Abstract: The invention provides assays for detecting the presence of the maize DAS-59132 event based on the DNA sequence of the recombinant construct inserted into the maize genome and the DNA sequences flanking the insertion site. Kits and conditions useful in conducting the assays are provided.

Abstract: Methods of identifying the genotypes of a plurality of single cells, wherein each cell includes a plurality of DNA barcodes, each associated with a genetic mutation or marker, are provided. In particular, methods including linking a plurality of DNA barcodes together to create a stitched barcode, amplifying the stitched barcode and sequencing the stitched barcode are provided. Also provided are methods of determining the presence of at least one genetic mutation in a population of cells.

Abstract: The invention relates to the detection of Salmonella by nucleic acid amplification. The invention provides primer and probe oligonucleotides that can be used in multiplex to detect Salmonella in real-time amplification. The oligonucleotides of the invention detect all group I serovars, and have an increased Salmonella detection range: they enable to cover the seven Salmonella groups. They also have an increased sensitivity, without loss in specificity.

Abstract: An apparatus for detecting the presence of a microorganism in a sample includes a housing that includes a base fixed with a first DNA primer having a nucleotide sequence that is complementary to a DNA sequence of the microorganism of interest, a fibrinogen-splitting agent that is bound with a second DNA primer having a nucleotide sequence that is also complementary to a DNA sequence of the microorganism of interest, a rinsing unit configured to rinse the housing; and a fibrinogen adding unit configured to add fibrinogen to the housing so that the fibrinogen chemically reacts with the fibrinogen-splitting agent to produce a viscous substance, an ultrasonic emitter configured to emit ultrasonic signal to the housing, and an ultrasonic receiver configured to receive ultrasonic signal from the housing and transmit the received ultrasonic signal to an ultrasonic analyzer, wherein the ultrasonic analyzer determines whether the microorganism of interest exists.

Abstract: A method to detect a messenger ribonucleic acid (mRNA) sequence is provided including annealing a first probe and a second probe to at least a portion of the mRNA, wherein the first and second probes do not comprise the same nucleotide sequence, wherein each probe sequence is complimentary to at least a portion of the mRNA and the second probe is a T-shaped probe having 1) a probe sequence complementary to at least a portion of the mRNA sequence and 2) a rolling circle amplification primer that is linked to an internal reactive group of the probe sequence of the second probe so as to provide physical separation of probe ligation and rolling circle amplification, said probe-connected rolling circle primer comprising a circle recognition sequence.

Abstract: The present invention generally relates to methods for identifying nucleic acid ligands of a target molecule. In certain embodiments, the invention provides methods for identifying a nucleic acid ligand of a target molecule from a candidate mixture of nucleic acids, including contacting at least one target molecule with a candidate mixture of nucleic acids, in which the nucleic acids have different affinities for the target molecule, and separating in a single step nucleic acids that bind the target molecule with greatest affinity from nucleic acids that bind the target molecule with a lesser affinity and nucleic acids that do not bind the target molecule, thereby identifying the nucleic acid ligand of the target molecule.

Abstract: A method of generating a double stranded (ds) recombinant nucleic acid molecule covalently linked in both strands by contacting two or more ds nucleotide sequences with a topoisomerase under conditions such that both termini of at least one end of a first ds nucleotide sequence are covalently linked by the topoisomerase to both termini of at least one end of a second ds nucleotide sequence is provided. Also provided is a method for generating a ds recombinant nucleic acid molecule covalently linked in one strand, by contacting two or more ds nucleotide sequences with a type IA topoisomerase under conditions such that one strand, but not both strands, of one or both ends of a first ds nucleotide sequence are covalently linked by the topoisomerase. Compositions for performing such methods, and compositions generated from such methods also are provided, as are kits containing components useful for conveniently practicing the methods.

Abstract: A method for detecting ribosome inactivating protein (RIP) activity in a sample is provided that involves contacting a sample that contains an RIP with an inventive substrate that is depurinated to form product. The product is hybridized to a template and cleaved by an apurinic/apyrimidinic endonuclease such that releasing the blocked 3? end only in a sample that contains RIP activity. The 5? end of the product serves as a primer for extension by a polymerase reaction. The newly synthesized strand complementary to the template is detected by RT-PCR processes. A kit is provided suitable for field or laboratory use.

Abstract: The present invention provides novel compositions, kits and methods employing RNA 5? polyphosphatases, RNA 5? monophosphatases, capping enzymes, decapping enzymes, nucleic acid pyrophosphatases and RNA ligases, as well as other enzymes, for selective 5? ligation tagging of desired classes of RNA molecules that differ with respect to particular chemical moieties on their 5? ends. The 5?tagged RNA molecules can be used for synthesis of tagged first-stand cDNA, double-stranded cDNA, and sense or antisense RNA for a variety of uses.

Abstract: A method of providing an indication of an instance of expression of a gene is described herein, the method which may comprise the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.

Abstract: The present invention relates to a method for identifying a subject at risk of developing heart failure, comprising: (a) determining the level of one or more biological markers in a biological sample of said subject; (b) comparing the level of said biological marker to a standard level of the same biological marker; and (C) determining whether the level of the marker is indicative of a risk for developing heart failure, wherein the biological marker is Krüppel Like Factor 15 (KLF-15) and/or lysosomal integral membrane protein-2 (LIMP-2) and/or fragments and/or variants thereof, and/or wherein the biological marker is a gene coding for KLF15 and/or LIMP-2, and/or fragments and/or variants thereof.

Abstract: Methods and compositions for identifying novel genes that share regions of homology with known genes from target groups of genes of interest are provided. The methods comprise systematically designing oligonucleotide primers that are specific for regions of homology within the nucleotide sequences of a target group of known genes and performing successive rounds of PCR amplification of nucleic acid material from an organism of interest. The PCR steps are intended to identify and amplify nucleic acids comprising both known and novel genes. Nucleic acid molecules comprising known genes are detected and eliminated from further consideration by dot blot analysis using oligonucleotide probes specific for the known genes in the target group. Potentially novel genes are subjected to further sequence analysis to confirm novelty and assayed for biological activity.

Abstract: This invention describes methods for the generation of nucleic acid probes that improve the sensitivity of hybridization assays. The sensitivity increase results from structural modifications of nucleic acids that promote network formation during hybridization with the result that a single target molecule becomes attached to a complex of many probe molecules. The structural modification involves fragmentation of the probe nucleic acid followed by joining the fragments together such that their order and orientation and number is altered from the original probe molecule. The result is the generation of permuted probe libraries. Probes made according to this invention can be used in many kinds of hybridization assays including Southern blots. Northern blots. Dot blots. Nucleic acid Array hybridization, ‘in situ’ hybridization with fluorescent or other labels (FISH) and various kinds of sandwich hybridization assays.

Abstract: The invention provides methods and compositions for selectively amplifying one or more target polynucleotides in a sample. In one aspect, a plurality of selection oligonucleotides are provided that are capable of simultaneously annealing to separate regions of a target polynucleotide to form a complex that is enzymatically converted into a closed double stranded DNA circle that incorporates the sequence region between the two separate regions. Sequences that fail to form such complexes may be removed by nuclease digestion and the sequences of the remaining DNA circles may be amplified by a variety of techniques, such as rolling circle replication after nicking, PCR amplification after linearization, or the like.

Abstract: The invention is directed to systems, methods, and apparatus for carrying out multi-stage amplification reactions, especially under fluidly closed conditions. In one aspect, methods of the invention are carried out in a fluidly closed reaction system that permits the isolation of a portion of a first (or prior) reaction mixture and its use as a sample or specimen in a second (or subsequent) reaction mixture, thereby substantially avoiding interfering effects that first reaction components may have in the second reaction if both reaction mixtures were simply combined together. In this aspect, systems, methods, and apparatus of the invention may be used with any amplification reaction that permits multiple stages of amplification based on the use of nested primers.

Abstract: The invention relates to composition or a kit containing an enzyme that is reversibly inhibited by means of a chemical modification and an enzyme which is reversibly inhibited using non-covalent binding, the use of a mixture of enzymes reversibly inhibited in such a manner for processing or multiplying polynucleotides, and a method for specifically amplifying DNA by simultaneously using both types of reversibly inhibited enzymes.

Abstract: Methods and compositions for amplification of a target sequence by suppressing amplification of related sequences are provided.

Abstract: The present invention relates to a method for screening an individual for the presence in his/her genome of a genetic marker that is indicative of an increased risk of deep venous thrombosis, wherein the genetic marker is haplotype 2 of the fibrinogen ? gene (FGG-H2) as given in FIG. 5A. The genetic marker comprises a set of one, two, three or four mutations in the nucleic acid material encoding fibrinogen ?, the mutations being selected from the group consisting of 129A/T (rs2066854), 7874G/A (rs20668?1), 9615?C/T (rs2066864) and 10034C/T (rs2066865).

Abstract: The present invention relates to a method for amplifying an unknown nucleotide sequence adjacent to a known nucleotide sequence, which comprises the step of (a) performing a primary amplification of said unknown nucleotide sequence using a DNA walking annealing control primer (DW-ACP) and a first target-specific primer; in which said step (a) comprises: (a-1) performing a first-stage amplification of said unknown nucleotide sequence at a first annealing temperature, comprising at least one cycle of primer annealing, primer extending and denaturing using a first degenerate DW-ACP containing a degenerate random nucleotide sequence to hybridize with said unknown nucleotide sequence and a hybridizing nucleotide sequence substantially complementary to a site on said unknown nucleotide sequence; and (a-2) performing a second-stage amplification at a second annealing temperature to render said first degenerate DW-ACP not to function as a primer.

Abstract: The present invention provides a nucleic acid sequence amplification method and apparatuses thereof that are simple in the design and easy to miniaturize and integrate into complex apparatuses, with capability of using DNA polymerases that are not thermostable. In the present invention, a plurality of heat sources are combined to supply heat to, or remove heat from specific regions of the sample such that a specific spatial temperature distribution is maintained inside the sample by locating a relatively high temperature region lower in height than a relatively low temperature region.