Abstract: The present invention relates to compositions, apparatus and methods useful for concurrently performing multiple, high throughput, biological or chemical assays, using repeated arrays of probes. A combination of the invention comprises a surface, which comprises a plurality of test regions, at least two of which, and in a preferred embodiment, at least twenty of which, are substantially identical, wherein each of the test regions comprises an array of generic anchor molecules. The anchors are associated with bifunctional linker molecules, each containing a portion which is specific for at least one of the anchors and a portion which is a probe specific for a target of interest. The resulting array of probes is used to analyze the presence or test the activity of one or more target molecules which specifically interact with the probes. In a preferred embodiment, a sample to be tested is subjected to a nuclease protection procedure before it is contacted with a combination of the invention.

Abstract: Methods and compositions for high-throughput identification of protein/nucleic acid binding pairs are provided. In the subject methods, a nucleic acid probe array, e.g., a molecular beacon probe array, is contacted with a target nucleic acid population to produce a hybridized array. The resultant hybridized array is then contacted with a population of proteins to produce a protein bound array. Any resultant array surface bound target nucleic acid/protein complexes are then detected to identify protein/nucleic acid binding pairs. In certain embodiments, the protein and/or nucleic acid members of the identified protein/nucleic acid binding pairs are further characterized. Also provided are systems and kits for use in practicing the subject methods. The subject invention finds use in a variety of different applications.

Abstract: The present invention relates to apparatus and methods for quantitative protein design and optimization.

Abstract: The present invention relates to Drosophila genes and methods for their use. The invention provides nucleotide sequences of Drosophila genes, amino acid sequences of the encoded proteins, and derivatives (e.g., fragments) and analogs thereof. The invention further relates to fragments (and derivatives and analogs thereof) of proteins which comprise one or more domains of a Drosophila protein. Antibodies to Drosophila proteins, and derivatives and analogs thereof, are also provided. Also provided herein are vectors and host cells comprising such nucleic acids. Methods of production of a Drosophila protein (e.g., by recombinant means), and derivatives and analogs thereof, are provided. Chimeric polypeptide molecules comprising polypeptides of the invention fused to heterologous polypeptide sequences are provided. Methods to identify the biological function of a Drosophila gene are provided, including various methods for the functional modification (e.g.

Abstract: A technique is described for quantitating biological indicators, such as viral load, using interferometric interactions such as quantum resonance interferometry. A biological sample is applied to an array information structure that has a plurality of elements that emit data indicative of viral load. A digitized output pattern of the arrayed information structure is interferometrically enhanced by generating interference between the output pattern and a reference wave. The interferometrically enhanced output pattern is then analyzed to identify emitted data indicative of viral load which in turn is used to determine viral load.

Abstract: Described herein are methods that can be used for diagnosis and prognosis of colorectal cancer. Also described herein are methods that can be used to screen candidate bioactive agents for the ability to modulate colorectal cancer. Additionally, methods and molecular targets (genes and their products) for therapeutic intervention in colorectal cancer are described.

Abstract: A new method to analyze and predict the binding energy for enzyme-transition state inhibitor interactions is presented. Computational neural networks are employed to discovery quantum mechanical features of transition states and putative inhibitors necessary for binding. The method is able to generate its own relationship between the quantum mechanical structure of the inhibitor and the strength of binding. Feed-forward neural networks with back propagation of error can be trained to recognize the quantum mechanical electrostatic potential at the entire van der Waals surface, rather than a collapsed representation, of a group of training inhibitors and to predict the strength of interactions between the enzyme and a group of novel inhibitors. The experimental results show that the neural networks can predict with quantitative accuracy the binding strength of new inhibitors.

Abstract: The invention provides methods, compositions, apparatus, and a computer data retrieval system for conducting proteomics.

Abstract: The present invention discloses a methodology which is directed to providing positive confirmation that nucleic acids, possessing putatively identified sequences predicted to generate observed GeneCalling™ signals, are actually present within the sample from which the signal was originally derived. The putatively identified nucleic acid fragment within the sample possesses 3′- and 5′-ends with known terminal subsequences. The method involves contacting nucleic acid fragments in a sample in amplifying conditions with (i) a nucleic acid polymerase; (ii) “regular” primer oligonucleotides having sequences comprising hybridizable portions of known terminal subsequences; and (iii) a “poisoning” oligonucleotide primer. Nucleic acids amplified with a poisoning primer are distinguishable upon detection from nucleic acids amplified with regular primers.

Abstract: The present invention provides methods and systems, particularly computer systems, for determining the relative specificity with which a particular polynucleotide molecule hybridizes to a polynucleotide probe. For example, the methods and systems of the invention enable a user to compare the specificity with which different polynucleotides hybridize to a given probe and/or rank these polynucleotides according to their specificity to that probe. The methods and systems of the invention also enable a user to compare the specificity with which a particular polynucleotide hybridizes to different probes, and/or rank those different probes according to their specificity for that particular polynucleotide.

Abstract: The invention provides nucleic acids containing single-nucleotide polymorphisms identified for transcribed human sequences, as well as methods of using the nucleic acids.

Abstract: The present invention describes novel compounds of the formula Wherein Q is H or a sugar or a sugar analogue or a nucleic acid backbone or backbone analogue, Y=O, S, NR10, where R10 is H, alkyl alkenyl, alkynyl, X is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl or a combination thereof or, preferably, a reporter group. The novel compounds are suitable for incorporation in oligonucleotides and polynucleotides.

Abstract: Compounds and methods for treating prostate cancer are provided. The inventive compounds include polypeptides containing at least a portion of a prostate tumor protein. Vaccines and pharmaceutical compositions for immunotherapy of prostate cancer comprising such polypeptides, or DNA molecules encoding such polypeptides, are also provided, together with DNA molecules for preparing the inventive polypeptides.

Abstract: Described herein are methods that can be used for diagnosis and prognosis of breast cancer. Also described herein are methods that can be used to screen candidate bioactive agents for the ability to modulate breast cancer. Additionally, methods and molecular targets (genes and their products) for therapeutic intervention in breast cancer are described.

Abstract: The present invention relates to the use of primers in polymerase chain reaction assays for the detection of fungal pathogens Colletotrichum acutatum, Alternaria spp., and Cladosporium carpophilum. Specific primers are identified as being useful for the identification of fungal isolates using PCR based techniques. Also described are novel extraction buffer solutions for use in isolating DNA from an organism, methods of extracting DNA from tissue, and methods of performing PCR analysis on DNA extracted from tissue.

Abstract: The invention concerns gene banks and combinatorial derivatives thereof, prepared using phagemid- or phage-display in combination with type IIS restriction enzymes and cosmid packaging; their use for the isolation of ligands, including enzyme inhibitors, agonists and antagonists for receptors, competitive binding peptides to a defined target, diagnostic ligands for diseases and autoimmune syndromes, including surveillance tools for immune status, post-translationally modified peptides, and such ligands generated by this technology.

Abstract: A method and system for generating and searching a tree-structured index of window vectors that represent database sequences comprise a window vector generation module, a tree-structured index generation module, a query sequence partitioning module, and a retrieval component. The window vector generation module partitions a database sequence into a plurality of overlapping windows. Each window has a fixed length W comprising a fixed number of nucleotides, and the offset among windows is determined by a parameter &Dgr;. The window vector generation module then maps each database sequence window into a window vector. The database sequence window vector indicates the frequency of appearance of each k-tuple in the corresponding database sequence window. The tree-structured index generation module then generates a tree-structured index using the database sequence window vectors.

Abstract: The present invention relates to methods for identifying novel genes comprising: (i) generating one or more specialized databases containing information on gene/protein structure, function and/or regulatory interactions; and (ii) searching the specialized databases for homology or for a particular motif and thereby identifying a putative novel gene of interest. The invention may further comprise performing simulation and hypothesis testing to identify or confirm that the putative gene is a novel gene of interest.

Abstract: The present invention is directed to novel exocytotic polypeptides, such as Exo1 and Exo2 polypeptides and related molecules, which have an inhibitory effect on exocytosis and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention. Further provided by the present invention are method for identifying novel compositions which mediate exocytotic polypeptide bioactivity, and the use of such compositions in diagnosis and treatment of disease.

Abstract: Compounds and methods for treating prostate cancer are provided. The inventive compounds include polypeptides containing at least a portion of a prostate tumor protein. Vaccines and pharmaceutical compositions for immunotherapy of prostate cancer comprising such polypeptides, or DNA molecules encoding such polypeptides, are also provided, together with DNA molecules for preparing the inventive polypeptides.