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Inventi Impact - Bioinformatics

Patent Watch

  • METHOD FOR DETECTION OF AUTOIMMUNE DISEASES

    The present invention relates to the field of diagnostics, especially to the detection of autoimmune diseases such as rheumatoid arthritis. Particularly, the invention provides a method for detecting the presence or absence of rheumatoid arthritis, or of a predisposition therefore or for monitoring rheumatoid arthritis in a subject using expression data of target genes related to immune system and tools of bioinformatics.

  • Differential Filtering of Genetic Data

    Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions). These differential filters may be applied by the user to the entire set of genetic data and/or only to the specific CytoRegions of interest.

  • SECONDARY STRUCTURE DEFINING DATABASE AND METHODS FOR DETERMINING IDENTITY AND GEOGRAPHIC ORIGIN OF AN UNKNOWN BIOAGENT THEREBY

    The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.

  • Engineering intracellular sialylation pathways

    Methods for manipulating carbohydrate processing pathways in cells of interest are provided. Methods are directed at manipulating multiple pathways involved with the sialylation reaction by using recombinant DNA technology and substrate feeding approaches to enable the production of sialylated glycoproteins in cells of interest. These carbohydrate engineering efforts encompass the implementation of new carbohydrate bioassays, the examination of a selection of insect cell lines and the use of bioinformatics to identify gene sequences for critical processing enzymes. The compositions comprise cells of interest producing sialylated glycoproteins. The methods and compositions are useful for heterologous expression of glycoproteins.

  • POLYMER ENCAPSULATED ALUMINUM PARTICULATES

    The present invention relates to use of novel bioinformatics approach for predicting and identifying Scaffold/Matrix attachment regions (S/MARs) from different genomic database.

  • Efficiently Determining Condition Relevant Modifiable Lifestyle Attributes

    A bioinformatics method, software, system and database are presented in which attribute profiles containing pangenetic and non-pangenetic information are created and used to identify sets of attributes, including lifestyle attributes that are associated with a condition. The lifestyle attributes which can be modified and which result in a significant change in the probability of having the condition are identified and used as the basis for recommendations for lifestyle modification.

  • Secondary Structure Defining Database And Methods For Determining Identity And Geographic Origin Of An Unknown Bioagent Thereby

    The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.

  • Medical Laboratory Report Message Gateway

    A gateway enables medical (including genetic and genomic) laboratories and health care providers (collectively "clients") to communicate electronic messages with each other without developing and maintaining an interface for each peer. The gateway translates messages sent between the parties. The gateway receives messages from each sender in a form, and containing diagnostic codes, preferred by the sender. For each received message, the gateway ascertains an intended receiving client. Each client may specify one or more receivers (such as applications) that are to receive messages sent to the client, as well as a separate form, and optionally a set of codes, for each receiver. For each receiver, the gateway generates translated messages, according to the receiver's preferred form and/or codes. The gateway sends the translated messages to each of the designated receivers. The gateway may include a validation component to cheek incoming messages to ensure the messages include required information and that information values are valid or acceptable. The gateway may include an exception handler that notifies a sending client if a message from the client fails to be translated or sent correctly. The gateway may maintain a repository in which the gateway stores copies of messages the gateway sent or would have sent to clients. The gateway provides an interface, such as a secure web interface, to this repository. Clients may access messages or lists of messages, especially messages the clients are not otherwise capable of receiving, through this interface. The gateway may store copies of some of the data that flows through the gateway in a bioinformatics database, which may be automatically analyzed by the gateway or queried for research or patient care purposes.

  • Sequential Addition of Short DNA Oligos In DNA-Polymerase-Based Synthesis Reactions

    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  • Compiling Co-associating Bioattributes Using Expanded Bioattribute Profiles

    A bioinformatics method, software, database and system for compiling attribute combinations that co-associate with a query attribute (i.e., an attribute of interest) are presented in which expanded attribute profiles associated with a group of query-attribute-positive individuals and expanded attribute profiles associated with a group of query-attribute-negative individuals are accessed, and combinations of attributes having a higher frequency of occurrence in the set of expanded attribute profiles associated with the group of query-attribute-positive individuals are identified and stored to generate a compilation of attribute combinations that co-associate with the query attribute.

  • Methods for direct biomolecule identification by matrix-assisted laser desorption ionization (MALDI) mass spectrometry

    The present invention relates to the use of post source decay (PSD) or collision induced dissociation (CID) direct tissue (DT) MALDI-TOF or DT-MALDI-TOF-TOF mass spectrographic identification of biological molecules in a tissue or cellular sample without the need for further protein extraction. This method provides for studying cells or tissues by direct tissue MALDI (DT-MALDI), thereby substituting in situ protein release for further protein extraction. Mass/intensity data was processed with Mascot.COPYRGT. software interrogation of the NCBI database. These results are proof of principle that DT-MALDI, combined with bioinformatics, can directly identify proteins in cells and tissues from their mass spectra.

  • Method of network-based identification of multicomponent synergy and compositions for use as effective component of anti-angiogenesis medicines

    A method for determining synergistic effect of a medicine combination including two medicines relating to a disease on the basis of a gene network and medicine-effective genes of each and/or any of said two medicines, comprising: determining a synergy factor (ST.sub.1,2) of two medicines on the basis of distribution of medicine-effective genes of two medicines; determining a medicine similarity factor (AS.sub.1,2) of two medicines on the basis of similarity between a set of symptoms which two medicines relates to; and, determining synergistic effect of two medicines according to a product of the synergy factor and similarity factor. Proposed is constructing a disease-related gene network, mapping medicine-effective genes onto the network, and determining the synergistic effect of medicines on the basis of the genes. The present invention also relates to medicine composition of sinomenine and honokiol and of sinomenine and luteolin, each with anti-angiogenesis effect and having good synergistic effect.

  • Oligomeric compounds and compositions for use in modulation of small non-coding RNAS

    Compounds, compositions and methods are provided for modulating the expression and function of small non-coding RNAs. The compositions comprise oligomeric compounds, targeted to small non-coding RNAs. Methods of using these compounds for modulation of small non-coding RNAs as well as downstream targets of these RNAs and for diagnosis and treatment of disease associated with small non-coding RNAs are also provided.

  • Expression profiles to predict relapse of prostate cancer

    The present invention provides a method for preparing a reference model for cancer relapse prediction that provides higher resolution grading than Gleason score alone. The method encompasses obtaining from different individuals a plurality of prostate carcinoma tissue samples of known clinical outcome representing different Gleason scores; selecting a set of signature genes having an expression pattern that correlates positively or negatively in a statistically significant manner with the Gleason scores; independently deriving a prediction score that correlates gene expression of each individual signature gene with Gleason score for each signature gene in said plurality of prostate carcinoma tissue samples; deriving a prostate cancer gene expression (GEX) score that correlates gene expression of said set of signature genes with the Gleason score based on the combination of independently derived prediction scores in the plurality of prostate cancer tissue samples; and correlating said GEX score with the clinical outcome for each prostate carcinoma tissue sample. A set of signature genes is provided that encompasses all or a sub-combination of GI_2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B, and PROK1. Also provided a methods for predicting the probability of relapse of cancer in an individual and methods for deriving a prostate cancer gene expression (GEX) score for a prostate carcinoma tissue sample obtained from an individual.

  • Human Bocavirus and methods of diagnosis and treatment

    Human parvovirus, genus Bocavirus, associated with respiratory tract infections in children. Nucleic acid and polypeptide sequences of the virus. Methods and products for diagnosing presence of bocavirus in a sample using nucleic acid probes or primers, or specific binding members such as antibodies. Methods and products for diagnosing past or present infection of bocavirus in an individual e.g. by serology testing. Viral nucleic acid, polypeptide and/or viral particles for generating immune response in an individual, including vaccine compositions.

  • Managing biological databases

    Methods and systems for managing biological databases. The methods and systems can comprise creation, organization, and presentation of biological databases. The biological databases can be created using data obtained from a plurality of other databases and periodically updated. An executive summary can be created for a biological sequence using the biological database.

  • Artificial intelligence system for genetic analysis

    The present invention provides a complete artificial intelligence system for the acquisition and analysis of nucleic acid array hybridization information. The system includes a central data processing facility and one or more user facilities, linked by encrypted connections. Each user facility may include an optical scanning system to collect hybridization signals from a nucleic acid array, an image processing system to convert the optical data into a set of hybridization parameters, a connection to a data network, and a user interface to display, manipulate, search, and analyze hybridization information. This system reads data from a nucleic acid microarray, analyzes test results, evaluates patient risk for various ailments, and recommends methods of treatment. The automated artificial intelligence system is a real time, dynamic decision making tool that can be used in conjunction with a clinical analysis system, and with the information obtained in a research and development environment.

  • NOVEL GENE DISRUPTIONS, COMPOSITIONS AND METHODS RELATING THERETO

    The present invention relates to transgenic animals, as well as compositions and methods relating to the characterization of gene function. Specifically, the present invention provides transgenic mice comprising disruptions in PRO69122, PRO204, PRO214, PRO222, PRO234, PRO265, PRO309, PRO332, PRO342, PRO356, PRO540, PRO618, PRO944, PRO994, PRO1079, PRO1110, PRO1122, PRO1138, PRO1190, PRO1272, PRO1286, PRO1295, PRO1309, PRO1316, PRO1383, PRO1384, PRO1431, PRO1434, PRO1475, PRO1481, PRO1568, PRO1573, PRO1599, PRO1604, PRO1605, PRO1693, PRO1753, PRO1755, PRO1777, PRO1788, PRO1864, PRO1925, PRO1926, PRO3566, PRO4330, PRO4423, PRO36935, PRO4977, PRO4979, PRO4980, PRO4981, PRO5801, PRO5995, PRO6001, PRO6095, PRO6182, PRO7170, PRO7171, PRO7436, PRO9912, PRO9917, PRO37337, PRO37496, PRO19646, PRO21718, PRO19820, PRO21201, PRO20026, PRO20110, PRO23203 or PRO35250 genes. Such in vivo studies and characterizations may provide valuable identification and discovery of therapeutics and/or treatments useful in the prevention, amelioration or correction of diseases or dysfunctions associated with gene disruptions such as neurological disorders; cardiovascular, endothelial or angiogenic disorders; eye abnormalities; immunological disorders; oncological disorders; bone metabolic abnormalities or disorders; lipid metabolic disorders; or developmental abnormalities.

  • Systems, methods, and computer program products for analysis of vessel attributes for diagnosis, disease staging, and surgical planning

    Systems, methods, and computer program products for analysis of vessel attributes for diagnosis, disease staging, and surgical planning are disclosed. A method for analyzing blood vessel attributes may include developing an atlas including statistical measures for at least one blood vessel attribute. The statistical measures can be developed from blood vessel image data from different individuals. Blood vessel attribute measurements can be obtained from an individual subject. The individual subject's blood vessel attribute measurements can be compared to the statistical measures in the atlas. Output may be produced indicative of a physical characteristic of the individual based on results from the comparison.

  • PLANTS WITH ALTERED ROOT ARCHITECTURE, RELATED CONSTRUCTS AND METHODS INVOLVING GENES ENCODING LEUCINE RICH REPEAT KINASE (LLRK) POLYPEPTIDES AND HOMOLOGS THEREOF

    Isolated polynucleotides and polypeptides and recombinant DNA constructs particularly useful for altering root structure of plants, compositions (such as plants or seeds) comprising these recombinant DNA constructs, and methods utilizing these recombinant DNA constructs. The recombinant DNA construct comprises a polynucleotide operably linked to a promoter functional in a plant, wherein said polynucleotide encodes a polypeptide useful for altering plant root architecture.

  • Cand45 tRNA-Derived Expression System for Gene Modulation

    The present invention relates to systems and methods for modulating gene expression and applications thereof. Provided is a novel expression system to generate RNaseZ and RNA polymerase III dependent RNAs to regulate genes and control the timing and the location of the regulation by supplying synthetic or expressed oligonucleotide antisense to a small RNA.

  • MODULAR DNA-BINDING DOMAINS AND METHODS OF USE

    The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.

  • PRODUCTION OF DEFINED MONODISPERSE HEPAROSAN POLYMERS AND UNNATURAL POLYMERS WITH POLYSACCHARIDE SYNTHASES

    A methodology for polymer grafting by a polysaccharide synthase allows the creation of a variety of glycosaminoglycan oligosaccharides that have a natural, chimeric, hybrid and/or unnatural sugar structure and/or a targeted size (i.e., substantially monodisperse in size).

  • MICRO RNA MARKERS AND METHODS RELATED THERETO

    The present invention provides methods of diagnosis of Alzheimer's disease including assessing the levels of certain microRNAs in a subject and comparing these to levels in subjects not exhibiting the disease. The identified measurements provide input for improved diagnoses of Alzheimer's disease as compared to certain other forms of dementias, which allows more effective treatment regimens.

  • PROGNOSTIC GENE EXPRESSION SIGNATURE FOR SQUAMOUS CELL CARCINOMA OF THE LUNG

    Provided is a gene expression signature consisting of 12 biomarkers for use in prognosing or classifying a subject with lung squamous cell carcinoma into a poor survival group or a good survival group. The 12-gene signature specific for squamous cell carcinoma consists of the biomarkers RPL22, VEGFA, G0S2, NES, TNFRSF25, DKFZP586P0123, COL8A2, ZNF3, PJPK5, RNFT2, ARHGEF12 and PTPN20A.

  • GENETIC MARKER IDENTIFICATION IN ATLANTIC COD

    The present application describes SNPs useful for the genetic analysis of Atlantic cod. Also described are QTLs and SNP marker associations for commercially important traits such as weight, nodavirus resistance, resistance to stress and for determining geographic origin. The application also provides methods and uses of the SNPs for identifying family members and/or estimating relatedness, marker assisted selection, breeding programs, population management, identification of geographic origin and trait-association studies. A SNP-based linkage map for Atlantic cod is also provided.

  • USE OF INTERFERING RNA FOR TREATING AN HIV INFECTION

    The present invention relates to interfering RNAs, in particular miRNAs, capable of specifically blocking the replication of a strain of the HIV virus that is resistant to an antiretroviral compound, and use thereof for treating infections by this type of virus.

  • Method for Analysis of DNA Methylation Profiles of Cell-Free Circulating DNA in Bodily Fluids

    The invention can be summarized as follows. There is provided a method for analyzing DNA methylation profiles of cell-free DNA in body fluids by enriching a methylated or unmethylated fraction of DNA from cell-free DNA and subjecting the enriched DNA to microarray based methylome profiling and bioinformatics data analysis.

  • WOODY PLANTS HAVING IMPROVED GROWTH CHARACTERISTICS AND METHOD FOR MAKING THE SAME

    The present invention pertains to a novel and extensive analytical platform for selecting genes with a possible commercial phenotype from a large group of candidate genes identified using tools in bioinformatics, data from EST sequencing and DNA array. An aspect of the invention provides a method of producing a transgenic plant having an increased growth compared to its wild type. The method comprises altering in the plant the level of a gene product of at least one gene specifically expressed during different phases of wood formation. Further aspects of the invention provide a plant cell or plant progeny of a transgenic plant comprising a recombinant polynucleotide according to the invention. Other aspects pertain a DNA construct comprising a nucleotide sequence of the invention and a plant cell or plant progeny comprising the DNA construct

  • SECONDARY STRUCTURE DEFINING DATABASE AND METHODS FOR DETERMINING IDENTITY AND GEOGRAPHIC ORIGIN OF AN UNKNOWN BIOAGENT THEREBY

    The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.

  • UNIVERSAL FIBRONECTIN TYPE III BOTTOM-SIDE BINDING DOMAIN LIBRARIES

    The invention pertains to a natural-variant combinatorial library of fibronectin Type 3 domain (Fn3) polypeptides useful in screening for the presence of one or more polypeptides having a selected binding or enzymatic activity. The library polypeptides include (a) regions A, AB, B, C, CD, D, E, EF, F, and G having wildtype amino acid sequences of a selected native fibronectin Type 3 polypeptide or polypeptides, and (b) loop regions AB, CD, and EF having selected lengths (Bottom Loops). The Fn3 may also have loop regions BC, DE, and FG having wildtype amino acid sequences, having selected lengths, or mutagenized amino acid sequences (Top Loops).

  • COMPUTER-FACILITATED PARALLEL INFORMATION ALIGNMENT AND ANALYSIS

    Described herein, Smith-Waterman using Associative Massive Parallelism (SWAMP) extends the single, highest scoring subsequence alignment the traditional Smith-Waterman algorithm and variations return to discover the top k highest scoring non-overlapping, non-intersecting subalignments in parallel. Embodiments provided herein provide synergistic work, accelerating the high quality of alignments, in addition to providing multiple subsequence discovery that is handled in an automated fashion within the algorithm. SWAMP and SWAMP+ (and related algorithms such as are described herein) are parallel algorithms that are designed to run in an accelerated manner, inter alia, on single-instruction, multiple-data (SIMD) machines. Not only is the alignment/matching process accelerated for the single, highest matching alignment, in embodiments the algorithm can analyze deeper into the sequences for additional high-quality alignments. Envisioned uses include bioinformatics, for instance for nucleic acid or amino acid sequence alignments, as well as alignments of other data strings or other packets or lines of information.

  • COMPOSITIONS HAVING ANTIANGIOGENIC ACTIVITY AND USES THEREOF

    The invention generally features compositions and methods that are useful for modulating blood vessel formation, as well as methods that provide for the systematic and efficient identification of angiogenesis modulators. As described in more detail below, a systematic computational methodology based on bioinformatics was used to identify novel peptide modulators of angiogenesis that have been characterized in vitro and/or in vivo.

  • Method for Analysis of DNA Methylation Profiles of Cell-Free Circulating DNA in Bodily Fluids

    The invention can be summarized as follows. There is provided a method for analyzing DNA methylation profiles of cell-free DNA in body fluids by enriching a methylated or unmethylated fraction of DNA from cell-free DNA and subjecting the enriched DNA to microarray based methylome profiling and bioinformatics data analysis.

  • TRANSGENIC PLANTS HAVING INCREASED BIOMASS

    Methods and materials for modulating biomass levels in plants are disclosed. For example, nucleic acids encoding biomass-modulating polypeptides are disclosed as well as methods for using such nucleic acids to transform plant cells. Also disclosed are plants having increased biomass levels and plant products produced from plants having increased biomass levels.

  • Photoacid Generators for the Synthesis of Oligo-DNA in a Polymer Matrix

    Compounds represented by the following structural formulas can be used as photoacid generators: ##STR00001## Such compounds are useful, for example, in fabricating arrays of polymers.

  • Non-Invasive Diagnosis of Graft Rejection in Organ Transplant Patients

    The disclosure provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant. The methods comprise determining the presence or absence of one or more nucleic acids from a donor transplant, wherein said one or more nucleic acids from said donor are identified based on a predetermined marker profile, and diagnosing or predicting transplant status or outcome based on the presence or absence of said one or more nucleic acids.

  • TOLEROGENIC SYNTHETIC NANOCARRIERS FOR ALLERGY THERAPY

    Disclosed are synthetic nanocarrier compositions, and related methods, comprising immunosuppressants and MHC Class II-restricted epitopes of an allergen that provide tolerogenic immune responses specific to the allergen.

  • Genetic Inhibition by Double-Stranded RNA

    A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The process may be practiced ex vivo or in vivo. The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods.

  • GENETIC ELEMENTS, PROTEINS, AND ASSOCIATED METHODS INCLUDING APPLICATION OF ADDIITNAL GENETIC INFORMATION TO GRAM (+) THERMOACIDOPHILES

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for modulating or altering recombination inside or outside of a cell using isolated and/or purified polypeptides and/or nucleic acid sequences from Alicyclobacillus acidocaldarius.

  • Compositions and Methods for Genetic Manipulation and Monitoring of Cell Lines

    The disclosure relates generally to stem cell biology and more specifically to genetic manipulation of stem cells. Methods and compositions using recombinational cloning techniques are disclosed which allow the construction and insertion of complex genetic constructs into embryonic and adult stem cells and progenitor cells. The methods disclosed will allow the harvesting of adult stem cells pre-engineered with integration sites to facilitate early passage genetic modification.

  • GENETIC MODIFICATION FOR PRODUCTION OF 3-HYDROXYPROPIONIC ACID

    A method of increasing 3-HP production efficiency by inhibiting expression of a lactate dehydrogenase, a phosphotransacetylase, and an alcohol dehydrogenase in production of 3-HP using a malonic semialdehyde reduction pathway to prevent metabolite leak and increase a malonyl-CoA pool is disclosed.

  • Gene re-cycling

    Through ecological re-cycling, plants take up the nutrients from the cadavers. But it is not understood whether the plant roots can take the nutrients and the genes of the dead plants and cadavers, to develop into a transgenic plants. Biotechnology has successfully developed transgenic plants and animals. Recently, gene sequencing studies, have shown that animals carry foreign genes making them as natural transgenic animals. Reason for the presence of transgenes not investigated. Further studies will enable us to learn more about the existence of transgenic flora and fauna and the role of gene re-cyling. Corroborating the Nature's hidden biological phenomena, like ethnicity, cyclic occurrence of diseases, re-appearance of extinct animals, Biblical citations etc., with modern literature on transgenic plants/animals, human genomic studies. gene sequencing, etc. it is hypothesized that genes of flora and fauna are recycled from generation to generation through immortal DNA. It will change the present concept of organism's mortality to immortality.

  • NOVEL CELLULASE GENE

    An object is to identify endoglucanase and .beta.-glucosidase genes by isolating genomic DNA containing cellulase genes, which are classified into endoglucanases or .beta.-glucosidases, from Acremonium cellulolyticus, and sequencing the nucleotide sequences thereof. The inventors intensively compared the amino acid sequences of known endoglucanases and .beta.-glucosidases with each other to find conserved region of amino acid sequences in Acremonium cellulolyticus, and various primers were designed based on the information. PCR was carried out using the various primers thus designed and genomic DNA or cDNA as a template. As a result, gene fragments of endoglucanases and .beta.-glucosidases were obtained. Primers were designed based on the gene fragments, and PCR was carried out to amplify nine genes of endoglucanases and .beta.-glucosidases. The nucleotide sequences thereof were sequenced, and the present invention was completed.

  • GENOME-SCALE ANALYSIS OF REPLICATION TIMING

    Methods for identifying and/or distinguishing a homogeneous population of cells based on their replication domain timing profile using high resolution genomic arrays or sequencing procedures are provided. These methods may be used to compare the replication timing profile for a population of cells to another replication timing profile(s), a replication timing fingerprint, and/or one or more informative segments of a replication timing fingerprint, which may be simultaneously or previously determined and/or contained in a database, to determine whether there is a match between them. Based on such information, the identity of the population of cells may be determined, or the identity of the population of cells may be distinguished from other populations of cells or cell types. Methods for determining a replication timing fingerprint for particular cell types are also provided.

  • CORN EVENT MZDT09Y

    A novel transgenic corn event designated MZDT09Y is disclosed. The invention relates to nucleic acids that are unique to event MZDT09Y and to methods of detecting the presence of event MZDT09Y based on DNA sequences of the recombinant constructs inserted into the corn genome that resulted in the MZDT09Y event and of genomic sequences flanking the insertion site. The invention further relates to corn plants comprising the transgenic genotype of event MZDT09Y and to methods for producing a corn plant by crossing a corn plant comprising the MZDT09Y genotype with itself or another corn variety. Seeds of corn plants comprising the MZDT09Y genotype are also objects of the invention.

  • SITE-SPECIFIC INTEGRATION AND STACKING OF TRANSGENES IN SOYBEAN VIA DNA RECOMBINASE MEDIATED CASSETTE EXCHANGE

    A targeting method is described that allows precise cassette replacement at a previously characterized genetic locus. A target DNA construct containing a pair of incompatible FRT sites flanking a target cassette was introduced into soybean by regular biolistic transformation. Transgenic events containing a single complete copy of the target site were then selected and retransformed with a donor DNA construct containing the identical pair of incompatible FRT sites flanking a donor cassette. Precise DNA cassette exchange happened between the target cassette and the donor cassette via recombinase mediated cassette exchange (RMCE) so that the donor cassette was introduced at the exact genomic site previously occupied by the target cassette. Through repeated RMCE using additional incompatible FRT sites, multiple groups of transgenes can be stacked at the same genomic locus.

  • METHODS AND SYSTEMS FOR GENOME-SCALE KINETIC MODELING

    Embodiments of the present invention generally relate to the construction, analysis, and characterization of dynamical states of biological networks at the cellular level. Methods are provided for analyzing the dynamical states by constructing matrices using high-throughput data types, such as fluxomic, metabolomic, and proteomic data. Some embodiments relate to an individual, while others relate to a plurality of individuals.

  • METHODS FOR CELL REPROGRAMMING AND GENOME ENGINEERING

    Methods for producing engineered induced pluripotent stem (iPS) cells are provided comprising introducing a first nucleic acid into somatic cells for integration into their genome and reprogramming the cells to produce engineered iPS cells having the nucleic acid integrated into their genome. For example, in certain aspects the cells are reprogrammed by introduction of a genetic element that expresses one or more reprogramming factor and culturing of the cells under conditions sufficient to produce reprogrammed cells.

  • Genome-Wide Association Study Identifying Determinants Of Facial Characteristics For Facial Image Generation

    The present invention relates to a method for the generation of a facial composite from the genetic profile of a DNA-donor. The method comprises the steps of a) subjecting a biological sample to genotyping thereby generating a profile of genetic markers associated to numerical facial descriptors (NFD) for said sample, b) reverse engineer a NFD from the profile of the associated genetic variants and constructing a facial composite from the reverse engineered numerical facial descriptors (NFDs). The present invention also relates to a method for identifying genetic markers and/or combinations of genetic markers that are predictive of the facial characteristics, (predictive facial markers) of a person, said method comprising the steps of: a) capturing images of a group of individual faces; b) performing image analysis on facial images of said group of individual faces thereby extracting phenotypical descriptors of the faces; c) obtaining data on genetic variation from said group of individual and d) performing a genome-wide association study (GWAS) to identify said predictive facial markers.

  • METHOD OF GENERATING GENE MOSAICS

    The invention relates to a method for generating a gene mosaic by somatic in vivo recombination, comprising: e) in a single step procedure (vii) transforming a cell with at least one gene A having a sequence homology of less than 99.5% to another gene to be recombined that is an integral part of the cell genome or presented in the framework of a genetic construct, (viii) recombining said genes, (ix) generating a gene mosaic of the genes at an integration site of a target genome, wherein said at least one gene A has a single flanking target sequence either at the 5' end or 3' end anchoring to the 5' or 3' end of said integration site, and f) selecting clones comprising the gene mosaic, as well as a method of producing a diversity of gene mosaics and gene assembly.

  • Nucleic Acids Useful in the Manufacture of Oil

    Novel gene sequences from microalgae are disclosed, as well as novel gene sequences useful in the manufacture of triglyceride oils. Also disclosed are sequences and vectors that allow microalgae to be cultivated on sugar cane and sugar beets as a feedstock. In some embodiments, the vectors are useful for the purpose of performing targeted modifications to the nuclear genome of heterotrophic microalgae.

  • Methods For Increasing Homologous Recombination Of A Nucleic Acid Sequence

    The present invention relates to methods for increasing homologous recombination of a nucleic acid sequence introduced into a host cell, comprising: (a) introducing into a population of filamentous fungal host cells a first nucleic acid sequence encoding a recombination protein and a second nucleic acid sequence comprising one or more regions which are homologous with the genome of the filamentous fungal host cell, wherein (i) the recombination protein promotes the recombination of the one or more regions with the corresponding homologous region in the host's genome to incorporate the second nucleic acid sequence by homologous recombination, and (ii) the number of host cells comprising the incorporated second nucleic acid sequence in the population is increased at least 20% compared to the same population without the first nucleic acid sequence; (b) and isolating from the population a filamentous fungal cell comprising the incorporated second nucleic acid sequence.

  • USE OF ENDOGENOUS PROMOTERS TO EXPRESS HETEROLOGOUS PROTEINS

    The present invention provides methods for using endogenous transcriptional control systems to regulate the expression of heterologous protein(s). In particular, targeted genome editing is used to integrate a sequence encoding the heterologous protein(s) in-frame with an endogenous coding sequence such that the expression of the heterologous and endogenous sequences is regulated by the endogenous control system.

  • GENETIC ENGINEERING OF NON-HUMAN ANIMALS FOR THE PRODUCTION OF CHIMERIC ANTIBODIES

    The invention provides non-human cells and mammals having a genome encoding chimeric antibodies and methods of producing transgenic cells and mammals. Certain aspects of the invention include chimeric antibodies, humanized antibodies, pharmaceutical compositions and kits. Certain aspects of the invention also relate to diagnostic and treatment methods using the antibodies of the invention.

  • CELLULAR ARRAYS AND METHODS OF DETECTING AND USING GENETIC DISORDER MARKERS

    A method is disclosed for rapid molecular profiling of tissue or other cellular specimens by placing a donor specimen in an assigned location in a recipient array, providing copies of the array, and performing a different biological analysis of each copy. The results of the different biological analyses are compared to determine if there are correlations between the results of the different biological analyses at each assigned location. In some embodiments, the specimens may be tissue specimens from different tumors, which are subjected to multiple parallel molecular (including genetic and immunological) analyses. The results of the parallel analyses are then used to detect common molecular characteristic of the genetic disorder type, which can subsequently be used in the diagnosis or treatment of the disease. The biological characteristics of the tissue can be correlated with clinical or other information, to detect characteristics associated with the tissue.

  • METHOD FOR TARGETED GENOMIC EVENTS IN ALGAE

    The invention relates to endonucleases cleaving DNA target sequences from algae genomes, to appropriate vectors encoding such endonucleases, to cells or to algae modified by such vectors and to the use of these endonucleases and products derived therefrom for targeted genomic engineering in algae.

  • GENOMIC MARKERS FOR PREDICTION OF LONG-TERM RESPONSE TO GROWTH HORMONE (GH) THERAPY

    The present invention relates to the use of genetic markers to identify the response to growth hormone treatment in Growth Hormone Deficiency (GHD) or Turner Syndrome (TS) patients as well as a method of treating GHD or TS patients and kits for genotyping.

  • SYSTEM AND METHOD FOR REAL WORLD BIOMETRIC ANALYTICS THROUGH THE USE OF A MULTIMODAL BIOMETRIC ANALYTIC WALLET

    A system and method for real world biometric analytics through the use of a multimodal analytic wallet. The system includes a biometric wallet comprising a pervasive repository for storing biometric data, the pervasive repository including at least one of a biometric layer, a genomic layer, a health layer, a privacy layer, and a processing layer. The biometric wallet further comprises a biometric analytic interface configured to communicate the biometric data to one or more devices.

  • METHOD FOR DETECTING NUCLEIC ACIDS BASED ON AGGREGATE FORMATION

    The invention provides methods to detect or determine the presence or amount of a pathogen, such as a virus or bacterium, in a sample or the amount of cells based on the detection of their genomic DNA. The method employs magnetic substrates and subjects the sample and the magnetic substrate to forms of energy so as to induce aggregate formation and detects the aggregates.

  • METHODS AND COMPOSITIONS FOR GENERATING COMPLEX TRAIT LOCI

    Compositions and methods are provided for stacking multiple independent transgenic loci into the genome of a plant. Compositions include plants, seeds or plant cells comprising at least one transgenic target site and at least one genomic locus of interest integrated at different genomic sites within a genomic window. Plant breeding techniques can be employed such that the transgenic target site and the genomic locus of interest can be bred together. In this way, multiple independent transgene integrations can be generated within a genomic window to create a complex trait locus. The complex trait locus is designed such that the transgenic target sites and/orgenomic loci of interest can segregate independently of each other, thus providing the benefit of altering a complex trait locus by breeding-in and breeding-away specific elements. Various methods can also be employed to modify the target sites such that they contain a variety of polynucleotides of interest.

  • BRASSICA GENOMIC ASSAYS

    Methods and compositions for detecting, identifying, and quantifying Brassica A genomic DNA are described. The methods are specific to the Brassica A genome and do not cross-react with other Brassica species, crops or weedy relatives that could contribute to contamination of a canola field.

  • Unnatural Reactive Amino Acid Genetic Code Additions

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  • Y-SHAPED PROBE AND VARIANT THEREOF, AND DNA MICROARRAY, KIT AND GENETIC ANALYSIS METHOD USING THE SAME

    The present disclosure relates to a Y-shaped nucleotide probe having two probe parts in one body, which provides improved sensitivity, specificity and accuracy in genotype and genetic analysis and thus is widely applicable to diagnosis and a variant thereof (d- or b-shaped probe), and a DNA microarray, a kit and a genetic analysis method using the same. The Y-shaped probe comprises a left-side probe part, a left-side stem part, a linker part, a right-side stem part and a right-side probe part. The DNA microarray of the present disclosure can improve accuracy of test by testing the same gene simultaneously or by testing two different target genes at once. Especially, since both the target gene and the control gene can be tested simultaneously from one spot, error can be reduced, quantitative analysis is possible and standardization is easy. The Y-shaped probe of the present disclosure may be widely used for genotyping, analysis of gene expression, analysis of mutation or SNP, diagnosis and prediction of diseases, determination of therapeutic regimen, or the like.

  • Novel Pharmacogene Single Nucleotide Polymorphisms and Methods of Detecting Same

    The present invention provides pharmacogene polymorphisms and their use in predicting therapeutic effectiveness. The present invention also provides methods comprising targeted analysis of selected pharmacogenes in thousands of compiled whole human genome sequences for identifying polymorphic sequences associated with drug response are described. The methods also provide confirmation and validation of these pharmacogene polymorphisms, based on concordance between different sequencing technologies, and statistical error-checking. Imputation of the deleterious consequences of novel variants is predicted by bioinformatics analysis.

  • ENGINEERED INTRACELLULAR SIALYLATION PATHWAYS

    Methods for manipulating carbohydrate processing pathways in cells of interest are provided. Methods are directed at manipulating multiple pathways involved with the sialylation reaction by using recombinant DNA technology and substrate feeding approaches to enable the production of sialylated glycoproteins in cells of interest. These carbohydrate engineering efforts encompass the implementation of new carbohydrate bioassays, the examination of a selection of insect cell lines and the use of bioinformatics to identify gene sequences for critical processing enzymes. The compositions comprise cells of interest producing sialylated glycoproteins. The methods and compositions are useful for heterologous expression of glycoproteins.

  • COMPOSITIONS HAVING ANTIANGIOGENIC ACTIVITY AND USES THEREOF

    Compositions and methods that are useful for modulating blood vessel formation, as well as methods that provide for the systematic and efficient identification of angiogenesis modulators are described. As discussed in more detail below, a systematic computational methodology based on bioinformatics was used to identify novel peptide modulators of angiogenesis that have been characterized in vitro and/or in vivo.

  • SYSTEMS AND METHODS FOR SEARCHING GENOMIC DATABASES

    The invention described herein solves the challenges encountered in searching for clinical and genomic information from multiple data sources. Systems, methods, and devices of the invention allow a user to search a number of dissimilar information sources simultaneously, and view, process, and perform correlations on the information. The invention uses faceted search to process clinical values, genomic data, subject characteristics, and population characteristics, thereby providing a user with an array of information useful for monitoring or improving the state of health of a subject or a subject population. The invention allows a user to evaluate clinical and research information in a subject-centric way, and analyze information at either the individual or the population level.

  • Techniques for Determining Haplotype by Population Genotype and Sequence Data

    A novel phasing algorithm harnesses sequencing read information from next generation sequencing technologies to guide and improve local haplotype reconstruction from genotypes. Techniques include determining correlated occurrences of single nucleotide polymorphisms (SNPs) in genes of a population of individuals. A plurality of sequences of nucleotide bases in one or more individuals from the populations of individuals is determined based on ultra-high throughput sequencing of a sample from the one or more individuals. Haplotypes included in the population of individuals are determined based on both the correlated occurrences and the plurality of sequences. The inclusion of paired end read data is especially advantageous for the phasing of rare variants, including singletons.

  • METHODS FOR TREATING LYSOSOMAL ACID LIPASE DEFICIENCY

    The present invention provides compositions and methods for effective treatment of a lysosomal acid lipase deficiency (LALD) disease, in particular, Wolman's disease and Cholesteryl Ester Storage Disease (CESD). Among other things, the present invention provides a method of treating developmental impairment or malnutrition in an individual suffering from a lysosomal acid lipase deficiency (LALD) disease, comprising administering to the individual a therapeutic effective amount of a lysosomal acid lipase.