Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.

Abstract: The present invention provides compositions and improved methods for multi-site directed mutagenesis and DNA shuffling. The present compositions and methods provide increased mutation frequency and increased number of transformants which allow one to sequence only a few clones in order to identify the correct mutants and to obtain the desired mutant by screening large number of transformants in a short time. Moreover, the inclusion of FEN-1, PEF and optimized buffer and cycling conditions provided in the present invention should also facilitate random mutagenized library construction and the mutagenesis of large or difficult templates.

Abstract: The invention relates to a method for the detection of the occurrence of initiation of replication events in genomic DNA in a eukaryotic cell, involving contacting said eukaryotic cell comprising said genomic DNA with a first nucleotide probe, under conditions enabling in situ hybridization of said first nucleotide probe with a target region in the DNA genome, wherein said target region comprises a nucleic acid sequence which has no identified corresponding annealing RNA in a metabolically active cell and therefore remains RNA-free during transcription and replication of said DNA genome and detecting said first nucleotide probe hybridized to said DNA. Further detection of at least one RNA molecule can be achieved.

Abstract: Disclosed are biomolecule based bioprobes that exhibit improved water solubility and monolayer-forming properties with substantially little or no aggregation that can appreciably interfere with binding of the bioprobes to a target nucleotide. The bioprobes may be used in conjunction with a suitable reporter system to detect very small quantities of biological markers. The bio-probes comprise a nucleobase sequence capable of hybridizing to a target nucleotide; and at least one charged functional group attached to said nucleobase sequence. Also disclosed are biosensors, and sensing devices that comprise the bio-probe. Further disclosed are suitable electrochemical reporter systems for use with bioprobes. Methods of use of these devices and probes, including for the detection of target biomarkers, including biomarkers for cancer cells or pathogens, are also included.

Abstract: A kit to execute a method of simultaneously performing comparative transcript analysis in a multitude of samples. The kit includes a blocking adapter. The blocking adapter includes an inert 3? end.

Abstract: The invention herein disclosed provides for devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore in the absence of requiring a terminating nucleotide. The devices and methods are also used to determine rapidly (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of drug discovery, molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

Abstract: Compounds, compositions and methods are provided for modulating the expression of apolipoprotein(a). The compositions comprise oligonucleotides, targeted to nucleic acid encoding apolipoprotein(a). Methods of using these compounds for modulation of apolipoprotein(a) expression and for diagnosis and treatment of disease associated with expression of apolipoprotein(a) are provided.

Abstract: A method for detecting the bacteria Staphylococcus epidermidis includes isolating DNA from a biological sample suspected of containing the bacteria. The method further includes subjecting the DNA to a Polymerase Chain Reaction (PCR) amplification method utilizing at least one primer derived from a cell division gene. The method may further include characterizing an indicator of a Staphylococcus epidermidis phenotype of interest. The method additionally includes detecting the bacterium Staphylococcus epidermidis by visualizing the product of the polymerase chain reaction. Amplification products of cell division genes and virulence genes are also provided.

Abstract: The object of the present invention is to provide a gene amplification method, wherein the method can amplify both methylated and unmethylated nucleic acids present in a biological sample, and further regulate the amplification ratio of the methylated and/or unmethylated nucleic acid as needed. Such objects can be solved by an amplification method using a nonspecific primer which can hybridize both with methylated and unmethylated nucleic acids and a specific primer which specifically hybridizes with either methylated or unmethylated nucleic acid, and further by an amplification method which can change the amplification ratio of methylated or unmethylated nucleic acid by changing the mixing rate of these primers.

Abstract: A method and kit for detecting the presence of a target sequence in a polynucleotide analyte contained in a sample are disclosed. In practicing the method, the sample is mixed with a single-stranded DNA target probe having a sequence capable of hybridizing with the target sequence, under conditions effective to form a double-stranded complex of the analyte and the single-stranded DNA target probe, and the single-stranded DNA target probe in the complex is reacted in the presence of a polymerase and one to three nucleotide triphosphates, to add a selected one or more target-directed nucleotide bases to single-stranded DNA target probe's 3? end to produce a modified probe. The modified probe is hybridized with a single-stranded DNA detection probe, the two probes are ligated to form a two-probe ligation product, and the presence of the ligation product is detected.

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 discloses a method for the treatment of Flaviviridae infection that includes the administration of a 2?-branched nucleoside, or a pharmaceutically acceptable prodrug and/or salt thereof, to a human in need of therapy in combination or alternation with a drug that directly or indirectly induces a mutation in the viral genome at a location other than a mutation of a nucleotide that results in a change from serine to a different amino acid in the highly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA polymerase region, or is associated with such a mutation. The invention also includes a method to detect a mutant strain of Flaviviridae and a method for its treatment.

Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.

Abstract: The present patent application describes a cantilever for atomic force microscopy (AFM), which includes a cantilever body having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendron are bound to the surface, and a terminus of the linear region of the dendron is functionalized.

Abstract: Provided is a method for inducing, stimulating and/or otherwise promoting and/or modulating flavonoid and/or lignin biosynthesis in a plant by using a microbial based soil additive or amendment.

Abstract: The invention provides compositions comprising one or more isolated factors from a microenvironment of human embryonic stem cells (hESCs), including, but not limited to, Lefty and inhibitors of Nodal. The invention also provides methods of utilizing factors derived from human embryonic stem cells (hESC) and their microenvironment to treat and prevent tumor formation and progression and to inhibit tumor cell aggressiveness. The invention further provides methods of inhibiting tumor cell growth and/or treating aggressive tumors in a mammal comprising administering to the mammal, having at least one tumor cell present in its body, an effective amount of an inhibitor of Nodal activity.

Abstract: Point-of-care binding assays include at least one target nucleic acid binding in a multiplex structure with at least one sequence in a partner nucleic acid associated with a label, due to complementary base pairings between at least one sequence in the target nucleic acid and at least one sequence in the partner nucleic acid. The assays overcome the inherent deficiencies of antibody-protein antigen assays. In a preferred embodiment, color tagged nucleic acid sequences are used to bind a complementary target nucleic acid. The tagged nucleic acid sequences are preferably made from deoxyribonucleotides, ribonucleotides, or peptide nucleotides.

Abstract: Methods are provided for detection of cancers associated with methylation of hMLH1 promoter DNA in a subject. The method comprise assaying for the presence of methylated hMLH1 promoter DNA in a bodily fluid from a subject. In one embodiment, the method comprises reacting DNA from the sample with a chemical compound that converts non-methylated cytosine bases but not methylated cytosine bases, to a different nucleotide base. The compound-converted DNA is then amplified using a methylation-sensitive polymerase chain reaction (MSP) employing primers that amplify the compound-converted DNA template. The present invention also provides nucleotide primer sequences for use in the methylation-sensitive PCR assay.

Abstract: Genetic diseases can be diagnosed by detection of mutations in causative genes. Protein truncation assays can be used to detect gene products of truncation-type mutations. However, the sensitivity of the assays is often insufficient to detect mutations present in a sample of DNA at a low frequency. Sensitivity can be increased by dividing samples so that the signal generated by a mutant allele comprises a larger fraction of the total alleles than prior to dividing. Thus a previously undetectable signal generated by the mutant allele can become detectable in the assay. Such increased sensitivity permits detection at early stages and in samples having high levels of other alleles.

Abstract: The invention further relates to conjugated polymers, and methods, articles and compositions employing them as described herein. In some aspects, the invention relates to methods, articles and compositions for the detection and analysis of biomolecules in a sample. Provided assays include those determining the presence of a target biomolecule in a sample or its relative amount, or the assays may be quantitative or semi-quantitative. The methods can be performed on a substrate. The methods can be performed in an array format on a substrate, which can be a sensor. In some embodiments, detection assays are provided employing sensor biomolecules that do not comprise a fluorophore that can exchange energy with the cationic multichromophore. In some aspects biological assays are provided in which energy is transferred between one or more of the multichromophore, a label on the target biomolecule, a label on the sensor biomolecule, and/or a fluorescent dye specific for a polynucleotide, in all permutations.

Abstract: Disclosed herein are compounds and methods for decreasing PrP and preventing, ameliorating, or treating a prion disease or conformational neurodegenerative disorder, in an individual in need thereof. Examples of disease conditions that can be ameliorated with the administration of antisense compounds targeted to PrP include Creutzfeldt-Jakob disease (CJD); variant Creutzfeldt-Jakob Disease (vCJD); Gerstmann-Straussler-Scheinker syndrome; fatal familial insomnia; kuru; Bovine Spongiform Encephalopathy (BSE), e.g. “mad cow disease”; Chronic Wasting Disease (CWD); scrapie; transmissible mink encephalopathy; feline spongiform encephalopathy; ungulate spongiform encephalopathy; Alzheimer's disease; Parkinson's disease; Huntington's disease; and Amyotrophic Lateral Sclerosis (ALS).

Abstract: The present invention provides a method and compositions for high throughput screening of genetically modified photosynthetic organisms for plasmic state. The present invention provides methods of producing one or more proteins, including biomass degrading enzymes in a plant. Also provided are the methods of producing biomass degradation pathways in alga cells, particularly in the chloroplast. Single enzymes or multiple enzymes may be produced by the methods disclosed. The methods disclosed herein allow for the production of biofuel, including ethanol.

Abstract: A nucleotide probe permitting the detection of nucleic acids and constituted of a labeled nucleotide strand having three fragments: a first fragment having a first closing sequence, a second fragment, all or part of which has a recognition sequence for the molecular recognition of the target nucleic acid and a third fragment having a second closing sequence, and at least two markers, one of the ends of the strand of the detection probe being free of any marker, in which, when the two closing sequences are hybridized together, the detection probe has a completely circular shape, the closing sequences thus maintaining the probe in a conformation that cannot be detected in the absence of the target nucleic acid.

Abstract: It is an object of the present invention to provide a solution to problems associated with the use of microarray technology for the analysis DNA. The present invention provides compositions and methods for the use of simple and compound representations of DNA in microarray technology. The present invention is also directed to methods for the production of High Complexity Representations (HCRs) of the DNA from cells.

Abstract: The invention is directed to binary oligonucleotide probes for nucleic analysis, which probes can be made of DNA or RNA that recognize nucleic acid analytes (both DNA and RNA) with unprecedented high selectivity under mild conditions and are highly sensitive to single nucleotide mismatches (SNP single nucleotide polymorphisms) without PCR amplification. In one group, the binary probes indicate that they have hybridized to a particular nucleic analyte by binding to a molecular beacon that gives off a fluorescent signal. A second group of binary probes bind to a dye such as malachite green, where upon hybridization to analyte the fluorescence of the dye increases dramatically and is easily detected and measured. The new binary probes require only about five minutes at room temperature to generate a detectable signal.

Abstract: The invention relates to a method for detecting a nucleic acid of an organism in a composition, comprising the steps of, (i) amplifying the nucleic acid to be detected, (ii) during or after amplification, hybridizing to said nucleic acid to be detected a first probe that comprises an abasic site additionally optionally carrying a detectable label, (iii) wherein the position of the abasic site corresponds to a position in said nucleic acid to be detected, known to have a polymorphism in said organism, and wherein said nucleic acid is detected if hybridization occurs.

Abstract: An isolated nucleic acid molecule that selectively binds to an E-selectin protein comprises a contiguous 29-30 nucleotide sequence that includes at least one monothiophosphate or a dithiophosphate modified nucleotide. Also disclosed are methods of inhibiting an E-selectin mediated interaction with a natural E-selectin ligand, and methods of targeting an imaging agent or therapeutic agent to a target tissue bearing E-selectin.

Abstract: The invention provides a method for rapidly detecting a pathogen in fish comprising conducting loop-mediated isothermal amplification with a specific primer set and a nucleic acid in a test sample. If at least one amplification is carried out, the test sample comprises the pathogen in fish. The invention also provides a primer set, probe and kit for detecting a pathogen in fish.

Abstract: Disclosed is a method for in situ detection of one or more target nucleic acids based on a combination of an in situ hybridization (ISH) assay method and a general ISH signal amplification method. This new method produces high signal intensity and while keeps low background noise of signal amplification. The result can be consistently reproduced and the method can be easily adopted for routine clinic diagnostic use. Further, the invention relates to a kit, comprising the components of the ISH assay and a general ISH signal amplification assay, for sensitive detection of one or more target nucleic acids.

Abstract: The present invention relates to the use of cross-linking probes to covalently bind probes to nucleic acid targets. In some embodiments, the probe comprises an initiator region that is able to bind to a first portion of a target nucleic acid, a probe region linked too the initiator region that is able to bind to a second region of the target nucleic acid and that comprises one or more cross-linkers, and a blocking region hybridized to the probe region.

Abstract: Provided herein are methods, compounds, and compositions for reducing expression of PTP1B mRNA and protein in an animal. Such methods, compounds, and compositions are useful to treat, prevent, delay, or ameliorate metabolic disease, for example, diabetes, or a symptom thereof.

Abstract: The Application relates to compositions, kits, methods, and systems for nucleotide sequencing comprising producing polymerase reactions that comprise both catalytic and non-catalytic divalent metal ions. Effective ratios and amounts of catalytic and non-catalytic divalent metal ions are described.

Abstract: The present invention relates to a control method of a wheel alignment apparatus using an MDPS, which determines whether or not to cancel center alignment control due to a trouble or error is preferentially determined prior to each control step and then performs control when wheels of a vehicle having an MDPS mounted therein are aligned, such that the trouble or error is preferentially considered in the control priority, thereby increasing driver's convenience and improving safety performance for protecting the driver.

Abstract: Compounds of general formula I are used as labels in an electrochemical assay: (I) in which: Fc and Fc? are substituted or unsubstituted ferrocenyl moieties, X is a C1 to C6 alkylene chain which is optionally interrupted by —O— or —NH—; Y is a C1 to C6 alkylene chain which is optionally interrupted by —O— or —NH—; Z is a C1 to C12 alkylene chain which may optionally be substituted and/or may optionally be interrupted by —O—, —S—, cycloalkyl, —CO—, —CON R1—, —NR1CO— or —NR1— in which R1 represents hydrogen or C1 to C4 alkyl; and R is a linker group. Compounds I are used to make labelled substrates, as well as functionalised compounds for making the labelled substrates.

Abstract: The present invention relates to the prediction of QT prolongation following administration of a compound capable of increasing an individual's QT interval based on the individual's genotype at one or more single nucleotide polymorphism (SNP) loci and to the treatment of a patient based on such prediction.

Abstract: Compositions and methods are provided for amplifying nucleic acid molecules. The nucleic acid molecules can be used in various research and diagnostic applications, such as gene expression studies involving nucleic acid microarrays.

Abstract: Methods for amplification and sequencing of at least one nucleic acid comprising the following steps: (1) forming at least one nucleic acid template comprising the nucleic acid(s) to be amplified or sequenced, wherein said nucleic acid(s) contains at the 5? end an oligonucleotide sequence Y and at the 3? end an oligonucleotide sequence Z and, in addition, the nucleic acid(s) carry at the 5? end a means for attaching the nucleic acid(s) to a solid support; (2) mixing said nucleic acid template(s) with one or more colony primers X, which can hybridize to the oligonucleotide sequence Z and carries at the 5? end a means for attaching the colony primers to a solid support, in the presence of a solid support so that the 5? ends of both the nucleic acid template and the colony primers bind to the solid support; (3) performing one or more nucleic acid amplification reactions on the bound template(s), so that nucleic acid colonies are generated and optionally, performing at least one step of sequence determination of

Abstract: Provided is an HPV E6, E7 mRNA assay, referenced herein as the “In Cell HPV Assay,” that is capable of sensitive and specific detection of normal cervical cells undergoing malignant transformation as well as abnormal cervical cells with pre-malignant or malignant lesions. The In Cell HPV Assay identifies HPV E6, E7 mRNA via in situ hybridization with oligonucleotides specific for HPV E6, E7 mRNA and quantitates the HPV E6, E7 mRNA via flow cytometry. The In Cell HPV Assay can be carried out in less than three hours directly from liquid-based cervical (“LBC”) cytology specimens. The In Cell HPV Assay provides an efficient and highly sensitive alternative to the Pap smear for determining abnormal cervical cytology.

Abstract: An oligonucleotide-based molecular probe includes at least one pin loop, the pin loop including a loop sequence complementary to a target sequence. A first stem sequence is attached to one end of the pin loop, the first stem having at least one fluorescent label attached thereto. A second stem sequence is attached to the other end of the pin loop. The second stem has a plurality of quencher molecules attached thereto.

Abstract: The present invention provides 2-aminopyridine and 2-pyridone C-nucleosides and oligonucleotides containing the subject nucleosides. The nucleosides are useful in the preparation of the subject oligonucleotides. The oligonucleotides are useful in oligonucleotide-based diagnosis and separation through triplex binding.

Abstract: The present invention provides a circular dumbbell oligodeoxynucleotide (CDODN) comprising two loop structures and a stem structure, wherein the stem structure comprises a nucleotide sequence capable of binding the DNA-binding domain of a transcriptional factor. The present invention further provides a pharmaceutical composition comprising said CDODN. The pharmaceutical composition can be used for treating and/or preventing a disease or disorder related to such a transcriptional factor. The present invention also provides a method for treating and/or preventing a disease or disorder related to such a transcriptional factor, comprising administering to the subject a therapeutically effective amount of a CDODN comprising two loop structures and a stem structure, wherein the stem structure comprises a nucleotide sequence capable of binding the DNA-binding domain of the transcriptional factor.

Abstract: Polymorphic corn DNA loci useful for genotyping between at least two varieties of corn. Sequences of the loci are useful for providing the basis for designing primers and probe oligonucleotides for detecting polymorphisms in maize DNA. Polymorphisms are useful for genotyping applications in corn. The polymorphic markers are useful to establish marker/trait associations, e.g. in linkage disequilibrium mapping and association studies, positional cloning and transgenic applications, marker-aided breeding and marker-assisted selection, hybrid prediction and identity by descent studies. The polymorphic markers are also useful in mapping libraries of DNA clones, e.g. for corn QTLs and genes linked to polymorphisms.

Abstract: This invention relates in part to soybean event pDAB8264.44.06.1 and includes a novel expression cassettes and transgenic inserts 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 endpoint TaqMan PCR assays for the detection of Event pDAB8264.44.06.1 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: The invention relates to a new resistance gene, Rpi-edn2 and functional homologues or functional fragments thereof isolated from S. x edinense. Moreover, the invention relates to the use of said resistance gene, for example the use of said resistance gene in a method to increase or confer at least partial resistance in a plant to an oomycete infection. The invention provides an isolated or recombinant nucleic acid sequence comprising a nucleic acid sequence encoding one of the amino acid sequences of FIG. 4 or a functional fragment or a functional homologue thereof.

Abstract: A signal-off-quantum-dot-based sensor for detecting the presence of a target molecule comprising: an aptamer probe having a nucleotide sequence which specifically interacts with the target molecule by sequence-dependent interaction, wherein the aptamer probe is sandwiched between (a) an oligonucleotide which is immobilized on the surface of a quantum dot (QD), and (b) a fluorophore-labeled oligonucleotide, wherein when the sensor is excited by an energy source: (i) in the absence of specific interaction between the target molecule and the aptamer probe, a baseline signal is emitted, and (ii) in the presence of specific interaction between the target molecule and the aptamer probe, a detection signal is emitted, wherein the baseline signal is greater than the detection signal, whereby the presence of the target molecule is detected.

Abstract: The invention provides compositions and methods for the differential detection of high risk forms of HPV from a urine sample provided by a patient. Specifically, the invention provides primers and probes that specifically recognize and bind sequences within the E1 gene of HPV. Detection of high risk forms of HPV identify individuals at risk of developing or in the early stages of cervical carcinoma.

Abstract: The present invention provides a manufacturing method that can easily manufacture a compound known as photoresponsive (photocoupling) nucleic acids at high yield in a shorter period of time than that of the conventional technology. The present invention relates to a method of manufacturing a photoresponsive nucleic acid which includes a step of reacting a nucleic acid having groups represented by the Formula I, the Formula III, the Formula IV, or the Formula V and a compound represented by the Formula II, or reacting a nucleic acid having groups represented by the Formula VI, the Formula VIII, the Formula IX, or the Formula X and a compound represented by the Formula VII by heating them by microwaves in the presence of a metal catalyst, a basic substance, and a solvent.

Abstract: Disclosed herein are polynucleotides which may be used to calibrate or standardize quantitative nucleic acid assays. As disclosed, the polynucleotides comprise a sequence derived from a plant viroid polynucleotide or a bacterial or chloroplast Type II intron polynucleotide. Also disclosed are methods of making and using the polynucleotides.

Abstract: A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of apolipoprotein B. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding apolipoprotein B. Methods of using these compounds for modulation of apolipoprotein B expression and for treatment of diseases associated with expression of apolipoprotein B are provided.