Abstract: The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers.

Abstract: The present invention provides pharmaceutical formulations for oral administration of antisense oligonucleotides, such as antisense oligonucleotides against SMAD7. The pharmaceutical formulations can be used to treat Crohn's disease, ulcerative colitis and chronic inflammatory bowel disease.

Abstract: The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3? end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.

Abstract: Labeled reactant compositions, and particularly labeled nucleic acid reaction compositions, that include structural components that maintain potentially damaging labeling components sufficiently distal from the reactant portion of the molecule such that damaging effects of the label group on other reaction components, such as enzymes, are reduced, minimized and/or eliminated.

Abstract: The invention provides a novel class of scaffold-based labeled polymerase enzyme substrates. The polymerase enzyme substrates have a multivalent core or scaffold to which is attached fluorescent dye moieties and nucleoside phosphate moities. The polymerase enzyme substrates have multiple fluorescent dye moities and/or multiple nucleoside phosphate moieties. Preferred multivalent cores comprise trifunctional six membered aromatic moities. The invention also provides for sequencing methods and kits with scaffold-based labeled polymerase enzyme substrates.

Abstract: The present invention concerns methods for controlling insect infestation via RNAi-mediated gene silencing, whereby the intact insect cell(s) are contacted with a double-stranded RNA from outside the insect cell(s) and whereby the double-stranded RNA is taken up by the intact insect cell(s). In one particular embodiment, the methods of the invention are used to alleviate plants from insect pests. Alternatively, the methods are used for treating and/or preventing insect infestation on a substrate or a subject in need of such treatment and/or prevention. Suitable insect target genes and fragments thereof, dsRNA constructs, recombinant constructs and compositions are disclosed.

Abstract: The invention concerns nucleic acid molecules derived from novel hepatitis D virus strains or isolates constituting genotypes different from known I, II and III genotypes, their fragments, corresponding proteins and their uses as diagnostic reagents. The invention also concerns a method for sensitive diagnosis of the hepatitis D virus (or delta hepatitis virus) and a method for epidemiologic monitoring of HDV-related infections.

Abstract: The present invention relates to the selective inhibition of protein expression of CAG repeat-related disease proteins such as Huntingtin using nucleic acid analogs. Peptide nucleic acids and locked nucleic acids are particularly useful analogs.

Abstract: Disclosed are oligonucleotides and methods related to identifying Escherichia coli serotypes by gene sequence polymorphisms. More specifically disclosed is oligonucleotides and methods to detecting a genotype of a single-nucleotide polymorphism in the O-antigen operon to identify Shiga toxin-producing serotypes O26, O111, O103, O145, O45, and O121.

Abstract: A method of sequencing nucleic acids is provided using sequencing by ligation and/or sequencing by hybridization.

Abstract: This invention relates to crop plants of which the fruit dehiscence properties are modulated. More specifically the invention relates to improved methods and means for reducing seed shattering, or delaying seed shattering until after harvest, while maintaining at the same time an agronomically relevant treshability of the pods, and for increasing yield.

Abstract: A reagent for detecting gene product, the reagent comprising a probe or chemical modulation that specifically binds to an alternative splicing junction of a gene product of human PTCH1 gene, the expression of the gene product from gene products of the human PTCH1 gene being varied due to the unusual alternative splicing, for use for measuring the abundance of the gene product contained in a human sample.

Abstract: This invention is directed to mutated Activin A type I receptor proteins (ACVR1) and isolated nucleic acids encoding same. The invention also relates to the use of mutated ACVR1 in the diagnosis and treatment of Fibrodysplasia Ossificans Progressiva (FOP).

Abstract: The present invention provides a double-stranded nucleic acid in which at least one nucleic acid strand includes an unnatural base that forms a self-complementary base pair or an unnatural base that forms a base pair with any natural base with substantially the same thermal stability. The present invention also provides a method of hybridizing a first nucleic acid strand with a second nucleic acid strand, wherein the first nucleic acid strand includes an unnatural base that forms a self-complementary base pair or an unnatural base that forms a base pair with any natural base with substantially the same thermal stability, and a method of applying the nucleic acid to SNP detection, a DNA chip, DNA/RNA computing, or an in vitro translation system. The present invention provides a method of introducing an unnatural base into a nucleic acid strand and thereby controlling the thermodynamic stability in hybridization of the nucleic acid strand.

Abstract: This invention relates to a method, kit and system for collecting and processing of samples to release and treat DNA and RNA for gene sequence detection. The method described here in provides for rapid and convenient release, and recovery of DNA and RNA from tissues and cellular materials.

Abstract: The invention relates to inhibition of wild-type and certain mutant forms of human histone methyltransferase EZH2, the catalytic subunit of the PRC2 complex which catalyzes the mono- through tri-methylation of lysine 27 on histone H3 (H3-K27). In one embodiment the inhibition is selective for the mutant form of the EZH2, such that trimethylation of H3-K27, which is associated with certain cancers, is inhibited. The methods can be used to treat cancers including follicular lymphoma and diffuse large B-cell lymphoma (DLBCL). Also provided are methods for identifying small molecule selective inhibitors of the mutant forms of EZH2 and also methods for determining responsiveness to an EZH2 inhibitor in a subject.

Abstract: Provided herein are methods, kits and compositions to classify fungi. Methods are provided for classification of fungi according to established phenotypes, for example, antimicrobial susceptibility profiles. More specifically, the invention provides methods for the use of PNA probes in diagnostic applications, which will aid in the direction of appropriate therapy against fungi.

Abstract: Methods of isolating target double-stranded polynucleotides with internal single-stranded regions are provided. Compositions and kits comprising double-stranded polynucleotides with internal single-stranded regions are also provided.

Abstract: Ligation-enhanced nucleic acid detection assay embodiments for detection of RNA or DNA are described. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection. The assay embodiments are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. Very little background amplification is observed and as few as 1000 copies of target nucleic acid can be detected. Method embodiments are particularly adept for detection of RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. Heavily degraded and cross-linked nucleic acids of compromised samples, in which classic quantitative real time PCR assays typically fail to adequately amplify signal, can be reliably detected and quantified.

Abstract: Methods for the detection of ddPCR assay-generated amplicons by short minor groove binder-fluororophore-oligonucleotide-quencher (MGB-Fl-oligo-Q) probes. The short MGB-Fl-oligo-Q probes not only reduce background, but also show improved mismatch discrimination when compared to the same length non-MGB probes for detecting the ddPCR generated targets at room temperature.

Abstract: Disclosed are novel primers for use in the molecular detection of food-threat agents and food-borne pathogens. The primers may be used in combination for the rapid, high-throughput screening PCR-based techniques to simultaneously detect multiple food safety biothreat agents. The multiplex-detection methods have improved sensitivity and specificity for the detection of multiple high-impact food-borne pathogens simultaneously. Real-time PCR assaying techniques using such primers include microarrays and multiplex single-tube arrays, the latter optionally simultaneously with TaqMan probes.

Abstract: A size standard, kit includes a size standard, method of defining a size standard and method of analysis using a size standard. The size standard is intended to include size standard elements which have a size greater than and/or less than and/or different from the components of a sample which are to be sized. This means that the same characteristic unit, such as a dye, can be used to label the component and the size standard. A further characteristic unit, from amongst a limited number of such characteristic units is liberated from use only on size standards for use on components. The method is therefore particularly useful in multiplex amplification of STRs.

Abstract: The invention relates generally to methods and apparatus for conducting analyses, particularly microfluidic devices for the detection of target analytes.

Abstract: A switch mode nucleic acid aptamer probe includes a probe main body, a fluorescence generating unit and a fluorescence quenching unit which are respectively connected to two ends of the probe main body. The probe main body includes a nucleic acid aptamer fragment with a function of specifically recognizing target tumor cell and a nucleic acid fragment linked to the nucleic acid aptamer fragment by a connection fragment with a length of 7˜15 nm so as to form a hairpin structure. The ability of competitive hybridization of the nucleic acid fragment with the nucleic acid aptamer fragment is weaker than that of the target tumor cell. The use of the probe of the invention can be at least one of specific detection of tumor living cell in buffer solution, effective detection of tumor living cell in serum, and real-time fluorescence imaging and intravital detection of tumor in living body.

Abstract: An automated method for detecting the presence of a nucleic acid in a sample, where the method is performed within a housing of a self-contained, stand-alone analyzer. The method includes purifying the nucleic acid after it has been immobilized on a magnetically-responsive solid support. A pipette of the analyzer is used to form a reaction mixture comprising the purified nucleic acid and all reagents required to perform a nucleic acid amplification. Amplification products are synthesized that include a nucleotide sequence contained in the nucleic acid or the complement of the nucleic acid. The amplification products are exposed to a probe in a mixture, where the probe forms a hybrid with one of the amplification products. The formation of the hybrid in the mixture provides an indication of the presence of the nucleic acid in the sample.

Abstract: The present invention relates to surface-patterned microgels to which molecular beacon probes are immobilized. The immobilized molecular beacon probes exhibit both low non-specific background and high specific fluorescence. Also disclosed are related arrays, related detection methods, and preparation methods.

Abstract: Described herein are oligonucleotides useful for detecting, isolating, amplifying, quantitating, monitoring, screening and sequencing GBS genes and methods of using the described oligonucleotides.

Abstract: The present application provides polynucleotide structures such as nucleic acid ribbons and nucleic acid tubes, methods for making the polynucleotide structures, and methods for making two-dimensional or three-dimensional objects comprising the nucleic acid ribbons and nucleic acid tubes.

Abstract: The present invention relates to probes which detect a polymorphism(s) in exon 12 of the NPM1 gene, a kit therefor, and the method of detecting the polymorphism(s) thereof.

Abstract: Methods of using dyes and associated technology are provided. A dye, such as a monomeric dye or a dimeric dye, may be used in a nucleic acid gel staining application and/or a nucleic acid detection application. A dimeric dye, such as a dimeric dye capable of forming a hairpin-like structure, may be used to stain and/or detect nucleic acids via a release-on-demand mechanism. A dimeric dye having low background fluorescence in the absence of nucleic acids and high fluorescence in the presence of nucleic acids, upon binding therewith, may be used to stain and/or detect nucleic acids. Buffers comprising a weak acid and a salt of the weak acid, such as a lithium salt, are also provided to allow for effective prestaining of nucleic acids.

Abstract: Methods and means are provided for producing chimeric nucleic acid constructs capable of producing dsRNA for silencing target nucleic acid sequences of interest using recombinational cloning.

Abstract: The invention relates to methods and kits for performing in situ hybridization on a biological sample on a solid surface using nucleic acid probes that are embedded in or sorbed to a dry, fibrous matrix.

Abstract: The present invention relates to the field of plant transformation with genes conferring tolerance to glyphosate. The invention particularly relates to a maize (corn) plant transformed with a gene encoding an EPSPS providing the plant tolerance to an application of glyphosate under conditions where this herbicide is effective in killing weeds. The invention particularly concerns an elite transformation event VCO-Ø1981-5 comprising the gene construct and means, kits and methods for detecting the presence of the said elite event.

Abstract: Embodiments of the present disclosure relate generally to reporter compositions which are synthetic nucleotides that comprise nucleotides with a high charge mass moiety attached thereto via a linker molecule. The linker molecules can vary in length in part to enable the high charge mass moiety to extend out from a DNA polymerase complex so that polymerization may not be influenced.

Abstract: Methods and reagents for detection and analysis of nucleic acids are provided. Certain methods involves an encoding amplification in which a target sequence is associated with probe-binding sequences and optionally with indexing sequences, (2) an optional distribution step in which the product of the encoding amplification is split into multiple aliquots, and (3) a decoding and detection step in which the presence, absence, quantity, or relative amount of the target sequence in the aliquots is determined. The detection step makes use of a multifunctional “self-digesting” molecular probe comprising a primer polynucleotide and a probe oligonucleotide, linked in a 5?-5? orientation.

Abstract: The invention relates to a mediator probe comprising a probe region and a mediator region. Furthermore, the invention relates to a system comprising a mediator probe and a detection molecule, use of that system and a method for detection of at least one target molecule.

Abstract: The present invention provides probes and methods of use thereof in the diagnosis and/or prognosis of certain types of cancers, particularly human papillomavirus (HPV)-associated cancers. The probes are designed for hybridization with genomic material in a manner indicative of one or more aberrations in the genetic material present in the test sample. The identified aberrations are biomarkers of HPV-associated cancer. The methods of the invention comprise contacting a sample to one or more probes, allowing any genetic material in the sample to hybridize to the genomic regions provided in the probes, analyzing the hybridizations, and analyzing the hybridizations to identify detected aberrations as biomarkers indicative of HPV-associated cancer progression.

Abstract: The present disclosure relates to Birt-Hogg-Dubé syndrome, nucleic acids encoding the BHD gene, and methods of using the nucleic acids and proteins encoded thereby. In particular, the present disclosure relates to methods of diagnosing BHD disease and related conditions, such as spontaneous pneumothorax and kidney cancer, and methods of treating BHD skin lesions.

Abstract: The present invention is characterized by certain genetic variants being susceptibility variants for prostate cancer. The invention relates to methods of determining increased susceptibility to prostate cancer, as well as methods of determining decreased susceptibility to prostate cancer, using such variants. The invention further relates to kits for determining a susceptibility to prostate cancer.

Abstract: The invention relates to methods for isolating and/or identifying nucleic acids. The invention also provides kits for isolating and/or identifying nucleic acids.

Abstract: This document provides methods and materials for detecting target nucleic acid. For example, methods and materials for detecting the presence or absence of target nucleic acid, methods and materials for detecting the amount of target nucleic acid present within a sample, kits for detecting the presence or absence of target nucleic acid, kits for detecting the amount of target nucleic acid present within a sample, and methods for making such kits are provided.

Abstract: The invention provides a combination of reagents as a test kit containing a detection conjugate having a binding portion and a reagent for deactivating of the fluorochrome portion by interaction with the linker. The binding portion especially is an antibody portion. The detection conjugate has a fluorochrome portion connected to the antibody portion, and a linker connected to the fluorochrome portion, wherein the linker comprises an oligonucleotide. The fluorochrome portion can be deactivated by hydrolysis of the linker or by specific hybridization of a quencher having an oligonucleotide to the linker.

Abstract: The present invention provides a new and improved multiplexed oligonucleotide detection method based on the nanopore technology with one or more probes containing a sequence with complementarity to the target oligonucleotide, a terminal extension at the probe's 3? terminus, 5? terminus, or both termini and a label attached to the terminus. The improved probes and probe sets enable sensitive, selective, and direct multiplex detection, differentiation and quantification of distinct target oligonucleotides such as miRNAs. The inventive detection method may also be employed as a non-invasive and cost-effective diagnostic method based on miRNA levels in the patient's tissue sample.

Abstract: The invention provides improved nucleic acid ligands that inhibit coagulation and improved modulators of the nucleic acid ligands to provide ideal modulators of coagulation. These improved nucleic acid ligands and modulators are particularly useful for inhibiting coagulation in a host undergoing a therapeutic regime such as surgery or coronary artery bypass.

Abstract: The present disclosure encompasses systems, and their methods of use, for detecting a target analyte. The systems include a first and second oligonucleotide probe that associate together to form a complex that binds to a target analyte; a cleavable reporter molecule that binds to the complex; and cleaving agent.

Abstract: The identification of pre-defined mutations expected to be present in a minor fraction of a cell population is important for a variety of basic research and clinical applications. The exponential, analog nature of the polymerase chain reaction is transformed into a linear, digital signal suitable for this purpose. Single molecules can be isolated by dilution and individually amplified; each product is then separately analyzed for the presence of pre-defined mutations. The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample.

Abstract: The present invention is directed towards the synthesis of high purity deuterated sugars, deuterated phosphoramidites, deuterated nucleobases, deuterated nucleosides, deuterated oligonucleotides, and deuterated RNA's of defined sequences which can exhibit biochemically useful and biologically valuable properties, thus having potential for therapeutic uses.

Abstract: Molecular constructs, populations thereof, arrays, compositions, methods and kits for differentiating a target molecule from an off-target molecule are provided.

Abstract: A detection probe for detecting single base mutations or alterations in a double stranded target nucleic acid molecule is provided. In some aspects, the detection probe may include a double-stranded probe nucleic acid molecule having a first end and a second end; at least one probe initiation toehold at the first end; at least one substance capable of emitting a detectable signal at the second end; and optionally, at least one dissociation toehold at the second end. The detection probe is designed to hybridize with a double stranded target nucleic acid in a reaction which proceeds at approximate thermodynamic equilibrium (?G?0) when no single base mutations or alterations are present in the double stranded target nucleic acid molecule. The probe may be used in detection systems and methods to identifying the presence or absence of one or more single base mutations or alterations in a double-stranded nucleic acid target molecule.

Abstract: Methods, compositions, and kits for predicting and controlling fruit color in palm.