Abstract: The present teachings provide methods, compositions, and kits for synthesizing and sequencing nucleic acids. In some embodiments, reversible di-nucleotide compounds are employed along with cleaving reactions that remove a label and a blocking moiety. Improved sequencing efficiency is achieved by the rapid polymerase-mediated incorporation of reversible di-nucleotide compounds. In some embodiments, the di-nucleotides do not contain conventional nucleotide triphosphates, but rather employ amino acid phosphoramidate nucleotides (AAPNs).

Abstract: A process is disclosed for determining the concentration of nucleic acids in a sample in a microfluidic device. In at least one embodiment, the method includes a) introducing the sample into a first chamber, b) carrying out a number of cycles of an amplification reaction to be carried out in cycles for amplifying nucleic acids, c) transferring a defined volume which is a fraction of the volume of the first chamber and which has amplified nucleic acids into a second chamber and replacing the transferred defined volume with fresh reagents for the amplification reaction, d) determining the concentration of the amplified nucleic acids in a second chamber equipped with an element to determine concentrations, and e) repeating steps b)-d) until a concentration of the amplified nucleic acids which is within a range is determined in the second chamber. An arrangement is further disclosed.

Abstract: Polynucleotides useful for detecting Chlamydia trachomatis and/or Neisseria gonorrhoeae in a test sample, kits, a nucleic acid amplification method and detection method including the same.

Abstract: The characterization of a new strain of human rhinovirus of genetic group C (HRV-C) as well as methods and kits for detecting the presence of HRV-C by PCR amplification are provided.

Abstract: The current disclosure generally relates to the field of saxitoxins and the identification of microorganisms capable of producing them. In particular, the saxitoxin A (sxtA) gene comprising catalytic domain sequences saxitoxin A1 (sxtA1) and saxitoxin A4 (sxtA4) is identified in a number of dinoflagellate species. The disclosure relates to methods of detection of saxitoxin-producing dinoflagellates by amplification and detection of the sxtA gene (in particular by PCR) and kits and primers for use in the method are also disclosed. Saxitoxin-producing dinoflagellate genera detected by the method include Alexandrium, Pyrodinium or Gymnodinium.

Abstract: A purified polynucleotide having a chain of nucleotides corresponding to a mutated sequence, which in a wild form encodes a polypeptide implicated in hereditary sensory defect, wherein said mutated purified polynucleotide presents a mutation responsible for prelingual non-syndromic deafness selected from the group consisting of a specific deletion of at least one nucleotide.

Abstract: The present application provides for an enhanced method for sequencing, or amplifying and detecting nucleic acids comprising the steps of: i) providing at least one nucleic acid primer comprising at least one labelled nucleotide, ii) providing enzymes and reagents for amplification of a target nucleic acid using said at least one labelled nucleic acid primer, iii) incubating the components of the reaction under conditions suited for amplification of the target nucleic acid primer, iv) detecting the amplified nucleic acids via the labelled nucleotide, wherein the nucleic acid primer comprises the following sequence: 5?-NaXNb-3?, wherein in N may be any nucleotide, wherein “a” and “b” represent the number of nucleotides and may range from 1 to 150 and wherein X is said at least one labelled nucleotide. Furthermore a kit comprising such a nucleic acid primer and the use of said kit or nucleic acid primer in a method for sequencing or amplifying and detecting nucleic acids is disclosed herein.

Abstract: Provided are compositions, kits, and methods for the identification of Salmonella. In certain aspects and embodiments, the compositions, kits, and methods may provide improvements in relation to specificity, sensitivity, and speed of detection.

Abstract: The present invention provides a method of detecting a functional filamentous fungus, wherein the functional filamentous fungus, Coprinellus curtus, in a sample is detected using at least one polynucleotide selected from the group consisting of polynucleotides having a nucleotide sequence shown in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 4 and polynucleotides having a nucleotide sequence complementary thereto, and polynucleotides having a nucleotide sequence substantially homologous to these sequences; and a method of evaluating a product containing a functional filamentous fungus wherein the existence or concentration of the functional filamentous fungus, Coprinellus curtus, in a product containing a functional filamentous fungus is evaluated.

Abstract: The invention relates to an in vitro method for the detection of bacteria of the Salmonella spp. genus by means of a quantitative polymerase chain reaction using specific primers for the pathogen from DNA and RNA samples from the microorganism. The method is useful in the detection of viable and non-viable microorganisms of Salmonella spp. in environmental, clinical and food samples. Likewise, the invention also relates to a kit used for putting the method into practice.

Abstract: The present invention relates to a method for the diagnosis and prognosis of cancers using an epigenetic marker consisting of a specific single CpG site in TTP (Tristetraprolin) promoter and treatment of cancers by regulating its epigenetic status. Particularly, the present invention relates to a method for the diagnosis and prognosis of liver cancer by measuring specific methylation of C, the 32nd residue of the nucleic acid sequence represented by SEQ. ID. NO. 41, and a method for treatment of cancer by regulating the same. The present invention can be effectively used for the diagnosis and/or treatment of liver cancer characterized by TTP down-regulation and methylation of C, the 32nd residue of the nucleic acid sequence represented by SEQ. ID. NO. 41. The present invention can be further applied for the diagnosis and treatment of other cancers or inflammatory diseases that are characterized by TTP down-regulation and methylation of C, the 32nd residue of the nucleic acid sequence represented by SEQ. ID.

Abstract: The present invention generally relates to a molecular test of Influenza A, Influenza B, Respiratory Syncytial Virus A, and Respiratory Syncytial Virus B in order to identify patients with a viral infection. Accordingly methods and compositions are disclosed to determine the presence or absence of a viral pathogen in a sample containing one or more target nucleic acids from the M gene of Influenza A, Influenza B, Respiratory Syncytial Virus A, and/or Respiratory Syncytial Virus B.

Abstract: Isolated nucleotides encoding polypeptides with mutations leading to amino acid substitutions linked to hereditary kidney disease or malformation of the urinary tract are provided herein. Constructs, cells, probes and inhibitory molecules comprising these mutations are also provided and may be used in screening assays for candidate agents to treat or reverse these diseases or alternatively to provide diagnostic tests. Methods of diagnosing subjects likely to develop these diseases or to be carriers of these diseases are also provided.

Abstract: Methods and materials are disclosed for use in simultaneously amplifying at least 11 specific STR loci of genomic DNA in a single multiplex reaction, as are methods and materials for use in the analysis of the products of such reactions. Included in the present invention are materials and methods for the simultaneous amplification of 16 specific loci in a single multiplex reaction, comprising the 10 AmpFlSTR® SGMplus® STR loci, the Amelogenin locus, and 5 new STR loci, including methods and materials for the analysis of these loci.

Abstract: Nucleic acid molecules derived from sequences of novel human parvovirus B19 variant genomes are provided. Also provided are assays and kits comprising the nucleic acid molecules.

Abstract: The invention relates to isolated DNA or RNA molecules comprising at least ten contiguous bases having a sequence in a pancreatic islet microRNA. In another embodiment, the invention relates to isolated single stranded pancreatic islet microRNA molecules or anti-pancreatic islet microRNA molecules.

Abstract: The present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immuno-deficiency Virus (HIV). With the present invention nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid. The oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained. The benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity.

Abstract: A marker for the detection of liver cancer and application of the marker thereof. The application includes use of cytochrome p450 family 17 subfamily A polypeptide 1 (CYP17A1 protein) in the preparation of diagnostic reagents or kits for the detection of liver cancer kit. Studies have shown that CYP17A1 expression levels are higher in liver cancer tissues than in the adjacent healthy tissues, and the amount of CYP17A1 in sera of liver patients is significantly higher than that of healthy human population. Therefore, CYP17A1 can be used as a marker for the diagnosis of liver cancer (especially serological diagnosis).

Abstract: Compositions and methods related to transgenic high oleic acid/ALS inhibitor-tolerant soybean plants are provided. Specifically, the present invention provides soybean plants having a DP-305423-1 event which imparts a high oleic acid phenotype and tolerance to at least one ALS-inhibiting herbicide. The soybean plant harboring the DP-305423-1 event comprises genomic/transgene junctions having at least the polynucleotide sequence of SEQ ID NO:8, 9, 14, 15, 20, 21, 83 or 84. The characterization of the genomic insertion site of the DP-305423-1 event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the soybean DP-305423-1 events are provided.

Abstract: The present invention relates to primer sets for diagnosing ankylosing spondylitis and the method for diagnosing ankylosing spondylitis using the same. Particularly, the present invention provides primer sets for diagnosing ankylosing spondylitis as follows: (a) a primer set comprising a primer having at least 95% sequence homology with SEQ ID NO: 7, and at least one primer selected from the group consisting of primers of SEQ ID NOs: 9 to 13; (b) a primer set comprising at least one primer selected from the group consisting of primers of SEQ ID NOs: 15 to 17, and a primer having at least 95% sequence homology with SEQ ID NO: 19 and (c) a primer set comprising a primer having at least 95% sequence homology with SEQ ID NO: 18, and a primer having at least 95% sequence homology with SEQ ID NO: 20. The primer sets and the kit for diagnosing ankylosing spondylitis of the present invention can be effectively used for early diagnosis. tracking progress and prognosis of ankylosing spondylitis.

Abstract: A composition is provided comprising a negatively charged group, an oligonucleotide sequence and at least none or one nuclease-resistant linkage group to form a chemically-enhanced primer. The chemically-enhanced primer can be used for sequencing and fragment analysis. Methods for synthesizing the primer as well as a method of preparing DNA for sequencing and a method of sequencing DNA and kits containing the chemically-enhanced primer are also provided. The method of sequencing DNA can comprise contacting amplification reaction products with the composition under conditions in which excess amplification primer is degraded by the nuclease and the chemically-enhanced primer is essentially non-degraded.

Abstract: The present invention provides transgenic soybean event MON87769, and cells, seeds, and plants comprising DNA diagnostic for the soybean event. The invention also provides compositions comprising nucleotide sequences that are diagnostic for said soybean event in a sample, 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 in a sample, growing the seeds of such soybean event into soybean plants, and breeding to produce soybean plants comprising DNA diagnostic for the soybean event.

Abstract: The invention relates to determining the presence of an EZH2 gene mutation in a sample from a subject and 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: The present invention provides screening kits, compositions, and diagnostic methods for determining whether a subject has a predisposition to, or likelihood of having, a substance use disorder by determining a nucleic acid methylation profile from a biological sample from the subject, wherein a given profile indicates that the subject has a predisposition to a substance use disorder.

Abstract: A gene expression signature of colon cancer, microarrays including them and methods of using the colon gene expression signature are provided. The gene expression signature is especially useful for determining the prognosis of a patient diagnosed with colon cancer, such as stage II colon cancer. The gene signature described herein is also useful for determining effectiveness of surgical resection with or without adjuvant chemotherapy, and determining possibility of cancer recurrence in patients with colon cancer.

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: 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: Methods of detecting D. gatoi or D. cati, are disclosed. A sample suspected of containing a nucleic acid of D. gatoi or D. cati is screened for the presence or absence of that nucleic acid. The presence of the D. gatoi or D. cati nucleic acid indicates the presence of D. gatoi or D. cati. Determining whether the D. gatoi or D. cati nucleic acid is present in the sample can be accomplished by detecting hybridization between a D. gatoi or D. cati probe. Probes and primers for the detection of D. gatoi or D. cati are also disclosed. Disclosed are isolated nucleic acids that encode a D. gatoi or D. cati rRNA gene sequence. Kits and arrays that contain the disclosed probes and/or primers also are disclosed.

Abstract: Methods for the rapid detection of the presence or absence of Clostridium difficile in a biological or nonbiological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes, and kits are provided that are designed for the detection of Clostridium difficile.

Abstract: This disclosure relates to methods of determining the presence and position of AGG or interruptor elements within a trinucleotide (for example, CGG) repeat region, and to methods of determining the number of repeats present in this region, by amplifying a set of products with a set of primers of which at least one comprises a portion of the CGG repeat region, and resolving the products to produce a representation of product size and abundance.

Abstract: The invention provides methods permitting the detection of small amounts of different nucleic acids in the presence of an excess amount of wild-type nucleic acids. Also provided herein are method so detecting infectious disease minority variants, methods of forensic identification, methods of diagnosing cancer and monitoring disease progress.

Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

Abstract: A method for predicting ADCC activity in a subject, the method comprising the steps of: (a) preparing a biological sample from the subject, said sample including a leukocyte, (b) bringing a portion of the biological sample and an antibody into contact with each other, (c) detecting expression of at least one marker of ADCC activity selected from the group consisting of tumor necrosis factor super family 15, chemokine CXCL3, and interleukin 6 in the leukocyte in (i) the portion of the sample brought into contact with the antibody and in (ii) another portion of the sample not brought into contact with the antibody, (d) comparing an expression level in portion (i) with the expression level in portion (ii); and (e) predicting presence of the cytotoxic activity when the expression level in portion (i) is higher than the expression level in portion (ii)

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: Provided herein are molecular assays, including oligonucleotides and other reagents, for the detection and analysis of PRAME (Preferentially Expressed Antigen in Melanoma). The assays find use, for example, as diagnostic and prognostic applications, including use in assessing therapeutic courses of action.

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 is directed to novel reductive dehalogenase genes encoding for reductive dehalogenases, which are capable of dehalogenating halogenated organic compounds and may be useful for environmental assessment and monitoring, and in the bioremediation of pollutants. In particular, the invention provides isolated polynucleotides of novel reductive dehalogenase genes dcpA and dcpB and fragments thereof as well as isolated polypeptides encoding the DcpA and DcpB proteins or fragments thereof. The invention is also directed to methods of identifying and/or quantifying dechlorinating bacterial organisms or polynucleotides encoding a reductive dehalogenase, such as the dcpA or dcpB polynucleotides or fragments thereof, in a sample.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with liver fibrosis and related pathologies. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, 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: 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: 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: Provided is a new polyomavirus, provisionally named MX polyomavirus, (MXPyV). Further provided are cDNA nucleic acid sequences, recombinant proteins, expression vectors and host cells, recombinant anti-MXPyV antibodies, vaccines, compositions, methods of detecting MXPyV, methods for assaying for anti-MXPyV compounds, and methods for treating or preventing a MXPyV infection.

Abstract: The present invention provides a method for detecting or enriching for a target deoxyribonucleic acid (DNA) present in a nucleic acid sample, said method comprising: (a) fragmenting a nucleic acid sample to generate nucleic acid fragments including a target fragment containing said target DNA and non-specifically ligating an adaptor sequence to an end of said fragments; (b) rendering said fragments at least partially single-stranded; (c) contacting the at least partially single-stranded fragments of step (b) with oligonucleotides A and B of a single target-specific nucleic acid probe; (d) ligating oligonucleotide B of said probe to the part of the single-stranded portion of said target fragment which is hybridised to oligonucleotide A of said probe to produce a probe-target fragment hybrid; and (e) detecting or enriching for said probe-target fragment hybrid.

Abstract: Disclosed herein are antisense compounds and methods for decreasing LDL-C in an individual having elevated LDL-C. Additionally disclosed are antisense compounds and methods for treating, preventing, or ameliorating hypercholesterolemia and/or atherosclerosis. Further disclosed are antisense compounds and methods for decreasing coronary heart disease risk. Such methods include administering to an individual in need of treatment an antisense compound targeted to a PCSK9 nucleic acid. The antisense compounds administered include gapmer antisense oligonucleotides.

Abstract: Methods and kits for diagnosis, prognosis and treatment of metastatic tumors are provided where the metastatic tumor is characterized by changes in expression of +++, ++ and/or 11a variants of Mena.

Abstract: Disclosed is a method for quantitative determination of CK-19 mRNA positive cells in a biological sample. The method can be used, for instance, with peripheral blood to detect cancer in a patient. In one embodiment, the method can be used to detect the cancer before initiation of adjuvant treatment, thereby providing information about therapeutic efficacy. Practice of the invention method is sensitive, reliable, and easy to perform.

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 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: 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: Hence, the invention relates to a method for diagnosis and/or prognosis of cancer, comprising the steps of analyzing in a sample of a subject the DNA methylation status of a genomic region of at least one member of the group of, (i) SFN according to SEQ ID NO. 1, (ii) SLIT2 according to SEQ ID NO. 2, (iii) SERPINB5 according to SEQ ID NO. 3; and (iv) TWIST 1 according to SEQ ID NO 4; wherein, if (i) SFN shows a methylation cut off value of above 80% and/or, (ii) SLIT2 shows a methylation cut-off value of above 45% and/or, (iii) SERPBINB5 shows a methylation cut-off value of above 70%, and/or (iv) TWIST 1 shows a methylation level below 15% the sample is categorized as a sample from a patient with cancer and/of a poor prognosis.