Abstract: This invention relates to a novel alpha-amylase, a process for its preparation and the use of the amylase. The invention relates to a newly identified polynucleotide sequence from Alicyclobacillus pohliae comprising a gene that encodes the novel alpha-amylase enzyme. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional protein of the gene. The invention also relates to methods of using these proteins in industrial processes, for example in food industry, such as the baking industry. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins and cells.

Abstract: The present invention provides novel transgenic nonhuman mammals capable of producing human sequence antibodies, as well as methods of producing and using these antibodies.

Abstract: This invention provides a method for enhancing utrophin protein production in a cell by inhibiting an utrophin microRNA molecule. Moreover, the invention provides that methods for enhancing utrophin protein production in a muscle cell are used for treating a muscular dystrophy and/or other myopathies.

Abstract: A polynucleotide device is provided that adds one or more bases to a single stranded polynucleotide. Methods of using the device are provided, comprising contacting a single stranded target molecule with an extension reaction mixture comprising (i) a device or composition of the disclosure, (ii) a polymerase, and (iii) free nucleotides, whereupon an extension reaction product is generated. Kits comprising a device of the disclosure are also provided.

Abstract: The invention provides for sequencing a nucleic acid molecule based on the detection of base incorporation by the release of pyrophosphate (PPi) using a new enzyme system comprising adenosine diphosphate (ADP)-glucose pyrophosphorylase (AGPase) and its substrate ADP-glucose.

Abstract: In certain embodiments, the invention provides methods for treating cancer, comprising: (a) obtaining a specimen of cancer tissue and normal tissue from a patient; (b) extracting total protein and RNA from the cancer tissue and normal tissue; (c) obtaining a protein expression profile of the cancer tissue and normal tissue; (d) identifying over-expressed proteins in the cancer tissue; (e) comparing the protein expression profile to a gene expression profile; (f) identifying at least one prioritized protein target by assessing connectivity of each said over-expressed protein to other cancer-related or stimulatory proteins; (g) designing a first RNA interference expression cassette to modulate the expression of at least one gene encoding the prioritized target protein; (h): designing a first RNA interference expression cassette to modulate the expression of at least one gene encoding a protein of higher priority in the signaling pathway in which the first protein is a component; (i) incorporating the first cass

Abstract: The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.

Abstract: A composition comprising an oligonucleotide having the structure 5?-Y1-L1-X-L2-Y2-3?. Y1 comprises a sequence of one or more DNA or RNA nucleotides, including a first nucleotide N1 having a 3? phosphate covalently linked to L1. Y2 comprises a sequence of one or more DNA or RNA nucleotides, including a second nucleotide N2 having a 5? phosphate covalently linked to L2. L1 and L2 each independently are a direct bond or a C1-C7 alkyl, alkynyl, alkenyl, heteroalkyl, substituted alkyl, aryl, heteroaryl, substituted aryl, cycloalkyl, alkylaryl, or alkoxyl group. X is R1 is a hydrogen or a C1-C8 alkyl. M is a label or ligand comprising a fused polycyclic aromatic moiety.

Abstract: The present invention relates to compositions and methods for the detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled compositions comprising at least two probes hybridized to each other that are capable of binding to and identifying target molecules based on the probes' label codes. Methods of making and using such compositions are also provided. The compositions can be used in diagnostic, prognostic, quality control and screening applications.

Abstract: Described herein are compositions and methods for the inhibition of miR-21 activity. The compositions have certain nucleoside modification patterns that yield potent inhibitors of miR-21 activity. The compositions may be used to inhibit miR-21, and also to treat diseases associated with abnormal expression of miR-21, such as fibrosis and cancer.

Abstract: Method of detecting methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) in a nucleic acid coamplification assay. The invention advantageously reduces the incidence of false-positive MRSA determinations in real-time assays by requiring satisfaction of a threshold criterion that excludes certain co-infections from the MRSA determination. The invention further provides for determination of MSSA, even when the MSSA is present in combination with methicillin-resistant coagulase-negative (MR-CoNS) bacteria at high or low levels.

Abstract: Sequences of ribonucleic acid interference molecules are provided. For example, in one aspect, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ_ID NO: 1 through SEQ_ID NO: 3,197 and one or more corresponding mature sequences having SEQ_ID NO: 3,198 through SEQ_ID NO: 6,565 is provided. Techniques are also provided for regulating gene expression.

Abstract: The pharmaceutical composition producing the antioxidant, antimicrobal, antitoxic protein—human lactoferrin in which the therapeutic effect is achieved as a result of the antioxidant, antimicrobal, antitoxic protein—human lactoferrin on the human body different in what it contains human adenovirus 5 genome based non-replicating nanoparticles with the human lactoferrin gene insert expressing human lactoferrin in a therapeutically effective amount in the body and containing the formulating buffer. The non-replicating nanoparticles content makes no less than 2.33×1011 virus particle (v.p.) per ml of the formulating buffer.

Abstract: Provided are novel binding molecules of human origin, particularly human antibodies as well as fragments, derivatives and variants thereof that recognize antigens such as native endogenous proteins associated with, e.g., immune response, autoimmune disorders, inflammatory diseases, metabolic disorders, vascular function, neurodegenerative diseases or tumors. More particularly, a human Auto-Immunosome and corresponding monoclonal antibody reservoir are provided. In addition, pharmaceutical compositions, kits and methods for use in diagnosis and therapy of are described.

Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties include increased resistance to photodamage, and can also include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.

Abstract: A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.

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: This invention provides for an improved generation of novel nucleic acid modifying enzymes. The improvement is the fusion of a sequence-non-specific nucleic-acid-binding domain to the enzyme in a manner that enhances the ability of the enzyme to bind and catalytically modify the nucleic acid.

Abstract: This invention provides for an improved generation of novel nucleic acid modifying enzymes. The improvement is the fusion of a sequence-non-specific nucleic-acid-binding domain to the enzyme in a manner that enhances the ability of the enzyme to bind and catalytically modify the nucleic acid.

Abstract: This invention provides a novel method for amplifying and detecting a target gene rapidly with high sensitivity under isothermal conditions. In such method, a sequence to be amplified can be freely designed regardless of the template sequence, an amplified product can be amplified and detected within a short period of time with high sensitivity, and thus, the gene expression level can be determined more easily than is possible with prior art.

Abstract: The present invention provides thermostable enzymes, such as DNA polymerases and restriction endonucleases, that are substantially free from contamination with nucleic acids. The invention also provides methods for the production of these enzymes, and kits comprising these enzymes which may be used in amplifying or sequencing nucleic acid molecules, including through use of the polymerase chain reaction (PCR).

Abstract: The present invention relates to targeted conversion of alpha-hydroxyalkylated residues in biomolecules in the presence of a directing methyltransferase, namely to targeted removal of the alpha-hydroxyalkyl moieties to give unmodified residues, or targeted derivatization of the alpha-hydroxyalkyl groups by covalent coupling of non-cofactor compounds represented by formula HQ-LX1 wherein X represents a functional group or a reporter group attached via a linker moiety L, and QH is selected from HS—, HSe—, HO—H2N—, HN3 or HCN in the presence of a directing methyltransferase. Further development of the method of targeted conversion comprises methods for targeted labeling a biomolecule and method for detecting hydroxymethylated target sites in a biomolecule according to the present invention.

Abstract: The invention relates to a method for rapid detection of a target nucleic acid amplification product while preventing cross-contamination between target nucleic acid amplification products and avoiding false positives, comprising the steps of: a) leaving the reaction tube unopened after the amplification reaction is finished, so as to prevent the target nucleic acid amplification product from leaking out and resulting in contamination; b) placing the unopened reaction tube inside an enclosed unit, making the target nucleic acid amplification product be transferred to a test strip from the reaction tube in a physically enclosed environment; c) performing detection in a visual read-out manner, and determining the result; d) discarding the enclosed unit in a safety place as a whole without opening it after the detection.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Abstract: The present disclosure provides novel beta-alanine/alpha ketoglutarate aminotransferase nucleic acid and protein sequences having increased biological activity. Also provided are cells containing such enzymes, as well as methods of their use, for example to produce malonyl semialdehyde and downstream products thereof, such as 3-hydroxypropionic acid and derivatives thereof.

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: The invention relates to a double-stranded ribonucleic acid (dsRNA) targeting a G-alpha q subunit (GNAQ) of a heterotrimeric G gene, and methods of using the dsRNA to inhibit expression of GNAQ.

Abstract: A novel soybean variety, designated XB79B13 is provided. Also provided are the seeds of soybean variety XB79B13, cells from soybean variety XB79B13, plants of soybean XB79B13, and plant parts of soybean variety XB79B13. Methods provided include producing a soybean plant by crossing soybean variety XB79B13 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB79B13, methods for producing other soybean varieties or plant parts derived from soybean variety XB79B13, and methods of characterizing soybean variety XB79B13. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB79B13 are further provided.

Abstract: Recombinant proteins for siRNA delivery and a composition including same. These recombinant proteins include a p19 RNA binding protein and a target oriented peptide and can secure the stability of siRNAs from external attacks such as various degradation enzymes, have selective binding affinity to cancer cells by virtue of target-oriented peptides having various cancer cells as their target, and silence target genes by effectively delivering the siRNAs to cells and biological tissues by the release of the siRNAs to the cytoplasms after the cell penetration thereof. Therefore, they are expected to be effectively employed as siRNA delivery vehicles for siRNA therapeutic agents, cell-based drug screening compositions and research.

Abstract: The present invention relates to a method for monitoring the progression of the bisulfite-mediated conversion of DNA during DNA methylation analysis. The method is based on the reaction of the enzyme uracil-DNA-glycosylase (UNG) with at least one labeled DNA reporter molecule, the reporter molecule comprising at least one unmethylated cytosine residue in its sequence. After bisulfite-mediated conversion of unmethylated cytosine residues in uridin residues UNG removes the uracil bases from the DNA backbone, thus making it susceptible to heat-induced hydrolytic cleavage. Finally, the labels released from the DNA reporter molecule during this fragmentation process are detected.

Abstract: The present disclosure relates to a nucleic acid assembly (NAA), comprising sensor domain and handle domain; an assembly interfaceable motif (AIM) sequence optionally along with intracellular targeting motif (ITM) sequence; and an AIM-NAA complex. It also relates to a vector comprising assembly interfaceable motif sequence optionally along with intracellular targeting motif sequence and a cell comprising the vector. Further, the instant disclosure also provides a method to obtain the nucleic acid assembly, method of intracellular targeting and kit thereof.

Abstract: The present invention relates generally to the fields of genomics, synthetic biology and genetic engineering. More particularly, the present invention concerns the methods that enable parallel multiplex ligation and amplification on surface for making assemblies of nucleic acids of various biological applications and for analysis of biological samples such as DNA, RNA, and proteins.

Abstract: An object is to provide a novel enzyme that exhibits glucose dehydrogenase activity. Furthermore, another object is to provide a novel method pertaining to enzyme modification.

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 a bacterial cell of the genus Pasteurella comprising a heterologous polypeptide having formate dehydrogenase activity. The present invention also relates to a method of manufacturing succinic acid and the use of the bacterial cell for the manufacture of succinic acid.

Abstract: A novel soybean variety, designated XB86G13 is provided. Also provided are the seeds of soybean variety XB86G13, cells from soybean variety XB86G13, plants of soybean XB86G13, and plant parts of soybean variety XB86G13. Methods provided include producing a soybean plant by crossing soybean variety XB86G13 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB86G13, methods for producing other soybean varieties or plant parts derived from soybean variety XB86G13, and methods of characterizing soybean variety XB86G13. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB86G13 are further provided.

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: 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: 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 present invention is concerned with bacteria for the production of succinic acid. Specifically, the invention relates to a bacterial cell of the genus Pasteurella comprising a heterologous polypeptide having isocitrate lyase activity and a heterologous polypeptide having malate synthase activity. Further, the present invention contemplates a polynucleotide comprising a nucleic acid encoding a polypeptide having isocitrate lyase activity and a nucleic acid encoding a polypeptide having malate synthase activity. Finally, the present invention relates to the use of a bacterial cell of the invention for the manufacture of succinic acid.

Abstract: It is an object of the present invention to provide a method of evaluating whether or not a subject has a predisposition to obesity or an obesity-related condition or disease, a kit for conducting the method, an anti-obesity drug having an effect of preventing or treating obesity or an obesity-related condition or disease, a method of screening the anti-obesity drug, a non-human animal having a deficiency in the gene associated with obesity, and an adipose tissue or adipocyte of the animal. The method of evaluating a predisposition to obesity of the present invention is a method of evaluating whether or not a subject has a predisposition to obesity or an obesity-related condition or disease. The method includes the step of detecting a copy number variation (CNV) in intron 1 of SLC25A24 gene or a gene polymorphism having a linkage disequilibrium relationship with the CNV in a sample containing a human gene of the subject.

Abstract: This invention concerns self-avoiding molecular recognition systems (SAMRS), compositions that bind to natural DNA and RNA, but do not bind to compositions at sites that incorporate other SAMRS components, and processes dependent on them. Their utility is shown by discoveries that DNA polymerases accept these compositions as primers and templates, where standard triphosphates are added to primers containing SAMRS components, and added opposite to SAMRS components in the template. A critical mass of data are provided in 16 examples to provide first-generation heuristic rules to permit design of SAMRS sequences can be used as primers and templates that are accepted by DNA polymerases. The presently preferred primers are at least 12 nucleotide units in length, and more preferably between 15 and 30 nucleotides in length. Also preferred are chimeric primers that have standard nucleotides in their 5?-segments, and SAMRS nucleotides in their 3?-segments, and in multiplexed priming.

Abstract: An object of the present invention is to provide an RNAi control system using an RNA-protein interaction motif. The present invention provides an shRNA comprising: a guide strand having a sequence complementary to a target sequence; a passenger strand which forms a duplex with the guide strand; and a linker strand which links the guide strand and the passenger strand, wherein the linker strand comprises an RNP-derived protein-binding motif sequence. The present invention also provides an RNAi control system comprising: the shRNA; and an RNP-derived protein which specifically binds to a protein-binding motif sequence in the shRNA.

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: The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: Amplification-based methods and kits for rapidly producing siRNA expression cassettes are provided. Also provided are methods for expressing amplified siRNA expression cassettes in cells.

Abstract: An object of the present invention relates to distinguishing, from a fluorophore of an unreacted substrate, a single fluorophore attached to a nucleotide that is incorporated into a probe by a nucleic acid synthesis. The present invention relates to a nucleic acid analyzing device that analyzes a nucleic acid in sample by fluorescence, wherein a localized surface plasmon is generated by illumination, and a probe for analyzing the nucleic acid in the sample is on the site where the surface plasmon is generated. According to the present invention, since it is possible to efficiently produce fluorescence intensifying effects due to the surface plasmon and to immobilize the probe to a region within the reach of the fluorescence intensifying effects, it becomes possible to measure a nucleic acid synthesis without removing unreacted nucleotide to which fluorophores are attached.

Abstract: Recombinant lentiviral vectors containing at least: a lentiviral backbone comprising essential lentiviral sequences for integration into a target cell genome; a nucleic acid encoding a CCR5 RNAi; and an expression control element that regulates expression of the nucleic acid encoding the CCR5 RNAi element, are provided by this invention. In an alternative aspect, the vector also contains polynucleotides encoding TRIM5 alpha and HIV TAR decoy sequences along with gene expression regulation elements such as promoters operatively linked to the polynucleotides. The vectors are combined with packaging plasmid and envelope plasmids and optionally conjugated to cell-specific targeting antibodies. Diagnostic and therapeutic methods for using the compositions are further provided herein.

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 invention discloses a method for production of polyhydroxybutyrate-co-polyhydroxyvalerate (PHBV) by recombinant Escherichia coli harboring plasmid containing both phaCAB and prpE. Different percentage of hydroxyvalerate can be obtained from the recombinant E. coli when cultivated in the medium containing different concentrations of propionic acid. In this patent, we provide a method that integrated all of the genes (i.e. phaCAB, vgb and prpE) required for PHBV production into a single plasmid. The plasmids were then transformed into an E. coli host. Results showed that PHBV can be produced by this recombinant E. coli, and the ration of HV to HB in the co-polymers can be regulated by addition of different concentrations of propionic acid in the medium. The percentage of HV in the co-polymers can be adjusted from about 3% up to more than 35%.