Patents Assigned to Diversa Corporation
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Patent number: 7056691Abstract: The invention relates to ?-galactosidase and to polynucleotides encoding the ?-galactosidase. In addition methods of designing new ?-galactosidases and method of use thereof are also provided. The ?-galactosidases have increased activity and stability at increased pH and temperature.Type: GrantFiled: April 3, 2002Date of Patent: June 6, 2006Assignee: Diversa CorporationInventors: Jay M. Short, Dennis Murphy, John Reid, Eric J. Mathur
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Patent number: 7056703Abstract: The invention relates to thermostable polymerases that have polymerase activity temperatures in the range from 90° C. up to 113° C., such as those derived from Pyrolobus fumaria, and to polynucleotides encoding the polymerases In addition, methods of designing new thermostable DNA polymerases and methods of use thereof are also provided. The polymerases have increased activity and stability at increased pH and temperature.Type: GrantFiled: September 6, 2001Date of Patent: June 6, 2006Assignee: Diversa CorporationInventors: Walter Callen, Eric J. Mathur, Jay Short
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Patent number: 7049101Abstract: The invention relates to thermostable polymerases that have polymerase activity temperatures in the range from 90° C. up to 113° C., such as those derived from Pyrolobus fumaria, and to polynucleotides encoding the polymerases In addition, methods of designing new thermostable DNA polymerases and methods of use thereof are also provided. The polymerases have increased activity and stability at increased pH and temperature.Type: GrantFiled: September 6, 2000Date of Patent: May 23, 2006Assignee: Diversa CorporationInventors: Walter Callen, Eric J. Mathur
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Publication number: 20060088821Abstract: A process for constructing a catalogued nucleic acid library in which the proportional representation of the constituents is adjusted to advantage through the use of disclosed technologies for positive and negative selection. The resultant benefit is that significantly fewer library constituents will need to be screened in order to identify a potentially desired constituent. Moreover, library constituents that previously would have been essentially “lost” are now recoverable. Preferred embodiments of this invention include the cataloguing, normalization, and enrichment of library constituents. By way of example, but not limitation, this technology is serviceable for constructing a library that contains an adequate representation of desirable constituents that (1) are initially found in low-copy numbers within a sample source or (2) originate from an organism that is problematic to culture. Applicable uses of this invention include any library-screening endeavor previously hindered by logistical impediments.Type: ApplicationFiled: December 21, 2001Publication date: April 27, 2006Applicant: Diversa CorporationInventor: Jay Short
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Patent number: 7033781Abstract: An invention comprising cellular transformation, directed evolution, and screening methods for creating novel transgenic organisms having desirable properties. Thus in one aspect, this invention relates to a method of generating a transgenic organism, such as a microbe or a plant, having a plurality of traits that are differentially activatable. Also, a method of retooling genes and gene pathways by the introduction of regulatory sequences, such as promoters, that are operable in an intended host, thus conferring operability to a novel gene pathway when it is introduced into an intended host. For example a novel man-made gene pathway, generated based on microbially-derived progenitor templates, that is operable in a plant cell. Furthermore, a method of generating novel host organisms having increased expression of desirable traits, recombinant genes, and gene products.Type: GrantFiled: September 30, 2000Date of Patent: April 25, 2006Assignee: Diversa CorporationInventor: Jay M. Short
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Patent number: 7019827Abstract: A GigaMatrix plate for holding a large number of small-volume fluid samples includes a base for supporting a plurality of substantially parallel, elongated capillary tubes. Each tube defines a lumen that extends through the base, and each lumen has an aspect ratio greater than about 5:1. Dimensionally, each lumen has an inner diameter that is less than approximately five hundred microns and it has a length greater than about five millimeters. Further, each tube acts to optically distinguish light that is directed toward it from the sample whenever the sample fluoresces inside the tube lumen. Also, however, light from the sample that is directed axially through the tube is emitted therefrom for optical detection of the tube and the sample therein.Type: GrantFiled: February 25, 2002Date of Patent: March 28, 2006Assignee: Diversa CorporationInventor: William Michael Lafferty
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Patent number: 7018793Abstract: Provided is a method of screening gene libraries derived from a mixed population of organisms for a bioactivity or biomolecule of interest. The mixed population of organisms can be a cultured population or an uncultured population from, for example, the environment. Also provided are methods of screening isolates or enriched populations of organisms, which isolates include a population that is spatially, temporally, or hierarchical, for example, of a particular species, genus, family, or class of organisms. Identified clones containing a biomolecule or bioactivity of interest can be further variegated or the DNA contained in the clone can be variegated to create novel biomolecules or bioactivities of interest.Type: GrantFiled: September 15, 2000Date of Patent: March 28, 2006Assignee: Diversa CorporationInventor: Jay M. Short
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Patent number: 6987016Abstract: The invention relates to ?-galactosidase and to polynucleotides encoding the ?-galactosidase. In addition methods of designing new ?-galactosidases and method of use thereof are also provided. The ?-galactosidases have increased activity and stability at increased pH and temperature.Type: GrantFiled: June 20, 2001Date of Patent: January 17, 2006Assignee: Diversa CorporationInventors: Dennis Murphy, John Reid, Dan E. Robertson
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Patent number: 6987009Abstract: A thermostable alpha-glycosidase derived from various Thermococcus, alcaliphilus AEDII12RA is disclosed. The enzymes are produced from native or recombinant host cells and can be utilized in the food processing industry.Type: GrantFiled: July 19, 2000Date of Patent: January 17, 2006Assignee: Diversa CorporationInventors: Dennis Murphy, John Reid
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Patent number: 6979733Abstract: The invention is directed to polypeptides having epoxide hydrolase activity, polynucleotides encoding the polypeptides, antibodies that bind to these polypeptides, and methods for making and using these polynucleotides and polypeptides. The epoxide hydrolases are used to catalyze the hydrolysis of epoxides and arene oxides to their corresponding diols.Type: GrantFiled: August 5, 2002Date of Patent: December 27, 2005Assignee: Diversa CorporationInventors: Lishan Zhao, Eric J. Mathur, David Weiner, Toby Richardson, Aileen Milan, Mark J. Burk, Bin Han, Jay M. Short
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Patent number: 6972183Abstract: A process for screening an expression library to identify clones expressing enzymes having a desired activity is provided. The process involves first generating from genomic DNA samples of one or more microorganisms an expression library comprising a plurality of recombinant cell clones, and then introducing into capillaries in a capillary array a substrate and at least a subset of the clones, either individually or as a mixture. Interaction of the substrate and a clone expressing an enzyme having the desired activity produces an optically detectable signal, which can then be spatially detected to identify capillaries containing clones producing such a signal. The signal-producing clones can then be recovered from the identified capillaries.Type: GrantFiled: November 22, 1999Date of Patent: December 6, 2005Assignee: Diversa CorporationInventors: William Michael Lafferty, Jay M. Short, Martin Keller
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Patent number: 6949369Abstract: The invention relates to ?-galactosidase and to polynucleotides encoding the ?-galactosidase. In addition methods of designing new ?-galactosidases and method of use thereof are also provided. The ?-galactosidases have increased activity and stability at increased pH and temperature.Type: GrantFiled: April 1, 2002Date of Patent: September 27, 2005Assignee: Diversa CorporationInventors: Dennis Murphy, John Reid, Dan E. Robertson
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Patent number: 6943001Abstract: The invention is directed to polypeptides having epoxide hydrolase activity, polynucleotides encoding the polypeptides, antibodies that bind to these polypeptides, and methods for making and using these polynucleotides and polypeptides. The epoxide hydrolases are used to catalyze the hydrolysis of epoxides and arene oxides to their corresponding diols.Type: GrantFiled: October 10, 2002Date of Patent: September 13, 2005Assignee: Diversa CorporationInventors: Lishan Zhao, Eric J. Mathur, David Weiner, Toby Richardson, Aileen Milan, Mark J. Burk, Bin Han, Jay M. Short
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Patent number: 6939689Abstract: This invention provides methods of obtaining novel polynucleotides and encoded polypeptides by the use of non-stochastic methods of directed evolution (DirectEvolution™). A particular advantage of exonuclease-mediated reassembly methods is the ability to reassemble nucleic acid strands that would otherwise be problematic to chimerize. Exonuclease-mediated reassembly methods can be used in combination with other mutagenesis methods provided herein. These methods include non-stochastic polynucleotide site-saturation mutagenesis (Gene Site Saturation Mutagenesis™) and non-stochastic polynucleotide reassembly (GeneReassembly™). This invention provides methods of obtaining novel enzymes that have optimized physical &/or biological properties. Through use of the claimed methods, genetic vaccines, enzymes, small molecules, and other desirable molecules can be evolved towards desirable properties. For example, vaccine vectors can be obtained that exhibit increased efficacy for use as genetic vaccines.Type: GrantFiled: December 21, 2001Date of Patent: September 6, 2005Assignee: Diversa CorporationInventors: Jay M. Short, Tsotne David Djavakhishvili, Gerhard Johann Frey
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Patent number: 6918738Abstract: A holding plate includes a flat base member with a surface that is formed with a plurality of stations (wells or depressions) for holding specimens. A panel extends downwardly from the edge of the surface to create a concavity for receiving a lid member therein. The panel also has a flange extending outwardly from the concavity. The flat lid member has a skirt with a rim that extends from the edge of the lid member to create a hollow for receiving a base member therein. In operation, a robot or mechanical device selectively engages the flange of the base member and the rim of the lid member to engage or disengage the base and lid members. This allows for individual movement of either the base member or the lid member. This also allows for collective movement of the engaged base and lid members for stacking and storage.Type: GrantFiled: March 11, 2002Date of Patent: July 19, 2005Assignee: Diversa CorporationInventors: William Michael Lafferty, Scott Wayne Beaver, Charles Wilson Tweedy
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Publication number: 20050108789Abstract: The invention provides novel polypeptides having phospholipase activity, including, e.g., phospholipase A, B, C and D activity, patatin activity, lipid acyl hydrolase (LAH) activity, nucleic acids encoding them and antibodies that bind to them. Industrial methods, e.g., oil degumming, and products comprising use of these phospholipases are also provided.Type: ApplicationFiled: March 8, 2004Publication date: May 19, 2005Applicant: Diversa CorporationInventors: Svetlana Gramatikova, Geoff Hazlewood, David Lam, Nelson Barton
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Patent number: 6872526Abstract: Disclosed is a process for identifying clones having a specified activity of interest, which process comprises (i) generating one or more expression libraries derived from nucleic acid directly isolated from the environment; and (ii) screening said libraries utilizing a fluorescence activated cell sorter to identify said clones. More particularly, this is a process for identifying clones having a specified activity of interest by (i) generating one or more expression libraries derived from nucleic acid directly or indirectly isolated from the environment; (ii) exposing said libraries to a particular substrate or substrates of interest; and (iii) screening said exposed libraries utilizing a fluorescence activated cell sorter to identify clones which react with the substrate or substrates.Type: GrantFiled: May 3, 2001Date of Patent: March 29, 2005Assignee: Diversa CorporationInventors: Jay M. Short, Martin Keller
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Patent number: 6866824Abstract: Provided are methods of screening and identification of bioactivities and bioactive molecules of interest using a capillary array system. More specifically, disclosed are methods of using optical detection and capillary array-based techniques for screening libraries and recovering bioactive molecules having a desired activity or a nucleic acid sequence encoding such bioactive molecules.Type: GrantFiled: May 28, 2002Date of Patent: March 15, 2005Assignee: Diversa CorporationInventors: William Michael Lafferty, Jay M. Short, Martin Keller
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Publication number: 20050040550Abstract: Disclosed is a process for identifying clones having a specified activity of interest, which process comprises (i) generating one or more expression libraries derived from nuclei acid directly isolated from the environment; and (ii) screening said libraries utilizing a fluorescence activated cell sorter to identify said clones. More particularly, this is a process for identifying clones having a specified activity of interest by (i) generating one or more expression libraries derived from nucleic acid directly or indirectly isolated from the environment; (ii) exposing said libraries to a particular substrate or substrates of interest; and (iii) screening said exposed libraries utilizing a fluorescence activated cell sorter to identify clones which react with the substrate or substrates.Type: ApplicationFiled: September 23, 2004Publication date: February 24, 2005Applicant: Diversa CorporationInventors: Jay Short, Martin Keller
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Patent number: 6855365Abstract: A purified and modified phytase enzyme from Escherichia coli K12 appA phytase is provided. The enzyme has phytase activity and improved thermal tolerance as compared with the wild-type enzyme. In addition, the enzyme has improved protease stability at low pH. Glycosylation of the modified phytase provided a further improved enzyme having improved thermal tolerance and protease stability. The enzyme can be produced from native or recombinant host cells and can be used to aid in the digestion of phytate where desired. In particular, the phytase of the present invention can be used in foodstuffs to improve the feeding value of phytate rich ingredients.Type: GrantFiled: May 24, 2001Date of Patent: February 15, 2005Assignee: Diversa CorporationInventors: Jay M. Short, Keith A. Kretz, Kevin A. Gray, Nelson Robert Barton, James B. Garrett, Eileen O'Donoghue, Eric J. Mathur