Abstract: The invention describes methods for labeling or detecting of immobilized poly(amino acids), including peptides, polypeptides and proteins, on membranes and other solid supports, using fluorescent dipyrrometheneboron difluoride dyes. Such immobilized poly(amino acids) are labeled or detected on blots or on arrays of poly(amino acids), or are attached to immobilized aptamers.

Abstract: Provided is a method for controlling the degree of labeling (DOL) of a carrier molecule or solid support by the addition of a reactive label competitor to the labeling reaction. When the reactive label competitor is added to the labeling solution the competitor competes with the carrier molecule or solid support for the label, reducing the number of labels available to conjugates to the carrier molecule or solid support. This provides for a facile method that predictably alters the DOL of a carrier molecule or solid support.

Abstract: The present invention relates to nucleic acid inhibitors, compositions and method for enhancing synthesis of nucleic acid molecules. In a preferred aspect, the invention relates to inhibition or control of nucleic acid synthesis, sequencing or amplification. Specifically, the present invention discloses nucleic acids having affinity for polypeptides with polymerase activity for use in such synthesis, amplification or sequencing reactions. The nucleic acid inhibitors are capable of inhibiting nonspecific nucleic acid synthesis under certain conditions (e.g., at ambient temperatures). Thus, in a preferred aspect, the invention relates to “hot start” synthesis of nucleic acid molecules. Accordingly, the invention prevents, reduces or substantially reduces nonspecific nucleic acid synthesis. The invention also relates to kits for synthesizing, amplifying, reverse transcribing or sequencing nucleic acid molecules comprising one or more of the nucleic acid inhibitors or compositions of the invention.

Abstract: The present invention includes a fluorescent compound that can detect an activity, such as an enzymatic activity, and exhibits quenching. The fluorescent compound can include a fluorescent protein, such as an Aequorea-related green fluorescent protein. The fluorescent compound can include a substrate site for an enzymatic activity such as a kinase activity, a phosphatase activity, a protease activity, and a glycosylase activity. The fluorescent compound of the present invention can be used to detect such enzymatic activities in samples, such as biological samples, including cells. The present invention also includes nucleic acids that encode the fluorescent compounds of the present inventions, and cells that include such nucleic acids or fluorescent compounds.

Abstract: Methods for delivering ligands to a cell by using light to activate fluorescent ligands causing their release from endosomes. The instant methods thus increasing the efficiency of ligands, e.g. in vitro or at localized sites within a subject. The invention provides for the release of ligands by shining a light source on a cell to promote release of ligands into the cell where they can effect their function.

Abstract: The present invention provides fluorogenic probes and corresponding fluorescent compounds, methods of using the probes, compounds and kits that include the probes.

Abstract: The invention relates generally to standard sets of proteins, polypeptides, or peptides, and methods of using the standard sets to standardize laboratories, laboratory procedures, or laboratory equipment, and to certify laboratories and laboratory technicians. In certain aspects, the invention relates to standard sets of proteins, polypeptides, or peptides, that may be used in mass spectrometry.

Abstract: This invention provides an optical probe useful as an optical probe or sensor of post translational type modifications, such as phosphorylation. The invention comprises a polypeptide moiety, which contains a recognition motif for a post translational type activity and a protease site, which is coupled to a probe moiety. Modification of the polypeptide, by the post translational type activity, results in a modulation of the rate at which a protease cleaves the polypeptide which is sensed by a measurable change in at least one optical property of the optical probe upon cleavage. The present invention also includes a recombinant nucleic acid molecule that encodes an optical probe and a vector and host cell or library of cells that include the recombinant nucleic acid molecule. The optical probe can be used in methods to determine whether a sample, including a cell or a sample from an organism, contains a post-translational type modification activity.

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

Abstract: The present invention provides improved methods for amplifying a nucleic acid molecule. More specifically, the invention provides methods for nucleic acid amplification which use primers having equivalent priming efficiency.

Abstract: Control beads are disclosed that allow for improved quantitation of analytes in multiplexed bead assays. The control beads have a range of concentrations of calibration moieties that provide for the preparation of a titration curve. The titration curve can be used to quantify the concentration of the analytes. The titration curve can be used to correlate the signal obtained from a bead with the concentration (or absolute number of molecules) of the analyte bound to the bead.

Abstract: The present disclosure relates to methods of DNA amplification with a first primer that has a random sequence of nucleotides at its 3? end and a generic sequence 5? of the random nucleotides, as well as a second primer with the generic sequence of the first primer. The disclosure further relates to a method of precipitating DNA on a solid medium to improve DNA amplification. In a preferred embodiment, the presently disclosed methods are used for high-throughput genotyping of DNA samples, such as bloodstains or trace amounts of DNA.

Abstract: The invention provides a compound, useful as an optical probe or sensor of the activity of at least one cytochrome P450 enzyme, and methods of using the compound to screen candidate drugs, and candidate drugs identified by these methods.

Abstract: Methods and compositions for determining whether a subject at least has a neoplastic disease are provided. In practicing the subject methods, a sample from a subject is assayed for a soluble filamin analyte, such as a filamin A analyte, to determine whether the subject at least has the neoplastic disease. Also provided are kits, systems, and devices for practicing the subject methods.

Abstract: The invention provides novel fluorinated resorufin compounds that are of use in a variety of assay formats. Also provided are methods of using the compounds and kits that include a compound of the invention and instructions detailing the use of the compound in one or more assay formats.

Abstract: Functionalized fluorescent nanocrystal compositions and methods for making and using these compositions are disclosed. The compositions are fluorescent nanocrystals coated with at least one material. The coating material has chemical compounds or ligands with functional groups or moieties with conjugated electrons and moieties for imparting solubility to coated fluorescent nanocrystals in aqueous solutions. The coating material provides for functionalized fluorescent nanocrystal compositions which are water soluble, chemically stable, and emit light with a high quantum yield and/or luminescence efficiency when excited with light. The coating material may also have chemical compounds or ligands with moieties for bonding to target molecules and cells as well as moieties for cross-linking the coating.

Abstract: An analysis data interpretation system configured to automatically identify a test kit type used to generate a laboratory system output file. The system includes an analysis data interpretation processor configured to receive a laboratory system output file including a test kit identifier to identify the test kit that was used to generate the laboratory system output file.

Abstract: Methods for enhancing the dynamic range for specific detection of one or more analytes in assays using scattered-light detectable particle labels. The methods involve utilizing variations in detection technique and/or signal processing to extend the dynamic range to either or both of lower and higher concentrations.

Abstract: The invention provides compositions and methods useful in the analysis of tissues and cells. More specifically, the invention provides compositions, referred to as “pseudo-tissue samples,” which comprise aggregated fixed cells embedded in an embedding medium. The invention also provides histological specimens comprising pseudo-tissues, as well as histological specimen-substrate compositions, such as microscope slides upon which pseudo-tissues and histological specimens prepared therefrom are placed. The histological specimen-substrate compositions may comprise arrays (or microarrays) of pseudo-tissues and/or histological specimens. The invention also provides methods for preparing pseudo-tissues, histological specimens, and histological specimen-substrate compositions containing the same.

Abstract: Division arrested cells are used in screening assays to determine the effect of a substance of interest on the cells. The division arrested cells can be used in drug screening assays, signal transduction assays, and are especially useful in large scale, high throughput assays.