Abstract: The invention is directed to modified oligonucleotide compositions and methods for selectively reducing unwanted nucleic acid contaminants and enriching for desired nucleic acid targets from complex genomic nucleic acid mixtures for sequencing applications. The modified oligonucleotide compositions include one or more modified groups that increase the Tm of the resultant oligonucleotide composition.

Abstract: The present invention relates to methods for treating chronic kidney disease (CKD) including methods for preventing or delaying onset of CKD and methods for preventing exacerbation and progression of CKD. In particular embodiments, the invention provides methods for treating a subject at risk of developing CKD comprising administering to the subject a composition comprising a) a therapeutically effective amount of at least one oligonucleotide compound which inhibits the expression of a human target gene associated with the kidney disease; and b) a pharmaceutically acceptable excipient or carrier, or mixtures thereof, thereby reducing the risk of CKD in the subject.

Abstract: This invention relates to a ribonucleic acid (RNA) based assay system for body fluid identification, and in particular to a novel, multiplex, parallel assay system based on messenger RNA expressed in human tissue, and to a method for using the same.

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 relates to methods of inhibiting S. aureus comprising inhibiting siderophore-mediated iron uptake, for example, staphyloferrm-mediated iron uptake Such methods of inhibiting S. aureus include the inhibition of staphyloferrm A- and staphyloferrm B-mediated uptake either by inhibiting expression or activity of staphyloferrm A and B or by inhibiting transport of staphyloferrm A and B The methods as provided would be useful for treating S. aureus infection.

Abstract: The present invention provides compositions, methods and kits for use in the detection of small RNA sequences, which allow for rapid and robust amplification and detection. The methods provide improved sensitivity and efficiency in the amplification-based detection of small RNA sequences by incorporating one or more base-modified duplex-stabilizing dNTPs during reverse transcription and/or amplification.

Abstract: A method is provided in which with respect to an optical detection apparatus including an optical detection unit and a temperature control unit, whether optical signal detection and temperature control are performed accurately, i.e. the performance thereof, can be verified simply with high reliability. With respect to an optical detection apparatus including an optical detection unit for detecting an optical signal of a sample and a temperature control unit for controlling temperature of the sample, the optical signal detection performance and temperature control performance are verified by the following method. First, a standard sample containing a nucleic acid sequence and a strand complementary thereto that have a known optical signal intensity and Tm value is provided, the temperature of the standard sample is increased or decreased with the temperature control unit, and optical signal intensity of the standard sample is measured with the detection unit.

Abstract: The present invention concerns the V617F variant of the protein-tyrosine kinase JAK2, said variant being responsible for Vaquez Polyglobulia. The invention also relates to a first intention diagnostic method for erythrocytosis and thrombocytosis allowing their association with myeloproliferative disorders, or to the detection of the JAK2 V617F variant in myeloproliferative disorders allowing their reclassification in a new nosological group.

Abstract: The invention relates to novel classes of nucleotides that can be used as substrates for enzymes, e.g. for labeling nucleic acids.

Abstract: Tools are provided which allow rapid and unequivocal identification elite event A2704-12 in biological samples.

Abstract: The present invention relates to assays and kits for carrying out said assays for the rapid, automated detection of infectious pathogenic agents and normal and abnormal genes. The present invention further relates to methods for general amplification of total mRNAs and for analyzing differential mRNA expression using the amplification methods disclosed herein.

Abstract: The present invention provides an oligonucleotide derivative that enables to easily synthesize an oligonucleotide derivative chemically modified at the 3?-end with two moieties each having a benzene or pyridine structure with a few steps, an aromatic compound serving as a precursor for preparing the modification carrier for synthesizing oligonucleotide derivative, and the oligonucleotide derivative and the oligonucleotide construct using the same, that is chemically modified at the 3?-end with two moieties each having a benzene or pyridine structure, and has good permeability through a cell membrane and excellent nuclease resistance. The modification carrier for synthesizing oligonucleotide derivative, comprising a unit and a carrier carrying the unit directly or via a linker, wherein the unit is represented by the formula (a): wherein, R1 to R6 each independently represent hydrogen or a substituent other than hydrogen; Z1 and Z2 each independently represent CH or nitrogen; and X represents oxygen or sulfur.

Abstract: The present invention relates generally to a method of identifying micro-organisms in a sample and in particular to the identification of prokaryotic micro-organisms. In some embodiments, the present invention relates to a method for the detection and/or identification of at least one microorganism or for the simultaneous detection and/or identification of several microorganisms in a test sample wherein the test sample is contacted with one or more probes derived from a tuf gene variable region.

Abstract: The present invention relates to an annealing control primer for improving annealing specificity in nucleic acid amplification and its applications to all fields of nucleic acid amplification-involved technology. The present primer comprises (a) a 3?-end portion having a hybridizing nucleotide sequence substantially complementary to a site on a template nucleic acid to hybridize therewith; (b) a 5?-end portion having a pre-selected arbitrary nucleotide sequence; and (c) a regulator portion positioned between said 3?-end portion and said 5?-end portion comprising at least one universal base or non-discriminatory base analog, whereby said regulator portion is capable of regulating an annealing portion of said primer in association with annealing temperature.

Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Methods of capturing one or more long nucleic acids and methods of capturing one or more nucleic acid for sequencing are also provided. Compositions, kits, and systems related to the methods are also described.

Abstract: Described herein are novel polynucleotides associated with prostate and lung cancer. The polynucleotides are miRNAs and miRNA precursors. Related methods and compositions that can be used for diagnosis, prognosis, and treatment of those medical conditions are disclosed. Also described herein are methods that can be used to identify modulators of prostate and lung cancer.

Abstract: Disclosed herein are methods and kits relating to detection and quantitation of helicase activity.

Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.

Abstract: A method and a kit for the identification of chromosomal inversions are described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Compositions, kits, and systems related to the methods are also described.

Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.

Abstract: Provided is a probe set that is useful for identifying each allele of HLA individually, and a method of identification of an allele of HLA by the use thereof for each type. The probe set is composed of probes that cover all of the partial sequences that contain a unique base to each allele. Using this probe set HLA contained in a specimen is identified.

Abstract: The present invention provides a transgenic soybean comprising event MON87712 that exhibits increased yield. The invention also provides cells, plant parts, seeds, plants, commodity products related to the event, and DNA molecules that are unique to the event and were created by the insertion of transgenic DNA into the genome of a soybean plant. The invention further provides methods for detecting the presence of said soybean event nucleotide sequences in a sample, probes and primers for use in detecting nucleotide sequences that are diagnostic for the presence of said soybean event.

Abstract: Two genes, A622 and NBB1, can be influenced to achieve a decrease of nicotinic alkaloid levels in plants. In particular, suppression of one or both of A622 and NBB1 may be used to decrease nicotine in tobacco plants.

Abstract: The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to improved, stable nanoreporter probes that are capable of binding to and identifying target molecules based on the probes' uniquely detectable signal. Methods for identifying target-specific sequences for inclusion in the probes are also provided, as are methods of making and using such probes. Polynucleotide sequences of certain nanoreporter components are also provided. The probes can be used in diagnostic, prognostic, quality control and screening applications.

Abstract: There is provided an oligonucleotide sequence capable of binding to a portion of a CAstV genome, wherein the oligonucleotide sequence has binding specificity to the precapsid region of CAstV or to cDNA of the precapsid region. The oligonucleotide sequence can be one of a primer pair for use in a method for detecting the presence of CAstV in a biological sample by reverse transcription followed by amplification of the reverse transcription products using such primer pair, or a method for amplifying CAstV cDNA using such primer pair.

Abstract: The present invention provides a transgenic rice event 17314 and plants, plant cells, seeds, plant parts, and commodity products derived from event 17314. The present invention also provides polynucleotides specific for event 17314 and plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides specific for event 17314. The invention also provides methods related to event 17314.

Abstract: The invention provides transgenic maize event MON 87427 and plants, plant cells, seeds, plant parts, and commodity products derived from event MON 87427. The invention also provides nucleotides specific for transgenic maize event MON 87427 and plants, plant cells, seeds, plant parts, and commodity products comprising nucleotides specific for transgenic maize event MON 87427. The invention also provides methods related to transgenic maize event MON 87427 and to the Roundup® Hybridization System (RHS). The invention also provides a Relative Development Scale useful for monitoring and determining reproductive development in maize that reconciles developmental differences across various maize varieties. This is useful for determining the optimal timing of a treatment regimen in which tassel development stage is an important factor, including various methods in making hybrid seed.

Abstract: The present invention provides a transgenic rice event 17053 and plants, plant cells, seeds, plant parts, and commodity products derived from event 17053. The present invention also provides polynucleotides specific for event 17053 and plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides specific for event 17053. The invention also provides methods related to event 17053.

Abstract: Methods, compositions and articles of manufacture for assaying a sample for a target polynucleotide are provided. A sample suspected of containing the target polynucleotide is contacted with a polycationic multichromophore and a sensor polynucleotide complementary to the target polynucleotide. The sensor polynucleotide comprises a signaling chromophore to receive energy from the excited multichromophore and increase emission in the presence of the target polynucleotide. The methods can be used in multiplex form. Kits comprising reagents for performing such methods are also provided.

Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

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: The present invention relates to methods and compositions for predicting drug responses. In particular, the present invention provides methods and compositions for determining individualized Warfarin dosages based on genotype of DNA polymorphisms and haplotypes derived from them in the VKORC1 gene.

Abstract: Substituting fish of lesser value for high priced fish such as grouper has become a major problem for restaurants, wholelsalers, and the general public. A method based upon nucleic acid amplification enables clear differentiation between grouper and potential substitutes. The nucleic acid is incubated with a molecular beacon probe thereby allowing detection of the hybridized molecular beacon probe. All grouper, including the fresh market sample, were successfully confirmed as grouper. Several non-grouper samples obtained fresh and frozen from the market were also tested; none were detected as grouper.

Abstract: Provided herein are sequences of the genomes and encoded proteins of new astrovirus species, and variants thereof. Also provided are methods of detecting the new astrovirus species and diagnosing astrovirus infection, methods of treating or preventing astrovirus infection, and methods for identifying anti-astrovirus compounds. Provided are two new astrovirus species named HMOAstV-A and HMOAstV-B, and both are distantly related to known astroviruses. Also provided is a new method of classifying astroviruses, where there are three groups of human astroviruses, including HAstV, AstV-MLB, and HMOAstV.

Abstract: The invention is directed towards methods and compositions for identifying the specific microorganisms present in a particular potion of a papermaking processes. The method involves obtaining a sample from the process which is such that little or no live examples of the microorganism remain. However because DNA from the organisms is still present, an analysis which identifies portions of DNA specific to the particular organism will correctly identify the microorganism present. This allows for analysis of infestations present on felts or paper sheets which typically no longer have many live microorganisms on them when samples are taken for analysis.

Abstract: Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.

Abstract: The invention provides corn event MON 87411, and plants, plant cells, seeds, plant parts, and commodity products comprising event MON 87411. The invention also provides polynucleotides specific for event MON 87411 and plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides specific for event MON 87411. The invention also provides methods related to event MON 87411.

Abstract: This invention relates to soybean event pDAB8291.45.36.2, which includes a novel expression cassette comprising multiple traits conferring resistance to glyphosate, aryloxyalkanoate, and glufosinate herbicides. This invention also relates in part to methods of controlling resistant weeds, plant breeding, and herbicide tolerant plants. In some embodiments, the event sequence can be “stacked” with other traits, including, for example, other herbicide tolerance gene(s) and/or insect-inhibitory proteins. This invention further relates in part to detection methods, including endpoint TaqMan PCR assays, for the detection of Event pDAB8291.45.36.2 in soybeans and related plant material. Some embodiments can perform high throughput zygosity analysis of plant material and other embodiments can be used to uniquely identify the zygosity of and breed soybean lines comprising the event of the subject invention. Kits and conditions useful in conducting these assays are also provided.

Abstract: Arrays of polypeptides are generated by translation of nucleic acid sequences encoding the polypeptides at a plurality of addresses on the array.

Abstract: Chemical field effect sensors comprising nanotube field effect devices having biopolymers such as single stranded DNA or RNA functionally adsorbed to the nanotubes are provided. Also included are arrays comprising the sensors and methods of using the devices to detect volatile compounds.

Abstract: The invention provides methods of detecting West Nile virus and oligonucleotide reagents derived from a West Nile virus consensus sequence that are useful in the methods of the invention.

Abstract: Compositions are disclosed as nucleic acid sequences that may be used as amplification oligomers, including primers, capture probes for sample preparation, and detection probes specific for Legionella pneumophila 16S or 23S rRNA sequences or DNA encoding 16S or 23S rRNA. Methods are disclosed for detecting the presence of L. pneumophila in samples by using the disclosed compositions in methods that include in vitro nucleic acid amplification of a 16S rRNA sequence or DNA encoding the 16S rRNA sequence, or of a 23S rRNA sequence or DNA encoding the 23S rRNA sequence to produce a detectable amplification product.

Abstract: The application relates to methods and systems for analysis of dissociation behavior of nucleic acids and identification of nucleic acids. In one aspect, methods and systems are disclosed for identifying a nucleic acid in a sample including an unknown nucleic acid and for detecting a single nucleotide polymorphism in a nucleic acid in a sample. Methods and systems are also disclosed for identification of a nucleic acid in a biological sample including at least one unknown nucleic acid by fitting denaturation data including measurements of a quantifiable physical change of the sample at a plurality of independent sample property points to a function to determine an intrinsic physical value and to obtain an estimated physical change function, and identifying the nucleic acid in the biological sample by comparing the intrinsic physical value for at least one unknown nucleic acid to an intrinsic physical value for a known nucleic acid.

Abstract: Methods are provided for detecting an aneuploidy in a fetus. These methods can be used to detect trisomy 13, 8 or 21, amongst other aneupoloidies. In some embodiments, the methods include selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence and genotyping the fetus using the purified fetal DNA, thereby detecting aneuploidy in the fetus.

Abstract: The present invention provides compositions comprising at least one oligomeric compound comprising an alternating motif and further include a region that is complementary to a nucleic acid target. The compositions are useful for targeting selected nucleic acid molecules and modulating the expression of one or more genes. In preferred embodiments the compositions of the present invention hybridize to a portion of a target RNA resulting in loss of normal function of the target RNA. The present invention also provides methods for modulating gene expression.

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: The present invention relates to methods and systems for single molecule based clonal amplification and subsequent detection of nucleic acid molecules, and particularly to the determination of SNPs, mutations, and to the diagnosis of diseases associated with the changes of these nucleic acid molecules.

Abstract: Parkinson's disease is caused by the preferential loss of substantia nigra dopamine neurons. A Parkin Interacting Substrate, PARIS (ZNF746) is identified. The levels of PARIS are regulated by the ubiquitin proteasome system via binding to and ubiquitination by the E3 ubiquitin ligase, parkin. PARIS is a KRAB and zinc finger protein that accumulates in models of parkin inactivation and in human brain Parkinson's disease patients. PARIS represses the expression of the transcriptional co-activator, PGC-1? and the PGC-1? target gene, NRF-1 by binding to insulin response sequences in the PGC-1? promoter. Conditional knockout of parkin in adult animals leads to progressive loss of dopamine (DA) neurons that is PARIS dependent. Overexpression of PARIS causes selective loss of DA neurons in the substantia nigra, which is reversed by either parkin or PGC-1? co-expression. The identification of PARIS provides a molecular mechanism for neurodegeneration due to parkin inactivation.

Abstract: Novel compositions comprised of at least one bead conjugated to a solid support and further conjugated to at least one nucleic acid and preferred methods for making the novel compositions are described. As compared to “flat” surfaces, beads linked to a solid support provide an increased surface area for immobilization of nucleic acids. Furthermore, by selecting a bead with the desired functionality, a practitioner can select a functionalization chemistry for immobilizing nucleic acids, which is different from the chemistry of the solid support.