Abstract: A method of determining the binding of an oligonucleotide probe to a test nucleic acid sequence comprises the steps of: (a) providing the test nucleic acid sequence in single-stranded form, (b) contacting the test nucleic acid sequence under hybridizing conditions with a solution containing an oligonucleotide probe which is complementary to a defined portion of a standard nucleic acid sequence, (c) immobilizing to a solid support a nucleic acid fragment at least part of which is complementary to said oligonucleotide probe, (d) contacting the solution from step (b) with said solid support, and (e) determining the amount of binding of oligonucleotide probe present in said solution to its complementary nucleic acid fragment on the second solid support, said amount being inversely related to the amount of binding of the oligonucleotide probe to the test nucleic acid sequence.

Abstract: Disclosed are methods and compositions for copying a target nucleic acid using a self-priming primer. Single and different target nucleic acids can be copied using the disclosed methods and compositions.

Abstract: Gene segment linking provides a simple, cost-effective way to produce an amplified DNA sequence containing linked segments of a single gene or multiple genes. The inventive method involves Multiplex PCR amplifications of gene sequences and linkage of the exons in a single reaction. Multiplex PCR of the gene segments is performed with primers having complementary tails which permit linkage of the gene segments and amplification of the linked gene in one polymerase chain reaction. The ability to construct an amplified DNA from genomic DNA containing several introns in two PCR steps allows the rapid production of DNA which heretofore required many time-consuming and expensive steps.

Abstract: Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising multiple sites capable of binding the binding ligand to complex the receptor to the binding ligand, and the receptor is contacted with an amplification reagent, comprising a plurality of the binding ligands, to complex the amplification reagent to the receptor. The presence of the complexed amplification reagent then is detected, for example, by detecting the presence of a detectable label, such as a fluorescent label, for example, on the receptor or the amplification reagent.

Abstract: The present invention relates to a method for selectively extending an oligonucleotide primer along a specific target polynucleotide sequence in a mixture of polynucleotides. A combination is provided comprising the mixture, an oligonucleotide primer having a modification, and a binding substance for the modification wherein the binding substance binds to the oligonucleotide and prevents the extension of the oligonucleotide along the target polynucleotide sequence. The temperature of the combination is adjusted to a level sufficient to irreversibly denature the binding substance and permit the extension of the oligonucleotide primer along the specific target polynucleotide sequence. The invention has particular application in the amplification of nucleic acids. Also disclosed are kits for carrying out a method in accordance with the present invention.

Abstract: The present invention relates, in general, to tristetraprolin (TTP) and, in particular, to methods of modulating levels of tumor necrosis factor &agr; (TNF&agr;) using TTP or nucleic acid sequences encoding same. The invention further relates to methods of screening for compounds for their ability to inhibit TNF&agr; biosynthesis.

Abstract: This invention relates to methods of amplifying nucleic acids to minimize contamination by products of earlier amplification reactions. More particularly, it relates to methods of using nucleic acid labels that inhibit further amplification of the amplicon, and compositions that are useful to accomplish this task. In particular, the present invention relates to photoreactive complexes of a binding ligand, a binding enhancer and a label.

Abstract: MyoD1 expression is found at early stages of embryonic myogenesis and in rhabdomyosarcoma, the most common soft-tissue cancer in children. Hypomethylation of a CpG island in the 5′ upstream region of the human MyoD1 gene occurs in a majority of alveolar rhabdomyosarcomas, and may be responsible for higher levels of the MyoD1 expression in this tumor type. The methylation status of the upstream CpG island may play a key role in regulation of the MyoD1 expression not only in alveolar rhabdomyosarcoma, but also during normal development. This invention provides for the assessment of the methylation status of the MyoD1 upstream CpG sites, which may have valuable implications for differential diagnosis of pediatric cancers and may results in potential therapeutic applications.

Abstract: Methods for preparing a biochip are provided herein wherein the biomolecular probe to be used with the biochip is alternatively bound to a hydrogel prepolymer prior to or simultaneously with polymerization of the prepolymer. In particularly preferred embodiments, a polyurethane-based hydrogel prepolymer is derivatized with an organic solvent soluble biomolecule, such as a peptide nucleic acid probe in aprotic, organic solvent. Following derivatization of the prepolymer, an aqueous solution, for example sodium bicarbonate, preferably buffered to a pH of about 7.2 to about 9.5, is added to the derivatized prepolymer solution to initiate polymerization of the hydrogel. Alternatively, a water soluble biomolecule, such as DNA or other oligonucleotide, is prepared in an aqueous solution and added to the polyurethane-based hydrogel prepolymer such that derivatization and polymerization occur, essentially, simultaneously.

Abstract: Protease-deficient strains of the methylotrophic yeast Pichia methanolica and materials and methods for generating such strains are disclosed. The strains have a functional deficiency in a vacuolar protease, such as proteinase A or proteinase B. The strains are useful as hosts for the expression of heterologous genes encoding proteins of commercial or other interest.

Abstract: We sequenced a 625 and 617 bp fragment of the inner spacer region of 16S-23S rDNA of a strain of Acidovorax avenae representing pathogens from several hosts, including foxtail, oats, corn, rice, millet, sugarcane, orchid, and watermelon and a strain of A. avenae subsp. citrulli pathogenic only to watermelon, respectively, for the purpose of designing PCR primers for their identification. These plant pathogens were previously considered as non-fluorescent pseudomonads and have been recently reclassified as Acidovorax avenae subsp. avenae, A. avenae subsp. cattleyae, and A. avenae subsp. citrulli. Several sets of primers were designed. Primers identified by SEQ ID NO:1 and SEQ ID NO:2 of subsp. avenae reacted with all strains of A. avenae subsp. avenae (previously named P. avenae or P. alboprecipitans) originating from foxtail, oats, corn, rice, sugarcane, and millet, A. avenae subsp. cattleyae from orchid, and A. avenae subsp. citrulli (previously named P. pseudoalcaligenes subsp. citrulli) from watermelon.

Abstract: A technique is described for identifying mutations, if any, present in a biological sample, from a pre-selected set of known mutations. The method can be applied to DNA, RNA and peptide nucleic acid (PNA) microarrays. The method analyzes a dot spectrogram representative of quantized hybridization activity of oligonucleotides in the sample to identify the mutations. In accordance with the method, a resonance pattern is generated which is representative of nonlinear resonances between a stimulus pattern associated with the set of known mutations and the dot spectrogram. The resonance pattern is interpreted to a yield a set of confirmed mutations by comparing resonances found therein with predetermined resonances expected for the selected set of mutations.

Abstract: Nucleic acids encoding each of three subunits, .alpha.1B, .alpha.2.delta., and .beta.3, of a calcium channel, are disclosed. Also disclosed are vectors containing the nucleic acids encoding the subunits; host cells containing the nucleic acids encoding the subunits; methods of isolating nucleic acids encoding related calcium channel subunits; the subunit proteins; fusion proteins comprising the subunit proteins; antibodies to the subunit proteins; assays to identify agents that modulate calcium channel activity, and agents identified thereby; methods of treating certain central nervous system disorders by altering calcium channel activity; and methods of diagnosing diseases associated with particular calcium channels, such as Lambert-Eaton syndrome.

Abstract: The present invention is directed to a mutation detection kit and method of analyzing multiple loci of one or more nucleic acid sequences for the presence of mutations or polymorphisms. More particularly, the present invention relates to the use of the polymerase chain reaction (PCR) and fluorescently labeled oligonucleotide hybridization probes to identify mutations and polymorphisms based on melting curve analysis of the hybridization probes.

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: The invention describes a method of quantitatively detecting specific nucleotide sequences. Said method is essentially characterized in that a single-stranded nucleic acid, particularly mRNA, which has been isolated from a mixture, e.g. a biological sample, is hybridized in solution, with a polynucleotide sequence which is essentially complementary to the sequence to be determined; the nucleic acid is then immobilized on a solid phase, and the amount of bound hybrid is determined. It has proven to be particularly advantageous if the binding to the coated solid phase is accomplished with the aid of the specifically bindable chemical group which is coupled to the sequence to be determined or to the polynucleotide probe sequence via a linker.

Abstract: A sample application method including the steps of: rotating a biochip including a plurality of regions bound with various probes; and dropping a sample onto generally a center of rotation of the rotating biochip so as to apply the sample to the plurality of regions.

Abstract: The invention provides two new zoogloeal strains, mz1t and mz2t. The invention provides an isolated nucleic acid consisting of the nucleic acid of SEQ ID NO:1. Examples of nucleic acids of mz1t include SEQ ID NO:2 and SEQ ID NO:3. An example of a nucleic acid of mz2t is SEQ ID NO:4. The invention also provides an isolated nucleic acid consisting of the nucleic acid of SEQ ID NO:5. A method of detecting the presence of zoogloeal clusters in a wastewater sample is provided, comprising: a) contacting RNA from a sample of the wastewater with a nucleic acid comprising the nucleic acid of SEQ ID Nos:1,2,3,4 or 5 under conditions that permit specific hybridization; and b) detecting the presence of hybridization, the presence of hybridization indicating the presence of zoogloeal clusters. A new Hyphomicrobium spp. strain, designated M3, is provided herein. The invention provides novel nucleic acids of a Hyphomicrobium sp. M3. For example SEQ ID NO:6 and SEQ ID NO:7 rDNAs of M3.

Abstract: A method of transcribing ribonucleic acids of a sample by treating the sample containing ribonucleic acid with a DNA digesting enzyme in the presence of Mn.sup.2+ ions followed by transcribing the ribonucleic acids into deoxyribonucleic acids and suitable reagents.

Abstract: The object of the present invention is to provide a method capable of analyzing the presence or absence of a target DNA sequence, the level and sequence characteristics thereof at a high sensitivity, and a device therefor, wherein the overall process from pretreatment to the recovery of DNA information and the analysis thereof can be completed in a speedy fashion by the simple device structure and procedures.Therefore, by preparing a single-stranded DNA fragment of a target DNA region, detecting the change in the absorbance of the single-stranded DNA sample while changing the denaturing condition of the conformation of the single-stranded DNA fragment by a denaturing condition regulatory means, and analyzing the curve of the change in the absorbance over the modification in the denaturing condition, the sequence information of the single-stranded DNA, namely the target DNA, can be generated in a rapid and simple manner.