Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with psoriasis and related pathologies. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, including groups of nucleic acid molecules that may be used as a signature marker set, such as a haplotype, a diplotype, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Abstract: A technology is described that is capable of generating high-throughput sequencing (HTS) read length DNA products to accurately and reliably provide exon connectivity information for alternatively spliced isoforms. The method is not limited by the initial size of the isoform as the technology removes the template oligonucleotide sequence and a newly formed full length ligated product provides an HTS-compatible read length sequence that comprises information that corresponds to the consecutive order of the exons in the original template oligonucleotide.

Abstract: Solid support assays using non-standard bases are described. A capture oligonucleotide comprising a molecular recognition sequence is attached to a solid support and hybridized with a target. In some instances, the molecular recognition sequence includes one or more non-standard bases and hybridizes to a complementary tagging sequence of the target oligonucleotide. In other instances, incorporation of a non-standard base (e.g., via PCR or ligation) is used in the assay.

Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

Abstract: The invention provides methods and compositions for the expression of small RNA molecules within a cell using a lentiviral vector. The methods can be used to express doubles stranded RNA complexes. Small interfering RNA (siRNA) can be expressed using the methods of the invention within a cell, which are capable of down regulating the expression of a target gene through RNA interference. A variety of cells can be treated according to the methods of the invention including embryos, embryogenic stem cells, allowing for the generation of transgenic animals or animals constituted partly by the transduced cells that have a specific gene or a group of genes down regulated.

Abstract: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.

Abstract: Compositions and methods for diagnosis and treatment of ALS are provided.

Abstract: Disclosed are an oligonucleotide primer with an omega structure for detecting short-chain RNAs and the use thereof. The primer from the 5? end to the 3? end sequentially is: a PCR primer target region of 20-30 bases, a variable coding region of 0-50 bases, an omega stem-loop, a probe spacer of at least one base and a probe region of 4-11 bases. The length of the stem of the omega stem-loop is 4-12 paired bases, and the length of the loop of the omega stem-loop is 3-20 unpaired bases.

Abstract: The present invention relates to combinations of fluorescent dyes used in molecular biology, particularly in multiplex PCR. In particular, the present invention relates to a combination of dyes for amplification reactions, wherein at least four different dyes are used, wherein the first dye is 5-FAM or 6-FAM or a blend thereof, the second dye is selected from the group consisting of DY-530, HEX, CAL Fluor Orange 560 and ATTO 532, the third dye is selected from the group consisting of ATTO 550, DY-555 and DY-556, the fourth dye is selected from the group consisting of ROX, DY-510XL and ATTO 565, and optionally a fifth dye is selected from the group consisting of DY 632 and DY-520XL.

Abstract: This invention relates to DNA microarray technology, and more specifically to methods and kits for identifying autism and autism spectrum disorders in humans.

Abstract: The present invention relates to methods that utilize multi-component nucleic acid complex (MNA complex) cascades. The MNA complexes may have cleavage or ligase activity. Further, the invention provides cascades which may include one or more DNAzymes. The invention also provides methods which use these cascades for the identification, detection and quantification of targets.

Abstract: The present embodiments relate to engineering imaging probes based on “triggered molecular geometry.” Upon detection of a molecular signal, nucleic acid hairpin monomers assemble an imageable molecular shape with prescribed geometry. In some embodiments the prescribed shape can be imaged directly. In some embodiments, the prescribed shape can serve as a spatial organizer or amplification scheme for other imaging entities, such as fluorophore and fluorescent proteins.

Abstract: The present application relates to the use of hybridization chain reaction (HCR) to form double stranded RNA polymers in the presence of a target, such as a nucleic acid associated with a disease or disorder. The RNA polymers are preferably able to activate the RNA-dependent kinase PKR. Activation of PKR via RNA-HCR can be used to treat a wide variety of diseases and disorders by specifically targeting diseased cells.

Abstract: A method for detecting a target nucleic acid, comprising: (a) contacting a nucleic acid sample comprising a target nucleic acid, comprising a first portion and a second portion, with: (i) a detection probe, wherein the detection probe is labeled with a labeling substance and comprises a nucleic acid sequence that forms a stem-loop structure and having a 5? protruding end or a 3? protruding end that is capable of hybridizing to the second portion, and (ii) a capture probe comprising a nucleic acid sequence capable of hybridizing to the first portion, wherein the capture probe is immobilized to a substrate, under conditions to form a target nucleic acid-detection probe-capture probe complex by hybridizing the second portion to the detection probe and hybridizing the first portion to the capture probe; (b) ligating a first end of the detection probe with an end of the target nucleic acid and ligating a second end of the detection probe with an end of the capture probe; and (c) detecting the labeling substance of

Abstract: The invention generally provides three-component molecular biosensors. The molecular biosensors are useful in several methods including in the identification and quantification of target molecules.

Abstract: The present invention refers to a method for detecting molecules and/or substances within a sample based on the use of a microcantilever system. The method comprises the variation of a certain condition such as humidity so as the mechanical feature analyzed varies with a characteristic pattern while the target molecule is bound to the detector. The invention also refers to the system used to carry out such method.

Abstract: Disclosed are methods and compositions for conducting assays utilizing real-time polymerase chain reactions (“PCRs”) in detection of serotypes L I, L II, and L III, but not stereotype B, of Chlamydia trachomatis, capable of causing lymphogranuloma venereum (“LGV”). These assays take advantage of a deletion occurring in the cytotoxin gene locus specific to the L I, L II, and L III serotypes. Each assay employs a first primer having a nucleotide sequence flanking one side of the deletion point and a second primer having a nucleotide sequence flanking the other side of the deletion point, wherein the first primer and the second primer are capable of hybridizing respectively to the plus strand and the minus strand of the genome of Chlamydia trachomatis during PCR. Synthesis during PCR of a sequence-specific amplicon containing this deletion point indicates that the sample contains nucleic acid specific to an LGV-causing serotype of Chlamydia trachomatis.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of a Reprogramming factor, in particular, by targeting natural antisense polynucleotides of a Reprogramming factor. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of Reprogramming factors.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: The invention provides methods for identifying early stage non-small cell lung cancer (NSCLC) patients who will have a favorable prognosis for the recurrence of lung cancer after surgical resection. The invention is based on the discovery that assessment of chromosomal copy number abnormalities at two or more of chromosome 5p15, 7p12, 8q24 and centromere 6 can be used for prognostic classification. The invention preferably uses fluorescence in situ hybridization with fluorescently labeled nucleic acid probes to hybridize to patient samples to quantify the chromosomal copy number of the these genetic loci.

Abstract: The invention provides DNA compositions that relate to transgenic insect resistant maize plants. Also provided are assays for detecting the presence of the maize DAS-59122-7 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: The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of: a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c).

Abstract: Methods of detecting nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Nucleic acids captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label with the nucleic acids. Compositions, kits, and systems related to the methods are also described.

Abstract: Hybridization assay detection probes targeted to HPV Type 16 nucleic acid sequences which are particularly useful to aid in detecting HPV type 16 are described. The oligonucleotides can aid in detecting HPV Type 16 by acting singly or as part of a detection probe mixture. Compositions, reaction mixtures and methods of use are provided.

Abstract: The present disclosure describes methods, devices, reagents, and kits for the detection of one or more target molecules that may be present in a test sample. In one embodiment, a test sample is contacted with an aptamer that includes a tag and has a specific affinity for a target molecule. An aptamer affinity complex that includes an aptamer bound to its target molecule is allowed to form. If the test sample contains the target molecule, an aptamer affinity complex will generally form in the test sample. The aptamer affinity complex is optionally converted to an aptamer covalent complex that includes an aptamer covalently bound to its target molecule. The aptamer affinity complex (or optional aptamer covalent complex) can then be detected and/or quantified using any of a variety of methods known to one skilled in the art, including using a solid support, using mass spectrometry, and using quantitative polymerase chain reaction (Q-PCR).

Abstract: Provided are methods for the treatment of disorders of the central nervous system (CNS) and the eye. In particular, use of compositions comprising a compound capable of modulating a target gene or gene product is described for the preparation of a pharmaceutical composition for the treatment of disorders of the CNS and/or the eye, wherein the composition is designed to be administered outside the blood-CNS and the blood-retina barriers. Furthermore, methods are provided for identifying and obtaining nucleic acid molecules encoding polypeptides involved in CNS disorders or of the eye, methods for diagnosing said disorders as well as transgenic animal deficient in the expression of target genes identified in accordance with the described method. In addition, methods of identifying and isolating drugs that are particularly useful for the treatment of disorders related to the CNS and/or the eye are disclosed.

Abstract: Reagents, systems and methods for the detection of nucleic acids are described herein, including such methods which may be performed in a single reaction. Such reagents include a target specific indexing probe (TSIP) synthetic DNA structure comprising a detectable moiety and a quencher thereof, wherein in the presence of a target nucleic acid a portion (a tag) of the (TSIP) synthetic DNA structure comprising the detectable moiety is released, thereby increasing the signal emitted therefrom. The tag may in turn bind to a capture probe, facilitating signal detection.

Abstract: The present invention relates to compositions comprising a porous nanostructure of a known characteristics and a fragment of nucleic acid having a known sequence. Methods of use of the compositions were also provided, for example in DNA amplification, detection, and DNA sequencing.

Abstract: The invention provides allelic ladder mixtures and individual alleles suitable for use in such mixtures. The allelic ladder mixtures give improved identification and distinguishing capabilities, particularly suitable in forensic investigations.

Abstract: A detector oligonucleotide comprises multiple pairs of a donor fluorophore and a quencher molecule, which donor fluorophores and quencher molecules are separated by a site that is capable of being cleaved when in double-stranded form. The detector oligonucleotide may be made double-stranded in a manner that depends on the presence of a target nucleic acid, allowing the cleavage sites to be cleaved. Separation of the donor fluorophores and the quencher molecules decreases fluorescence quenching and generates a detectable change in a fluorescence parameter of the fluorophores of the detector oligonucleotide. By using multiple donor/quencher pairs, the present detector oligonucleotide advantageously generates a high signal to noise ratio and high efficiency in detection of a target nucleic acid.

Abstract: Provided herein are nucleic acids and methods for selectively amplifying in parallel tens of thousands of high quality oligonucleotides without common sequences. The resultant oligonucleotides can be used for a variety of purposes and applications including but not limited to DNA nano structure synthesis.

Abstract: The present invention provides a nucleic-acid-responsive gel which allows (i) a larger volumetric change through structural design, (ii) adjustment of its recognition ability to recognize a nucleic acid, (iii) improvement of sensitivity, and (iv) flexible design according to, e.g., a sequence of target DNA. The nucleic-acid-responsive gel includes a probe formed of two single-stranded nucleic acids which are hybridized with each other. The probe is fixed within a network structure of a polymer gel. The two single-stranded nucleic acids are bound reversibly with each other.

Abstract: Methods, Compositions, and Systems are provided for obtaining polymerase-template complex mixtures with improved levels of active polymerase. In some aspects, methods are described in which a polymerase-template complex is exposed to reaction conditions in which a complementary strand to the template is produced. The extended reaction mixture is purified, for example by gel filtration chromatography to produce a mixture of polymerase-template complex having a higher active fraction. This purified mixture can be used for further analyses including single molecule sequencing.

Abstract: Disclosed is a means for improving the clinical outcomes of cancer therapy. Specifically disclosed is an activity potentiator comprising a compound capable of inhibiting the expression of RFP (RET finger protein) gene or the activity of RFP as an active ingredient. The activity of an anti-cancer agent having an oxidative stress inducing ability can be potentiated by using the anti-cancer agent in combination with the activity potentiator. Further specifically disclosed are a biomarker useful for the recognition of prognosis in a cancer patient and use of the biomarker.

Abstract: The invention provides glyphosate tolerant transgenic turfgrass plants, plant material, and seeds that have a specific transformation event. Also provided are assays for detecting the presence of the event. The invention also provides sequences for a variant EPSPS gene and a GAO2X gene, cassettes, and plants comprising the variant EPSPS gene and a GAO2X gene.

Abstract: The present invention relates to a method for determining the sequence of a nucleic molecule. Herein a capture oligonucleotide probe is attached to an encoded microcarrier, wherein the code of said microcarrier identifies the sequence of said oligonucleotide probe. The capture oligonucleotide probe is hybridized with a sample comprising nucleic acids molecules, wherein said DNA fragment comprises a sequence which is complementary to the sequence of the capture oligonucleotide probe. The sequence of the DNA molecule is determined, wherein the capture oligonucleotide probe serves as a primer for a DNA polymerase, in the case of single molecule sequencing this is a sequencing primer. After the sequence determination, the nucleotide sequence of the capture oligonucleotide probe is identified by determining the code on the microcarrier, which corresponds with the capture oligonucleotide probe.

Abstract: The invention generally relates to methods and kits for isolating nucleic acids from an organism. In certain embodiments, methods of the invention involve contacting a plurality of lytic enzymes to an organism, thereby lysing a cell wall of the organism to release the nucleic acid, and introducing at least one agent to separate the nucleic acid from the lysed cells, thereby isolating the nucleic acid.

Abstract: Provided is a method for determining whether a horse is normal, a carrier, or is affected with Lavender Foal Syndrome (LFS). The method entails, in a biological sample obtained or derived from a horse, determining a single nucleotide deletion which introduces a translational stop codon in the 49th codon of exon 30 of the equine MYO5A gene. Homozygosity for the absence of the deletion is indicative that the horse is normal for LFS. Heterozygosity for the deletion is indicative that the horse is a carrier of LFS. Homozygosity for the deletion is indicative that the horse is affected with LFS. Methods for selecting horses for breeding and kits for determining the LFS-associated deletion are also provided.

Abstract: A general methodology to design label-free fluorescent functional nucleic acid sensors using a vacant site approach and an abasic site approach is described. In one example, a method for designing label-free fluorescent functional nucleic acid sensors (e.g., those that include a DNAzyme, aptamer or aptazyme) that have a tunable dynamic range through the introduction of an abasic site (e.g., dSpacer) or a vacant site into the functional nucleic acids. Also provided is a general method for designing label-free fluorescent aptamer sensors based on the regulation of malachite green (MG) fluorescence. A general method for designing label-free fluorescent catalytic and molecular beacons (CAMBs) is also provided. The methods demonstrated here can be used to design many other label-free fluorescent sensors to detect a wide range of analytes. Sensors and methods of using the disclosed sensors are also provided.

Abstract: A method of selecting nucleic acid samples from a plurality of nucleic acid samples based on desired alleles including the steps of performing a first reaction in a plurality of pools of the alleles to be identified to produce reaction products including a source tag identifying said each pool; pooling the pools to provide pooled pools; for each of the desired alleles to be identified, performing a second reaction using said reaction products to produce allele-specific second reaction products comprising a marker tag and a derived source tag; identifying said allele-specific second reaction products to select nucleic acid sample. In some embodiments, the first reaction may not be performed. A source tag sharing number “d” may be determined for each of the alleles. Alleles may be binned together.

Abstract: The present invention provides a method for stably correcting a detection signal in an isothermal nucleic acid amplification reaction, particularly an isothermal nucleic acid amplification reaction performed at low temperature. Specifically, the present invention provides a method for detecting a target nucleic acid in an isothermal nucleic acid amplification reaction, comprising the following (1) and (2): (1) subjecting a nucleic acid sample to an amplification reaction of a target nucleic acid under an isothermal condition in the presence of a nucleic acid probe for correction and a nucleic acid probe for detection of the target nucleic acid; and (2) correcting a detection signal due to the nucleic acid probe for detection with a detection signal due to the nucleic acid probe for correction in the amplification reaction.

Abstract: The present invention relates to novel conjugate complexes for immunoassays as well as kits comprising these conjugate complexes, methods of producing these complexes, and methods of detecting an analyte by use of these complexes. The conjugate complexes of the invention comprise one or more non-nucleic acid receptors capable of specifically binding an analyte, one or more nucleic acid markers comprising a predetermined nucleotide sequence, one or more first linker molecules capable of specifically binding the non-nucleic acid receptor and the nucleic acid marker, and one or more second linker molecules capable of specifically binding the first linker molecules.

Abstract: The present invention provides a novel method for detection of liver cancer. This method detects high-sensitively, high-specifically, simply and accurately liver cancer, especially that in early stage by identifying and/or quantifying methylation on particular genes and/or their DNA fragments in clinical specimens, and by combining said methylated DNA values with existing tumor marker values and/or DNA amounts in blood. This invention also detects a precancerous lesion, detects a risk of recurrence after treatment of liver cancer, detects malignancy of liver cancer and monitors progression of liver cancer with time by the same method. As for particular genes, BASP1 gene, SPINT2 gene, APC gene, CCND2 gene, CFTR gene, RASSF1 gene and SRD5A2 gene are mentioned.

Abstract: FRET-labeled compounds are provided for use in analytical reactions. In certain embodiments, FRET-labeled nucleotide analogs are used in place of naturally occurring nucleoside triphosphates or other analogs in analytical reactions comprising nucleic acids, for example, template-directed nucleic acid synthesis, DNA sequencing, RNA sequencing, single-base identification, hybridization, binding assays, and other analytical reactions.

Abstract: The invention provides new probes that are useful in a method to analyze beta-PV types based on hybridization to these probes.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Nuclear Respiratory Factor 1 (NRF1), in particular, by targeting natural antisense polynucleotides of Nuclear Respiratory Factor 1 (NRF1). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of NRF1.

Abstract: the Present Invention Provides Vectors, Including a Novel Attenuated Strain of Salmonella, for Efficient Gene Transfer into an Animal, e.g. a Mammalian Host.

Abstract: The invention provides a transgenic Glycine max event MON87751, plants, plant cells, seeds, plant parts, progeny plants, and commodity products comprising event MON87751. The invention also provides polynucleotides specific for event MON87751, plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides for event MON87751. The invention also provides methods related to event MON87751.

Abstract: The invention provides an improved stem-loop target capture oligomer and methods of use. Such a target capture oligomer has a target-binding segment forming a loop flanked by stem segments forming a stem. The stem segments are of unequal length. Such probes show little or no binding to immobilized probes in the absence of a target nucleic acid but offer good target sensitivity. The probes are particularly useful in multiplex methods of detection in which multiple target capture oligomers are present for detecting of multiple target nucleic acids (for example, detecting multiple polymorphic forms of a target gene).

Abstract: The present invention provides methods of detecting and mapping chromosomal or genetic abnormalities associated with various diseases or with predisposition to various diseases, or to detecting the phenomena of large scale copy number variants. In particular, the present invention provides advanced methods of performing array-based comparative hybridization that allow reproducibility between samples and enhanced sensitivity by using the same detectable label for both test sample and reference sample nucleic acids. Invention methods are useful for the detection or diagnosis of particular disease conditions such as cancer, and detecting predisposition to cancer based on detection of chromosomal or genetic abnormalities and gene expression level. Invention methods are also useful for the detection or diagnosis of hereditary genetic disorders or predisposition thereto, especially in prenatal samples.