Abstract: The present invention provides for the nucleic acid sequences of plant centromeres. This will permit construction of stably inherited recombinant DNA constructs and minichromosomes which can serve as vectors for the construction of transgenic plant and animal cells.

Abstract: Connexin modulation for the treatment of wounds that do not heal at expected rates, including delayed healing wounds, incompletely healing wounds, and chronic wounds, and associated methods, compositions and articles.

Abstract: Recombinant lentiviral vectors having a region encoding a functional ?-globin gene; and large portions of the ?-globin locus control regions which include DNase I hypersensitive sites HS2, HS3 and HS4 provides expression of ?-globin when introduced into a mammal, for example a human, in vivo. Optionally, the vector further includes a region encoding a dihydrofolate reductase. The vector may be used in treatment of hemoglobinopathies, including ?-thalessemia and sickle-cell disease. For example, hematopoietic progenitor or stem cells may be transformed ex vivo and then restored to the patient. Selection processes may be used to increase the percentage of transformed cells in the returned population. For example, a selection marker which makes transformed cells more drug resistant than untransformed cells allows selection by treatment of the cells with the corresponding drug.

Abstract: A nucleic acid construct that includes (i) a first nucleic acid sequence encoding TNF alpha; (ii) a second nucleic acid sequence encoding a Diphtheria toxin; and (iii) at least one additional nucleic acid sequence of a cancer specific promoter. The TNF alpha and Diphtheria toxin encoding sequences are under an expression control of the cancer specific promoter. Also provided are construct systems and methods and uses of same.

Abstract: A compound having the general formula shown below: where R1-6 are independently selected from the group consisting of an electron withdrawing group, an alkyl group, an aryl group, hydrogen, a heteroaryl group, and a five or six member ring structure formed from the R1 and R2 pair, the R3 and R4 pair, the R4 and R5 pair, or the R5 and R6 pair; R7 is a substituted or unsubstituted aryl group; and Y is a nucleophile.

Abstract: One aspect of the present invention relates to a ribonucleoside substituted with a phosphonamidite group at the 3?-position. In certain embodiments, the phosphonamidite is an alkyl phosphonamidite. Another aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-phosphate linkage. Representative non-phosphate linkages include phosphonate, hydroxylamine, hydroxylhydrazinyl, amide, and carbamate linkages. In certain embodiments, the non-phosphate linkage is a phosphonate linkage. In certain embodiments, a non-phosphate linkage occurs in only one strand. In certain embodiments, a non-phosphate linkage occurs in both strands. In certain embodiments, a ligand is bound to one of the oligonucleotide strands comprising the double-stranded oligonucleotide. In certain embodiments, a ligand is bound to both of the oligonucleotide strands comprising the double-stranded oligonucleotide.

Abstract: The invention provides engineered plant minichromosomes generated by telomere mediated truncation of native chromosomes. These minichromosomes are faithfully transmitted from one generation to the next and provide an ideal platform for breeding genes into desired plant varieties with out problems, such as linkage drag, associated with standard breeding methods.

Abstract: The present invention provides for the nucleic acid sequences of plant centromeres. This will permit construction of stably inherited recombinant DNA constructs and minichromosomes which can serve as vectors for the construction of transgenic plant and animal cells.

Abstract: The present invention provides a method for identifying a compound of interest by screening libraries of molecules which include an encoding oligonucleotide tag.

Abstract: The electrical conductivity of DNA and other oligonucleotide constructs is dependent on its conformational state. Such a dependence may be harnessed for the electronic sensing of external analytes, for instance, adenosine or thrombin. Such a DNA sensor incorporates an analyte receptor, whose altered conformation in the presence of bound analyte switches the conformation, and hence, the conductive path between two oligonucleotide stems, such as double-helical DNA. Two distinct designs for such sensors are described that permit significant electrical conduction through a first or “detector” double-helical stem only in the presence of the bound analyte. In the first design, current flows through the analyte receptor itself whereas, in the second, current flows in a path adjacent to the receptor.

Abstract: The electrical conductivity of DNA and other oligonucleotide constructs is dependent on its conformational state. Such a dependence may be harnessed for the electronic sensing of external analytes, for instance, adenosine. Such a DNA sensor incorporates an analyte receptor, whose altered conformation in the presence of bound analyte switches the conformation, and hence, the conductive path between two oligonucleotide stems, such as double-helical DNA. Two distinct designs for such sensors are described that permit significant electrical conduction through a first or “detector” double-helical stem only in the presence of the bound analyte. In the first design, current flows through the analyte receptor itself whereas, in the second, current flows in a path adjacent to the receptor.

Abstract: The present invention provides methods of synthesizing libraries of molecules comprising a functional moiety which is operatively linked to an encoding oligonucleotide.

Abstract: A probe and a primer capable of collectively detecting microorganisms of the same species while differentiating microorganisms of other species with an object of classification by species of fungus. An oligonucleotide probe for detecting an infectious etiologic microorganism gene includes at least one base sequence selected from the base sequences belonging to one group of the following first to ninth groups. The base sequence groups of first to ninth groups are: first group (SEQ ID NOS:1 to 5); second group (SEQ ID NOS:6 to 10); third group (SEQ ID NOS:11 to 15); fourth group (SEQ ID NOS:16 to 21); fifth group (SEQ ID NOS:22 to 26); sixth group (SEQ ID NOS:27 to 31); seventh group (SEQ ID NOS:32 to 36); eighth group (SEQ ID NOS:37 to 41); and ninth group (SEQ ID NOS:42 to 46).

Abstract: The invention provides a Dre/rox recombinase system. In particular, the invention provides Dre polypeptides that can catalyze site-specific recombination at rox sites but not at lox sites. The Dre/rox system can be utilized in a number of genetic manipulations either alone or in combination with other recombinase systems.

Abstract: Novel calcium-independent phospholipases A2; genes encoding the same; an antibody against them; an inherent promoter or a regulator gene which comprises a base sequence occurring in intron and inducing site-specific expression in response to an external stimulus; a method of expressing a target protein in response to an external stimulus; and an organism having this gene transferred thereinto. Novel calcium-independent phospholipases A2 having an amino acid sequence represented by SEQ ID NO: 1, 3 or 5 or an amino acid sequence derived from such an amino acid sequence by the substitution, deletion or addition of one or more amino acids; a gene having a base sequence occurring in an intron and being capable of initiating RNA transcription due to an external stimulus such as a stimulus with kainic acid or an electrical stimulus; a method of regulating expression by using the gene; and an organism having the gene transferred thereinto.

Abstract: A nucleotide leader sequence 5?-UTR comprises elements favorable to gene expression, such as repeated CAA trinucleotide elements in combination with repeated CT dinucleotide elements.

Abstract: An object of the present invention is to provide a transformation system for Labyrinthulomycota that allows the elucidation of biosynthetic mechanisms of lipids such as PUFA and carotenoids as well as for the construction of a high production system and the design and development of novel functional lipid molecules by the control of the mechanisms. The present invention provides a method for introducing a transgene into a cell of Labyrinthulomycota, which comprises introducing into a cell of Labyrinthulomycota a recombinant vector comprising a transgene and a nucleotide sequence which is homologous to a part of chromosomal DNA of Labyrinthulomycota and is capable of homologous recombination with the chromosomal DNA, and then inducing homologous recombination in this homologous nucleotide sequence.

Abstract: A modified bioluminescent system comprising a fluorescent molecule covalently linked with a photoprotein, wherein said link between the two proteins has the function to stabilize the modified bioluminescent system and allowing the transfer of the energy by Chemiluminescence Resonance Energy Transfer (CRET).

Abstract: Cytomegalovirus (CMV) Intron A fragments for expressing gene products are disclosed. Also described are expression vectors including the fragments, as well as methods of using the same.

Abstract: The present invention relates to methods and compositions for treatment of cardiovascular and peripheral vascular diseases using ex vivo and in vivo gene delivery technologies. One aspect of the present invention relates to a method for treating a vascular disease by introducing a DNA sequence encoding a TM protein or its variant into a segment of a blood vessel in vivo using a gutless adenovirus vector. Another aspect of the present invention is to provide a method to deliver a gutless adenovirus vector carrying a DNA sequence encoding a TM protein or its variant using a stent.

Abstract: A pair of asymmetrical, partially double-stranded oligonucleotide adapters are provided wherein the pair of adapters comprise a first asymmetrical oligonucleotide adapter comprising a single-stranded 3? overhang and a second asymmetrical double-stranded oligonucleotide adapter comprising a single-stranded 5? overhang and at least one blocking group on the strand of said second asymmetrical oligonucleotide adapter that does not comprise the 5? overhang. Also provided are a pair of double-stranded Y oligonucleotide adapters and a pair of double-stranded bubble oligonucleotide adapters and methods of using said asymmetrical adapters for amplification of at least one double stranded nucleic acid molecule, wherein the amplification produces a plurality of amplified nucleic acid molecules having a different nucleic acid sequence at each end are also described. Also provided is a method for exponentially amplifying one strand in a double-stranded nucleic acid molecule.

Abstract: Provided herein are libraries of nucleic acid species each comprising a transcription unit having a promoter region operatively linked to a coding sequence. The coding sequence of each nucleic acid species encodes a RNA cleavage substrate comprising a unique compomer species and a cleavage site. Each compomer species has a molecular mass distinguishable from the molecular mass of other compomer species in the library, and cleavage at a cleavage site releases a polynucleotide comprising the compomer species from the RNA cleavage substrate.

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: Disclosed is a method for producing a protein involving infecting a culture of eukaryotic cells with a recombinant vaccinia virus.

Abstract: A probe suitable for coupling with a particulate support such as a microbead, the probe comprising: a) a coupling group which permits coupling of the probe to the surface of the particulate support; b) a spacer; and c) a target-specific oligonucleotide probe sequence, wherein the spacer comprises: i) an oligonucleotide spacer of at least 15 nucleotides between the target specific probe sequence and the support coupling group; and optionally ii) a carbon spacer of between 3 and 50 carbon units between the target specific probe sequence and the support coupling group.

Abstract: An object of the present invention is to provide a transformation system for Labyrinthulomycota that allows the elucidation of biosynthetic mechanisms of lipids such as PUFA and carotenoids as well as for the construction of a high production system and the design and development of novel functional lipid molecules by the control of the mechanisms. The present invention provides a vector for the transformation of Labyrinthulomycota with a transgene, which comprises at least (1) a nucleotide sequence which is homologous to a part of chromosomal DNA of Labyrinthulomycota and is capable of homologous recombination with the chromosomal DNA, (2) a selection marker gene having a promoter sequence located upstream and a terminator sequence located downstream, and (3) a cloning site for transgene insertion having a promoter sequence located upstream and a terminator sequence located downstream.

Abstract: Synthetic modular polynucleotide constructs are useful for gene expression in plants, methods for making and using such constructs, and plants transformed with such constructs. The constructs comprise unique restriction sites for each modular element and may further comprise polynucleotide identifier sequences.

Abstract: A method for controlling the use of oligonucleotide sequences released from arrays, comprises synthesizing a chemical array of oligonucleotides on a substrate under conditions for producing an array of cleavable oligonucleotides that are blocked from enzymatic reactions after cleavage. Methods may also include receiving a chemical array of cleavable oligonucleotides on a substrate, and cleaving the oligonucleotides from the array, wherein the oligonucleotides are blocked from enzymatic reactions after cleavage. Arrays, populations of oligonucleotides and kits are also provided to facilitate the methods.

Abstract: The present invention relates to T-DNA vectors and methods for obtaining transgenic eukaryotes using said vectors. The transgenic eukaryotes are characterized in that they contain the T-DNA but not the illegitimately transferred vector backbone sequence. This is achieved by modifying the T-DNA borders such that they are more efficiently nicked or such that they allow elimination of illegitimately transferred vector backbone sequences by means of recombination.

Abstract: The present invention provides for compositions, methods and systems for targeted sequence enrichment. In particular, the present invention provides for enriching for targeted nucleic acid sequences during hybridizations in microarray assays by suppressing secondary capture of non-target nucleic acid sequences.

Abstract: This invention relates to nucleic acid-based logic gates. The invention further relates to circuits comprising nucleic acid-based logic gates and methods of performing operations with the gates and circuits provided herein.

Abstract: The invention relates to a new “gene-switch” (cumate-inducible switch) for mammalian cells. This switch is as useful in the development of expression systems and cell-based assays for functional genomics as in the generation of viral vectors for gene therapy.

Abstract: The invention provides immunomodulatory polynucleotides and methods for immunomodulation of individuals using the immunomodulatory polynucleotides.

Abstract: The present invention relates to a method for producing a DNA chip, which comprises the steps of: (a) cloning a probe, where a linker is coupled to one or both ends of an oligonucleotide to be integrated on a slide, into a vector; (b) transforming host cells with the vector; (c) culturing the transformed host cells, to recover the probe where the linker is coupled to one or both ends of the oligonucleotides; and (d) integrating the recovered double-helical probes on a slide. Also, the present invention relates to a DNA chip for HPV diagnosis produced by the method, and a method for diagnosing the presence or genotype of HPV using the DNA chip.

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: A computational method is described which uses the process of cis-regulatory module evolution to identify conserved sequence patches which exhibit suppression of change by snp/indel occurrence, including determining sequence similarities significantly greater than random expectation on selected genome sequences from two or more species in sequences that lie outside of protein coding regions, sorting the similarities for conserved patches of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels). and selecting such patches to identify cis-regulatory modules. Further, the disclosed method is practiced in the absence of having to execute multiple interspecific sequence comparison analysis, where such identified cis-regulatory modules are used to produce libraries and arrays containing such cis-regulatory modules.

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.

Abstract: In one embodiment, the present invention relates to fluorescent nucleic acid constructs and methods of using these switchable constructs to rapidly screen for target molecule interactions. More particularly, an RNA/DNA chimera comprising a fluorophore-quencher pair and a nucleic acid construct is disclosed for the rapid screening of interactions between the HIV-1 nucleocapsid protein, NCp7, and a stem-loop region, SL3, of the HIV-1 RNA, or antagonists thereof. The compositions and methods disclosed herein can be used in preferred aspects of the present invention for diagnosing disease states, distinguishing the presence of infectious or toxic agents, drug discovery and design, and molecular electronic applications.

Abstract: The present invention relates to methods and compositions for treatment of cardiovascular and peripheral vascular diseases using ex vivo and in vivo gene delivery technologies. One aspect of the present invention relates to a method for treating a vascular disease by introducing a DNA sequence encoding a TM protein or its variant into a segment of a blood vessel ex vivo using a gutless adenovirus vector. Another aspect of the present invention is to provide a gutless adenovirus vector carrying a transgene, such as a gene encoding TM protein or its variant.

Abstract: A novel gene of Bifidobacteria and the polypeptides encoded thereby. In particular, a gene belonging to the Serpin superfamily and its use in the production of bacterial Serpins is provided. Also provided are vectors, host cells, and methods for producing bacterial Serpin polynucleotides and/or polypeptides.

Abstract: The invention provides new methods for modulating specific CMI-inducing cytokines in vivo. Such new methods result in stimulation of the cytokines IL-6, IL-12 MIP-1? and MCP without substantially inducing undesired cytokines. The methods according to the invention are based upon administration of oligonucleotides containing particular structural motifs which lead to specific cytokine induction.

Abstract: The invention provides methods, kits, and compositions comprising novel mutant loxP sites. Such sites are particularly useful for procedures requiring multiple site-specific recombination reactions, including deletions or insertions of multiple genes or other sequences in the same organism, staged insertions or deletions of genes of the same organism at different times, assembly of large polynucleotide constructs by serial site-specific recombination, and the like. In one aspect, compositions of the invention includes particular mutant spacer oligonucleotides of loxP recombination elements, the recombination elements themselves, and pairs of non-promiscuous mutant loxP sites.

Abstract: The present invention relates to methods and compositions for treatment of cardiovascular and peripheral vascular diseases using ex vivo and in vivo gene delivery technologies. One aspect of the present invention relates to a method for treating a vascular disease by introducing a DNA sequence encoding a TM protein or its variant into a segment of a blood vessel ex vivo using a gutless adenovirus vector. Another aspect of the present invention is to provide a gutless adenovirus vector carrying a transgene, such as a gene encoding TM protein or its variant.

Abstract: Nucleic acids containing unmethylated CpG dinucleotides and therapeutic utilities based on their ability to stimulate an immune response and to redirect a Th2 response to a Th1 response in a subject are disclosed. Methods for treating atopic diseases, including atopic dermatitis, are disclosed.

Abstract: The hsp70 gene from an Arthrobacter species has been isolated and sequenced. The encoded protein is believed to be highly immunogenic, especially in fish, and also has utility as a non-specific adjuvant, and as an adjuvanting carrier for heterologous antigens.

Abstract: The present invention relates generally to compositions and methods for use in recombinational cloning of nucleic acid molecules. In particular, the invention relates to nucleic acid molecules encoding one or more recombination sites or portions thereof, to nucleic acid molecules comprising one or more of these recombination site nucleotide sequences and optionally comprising one or more additional physical or functional nucleotide sequences. The invention also relates to vectors comprising the nucleic acid molecules of the invention, to host cells comprising the vectors or nucleic acid molecules of the invention, to methods of producing polypeptides using the nucleic acid molecules of the invention, and to polypeptides encoded by these nucleic acid molecules or produced by the methods of the invention. The invention also relates to antibodies that bind to one or more polypeptides of the invention or epitopes thereof.

Abstract: The invention provides immunostimulatory compositions and use of those compounds in the preparation of medicaments for the treatment of disease as well as in vitro uses. In particular, the compositions of the invention include immunostimulatory oligoribonucleotides that incorporate a sequence-dependent immunostimulatory sequence motif. Specific modifications involving phosphate linkages, nucleotide analogs, adducts, and combinations thereof are provided. Compositions of the invention, which optionally can include an antigen, can be used alone or together with other treatments to stimulate or enhance an immune response. Also provided are compositions and methods useful for treating a subject having an infection, a cancer, an allergic condition, asthma, airway remodeling, or immunodeficiency. Immunostimulatory oligoribonucleotides of the invention are believed to stimulate Toll-like receptor 8 (TLR8).

Abstract: Vector constructs for expression of two or more functional proteins or polypeptides under operative control of a single promoter and methods of making and using the same are described. The vectors comprise a self-processing cleavage site between each respective protein or polypeptide coding sequence. The vector constructs include the coding sequence for a self-processing cleavage site and may further include an additional proteolytic cleavage sequence which provides a means to remove the self processing peptide sequence from expressed protein(s) or polypeptide(s). The vector constructs find utility in methods for enhanced production of biologically active proteins and polypeptides in vitro and in vivo.

Abstract: This invention pertains to BIV constructs encompassing BIV combination vectors, BIV vectors and BIV packaging vectors and particularly the invention pertains to a three vector system comprising: a) a BIV vector construct including a DNA segment from a BIV genome, a packaging sequence to package RNA into virions; a promoter operably linked to the DNA segment; and a transgene operably linked to a second promoter; b) a BIV packaging vector construct comprising a BIV DNA sequence fragment comprising at least a gag gene or pol gene of BIV; a promoter operably linked to the BIV DNA fragment; and a polyadenylation sequence located downstream of the BIV DNA fragment; and c) an expression vector construct comprising a gene encoding a viral surface protein. Also provided is a method for transferring a gene of interest into a mammalian cell.

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