Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.

Abstract: The invention provides a method of generating nested sets of double stranded DNA (dsDNA) circles that may be used as size ladders in nucleic acid separations and as templates in DNA sequencing operations. In one aspect, the invention provides methods for generating nested sets of double stranded DNA circles in a self-sustaining enzymatic reaction comprising the activities of at least one endonuclease, at least one single stranded exonuclease, and at least one ligase. In another embodiment, such nested sets are generated from linear dsDNA fragments having ligatable terminators that are self-ligated to form corresponding dsDNA circles.

Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.

Abstract: Immunoliposomes and use thereof in highly specific and sensitive nucleic acid amplification assays relying on amplification of specific nucleic acid sequences released from encapsulation within a liposome after a receptor on the liposome couples with a targeted analyte/antigen immobilized on a select surface. The immunoliposome nucleic acid amplification assay permits both quantitative and qualitative analyte detection.

Abstract: Multiple species of fungi in an environment can be identified in one sample by extracting and purifying fungal DNA in the sample. PCR is then performed followed by cloning the amplifed DNA and transforming the DNA into bacteria for purposes of growing the organisms. Colonies of the growth containing transformed bacteria are then chosen on the basis of coloration. Plasmids from the chosen colonies were then purified and the DNA is analyzed to identify fungi present in the sample.

Abstract: The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether PPi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an ?-thio triphosphate analogue of said nucleotide is used, ant the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.

Abstract: A herbicide resistant transformed sugar beet that is detectable by the specific primers developed to match the DNA sequences that flank the left and/or right border region of the inserted transgenic DNA and the method of identifying primer pairs containing plant genomic DNA/plasmid DNA. More specifically, the present invention covers a specific glyphosate resistant sugar beet plant having an insertion of the transgenic material identified as the T227-1 event. The present invention additionally covers primer pairs: plant genomic DNA/Plasmid DNA that are herein identified. Additionally, these primer pairs for either the left or the right flanking regions make an event specific test for the T227-1 insert of transgenic material.

Abstract: Aptamers bind to Listeria surface proteins. A method of assaying a sample for the presence of Listeria monocytogenes includes exposing the sample to an aptamer that specifically binds one of the following proteins: Listeria monocytogenes internalin A protein, Listeria monocytogenes internalin E protein, and Listeria monocytogenes 0610 protein. The presence of Listeria monocytogenes in the sample is detected when the aptamer binds the protein present in the sample. A method of treating Listeria monocytogenes infection includes administering the aptamers to the mammal at a concentration sufficient to reduce Listeria monocytogenes infection.

Abstract: The method of the present invention is based on a method wherein a nucleic acid is synthesized utilizing the hybridized 3?-end, which is synthesized by complementary strand synthesis, on a specific region of a target nucleotide sequence existing as the nucleotide sequence of the same strand as the origin for the next round of complementary strand synthesis. The hybridization to a specific region, which region is searched for mutations and polymorphisms, is repeatedly carried out according to the present invention. Thus, mutations and polymorphisms in a target nucleotide sequence are exactly copied to the reaction products.

Abstract: A method for designing an array is provided. In certain embodiments, this method includes grouping probes into a plurality of ranked groups of probes; and designing an array comprising the ranked groups of probes, wherein the array contains more replicates of probes in a higher ranked group as compared to probes of a lower ranked group of probes.

Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.

Abstract: A process for assembling a series of DNA fragments generated by PCR into an ordered circular arrangement for replication and genetic work in cells. The PCR fragments are made with a modified nucleotide in the primers that can be removed with a DNA excision repair enzyme to generate a 3? overhang. The 3? overhangs are designed to allow directional annealing and thus sequential PCR fragments can be assembled by annealing the overhangs and subsequent ligation. Sequential addition of PCR fragments is facilitated by growing the chain on a solid support, and the assembled chain can be removed with a site specific recombinase if the first and last primers contain the recombinase site. The circularized assembled fragment can be directly used for cell transformation if the appropriate sequences are included, such as an origin of replication and a selectable marker.

Abstract: This invention relates to a body fluids identification method and kit. A parallel, multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay for the definitive identification of body fluids commonly encountered in forensic casework analysis, namely blood, saliva, semen, and vaginal secretions. The methodology is based on gene expression profiling analysis in which the body fluid-specific genes are identified by detecting the presence of appropriate messenger RNA species. Gene-specific primers are labeled with fluorescent dyes, separated and subjected to laser induced fluorescence for identification of body fluid-specific genes present in a sample stain.

Abstract: Immunoliposomes and use thereof in highly specific and sensitive nucleic acid amplification assays relying on amplification of specific nucleic acid sequences released from encapsulation within a liposome after a receptor on the liposome couples with a targeted analyte/antigen immobilized on a select surface. The immunoliposome nucleic acid amplification assay permits both quantitative and qualitative analyte detection.

Abstract: The present invention provides for amplification of one or more polynucleotides by multi-staged linear amplifications using one or more RNA polymerases. At each stage RNA transcripts are accumulated at a linear rate, so that multiple stages provide for faster than linear transcript accumulation. In one aspect, the invention provides for polynucleotide amplification by ligating hairpin adaptors to an end of polynucleotides wherein the hairpin adaptors each contain a promoter sequence oriented so that transcription proceeds in the direction of the loop of the hairpin adaptor. Upon transcription through such loop region and to the complementary strand a replicate is made of the promoter sequence as well as the polynucleotide, thereby permitting exponential amplification upon reverse transcription, second strand synthesis, and repetition of the above cycle. Preferably such amplification is carried out under isothermal reaction conditions.

Abstract: The present invention concerns oligonucleotides containing one or more modified nucleotides which increase the binding affinity of the oligonucleotides to target nucleic acids having a complementary nucleotide base sequence. These modified oligonucleotides hybridize to the target sequence at a faster rate than unmodified oligonucleotides having an identical nucleotide base sequence. Such modified oligonucleotides include oligonucleotides containing at least one 2?-O-methylribofuranosyl moiety joined to a nitrogenous base. Oligonucleotides can be modified in accordance with the present invention to preferentially bind RNA targets. The present invention also concerns methods of using these modified oligonucleotides and kits containing the same.

Abstract: The present invention concerns oligonucleotides containing one or more modified nucleotides which increase the binding affinity of the oligonucleotides to target nucleic acids having a complementary nucleotide base sequence. These modified oligonucleotides hybridize to the target sequence at a faster rate than unmodified oligonucleotides having an identical nucleotide base sequence. Such modified oligonucleotides include oligonucleotides containing at least one 2?-O-methylribofuranosyl moiety joined to a nitrogenous base. Oligonucleotides can be modified in accordance with the present invention to preferentially bind RNA targets. The present invention also concerns methods of using these modified oligonucleotides and kits containing the same.

Abstract: The invention provides polynucleotides and methods for detecting and quantifying RNA viruses, such as enteroviruses and noroviruses. In one aspect, the invention provides amplification primers and labeled molecular beacons for amplification of viral nucleic acid sequences. In another aspect, the invention provides a synthetic RNA internal control. In another aspect, the invention provides a kit for detecting the presence of enterovirus and/or norovirus in a sample.

Abstract: A process for preparing a processed sample liquid solution for gel electrophoresis, comprising (a) treating a sample comprising a cell suspension in a non-shearing manner to produce a processed sample liquid solution comprising a mixture of DNA fragments extracted from the cell suspension, wherein at least one of the DNA fragments is greater than 200 kilobase pairs and (b) transferring the processed sample liquid solution in a non-shearing manner directly to an electrophoresis medium for conducting electrophoresis.

Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.