Abstract: The present invention provides for the identification and cloning of functional plant centromeres in Arabidopsis. This will permit construction of stably inherited minichromosomes which can serve as vectors for the construction of transgenic plant and animal cells. In addition, information on the structure and function of these regions will prove valuable in isolating additional centromeric and centromere related genetic elements and polypeptides from other species.

Abstract: Methods for isolating microbial species, particularly previously uncultured species, from non-laboratory source environments (such as soil, freshwater, seawater, etc.) are disclosed. These methods can include the use of cultures in arrays, and cells deposited on solid surfaces in arrays for detection, and flow cytometry and/or cell sorting and/or dilution cultures.

Abstract: A rapid and sensitive PCR-based assay is provided to facilitate early detection of Edwardsiella ictaluri in channel catfish. This bacteria is the causative agent in the disease, Enteric septicemia of catfish (ESC). Also provided is a method of selecting breeding stock for use in selective breeding programs to improve disease resistance in channel catfish. Also provided is a method of determining the efficacy of vaccines produced against ESC.

Abstract: The invention provides materials and methods for detection and typing of HPV infection using PNA probes. More specifically, methods are provided for detecting high-risk types of HPV infection with minimal numbers of PNA probes or using PNA probes to selectively amplify only high-risk types of HPV. Novel primer sequences are also provided.

Abstract: An aqueous composition containing primers for opposing strands of two or more target nucleic acids can be used in polymerase chain reaction to provide simultaneously rapid and efficient amplification and detection of those nucleic acids. The primers for each target DNA differ in length by no more than 5 nucleotides and have a Tm within the range of from about 65 to about 74° C., while the Tm's are within about 5° C. of each other. Such compositions are useful in diagnostic test kits and methods for amplification and detection of multiple nucleic acids, or in “multiplexing”, using multiple capture probes. All of the capture probes have Tm's which are greater than 50° C. and are within 15° C. of each other.

Abstract: The invention provides novel reagents, reagent kits, and methods for automated hybridization. More particularly, the invention provides reagents, reagent kits, and methods for automated in situ hybridization and automated hybridization on a microarray. The use of automated instruments for in situ hybridization and microarray hybridization dramatically reduces the amount of labor and time involved and also facilitates standardization of protocols and consistency between results.

Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.

Abstract: The present invention provides compositions, methods, and kits for covalently linking nucleic acid molecules. The methods include a strand invasion step, and the compositions and kits are useful for performing such methods. For example, a method of covalently linking double stranded (ds) nucleic acid molecules can include contacting a first ds nucleic acid molecule, which has a topoisomerase linked to a 3? terminus of one end and has a single stranded 5? overhang at the same end, with a second ds nucleic acid molecule having a blunt end, such that the 5? overhang can hybridize to a complementary sequence of the blunt end of the second nucleic acid molecule, and the topoisomerase can covalently link the ds nucleic acid molecules. The methods are simpler and more efficient than previous methods for covalently linking nucleic acid sequences, and the compositions and kits facilitate practicing the methods, including methods of directionally linking two or more ds nucleic acid molecules.

Abstract: Methods useful for improving results obtained with enzyme-based polynucleotide amplification reactions. More particularly, the invented methods are useful for: (1) promoting amplification of template-specific products such that the amount of amplicon produced reflects the pre-amplification amount of analyte, even in reactions primed with low levels of analyte polynucleotide; (2) facilitating biological specimen processing such that the amount of amplicon produced in subsequent amplification reactions will be substantially independent of the efficiency of analyte polynucleotide isolation from the specimen; and (3) controlling the amount of analyte amplicon produced in the amplification reaction.

Abstract: The invention provides novel methods for characterizing the function of nucleic acids and polypeptides. The invention provides a novel method for identifying a nucleic acid or a polypeptide sequence that may be a target for a drug. The invention provides a novel method for identifying a nucleic acid or a polypeptide sequence that may be essential for the growth or viability of an organism. The characterization is based on use of methods of the invention comprising algorithms that can identify functional relationships between diverse sets of non-homologous nucleic acid and polypeptide sequences. The invention provides a computer program product, stored on a computer-readable medium, for identifying a nucleic acid or a polypeptide sequence that may be essential for the growth or viability of an organism. The invention provides a computer program product, stored on a computer-readable medium, for identifying a nucleic acid or a polypeptide sequence that may be a target for a drug.

Abstract: The invention relates to a process for the metallization 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 compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.

Abstract: Several types of DNA cuts are used as markers of apoptosis for detection of apoptotic cells in situ. The present invention includes a method to detect DNase II type DNA damage, bearing 5?OH using vaccinia topoisomerase I. The present invention also includes a method combining a ligase-based method to detect DNase I type DNA damage and the topoisomerase based method, resulting in simultaneous detection of two specific types of DNA damage in situ.

Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

Abstract: Disclosed herein are methods for detecting complex protein interactions and protein functional relationships, and reagents for carrying out those methods.

Abstract: The present invention is directed to isolated nucleic acid molecules that encode LIM mineralization protein, or LMP. The invention further provides vectors comprising nucleotide sequences that encode LMP, as well as host cells comprising those vectors. Moreover, the present invention relates to methods of inducing bone formation by transfecting osteogenic precursor cells with an isolated nucleic acid molecule comprising a nucleotide sequence encoding LIM mineralization protein. The transfection may occur ex vivo or in vivo by direct injection of virus or naked plasmid DNA. In a particular embodiment, the invention provides a method of fusing a spine by transfecting osteogenic precursor cells with an isolated nucleic acid molecule having a nucleotide sequence encoding LIM mineralization protein, admixing the transfected osteogenic precursor cells with a matrix and contacting the matrix with the spine.

Abstract: The present invention provides in situ hybridization probes which include a marker and a nucleic acid molecule able to hybridize exclusively with only one species of Encephalitozoon. The nucleic acid molecule may be, for example, complimentary to segment 878-896 of 16S rRNA of Encephalitozoon hellem spores. Specifically disclosed probes are those including the following nucleotides: (1) 5?-ACT CTC ACA CTC ACT TCA G-3? (Seq. I.D. No. 1) which is species specific for Encephalitozoon hellem, (2) 5?-CAG ACC ACT ATC TGC A-3? (Seq. I.D. No. 2) which is species specific for Encephalitozoon cuniculi and (3) 5?-GTT CTC CTG CCC GCT TCA G-3? (Seq. I.D. No. 3) which is species specific for Encephalitozoon intestinalis. The assay of the present invention utilizes a sample such as surface, ground or drinking water, suspected of containing one of the aforementioned species as a target organism.

Abstract: Included is a method for detecting spinocerebellar ataxia type 10 (SCA10) by measuring the presence or absence of a DNA expansion in a gene locus associated with spinocerebellar ataxia type 10. The method employs extracting DNA from a sample to be tested, amplifying the extracted DNA; and identifying the presence or absence of a DNA expansion in the amplified extension products. Also included in the present invention are a kit for diagnosis of SCA10 and non-human transgenic eukaryotes that are not expressing or overexpressing SCA10.

Abstract: The methods, compositions and apparatus disclosed herein are of use for nucleic acid sequence determination. The methods involve isolation of one or more nucleic acid template molecules and polymerization of a nascent complementary strand of nucleic acid, using a DNA or RNA polymerase or similar synthetic reagent. As the nascent strand is extended one nucleotide at a time, the disappearance of nucleotide precursors from solution is monitored by Raman spectroscopy or FRET. The nucleic acid sequence of the nascent strand, and the complementary sequence of the template strand, may be determined by tracking the order of incorporation of nucleotide precursors during the polymerization reaction. Certain embodiments concern apparatus comprising a reaction chamber and detection unit, of use in practicing the claimed methods. The methods, compositions and apparatus are of use in sequencing very long nucleic acid templates in a single sequencing reaction.

Abstract: Methods, compositions, kits, and apparatus are provided wherein the aminoacyl-tRNA synthetase system is used to analyze amino acids. The method allows very small devices for quantitative or semi-quantitative analysis of the amino acids in samples or in sequential or complete proteolytic digestions. The methods can be readily applied to the detection and/or quantitation of one or more primary amino acids by using cognate aminoacyl-tRNA synthetase and cognate tRNA. The basis of the method is that each of the 20 synthetases and/or a tRNA specific for a different amino acid is separated spatially or differentially labeled. The reactions catalyzed by all 20 synthetases may be monitored simultaneously, or nearly simultaneously, or in parallel. Each separately positioned synthetase or tRNA will signal its cognate amino acid. The synthetase reactions can be monitored using continuous spectroscopic assays.