Abstract: Titration is an important and critical step in dosing recombinant virus for gene therapy. A relatively fast, convenient and sensitive method that allows for precise quantification of recombinant retrovirus is presented. The method is based on PCR amplification of a foreign gene by the PRINS (primer in situ DNA synthesis) technique. The PRINS technique is based on the sequence-specific annealing of unlabeled oligonucleotide DNA in situ. This oligonucleotide operates as a primer for in situ chain elongation catalyzed by the Taq I polymerase. Using -labeled nucleotides as a substrate for chain elongation, the neo-synthetic DNA is labeled by an FITC-conjugated anti-antibody. To avoid the possibility of false positives, the puromycin resistance gene, which is associated with the transgene in the same viral vector and is not normally present in mammalian cells was amplified.

Abstract: The invention provides methods to detect EBV in biological samples using real-time PCR. Primers and probes for the detection of EBV are provided by the invention. Articles of manufacture containing such primers and probes for detecting EBV are further provided by the invention.

Abstract: HCV immunoassays comprising an NS3/4a conformational epitope and a multiple epitope fusion antigen are provided, as well as immunoassay solid supports for use with the immunoassays.

Abstract: The present invention relates to polypeptides and proteins useful in the diagnosis and prevention of disease caused by feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV).

Abstract: A herpes simplex virus (HSV) comprising (i) an HSV LAT sequence inserted into an essential gene of the HSV; and (ii) a deletion in the endogenous LAT region of the HSV strain. The HSV of the invention can be used in the treatment of disorders of, or injuries to, the nervous system of a mammal.

Abstract: This invention relates to Equine Herpes Viruses (EHV) wherein the protein gM is essentially absent or modified and non-functional with respect to its immunomodulatory capacity. Further aspects of the invention relate to nucleic acids coding said viruses, pharmaceutical compositions comprising these viruses or nucleic acids and uses thereof. The invention also relates to methods for improving the immune response induced by an EHV vaccine against wild type EHV infections, methods for the prophylaxis and treatment of EHV infections and methods for distinguishing wild type EHV infected animals from animals treated with EHV's according to the invention.

Abstract: Nucleic acid sequences, oligonucleotides and a method for detection of SRSV, in particular, a virus which belongs to Genotype II (GII), in clinical examinations, public health examinations, food evaluations and food poisoning examinations are provided.

Abstract: The invention provides a basic genetic operating system for an autonomous prototrophic nanomachine having a nanomachine genome encoding a minimal gene set sufficient for viability. Also provided is a basic genetic operating system for an autonomous auxotrophic nanomachine having a nanomachine genome encoding a minimal gene set sufficient for viability in the presence of an auxotrophic biomolecule. The minimal gene set encoded by the basic genetic operating system can contain the functional categories of transcription, translation, aerobic metabolism, glycolysis/pyruvate dehydrogenase/pentose phosphate pathways, carbohydrate metabolism, central intermediary metabolism, nucleotide metabolism, transport and binding proteins, and housekeeping functions. Functional categories can be arranged in a predetermined physical or temporal order.

Abstract: Methods for producing ligand arrays, e.g., peptide and nucleic acid arrays, as well as the arrays produced thereby, methods for use of the arrays and kits that include the same are provided. In one embodiment of the methods, a substrate having a surface displaying acetate functional groups that produce surface bound hydroxyl functional groups upon hydrolysis is first provided, where the acetate groups are then hydrolyzed to hydroxyl functional groups. The process is then repeated to form a multilayer with hydrolytic stability. In another embodiment of the methods, a multilayer having hydroxyl groups is contacted with alkenyl functional groups, where the alkenyl functional groups are then converted to carboxylic functional groups. The resultant substrates, optionally after an additional functionalization step, are then contacted with ligands, e.g., via deposition of each different ligand onto a different region of the surface, resulting in covalent attachment of the contacted ligands to the surface.

Abstract: Methods, computer software and systems are provided for biological data analysis. In one embodiment, significantly changed measurements are mapped to a biological function, such as a GO (Gene Ontology) annotation, category or biological pathway.

Abstract: The invention relates to a nanoneedle chip, which comprises a support having an interface region; and a plurality of shafts connected to and extending from said interface region of the solid support, wherein each said shaft is in a cone-like or cylinder shape, the tip of each shaft ranges from about 0.1 nm to less than about 1 &mgr;m in diameter, the base of each shaft ranges from about 1 nm to less than about 1 &mgr;m in diameter and the height of shaft is at least three times than the diameter of the base. Also disclosed in the processes for producing the nanoneedle array of the invention.

Abstract: The invention relates to sarcoma-associated antigens and the nucleic acid molecules that encode them. The invention further relates to the use of the nucleic acid molecules, polypeptides and fragments thereof associated with sarcoma in methods and compositions for the diagnosis and treatment of diseases, such as cancer More specifically, the invention relates to the discovery of a novel cancer/testis (CT) antigen, NY-SAR-35.

Abstract: A method of determining the susceptibility of a vertebrate to a bone-related disorder, the method comprising the steps of obtaining a DNA sample from the vertebrate; and analysing the DNA sample to determine whether the vertebrate has a polymorphism in the 1&agr;-hydroxylase gene. Presence of the polymorphism indicates susceptibility of the vertebrate to the bone-related disorder.

Abstract: The invention provides methods to detect mecA-containing Staphylococcus spp. in biological samples using real-time PCR. Primers and probes for the detection of S. aureus are provided by the invention. Articles of manufacture containing such primers and probes for detecting mecA-containing Staphylococcus spp. are further provided by the invention.

Abstract: Methods and compositions for producing labeled probe nucleic acids from genomic nucleic acid template are provided. In the subject methods, a conserved coding consensus region primer is employed to enzymatically generate a select set of labeled probe nucleic acids corresponding to coding regions of genes from a genomic template via a primer extension protocol. The subject methods find use in a variety of different applications, and are particularly suited for use in the preparation of labeled probe nucleic acids for use in array based comparative genomic hybridization applications. Also provided are kits for use in practicing the subject methods.

Abstract: Optical scanner system approaches are described in which signal saturation data is produced in real-time. The data generated may be used for tuning a subsequent scan, in protection of optical detector components from damage or otherwise. Approaches for obtaining and storing or expressing the data are also disclosed. Also provided are methods of using the subject system is biopolymer array based application, including genomic and proteomic applications.

Abstract: Array scanning methods that focus on the far side and devices configured for use in the same are provided. In reading arrays according to the subject methods, an array is placed in a reading position of a scanning device so that the nominal focal plane of the scanning device is present within the array substrate at a predetermined fixed substrate thickness fraction distance from the far-side of the array, and the array is then read by the device. As such, the subject scanner devices of the present invention are configured to hold an array substrate in a reading position of the device in which the device's nominal focal plane is present within the array substrate. The subject methods and devices find use in a variety of different applications, including both genomic and proteomic applications.

Abstract: The present invention relates to protease polypeptides, nucleotide sequences encoding the protease polypeptides, as well as various products and methods useful for the diagnosis and treatment of various protease-related diseases and conditions. Through the use of a bioinformatics strategy, mammalian members of the of PTK's and STK's have been identified and their protein structure predicted.

Abstract: Described herein are methods and compositions that can be used for diagnosis and treatment of colorectal cancer. Also described herein are methods that can be used to identify modulators of colorectal cancer.

Abstract: An assay kit is provided that includes assay reagents stored in a single-tube container, and a data storage medium containing information about the contents of the container. Methods are provided for using the data provided with the kit to direct instruments and/or processes, for example, to control an instrument to perform amplification and/or sequencing reactions.

Abstract: Novel hybridisation assay probes and mixtures of such probes for detecting a target sequence of one or mycobacteria optionally present in a sample. The probes may suitable be directed to target sequences of mycobacterial rDNA, precursor rRNA, or rRNA, said probes being capable of forming detectable hybrids. The probes are in particular directed to mycobacterial rDNA, to precursor rRNA, or to 23S, 16S or 5S rRNA. The probes are useful for detecting the organisms in test samples such as sputum, laryngeal swabs, gastric lavage, bronchial washings, biopsies, aspirates, expectorates, body fluids (spinal, pleural, pericardial, synovial, blood, pus, bone marrow), urine, tissue sections as well as food samples, soil, air and water samples, and cultures thereof.

Abstract: It is an objective of the present invention to provide a method capable of protecting personal information.

Abstract: A template (a molecule preferably of molecular size >500 Da, or a larger entity such as a cell, virus or tissue sample) is dissolved or suspended in a fluid. The fluid is frozen, and the template is removed (e.g. by dissolution or electrophoresis, or mechanically) to leave an “imprinted” frozen fluid. This is capable of selectively adsorbing the template substance. It is usable as a separation medium, a recognition element in sensors and assays, and as a catalyst.

Abstract: A method and apparatus for producing a discrete particle for subsequent analysis (such as mass spectrometry) or manipulation is disclosed. A discrete particle is generated by a particle generator. A net charge is induced onto the particle by an induction electrode. The particle is delivered to a levitation device where it is then electrodynamically levitated. If the particle is a droplet, desolvation will occur, leading to Coloumbic fissioning of the droplet into smaller droplets. The movement of the levitated droplet(s) can be manipulated by an electrode assembly. The droplet(s), and the charge thereon, can be delivered to a mass spectrometer in one aspect of the invention, providing an ion source for mass spectrometry without the detrimental space charge effects of electrospray ionization techniques.

Abstract: Families of compositions are provided as labels, referred to as eTag reporters for attaching to polymeric compounds and assaying based on release of the eTag reporters from the polymeric compound and separation and detection. For oligonucleotides, the eTag reporters are synthesized at the end of the oligonucleotide by using phosphite or phosphate chemistry, whereby mass-modifying regions, charge-modifying regions and detectable regions are added sequentially to produce the eTag labeled reporters. By using small building blocks and varying their combination large numbers of different eTag reporters can be readily produced attached to a binding compound specific for the target compound of interest for identification. Protocols are used that release the eTag reporter when the target compound is present in the sample.

Abstract: The invention provides human enzymes (NZMS) and polynucleotides which identify and encode NZMS. 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 NZMS.

Abstract: An enzyme is re-engineered to be a zymogen, an enzyme precursor which is converted into an enzyme by protease cleavage. In the example described here, an RNase A enzyme is converted into a zymogen by adding to the enzyme a bridge of amino acids linking the amino and carboxyl termini of the enzyme. The bridge has built in it a protease cleavage site for a specific protease, for example the protease plasmepsin II, produced by the malaria parasite. Since RNase A can be made cytotoxic, this permits a cytotoxic enzyme to be made in the form of a zymogen that becomes active only when it is acted on by a protease only present in a particular target cell such as a pathogen.

Abstract: Paper (1) characterized by the fact that it includes bodies (3) carrying at least one biochemical marker and of sufficient size to be capable of being taken individually.

Abstract: A method for determination of at least one of the triglyceride molecular species in a biological sample comprising the subjecting sample to lipid extraction to obtain a lipid extract and subjecting the resulting lipid extract to 2D electrospray ionization tandem mass spectrometry (ESI/MS/MS) with neutral loss scanning of all naturally occurring aliphatic chains and contour analysis of 2D intercept peaks. A method for determination of tricylglyceride content and/or TG molecular species directly from a lipid extract of a biological sample comprising subjecting said lipid extract to electrospray ionization tandem mass spectrometry.

Abstract: The subject invention identifies changes in gene expression related to treatment of marine invertabret cell cultures.

Abstract: The present invention relates to compositions and methods for cancer diagnostics, including but not limited to, cancer markers. In particular, the present invention provides gene expression profiles associated with lung cancers. Genes identified as cancer markers find use in the diagnosis and characterization of lung cancer. In addition, the genes provide targets for cancer drug screens and therapeutic applications.

Abstract: An object of the present invention is to provide a method for separating and purifying a nucleic acid by adsorbing the nucleic acid in a test sample to a surface of a membrane and desorbing the nucleic acid by washing and the like.

Abstract: An object of the present invention is to provide a method for separating and purifying a nucleic acid by adsorbing the nucleic acid in a test sample to a surface of a solid phase and desorbing the nucleic acid by washing and the like. The present invention provides a method for separating and purifying a nucleic acid having a predetermined length from a nucleic acid mixture, comprising a step of: adsorbing and desorbing a nucleic acid in the nucleic acid mixture containing nucleic acids having different lengths to and from a solid phase of an organic macromolecule having a hydroxyl group on surface thereof.

Abstract: A method is provided, which comprises examining the regulating activity of a defensin gene promoter closely associated with the expression activity of defensin, an antibacterial peptide, on the basis of the detection of a gene mutation, and estimating future susceptibility to periodontal disease. The sequence homology between DNA derived from a defensin gene promoter existing in a sample obtained from the gingival tissues of a subject and a nucleotide sequence comprising a mutation site in the promoter region, and/or compatibility in PCR amplification, are determined. Thereby a gene mutation is detected and then the site of the gene mutation is determined, so that data for the estimation can be collected.

Abstract: The present invention discloses methods and apparatus for the detection of biological molecules in various samples. In particular, a method for detecting a hapten-labeled analyte in a solution wherein substantially all other solution constituents are labeled with a hapten is disclosed. The method may be used to detect single or multiple analytes in solution. Apparatus to detect such analytes are also disclosed.

Abstract: The present invention discloses DNAs comprising nucleotide sequences set forth as SEQ ID NO:1 or NO:3 encoding Na+-driven Cl-/HCO3- exchanger, proteins comprising amino acid sequences set forth as SEQ ID NO:2 or NO:4, and their homologous proteins comprising an amino acid sequence having deletion, substitution, addition or insertion amino acids, which proteins, when expressed in a cell, functions as Na+-driven Cl-/HCO3- exchanger, and cells in which the proteins exogenously expressed.

Abstract: Compositions and methods for electrochemical detection and localization of genetic point mutations, common DNA lesions and other base-stacking perturbations within oligonucleotide duplexes adsorbed onto electrodes and their use in biosensing technologies are described. An intercalative, redox-active moiety (such as an intercalator or nucleic acid-binding protein) is adhered and/or crosslinked to immobilized DNA duplexes at different separations from an electrode and probed electrochemically in the presence or absence of a non-intercalative, redox-active moiety. Interruptions in DNA-mediated electron-transfer caused by base-stacking perturbations, such as mutations or binding of a protein to its recognition site are reflected in a difference in electrical current, charge and/or potential.

Abstract: The present invention relates to a novel hematopoietic signaling factor (HSF) protein which is a member of the cytokine superfamily. In particular, isolated nucleic acid molecules are provided encoding the human HSF protein. HSF polypeptides are also provided as are vectors, host cells and recombinant methods for producing the same.

Abstract: The present invention relates to novel human secreted proteins and isolated nucleic acids containing the coding regions of the genes encoding such proteins. Also provided are vectors, host cells, antibodies, and recombinant methods for producing human secreted proteins. The invention further relates to diagnostic and therapeutic methods useful for diagnosing and treating disorders related to these novel human secreted proteins.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of PPAR-delta. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding PPAR-delta. Methods of using these compounds for modulation of PPAR-delta expression and for treatment of diseases associated with expression of PPAR-delta are provided.

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

Abstract: The present invention provides polynucleotides which identify and encode two novel human NSP-like proteins (NSPLP). The invention provides for genetically engineered expression vectors and host cells comprising the nucleic acid sequences encoding NSPLP. The invention also provides for the use of substantially purified NSPLP, antagonists, and in pharmaceutical compositions for the treatment of diseases associated with the expression of NSPLP. Additionally, the invention provides for the use of antisense molecules to NSPLP in pharmaceutical compositions for treatment of diseases associated with the expression of NSPLP. The invention also describes diagnostic assays which utilize diagnostic compositions comprising the polynucleotide, fragments or the complement thereof, which hybridize with the genomic sequence or the transcript of polynucleotides encoding NSPLP or anti-NSPLP antibodies which specifically bind to NSPLP.

Abstract: Novel secreted and membrane bound tumor necrosis factor receptor (TNFR) polypeptides, polynucleotides encoding the polypeptides, antibodies and related compositions and methods are disclosed. The polypeptides may be used for detecting ligands, agonists and antagonists. The polypeptides, polynucleotides and antibodies may also be used in methods that modulate inflammation, tumor growth and metastasis, infection, immunity, and cellular maturation.

Abstract: Data concerning gene expression quantities, which have been obtained for first and second samples, are indicated with points plotted on a logarithmic coordinate system, in which a horizontal axis represents logarithms of the expression quantities obtained for the first sample, and in which a vertical axis represents logarithms of the expression quantities obtained for the second sample. A coefficient is calculated from a value of an intercept of an approximate straight line, which is obtained from approximate representation of the plotted points with a straight line having a slope of 1, on the vertical axis. The data concerning the expression quantities with respect to a plurality of genes, which expression quantities have been obtained for the second sample, are divided by the coefficient and are thus normalized.

Abstract: The invention provides isolated nucleic acids that encode three novel isoforms of human pregnancy associated plasma protein E, hPAPP-E, and fragments thereof, vectors for propagating and expressing PAPP-E nucleic acids, host cells comprising the nucleic acids and vectors of the present invention, proteins, protein fragments, and protein fusions of the novel PAPP-E isoforms, and antibodies thereto. The invention further provides transgenic cells and non-human organisms comprising human PAPP-E isoform nucleic acids, and transgenic cells and non-human organisms with targeted disruption of the endogenous orthologue of the human PAPP-E gene. The invention further provides pharmaceutical formulations of the nucleic acids, proteins, and antibodies of the present invention, and diagnostic, investigational, and therapeutic methods based on the PAPP-E nucleic acids, proteins, and antibodies of the present invention.

Abstract: A variety of heparanase specific molecular probes which can be used for research and medical applications including diagnosis and therapy. Specific applications include the use of a heparanase specific molecular probe for detection of the presence, absence or level of heparanase expression; the use of a heparanase specific molecular probe for therapy of a condition associated with expression of heparanase; the use of a heparanase specific molecular probe for quantification of heparanase in a body fluid; the use of a heparanase specific molecular probe for targeted drug delivery; and the use of a heparanase specific molecular probe as a therapeutic agent.

Abstract: A technique is disclosed that is useful for determining the presence of specific hybridization expression within an output pattern generated from a digitized image of a biological sample applied to an arrayed platform. The output pattern includes signals associated with noise, and signals associated with the biological sample, some of which are degraded or obscured by noise. The output pattern is first segmented using tessellation. Signal processing, such as interferometry, or more specifically, resonance interferometry, and even more specifically quantum resonance interferometry or stochastic resonance interferometry, is then used to amplify signals associated with the biological sample within the segmented output pattern having an intensity lower than the intensity of signals associated with noise so that they may be clearly distinguished from background noise. The improved detection technique allows repeatable, rapid, reliable, and inexpensive measurements of arrayed platform output patterns.

Abstract: A method is provided for determining a concentration of a target nucleic acid by using a nucleic acid probe labeled with a fluorescent dye.

Abstract: Disclosed is a method for determining a sequence of one or more nucleotides in a target polynucleotide. In the method, a target-specific primer is contacted with a polynucleotide sample under conditions effective for the primer to anneal specifically to a primer-complementary region in one or more target polynucleotides, to form one or more target-primer hybrid(s), wherein each target-specific primer contains (i) a target binding segment and (ii) a mobility-reducing moiety which does not bind the target. The hybrid(s) are reacted with a primer extension reagent in the presence of at least one labeled 3′-nucleotide terminator complementary to a selected nucleotide base-type, optionally in the presence of one or more extendable nucleoside monomers, under conditions effective to form one or more primer extension products which terminate with at least one labeled 3′-nucleotide terminator.

Abstract: The invention provides probes, antibodies and methods for detecting a gene that is only found in Enterobacteriaceae, the deoxyguanosine triphosphate triphosphohydrolase gene. These probes and methods are useful for the detecting whether test samples, including food and water samples, are infected with enteric bacteria.