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

Abstract: A method of mRNA production for use in transfection is provided, that involves in vitro transcription of PCR generated templates. This RNA can efficiently transfect different kinds of cells. This approach results in increased efficiency (fidelity and productivity) of mRNA synthesis and is less time consuming because it does not require cloning, and also consequently eliminates the unwanted errors and effects related to RNA made on DNA templates obtained with cloning techniques. The results of transfection of RNAs demonstrate that RNA transfection can be very effective in cells that are exceedingly difficult to transfect efficiently with DNA constructs. The method can be used to deliver genes into cells not- or only poorly transfectable for DNA, in vitro and in vivo.

Abstract: The invention relates to siRNA compounds comprising one non-nucleotide moiety covalently attached to at least one of the sense or antisense strands to down-regulate the expression of human genes. The invention also relates to pharmaceutical compositions comprising such compounds and a pharmaceutically acceptable carrier and to methods of treating and/or preventing the incidence or severity of various diseases or conditions associated with the target genes and/or symptoms associated with such diseases or conditions.

Abstract: The present invention provides a method that combines the construction of double-stranded target amplification products with one or two single-stranded overhangs with improved production of such target amplification products. The single-stranded overhang(s) can be used for post-amplification capture and subsequent detection/manipulation. The single-stranded overhang(s) enable capture/detection/manipulation without interference from the complementary strand in the double-stranded target amplification product.

Abstract: A method for the manufacture of products by biotechnological methods in bacterial cell culture is disclosed as well as products obtained, the use of certain additives to the media used in the manufacture of said products in bacterial cell culture media, and the use of said additives in reducing the detrimental effects of radicals in the manufacture of the products, as well as aspects related to these invention embodiments. The manufacturing process or method comprises adding one or more radical scavenging and/or antioxidative additive preferably selected from the group consisting of sterically hindered nitroxyls, sterically hindered hydroxylamines, sterically hindered hydroxylamine salt compounds, sterically hindered amino compounds and sterically hindered N-hydrocarbyloxyamines, benzofuranone compounds, as obligatory component(s) to the medium used during biosynthesis.

Abstract: The present disclosure provides nucleic acids encoding an RNA recognition sequence positioned proximal to an insertion site for the insertion of a sequence of interest; and host cells genetically modified with the nucleic acids. The present disclosure also provides methods of modifying the activity of a target RNA, and kits and compositions for carrying out the methods.

Abstract: Methods of treating a wound in a subject are provided comprising administering to the subject an amount of an inhibitor of Fidgetin-like 2. Compositions and pharmaceutical compositions comprising an amount of an inhibitor of Fidgetin-like 2 are also provided. Methods are also provided for identifying an inhibitor of Fidgetin-like 2.

Abstract: The present invention relates to a novel N-acetylglucosamine-2-epimerase and a method for preparing CMP-N-acetylneuraminic acid, more specifically, relates to a N-acetylglucosamine-2-epimerase derived from Bacteroides fragilis NCTC 9343, and a method for preparing CMP-N-acetylneuraminic acid using said N-acetylglucosamine-2-epimerase. According to the present invention, CMP-N-acetylneuraminic acid can be produced economically in a large amount through a one-step reaction using cytidine monophosphate and N-acetyl-D-glucosamine which are inexpensive substrates.

Abstract: Provided is a nucleic acid substrate which has nucleic acid substrate characteristics equivalent to those of dATP, has a low substrate specificity for luciferase, exerts no negative effect on enzymatic reactions such as a complementary-strand synthesis, and therefore is particularly suitable for the pyrosequencing method. As a nucleic acid substrate complementary to nucleotide T, a 7-substituted deoxyribonucleotide triphosphate whose 7-position of a purine group is modified by a substituent is used as a substitute for a nucleotide ?-thiotriphosphate analog.

Abstract: A cyanobacterial host cell, Cyanobacterium sp., that harbors at least one recombinant gene for the production of a chemical compounds is provided, as well as vectors derived from an endogenous plasmid isolated from the cell.

Abstract: Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types, through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.

Abstract: Oligonucleotide chemistry is central to the advancement of core technologies such as DNA sequencing, forensic and genetic analysis and has impacted greatly on the discipline of molecular biology. Oligonucleotides and their analogues are essential tools in these areas. They are often produced by automated solid-phase phosphoramidite synthesis but it is difficult to synthesize long DNA and RNA sequences by this method. Methods are proposed for ligating oligonucleotides together, in particular the use of an azide-alkyne coupling reaction to ligate the backbones of oligonucleotides together to form longer oligonucleotides that can be synthesized using current phosphoramidite synthesis methods.

Abstract: Novel simian adenovirus 41 and two isolates thereof are described. Various uses of these isolates, including construction of a recombinant vector which comprises simian adenovirus 41 sequences and a heterologous gene under the control of regulatory sequences are provided. A cell line which expresses simian adenovirus 41 gene(s) is also disclosed. Methods of using the vectors and cell lines are provided.

Abstract: The invention provides methods of cultivating oil-bearing microbes using xylose as a fixed carbon source. Also provided are microorganisms that have been genetically engineered to metabolize xylose as a fixed carbon source allowing them to convert xylose into oils. Particular advantages of the processes provided herein include production of oils rather than alcohols through the microbial fermentation processes utilizing xylose.

Abstract: The present invention relates to kits and methods for efficiently generating 5? capped RNA having a modified cap nucleotide and for use of such modified-nucleotide-capped RNA molecules. In particular, the present invention provides kits and methods for capping RNA using a modified cap nucleotide and a capping enzyme system, such as poxvirus capping enzyme. The present invention finds use for in vitro production of 5?-capped RNA having a modified cap nucleotide and for in vitro or in vivo production of polypeptides by in vitro or in vivo translation of such modified-nucleotide-capped RNA. The invention also provides methods and kits for capturing or isolating uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate, and methods and kits for using a capping enzyme system and modified cap nucleotides for labeling uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate with detectable dye or enzyme moieties.

Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: A method of treating a disease associated with a cell population which proliferates abnormally in a subject is disclosed. The method comprises administering to the subject a therapeutically effective amount of at least one modulator capable of modulating in the cell population a level and/or activity of a polypeptide having an amino acid sequence at least 60 percent similar to SEQ ID NO: 5, as determined using the Standard protein-protein BLAST [blastp] software of the NCBI.

Abstract: Agents that reduce the amount of IGFBP-2 and/or IGFBP-5 and that are known to be useful in the treatment of cancer result in increased expression of the protein clusterin. Since clusterin can provide protection against apoptosis, this secondary effect detracts from the efficacy of the therapeutic agent. In overcoming this, the present invention provides a combination of therapeutic agents that is useful in the treatment of cancer. The combination includes an agent that reduces the amount of IGFBP-2 and/or IGFBP-5 and that stimulates expression of clusterin as a secondary effect, and an oligonucleotide that is effective to reduce the amount of clusterin in cancer cells. In some embodiments of the invention, the agent that reduces IGFBP-2 and/or IGFBP-5 is a bispecific antisense species. The oligonucleotide may be an antisense oligonucleotide or an RNAi oligonucleotide.

Abstract: The present invention provides compositions and methods for reducing steric hindrance in the product of nucleic acid polymerase reaction. Methods and compositions of the invention encompass application of exonucleases, endonucleases, and uracil-DNA glycosylases to a nucleic acid polymerase reaction such that newly formed nucleic acid strands are modified (e.g., cleaved) while the polymerase reaction continues to proceed.

Abstract: The present invention provides an Influenza A H1N1 subtype-specific aptamer. The aptamer was selected in vitro using SELEX and a microfluidic chip system. The aptamer is stable, establishing sensitivity about 100 times higher than antibody and high specificity to Influenza A H1N1 subtype. Thus, the aptamer can be effective in detection of H1N1 influenza virus.

Abstract: Recombinant vectors comprise simian adenovirus A1321 (SAdV-A1321), SAdV-A1325, SAdV-A1295, SAdV-A1309, SAdV-A1316, and/or SAdV-A1322 sequences and a heterologous gene under the control of regulatory sequences. A cell line which expresses simian adenovirus SAdV-A1321, SAdV-A1325, SAdV-A1295, SAdV-A1309, SAdV-A1316, and/or SAdV-A1322 gene(s) is also disclosed. Methods of using the vectors and cell lines are provided.

Abstract: The present disclosure provides methods of identifying subjects having an increased likelihood of developing one or more adverse side effects resulting from administration of a microtubule-stabilizing agent. In particular examples, the method includes determining whether the subject has an ABCB1 predictive polymorphism for microtubule-stabilizing agent-induced toxicity, wherein the presence of such a polymorphism indicates that the subject has an increased risk of developing microtubule-stabilizing agent induced adverse effects. Examples of ABCB1 predictive polymorphisms include 2677G>T/A and 3435C>T. Also provided are methods of modifying microtubule-stabilizing agent therapy in a subject identified as having one or more ABCB1 predictive polymorphisms. Kits and isolated nucleic acid molecules that can be used in the disclosed methods are also provided.

Abstract: Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for allelic imbalance, imprinting and imprinting errors.

Abstract: The present disclosure provides nucleic acid probes, as well as kits that include such probes. Methods for producing and using (for example in chromosomal in situ hybridization) the probes are also provided. Such probes in some examples are used to detect chromosomal abnormalities or the presence of a pathogen.

Abstract: Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms.

Abstract: A method of producing lycopene, with high productivity by means of a recombinant bacterial strain includes preparing the recombinant vector containing genes encoding proteins, which are required for lycopene biosynthesis. The genes involved in lycopene biosynthesis are crtE with the nucleotide SEQ ID NO: 8, crtB with the nucleotide SEQ ID NO: 3 and crtI with the nucleotide SEQ ID NO: 5 of the Sequence List. The said recombinant vector is transformed into Escherichia coli (hereafter E. coli). The E. coli transformant is cultured to recover lycopene from the culture medium.

Abstract: Disclosed are: a eukaryotic amadoriase which is prepared by introducing a mutation into DNA encoding a eukaryotic amadoriase derived from a microorganism belonging to the genus Coniochaeta or Eupenicillium so as to introduce a substitution into a specific amino acid residue in the eukaryotic amadoriase, thereby overcoming the defect associated with thermal stability; a gene or recombinant DNA for the eukaryotic amadoriase; and a process for production of a eukaryotic amadoriase having excellent thermal stability.

Abstract: The present invention relates to variants of a parent cellobiohydrolase. The present invention also relates to polynucleotides encoding the cellobiohydrolase variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the cellobiohydrolase variants.

Abstract: The present invention is in the field of nucleic acid amplification, and in particular in transcription-based amplification, providing improvements thereof. Specifically, the present invention provides primers, and methods for using them, that improve transcription-based amplification reactions, in particular multiplex reactions.

Abstract: A novel soybean variety, designated 95Y21 is provided. Also provided are the seeds of soybean variety 95Y21, cells from soybean variety 95Y21, plants of soybean 95Y21, and plant parts of soybean variety 95Y21. Methods provided include producing a soybean plant by crossing soybean variety 95Y21 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety 95Y21, methods for producing other soybean varieties or plant parts derived from soybean variety 95Y21, and methods of characterizing soybean variety 95Y21. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety 95Y21 are further provided.

Abstract: Provided are isolated genomic polynucleotide fragments that encode human SNARE YKT6, human glucokinase, human adipocyte enhancer binding protein (AEBP1) and DNA directed 50 kD regulatory subunit (POLD2), vectors and hosts containing these fragments and fragments hybridizing to noncoding regions as well as antisense oligonucleotides to these fragments. The invention is further directed to methods of using these fragments to obtain SNARE YKT6, human glucokinase, AEBP1 protein and POLD2 and to diagnose, treat, prevent and/or ameliorate a pathological disorder.

Abstract: A novel soybean variety, designated XB78B13 is provided. Also provided are the seeds of soybean variety XB78B13, cells from soybean variety XB78B13, plants of soybean XB78B13, and plant parts of soybean variety XB78B13. Methods provided include producing a soybean plant by crossing soybean variety XB78B13 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB78B13, methods for producing other soybean varieties or plant parts derived from soybean variety XB78B13, and methods of characterizing soybean variety XB78B13. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB78B13 are further provided.

Abstract: A novel soybean variety, designated XB85F13 is provided. Also provided are the seeds of soybean variety XB85F13, cells from soybean variety XB85F13, plants of soybean XB85F13, and plant parts of soybean variety XB85F13. Methods provided include producing a soybean plant by crossing soybean variety XB85F13 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB85F13, methods for producing other soybean varieties or plant parts derived from soybean variety XB85F13, and methods of characterizing soybean variety XB85F13. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB85F13 are further provided.

Abstract: The invention relates to a recombinant DNA molecule encoding a polypeptide having phytase activity and increased temperature stability and increased proteolytic stability of the enzyme activity. The DNA sequence has been obtained by variation of the mature wild-type E. coli phytase sequence with defined amino acid positions being modified in comparison to the wild-type sequence or with the sequences having N- and/or C-terminal extensions, respectively. The invention further relates to a method for expressing the recombinant phytase as well as its use in the food and animal feed technologies.

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

Abstract: Gene expression can be selectively modulated by contacting a cell with an oligomer that targets a gene region downstream of a ?3-UTR, thereby increasing or decreasing the expression of the target gene.

Abstract: A two-stranded intermediary complex and cooperative hybridization method are provided. The complex has been designed so that target oligonucleotides of independent sequence can cooperatively and simultaneously hybridize to it. The cooperative hybridization mechanism is robust and modular, smoothly integrating with other dynamic DNA components to form cascaded reaction networks that can perform a variety of functions.

Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.

Abstract: The invention provides methods for treating asthma by using multiple rounds of administration of ISS over a period of time to confer long term disease modification.

Abstract: The invention encompasses a lentiviral packaging vector comprising a non-subtype B gag-pol sequence, particularly a subtype D gag-pol sequence. The invention further encompasses methods for making and using these vectors. The invention further encompasses lentiviral vector particles comprising HIV-1 non-subtype B Gag and/or Pol proteins.

Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template. Because the nucleotide analogs have an unmodified 3? OH, i.e., as found in “natural” deoxyribose and ribose molecules, the analogs result in natural polynucleotides suitable for incorporation into biological systems.

Abstract: The present disclosure relates to new polymethine compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

Abstract: The invention provides nucleoside and nucleotide molecules containing cleavable linkers linking a label such as a dye. The invention also provides nucleosides and nucleotide molecules containing a blocking group, either removable or non-removable. The invention additionally provides methods of using the nucleoside and nucleotide molecules containing a cleavable linker and/or a blocking group.

Abstract: The present invention relates to certain novel shRNA molecules and methods of use thereof. According to certain embodiments of the present invention, methods for reducing the expression level of a target gene are provided. Such methods generally comprise providing a cell with one or more precursor nucleic acid sequences that encode two or more RNA molecules. A first RNA molecule comprises a double stranded sequence, which includes a guide strand sequence that is complementary to a portion of an mRNA transcript encoded by the target gene. In addition, a second RNA molecule comprises a second double stranded sequence, which includes a second guide strand sequence that is partially complementary to a portion of the mRNA transcript encoded by the target gene. Preferably, the second guide strand sequence comprises one or more bases that are mismatched with a nucleic acid sequence of the mRNA transcript encoded by the target gene.

Abstract: This invention relates to the use of tumor-derived or associated extracellular ribonucleic acid (RNA) found circulating in blood plasma or serum fraction for the detection, monitoring, or evaluation of cancer or premalignant conditions. Specifically, this invention enables the extraction of circulating RNA from plasma or serum and utilizes nucleic acid amplification assays for the identification, detection, inference, monitoring, or evaluation of any neoplasm, benign, premalignant, or malignant, in humans or other animals, which might be associated with that RNA. Further, this invention allows the qualitative or quantitative detection of tumor-derived or associated extracellular RNA circulating in the plasma or serum of humans or animals with or without any prior knowledge of the presence of cancer or premalignant tissue.

Abstract: An automated nucleic acid analysis method and analytical system are described comprising separate modules, wherein the air flow of any one of said modules is controlled and wherein at least the air flow between the module for isolation and purification of the analyte and the module for analysis of the analyte are separated.

Abstract: The present invention relates to a method for identifying a target nucleotide sequence. This method involves forming a ligation product on a target nucleotide sequence in a ligation detection reaction mixture, amplifying the ligation product to form an amplified ligation product in a polymerase chain reaction (PCR) mixture, detecting the amplified ligation product, and identifying the target nucleotide sequence. Such coupling of the ligase detection reaction and the polymerase chain reaction permits multiplex detection of nucleic acid sequence difference.

Abstract: The invention relates to compositions comprising double-stranded oligonucleotides of identical or different sequences and/or length, said oligonucleotides having sequences 3?N1N2 . . . Ni-1Ni . . . Nj5? wherein—3?Ni . . . Nj5? is half of a double-stranded 19-28mer oligonucleotide of sequence complementary to a target nucleic acid sequence present in a living cell, and—3?N1 . . . Ni-15? is a 3-50mer overhang of sequence allowing oligomerization of said double-stranded oligonucleotide. Compositions of transfection comprising said oligonucleotide compositions and there used for therapeutical application.

Abstract: The subject invention concerns a method of inhibiting an RNA virus infection within a patient by increasing the amount of 2-5 oligoadenylate synthetase (2-5 AS) activity within the patient. Preferably, the preventative and therapeutic methods of the present invention involve administering a nucleotide encoding 2-5 AS, or at least one catalytically active fragment thereof, such as the p40, p69, p100 subunits, to a patient in need thereof. The present inventors have determined that overexpression of 2-5AS causes a reduction in epithelial cell damage, reduction in infiltration of mononuclear cells in the peribronchiolar and perivascular regions, and reduction in thickening of the septa in the lungs. Levels of chemokines, such as MIP1-?, are also reduced upon overexpression of 2-5AS. The subject invention also pertains to pharmaceutical compositions containing a nucleotide sequence encoding 2-5 AS and a pharmaceutically acceptable carrier, as well as vectors for delivery of the 2-5 AS nucleotide sequence.

Abstract: The present invention features methods for decreasing the size and density of amyloid plaques, decreasing cognitive decline associated with amyloid pathology, and treating Alzheimer's disease by selectively inhibiting the activity of Acyl-CoA:Cholesterol Acyltransferase 1, but not Acyl-CoA:Cholesterol Acyltransferase 2.