tissue microarrays from a plurality of patients. In one aspect, a tissue information system is provided comprising a specimen-linked database and an information management system for accessing, organizing, and displaying tissue information obtained from tissue microarrays. Preferably, the system is used to model and validate GPCR pathways affected during one or more physiological responses to a condition.

Abstract: The present invention relates, in general, to immunosuppression and, in particular, to a method of inducing an immunosuppressive effect. The invention further relates to a method of screening compounds for immunosuppressive activity.

Abstract: The present invention provides systems, devices and methods for performing fast and efficient separation and collection of components of a sample mixtures. The present invention provides integrated systems for performing separation using a multi port control system to sort and collect components of sample mixtures.

Abstract: The present invention pertains to a monoclonal antibody, or fragment thereof, having an antigen-binding specific region for NKX3.1 and to a hybridoma cell line for producing the monoclonal antibody. The present invention also pertains to a method for detecting the presence of NKX3.1 in a sample. The method comprises (a) contacting a biopsy tissue sample with a monoclonal antibody, or a fragment thereof, having an antigen-binding specific region for NKX3.1, under conditions permitting immunospecific binding between the monoclonal antibody, or a fragment thereof, and NKX3.1 in the sample; and (b) detecting whether immunospecific binding has occurred to detect the presence of NKX3.1 in the sample.

Abstract: Novel human prostate cancer-associated neuroendocrine (NE)-like cell lines are provided that were derived via a process that resembles clinical androgen ablation therapy for advanced prostate cancer.