Abstract: The present invention relates to novel human secreted proteins and isolated nucleic acids containing the coding regions of the genes encoding such proteins. Also provided are vectors, host cells, antibodies, and recombinant methods for producing human secreted proteins. The invention further relates to diagnostic and therapeutic methods useful for diagnosing and treating disorders related to these novel human secreted proteins.

Abstract: The present disclosure describes methods for the computational analysis of genetic variances in the coding and non-coding regions of particular genes.

Abstract: Systems and methods for detecting molecular binding events and other environmental effects using the unique dielectric properties of the bound molecular structure or structures are presented. A molecular binding layer is coupled along the surface of a signal path. A test signal is propagated along the signal path, whereby the test signal couples to the molecular binding layer, and in response, exhibits a signal response.

Abstract: The present invention relates to peptides immunochemically reactive with antibodies to the Epstein-Barr virus (EBV), nucleic acid sequences encoding these peptides, monoclonal antibodies against these peptides, cell lines capable of producing monoclonal antibodies and anti-idiotype antibodies. The invention also relates to recombinant vector molecules comprising a nucleic acid sequence according to the invention and host cells transformed or transfected with these vector molecules. The invention is further concerned with immunological reagents and methods for the detection of EBV or anti-EBV antibodies and a method for the amplification and detection of Epstein Barr viral nucleic acid.

Abstract: A method of making a synthetic nucleic acid sequence comprises providing a starting nucleic acid sequence, which optionally encodes an amino acid sequence, and determining the predicted &Dgr;Gfolding of the sequence. The starting nucleic acid sequence can be a naturally occurring sequence or a non-naturally occurring sequence. The starting nucleic acid sequence is modified by replacing at least one codon from the starting nucleic acid sequence with a different corresponding codon to provide a modified nucleic acid sequence. As used herein, a “different corresponding codon” refers to a codon which does not have the identical nucleotide sequence, but which encodes the identical amino acid. The predicted &Dgr;Gfolding of the modified nucleic acid sequence is determined and compared with the &Dgr;Gfolding of the starting nucleic acid sequence.

Abstract: The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to model enzymatic reactions in order to determine experimental conditions before conducting actual experiments.

Abstract: The inventors have modified the amino acid sequence of a pullulanase to obtain variants with improved properties, based on the three-dimensional structure of the pullulanase Promozyme®. The variants have altered physicochemical properties, e.g. an altered pH optimum, improved thermostability, altered substrate specificity, increased specific activity or an altered cleavage pattern.

Abstract: A biochemical reaction detection chip capable of controlling the temperature for biochemical reactions including hybridizations and its substrate. The function of the chip is performed by comprising a plurality of islands of a heat conducting material on the membrane of the substrate, the islands being spaced from each other and individually provided with temperature controllers, and the probes immobilized on the substrate.

Abstract: A 2.4 Å crystal structure of a protein construct containing the catalytic kinase domain of vascular endothelial growth factor receptor 2 (VEGFR2/KDR), a key enzyme in angiogenesis, has been determined in an unliganded, phosphorylated state. This protein construct, contains a modified catalytic linker and has comparable in vitro kinase activity to constructs containing the entire KID. The resulting construct retains comparable in vitro kinase activity to that of the wild-type KID, and more importantly, allows complete crystallization of the protein such that it may be characterized by X-ray crystallography. The present invention further discloses the use of x-ray crystallographic data for identification and construction of possible therapeutic compounds in the treatment of various disease conditions.

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, molecular targets (genes and their products) for therapeutic intervention in colorectal and other cancers are described.

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: The present invention discloses the amino acid and nucleic acid sequences of a new CNGC and Myosin that map to the region of the human chromosome associated with Bardet-Biedl Syndrome. Cyclic nucleotide gated channels (CNGCs) comprise a family of multimeric protein ion channels that open in response to the binding of a cyclic nucleotide to an intracellular domain. The two new proteins, CNGC-15 and Myosin IXa, are useful in the study, diagnosis and treatment of Bardet-Biedl Syndrome and Usher Syndrome. Other indications that can be treated by CNGC-15 and/or Myosin IXa polypeptides, or agonists or antagonists include hearing loss, retinis pigmentosa, obesity, hypogonadism, sterility, polydactyly, brachydactyly, syndactyly, mental retardation, renal abnormalities, hypertension, diabetes and cardiovascular abnormalities. Compositions and methods for expressing cyclic nucleotide gated channel-15 (CNGC-15) and Myosin IXa are provided.

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 and other cancers are described.

Abstract: The present invention relates to methods, software, and apparati for determining whether a genomic region harbors a gene associated with a detectable trait.

Abstract: Novel proteins which have cell death inducing activity or proliferation inhibitory activity on cancer cells; fragments of such proteins; genes coding such proteins; monoclonal antibodies to such proteins; reagents which induce apoptosis on cells including cancer cells in vitro for investigation of the mechanism of cell death induction, and which are obtained from the proteins including the amino acid sequence of SEQ ID No. 1 of the sequence listing, fragments thereof, genes coding these; and carcinostatic agents.

Abstract: Disclosed herein are methods and apparatuses for sequencing a nucleic acid. The method includes annealing a population of circular nucleic acid molecules to a plurality of anchor primers linked to a solid support, and amplifying those members of the population of circular nucleic acid molecules which anneal to the target nucleic acid, and then sequencing the amplified molecules by detecting the presence of a sequence byproduct.

Abstract: The present invention describes the development and evaluation of the sensitivity and specificity of a PCR-based 5′ nuclease assay for presumptively detecting E. coli O157:H7 DNA. The specificity of the eaeA-based, 5′ nuclease assay system was sufficient to correctly identify all E. coli O157:H7 strains evaluated, mirroring the previously described specificity of the PCR primers. The SZ-primed, eaeA-targeted, 5′ nuclease detection assay was capable of rapid, semiautomated, presumptive detection of E. coli O157:H7 when ≧103 CFU/ml were present in modified tryptic soy broth (mTSB) or modified E. coli broth (mEC), and when ≧104 CFU/ml were present in ground beef-mTSB mixtures. Incorporating an immunomagnetic separation step (IMS), followed by a secondary enrichment culturing step and with DNA recovery, improved the detection threshold to ≧102 CFU/ml.

Abstract: Methods are provided for purifying non-chromosomal nucleic acid molecules from cells, comprising: the general steps of (a) lysing cells to form a nucleic acid-containing lysate, and (b) applying the lysate to a depth filter in order to obtain a clarified solution containing purified non-chromosomal nucleic acid molecules.

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

Abstract: A method and a system for identifying mutations within nucleic acid sequences. Using raw data signals from conventional nucleic acid sequencing equipment, a method to create input signals that enables a properly trained neural network to output a mutation/no mutation signal is provided. Further, an instrument system to perform the method is provided.