Abstract: Compositions and methods are provided for antisense modulation of interleukin-5 signal transduction. Antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding interleukin-5 and interleukin-5 receptor.alpha. are preferred. Methods of using these compounds for modulation of interleukin-5 signal transduction and for treatment of diseases associated with interleukin-5 signal transduction are also provided.

Abstract: Automated sample analysis is performed by a computer-implemented apparatus and method for distinguishing objects of interest in an optical field from other objects and background in the optical field, collectively called background. Once an object has been identified, the color comprised of a combination of the red, green and blue components of the pixels occupied by the image of the object of interest, or another parameter of interest relative to that object can be measured and stored. This computer-implemented analysis apparatus and method is performed on objects of interest in the sample which are tagged using fluorescent tags. The sample may be a cell sample containing a nucleic acid target and the tagging achieved by fluorescence in situ hybridization.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of PI3 kinase p110 beta. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding PI3 kinase p110 beta. Methods of using these compounds for modulation of PI3 kinase p110 beta expression and for treatment of diseases associated with expression of PI3 kinase p110 beta are provided.

Abstract: A DNA probe has been isolated which is capable of hybridizing to an oligonucleotide sequence coding for a polypeptide from a major 64 Kilodalton protein of human cytomegalovirus (HCMVgp64). The probe has a sequence of at least seventeen (17) to as many as seven hundred twenty-one (721) nucleotides. The DNA fragments coding for the major late protein of human cytomegalovirus (HCMVgp64) may be hybridized to DNA fragments of HCMV DNA from an individual having human cytomegalovirus infection. The major late protein of human cytomegalovirus (HCMVgp64) also reacts with T-lymphocytes of an individual after natural infection of that individual with human cytomegalovirus. Thus, the HCMVgp64 protein may be used as a vaccine to prevent HCMV infection.

Abstract: Methods for linearly amplifying mRNA to produce antisense RNA are provided. In the subject methods, mRNA is converted to double-stranded cDNA using a promoter-primer having a poly-dT primer site linked to a promoter sequence so that the resulting double-stranded cDNA is recognized by an RNA polymerase. The resultant double-stranded cDNA is then transcribed into antisense RNA in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods find use a variety of different applications in which the preparation of linearly amplified amounts of antisense RNA is desired. Also provided are kits for practicing the subject methods.

Abstract: A novel method and composition is provided to control Fusarium root rot and damping off on conifer seedlings. When certain bacteria and an ectomycorrhizal fungus are placed in contact with the conifer seed or seedling, the combination reduces or eliminates disease symptoms caused by several Fusarium species.

Abstract: A method for determining the activity of a nucleotide polymerizing enzyme in a sample, and use of the method for determining HIV 1 RT- and Herpes Simplex DNA-polymerase activity. The enzyme is captured by means of a nonoclonal antibody which is immobilized to a solid carrier and is capable of binding the enzyme without detrimentally effecting the enzyme activity. Contaminants and disturbing factors are removed and the nucleotide polymerization starts by the addition of a reaction solution containing a primer/template construct and nucleotides substrate, the reaction conditions being chosen such that they promote permanent association between antibody enzyme- and primer/template constructs. When necessary a nucleotide substrate, primer/template and reaction solution are washed away from the newly synthesized polymer, and the amount of nucleotide which as been incorporated into the polymer is determined, and the activity of the enzyme is determined with the guidance of this determination.

Abstract: Disclosed are diagnostic and prognostic kits for the detection and treatment of proliferative diseases such as ovarian cancer, breast cancer, and lymphoma. Also disclosed are cancer therapeutics utilizing IAP antisense nucleic acids IAP fragments, and antibodies which specifically bind IAP polypeptides.

Abstract: A method and compounds are provided for inhibiting the synthesis of extracellular matrix proteins. Compounds of the invention comprise antisense oligonucleotides specific for nuclear proto-oncogenes. Preferably, antisense compounds of the invention are selected from the group consisting of c-myc and c-myb and are locally administered. The invention finds use in the treatment of a variety of disorders, including sclerotic disorders and restenosis, associated with the inappropriate synthesis of extracellular matrix proteins, particularly collagen.

Abstract: Expression vectors capable of being replicated in lactic acid bacterial cells comprising a promoter region comprising (a) a promoter sequence element the function of which is regulatable by an environmental or growth condition factor and (b) at least one further nucleotide sequence element, the position, orientation, presence and/or sequence of which element has a regulatory effect on the expression of a gene operably linked to the promoter region in which vectors the position, orientation, presence and/or sequence of at least one of said elements (a) or (b) is modified relative to the position, orientation, presence and/or sequence of the corresponding non-modified element whereby the expression of the gene is altered, and a lactic acid bacterium which is transformed with such a vector as defined above are provided.

Abstract: Compounds, compositions and methods are provided for inhibiting FAK mediated signaling. The compositions comprise antisense compounds targeted to nucleic acids encoding FAK. Methods of using these antisense compounds for inhibition of FAK expression and for treatment of diseases, particularly cancers, associated with overexpression or constitutive activation of FAK are provided.

Abstract: Detector nucleic acids are employed for detection of nucleic acid target sequences by fluorescence quenching mechanisms. The detector nucleic acid comprises at least two oligonucleotides and is partially single-stranded and partially double-stranded. One of the two dyes of a donor/acceptor dye pair is linked to the first oligonucleotide and the other is linked to a second oligonucleotide such that they are in close spatial proximity when the first and second oligonucleotides are base-paired and donor fluorescence is quenched. A single second oligonucleotide may be hybridized to the first oligonucleotide or multiple second oligonucleotides may be hybridized to the first oligonucleotide and to each other, forming a junction structure comprising multiple donor/acceptor dye pairs. The detector oligonucleotide retains its partially single-stranded and partially double-stranded conformation in the absence of target.

Abstract: A method based on polymerase chain reaction (PCR) amplification and oligonucleotide ligase assay (OLA) reaction is provided for analyzing complex genetic systems in a single reaction vessel. The method involves simultaneously incubating a sample containing one or more target polynucleotides with PCR primers and OLA probes in a single reaction mixture. The presence of variant polynucleotide sequences in the sample is determined by detecting and identifying the products of the OLA reaction.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of Telomeric Repeat Binding Factor 1. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding Telomeric Repeat Binding Factor 1. Methods of using these compounds for modulation of Telomeric Repeat Binding Factor 1 expression and for treatment of diseases associated with expression of Telomeric Repeat Binding Factor 1 are provided.

Abstract: The present invention is based at least in part on the discovery of the genomic structure of the human SR-BI gene and on the identification of polymorphic regions within the gene. Accordingly, the invention provides nucleic acids having a nucleotide sequence of an allelic variant of an SR-BI gene and nucleic acids having an SR-BI intronic sequence. The invention also provides methods for identifying specific alleles of polymorphic regions of an SR-BI 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 SR-BI gene, and kits for performing such methods.

Abstract: The present invention provides a fast, simple and direct covalent bond formation between two strands of nucleotide sequences. Non-modified first strand nucleotide sequences are hybridized with second strand nucleotide sequences, of which certain specific base structure(s) is modified by chemical reagents in order to generate covalent bonding with the first strand. While the hybridization of these two strand nucleotide sequences generates double-stranded hybrid duplexes between their homologues, covalent bond formation occurs in the region of modified base-pairs. Since neither a polymerase chain restriction nor a restriction enzyme digestion can be performed with the covalently bonded hybrid duplexes, the present invention can be used to subtract common sequences during subtractive hybridization, to inhibit nonspecific contamination during subcloning and to increase binding stability of antisense probes during in situ hybridization as well as gene therapy.

Abstract: Techniques for designing polymer probes to verify the integrity of the probe synthesis are provided. Multiple probes with identical sequences are designed so that the probes will be formed utilizing at least one different monomer addition cycle. Based on the probes affinity to a control target, variations (e.g., errors) in probe synthesis may be identified.

Abstract: Methods for the determination of nuclease stability of an oligomeric compound and its deletion sequences by capillary gel electrophoresis using laser-induced fluorescence detection (LIF CGE) are provided. Fluorescently labeled oligomeric compounds are treated with one or more agents having nuclease activity resulting in an assay mixture of the original oligomeric compound and its deletion sequences. A diluted aliquot taken directly from the assay mixture is analyzed using LIF CGE. Results of the assay yield quantitative concentrations of the oligomeric compound and each of the deletion sequences. In further embodiments, the invention provides methods for determining the relative binding affinity of one or more oligomeric compounds for a substrate having nuclease activity, and methods for determining the nuclease activity of an enzyme.

Abstract: A purified thermostable nucleic acid polymerase is obtained that has unique characteristics. Preferably the nucleic acid polymerase is DNA polymerase isolated from a Thermus aquaticus species and has a molecular weight of about 86,000-95,000 daltons. The thermostable nucleic acid polymerase may be native or recombinant and may be used in a temperature-cycling chain reaction wherein at least one nucleic acid sequence is amplified in quantity from an existing sequence with the aid of selected primers and nucleotide triphosphates. The nucleic acid polymerase is preferably stored in a buffer containing non-ionic detergents that lends stability to the nucleic acid polymerase. A preferred buffer contains glycerol, polyoxyethylated sorbitan monolaurate, ethoxylated nonyl phenol and gelatin.

Abstract: The invention relates to cells usable for the production of defective adenoviruses comprising, inserted into their genome, a portion of the region E4 of an adenovirus genome carrying the reading phase ORF6 under the control of a functional promoter.

Abstract: Oligonucleotides in which one or more purine residues are substituted by pyrazolo[3,4-d]pyrimidines exhibit improved hybridization properties. Oligonucleotides containing pyrazolo[3,4-d]pyrimidine base analogues have higher melting temperatures than unsubstituted oligonucleotides of identical sequence. Thus, in assays involving hybridization of an oligonucleotide probe to a target polynucleotide sequence, higher signals are obtained. In addition, mismatch discrimination is enhanced when pyrazolo[3,4-d]pyrimidine-containing oligonucleotides are used as hybridization probes, making them useful as probes and primers for hybridization, amplification and sequencing procedures, particularly those in which single- or multiple-nucleotide mismatch discrimination is required.

Abstract: A method and apparatus is disclosed to reduce evaporation of solutions, particularly aqueous solutions, using a polymeric material such as polysucrose, polyvinylpyrrolidone and polyethylene glycol. A microscope slide and cover glass assembly utilizing the polymeric material in solution and method of use are described.

Abstract: The invention relates to the detection of target nucleic acids or nucleic acid units in a sample, by obtaining a SER(R)S spectrum for a SER(R)S-active complex containing, or derived directly from, the target. The complex includes at least a SER(R)S-active label, and optionally a target binding species containing a nucleic acid or nucleic acid unit. In this detection method, the concentration of the target present in the SER(R)S-active complex, or of the nucleic acid or unit contained in the target binding species in the SER(R)S-active complex, is no higher than 10.sup.-10 moles per liter. Additionally or alternatively, one or more of the following features may be used with the method: i) the introduction of a polyamine; ii) modification of the target, and/or of the nucleic acid or nucleic acid unit contained in the target binding species, in a manner that promotes or facilitates its chemi-sorption onto a SER(R)S-active surface; iii) inclusion of a chemi-sorptive functional group in the SER(R)S-active label.

Abstract: Nucleic acid molecules with new motifs having catalytic activity, methods of synthesis, and use thereof are also described.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of fra-1. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding fra-1. Methods of using these compounds for modulation of fra-1 expression and for treatment of diseases associated with expression of fra-1 are provided.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of PDK-1. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding PDK-1. Methods of using these compounds for modulation of PDK-1 expression and for treatment of diseases associated with expression of PDK-1 are provided.

Abstract: Disclosed are compositions and a method for amplification of nucleic acid sequences of interest. The method is based on stand displacement replication of the nucleic acid sequences of interest by multiple primers. In one preferred form of the method, referred to as multiple strand displacement amplification, two sets of primers are used, a right set and a left set. The primers in the right set are complementary to one strand of the nucleic acid molecule to be amplified and the primers in the left set are complementary to the opposite strand. The 5' end of primers in both sets are distal to the nucleic acid sequence of interest when the primers have hybridized to the nucleic acid sequence molecule to be amplified. Amplification proceeds by replication initiated at each primer and continuing through the nucleic acid sequence of interest. A key feature of this method is the displacement of intervening primers during replication by the polymerase.

Abstract: A nucleotide sequence encoding a katG/lacZ fusion protein is useful for assaying the enzymatic activity of the katG gene product. A process of selecting a compound that is toxic against an isoniazid-resistant mycobaterial strain comprises incubating a catalase peroxidase enzyme with an isoniazid to produce a compound that restores isoniazid susceptability to the isoniazid-resistant mycobaterial strain.

Abstract: The present invention provides a partial cDNA corresponding to an RNA containing double stranded regions (R-RNA), which, when transcribed in vitro, gives rise to an RNA transcript that activates PKR. An approximately 226-252 bp nucleotide (nt) sequence responsible for activation of PKR (the activation sequence) has been identified within the cDNA and isolated. Antisense oligonucleotides corresponding to specific portions of the 252 nt cDNA fragment stimulate proliferation of different cells in culture. Various portions of the cDNA or R-RNA may also be used to inhibit cell proliferation in cell cultures.The present invention further provides pharmaceutical compositions comprising the subject nucleic acid fragments and oligonucleotides. Kits which comprise at least one of the subject isolated nucleic acid molecules or oligonucleotides and a pharmaceutically acceptable carrier are also provided.

Abstract: DNA sequences optimized for expression in plants are disclosed. The DNA sequences preferably encode for an insecticidal polypeptides, particularly insecticidal proteins from Bacillus thuringiensis. Plant promoters, particular tissue-specific and tissue-preferred promoters are also provided. Additionally disclosed are transformation vectors comprising said DNA sequences. The transformation vectors demonstrate high levels of insecticidal activity when transformed into maize.

Abstract: A synthetic nuclease resistant antisense oligodeoxynucleotide (AS-ODN) capable of selectively modulating human acetylcholinesterase (AChE) production and a composition comprising at least one AS-ODN as an active ingredient. A nuclease resistant antisense targeted against the splice junction in the AChE mRNA post-splice message is disclosed. The synthetic nuclease resistant AS-ODNs are capable of selectively modulating human AChE production in the central nervous system or capable of selectively reducing human AChE deposition of the neuromuscular junction. The present invention also provides a method to restore balanced cholinergic signalling in the brain and spinal cord or reduce AChE in the neuromuscular junction in patients in need of such treatment by administering to a patient in need of such treatment a therapeutically effective amount of at least one of the synthetic nuclease resistant AS-ODN capable of selectively modulating human AChE production.

Abstract: The invention provides a method of preventing or reducing the severity of a cancer in a subject by stimulating the subject's immune response against the cancer. The invention provides, for example, a method of stimulating an immune response in a subject by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to reduce or inhibit the expression of one or more immunosuppressive agents. The invention also provides a method of preventing or reducing the severity of cancer in a subject by stimulating the subject's immune response against the cancer by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to prevent the expression of an immunosuppressive agents and, in combination with the genetically modified tumor cells, an immunostimulatory agent. The invention further provides compositions useful for practicing the claimed methods.

Abstract: Endo-xyloglucan transferases responsible for growth of plant cell wall, genes coding for the enzymes, a method of transferring xyloglucan molecules by using the enzyme, and methods of using the gene are described.

Abstract: An isothermal transcription based amplification assay for the detection or quantification of chemokine RNA uses primers and probes for sequences within the gene for RANTES, MIP-l.alpha. and MIP-1 .beta.. The quantitative system uses an internal control Q of a mutant version of each gene. Target specific primers and probes are also disclosed.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of SHP-1. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding SHP-1. Methods of using these compounds for modulation of SHP-1 expression and for treatment of diseases associated with expression of SHP-1 are provided.

Abstract: Compounds of the formula: ##STR1## are provided, in which R.sup.1 and R.sup.2 each independently represent a C.sub.8 -C.sub.24 saturated or unsaturated hydrocarbon chain, which is optionally interrupted by from 1 to 3 heteroatom moieties, such as --O--, --S--, --NH-- and --NR--. The symbol X represents --CH.sub.2 --, --O--, --S--, --NH-- or --NR--. The R group for each of the --NR-- moieties represents an alkyl group having from 1 to 4 carbon atoms. Finally, the subscript n represents the integer 1 or 2, and A.sup.- represents an anion, preferably chloride or citrate.

Abstract: The invention relates to a method for diagnosing an individual as having atopy or a predisposition thereto. The method involves demonstrating in the individual the presence or absence of either: (i) an unusual variant form of the gene which codes for the beta sub-unit of the high affinity receptor for IgE (Fc.epsilon.RI.beta.), the variant form comprising a variation in exon (7) which encodes a glycine at amino acid residue 237 instead of glutamic acid which appears at residue 237 in individuals without atopy: or (ii) an unusual polymorphic form of the amino acid sequence for Fc.epsilon.RI.beta., the polymorphic form comprising glycine at amino acid residue 237 instead of glutamic acid which appears at residue 237 in individuals without atopy. Materials and other methods relating to the above diagnostic method are also described.

Abstract: The invention features a synthetic gene encoding a protein normally expressed in a mammalian cell wherein at least one non-preferred or less preferred codon in the natural gene encoding the protein has been replaced by a preferred codon encoding the same amino acid.

Abstract: A method of amplifying a mixture of different-sequence DNA fragments which may be formed from RNA transcription, or derived from genomic single- or double-stranded DNA fragments. The fragments are treated with terminal deoxynucleotide transferase and a selected deoxynucleotide, to form a homopolymer tail at the 3' end of the anti-sense strands, and the sense strands are provided with a common 3'-end sequence. The fragments are mixed with a homopolymer primer which is homologous to the homopolymer tail of the anti-sense strands, and a defined-sequence primer which is homologous to the sense-strand common 3'-end sequence, with repeated cycles of fragment denaturation, annealing, and polymerization, to amplify the fragments. In one embodiment, the defined-sequence and homopolymer primers are the same, i.e., only one primer is used. The primers may contain selected restriction-site sequences, to provide directional restriction sites at the ends of the amplified fragments.

Abstract: Methods are provided for inhibiting the expression of cell adhesion molecules using inhibitors of signaling molecules involved in human TNF-.alpha. signaling. These inhibitors include monoclonal antibodies, peptide fragments, small molecule inhibitors, and, preferably, antisense oligonucleotides. Methods for treatment of diseases, particularly inflammatory and immune diseases, associated with overexpression of cell adhesion molecules are provided.

Abstract: The present invention provides a reagent which can be used as a marker to identify individual lanes on an electrophoresis gel which is run on an Automated DNA Sequencer. This reagent is may be included in the loading dye for samples in DNA sequencing, DNA fragment analysis, or linkage mapping analysis. Inclusion of the reagent aids in the identification of the lane in which each sample is individually loaded on the acrylamide gel, such that the data read from each lane by the instrument is correctly applied to the appropriate sample.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of G-alpha-S1. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding G-alpha-S1. Methods of using these compounds for modulation of G-alpha-S1 expression and for treatment of diseases associated with expression of G-alpha-S1 are provided.

Abstract: This invention relates to a novel Solvent Extraction and Direct Hydration (SEDH) method for preparing lipid-nucleic acid particles which are useful for the introduction of nucleic acids (e.g., plasmid DNA, antisense molecules, ribozymes, etc.) into cells. The lipid-nucleic acid particles prepared using the methods of the present invention have enhanced circulation characteristics and serum stability and, thus, they are extremely effective as nucleic acid delivery vehicles.

Abstract: The invention consists of a method for inducing production of a mucosal immune response in a host by administration of an antigen-encoding polynucleotide preparation, comprising DNA or RNA encoding an antigenic epitope to a mucosal inductor site in the mucosal tissue of the host. Naked DNA may be administered directly to mucosa, for instance in saline drops, or in a recombinant gene expression vector. Preferably, the recombinant gene expression vectors are not capable of replication or dessimination. The invention also includes the use of live viral vaccines wherein the viruses include immunostimulatory polynucleotides of the invention. According to a preferred method of the invention, a target protein antigen is administered through its expression by a recombinant gene expression vector.

Abstract: The present invention discloses catalytic or enzymatic DNA molecules that contain a modified nucleotide and that are capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

Abstract: A synthetic nuclease resistant antisense oligodeoxynucleotide (AS-OND) capable of selectively modulating human acetylcholinesterase production in the central nervous system is provided. In an embodiment the antisense oligodeoxynucleotide can be selected from5'ACGCTTTCTTGAGGC 3' SEQ ID No:1, or - 5'GGCACCCTGGGCAGC 3' SEQ ID No:2.The present invention also discloses a pharmaceutical or medical composition comprising as active ingredient at least one synthetic nuclease resistant antisense oligodeoxynucleotide capable of selectively modulating human acetylcholinesterase production in the central nervous system in a physiologically acceptable carrier or diluent.

Abstract: This invention relates to methods, kits and compositions suitable for the improved detection, analysis and quantitation of nucleic acid target sequences using probe based hybridization assays. The invention is more specifically directed to methods, kits and compositions suitable for suppressing the binding of detectable nucleic acid probes or detectable PNA probes to non-target nucleic acid sequences in an assay for a target nucleic acid sequence to thereby improve the reliability, sensitivity and specificity of the assay. The methods, kits and compositions of this invention are particularly well suited to the detection and analysis of nucleic acid point mutations.

Abstract: The invention features methods for detecting polymorphic restriction sites and single nucleotide polymorphisms in nucleic acid molecules and kits for carrying out these methods.

Abstract: The present invention provides a method for producing erythritol comprising cultivating microorganisms, which produce erythritol, belonging to Trichosporonoides megachiliensis in a culture medium having a high saccharide concentration and then recovering the erythritol accumulated in the culture medium. According to the present invention, cultivation period for producing erythritol can be shortened remarkably, and saccharide-based erythritol yield is excellent. Moreover, a large amount of erythritol can be produced efficiently, without much cost, since the same effect can be confirmed in case of using a culture medium at high saccharide concentration.

Abstract: A process for producing high yields of .gamma.-hexalactone and 2-pentanone from the corresponding hexanoic acid starting material is carried out with high amounts of oxygen and sugar in the presence of a mold microorganism. Fragrance compositions and foodstuff compositions are augmented and enhanced by the presence of the product compounds.