Abstract: A method of modifying a test nuclear receptor (NR) polypeptide is disclosed. The method provides a test NR polypeptide sequence having a characteristic that is targeted for modification; aligning the test NR polypeptide sequence with at least one reference NR polypeptide sequence for which an X-ray structure is available; building a three-dimensional model for the test NR polypeptide using the three-dimensional coordinates of the X-ray structure(s) of at least one reference polypeptide and its sequence alignment with the test NR polypeptide sequence; examining the three-dimensional model of the test NR polypeptide sequence for characteristic differences with the reference polypeptide; and mutating at least one amino acid residue in the test NR polypeptide sequence at a characteristic difference, whereby the test NR polypeptide is modified.

Abstract: The present invention provides methods for determining the structure and/or function of one or more domains of a cation-dependent (and preferably calcium-dependent) polypeptide (particularly a calcium-dependent enzyme, which may be a protease such as calpain) in the presence of one or more cations. The invention further provides methods for identifying a ligand having the ability to bind to one or more ligand-binding domains (LBDs) of a cation-dependent (and preferably calcium-dependent) polypeptide, and ligands identified by these methods. The invention also provides methods of treating or preventing physical disorders in animals using these ligands.

Abstract: The present application provides a method for predicting the functional site of a protein using data of the entire proteins of an organism of which genome data or cDNA data is known. More specifically, the present application provides a method for predicting a protein functional site, comprising the steps of calculating the frequency of occurrence of an oligopeptide in the entire proteins, calculating the value of each amino-acid residue contributing to the frequency of occurrence as the representative value of the function, and predicting the protein functional site by using the representative value of function as an indicator. The present also provides a system for predicting a functional site for automatically performing said methods.

Abstract: Provided are proteins having NF-?B activity, which are used for diagnosing, treating or preventing diseases associated with the excessive activation or inhibition of NF-?B. Using plasmid pNF?B-Luc, cDNA encoding a protein capable of activating NF-?B has been cloned from a cDNA library constructed from human lung fibroblasts, and the DNA sequence and the deduced amino acid sequence determined. The protein, the DNA encoding the protein, a recombinant vector containing the DNA, and a transformant containing the recombinant vector are useful for screening a substance inhibiting or promoting NF-?B activation.

Abstract: The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.

Abstract: The invention discloses a system and methods for quantitating the presence of nucleic acid sequences by evaluation of amplification data generated using real-time PCR. In one aspect, the methods may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction. The methodology used in the analysis may be readily automated such that subjective user interpretation of the data is substantially reduced or eliminated.

Abstract: A novel class of peptide nucleic acids are described which include a conjugate attached thereto. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.

Abstract: Contortrostatin, a homodimeric disintegrin, modulates the adhesion, motility, and invasiveness of integrin expressing tumor cells. When formulated as a pharmaceutically acceptable composition, the proteins can be used to treat patients by inhibiting or disrupting disease processes associated with an integrin binding to an ?v?3 or ?v?5 integrin.

Abstract: Systems and methods for rapidly analyzing cell containing samples, for example to identify morphology or to localize and quantitate biomarkers are disclosed.

Abstract: A method for profiling and identifying persons by using data samples provides a collapsed list of one or more aggregated matching samples having consistent STR profiles. Each of the one or more aggregated matching samples are presented on a one-line display, the one-line display having a composite profile representing consensus of all STR profiles in an associated aggregate matching sample. The one-line display of an aggregated matching sample may be expanded, and the expanded one-line display provides a view of all member samples in the aggregated matching sample. A method for aggregating samples from a plurality of disparate samples, and combining the aggregated samples is also provided.

Abstract: Novel pseudopeptide analogs of the insect allatostatin neuropeptide family which possess biological activity mimicking that of the naturally occurring neuropeptides are disclosed. By addition of a hydrophobic moiety to an active portion of the allatostatin peptides, analogs are produced which exhibit an overall amphiphilic nature and which are capable of penetrating the insect cuticle while still retaining biological activity. Furthermore, by substituting sterically hindered amino acids or aromatic acids for any or all of the first, third or fifth amino acid residues of the allatostatin C-terminal pentapeptide, analogs may be produced which are resistant to degradation by insect peptidases while still retaining biological activity. The analogs may be used for insect control by disrupting critical reproductive and/or developmental processes normally regulated by allatostatins in insects.

Abstract: Provided are methods of identifying inhibitors of ?-secretase that employ modified ?-secretase substrates. The modified ?-secretase substrates have ?-secretase cleavage sites that are altered from wild type. The amino acid sequences of the altered ?-secretase cleavage sites contain different amino acids in at least one of the positions P2-P1-P1?-P2? of the ?-secretase cleavage site. Many of the modified ?-secretase substrates are more efficient substrates for ?-secretase than are corresponding substrates having wild-type sequences, that is, these modified substrates are more susceptible to enzymatic breakdown by ?-secretase. Recombinant polynucleotide molecules encoding the modified ?-secretase substrates are provided. Antibodies that recognize cleavage products of the modified ?-secretase substrates are provided. Stable cell lines expressing the modified ?-secretase substrates are provided. Transgenic animals expressing the modified ?-secretase substrates are provided.

Abstract: Methods and computer software products are provided for analyzing gene expression data. In one embodiment, methods, systems and computer software are provided for comparative gene expression analysis using intensity dependent normalization factors.

Abstract: Novel full-length cDNAs are provided. 2443 cDNA derived from human have been isolated. The full-length nucleotide sequences of the cDNA and amino acid sequences encoded by the nucleotide sequences have been determined. Because the cDNA of the present invention are full-length and contain the translation start site, they provide information useful for analyzing the functions of the polypeptide.

Abstract: Isolated peptides that are fragments of protein products arising from frameshift mutations in genes associated with cancer are disclosed. The isolated peptides of the invention are capable of eliciting T cell immunity against cells harboring genes with such frameshift mutations. Cancer vaccines and therapeutically effective compositions containing the peptides of the invention are also described.

Abstract: A method is disclosed for the direct synthesis of double stranded DNA molecules of a variety of sizes and with any desired sequence. The DNA molecule to be synthesis is logically broken up into smaller overlapping DNA segments. A maskless microarray synthesizer is used to make a DNA microarray on a substrate in which each element or feature of the array is populated by DNA of a one of the overlapping DNA segments. The DNA segments are released from the substrate and held under conditions favoring hybridization of DNA, under which conditions the segments will spontaneously hybridize together to form the desired DNA construct. This method makes possible the remote assembly of DNA sequence, through a process analogous to facsimile transmission of documents, since the information on DNA to be made can be transmitted remotely to an instrument which can then synthesize any needed DNA sequence from the information.

Abstract: The present invention provides methods and kits for mitigating radiation induced tissue damage, improving the effectiveness of radiation therapy, to support bone marrow transplantation, and promoting megakaryocyte production and mobilization and platelet production, each method comprising the administration of an effective amount of angiotensinogen, angiotensin I (AI), AI analogues, AI fragments and analogues thereof, angiotensin II (AII), AII analogues, AII fragments or analogues thereof or AII AT2 type 2 receptor agonists.

Abstract: Compositions and methods for prevention and treatment of uncontrolled formation of intravascular fibrin clots are provided wherein fibrinolytic or anticoagulant drugs are biocompatibly coupled to red blood cell carriers.

Abstract: The present invention is directed to novel polypeptides having sequence similarity to Stra6, a murine retinoic acid responsive protein, 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.

Abstract: A method is provided for identifying a search model to use in molecular replacement for determining a structure of a target biomolecule, such as a protein, from X-ray diffraction data, the method comprising: employing computer executable logic to perform multiple molecular replacement searches on X-ray diffraction data of the target biomolecule where a group of different biomolecule structures are used as search models for the multiple molecular replacement searches; and employing computer executable logic to compare solutions from the multiple molecular replacement searches, the comparison producing data from which biomolecule structures can be identified as having superior structural identity with the target biomolecule as compared to the other biomolecule structures in the group.