Abstract: The present invention relates to means for cleaving a nucleic acid cleavage structure in a site-specific manner. Enzymes, including 5? nucleases and 3? exonucleases, are used to detect and identify nucleic acids derived from microorganisms. Methods are provided which allow for the detection and identification of bacterial and viral pathogens in a sample.

Abstract: The present invention relates to nucleic acids and nucleic acid fragments encoding amino acid sequences for flavonoid biosynthetic enzymes in plants, and the use thereof for the modification of flavonoid biosynthesis in plants. More particularly, the flavonoid biosynthetic enzyme is selected from the group consisting of chalcone isomerase (CHI), chalcone synthase (CHS), chalcone reductase (CHR), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin reductase (LCR), flavonoid 3?, 5? hydrolase (F3?5?H), flavanone 3-hydroxylase (F3H), flavonoid 3?-hydroxylase (F3?H), phenylalanine ammonia-olyase (PAL) and vestitone reductase (VR), and functionally active fragments and variants thereof.

Abstract: A bacterial growth medium for promoting auto-induction of transcription of cloned DNA in cultures of bacterial cells grown batchwise is disclosed. The transcription is under the control of a lac repressor. Also disclosed is a bacterial growth medium for improving the production of a selenomethionine-containing protein or polypeptide in a bacterial cell, the protein or polypeptide being produced by recombinant DNA techniques from a lac or T7lac promoter, the bacterial cell encoding a vitamin B12-dependent homocysteine methylase. Finally, disclosed is a bacterial growth medium for suppressing auto-induction of expression in cultures of bacterial cells grown batchwise, said transcription being under the control of lac repressor.

Abstract: Disclosed are a method of preparing an active Nanoarchaeum equitans B-type DNA polymerase (Neq DNA polymerase), an active Neq DNA polymerase prepared according to the method, and a polymerase chain reaction (PCR) using the active Neq DNA polymerase. The active Neq DNA polymerase may be used in various nucleic acid polymerization reactions, such as PCR.

Abstract: Production of ethanol using a strain of xylose-utilizing Zymomonas with a genetic modification of the glucose-fructose oxidoreductase gene was found to be improved due to greatly reduced production of xylitol, a detrimental by-product of xylose metabolism synthesized during fermentation.

Abstract: A strain of xylose-utilizing Zymomonas was engineered with a genetic modification to the glucose-fructose oxidoreductase gene resulting in reduced expression of GFOR enzyme activity. The engineered strain exhibits reduced production of xylitol, a detrimental by-product of xylose metabolism. It also consumes more xylose and produces more ethanol during mixed sugar fermentation under process-relevant conditions.

Abstract: This invention relates to methods for altering the splicing of mRNA in cells. In particular, this invention also relates to methods for increasing the ratio of wild type to misspliced forms of mRNA and corresponding encoded proteins in cells possessing a mutant gene encoding either the i) misspliced mRNA corresponding to the mutant protein or ii) a component in the splicing machinery responsible for processing the misspliced mRNA. In addition, this invention relates to treating individuals having a disorder associated with a misspliced mRNA, such as Familial Dysautonomia or Neurofibromatosis 1, by administering to such an individual a cytokinin such as kinetin.

Abstract: The present invention describes methods of identifying altered recombinases and compositions thereof, wherein at least one amino acid is different from a parent, wild-type recombinase and the altered recombinase has improved recombination efficiency towards wild-type and/or pseudo att site sequences relative to the parent, wild-type recombinase. The present invention also includes methods of modifying the genomes of cells using the altered recombinases, including methods of site-specifically integrating a polynucleotide sequence of interest in a genome of a eucaryotic cell.

Abstract: The invention relates to hyperactive, non-phosphorylated, mutant transposases of mariner mobile genetic elements. The invention also relates to recombinant nucleotide sequences encoding such transposases. The invention further relates to a method of producing said transposases and to the use thereof for in vitro or in vivo transposition.

Abstract: The present invention provides a novel method of significantly promoting the ratio of homologous recombination in desirable cells. In order to enhance the ratio of homologous recombination in desirable cells such as eukaryotic cells, mutation is introduced into genes encoding factors necessary for non-homologous recombination, such as Ku70 or Ku80, or the above genes are disrupted, so as to cause the loss of the functions thereof. At the time, foreign DNA is introduced into the cells via the electroshock method or the like, so as to carry out homologous recombination, thereby promoting the frequency of homologous recombination in the cells.

Abstract: Compositions and methods are provided to identify functional mutant ribosomes that may be used as drug targets. The compositions and methods allow isolation and analysis of mutations that would normally be lethal and allow direct selection of rRNA mutants with predetermined levels of ribosome function. The compositions and methods of the present invention may be used to identify antibiotics to treat a large number of human pathogens through the use of genetically engineered rRNA genes from a variety of species. The invention further provides novel plasmid constructs to be used in the methods of the invention.

Abstract: Alterations in the genetic content of a cell underlie many human diseases, including cancers. A method called Digital Karyotyping provides quantitative analysis of DNA copy number at high resolution. This approach involves the isolation and enumeration of short sequence tags from specific genomic loci. Analysis of human cancer cells using this method identified gross chromosomal changes as well as amplifications and deletions, including regions not previously known to be altered. Foreign DNA sequences not present in the normal human genome could also be readily identified. Digital Karyotyping provides a broadly applicable means for systematic detection of DNA copy number changes on a genomic scale.

Abstract: Methods for promoting and suppressing auto-induction of transcription of cloned DNA in cultures of T7 expression strains are disclosed.

Abstract: A clarification system and method of using for plasmid DNA that is centrifugation-free. The system is comprised of a coarse filter, about 50 to about 200 microns pore size, followed by a prefilter of about 1 to about 2 micron pore size and then a final filter of about 0.22 micron. Preferably, the prefilter and final filter are combined into one filter housing to reduce system hold up volume and enhance recovery of the plasmid DNA. The method allows for continuous as well as batch operation.

Abstract: Bacteria are manipulated to create desirable output traits using dominant negative alleles of mismatch repair proteins. Enhanced hypermutation is achieved by combination of mismatch repair deficiency and exogenously applied mutagens. Stable bacteria containing desirable output traits are obtained by restoring mismatch repair activity to the bacteria.

Abstract: Methods are presented for enhancing the natural mutation rate of micro-organisms, particularly bacteria via a modified phosphate. The novel metabolite inhibits DNA repair mechanisms in vivo resulting in a 100-200 hundred fold increase in the mutation rate of bacteria. The method yields viable cells and allows for the continuous selection of incremental traits. The modified phosphate can also be used to randomly mutate specific genes. In particular, high rates of random mutagenesis can be readily achieved in vivo using recombinant DNA phage. The phage are amplified in mutator media containing the modified phosphate. The resultant phage can be further mutated by another round of infection and growth in mutator media. After two such rounds of amplification significant mutation rates are achieved such that each phage insert bears a novel mutation. The mutator media can also be used to mutagenize recombinant DNA plasmids in virtually any bacterial host.

Abstract: The present invention relates to means for cleaving a nucleic acid cleavage structure in a site-specific manner. Enzymes, including 5? nucleases and 3? exonucleases, are used to detect and identify nucleic acids derived from microorganisms. Methods are provided which allow for the detection and identification of bacterial and viral pathogens in a sample.

Abstract: The present invention relates to a promoter for high-throughput screening for inhibitors against Mycobacteria under low carbon or starved conditions. Further, the use of this novel 200 bp promoter open new vistas and provides a new system that would enable the TB drug developers to isolate and develop highly efficient inhibitors or medicines against ever evolving and changing M. tuberculosis mycobacteria.

Abstract: Described herein are methods for increasing the amount of protein secreted by a cell. In one case, a cell is provided which contains a heterologous nucleic acid encoding a protein having unfolded protein response modulating activity and a heterologous nucleic acid encoding a protein of interest to be secreted. In one case, the protein having unfolded protein response modulating activity is selected from the proteins selected from the group consisting of HAC1, PTC2 and IRE1. The protein of interest can be any secreted protein such as a therapeutic or an industrial enzyme. For example the protein can be selected from the group consisting of lipase, cellulase, endo-glucosidase H, protease, carbohydrase, reductase, oxidase, isomerase, transferase, kinase, phosphatase, alpha-amylase, glucoamylase, lignocellulose hemicellulase, pectinase and ligninase.

Abstract: The present invention provides an Ecoli host cell expressing a recombinant antibody characterized in that the Ecoli host cell has been genetically modified in order to change at least one physical property of one or more Ecoli proteins which in the wild type copurify with said recombinant antibody.