Abstract: Disclosed herein is a novel system and methods for expressing exogenous genes, such as genes encoding fluorescent proteins, in mammalian cells. In one embodiment of this system and methods, a gene essential for viral infectivity or replication in cell culture is deleted or inactivated in the genome of a non-mammalian DNA virus. The exogenous gene operably linked to a mammalian promoter is then inserted into the non-replicative non-mammalian DNA virus. The non-replicative virus is propagated in a host cell that expresses in trans the deleted or inactivated gene or a functional homolog.

Abstract: Fluidic methods and devices for conducting parallel chemical reactions are disclosed. The methods are based on the use of in situ photogenerated reagents such as photogenerated acids, photogenerated bases, or any other suitable chemical compounds that produce active reagents upon light radiation. The present invention describes devices and methods for performing a large number of parallel chemical reactions without the use of a large number of valves, pumps, and other complicated fluidic components. The present invention provides microfluidic devices that contain a plurality of microscopic vessels for carrying out discrete chemical reactions.

Abstract: Recombinational cloning is provided by the use of nucleic acids, vectors and methods, in vitro and in vivo, for moving or exchanging segments of DNA molecules using engineered recombination sites and recombination proteins to provide chimeric DNA molecules that have the desired characteristic(s) and/or DNA segment(s).

Abstract: The present invention relates generally to methods for stimulating, activating, and maintaining or increasing the polyclonality of expressed TCRs in a population of T cells. In the various embodiments, cells are stimulated with a surface, wherein the surface has attached thereto one or more agents that ligate a cell surface moiety of at least a portion of the T cells and stimulates at least a portion of the T cells, yielding enhanced proliferation, cell signal transduction, and/or cell surface moiety aggregation. In certain aspects methods for stimulating a population of cells such as T-cells, by cell surface moiety ligation are provided by contacting the population of cells with a surface, that has attached thereto one or more agents that ligate a cell surface moiety thereby inducing cell stimulation, cell surface moiety aggregation, and/or receptor signaling enhancement.

Abstract: A method is provided for measuring competitive binding activity of molecules to nuclear receptors comprising mixing a fluorescence-emitting compound that specifically binds to steroid hormone receptors in a solution wherein the fluorescence-emitting compound is in concentration below the dissociation constant and the steroid hormone receptors are at or above the dissociation constant using fluorescence polarization.

Abstract: The present invention is generally related to compositions and methods for the reverse transcription of nucleic acid molecules, especially messenger RNA molecules. Specifically, the invention relates to compositions comprising mixtures of polypeptides having reverse transcriptase (RT) activity, and to methods of producing, amplifying or sequencing nucleic acid molecules (particularly cDNA molecules) using these compositions or polypeptides, particularly at temperatures above about 55° C. The invention also relates to nucleic acid molecules produced by these methods, to vectors and host cells comprising these nucleic acid molecules, and to the use of such nucleic acid molecules to produce desired polypeptides.

Abstract: Compositions, including antibodies, polypeptides, and organic molecules, kits, and methods for probing molecular interactions (e.g., deubiquination, ubiquination and kinase activity), e.g., using resonance energy transfer (RET) are provided.

Abstract: The present invention is directed generally to cell culture media (particularly serum free, non animal derived, and/or chemically defined media) which are useful for introducing macromolecules and compounds (e.g., nucleic acid molecules) into cells (e.g., eukaryotic cells). According to the invention, such introduction can take place in the presence of said medium. Cells containing such introduced materials can then be cultured in the medium and the effect of the introduced materials on the cells can be measured or determined. In particular, the invention allows introduction of nucleic acid molecules (e.g., vectors) into cells (particularly eukaryotic cells) and expression of proteins encoded by the nucleic acid molecules in the cells. The invention obviates the need to change the cell culture medium each time a different procedure is performed with the cells (e.g., culturing cells vs. transfecting cells).

Abstract: Provided in certain embodiments are new methods for forming azido modified biomolecule conjugates of reporter molecules, carrier molecules or solid support. In other embodiments are provided methods for enzymatically labeling a biomolecules with an azide group.

Abstract: Recombinational cloning is provided by the use of nucleic acids, vectors and methods, in vitro and in vivo, for moving or exchanging segments of DNA molecules using engineered recombination sites and recombination proteins to provide chimeric DNA molecules that have the desired characteristic(s) and/or DNA segment(s).

Abstract: The present invention provides ligand-detection reagents, ligand analogs and methods for determining the presence of a ligand in a sample. The ligand-detection reagent comprises a ligand-binding antibody and a ligand analog to form an antibody-ligand analog complex wherein the ligand analog is covalently bonded to a reporter molecule. This complex may additionally comprise a labeling protein non-covalently bonded to the antibody to form a ternary complex wherein the labeling protein comprises a monovalent antibody fragment or a non-antibody protein that is covalently bonded to a label moiety. The reporter molecule is either quenched by the ligand-binding antibody or by the label moiety of the labeling protein, depending on the reporter molecule and the ligand-binding antibody, wherein the amount of quenching is directly related to the amount of ligand present in the sample.

Abstract: Chemically reactive carbocyanine dyes incorporating an indolium ring moiety that is substituted at the 3-position by a reactive group or by a conjugated substance, and their uses, are described. Conjugation through this position results in spectral properties that are uniformly superior to those of conjugates of spectrally similar dyes wherein attachment is at a different position. The invention includes derivative compounds having one or more benzo nitrogens.

Abstract: A method for extracting nucleic acids from a biological material such as blood comprises contacting the mixture with a material at a pH such that the material is positively charged and will bind negatively charged nucleic acids and then eluting the nucleic acids at a pH when the said materials possess a neutral or negative charge to release the nucleic acids. The nucleic acids can be removed under mildly alkaline conditions to the maintain integrity of the nucleic acids and to allow retrieval of the nucleic acids in reagents that are immediately compatible with either storage or analytical testing.

Abstract: Compositions and methods are provided for generating three frame cDNA expression libraries for functional screening of proteins. The invention includes sets of 5? adapters for cloning cDNA molecules in which the sets include three adapters that can be used to clone a particular cDNA in all three reading frames. The libraries so generated have greater complexity of expressed open reading frames, and thus can improve the success of functional protein screens, such as two hybrid screens. The adapters also have recombination sites for efficient cloning and transfer between systems.

Abstract: A method is described for the manufacture of semiconductor nanoparticles. Improved yields are obtained by use of a reducing agent or oxygen reaction promoter.

Abstract: The invention relates, in part, to methods for detecting, monitoring, measuring or assessing an interaction between at least two proteins. The invention also relates, in part, to methods for determining if a test compound, or a mix of compounds, modulates an interaction between at least two proteins. In some embodiments, determination is made possible via the use of two recombinant molecules, e.g., one of which contains a first protein cleavage site for a proteolytic molecules, and an activator of a gene. A second recombinant molecule may include a second protein and the proteolytic molecule. Various other formats are provided by the invention. In some embodiments, if the test compound binds to the first protein, a reaction is initiated whereby the activator is cleaved, and activates a reporter gene.

Abstract: The invention is directed to one-tube nested nucleic acid amplification methods, as well as compositions for performing these methods, which employ one or more outer primers containing one or more exo-sample nucleotides and inner primers. Nested amplification reactions are performed in these methods in the presence of an agent that degrades the exo-sample-nucleotide-containing primers in time course fashion during the PCR cycles.

Abstract: The present invention provides cells and methods related to signaling receptors. The cells of the invention express the signaling receptors (e.g., in a constitutively active state). The cells are useful for analyzing the signaling receptors and their related pathways. The invention further provides methods for studying interactions of the signaling receptors and for small molecule screening, including high throughput methods. The invention further relates to expressing a signaling receptor (e.g., a GPCR) in a constitutively active state, even in the absence of the receptor's ligand. This allows for screening for inhibitors of the activated receptor's pathway without even knowing the ligand that activates the receptor, e.g., an orphan receptor. The invention further provides cell lines for expressing a signaling receptor in a constitutively active state. These cell lines are useful for high throughput screening assays of the invention.

Abstract: The present invention provides methods and non-fluorescent carbocyanine quencher compounds having the general formula: Wherein the A moiety is a substituted pyridinium, unsubstituted pyridinium, substituted quinolinium, unsubstituted quinolinium, substituted benzazolium, unsubstituted benzazolium, substituted indolinium, or unsubstituted indolinium. The invention further provides luminescent donor molecule-quencher pairs and luminescent donor molecule-quencher-luminescent acceptor molecule conjugates wherein the quencher is a cyanine compound of the present invention. The energy transfer pairs are used to detect an analyte of interest in a sample.

Abstract: The present invention relates generally to methods for generating, expanding, and isolating antigen-specific T cells. Compositions of antigen-specific T cells activated and expanded by the methods herein are further provided.