Patents by Inventor Jon E. Ness
Jon E. Ness has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 9359581Abstract: A substantially pure Candida host cell is provided for the biotransformation of a substrate to a product wherein the host cell is characterized by a first genetic modification class that comprises one or more genetic modifications that collectively or individually disrupt at least one alcohol dehydrogenase gene in the substantially pure Candida host cell.Type: GrantFiled: November 19, 2013Date of Patent: June 7, 2016Assignee: Synthezyme LLCInventors: Jon E. Ness, Jeremy Minshull
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Patent number: 9102944Abstract: Provided are methods, compositions, and kits for cloning of DNA using DNA topoisomerase. The methods comprise (I) combining into a mixture (A) a first polynucleotide comprising an origin of replication, a selectable marker, two topoisomerase recognition sequences, and two nicking agent recognition sequences, each of the topoisomerase recognition sequences being within 50 nucleotides of at least one of the nicking agent recognition sequences and each of the two nicking agent recognition sequences being nicked, with (B) a sequence-specific topoisomerase and (C) a second polynucleotide having 5? hydroxyl on each end; and (II) transforming the mixture into a host organism, thereby cloning the second polynucleotide. Formation or purification of a DNA-protein adduct prior to the addition of the second polynucleotide is not required. Also provided are vector sequences to facilitate performance of the methods and methods for modifying a vector of interest to render it useful in the disclosed methods.Type: GrantFiled: October 10, 2012Date of Patent: August 11, 2015Assignee: DNA Twopointo, Inc.Inventors: Jon E. Ness, Jeremy S. Minshull
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Publication number: 20150218486Abstract: An ?-carboxyl-?-hydroxyl fatty acid oxidized from a substantially pure Candida host cell, wherein the substantially pure Candida host cell is characterized by a first genetic modification class that comprises one or more genetic modifications that collectively or individually disrupt an alcohol dehydrogenase gene, and a second genetic modification class, wherein the second genetic modification class comprises an insertion of a first gene into the Candida host cell genome.Type: ApplicationFiled: April 6, 2015Publication date: August 6, 2015Applicant: SYNTHEZYME LLCInventors: JON E. NESS, JEREMY MINSHULL
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Publication number: 20150094483Abstract: A substantially pure Candida host cell is provided for the biotransformation of a substrate to a product wherein the host cell is characterized by a first genetic modification class that comprises one or more genetic modifications that collectively or individually disrupt at least one alcohol dehydrogenase gene in the substantially pure Candida host cell.Type: ApplicationFiled: November 19, 2013Publication date: April 2, 2015Inventors: Jon E. Ness, Jeremy Minshull
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Patent number: 8825411Abstract: Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.Type: GrantFiled: May 4, 2005Date of Patent: September 2, 2014Assignee: DNA Twopointo, Inc.Inventors: Sridhar Govindarajan, Jeremy S. Minshull, Jon E. Ness
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Patent number: 8597923Abstract: A substantially pure Candida host cell is provided for the biotransformation of a substrate to a product wherein the host cell is characterized by a first genetic modification class that comprises one or more genetic modifications that collectively or individually disrupt at least one alcohol dehydrogenase gene in the substantially pure Candida host cell.Type: GrantFiled: May 6, 2010Date of Patent: December 3, 2013Assignee: SyntheZyme, LLCInventors: Jon E. Ness, Jeremy Minshull
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Publication number: 20130196864Abstract: Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.Type: ApplicationFiled: February 8, 2013Publication date: August 1, 2013Applicant: DNA TWOPOINTO, INC.Inventors: Sridhar Govindarajan, Jeremy S. Minshull, Jon E. Ness
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Patent number: 8377681Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.Type: GrantFiled: December 2, 2011Date of Patent: February 19, 2013Assignee: Codexis Mayflower Holdings, LLCInventors: Stephen DelCardayre, Matthew B. Tobin, Willem P. C. Stemmer, Jon E. Ness, Jeremy S. Minshull, Phillip A. Patten, Venkiteswatan Mani Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Anthony R. Cox, Gjalt W. Huisman, Ling Yuan, Joseph A. Affholter
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Patent number: 8323930Abstract: Provided are methods, compositions, and kits for molecular cloning of DNA using DNA topoisomerase. The methods comprise (I) combining into a mixture (A) a first polynucleotide, comprising an origin of replication, a selectable marker, two topoisomerase recognition sequences, and two nicking agent recognition sequences, each of the topoisomerase recognition sequences being within 50 nucleotides of at least one of the nicking agent recognition sequences and each of two nicking agent recognition sequences being nicked, with (B) a sequence-specific topoisomerase and (C) a second polynucleotide, having a 5? hydroxyl on each end; and (II) transforming the mixture into a host organism, thereby cloning the second polynucleotide. Formation or purification of a DNA-protein adduct prior to the addition of the second polynucleotide is not required. Also provided are vector sequences to facilitate performance of the methods and methods for modifying a vector of interest to render it useful in the disclosed methods.Type: GrantFiled: July 23, 2008Date of Patent: December 4, 2012Assignee: DNA Twopointo, Inc.Inventors: Jon E. Ness, Jeremy S. Minshull
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Publication number: 20120252681Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.Type: ApplicationFiled: December 2, 2011Publication date: October 4, 2012Applicant: CODEXIS MAYFLOWER HOLDINGS, LLCInventors: Stephen del Cardayre, Matthew Tobin, Willem P.C. Stemmer, Jon E. Ness, Jeremy Minshull, Phillip Patten, Venkiteswaran Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Tony Cox, Gjalt Huisman, Ling Yuan, Joseph A. Affholter
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Publication number: 20120040871Abstract: Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.Type: ApplicationFiled: September 23, 2011Publication date: February 16, 2012Applicant: CODEXIS MAYFLOWER HOLDINGS, LLCInventors: Andreas Crameri, Willem PC Stemmer, Jeremy Minshull, Steven H. Bass, Mark Welch, Jon E. Ness, Claes Gustafsson, Phillip A Patten
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Patent number: 8076138Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.Type: GrantFiled: October 15, 2009Date of Patent: December 13, 2011Assignee: Codexis Mayflower Holdings, LLCInventors: Stephen DelCardayre, Matthew B. Tobin, Willem P. C. Stemmer, Jon E. Ness, Jeremy S. Minshull, Phillip A. Patten, Venkiteswatan Mani Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Anthony R. Cox, Gjalt W. Huisman, Ling Yuan, Joseph A. Affholter
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Patent number: 8029988Abstract: Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.Type: GrantFiled: November 30, 2007Date of Patent: October 4, 2011Assignee: Codexis Mayflower Holdings, LLCInventors: Andreas Crameri, Willem P. C. Stemmer, Jeremy Minshull, Steven H. Bass, Mark Welch, Jon E. Ness, Claes Gustafsson, Phillip A. Patten
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Publication number: 20110190140Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.Type: ApplicationFiled: October 15, 2009Publication date: August 4, 2011Applicant: Maxygen, Inc.Inventors: Stephen del Cardayre, Matthew Tobin, Willem P.C. Stemmer, Jon E. Ness, Jeremy Minshull, Phillip Patten, Venkiteswatan Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Tony Cox, Gjalt Huisman, Ling Yuan, Joseph A. Affholter
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Patent number: 7873477Abstract: Methods and systems for providing biological results in the form of systematically varied libraries of sequences or as data representing sequences or physical preparations of systematically varied libraries and/or selections from systematically varied libraries.Type: GrantFiled: August 20, 2002Date of Patent: January 18, 2011Assignee: Codexis Mayflower Holdings, LLCInventors: Claes Gustafsson, Sridhar Govindarajan, Jeremy S. Minshull, Jon E. Ness, Robin A. Emig
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Publication number: 20100291653Abstract: A substantially pure Candida host cell is provided for the biotransformation of a substrate to a product wherein the host cell is characterized by a first genetic modification class that comprises one or more genetic modifications that collectively or individually disrupt at least one alcohol dehydrogenase gene in the substantially pure Candida host cell.Type: ApplicationFiled: May 6, 2010Publication date: November 18, 2010Inventors: Jon E. Ness, Jeremy Minshull
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Patent number: 7805252Abstract: Computer systems, computer program products and methods for designing oligonucleotides are provided. A set of sequence elements is defined. Each sequence element represents an amino acid sequence segment or a nucleic acid sequence segment. The set of sequence elements collectively represent a design nucleic acid sequence. The set of sequence elements are displayed as a plurality icons in a linear or a near linear arrangement such that each respective icon in the plurality of icons uniquely represents a corresponding sequence element in the set of sequence elements. In this representation, neighboring icons in the plurality of icons represent neighboring sequence elements in the set of sequence elements. Each respective icon in the plurality of icons depicts a directional property for the corresponding sequence element in the set of sequence elements. An oligonucleotide selection module is used to identify oligonucleotides in the design nucleic acid sequence.Type: GrantFiled: August 16, 2005Date of Patent: September 28, 2010Assignee: DNA Twopointo, Inc.Inventors: Claes Gustafsson, Sridhar Govindarajan, Jon E. Ness, Alan Marco Villalobos, Jeremy Minshull
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Publication number: 20100105599Abstract: New subtilisin homologues (both nucleic acids and proteins) are provided. Compositions which include these new proteins, recombinant cells, shuffling methods involving the new homologues, antibodies to the new homologues, and methods of using the homologues are also provided.Type: ApplicationFiled: September 18, 2009Publication date: April 29, 2010Applicants: Novozymes A/S, Maxygen Inc.Inventors: Jon E. Ness, Mark Welch, Lorraine J. Giver, Joel R. Cherry, Torben V. Borchert, Jeremy S. Minshull
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Publication number: 20090317873Abstract: Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.Type: ApplicationFiled: May 4, 2005Publication date: December 24, 2009Inventors: Sridhar Govindarajan, Nicolay V. Kulikov, Jeremy S. Minshull, Jon E. Ness
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Patent number: 7629170Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.Type: GrantFiled: August 17, 2006Date of Patent: December 8, 2009Assignee: Maxygen, Inc.Inventors: Stephen delCardayre, Matthew B. Tobin, Willem P. C. Stemmer, Jon E. Ness, Jeremy S. Minshull, Phillip A. Patten, Venkiteswatan Mani Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Anthony R. Cox, Gjalt W. Huisman, Ling Yuan, Joseph A. Affholter