Abstract: The present invention provides compositions and methods for recombinational cloning. The compositions include vectors having multiple recombination sites with unique specificity. 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. Such molecules and/or compounds or combinations of such molecules and/or compounds can also be bound through recombination to various structures or supports according to the invention.

Abstract: The present invention provides highly accurate methods for cloning nucleic acids in a desired, pre-defined orientation, and additionally provides for a library of cloned oriented nucleic acids. The ability to control the orientation of a nucleic acid being cloned is highly important in various molecular biology applications.

Abstract: The present invention relates to nucleic acid molecules and in particular to vectors, comprising at least one gene of interest, at least one scaffold/matrix attached region (S/MAR), at least one origin of replication, and at least one replication initiation factor, cells comprising these, processes for their propagation, and their use, in particular for the high level expression of proteins which can be used as medicaments.

Abstract: The invention relates to a simple and rapid method for identifying mutations in a gene of interest indicating an alteration in the reading frame of the proteins derived therefrom. The inventive method more particularly relates to the use of said method for scanning the animal population.

Abstract: An attenuated feline recombinant herpesvirus 1 (FHV-1), which is prepared by identifying gene regions in the genome wherein inserted foreign genes can be expressed without affecting the replication of FHV-1 and has least two types of foreign nucleic acid sequences inserted thereinto, usable as a vector virus or a vaccine. In this attenuated recombinant FHV-1, at least two types of foreign genes are inserted in such a manner as allowing the expression into two different gene regions exerting no lethal effect on the proliferation of the virus in the feline herpesvirus 1 genome.

Abstract: Large circular (LC)-sense molecules in an array is disclosed. The LC-sense molecules array is combined with cDNA hybridization to detect differences in expression profile between different cells. LC-sense molecules were purified from nonredundant clones with recombinant phagemid and arrayed onto silanized slide glasses. By hybridization of LC-sense array with Cy3 or Cy5-labelled cDNA preparations at 60° C., 29 up-regulated and 6 down-regulated genes in cancerous liver tissue were detected.

Abstract: A method for providing an adenovirus from a serotype which does not grow efficiently in a desired cell line with the ability to grow in that cell line is described. The method involves replacing the left and right termini of the adenovirus with the corresponding termini from an adenovirus which grow efficiently in the desired cell line. At a minimum, the left terminus spans the 5? inverted terminal repeat, the left terminus spans the E4 region and the 3? inverted terminal repeat. The resulting chimeric adenovirus contains the internal regions spanning the genes encoding the penton, hexon and fiber from the serotype which does not grow efficiently in the desired cell. Also provided are vectors constructed from novel simian adenovirus sequences and proteins, host cells containing same, and uses thereof.

Abstract: The present invention relates to compositions comprising a novel recombinant virus which replicates selectively in cells or tissues that are hypoxic or have an activated HIF pathway. The novel compositions of the invention comprise a recombinant virus genetically engineered to have a hypoxia/HIF-responsive element, or a multiplicity of such elements, operably linked to a promoter which is in turn operably linked to a nucleic acid(s) encoding a peptide(s) which regulates or modulates replication of the virus and/or encode a therapeutic molecule. The invention also includes constructs useful for screening of agents which interact with proteins or genes in the hypoxia-inducible pathway or are jointly translated under hypoxia and animal models useful for monitoring a variety of hypoxic conditions in a non-invasive manner.

Abstract: The invention provides novel yeast promoters useful for controlling the expression of homologous and heterologous nucleic acid molecules in yeast cells. The yeast promoters are induced by a fermentable carbon source, such as glucose, or a non-fermentable carbon source, such as ethanol, or both. Therefore, expression of nucleic acid molecules encoding a polypeptide under the control of the novel yeast promoters may be regulated by varying the level of a fermentable carbon source, or a non-fermentable carbon source, or both.

Abstract: We disclose compositions and processes for enhancing transposon mediated integration of a nucleic acid molecule into another target nucleic acid molecule. Integration by an integrator complex is enhanced by cationic reagents.

Abstract: The present invention relates to a method of detecting a base at a pre-determined position in a nucleic acid molecule by performing enzymatic detection reactions using base-specific detection oligomers, where each oligomer is specific for a particular base at the predetermined position, and then comparing the enzymatic detection reactions to determine which base is present at the position, with an enzyme-disabling agent being present during the enzymatic detection reaction. In preferred embodiments the enzymatic detection reaction is an oligomer elongation extension reaction, catalysed by, among others, polymerase or ligase. Also disclosed are methods of performing the assay in a liquid phase and on microarrays.

Abstract: Promoters from male reproductive tissues were isolated from corn (Zea mays). These promoters can be used in plants to regulate transcription of target genes including genes for control of fertility, insect or pathogen tolerance, herbicide tolerance or any gene of interest.

Abstract: The invention relates to a process for the preparation of L-amino acids, in particular L-threonine.

Abstract: The present invention provides an isolated nucleic acid comprising a single retroviral LTR, a polypurine tract, a packaging signal, a primer binding site and a rev responsive element. Further provided is an isolated nucleic acid comprising a heterologous nucleotide sequence, a single retroviral long terminal repeat (LTR), a packaging signal, a rev responsive element, a polypurine tract, a eukaryotic promoter, a primer binding site, a bacterial origin of replication and a bacterial selection marker. In addition, the present invention provides an isolated nucleic acid comprising a 5? retroviral LTR and a 3? retroviral LTR, a heterologous nucleotide sequence, a packaging signal, a rev responsive element, a polypurine tract, a eukaryotic promoter, a primer binding site, a bacterial origin of replication and a bacterial selection marker cassette, wherein the bacterial origin of replication and bacterial selection marker are located between the two LTRs.

Abstract: The present invention relates to HSV-based amplicon vectors carrying a genomic DNA fragment, and methods of constructing and using the same. Included within the present invention is a method of converting any large capacity DNA cloning vector, such as a BAC or PAC, into an HSV amplicon or hybrid HSV amplicon using site-specific, or other types of recombination, so that genomic DNA inserts within the BAC or PAC clone can be delivered by infection to a cell, and efficiently expressed. The present invention also relates to a system for the rapid creation of viral vectors carrying transgenes of interest. This aspect of the invention is accomplished through recombination between: (a) a large-capacity cloning vector carrying a viral genome, and (b) a transfer vector containing the transgene of interest. Finally, an expression-ready genomic DNA library is disclosed.

Abstract: The present invention provides random cDNA expression vector libraries, comprising expression vectors which comprise random cDNAs positioned in sense and antisense orientation, which are useful for the delivery and expression of a combination of genetic effector types to host cells. Methods for producing these libraries through bi-directional cloning of random cDNAs are also provided. Also provided herein are methods of using these libraries to screen for agents capable of modulating cell phenotype in desirable ways.

Abstract: A method of providing papillomavirus like particles which may be used for diagnostic purposes or for incorporation in a vaccine for use in relation to infections causd by papillomavirus. The method includes an initial step of constructing one or more recombinant DNA molecules which each encode papillomavirus L1 protein or a combination of papillomavirus L1 protein and papillomavirus L2 protein followed by a further step of transfecting a suitable host cell with one or more of the recombinant DNA molecules so that virus like particles (VLPs) are produced within the cell after expression of the L1 or combination of L1 and L2 proteins. The VLPs are also claimed per se as well as vaccines incorporating the VLPs.

Abstract: Recombinant DNA vectors and methods for cloning and expressing nucleic acid molecules by using a combination of site-specific recombination and end-to-end joining or linking of nucleic acid molecules, such as endonuclease restriction digestion and ligation. The DNAs, vectors and methods can be used for inserting, exchanging, transferring a variety of DNA segment(s) both in vitro and in vivo. Also disclosed are linker molecules and methods using these linkers the can be used for cloning a gene of interest into an expression vector in one-step. The linker sequences comprise adapter sequences for cloning purposes, as well as eukaryotic and prokaryotic ribosome binding sites for increase translation efficiency.

Abstract: A new DNA vector is disclosed comprising a nucleic acid sequence useful for inserting heterologous sequences into the genome of poxviruses by homologous recombination. Also disclosed are recombinant poxviruses carrying heterologous coding sequences transferred by the DNA vector.

Abstract: The present invention relates to hepatitis virus core proteins and nucleic acids. In particular, the present invention provides compositions and methods comprising recombinant hepatitis virus core proteins or nucleic acids for use in vaccine formulations.

Abstract: The present invention provides virus vectors of the family Paramyxoviridae in which the transcription start (S) sequence has been modified so as to modify the expression of genes located downstream thereof, a method for producing the vectors, and uses thereof. By measuring the transcription initiation efficiency of the S sequence of each gene carried by Sendai viruses (SeV), it was clarified that the S sequence of F gene has a significantly lower ability to promote transcription than the other three S sequences. When the S sequence of the F gene of wild type Sendai virus was substituted by the S sequence of the P/M/HN gene-type showing a high transcription initiation efficiency, the F gene of the resultant Sendai virus mutant and genes located downstream thereof show elevated expression levels. It was also revealed that this mutant proliferates more quickly than the wild type.

Abstract: This invention relates to novel adenoviruses useful in the production of high titers of recombinant adeno-associated virus (rAAV) comprising a foreign DNA insert and methods of making these adenoviruses. The adenovirus comprises the AAV rep gene in which the p5 promoter is replaced by a minimal promoter or by no promoter. The invention also provides methods of producing high levels of rAAV as a substantially homogenous preparation and composition of rAAV.

Abstract: The subject invention concerns novel vectors for the rapid and robust selection for cDNA sequences that encode secreted or membrane-bound proteins. The invention also pertains to methods for cloning secreted or membrane-bound proteins, including proteins encoded by novel members of gene families.

Abstract: The invention provides methods of covalently joining nucleic acid molecules and methods of molecular cloning. The methods provide either sequential or simultaneous ligation of flanking or vector nucleic acid molecules to nucleic acid insert molecules by topoisomerase and DNA ligase. The methods provide for directional and non-directional covalent joining and cloning of nucleic acid molecules.

Abstract: The present invention provides efficient transfer of genes into host cells or embryos to transform the cells or embryos by transposition vectors using the minimal amount of nucleotide sequences in the transposon piggyBac required for gene transfer. The transformed cells or embryos may also be developed into transgenic organisms.

Abstract: The invention provides novel yeast promoters useful for controlling the expression of homologous and heterologous nucleic acid molecules in yeast cells. The yeast promoters are induced by a fermentable carbon source, such as glucose, or a non-fermentable carbon source, such as ethanol, or both. Therefore, expression of nucleic acid molecules encoding a polypeptide under the control of the novel yeast promoters may be regulated by varying the level of a fermentable carbon source, or a non-fermentable carbon source, or both.

Abstract: The present invention provides an HSV having a genome with a mutation of a TAATGARAT sequence such that, in the presence of a ICP4 gene product, a native immediate early gene is expressed from the genome with delayed kinetics, the genome having a further inactivating mutation of each of the genes encoding ICP4.

Abstract: The present invention encompasses methods of preparing a recombinant viral vector, within a procaryotic cell, by intermolecular homologous recombination, methods of preparing an infectious viral particle containing the recombinant viral vector and pharmaceutical compositions comprising said vector or particle. The invention also encompasses the therapeutic use of said vector or particle, especially in human gene therapy.

Abstract: The invention provides novel yeast promoters useful for controlling the expression of homologous and heterologous nucleic acid molecules in yeast cells. The yeast promoters are induced by a fermentable carbon source, such as glucose, or a non-fermentable carbon source, such as ethanol, or both. Therefore, expression of nucleic acid molecules encoding a polypeptide under the control of the novel yeast promoters may be regulated by varying the level of a fermentable carbon source, or a non-fermentable carbon source, or both.

Abstract: Methods of repressing expression of a recombinant gene in a cell are provided. The methods include the steps of introducing a transposase DNA binding motif into or adjacent to the gene, and introducing into the cell a transposase that is capable of binding to the transposase DNA binding motif. Methods of producing a population of cells of an organism that vary in their expression of a gene are also provided. The methods involve transfecting the cells with a first polynucleotide sequence encoding the target gene operably linked to a promoter such that the target gene is expressed in the cells, wherein the vector has at least one transposase DNA binding motif within or adjacent to the target gene; and transfecting some of the cells with a second polynucleotide encoding the transposable element operably linked to a second promoter such that the transposable element is expressed in the cells.

Abstract: Methods and compositions are provided for the use of vaccinia virus or other poxviruses as vectors for expression of foreign genes. Expression of foreign genes is obtained by combining vaccinia virus transcriptional regulatory sequence with uninterrupted foreign protein coding sequences in vitro to form a chimeric gene. The chimeric gene is flanked by DNA from a non-essential region of the vaccinia virus genome to provide sites for in vivo homologous recombination. These steps are facilitated by the construction of plasmids that contain multiple restriction endonuclease sites, next to the vaccinia transcriptional regulatory sequences, for insertion of any foreign protein coding sequence. Transfection procedures are used to introduce the DNA into cells where homologous recombination results in the insertion of the chimeric gene into a non-essential region of the vaccinia virus genome.

Abstract: The present invention provides a method for modulating expression of a genetic sequence by introducing, creating or deleting one or more pseudo-translation initiation sites in the nucleotide sequence of an mRNA, upstream of the authentic translation initiation site of an open reading frame. Expression of the genetic sequence can be further modulated by introducing, creating or removing Kozac or Kozac-like sequences proximal to the pseudo-translation initiation site(s). Moreover, expression can be manipulated by the introduction, creation or removal of a termination signal prior to the authentic translation initiation site or after this site but in a different reading frame relative to the reading frame determined by the authentic translation initiation site. Nucleic acid molecules useful for practicing the present methods are also provided. The present invention further provides a method for detecting a disease condition associated with a particular level of expression of a gene or other genetic sequence.

Abstract: A method of generating a double stranded (ds) recombinant nucleic acid molecule covalently linked in both strands by contacting two or more ds nucleotide sequences with a topoisomerase under conditions such that both termini of at least one end of a first ds nucleotide sequence are covalently linked by the topoisomerase to both termini of at least one end of a second ds nucleotide sequence is provided. Also provided is a method for generating a ds recombinant nucleic acid molecule covalently linked in one strand, by contacting two or more ds nucleotide sequences with a type IA topoisomerase under conditions such that one strand, but not both strands, of one or both ends of a first ds nucleotide sequence are covalently linked by the topoisomerase. Compositions for performing such methods, and compositions generated from such methods also are provided, as are kits containing components useful for conveniently practicing the methods.

Abstract: The invention provides an equine infectious anemia (EIA) vaccine that provides immunity to mammals, especially equines, from infection with equine infectious anemia virus (EIAV) and which allows differentiation between vaccinated and non-vaccinated, but exposed, mammals or equines. Preferably said vaccine encompasses at least one mutation in an EIAV which produces a non-functional gene in the vaccine virus that is always expressed in disease-producing wild-type EIA viruses. Additionally, said EIA vaccine virus cannot cause clinical disease in mammals or spread or shed to other mammals including equines.

Abstract: Recombinant poxviruses, such as vaccinia, are provided that comprises a segment comprised of (A) a first DNA sequence encoding a polypeptide that is foreign to poxvirus and (B) a poxvirus transcriptional regulatory sequence, wherein (i) said transcriptional regulatory sequence is adjacent to and exerts transcriptional control over said first DNA sequence and (ii) said segment is positioned within a nonessential genomic region of said recombinant poxvirus. Vaccines, carriers, cells, and media comprising recombinant poxviruses, and methods of immunization with recombinant poxviruses also are provided.

Abstract: The present invention relates to a novel promoter sequence which encodes an isolated DNA molecule comprising the polynucleotide sequence of SEQ ID NO: 1 and which encodes the promoter region of the myostatin gene, or a fragment thereof, or variant thereof which has been modified by the insertion, substitution or deletion of one or more nucleotides, said fragment and variant of said polynucleotide sequence having substantially equivalent function thereto.

Abstract: A vector expressing two foreign genes by using RRE sequence and controlling the ratio of the expression doses of these genes owing to the modification is provided. This vector, which can be provided as a lentivirus vector based on SIVagm, is constructed by modifying a virus-origin expression regulatory sequence into another expression regulatory sequence so as to eliminate the dependency on the virus-origin protein. Although this vector has a packaging signal, it has been modified so that the risk of the occurrence of wild strains due to gene recombination is lowered and no virus structural protein is expressed. This vector is highly useful as a gene therapeutic vector with a need for transferring two genes while controlling the expression doses or expression dose ration thereof.

Abstract: Methods are provided for producing a vector that includes at least one splicable intron. In the subject methods, intron containing vectors are produced from donor and acceptor vectors that each include a site specific recombinase site, where the subject donor and acceptor vectors further include splice donor and acceptor sites that, upon site specific recombination of the donor and acceptor vectors, define an intron in the product vector of the recombination step. Also provided are compositions for use in practicing the subject methods, including the donor and acceptor vectors themselves, as well as systems and kits that include the same. The subject invention finds use in a variety of different applications, including the production of expression vectors that encode C-terminal tagged fusion proteins, the production of expression vectors that encode pure protein and not a fusion thereof, and the like.

Abstract: The present invention relates to a method for isolating from the immunological gene repertoire a gene coding for a receptor having the ability to bind a preselected ligand. Receptors produced by the gene isolated by the method, particularly catalytic receptors, are also contemplated.

Abstract: The invention relates to Adeno-associated virus vectors. In particular, it relates to Adeno-associated virus vectors with modified capsid proteins and materials and methods for their preparation and use.

Abstract: Cloning systems are provided for constructing expression vectors. In one aspect of the invention, a kit is provided for constructing one or more recombinant expression vectors. The kit comprises: a linear driver DNA comprising a promoter sequence, a donor recombination site, and at least one selectable marker, the linear driver DNA being capable of being ligated with one or more linear donor DNA comprising a donor DNA sequence to form one or more circular donor DNA; and a circular acceptor vector comprising an origin of replication and an acceptor recombination site capable of recombining with the circular donor DNA to form the recombinant expression vector for expressing the donor DNA sequence.

Abstract: The present invention provides compositions, methods, and kits for covalently linking nucleic acid molecules. The methods include a strand invasion step, and the compositions and kits are useful for performing such methods. For example, a method of covalently linking double stranded (ds) nucleic acid molecules can include contacting a first ds nucleic acid molecule, which has a topoisomerase linked to a 3? terminus of one end and has a single stranded 5? overhang at the same end, with a second ds nucleic acid molecule having a blunt end, such that the 5? overhang can hybridize to a complementary sequence of the blunt end of the second nucleic acid molecule, and the topoisomerase can covalently link the ds nucleic acid molecules. The methods are simpler and more efficient than previous methods for covalently linking nucleic acid sequences, and the compositions and kits facilitate practicing the methods, including methods of directionally linking two or more ds nucleic acid molecules.

Abstract: The increased use of nucleotide sequence data mining techniques has amplified the demand for efficient methods of producing recombinant proteins in eukaryotic cells. A strategy is provided for enhancing the synthesis of recombinant amino acid sequences by polymerizing expression cassettes in vitro before producing recombinant hosts.

Abstract: The inventive method of producing a eukaryotic viral vector comprises contacting a eukaryotic cell, which comprises a unique enzyme that nicks or cleaves a DNA molecule, with a recombinant phage vector, or contacting a eukaryotic cell, which does not comprise a unique enzyme that nicks or cleaves a DNA molecule, simultaneously or sequentially, in either order, with (i) a unique enzyme that nicks or cleaves a DNA molecule, and (ii) a recombinant phage vector. The recombinant phage vector comprises the DNA molecule comprising (a) a eukaryotic viral vector genome comprising a coding sequence, (b) a phage packaging site that is not contained within the eukaryotic viral vector genome, and (c) a promoter that is operably linked to the coding sequence. Alternatively, the DNA molecule is not present within the recombinant phage vector. The eukaryotic cell is contacted with the first DNA molecule and a recombinant phage vector.

Abstract: The present invention relates to a polynucleotide comprising a ubiquitous chromatin opening element (UCOE) which is not derived from 13. The polynucleotide of any one of claims 1 to 7, wherein the UCOE comprises the sequence of FIG. 20 between nucleotides 1 to 7627 or a functional homologue or fragment thereof. an LCR. The present invention also relates to a vector comprising the polynucleotide sequence, a host cell comprising the vector, use of the polynucleotide, vector or host cell in therapy and in an assay, and a method of identifying UCOEs. The UCOE opens chromatin or maintains chromatin in an open state and facilitates reproducible expression of an operably-linked gene in cells of at least two different tissue types.

Abstract: Novel DNA sequences derived from a family of genes encoding ?-galactosidases in tomato are disclosed. ?-Galactosidase II has demonstrated enzyme activity in cell wall disassembly, leading to loss of tissue integrity and fruit softening. Modification of ?-galactosidase II gene expression in plants transformed for expression in the antisense direction results in improvement of the quality of fruit texture and firmness.

Abstract: The present invention provides tangible means and methods for stimulation of angiogenesis via enhanced endothelial expression of core proteins having a syndecan-4 cytoplasmic region intracellularly. The tangible means include a prepared DNA sequence fragment having separate and individual DNA sequenced portions coding for an heparan sulfate binding extracellular domain, a central transmembrane domain, and a cytoplasmic domain coding for the syndecan-4 polypeptide. The prepared DNA sequence unitary fragment may be delivered to endothelial cells in-situ, both under in-vivo and/or in-vitro conditions, using suitable expression vectors including plasmids and viruses. The resulting transfected endothelial cells overexpress heparan sulfate binding, core proteins; and the resulting overexpression of these proteoglycan entities causes stimulation of angiogenesis in-situ.

Abstract: Site-specific recombinase based methods for making a recombinant adenoviral genome, as well as kits for practicing the same and the recombinant adenovirus vectors produced thereby, are provided. In the subject methods, the subject genomes are prepared from donor and acceptor vectors that each include at least one site recombinase recognition site, where in certain preferred embodiments, one of the donor and acceptor vectors includes a single recombinase recognition site while the other includes two recombinase recognition sites. The acceptor vector includes an adenoviral genome having an E region deletion. The donor vector includes an insertion nucleic acid. In the subject methods, the donor and acceptor vectors are combined in the presence of a recombinase to produce an adenoviral genome that includes the insertion nucleic acid. The subject adenoviral genomes find use in a variety of applications, including as vectors for use in a variety of applications.

Abstract: The present invention provides vectors and methods which improve the efficiency of nucleic acid insertion into circular vectors, which generally facilitate nucleic acid cloning and specifically facilitate the preparation of DNA libraries. In general, the present invention involves separation of the cloning process into two distinct steps: (a) insertion which is done at a high nucleic acid concentration favoring intermolecular joining, and (b) circularization which is performed at a low nucleic acid concentration favoring intramolecular circularization. The present vectors generally have distinct insertion ends and circularization ends which are blocked from covalent joining during the insertion step. Circularization ends contemplated by the present invention include complementary cohesive ends and topoisomerase-linked ends. The present vectors and methods allow minute amounts of nucleic acid inserts to be efficiently cloned.

Abstract: A simple method for modifying genes in a recombination deficient host cell is disclosed. Such modifications include generating insertions, deletions, substitutions, and/or point mutations at any chosen site in the independent origin based cloning vector. The modified gene is contained in an independent origin based cloning vector that is used to introduce a modified heterologous gene into a cell. Such a modified vector may be used in the production of a germline transmitted transgenic animal, or in gene targeting protocols in eukaryotic cells. In particular, high throughput methodology is provided for generating the modified the independent origin based cloning vectors of the present invention.