Abstract: The present invention is directed to methods, reagents, kits, and compositions for detecting target polynucleotide sequences, especially small target polynucleotides such as miRNAs, between two samples. A pair of linker probes can be employed in two different reactions to query a particular species of target polynucleotide. A pair of detector probes, a single forward primer specific for the target polynucleotide, and a reverse primer can be employed in an amplification reaction to query the difference in expression level of the target polynucleotide between the two samples. In some embodiments a plurality of small miRNAs are queried with a plurality of linker probes. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.

Abstract: Provided are means and methods for in vitro and in vivo detection of chemically induced effects on embryonic development and differentiation for the purpose of embryotoxicity/teratogenicity screening as well as for the identification of pharmaceuticals such as growth and tissue promoting factors based on differentiating pluripotent embryonic stem (ES) cells. The assays are based on the use of transgenic ES cells and non-human animals comprising such ES cells or derivatives thereof, wherein said ES cells are characterized by the differentiation-dependent expression of a secreted reporter protein; in particular secreted embryonic alkaline phosphatase (SEAP).

Abstract: The present invention relates to detection of pathogenic mycobacteria in clinical specimens such as sputum, cerebrospinal fluid, gastric lavage and tissue biopsies etc., wherein the novel stretch of DNA that lies in the intergenic region between methyl mycolic acid synthase genes mmaA1 and mmaA2 and the flanking region in mmaA1 and mmaA2 genes and is the invention uses a pair of designed oligonucleotide primers that specifically amplifies the target DNA from the clinical specimens.

Abstract: Two dimensional polynucleic acid arrays are assembled from robust nucleic acid motifs as polygonal units. The polygonal units in an array have edges composed of nucleic acid multi-crossover domains and are joined together by double cohesion of adjacent polygonal units. A subset of polygonal units in the array have a nanoparticle or pendant molecule attached to an end of one edge of each polygonal unit within this subset.

Abstract: The described method provides, methods, and kits to produce, identify, catalog and classify a comprehensive collection of nucleic acid targets produced from a nucleic acid sample. The method, referred to as Cataloging and Classification of Sequence Tags, involves generating a set of target nucleic acid fragments; coupling the target nucleic acid fragments to a nucleic acid bridge comprising, for example, two or more primer binding sites and two recognition sites for cleavage at a site offset from the recognition site to the fragment's end; and cleaving the fragments to generate chimeric nucleic acids of known length. The nucleic acid bridge is thus disposed between the two nucleic acid fragments in the chimeric nucleic acid. The resulting duplex nucleic acids comprise a set of sequence tags (i.e., by amplification using universal primers), comprising an addressable portion, a target nucleic portion and a portion of the nucleic acid bridge.

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 present invention concerns methods and means to produce humanized antibodies from transgenic non-human animals. The invention specifically relates to novel immunoglobulin heavy and light chain constructs, recombination and transgenic vectors useful in making transgenic non-human animals expressing humanized antibodies, transgenic animals, and humanized immunoglobulin preparations.

Abstract: The invention provides for nucleic acid molecules enabling the synthesis of microginin and microginin analogues. The invention also provides for methods for identifying microginins as well creating microginins which may not be found in nature.

Abstract: The present invention relates to unique strategies and constructs for producing a nucleic acid product that downregulates or prevents expression of a desired target polynucleotide.

Abstract: The present invention relates to two primordial germ cell-specific expressed genes, Fragilis and Stella. The sequences and sues of human Stella and Fragilis are disclosed herein, as are several mouse sequences related to Fragilis. The present invention relates to the use of Stella and Fragilis as markers for primordial germ cells and can be used to identify such cells. Additionally, the present invention relates to the use of Stella and Fragilis for the diagnosis, treatment and/or prevention of disease.

Abstract: The invention relates to a process for the controlled amplification of at least one part of a starting DNA containing a plurality of restriction sites for a determined specific restriction endonuclease, and of which at least part of its nucleic acid is unknown. Application of this process to human, animal or plant DNA fingerprinting, to identification of restriction fragment length polymorphisms. Kit for the application of the process.

Abstract: A method of identifying at least a nucleic acid molecule fragment to which a protein of interest binds, comprising: (i) preparing at least one nucleic acid molecule fragment to which a protein binds; (ii) isolating the 5? terminus and the 3? terminus of the nucleic acid fragment(s) and linking the 5? terminus and 3? terminus to create the at least one ditag; (iii) sequencing the ditag; and (iv) mapping the ditag sequence(s) to the genome.

Abstract: The present invention concerns a method for identifying substances useful for treating inflammation, characterized in that it comprises the following steps: (a) placing said substance in contact with a nucleic acid construct containing the Retinoid-Related Orphan Receptor (ROR) receptor response element of the promoter of the I?B? gene, under conditions suitable for allowing said substance to bind to said response element, (b) measuring the possible binding of said substance to the response element or the transcriptional activity of the response element or of a promoter containing it, (c) optionally comparing the measurement of step (b) with a measurement carried out under conditions similar to those of steps (a) and (b) but with a nucleic acid construct containing the mutated response element.

Abstract: A Brucella bacterium is modified by partial or complete deletion of the pgm gene, rendering the bacterium incapable of synthesizing a key enzyme in the metabolism of bacterial sugars. A live vaccine for immunization, prophylaxis or treatment of brucellosis comprises such a bacterium, either lyophilized or in a pharmaceutical vehicle. Nucleotide sequence fragments having the aforementioned deletion are disclosed, with methods for making them.

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 un-transformed cells allows selection by treatment of the cells with the corresponding drug.

Abstract: Disclosed is a novel substance capable of regulating the expression of a telomerase reverse transcriptase gene in a cell of a mammal. A gene capable of regulating the expression of hTERT, comprising a nucleotide sequence depicted in SEQ ID No: 1 or 2. The expression of a telomerase reverse transcriptase gene can be inhibited by inhibiting the expression of the gene. By utilizing this mechanism, the expression of a telomerase reverse transcriptase gene can be regulated.

Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.

Abstract: The present invention provides novel isolated nucleic acids encoding antigenic proteins derived from Sarcocystis neurona, or unique fragments thereof. In particular, the invention provides novel isolated nucleic acids encoding membrane-associated polypeptides SnSAG2, SnSAG3, and SnSAG 4. Also provided are purified antigenic polypeptide fragments encoded by the novel nucleic acid sequences set forth herein that encode for SnSAG2, SnSAG3, and SnSAG 4. Also provided are isolated nucleic acids capable of selectively hybridizing with the nucleic acid from Sarcocystis neurona. The invention also provides vectors comprising the nucleic acids of the invention encoding an antigenic protein derived from Sarcocystis neurona or a unique fragment thereof and provides the vector in a host capable of expressing the polypeptide encoded by that nucleic acid.

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: The invention pertains to a method for targeted alteration of a duplex acceptor DNA sequence, comprising combining the duplex acceptor DNA sequence with a donor oligonucleotide, wherein the duplex acceptor DNA sequence contains a first DNA sequence and a second DNA sequence which is the complement of the first DNA sequence and wherein the donor oligonucleotide comprises a domain that comprises at least one mismatch with respect to the duplex acceptor DNA sequence to be altered, preferably with respect to the first DNA sequence, and wherein a section of the donor oligonucleotide is methylated to a higher degree than the second DNA sequence and/or wherein the second DNA is methylated to a lower degree than the corresponding section of the donor oligonucleotide, optionally in the presence of proteins that are capable of targeted nucleotide exchange and to oligonucleotides for use in the method.

Abstract: The present invention comprises a copper-inducible promoter system of yeast for the controlled expression of recombinant genes. The invention comprises a promoter element comprising at least two tandemly-repeated MRE sequences and a minimal TATA element from the 35S-promoter of the cauliflower mosaic virus.

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: 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 relates to chimeric molecules comprising portions of rat PEG-3 (“rPEG-3”) and human GADD34 (“hGADD34”) having apoptotic activity. It is based, at least in part, on the discovery that a chimeric protein comprising amino acids 1-347 of rat PEG-3 fused with residues 418-674 of human GADD34 exhibited anti-proliferative activity when expressed in transformed cells. The present invention provides for this and other rPEG3/hGADD34 chimeras, and the use of such proteins in inhibiting cell proliferation, angiogenesis, and tumor growth.

Abstract: This invention relates to a DNA containing uncoupling protein-2 (UCP-2) promoter region containing the regulator sequence, a transformant transformed with the DNA, a method for screening a compound or its salt that promotes or inhibits UCP-2 promoter activity characterized by use of the transformant, a method for screening an antiobestic drug, an antidiabetic drug, a depressor, an antihyperlipemic drug, and an antipyretic drug characterized by use of the transformant, a kit for screening a compound or its salt that promotes or inhibits UCP-2 promoter activity characterized by use of the transformant, and pharmaceutical composition containing a compound or its salt that promotes or inhibits UCP-2 promoter activity obtained using the screening method or the screening kit.

Abstract: The present invention provides a vector system comprising a mutated post-transcriptional regulatory element. In particular, the present invention relates to a mutated WPRE sequence that can efficiently express nucleotides of interest in a retroviral vector system. The present invention also relates to methods of delivering and expressing nucleotides of interest to a target cell.

Abstract: The present invention relates to expression cassettes comprising transcription regulating sequences with seed-preferential or seed-specific expression profiles in plants obtainable from Arabidopsis thaliana genes At4g12910, At1g66250, At4g00820, At2g36640, At2g34200, At3g11180, At4g00360, At2g48030, At2g38590, At1g23000, At3g15510, At3g50870, At4g00220, or At4g26320.

Abstract: Vector preparations and cloning constructs suitable for use in cloning are provided. Vector preparations are double-stranded DNA molecules having two 3? termini, each terminus having a single base pair overhang that is capable of hybridizing to a single base pair overhang on a double stranded polynucleotide sequence to be cloned. The overhang of the vector preparation is suitably a dCMP and the overhang of the polynucleotide sequence to be cloned is suitably a dGMP. In other embodiments, the overhang of the polynucleotide sequence to be cloned is any ddNTP and the corresponding overhang of the vector preparation is any base that pairs to the ddNTP. The latter embodiment is particularly suited to preparing recombinant molecules having only a single insert. Methods of cloning, methods of preparing libraries of recombinant molecules and kits for carrying out the methods are also provided.

Abstract: The invention relates to fluorescent N2,N3-etheno-purine (2?-deoxy) riboside derivatives and fluorescent oligonucleotide probes comprising one or more moieties thereof, their preparation and uses thereof for staining DNA/RNA and for detection and quantitation of genetic material.

Abstract: A protein toxin named Aeromonas salmonicida exoenzyme T (AcxT), which belongs to the family of ADP-ribosylating toxins, is disclosed as is a Calcium (or other cation concentration) dependent promoter of A. salmonicida. Also disclosed are diagnostic, preventive, and therapeutic techniques, including the preparation of bacterin vaccines based on AexT for inducing immunity against A. salmonicida infections.

Abstract: Disclosed are protein and peptide antigen and DNA compositions effective in generating immune responses against the pathogenic fungi Coccidioides spp., the causative agents of coccidioidomycosis and Valley Fever. The invention thus provides protein and peptide antigens, DNA constructs, combinations and related biological compositions, and prophylactic and therapeutic methods of using such components and combinations to generate effective and protective immune responses against Coccidioides spp., including C. immitis.

Abstract: The present invention provides a production method of a copolymeric polyester which comprises culturing an ACT1 gene promoter shown under SEQ ID NO: 9, a GAP3 gene promoter shown under SEQ ID NO: 10; a PMA1 gene promoter shown under SEQ ID NO: 11, and, a TEF1 gene promoter shown under SEQ ID NO: 12; a plasmid which contains the gene expression unit comprising said promoter; a transformed cell as resulting from transformation of the said plasmid; and said transformed cell.

Abstract: An apparatus and method for performing rapid DNA sequencing, such as genomic sequencing, is provided herein. The method includes the steps of preparing a sample DNA for genomic sequencing, amplifying the prepared DNA in a representative manner, and performing multiple sequencing reaction on the amplified DNA with only one primer hybridization step.

Abstract: The present invention relates to methods for detecting a change in chromosomal structure. These methods employ labeled probes that bind nucleic acids. For example, these probes may be comprised of nucleic acids or nucleic acid analogs and a detectable label.

Abstract: Disclosed are methods and compositions for creating a DNA, RNA or protein molecule with two or more nucleic acid or polypeptide domains, respectively, joined by a linker region. These methods are used to generate random linker libraries of nucleic acids that encode dual-domain or multi-domain polypeptides. The linker regions are characterized by both length and sequence variability.

Abstract: The present invention concerns a novel retinoic acid regulated gene whose expression product displays useful morphogenic/mitogenic properties. The present invention further concerns an isolated nucleic acid of SEQ ID NO:1 encoding a retinoic acid regulated expression product having an amino acid sequence of SEQ ID NO:2.

Abstract: A novel gene (designated 125P5C8) and its encoded protein are described. While 125P5C8 exhibits tissue specific expression in normal adult tissue, it is aberrantly expressed multiple cancers including prostate, bladder, kidney and colon cancers. Consequently, 125P5C8 provides a diagnostic and/or therapeutic target for cancers, and the 125P5C8 gene or fragment thereof, or its encoded protein or a fragment thereof used to elicit an immune response.

Abstract: The present invention provides compositions of novel polypeptides and polynucleotides encoding the polypeptides, which polypeptides are useful for generating an immunological response in an individual and in therapeutic application of Coccidioides spp. infection.

Abstract: The present invention relates to polypeptides of Streptococcus pneumoniae which may be used for prophylaxis, diagnostic and/or therapy purposes.

Abstract: The present invention provides novel isolated nucleic acids encoding antigenic proteins derived from Sarcocystis neurona, or unique fragments thereof. In particular, the invention provides novel isolated nucleic acids encoding membrane-associated polypeptides SnSAG2, SnSAG3, and SnSAG4. Also provided are purified antigenic polypeptide fragments encoded by the novel nucleic acid sequences set forth herein that encode for SnSAG2, SnSAG3, and SnSAG4. Also provided are isolated nucleic acids capable of selectively hybridizing with the nucleic acid from Sarcocystis neurona. The invention also provides vectors comprising the nucleic acids of the invention encoding an antigenic protein derived from Sarcocystis neurona or a unique fragment thereof and provides the vector in a host capable of expressing the polypeptide encoded by that nucleic acid.

Abstract: The invention provides new compositions and methods for immunomodulation of individuals. Immunomodulation is accomplished by administration of immunomodulatory polynucleotide/microcarrier (IMP/MC) complexes. The IMP/MC complexes may be covalently or non-covalently bound, and feature a polynucleotide comprising at least one immunostimulatory sequence bound to a biodegradable microcarrier or noncarrier.

Abstract: The present invention provides compositions and methods for recombinational cloning. The compositions include vectors having multiple recombination sites and/or multiple topoisomerase recognition sites. The methods permit the simultaneous cloning of two or more different nucleic acid molecules. In some embodiments the molecules are fused together while in other embodiments the molecules are inserted into distinct sites in a vector. The invention also generally provides for linking or joining through recombination a number of molecules and/or compounds (e.g., chemical compounds, drugs, proteins or peptides, lipids, nucleic acids, carbohydrates, etc.) which may be the same or different.

Abstract: To prepare high-performance specific gene-amplification primers for detecting, quantitatively determining or identifying Vibrio parahaeinolyticus having low possibility of mis-identification and practically sufficient amplification efficiency and amplification specificity. We have determined the nucleotide sequences of rpoD genes encoding RNA polymerase ?70 factor of type strains of the genus Vibrio and of stock strains of Vibrio parahaemolyticus (strains containing and those not containing toxin gene); elucidated the phylogenetic relation, and identified nucleotides which are characteristic in Vibrio parahaemolyticus, thereby enabling the design of probes containing them and having high specificity, and primers for gene amplification having high specificity and excellent amplification efficiency.

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 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 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 relates to the design and use of nucleic acid molecules to create novel materials. The present invention further relates to the use of DNA as a bulding block for DNA-materials that are of high yield and purity and that can be incorporated into larger structures.

Abstract: The presently claimed invention provides methods and kits for amplifying a target sequence from within a nucleic acid population. The presently claimed invention provides selection probes which are complementary to at least a portion of said target sequence and mechanisms for adding a probe sequence to the 3? end of a target sequence that is hybridized to a selection probe. The added 3? probe sequence and a probe sequence added at the 5? end of the target by adaptor ligation allow for selective amplification of the target sequence.

Abstract: The present teachings relate to methods, compositions, and kits for detecting one or more target polynucleotide sequences in a sample, and methods compositions and kits for forming concatameric ligation products. In some embodiments of the present teachings, oligonucleotides are hybridized to complementary target polynucleotides and are ligated together to form a concatameric ligation product. In some embodiments of the present teachings, the concatameric ligation product can be amplified, and the identity and quantity of the target polynucleotides determined based on sequence introduced in the ligation reaction. Some embodiments of the present teachings provide methods for removing unligated probes from the reaction mixture. Some embodiments of the present teachings provide for highly multiplexed detection, identification, and quantification of a plurality of target polynucleotides using a variety of analytical procedures.

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.