Abstract: A method for the rapid isolation and identification of the DNA sequence of transposable element-tagged genes is provided. The method comprises a modified AFLP approach using a transposable element-anchored amplification to identify and clone an amplification product that is associated with a mutant phenotype. Once cloned, the amplification product of interest may be used to screen a cDNA library directly or may be sequenced and compared to available databases for sequence homology. A modification of this approach provides a method for the identification of the location of an additional type of insertion event into genomic DNA, more specifically transgene insertion into the genome of a host organism.

Abstract: The invention provides isolated cellulose synthase nucleic acids and their encoded proteins. The present invention provides methods and compositions relating to altering cellulose synthase concentration and/or composition of plants. The invention further provides recombinant expression cassettes, host cells, and transgenic plants.

Abstract: The invention features a method for identifying a gene associated with a desired phenotype. This method includes the steps of: (a) providing a plurality of cell cultures that include plant, animal, or fungal cells capable of exhibiting a desired phenotype; (b) contacting each of at least a subset of said cells with a stimulus that (i) induces said cells to exhibit the phenotype, or (ii) does not induce said cell cultures to exhibit the phenotype; (c) determining the presence of the phenotype in the cell cultures of step (b); and (d) identifying a gene having increased expression in response to stimuli that induce the phenotype but do not have increased expression in response to stimuli that do not induce the phenotype.

Abstract: Methods and compositions for the stacking of multiple nucleotide sequences at precise locations in the genome of a plant or plant cell are provided. Specifically, transfer cassettes comprising nucleotide sequences of interest flanked by non-identical recombination sites are introduced into a plant comprising a target site. The target site contains at least a set of non-identical recombination sites corresponding to those on the transfer cassette. Exchange of the nucleotide sequences flanked by the recombination sites is effected by a recombinase. The transfer cassettes and target sites are designed so as to allow for the stacking or ordering of nucleotide sequences at precise locations in the plant genome.

Abstract: A nucleic acid sequence effectively expressing FLP recombinase in monocot plants, particularly in maize. Stable, transformed maize plants harboring a gene encoding FLP or harboring FRT nucleic acid sequences enable efficient site-directed recombination of nucleic acid sequences in a monocot's genome.

Abstract: The invention relates to the genetic manipulation of plants, particularly to the expression of galactomannan biosynthetic genes in transformed plants. Nucleotide sequences for the GDP-mannose pyrophosphorylase genes and methods for their use are provided. The sequences find use in the production of gum in plants. A nucleic acid encoding a GDP-mannose pyrophosphorylase from maize is taught, as are plants and plant cells transformed with it.

Abstract: Methods for the targeted integration of nucleotide sequences into a plant are provided. Transfer cassettes comprising nucleotide sequences of interest flanked by non-identical recombination sites are used to transform a plant comprising a target site. The target site contains at least a set of non-identical recombination sites corresponding to those on the transfer cassette. Exchange of the nucleotide sequences flanked by the recombination sites is effected by a recombinase.

Abstract: Methods for identifying organisms capable of degrading fumonisin. Fumonisin can be incorporated into culture medium for selection of organisms resistant to fumonisin and/or capable of growing on fumonisin as a sole carbon source. Using this method, several organisms have been identified. These organisms can be used to isolate the enzymes and the genes responsible for conferring fumonisin-resistance. The gene can be cloned and inserted into a suitable expression vector so that the protein can be further characterized. Additionally, the DNA encoding for fumonisin degrading enzymes can be used to transform plant cells normally susceptible to Fusarium or other toxin-producing fungus infection. Plants can be regenerated from the transformed plant cells. In this way, a transgenic plant can be produced with the capability of degrading fumonisin, as well as with the capability of producing the degrading enzymes.

Abstract: Methods for the targeted integration of nucleotide sequences into a plant are provided. Transfer cassettes comprising nucleotide sequences of interest flanked by non-identical recombination sites are used to transform a plant comprising a target site. The target site contains at least a set of non-identical recombination sites corresponding to those on the transfer cassette. Exchange of the nucleotide sequences flanked by the recombination sites is effected by a recombinase.

Abstract: Methods to find optimal integration sites within a plant genome are provided. More particularly, a plant is transformed with a target site having an expression cassette comprising a nucleotide sequence operably linked to a promoter active in the plant. The target site is flanked by non-identical recombination sites. Transformed protoplast, tissues, or whole plants can be tested to determine the levels of activity of the inserted gene. By comparison of cellular activities of the gene in different insertion sites, preferred integration sites may be found wherein the gene is expressed at high or acceptable levels. These plants can then be utilized with subsequent retargeting techniques to replace the nucleotide sequence with other genes or nucleotide sequences of interest contained in a transfer cassette.

Abstract: Genes, nucleic acids and polypeptides associated with growth traits in plants are provided. Related probes, antibodies, marker sets, and arrays are provided as well as methods for predicting plant growth traits.

Abstract: Genes, nucleic acids, proteins, antibodies, marker sets, and arrays are provided. Methods of detecting conditions associated with elevated cholesterol and lipid, as well as during adipogenesis, are also provided.

Abstract: Methods and compositions for the targeted integration of nucleotide sequences into a plant are provided. Particularly, the present invention is drawn to compositions comprising polynucleotide sequences having the following operably linked components: an intron, a nucleotide sequence of interest, and a terminator region, wherein the polynucleotide sequence comprises one or more recombination sites. The recombination sites are non-identical to one another and one of the recombination sites is contained within the intron.

Abstract: The invention features a method for identifying a gene associated with a desired phenotype. This method includes the steps of: (a) providing a plurality of cell cultures that include plant, animal, or fungal cells capable of exhibiting a desired phenotype; (b) contacting each of at least a subset of said cells with a stimulus that (i) induces said cells to exhibit the phenotype, or (ii) does not induce said cell cultures to exhibit the phenotype; (c) determining the presence of the phenotype in the cell cultures of step (b); and (d) identifying a gene having increased expression in response to stimuli that induce the phenotype but do not have increased expression in response to stimuli that do not induce the phenotype.

Abstract: Polynucleotides, proteins, antibodies, labeled probes, marker sets, and arrays related to secreted and cell surface proteins that are altered in response to cholesterol are provided. Methods of detecting alterations in secreted and cell surface proteins in response to alterations in cholesterol levels (exposure), modulating cholesterol phenotype in cells and for treating a subject with adverse effects of altered levels of cholesterol, e.g., elevated or high levels of cholesterol, are also provided.

Abstract: The invention provides isolated cellulose synthase nucleic acids and their encoded proteins. The present invention provides methods and compositions relating to altering cellulose synthase concentration and/or composition of plants. The invention further provides recombinant expression cassettes, host cells, and transgenic plants.

Abstract: Nucleic acids, proteins, antibodies, marker sets and arrays are provided for biomarkers for breast cancer. Methods for detecting breast cancer, modulating breast cancer phenotypes in cells, and for treating a subject with breast cancer are also provided.

Abstract: The present invention provides methods and compositions relating to altering lignin biosynthesis content and/or composition of plants. The invention provides isolated nucleic acids and their encoded proteins which are involved in lignin biosynthesis. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions.

Abstract: Methods for reducing the complexity of integration of nucleotide sequences into a plant are provided. Transfer cassettes comprising nucleotide sequences of interest flanked by non-identical recombination sites are used to transform a plant comprising a target site. The target site contains at least a set of non-identical recombination sites corresponding to those on the transfer cassette. Exchange of the nucleotide sequences flanked by the recombination sites is effected by a recombinase.

Abstract: Nucleic acid sequences encoding two RAD51 recombinases active in maize plants are provided. cDNA sequences including the ZmRAD51 coding sequences and unique 3′-untranslated regions which are useful as RFLP probes, are also provided. The production of plasmids containing a nucleic acid sequence encoding a ZmRAD51 fusion protein, as well as the use of the plasmids to introduce the ZmRAD51 coding sequence into a host cell, such as maize cell, are also disclosed.