Abstract: Provided is an in vitro method for making a recombinant DNA molecule. The method includes combining in vitro a recombination-site-mediated evolution (a SCRaMbLE) ready DNA polynucleotide that contains at least one transcription unit (TU) and an introduced site-specific recombinase recognition sites that can be recognized by a recombinase, with a recombinase that recognizes the site-specific recombinase recognition sites. The method results in a polynucleotide that is recombined to provide a recombined polynucleotide. The method may further include determining the sequence, or determining the expression of the recombined polynucleotide. Polynucleotides made by this process, and modified yeast that contain the modified polynucleotides, are also provided.

Abstract: Provided are compositions and methods for compound discovery. Modified yeast that have their endogenous yeast shikimate pathway disrupted or deleted, and replaced with homologous pathway genes from one or more distinct organisms, are provided and used in assays of test agents. The homologous pathway genes are designed to supplement the disrupted or deleted shikimate pathway genes. The assays are designed to identify whether or not the test agents can interfere with the function of enzymes in the shikimate pathway from organisms that are distinct from the yeast avatar hosts. In embodiments, the disruption/deletion of the yeast endogenous shikimate pathway results in the yeast being incapable of producing chorismic acid.

Abstract: Provided is an in vitro method for making a recombinant DNA molecule. The method includes combining in vitro a recombination-site-mediated evolution (a SCRaMbLE) ready DNA polynucleotide that contains at least one transcription unit (TU) and an introduced site-specific recombinase recognition sites that can be recognized by a recombinase, with a recombinase that recognizes the site-specific recombinase recognition sites. The method results in a polynucleotide that is recombined to provide a recombined polynucleotide. The method may further include determining the sequence, or determining the expression of the recombined polynucleotide. Polynucleotides made by this process, and modified yeast that contain the modified polynucleotides, are also provided.

Abstract: Provided are compositions and methods for compound discovery. Modified yeast that have their endogenous yeast shikimate pathway disrupted or deleted, and replaced with homologous pathway genes from one or more distinct organisms, are provided and used in assays of test agents. The homologous pathway genes are designed to supplement the disrupted or deleted shikimate pathway genes. The assays are designed to identify whether or not the test agents can interfere with the function of enzymes in the shikimate pathway from organisms that are distinct from the yeast avatar hosts. In embodiments, the disruption/deletion of the yeast endogenous shikimate pathway results in the yeast being incapable of producing chorismic acid.

Abstract: A system for controlling gene expression in yeast comprises a repressible gene expression plasmid that has a regulator binding sequence for camR and a target gene sequence. The system also includes a transcription enhancer expression plasmid; wherein said transcriptional activator protein binds to the regulator binding sequence in the absence of a transcriptional inhibitor. The system is used in a method for controlling expression of the target gene through the use of camphor. The target gene is expressed in the absence of camphor but unexpressed if camphor is added to a solution of cells containing the plasmids.

Abstract: Provided are compositions and methods for use in assembling and expressing a plurality of transcription units using, in one aspect, homologous recombination in yeast. Yeast containing the plurality of transcription units, and isolated transcription units, are also provided. Kits for use in making the yeast and the transcript units are further included.

Abstract: Provided are compositions and methods for use in assembling and expressing a plurality of transcription units using, in one aspect, homologous recombination in yeast. Yeast containing the plurality of transcription units, and isolated transcription units, are also provided. Kits for use in making the yeast and the transcript units are further included.

Abstract: Provided are compositions and methods for use in assembling and expressing a plurality of transcription units using, in one aspect, homologous recombination in yeast. Yeast containing the plurality of transcription units, and isolated transcription units, are also provided. Kits for use in making the yeast and the transcript units are further included.

Abstract: A system for controlling gene expression in yeast comprises a repressible gene expression plasmid that has a regulator binding sequence for camR and a target gene sequence. The system also includes a transcription enhancer expression plasmid; wherein said transcriptional activator protein binds to the regulator binding sequence in the absence of a transcriptional inhibitor. The system is used in a method for controlling expression of the target gene through the use of camphor. The target gene is expressed in the absence of camphor but unexpressed if camphor is added to a solution of cells containing the plasmids.

Abstract: This application describes an assay for immunoprecipitation that is quick, reliable, easy to perform, and that can be used in a high throughput fashion because it does not rely on western blotting analysis even if it can be included in a standard IP/WB procedure without affecting the output of the analysis. Because of these features the FLIP assay is ideal for the high-throughput screening of IP-grade antibodies. Here we present the basic concept of the invention and the application of the FLIP in high-throughput screening such as the quick identification of IP-proficient mouse monoclonal antibodies.

Abstract: Provided are compositions and methods for use in assembling and expressing a plurality of transcription units using, in one aspect, homologous recombination in yeast. Yeast containing the plurality of transcription units, and isolated transcription units, are also provided. Kits for use in making the yeast and the transcript units are further included.

Abstract: Disclosed are methods for identifying molecular interactions (e.g., protein/protein, protein/DNA, protein/RNA, or RNA/RNA interactions). All of the methods within the invention employ counterselection and at least two hybrid molecules. Molecules which interact reconstitute a transcription factor and direct expression of a reporter gene, the expression of which is then assayed. Also disclosed are genetic constructs which are useful in practicing the methods of the invention.

Abstract: The invention relates to synthetic transposon and retrotransposon genes that exhibit higher levels of expression relative to natural transposon and retrotransposon genes. The invention further relates to transposons and retrotransposons comprising such synthetic genes.

Abstract: The present invention provides a method of for identifying repeat insertion mutation, a method for identifying or classifying genetic diseases characterized by genome rearrangement, as well as a method for mapping complex traits controlled by repeat insertion mutations in a plant or mammalian subject.

Abstract: Disclosed are methods for identifying molecular interactions (e.g., protein/protein, protein/DNA, protein/RNA, or RNA/RNA interactions). All of the methods within the invention employ counterselection and at least two hybrid molecules. Molecules which interact reconstitute a transcription factor and direct expression of a reporter gene, the expression of which is then assayed. Also disclosed are genetic constructs which are useful in practicing the methods of the invention.

Abstract: The present invention relates to methods of treating fungal infections with a drug combination: a first compound that inhibits the activity or expression of the protein FKBP12 and a second compound that inhibits the activity or expression of homoserine dehydrogenase. Evidence indicates that dual inhibitors of proteins FKBP12 and homoserine dehydrogenase are lethal to fungi. Such an approach should be minimally toxic since this combination therapy targets a biosynthetic pathway that is conserved in fungi but not in mammals.

Abstract: A novel compound, 2?/3?-O-acetyl-ADP-ribose, is provided. The compound is a mixture of the 2? and 3? regioisomers of O-acetyl-ADP ribose, and is formed nonenzymatically from 2?-O-acetyl-ADP-ribose, which is the newly discovered product of the reaction of Sir2 enzymes with acetylated peptides and NAD+. Analogs of 2?/3?-O-acetyl-ADP-ribose are also provided. Additionally, methods of preparing 2?/3?-O-acetyl-ADP-ribose, methods of determining whether a test compound is an inhibitor of a Sir2 enzyme, methods of detecting Sir2 activity in a composition, methods of deacetylating an acetylated peptide, and methods of inhibiting the deacetylation of an acetylated peptide are provided. Prodrugs of 2?/3?-O-acetyl-ADP-ribose are also provided.

Abstract: Methods of identifying agents that modulate reverse transcriptase activity in a cell by affecting manganese ion transport across a membrane of the cell are provided, as are agents identified using such methods. Also provided are methods of modulating reverse transcriptase activity by effecting manganese ion concentration. In addition, methods of reducing or inhibiting infection of cells with a retrotransposable element are provided.

Abstract: Disclosed are methods for identifying molecular interactions (e.g., protein/protein, protein/DNA, protein/RNA, or RNA/RNA interactions). All of the methods within the invention employ counterselection and at least two hybrid molecules. Molecules which interact reconstitute a transcription factor and direct expression of a reporter gene, the expression of which is then assayed. Also disclosed are genetic constructs which are useful in practicing the methods of the invention.

Abstract: Disclosed are methods for identifying molecular interactions (e.g., protein/protein, protein/DNA, protein/RNA, or RNA/RNA interactions). All of the methods within the invention employ counterselection and at least two hybrid molecules. Molecules which interact reconstitute a transcription factor and direct expression of a reporter gene, the expression of which is then assayed. Also disclosed are genetic constructs which are useful in practicing the methods of the invention.