Abstract: The present invention provides a therapeutic or improving agent for a lifestyle-related disease, containing an expression vector encoding a chimeric Hepatitis B virus core antigen polypeptide inserted with an amino acid sequence containing a specific epitope of the lifestyle-related disease-related factor, wherein the amino acid sequence containing the specific epitope is inserted between the amino acid residues 80 and 81 of the hepatitis B virus core antigen polypeptide.

Abstract: Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest.

Abstract: Polynucleotides and polypeptides which participate in influenza virus infection of cells and nucleic acid molecules, which include a polynucleotide sequence capable of specifically binding the polypeptides of the present invention. Also provided are methods of using such nucleic acid molecules, polynucleotides and antibodies directed thereagainst for diagnosing, treating and preventing influenza virus infection.

Abstract: The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g.

Abstract: Provided is a method for selectively obtaining, for a given target gene, a “joined DNA fragment” wherein just a target gene fragment is joined with desired other DNA fragments, regardless of whether a DNA fragment containing a target gene sequence has been purified. In the provided method, a double-stranded joining DNA fragment containing a sequence A and/or a sequence B is selectively joined to the ends of a target gene fragment. A mixture of a double-stranded gene fragment, the 3? end of which is protruding, and the double-stranded joining DNA fragment, which are related in a prescribed manner, undergoes at least two cycles of thermal denaturation, reassociation, and DNA synthesis, resulting in a “joined DNA fragment,” which is a double-stranded DNA fragment including at least one instance of a sequence resulting from joining sequence A, the target gene sequence, and sequence B. A “single-side joined DNA fragment” can also be obtained, by a similar method.

Abstract: There is disclosed a photocleavable sense-antisense nucleobase polymer complex capable of modulating gene expression comprising an unnatural antisense nucleobase polymer that targets an mRNA, and a photocleavable sense nucleobase polymer noncovalently bound to the antisense nucleobase polymer, wherein the photocleavable sense nucleobase polymer comprises a plurality of nucleobase polymers connected by a photocleavable linkage. There is also disclosed a method for controlling the time and spatial position of gene expression comprising selecting a target mRNA, introducing the photocleavable sense-antisense nucleobase polymer complex into a cell, and selectively irradiating the cell with light.

Abstract: Compositions and methods related to transgenic glyphosate tolerant Brassica plants are provided. Specifically, the present invention provides Brassica plants having a DP-073496-4 event which imparts tolerance to glyphosate. The Brassica plant harboring the DP-073496-4 event at the recited chromosomal location comprises genomic/transgene junctions within SEQ ID NO: 2 or with genomic/transgene junctions as set forth in SEQ ID NO: 12 and/or 13. The characterization of the genomic insertion site of the 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 event are provided.

Abstract: Provided is an improved design of shRNA based on structural mimics of miR-451 precursors. These miR-451 shRNA mimics are channeled through a novel small RNA biogenesis pathway, require AGO2 catalysis and are processed by Drosha but are independent of DICER processing. This miRNA pathway feeds active elements only into Ago2 because of its unique catalytic activity. These data demonstrate that this newly identified small RNA biogenesis pathway can be exploited in vivo to produce active molecules.

Abstract: The present invention relates to the construction and utilization of a new mammalian expression vector that contains a unique multiple cloning site (MCS), designated pUHAB. The pUHAB vector comprises a high copy replication origin (ColE1), a drug resistance gene (TK-Hygromycin), and a human cytomegalovirus promoter operably associated with a unique intron (hCMV/intron). Further, pUHAB comprises a selectable marker conferring resistance to kanamycin in bacterial cells, and a phage f1(+) region. pUHAB can be used to transiently or stably express cloned genes when transfected into mammalian cells. The invention also encompasses kits and host cells and cell lines comprising pUHAB, and methods of producing a recombinant protein using pUHAB.

Abstract: Provided herein is a method of preparing an RNA sample comprising: a) obtaining an RNA sample comprising: i. long RNA molecules that may be unfragmented or fragmented to contain 5?-OH group and a 2?-3?-cyclic phosphate group; and ii. short RNA molecules that comprise a 5? phosphate group and a 3? OH group; and b) contacting the RNA sample with an adaptor comprising either a 2?-PO group and 3?-OH group or a 2?,3?-cyclic phosphate group in the presence of a eukaryotic tRNA ligase, thereby producing a ligated RNA sample in which a) the short RNA molecules are selectively ligated to the adaptor or b) the short RNA molecules and long RNA fragments are selectively ligated to the adaptor.

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: Methods and compositions using populations of randomized modified FRT recombination sites to identify, isolate and/or characterize modified FRT recombination sites are provided. The recombinogenic modified FRT recombination sites can be employed in a variety of methods for targeted recombination of polynucleotides of interest, including methods to recombine polynucleotides, assess promoter activity, directly select transformed organisms, minimize or eliminate expression resulting from random integration into the genome of an organism, such as a plant, remove polynucleotides of interest, combine multiple transfer cassettes, invert or excise a polynucleotide, and identify and/or characterize transcriptional regulating regions are also provided.

Abstract: The present invention relates to plasmid curing, and particularly to efficient and stress-free methods for displacing resident or endogenous plasmids from a host cell, such as a bacterium. The invention extends to method of displacing a plasmid comprising a post-segregational killing system from a host cell, the method comprising introducing a recombinant nucleic acid molecule into a host cell harboring a plasmid comprising a post-segregational killing (PSK) system, characterized in that the recombinant nucleic acid molecule is adapted to neutralize the toxic effects of the plasmid's post-segregational killing system, and wherein the nucleic acid molecule is also adapted to outcompete or inhibit replication of the plasmid. The invention further extends to recombinant nucleic acid molecules that can be used in this method, as well as further uses of the methods and nucleic acid molecules of the invention.

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 present invention provides a method for producing a circular DNA molecule having a specific structure that enables to distinguish circular DNA formed from a single DNA molecule (single-molecule circular DNA), from circular DNA formed from multiple DNA molecules (multiple-molecule circular DNA) and also from single-molecule circular DNA derived from the circular DNA formed from multiple DNA molecules. According to the present invention, only single-molecule circular DNA that is not derived from multiple-molecule circular DNA can be selected in the production of circular DNA.

Abstract: Lentiviral vectors modified at the 5? LTR or both the 5? and 3? LTR's are useful in the production of recombinant lentivirus vectors. Such vectors can be produced in the absence of a functional tat gene. Multiple transformation of the host cell with the vector carrying the transgene enhances virus production.

Abstract: Compositions and methods of treatments of cells are provided for altering the phenotype of a cell by administering an oligonucleotide complex to the cell, the complex having two strands and chemical modifications.

Abstract: The present invention relates to polynucleotides comprising a first nucleic acid sequence for a chromatin element, which is capable of enhancing expression, and at least one second nucleic acid sequence comprising a curved origin motif. Furthermore, the invention relates to a host cell, a non-human transgenic organism, a vector and a kit comprising the aforementioned polynucleotide. Moreover, the invention relates to methods for expressing a polynucleotide of interest.

Abstract: The present invention is related to a nucleic acid capable of binding to hepcidin.

Abstract: This invention relates to synthetic adeno-associated virus (AAV) inverted terminal repeats (ITRs) that exhibit altered activities compared to a naturally occurring AAV ITR and methods of using the same for delivery of nucleic acids to a cell or a subject. The synthetic ITRs provide a larger packaging capacity and the ability to manipulate activities such as transduction efficiency, cellular response to transduction, and transcription.

Abstract: Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

Abstract: Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids.

Abstract: We describe methods and DNA constructs/engineered mammalian promoters to enhance native promoter activity while retaining inherent regulation by inserting multi-copy response elements (REs) into non-adjacent locations. Multiple copies of REs are clustered in a group forming a transcription factor response element segment. The segment is at least duplicated in tandem upstream of the ATG start codon. Spacers of 0.2-0.7 kilo base pairs are introduced between the two segments and smaller spacers of about between 9-15 bp are introduced between the copies of REs within a segment.

Abstract: Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding multizymes (i.e., single polypeptides having at least two independent and separable enzymatic activities) along with a method of making long-chain polyunsaturated fatty acids (PUFAs) using these multizymes in plants and oleaginous yeast are disclosed.

Abstract: Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

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: The present invention is concerned with nuclease fusion proteins and various uses thereof. Specifically, it relates to a polynucleotide encoding a polypeptide comprising (i) a first module comprising at least a first DNA binding domain derived from a homing endonuclease, (ii) a linker, and (iii) a second module comprising at least a second DNA binding domain and a cleavage domain derived from a restriction endonuclease, wherein said polypeptide functionally interacts only with DNA comprising a DNA recognition site for the first DNA binding domain and a DNA recognition site for the second DNA binding domain, and wherein said cleavage domain cleaves DNA within a specific DNA cleavage site upon binding of the polypeptide. Further contemplated are a vector and a non-human transgenic organism comprising said polynucleotide as well as a polypeptide encoded by the polynucleotide of the invention.

Abstract: Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

Abstract: The identification of differentially expressed microRNAs in patients with Sjögren's syndrome is disclosed herein. Provided is a method of diagnosing a subject as having Sjögren's syndrome by measuring the level of at least one differentially expressed miR gene product identified herein. An alteration in the level of the at least one miR gene product in the biological sample of the subject relative to a control indicates the subject has Sjögren's syndrome. Also provided is a method of treating a patient with Sjögren's syndrome by administering to the patient a therapeutically effective amount of an agent that inhibits expression of a miR gene product that is up-regulated in the patient with Sjögren's syndrome relative to a control, or by administering to the patient a therapeutically effective amount of an isolated miR gene product that is down-regulated in the patient with Sjögren's syndrome relative to a control. A method of restoring salivary flow in a patient with Sjögren's syndrome is also provided.

Abstract: The present invention pertains to a supramolecular structure based on i-motif tetramers of Cm—X—Cn oligonucleotides, wherein m and n are integers comprised between 2 and 9, and X is a linker such as A, T, G, a modified deoxynucleotide or a diol spacer. These supramolecular structures can be dissociated, when necessary, by a mere pH change. The present invention also relates to methods for obtaining such a supramolecular structure.

Abstract: Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer.

Abstract: The present invention relates to microorganisms that express, or have attached to their surface, a TNF? binding polypeptide. Peptides expressed or attached on the surface of microorganism are more resistant to chemical and enzymatic degradation in the gastrointestinal tract. Such microorganisms are capable of binding TNF? and therefore reducing the content of free TNF? and alleviating its pro-inflammatory effects in the gut. The invention also relates to the use of such microorganisms as medicament in the treatment of inflammatory bowel disease.

Abstract: A method for detecting a target nucleic acid of a pathogen in a test sample, the method comprising preparing a target nucleic acid detecting reagent and contacting the target nucleic acid detecting reagent with an oligonucleotide microarray. A kit for detecting a target nucleic acid of a pathogen in a test sample is also described. The kit comprises at least one primer pair and an oligonucleotide microarray comprising at least one probe.

Abstract: The present teachings are generally directed to methods for normalizing at least one species of small nucleic acid that is present in a population of small nucleic acid species, wherein the relative concentration of at least one small nucleic acid species is substantially greater than the relative concentration of at least one other small nucleic acid species in the population. At least one small nucleic acid species is normalized using a multiplicity of primers comprising degenerate sequences. In some embodiments, a small nucleic acid species is identified by inserting at least part of an extension product from a normalized population into a vector and subsequently sequencing the insert. In some embodiments, a small nucleic acid species is identified by determining the sequence of at least part of an extension product.

Abstract: Disclosed herein is the identification of human DNA polymerase ? (pol ?) as the polymerase that mediates repair of DNA containing interstrand cros slinks (ICLs). The mechanism of action of a number of chemotherapeutic and antimicrobial agents is the induction of ICLs. Thus, provided herein is a method of enhancing the efficacy of a chemotherapeutic or antimicrobial agent in a subject, including selecting a subject in need of treatment with an ICL -inducing agent and administering to the subject an ICL-inducing agent and a therapeutically effective amount of an inhibitor of pol ?. Also provided is a composition for treating a hyperproliferative disease, an autoimmune disease or an infectious disease, comprising an ICL-inducing agent and an amount of an inhibitor of pol ? sufficient to enhance the efficacy of the ICL-inducing agent. Further provided is a method of identifying a DNA polymerase inhibitor.

Abstract: The present teachings provide methods, compositions, and kits for quantifying target polynucleotides. In some embodiments, a reverse stem-loop ligation probe is ligated to the 3? end of a target polynucleotide, using a ligase that can ligate the 3? end of RNA to the 5? end of DNA using a DNA template, such as T4 DNA ligase. Following digestion to form an elongated target polynucleotide with a liberated end, a reverse transcription reaction can be performed, followed by a PCR. In some embodiments, the methods of the present teachings can discriminate between polymorphic polynucleotides that vary by as little as one nucleotide.

Abstract: The invention provides a series of reagent compositions and methods for making and amplifying novel cDNA based probe sets from RNA samples to improve analysis with gene expression arrays. The methods globally produce probe sets with common universal linkers at one or both ends, called WRAP-Probes, wherein the linkers do not bind to the target sequences and they can efficiently bind added reporters to the probes. The universal linkers are also designed as primer binding sites for copying and amplifying the probes, either linearly with one linker, or exponentially with double linkers. The capacity to globally and exponentially amplify the probe set by PCR is a primary advantage. Adding reporters by terminal linkers also improves quantification since each probe gets equivalent signaling. The invention allows expression analysis of small research, clinical and forensic samples to enable improved diagnostics, drug discovery, therapeutic monitoring, and medical, agricultural and general research.

Abstract: The present invention belongs to the field of functional proteomics and more particularly to the field of protein aggregation. The invention discloses a method for interfering with the function of a target protein and uses a non-naturally, user-designed molecule, designated as interferor, that has a specificity for a target protein and which induces aggregation upon contact with said target protein. The present invention also discloses such interferor molecules and their use in agrobiotech applications.

Abstract: The present invention relates to non-steroidal ligands for use in nuclear receptor-based inducible gene expression system, and a method to modulate exogenous gene expression in which an ecdysone receptor complex comprising: a DNA binding domain; a ligand binding domain; a transactivation domain; and a ligand is contacted with a DNA construct comprising: the exogenous gene and a response element; wherein the exogenous gene is under the control of the response element and binding of the DNA binding domain to the response element in the presence of the ligand results in activation or suppression of the gene.

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: A family of minimally cross-hybridizing nucleotide sequences, methods of use, etc. A specific family of 1168 24mers is described.

Abstract: This invention provides monoclonal antibodies that recognize the Toll-like Receptor 4/MD-2 receptor complex, and monoclonal antibodies that recognize the TLR4/MD2 complex as well as TLR4 when not complexed with MD-2. The invention further provides methods of using the monoclonal antibodies as therapeutics. This invention also provides soluble chimeric proteins, methods of expressing and purifying soluble chimeric proteins, and methods of using soluble chimeric proteins as therapeutics, in screening assays and in the production of antibodies.

Abstract: The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.

Abstract: Provided are methods of making carrier polypeptide that include incorporating a first unnatural amino acid into a carrier polypeptide variant, incorporating a second unnatural amino acid into a target polypeptide variant, and reacting the first and second unnatural amino acids to produce the conjugate. Conjugates produced using the provided methods are also provided. In addition, orthogonal translation systems in methylotrophic yeast and methods of using these systems to produce carrier and target polypeptide variants comprising unnatural amino acids are provided.

Abstract: The present disclosure relates to RNAi agents useful in methods of treating Beta-ENaC-related diseases such as cystic fibrosis, pseudohypoaldosteronism type 1 (PHA1), Liddle's syndrome, hypertension, alkalosis, hypokalemia, and obesity-associated hypertension, using a therapeutically effective amount of a RNAi agent to Beta-ENaC.

Abstract: Methods and compositions using populations of randomized modified FRT recombination sites to identify, isolate and/or characterize modified FRT recombination sites are provided. The recombinogenic modified FRT recombination sites can be employed in a variety of methods for targeted recombination of polynucleotides of interest, including methods to recombine polynucleotides, assess promoter activity, directly select transformed organisms, minimize or eliminate expression resulting from random integration into the genome of an organism, such as a plant, remove polynucleotides of interest, combine multiple transfer cassettes, invert or excise a polynucleotide, and identify and/or characterize transcriptional regulating regions are also provided.

Abstract: The invention provides interfering RNA molecule-ligand conjugates useful as a delivery system for delivering interfering RNA molecules to a cell in vitro or in vivo. The conjugates comprise a ligand that can bind to a low density lipoprotein receptor (LDLR) or LDLR family member. Therapeutic uses for the conjugates are also provided.

Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.

Abstract: A method for analyzing biomolecular interactions, which method can be carried out without performing affinity selection using an immobilized bait, is provided. mRNA portions of assignment molecules that interacted with each other are linked together by annealing via a DNA linker for linking mRNA portions of assignment molecules together, the DNA linker comprising, at the 5?-end, an mRNA-complementary region complementary to a sequence at the 5?-end of each mRNA portion, and, at the 3?-end, a self-complementary region complementary between molecules of the DNA linker, the DNA linker being phosphorylated at the 5?-end.

Abstract: The present invention provides compositions comprising conjugate molecules that are structurally stable at a temperature of between about 2 degrees C. and 8 degrees C. In some examples, a conjugate molecule comprises an antigen, such as an allergen. In some examples, a conjugate molecule comprises the Ragweed antigen Amb a 1. The present invention provides methods for making and using such compositions. Provided herein are methods for modulating an immune response in an individual comprising administration of a composition comprising a structurally stable conjugate molecule as described herein.