76 results about "Gene Discovery" patented technology

Methods for preparing a biochip are provided herein wherein the biomolecular probe to be used with the biochip is alternatively bound to a hydrogel prepolymer prior to or simultaneously with polymerization of the prepolymer. In particularly preferred embodiments, a polyurethane-based hydrogel prepolymer is derivatized with an organic solvent soluble biomolecule, such as a peptide nucleic acid probe in aprotic, organic solvent. Following derivatization of the prepolymer, an aqueous solution, for example sodium bicarbonate, preferably buffered to a pH of about 7.2 to about 9.5, is added to the derivatized prepolymer solution to initiate polymerization of the hydrogel. Alternatively, a water soluble biomolecule, such as DNA or other oligonucleotide, is prepared in an aqueous solution and added to the polyurethane-based hydrogel prepolymer such that derivatization and polymerization occur, essentially, simultaneously. While the hydrogel is polymerizing, it is microspotted onto a solid substrate, preferably a silanated glass substrate, to which the hydrogel microdroplet becomes covalently bound. Most preferably the hydrogel microdroplets are at least about 30 mum thick, for example about 50 mum to about 100 mum thick. The resulting biochips are particularly useful for gene discovery, gene characterization, functional gene analysis and related studies.

A novel 3' gene trap cassette is described that does not encode a marker conferring antibiotic resistance and can be used to efficiently trap and identify cellular genes. Vectors incorporating the presently 3' gene trap cassette find particular application in gene discovery, the production of transgenic cells and animals, and gene activation.

Disclosed are methods for detecting and / or prioritizing phenotype-causing genomic variants and related software tools. The methods include genomic feature based analysis and can combine variant frequency information with sequence characteristics such as amino acid substation. The methods disclosed are useful in any genomics study; for example, rare and common disease gene discovery, tumor growth mutation detection, personalized medicine, agricultural analysis, and centennial analysis.

The invention relates to methods and systems (e.g., computer systems and computer program products) for identifying and characterizing genes using microarrays. In particular, the invention provides for improved, robust methods for detecting genes through the use of microarrays to analyze the expression state of the genome. Genes which are expressed can be mapped to their respective positions in the genome, and the structure of such genes can be determined.

Novel vectors are described that incorporate, inter alia, a novel 3' gene trap cassette which can be used to efficiently trap and identify previously unknown cellular genes. Vectors incorporating the described 3' gene trap cassette find particular application in gene discovery and in the production of mutated cells and animals.

The present invention describes a comprehensive system for gene discovery using retrovirus that have been engineered to exhibit increased accessibility to genomic DNA, or to mutate and identify the chromosomal target sequences of DNA binding proteins. The strategy employs the combination of retroviral integrase / DNA binding protein fusion constructs and gene-trapping methodologies. This novel technology provides the ability to establish proviral integration at any location within the genome. In addition, it allows for the generation of a collection of eukaryotic cells in which each cell contains a mutation in a target gene or sequence for a known DNA binding protein which also allow for rapid in vivo functional analysis. Sequence information obtained for genes identified using the described methods identify a collection of eukaryotic genes related by, or directly or indirectly regulated by, a given DNA binding protein.

Serial analysis of gene expression, SAGE, a method for the rapid quantitative and qualitative analysis of transcripts is provided. Short defined sequence tags corresponding to expressed genes are isolated and analyzed. Sequencing of over 1,000 defined tags in a short period of time (e.g., hours) reveals a gene expression pattern characteristic of the function of a cell or tissue. Moreover, SAGE is useful as a gene discovery tool for the identification and isolation of novel sequence tags corresponding to novel transcripts and genes.

Methods and compositions are provided for producing arrays of polymeric binding agents. In the subject methods, the individual polymers of the array are synthesized using solid phase synthesis techniques on the surface of a substrate. A critical feature of the invention is that one or more locations on the substrate surface are spatially and temporally protected by a protective bubble during the synthesis protocol, where the protective bubble may be produced using any convenient bubble producing means. The bubble producing means may be a component of either a substrate or a structure separate from the substrate. Also provided are the arrays produced by the subject methods, kits for use in practicing the subject methods, and methods of using the arrays in analyte detection assays, including hybridization assays, such as gene discovery, differential gene expression and gene sequencing assays.

The present invention pertains to a process for automatically analyzing nucleic acid samples. Specifically, the process comprises the steps of forming electrophoretic data of DNA samples with DNA ladders; comparing these data; transforming the coordinates of the DNA sample's data into DNA length coordinates; and analyzing the DNA sample in length coordinates. This analysis is useful for automating fragment analysis and quality assessment. The automation enables a business model based on usage, since it replaces (rather than assists) labor. This analysis also provides a mechanism whereby data generated on different instruments can be confidently compared. Genetic applications of this invention include gene discovery, genetic diagnosis, and drug discovery. Forensic applications include identifying people and their relatives, catching perpetrators, analyzing DNA mixtures, and exonerating innocent suspects.

The present invention provides hyperactive piggyBac transposons, in particular hyperactive piggyBac transposons from Trichoplusia ni (cabbage looper moth) that transpose at a higher frequency than wildtype. The invention also features integration defective piggyBac transposons. The piggyBac transposons and transposases can be used in gene transfer systems for stably introducing nucleic acids into the DNA of a cell. The gene transfer system can be used in methods, for example, but not limited to, gene therapy, insertional mutagenesis, or gene discovery.

The present invention provides polynucleotide vectors for high expression of heterologous genes, and methods for constructing such vectors. Some vectors further comprise novel transposons and transposases that further improve expression. Further disclosed are vectors that can be used in a gene transfer system for stably introducing nucleic acids into the DNA of a cell. The gene transfer systems can be used in methods, for example, but not limited to, gene expression, gene therapy, insertional mutagenesis, or gene discovery.

The present invention provides polynucleotide vectors for high expression of heterologous genes, and methods for constructing such vectors. Some vectors further comprise novel transposons and transposases that further improve expression. Further disclosed are vectors that can be used in a gene transfer system for stably introducing nucleic acids into the DNA of a cell. The gene transfer systems can be used in methods, for example, but not limited to, gene expression, gene therapy, insertional mutagenesis, or gene discovery.

The invention provides collections of transgenic animals and vectors for producing transgenic animals, which transgenic animals and vectors have a transgene comprising sequences encoding a detectable or selectable marker, the expression of which marker is under the control of regulatory sequences from an endogenous gene such that when the transgene is present in the genome of the transgenic animal, the detectable or selectable marker has the same expression pattern as the endogenous gene. Such transgenic animals can then be used to detect, isolate and / or select pure populations of cells having a particular functional characteristic. The isolated cells have uses in gene discovery, target identification and validation, genomic and proteomic analysis, etc.

Provided herein are methods for evaluating associations between candidate genes and a trait of interest in a population. The methods include a combination of genome-wide association analysis and one or more of nested association mapping (NAM), expression QTL analysis (eQTL), and allele epistastic analysis (AEA). Markers are selected or prioritized if they are shown to be positively-correlated with a trait of interest using GWA and a combination of one or both of NAM and eQTL. Also provided are models for evaluating the association between a candidate marker and a trait in a nested population of organisms. These methods include single marker regression and multiple marker regression models. Markers identified using the methods of the invention can be used in marker assisted breeding and selection, as genetic markers for constructing linkage maps, for gene discovery, for identifying genes contributing to a trait of interest, and for generating transgenic organisms having a desired trait.

The invention provides collections of transgenic animals and vectors for producing transgenic animals, which transgenic animals and vectors have a transgene comprising sequences encoding a detectable or selectable marker, the expression of which marker is under the control of regulatory sequences from an endogenous gene such that when the transgene is present in the genome of the transgenic animal, the detectable or selectable marker has the same expression pattern as the endogenous gene. Such transgenic animals can then be used to detect, isolate and / or select pure populations of cells having a particular functional characteristic. The isolated cells have uses in gene discovery, target identification and validation, genomic and proteomic analysis, etc.

An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5′-terminus sequence and the second tag comprises the 3′-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.

Biological samples undergo drastic changes during the execution of an experiment to aid in the determination of gene discovery, disease diagnosis, drug discovery, toxicological research, and so on. After a biological sample is processed, pieces of information about the state of a biological sample are generated. Pedigree information is also generated when a biological sample is sub-divided into multiple portions or when multiple biological samples are combined. These pieces of information illuminate the experiment process in a way that can help scientists to better understand the failure or the success of an experiment. Various pieces of information, such as the state and the pedigree of biological samples are tracked, traced, or searched, so as to allow scientists to piece together a picture of greater experimental clarity.

The present disclosure provides methods and systems for prioritizing phenotype-causing genomic variants. The methods include using variant prioritization analyses and in combination with biomedical ontologies using a sophisticated re-ranking methodology to re-rank these variants based on phenotype information. The methods can be useful in any genomics study and diagnostics; for example, rare and common disease gene discovery, tumor growth mutation detection, drug responder studies, metabolic studies, personalized medicine, agricultural analysis, and centennial analysis.

The present invention pertains to a process for automatically analyzing nucleic acid samples. Specifically, the process comprises the steps of forming electrophoretic data of DNA samples with DNA ladders; comparing these data; transforming the coordinates of the DNA sample's data into DNA length coordinates; and analyzing the DNA sample in length coordinates. This analysis is useful for automating fragment analysis and quality assessment. The automation enables a business model based on usage, since it replaces (rather than assists) labor. This analysis also provides a mechanism whereby data generated on different instruments can be confidently compared. Genetic applications of this invention include gene discovery, genetic diagnosis, and drug discovery. Forensic applications include identifying people and their relatives, catching perpetrators, analyzing DNA mixtures, and exonerating innocent suspects.

Compositions, methods and kits for genomic screening, genetic analysis, and gene discovery. In some embodiments the disclosed methods can detect large internal tandem duplications, or novel translocations, as well as identify the genomic breakpoint of novel translocations when only one of the two fusion partners is known or targeted. This is accomplished by employing a series of carefully selected capture probes to target genome-specific and disease-specific areas of target genes that harbor disease related somatic mutations, insertions / deletions or are involved in translocations.

The present invention provides polynucleotide vectors for high expression of heterologous genes, and methods for constructing such vectors. Some vectors further comprise novel transposons and transposases that further improve expression. Further disclosed are vectors that can be used in a gene transfer system for stably introducing nucleic acids into the DNA of a cell. The gene transfer systems can be used in methods, for example, but not limited to, gene expression, gene therapy, insertional mutagenesis, or gene discovery.

Development of an efficient and cost-effective doubled haploid production system and genetic transformation system are the prerequisite to initiate haploid breeding and genetic modification in flax respectively. Pre-culturing anthers on a high osmotic, high auxin and high mineral salt concentration for a period of time before transfer to a low osmotic, low auxin and low salt concentration significantly increased the overall efficiency of regeneration or anther efficiency than directly culturing anthers on a low osmotic, low auxin and low salt concentration medium. This culture procedure also dramatically reduced the frequency of shoot regeneration from somatic cells in anther culture. Using this procedure, a highly efficient anther culture-derived callus based transformation system was developed. The transformation efficiency of anther culture-derived callus based transformation system was four times higher than the best reported transformation efficiency using hypocotyls as the ex-plants in Agrobacterium tumefaciens based transformation system or particle bombardment based transformation system. The frequency of escape in anther culture-derived callus based transformation system was one third of that in hypocotyl-based transformation system using A. tumefaciens or one half using particle bombardment. This very high efficient transformation system will prove to be very valuable in basic research for gene discovery and practical applications in genetic engineering for improved traits.

The invention provides methods for identifying polymorphic markers for herbicide resistance in weeds and for generating herbicide susceptible and herbicide resistant weeds by mutagenizing weeds and comparing genetic differences between herbicide resistant and herbicide susceptible weeds. The methods may involve the inhibition of mismatch repair in the weeds through the introduction of dominant negative alleles of mismatch repair genes, through T-DNA insertional mutations, or the use of chemical inhibitors of mismatch repair. The invention also provides polymorphic markers of herbicide resistance and methods and kits to screen for herbicide resistant weeds, such as horseweed, goosegrass and rye grass.

The invention discloses an RFLP method for rapidly detecting the SNP of the cattle FGF21 gene. Using the whole genome DNA of the cattle to be tested containing the FGF21 gene as a template, using primer pairs P1, P2 and P3 as primers, the FGF21 gene of cattle is amplified by PCR, and 4 SNP sites; primer pairs F159, F297, F940, and F1151 were designed for these 4 SNP sites, and SalI, XhoI, XbaI, and MspI restriction sites were artificially introduced in turn for PCR amplification. The endonucleases digested the PCR amplification products respectively, and then detected the digested fragments by agarose gel electrophoresis, and identified the 159th, 297th, 940th, and 1151st units of the cattle FGF21 gene according to the electrophoresis results. Nucleotide polymorphism. Since the function of the FGF21 gene involves growth traits such as body weight, the detection method provided by the invention lays the foundation for the establishment of the relationship between the SNP of the FGF21 gene and the growth traits, so as to be used for marker-assisted selection of the growth traits of Chinese cattle, and to quickly establish cattle with excellent genetic resources. population.

The invention provides a PL-LbCpf1-RR gene with high mutagenic efficiency in gene targeting, and application thereof. A new PL-LbCpf1-RR gene is unexpectedly obtained in the rice gene targeting experiment process, and the PL-LbCpf1-RR gene can identify more genome sites and has high mutagenic efficiency when being used for performing rice shearing. In addition, the invention provides an expression box and an expression vector, as well as application of the expression box and the expression vector to a rice gene edition aspect. The obtained PL-LbCpf1-RR is used for constructing a plant expression vector and constructing a rice targeting vector, DNA double-chain shear of a rice specific gene site is caused after rice cells are imported, rice gene targeting is realized and high mutagenic efficiency is achieved.

The invention provides PL-LbCpf1-RVR gene for recognizing specific sites in rice gene targeting and application thereof. The novel PL-LbCpf1-RVR gene is accidentally acquired during a rice gene targeting experiment; it is discovered that the PL-LbCpf1-RVR gene can be used to shear rice to recognize specific sites, with more genome sites recognized. In addition, the invention provides an expression cassette and expression vector constructed based on the PL-LbCpf1-RVR gene, as well as application of the expression cassette and expression vector in rice gene editing. A plant expression vector is constructed by using the acquired PL-LbCpf1-RVR gene, a rice targeting vector is constructed, DNA double-chain shearing of rice specific gene sites is caused after the vector is introduced into rice cells, rice gene targeting is achieved, and transgenic rice plants are acquired under high mutation efficiency.

Novel genes that code for a family of feruloyl esterases that break down ferulic acid crosslinks between polysaccharide chains and between polysaccharides and lignins in plant cell walls are described herein as well as a method of rapid gene discovery.

According to the invention, there is provided a high throughput method for measuring total fermentables using a small amount of plan tissue. A high throughput screening tool for gene discovery aiming for increasing total fermentables is further provided.