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.

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.

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.

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.

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 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 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.