Abstract: The present invention relates generally to recombinant genetic technology. More particularly, the present invention relates to compositions and methods for use in selection and isolation of nucleic acid molecules. The invention further relates to methods for the preparation of individual nucleic acid molecules and populations of nucleic acid molecules, as well as nucleic acid molecules produced by these methods. The invention also relates to screening and/or selection methods for identifying and/or isolating nucleic acid molecules which have one or more common features (e.g., characteristics, activities, etc) and populations of nucleic acid molecules which share one or more features.

Abstract: The present invention relates to a method for cloning double-stranded DNA (ds DNA) molecules. In particular, the present invention relates to a method for cloning ds DNA molecules using terminal transferase to tail at least one 3? termini of the ds DNA molecules with nucleotides and ligating the tailed ds DNA molecules with a vector. Also provided are kits and compositions that can be used for cloning ds DNA molecules.

Abstract: Provided herein is a method for homologous end cloning using a 5?-exonuclease. One aspect provides a method of generating a recombinant DNA molecule comprising 5? exonuclease digestion of DNA molecules, exonuclease inactivation, annealing of 3? overhangs to form a annealed complex. Also provided is a method a method of generating a recombinant DNA molecule comprising 5? exonuclease digestion of DNA molecules, exonuclease inactivation, annealing of 3? overhangs to form a annealed complex, and extension of 3? ends to fill gaps corresponding to exonuclease removal to form a substantially non-gapped annealed complex. Also provided is a one reaction method in which no further additions need be made to the reaction mixture and the reaction mixture is only manipulated thereafter as to incubation time and incubation temperature. Complexes formed according to methods described herein can be transformed into a host cell without further in vitro processing.

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 polynucleoticle, 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: The invention relates to an immunogenic composition comprising a recombinant vector characterized in that it comprises a polynucleotide comprising the cis-acting central initiation region (cPPT) and the cis-acting termination region (CTS), these regions being of retroviral or retroviral-like origin, said vector comprising in addition a defined nucleotide sequence (transgene or sequence of interest) and regulatory signals of retrotranscription, expression and encapsidation of retroviral or retroviral-like origin, wherein the composition is capable of inducing or of stimulating a cell-mediated response for instance a CTL (Cytotoxic T Lymphocytes) response or a CD4 response, against one or several epitopes encoded by the transgene sequence present in the vector.

Abstract: The present invention concerns a novel recombinant eukaryotic expression plasmid pCMV-HA-pprI encoding the pprI gene isolated from Deinococcus radiodurans R1, the method for preparing pCMV-HA-pprI, and its expression in human 293T cells. The present invention also discloses the optimal method and process of pprI gene transfection by in vivo electroporation, and the radioprotective and therapeutic effects of the recombinant pCMV-HA-pprI on lethally irradiated mice.

Abstract: The present invention provides an agent that modulates physiological condition of pests, wherein the agent has an ability to modulate the activity of an insect vesicle-fusing ATPase; a method for assaying pesticidal activity of a test substance, which comprises measuring the activity of a vesicle-fusing ATPase in a reaction system in which the vesicle-fusing ATPase contacts with a test substance, and the like.

Abstract: Disclosed, among other things, are compounds having the structure wherein X comprises a bond or a linker, LABEL comprises at least one detectable label, W1 taken alone is —H or —OH, W2 is —OH or a non-extendable moiety, W3 when taken alone is —H or when taken together with W1 is —CH2—O—, and W4 is OH, monophosphate, diphosphate, or triphosphate. Also disclosed are labeled polynucleotide compounds and methods of use thereof.

Abstract: Disclosed is a method which can achieve the homologous recombination of a gene of interest selectively. Also disclosed is a recombinant DNA molecule produced by the method. Specifically disclosed is a homologous recombination method which uses a PCR product and a linearized vector. The PCR product comprises a sequence for a target gene and amplification primer sequences P1 and P2 attached to both termini of the sequence for the target gene.

Abstract: The present invention is directed generally to methods facilitating the cloning of nucleic acid molecules. In particular, the invention relates to the use of polymerase inhibitors, including but not limited to anti-polymerase antibodies (such as anti-Taq antibodies) and fragments thereof, to inactivate residual polymerase activity remaining after the amplification (particularly via PCR) of a target nucleic acid molecule. The invention further provides compositions, particularly storage-stable compositions, comprising one or more components, such as one or more restriction endonucleases and one or more polymerase inhibitors, that are useful in cloning amplified or synthesized nucleic acid molecules by the above-described methods. The invention also relates to nucleic acid molecules produced by these methods, and to genetic constructs (such as vectors) and host cells comprising these nucleic acid molecules.

Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Abstract: Method of preparing I-CreI meganuclease variants having a modified cleavage specificity, variants obtainable by said method and their applications either for cleaving new DNA target or for genetic engineering and genome engineering for non-therapeutic purposes. Nucleic acids encoding said variants, expression cassettes comprising said nucleic acids, vectors comprising said expression cassettes, cells or organisms, plants or animals except humans, transformed by said vectors.

Abstract: The present invention discloses nucleic acid sequences which encode infectious hepatitis C viruses and the use of these sequences, and polypeptides encoded by all or part of these sequences, in the development of vaccines and diagnostics for HCV and in the development of screening assays for the identification of antiviral agents for HCV.

Abstract: Disclosed herein are methods for generating recombinant DNA molecules in cells using homologous recombination mediated by recombinases and similar proteins. The methods promote high efficiency homologous recombination in bacterial cells, and in eukaryotic cells such as mammalian cells. The methods are useful for cloning, the generation of transgenic and knockout animals, and gene replacement. The methods are also useful for subcloning large DNA fragments without the need for restriction enzymes. The methods are also useful for repairing single or multiple base mutations to wild type or creating specific mutations in the genome. Also disclosed are bacterial strains and vectors which are useful for high-efficiency homologous recombination.

Abstract: A DNA sequence from the upstream region of cold-inducible hutU gene of the Antarctic Psychrotrophic Bacterium Pseudomonas syringae, comprising promoter elements and other regulatory sequences, with unique ‘CAAAA’ nucleotide sequence at ?10 site of multiple transcription start sites and using said promoter to express genes of interest in the said bacterium at temperature as low as 4° C. and using the said bacterium with generation time ranging between two and half to three hours, as a system to produce heat labile proteins of pharmaceutical significance.

Abstract: It is intended to provide a virus vector by which an exogenous nucleotide sequence can be inserted and easily transferred into a mammalian host cell and a gene encoded by the exogenous nucleotide sequence can be expressed in the host cell, and which has a low risk of pathogenicity and is appropriately usable in gene therapy of mammals. Namely, a recombinant vector originating in HHV-6 which has an exogenous nucleotide sequence in a portion corresponding to at least one region selected from the group consisting of U2, U3, U4, U5, U6, U7, U8, U24, and U25 regions of HHV-6; or a recombinant vector originating in HHV-7 which has an exogenous nucleotide sequence in a portion corresponding to at least one region selected from the group consisting of U2, U3, U4, U7, U8, U24, U24a, and U25 regions of HHV-7.

Abstract: The present invention provides duplexed parvovirus vector genomes that are capable under appropriate conditions of forming a double-stranded molecule by intrastrand base-pairing. Also provided are duplexed parvovirus particles comprising the vector genome. Further disclosed are templates and methods for producing the duplexed vector genomes and duplexed parvovirus particles of the invention. Methods of administering these reagents to a cell or subject are also described. Preferably, the parvovirus capsid is an AAV capsid. It is further preferred that the vector genome comprises AAV terminal repeat sequences.

Abstract: The present invention is a method for incorporating an integrase-fusion protein into a third-generation lentivirus vector, comprising: (i) transfecting a vector packaging plasmid into a producer cell, wherein the vector packaging plasmid contains a lentivirus transfer construct and a gene encoding the integrase-fusion protein, said gene being fused to the pol-polyprotein gene; (ii) transcription and translation of the genes; and (iii) release of the integrase-fusion protein from the pol-polyprotein.

Abstract: The present invention concerns an universal polypeptidic carrier for targeting directly or indirectly a molecule to Gb3 receptor expressing cells and having the following formula STxB-Z(n)-Cys, wherein: —STxB is the Shiga Toxin B subunit or a functional equivalent thereof, Z is an amino-acid devoided of sulfydryl group, n being 0, 1 or a polypeptide, Cys is the amino-acid Cysteine, and the use thereof for MHC class I and MHC class II presentation of antigens.

Abstract: Methods and compositions for cloning a donor DNA molecule into an acceptor vector at a predetermined location are described. The methods are based on homologous recombination mediated by in vitro treatment of the donor DNA and the acceptor vector with an enzyme cocktail containing an exonuclease and a single-stranded DNA binding protein.

Abstract: Improvements in plasmid DNA production technology are needed to insure the economic feasibility of future DNA vaccines and DNA therapeutics. General methods are described, by means of which it is possible to dramatically increase plasmid DNA productivity. These processes feature RNA based inducers of plasmid copy number.

Abstract: The present invention is directed generally to methods facilitating the cloning of nucleic acid molecules. In particular, the invention relates to the use of polymerase inhibitors, including but not limited to anti-polymerase antibodies (such as anti-Taq antibodies) and fragments thereof, to inactivate residual polymerase activity remaining after the amplification (particularly via PCR) of a target nucleic acid molecule. The invention further provides compositions, particularly storage-stable compositions, comprising one or more components, such as one or more restriction endonucleases and one or more polymerase inhibitors, that are useful in cloning amplified or synthesized nucleic acid molecules by the above-described methods. The invention also relates to nucleic acid molecules produced by these methods, and to genetic constructs (such as vectors) and host cells comprising these nucleic acid molecules.

Abstract: Methods, compositions and kits are disclosed for obtaining directionally truncated polypeptides by inserting a transposon. Preferably the transposon comprises a selectable marker and an ori, and optionally a promoter, a ribosome binding site and a translation start codon, into a target sequence in vitro or in vivo. Amplification products, varying in length depending on the transposon insertion site, are obtained using one primer that anneals to the target sequence and a second primer that anneals to the transposon. Amplification products are ligated to circular dsDNA, transformed into host cells, and individual colonies, each containing a directionally truncated clone of the target sequence, are obtained by plating on medium for which the selectable marker encodes resistance. Directionally truncated polypeptides encoded by the target sequence are obtained in vivo by inducing an RNAP in the host cells that uses the promoter or, in vitro by cell-free transcription and translation.

Abstract: The present invention relates to fungal ?-15 fatty acid desaturases that are able to catalyze the conversion of linoleic acid (18:2, LA) to alpha-linolenic acid (18:3, ALA). Nucleic acid sequences encoding the desaturases, nucleic acid sequences which hybridize thereto, DNA constructs comprising the desaturase genes, and recombinant host plants and microorganisms expressing increased levels of the desaturases are described. Methods of increasing production of specific omega-3 and omega-6 fatty acids by over-expression of the ?-15 fatty acid desaturases are also described herein.

Abstract: The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.

Abstract: The present invention relates to a method for in vitro recombining polynucleotides sequences of interest from at least two initial different polynucleotide sequences of interest by cleavage/ligation of circular DNA molecules.

Abstract: Methods and compositions using unprocessed (i.e., not deliberately or intentionally cleaved, circularized, or supercoiled) rolling circle amplification (RCA) product.

Abstract: Strong, constitutive plant promoters are provided, referred herein to as AA6 promoters, which remain strong and constitutive under biotic and/or abiotic stress conditions. Also provided are transgenic cells and organisms, especially plant cell and plants, comprising an AA6 promoter and methods for expressing nucleic acid sequences in cells and organisms using AA6 promoters.

Abstract: A process for the construction of plant transformation vector comprising: digesting a binary vector pCAMBIA 1304 with EcoRI and Sal I; subjecting the digested binary vector to the step of end filling by Klenow; re-ligating the said binary vector by known method; obtaining CaMV 35 8 promoter cassette with ? enhancer from pSH9; incorporating the said Camv35S promoter cassette into the Hind III site of the said binary vector to obtain modified pCAMBIA 1304 vector; subjecting pore DNA fragment (1206 bp) to the step of amplification using a pair of primers; introducing EcoRI restriction sites to both the primers; ligating the said amplified cDNA fragment to pGEM T-easy; extracting EcoRI digested porC cDNA fragment from cloned pGEM T-easy; inserting said EcoRI digested porC cDNA fragment into modified pCAMBIA 1304 plant transformation vector to produce recombinant plasmids construct (pCAMBIA 1304-AtporC).

Abstract: An herpes simplex virus wherein the herpes simplex virus genome comprises nucleic acid encoding an antisense to the squamous cell carcinoma related oncogene (asSCCRO); and an herpes simplex virus wherein the herpes simplex virus genome comprises nucleic acid encoding a short interfering ribonucleic acid (siRNA) molecule that is capable of repressing or silencing expression of squamous cell carcinoma related oncogene (SCCRO) nucleic acid or polypeptide are disclosed together with methods for generation and applications of such viruses.

Abstract: Transposase proteins that are modified relative to and have higher transposase activities than the wild-type Tn5 transposase are disclosed. A transposase protein of the present invention differs from the wild-type Tn5 transposase at amino acid position 41, 42, 450, or 454 and has greater avidity than the wild-type Tn5 transposase for at least one of a Tn5 outside end sequence as defined by SEQ ID NO:3, a Tn5 inside end sequence as defined by SEQ ID NO:4, and a modified Tn5 outside end sequence as defined by SEQ ID NO:5. Also disclosed are various systems and methods of using the transposase proteins of the present invention for in vitro or in vivo transposition.

Abstract: Linear vectors derived from bacteriophage of E. coli and host cells suitable for cloning are provided. The linear vectors include a left arm comprising a left telomere and a first selectable marker, a right arm comprising a right telomere and a second selectable marker and a cloning region located between the left arm and the right arm. Optional further components of the vector include transcriptional termination sequences, multiple cloning sites and reporter stuffer regions.

Abstract: The present invention relates to modified poxyiral vectors and to methods of making and using the same. In particular, the invention relates to recombinant avipox that expresses gene products of foot and mouth disease virus (FMDV), and to compositions or vaccines that elicit immune responses directed to FMDV gene products and which can confer protective immunity against infection by FMDV.

Abstract: A method for using cloning vector plasmids to produce DNA molecules, such as transgenes, in a single cloning step. The transgenes can be used for the purpose of gene expression or analysis of gene expression. The plasmid cloning vectors are engineered to minimize the amount of manipulation of DNA fragment components by the end user of the vectors and the methods for their use. Transgenes produced using the invention may be used in a single organism, or in a variety of organisms including bacteria, yeast, mice, and other eukaryotes with little or no further modification.

Abstract: The present invention provides a method for constructing recombinant translationally coupled operons, a method for producing useful metabolites using the bacterium containing the coupled operons, and a method for monitoring gene expression.

Abstract: Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

Abstract: A method for using cloning vector plasmids to produce DNA molecules, such as transgenes, in a single cloning step. The transgenes can be used for the purpose of gene expression or analysis of gene expression. The plasmid cloning vectors are engineered to minimize the amount of manipulation of DNA fragment components by the end user of the vectors and the methods for their use. Transgenes produced using the invention may be used in a single organism, or in a variety of organisms including bacteria, yeast, mice, and other eukaryotes with little or no further modification.

Abstract: The present invention relates to the generation of replication-competent viruses having therapeutic utility. The replication-competent viruses of the invention can express proteins useful in the treatment of disease.

Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid molecules using iterative activation of one or more vector-encoded traits to progressively assemble a longer nucleic acid insert. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using iterative activation of one or more vector-encoded traits.

Abstract: The present invention discloses a method of producing polypeptides, including insulinotropic GLP-1 (7-36) polypeptide and/or GLP-1 analogs, by ligating genes in a tandem way. Also disclosed are the recombinant polypeptides produced by such a method. Using the method of this invention, 1 to 32 copies of GLP-1 (7-36) and/or GLP-1 analog genes may be expressed in tandem and the desired polypeptide can be obtained after cleavage of a fusion protein and further processes of separation and purification thus making possible the production of recombinant polypeptides, including recombinant GLP-1 (7-36) and/or GLP-1 analogs on a large scale, at a significantly reduced production cost.

Abstract: The invention relates to methods of making modular chimeric protein expression products and compositions utilized in the methods. In particular, the invention relates to sequential, directional cloning of polynucleotides encoding polypeptide modules. Each clonable element or module contains an open reading frame of interest flanked by predetermined restriction sites. The methods include using modules and vectors containing these modules as starting materials for recombinant DNA techniques. One advantage of the invention is that it allows for many variations of fusion proteins to be made quickly and easily without needing to design and evaluate each subsequent cloning step.

Abstract: The invention features methods of analyzing the kinetics properties of transfection reactions. Also featured are methods for creating structural promoters which are effectively unregulated by enhancers and repressors. The structural promoters are significantly more active than the native promoter sequences upon which they are based.

Abstract: In one aspect, the invention provides a random or semirandom siRNA (encoding) library. Another aspect of the invention pertains to methods for construction of random or semirandom siRNA (encoding) libraries. Another aspect of the invention is vector systems for use in constructing siRNA libraries and/or that can express single siRNAs and siRNA libraries both constitutively and in an inducible fashion. In another aspect, the invention provides a method of using an siRNA library. The siRNA library is introduced into a population of cells. The population of cells then is subjected to a selection process to select a subpopulation of cells exhibiting a different behavioral, biochemical, chemical, functional, molecular, morphological, phenotypic, or physical property from the remainder of population. Following the selection process, the subpopulation of cells can be isolated, analyzed, and/or cloned as desired.

Abstract: The invention provides cells and methods of circularizing linear DNA molecules. The cell is an isolated Escherichia coli cell which transiently expresses the Cre recombinase protein from an integrated Cre recombinase gene, and which is at least transiently repressed for RecBCD activity. The cells are used in a method of circularizing a linear DNA molecule comprising at least two loxP sites. The DNA molecule is introduced into the cells, and the linear DNA molecule is joined at said loxp sites.

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: Methods and compositions are provided for generating a single-stranded extension on a polynucleotide molecule, the single-stranded extension having a desired length and sequence composition. Methods for forming single-stranded extensions include: the use of a cassette containing at least one nicking site and at least one restriction site at a predetermined distance from each other and in a predetermined orientation; or primer-dependent amplification which introduces into a polynucleotide molecule, a modified nucleotide which is excised to create a nick using a nicking agent. The methods and compositions provided can be used to manipulate a DNA sequence including introducing site specific mutations into a polynucleotide molecule and for cloning any polynucleotide molecule or set of joined polynucleotide molecules in a recipient molecule such as a vector of choice.

Abstract: The present invention provides duplexed parvovirus vector genomes that are capable under appropriate conditions of forming a double-stranded molecule by intrastrand base-pairing. Also provided are duplexed parvovirus particles comprising the vector genome. Further disclosed are templates and methods for producing the duplexed vector genomes and duplexed parvovirus particles of the invention. Methods of administering these reagents to a cell or subject are also described. Preferably, the parvovirus capsid is an AAV capsid. It is further preferred that the vector genome comprises AAV terminal repeat sequences.

Abstract: To provide a heterologous protein expression system which enables the fission yeast Schizosaccharomyces pombe as a host to produce of a heterologous protein which is almost impossible to express, or if possible, produced at low levels, under control of conventional promoters. The present invention provides an expression for use in the fission yeast Schizosaccharomyces pombe, a transformant carrying the expression vector, a method for producing a heterologous protein using the transformant, in particular a method for producing a heterologous protein in which a heat shock protein gene promoter in Schizosaccharomyces pombe is used to regulate gene expression by application of a specific form of stress, whereby the timing of the production of the desired heterologous protein can be controlled.

Abstract: The invention relates to the generation and characterization of stable MMLV reverse transcriptase mutants. The invention also discloses methods of using stable MMLV reverse transcriptase mutants.

Abstract: The invention relates to methods and means for producing adenoviral vectors on complementing cell lines, wherein the early region 4 open reading frame 6 (E4-orf6) encoding nucleic acid is present in the adenoviral vector and wherein the E4-orf6 gene product is compatible with one or more products of the E1 gene products provided by the complementing cell, such that the adenoviral vector can be efficiently produced by the complementing cell.