Patents by Inventor John J. Tomashek
John J. Tomashek 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: 10407705Abstract: The present invention provides an isolated fungal cell that is capable of producing one or more biomass-degrading enzymes and that exhibits increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. Also provided is a fermentation processes for producing one or more biomass-degrading enzymes comprising a fungal cells exhibiting increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. The biomass-degrading enzymes produced by the isolate fungal cell and fermentation processes of the present invention may be used in a process to produce soluble sugars from biomass.Type: GrantFiled: October 19, 2017Date of Patent: September 10, 2019Assignee: IOGEN ENERGY CORPORATIONInventors: Philippe J. Dufresne, Adam H. Colville, Barbara Fryzuk, Loreta Gudynaite-Savitch, Christopher M. D. Hindle, Boguslaw Ploch, John J. Tomashek
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Patent number: 10364422Abstract: Provided are modified cellulase enzymes exhibiting increase cellulose-hydrolyzing activity in the presence of lignin and/or reduced binding to lignin comprising modified linker peptides comprising one or more amino acid substitutions, insertions, or deletions that result in (a) a decrease in the calculated isoelectric point of the linker peptide and/or (b) an increase in the ratio of threonine:serine in the linker peptide relative to a parental linker peptide from which said modified linker peptide is derived. Also provided are genetic constructs comprising nucleic acid sequences encoding for modified cellulase enzymes, methods for the production of the modified cellulase enzymes from host strains and a process for hydrolysing cellulose with the modified cellulases in the presence of lignin.Type: GrantFiled: January 25, 2016Date of Patent: July 30, 2019Assignee: IOGEN ENERGY CORPORATIONInventors: Brian R. Scott, Patrick St-Pierre, James Lavigne, Nabil Masri, Theresa C. White, John J. Tomashek
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Patent number: 9885028Abstract: Provided is a modified Family 1 carbohydrate binding module (CBM) comprising amino acid substitutions at one or more of positions 10, 11, 12, 14, 17, 21, 24, 29, 31, 33, and 37, said position determined from alignment of a Family 1 CBM amino acid sequence with SEQ ID NO: 30, and exhibiting from about 50% to about 99.9% amino acid sequence identity to SEQ ID NO: 30. Also provided are modified glycosidase enzymes comprising the modified Family 1 CBM, genetic constructs and genetically modified microbes for expressing the modified Family 1 CBM or modified glycosidase enzyme. The modified Family 1 CBM confers reduced lignin binding and/or increased hydrolyzing activity in the presence of lignin to the modified glycosidase enzyme, which may be used in a process for hydrolyzing cellulose or hemicellulose in the presence of lignin.Type: GrantFiled: October 21, 2015Date of Patent: February 6, 2018Assignee: Iogen Energy CorporationInventors: John J. Tomashek, Brian R. Scott, Daniel Kolczynski
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Publication number: 20180030492Abstract: The present invention provides an isolated fungal cell that is capable of producing one or more biomass-degrading enzymes and that exhibits increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. Also provided is a fermentation processes for producing one or more biomass-degrading enzymes comprising a fungal cells exhibiting increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. The biomass-degrading enzymes produced by the isolate fungal cell and fermentation processes of the present invention may be used in a process to produce soluble sugars from biomass.Type: ApplicationFiled: October 19, 2017Publication date: February 1, 2018Inventors: Philippe J. Dufresne, Adam H. Colville, Barbara Fryzuk, Loreta Gudynaite-Savitch, Christopher M.D. Hindle, Boguslaw Ploch, John J. Tomashek
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Patent number: 9834804Abstract: The present invention provides an isolated fungal cell that is capable of producing one or more biomass-degrading enzymes and that exhibits increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. Also provided is a fermentation processes for producing one or more biomass-degrading enzymes comprising a fungal cells exhibiting increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. The biomass-degrading enzymes produced by the isolate fungal cell and fermentation processes of the present invention may be used in a process to produce soluble sugars from biomass.Type: GrantFiled: December 12, 2012Date of Patent: December 5, 2017Assignee: Iogen Energy CorporationInventors: Philippe J. Dufresne, Adam H. Colville, Barbara Fryzuk, Loreta Gudynaite-Savitch, Christopher M. D. Hindle, Boguslaw Ploch, John J. Tomashek
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Publication number: 20160201043Abstract: Provided are modified cellulase enzymes exhibiting increase cellulose-hydrolyzing activity in the presence of lignin and/or reduced binding to lignin comprising modified linker peptides comprising one or more amino acid substitutions, insertions, or deletions that result in (a) a decrease in the calculated isoelectric point of the linker peptide and/or (b) an increase in the ratio of threonine:serine in the linker peptide relative to a parental linker peptide from which said modified linker peptide is derived. Also provided are genetic constructs comprising nucleic acid sequences encoding for modified cellulase enzymes, methods for the production of the modified cellulase enzymes from host strains and a process for hydrolysing cellulose with the modified cellulases in the presence of lignin.Type: ApplicationFiled: January 25, 2016Publication date: July 14, 2016Inventors: Brian R. Scott, Patrick St-Pierre, James Lavigne, Nabil Masri, Theresa C. White, John J. Tomashek
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Publication number: 20160115464Abstract: Provided is a modified Family 1 carbohydrate binding module (CBM) comprising amino acid substitutions at one or more of positions 10, 11, 12, 14, 17, 21, 24, 29, 31, 33, and 37, said position determined from alignment of a Family 1 CBM amino acid sequence with SEQ ID NO: 30, and exhibiting from about 50% to about 99.9% amino acid sequence identity to SEQ ID NO: 30. Also provided are modified glycosidase enzymes comprising the modified Family 1 CBM, genetic constructs and genetically modified microbes for expressing the modified Family 1 CBM or modified glycosidase enzyme. The modified Family 1 CBM confers reduced lignin binding and/or increased hydrolysing activity in the presence of lignin to the modified glycosidase enzyme, which may be used in a process for hydrolysing cellulose or hemicellulose in the presence of lignin.Type: ApplicationFiled: October 21, 2015Publication date: April 28, 2016Inventors: John J. Tomashek, Brian R. Scott, Daniel Kolczynski
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Patent number: 9279163Abstract: Provided are isolated cellobiohydrolases comprising a modified Glycoside Hydrolase (GH) Family 7 catalytic domain, a GH Family 7 catalytic domain and a modified Family 1 carbohydrate binding module (CBM), or both a modified Family 7 catalytic domain and a modified Family 1 CBM. Such isolated cellobiohydrolases exhibit from 45% to about 99.9% amino acid sequence identity to amino acids 1-436 of SEQ ID NO: 1 or to amino acids 1-438 of SEQ ID NO: 2 and improved activity on process substrates. Also provided are genetic constructs and genetically modified microbes for expressing the isolated cellobiohydrolases, a process for producing the isolated cellobiohydrolases, cellulase enzyme mixtures comprising the isolated cellobiohydrolase and a process for hydrolyzing a cellulosic substrate with such cellulase enzyme mixtures.Type: GrantFiled: August 24, 2012Date of Patent: March 8, 2016Assignee: IOGEN ENERGY CORPORATIONInventors: Jacqueline Montalibet, Loreta Gudynaite-Savitch, Christopher Hill, Christopher D. Hindle, James A. Lavigne, Nabil Masri, Fuad Tahna, John J. Tomashek
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Patent number: 9279112Abstract: Provided are modified cellulase enzymes exhibiting increase cellulose-hydrolyzing activity in the presence of lignin and/or reduced binding to lignin comprising modified linker peptides comprising one or more amino acid substitutions, insertions, or deletions that result in (a) a decrease in the calculated isoelectric point of the linker peptide and/or (b) an increase in the ratio of threonine:serine in the linker peptide relative to a parental linker peptide from which said modified linker peptide is derived. Also provided are genetic constructs comprising nucleic acid sequences encoding for modified cellulase enzymes, methods for the production of the modified cellulase enzymes from host strains and a process for hydrolyzing cellulose with the modified cellulases in the presence of lignin.Type: GrantFiled: February 26, 2010Date of Patent: March 8, 2016Assignee: IOGEN ENERGY CORPORATIONInventors: Brian R. Scott, Patrick St-Pierre, James Lavigne, Nabil Masri, Theresa C. White, John J. Tomashek
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Patent number: 9238806Abstract: The present invention relates to a depilling composition comprising an enzyme mixture that comprises a Family 45 cellulase and one or more additional cellulases selected from a Family 5 cellulase, a Family 6 cellulase or a combination thereof. The enzyme mixture may be characterized in that the Family 45 and Family 5 cellulases or the Family 45 and Family 6 cellulases are present at a weight ratio that exhibits synergy in an assay that measures specific depilling activity. The enzyme mixture may be secreted by a genetically modified microbe overexpressing the foregoing cellulases. Also provided is a process for depilling that comprises a step of contacting cellulose-containing goods with the depilling composition.Type: GrantFiled: February 9, 2012Date of Patent: January 19, 2016Assignee: Novozymes A/SInventors: Christopher Hill, John J. Tomashek, Loreta Gudynaite-Savitch, Guylaine Therrien, Sophie Calixte
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Patent number: 9206406Abstract: Provided is a modified Family 1 carbohydrate binding module (CBM) comprising amino acid substitutions at one or more of positions 10, 11, 12, 14, 17, 21, 24, 29, 31, 33, and 37, said position determined from alignment of a Family 1 CBM amino acid sequence with SEQ ID NO: 30, and exhibiting from about 50% to about 99.9% amino acid sequence identity to SEQ ID NO: 30. Also provided are modified glycosidase enzymes comprising the modified Family 1 CBM, genetic constructs and genetically modified microbes for expressing the modified Family 1 CBM or modified glycosidase enzyme. The modified Family 1 CBM confers reduced lignin binding and/or increased hydrolyzing activity in the presence of lignin to the modified glycosidase enzyme, which may be used in a process for hydrolyzing cellulose or hemicellulose in the presence of lignin.Type: GrantFiled: February 11, 2011Date of Patent: December 8, 2015Assignee: IOGEN ENERGY CORPORATIONInventors: John J. Tomashek, Brian R. Scott, Daniel Kolczynski
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Publication number: 20150329841Abstract: The present invention relates to a cellulose-degrading enzyme composition comprising one or more cellobiohydrolase and/or endoglucanase enzyme, and an effective amount of an isolated GH16 polypeptide, where the presence of the isolated GH16 polypeptide in the enzyme composition increases the rate or extent of degradation of a cellulosic substrate compared to an equivalent dosage of a corresponding cellulose-degrading enzyme composition lacking the at least one isolated GH16 polypeptide. The present invention also relates to a method for producing fermentable sugars from a cellulosic substrate using the above cellulose-degrading enzyme composition and to genetically modified microbes for produced the above cellulose-degrading enzyme composition.Type: ApplicationFiled: May 31, 2013Publication date: November 19, 2015Inventors: Christopher M. D. Hill, John J. Tomashek, James A. Lavigne, Sandra Mortimer, Reginald Storms, Adrian Tsang, Greg Butler, Justin Powlowski
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Publication number: 20140356914Abstract: The present invention provides endoglucanase 1b (EG1b) suitable for use in saccharification reactions.Type: ApplicationFiled: August 27, 2012Publication date: December 4, 2014Applicant: Codexis, Inc.Inventors: Kripa Rao, Xiyun Zhang, Brian R. Scott, John J. Tomashek
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Publication number: 20140295504Abstract: The present invention provides an isolated fungal cell that is capable of producing one or more biomass-degrading enzymes and that exhibits increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. Also provided is a fermentation processes for producing one or more biomass-degrading enzymes comprising a fungal cells exhibiting increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. The biomass-degrading enzymes produced by the isolate fungal cell and fermentation processes of the present invention may be used in a process to produce soluble sugars from biomass.Type: ApplicationFiled: December 12, 2012Publication date: October 2, 2014Inventors: Philippe J. Dufresne, Adam H. Colville, Barbara Fryzuk, Loreta Gudynaite-Savitch, Christopher M.D. Hindle, Boguslaw Ploch, John J. Tomashek
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Publication number: 20130337542Abstract: The present invention relates to a depilling composition comprising an enzyme mixture that comprises a Family 45 cellulase enzyme component and one or more additional cellulase enzyme components selected from a Family 5 cellulase, a Family 6 cellulase or a combination thereof. The enzyme mixture may be characterized in that the Family 45 and the Family 5 cellulase enzyme components or the Family 45 and the Family 6 cellulase enzyme components are present at a weight ratio that exhibits synergy in an assay that measures specific depilling activity. The enzyme mixture may be secreted by a genetically modified microbe overexpressing theforegoing cellulase enzyme components. Also provided is a process for depilling that comprises a step of contacting cellulose-containing goods with the depilling composition.Type: ApplicationFiled: February 9, 2012Publication date: December 19, 2013Applicant: Novozymes A/SInventors: Christopher Hill, John J. Tomashek, Loreta Gudynaite-Savitch, Guylaine Therrien, Sophie Calixte
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Patent number: 8486683Abstract: Provided are modified beta-glucosidase enzymes, derived from the Trichoderma reesei Cel3A beta-glucosidase, that exhibit improvements in one or more kinetic parameters (KG, KG2, kcat) comprising amino acid substitutions at one or more of positions 43, 101, 260 and 543. Also provided are genetic constructs comprising nucleotide sequences encoding for modified beta-glucosidase enzymes, methods for the production of modified beta-glucosidase enzymes from host strains and the use of the modified beta-glucosidase enzymes in the hydrolysis of cellulose.Type: GrantFiled: May 28, 2010Date of Patent: July 16, 2013Assignee: Iogen Energy CorporationInventors: Brian R. Scott, Chengsong Liu, James Lavigne, John J. Tomashek
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Publication number: 20130052694Abstract: Provided are isolated cellobiohydrolases comprising a modified Glycoside Hydrolase (GH) Family 7 catalytic domain, a GH Family 7 catalytic domain and a modified Family 1 carbohydrate binding module (CBM), or both a modified Family 7 catalytic domain and a modified Family 1 CBM. Such isolated cellobiohydrolases exhibit from 45% to about 99.9% amino acid sequence identity to amino acids 1-436 of SEQ ID NO: 1 or to amino acids 1-438 of SEQ ID NO: 2 and improved activity on process substrates. Also provided are genetic constructs and genetically modified microbes for expressing the isolated cellobiohydrolases, a process for producing the isolated cellobiohydrolases, cellulase enzyme mixtures comprising the isolated cellobiohydrolase and a process for hydrolysing a cellulosic substrate with such cellulase enzyme mixtures.Type: ApplicationFiled: August 24, 2012Publication date: February 28, 2013Applicant: Iogen Energy CorporationInventors: Jacqueline Montalibet, Loreta Gudynaite-Savitch, Christopher Hill, Christopher D. Hindle, James A. Lavigne, Nabil Masri, Fuad Tahna, John J. Tomashek
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Publication number: 20120295308Abstract: Provided is a modified Family 1 carbohydrate binding module (CBM) comprising amino acid substitutions at one or more of positions 10, 11, 12, 14, 17, 21, 24, 29, 31, 33, and 37, said position determined from alignment of a Family 1 CBM amino acid sequence with SEQ ID NO: 30, and exhibiting from about 50% to about 99.9% amino acid sequence identity to SEQ ID NO: 30. Also provided are modified glycosidase enzymes comprising the modified Family 1 CBM, genetic constructs and genetically modified microbes for expressing the modified Family 1 CBM or modified glycosidase enzyme. The modified Family 1 CBM confers reduced lignin binding and/or increased hydrolysing activity in the presence of lignin to the modified glycosidase enzyme, which may be used in a process for hydrolysing cellulose or hemicellulose in the presence of lignin.Type: ApplicationFiled: February 11, 2011Publication date: November 22, 2012Applicant: IOGEN ENEGY CORPORATIONInventors: John J. Tomashek, Brian R. Scott, Daniel Kolczynski
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Patent number: 8143049Abstract: Provided are modified beta-glucosidase enzymes, derived from the Trichoderma reesei Cel3A beta-glucosidase, that exhibit improved stability at low pH, low pH and high aeration, low pH and high agitation, or low pH and elevated temperature. Also provided are genetic constructs comprising nucleotide sequences encoding for modified beta-glucosidase enzymes, methods for the production of modified beta-glucosidase enzymes from host strains and the use of the modified beta-glucosidase enzymes in the hydrolysis of cellulose.Type: GrantFiled: August 31, 2009Date of Patent: March 27, 2012Assignee: Iogen Energy CorporationInventors: Christopher Hill, James Lavigne, Martine Whissel, John J. Tomashek
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Patent number: 8110389Abstract: A modified Trichoderma reesei Family 6 (TrCel6A) cellulase enzyme comprising amino acid substitutions at one or more positions selected from the group consisting of 129, 322, 363 and 410 of SEQ ID NO: 1 is provided. Genetic constructs and genetically modified microbes comprising nucleic sequences encoding the modified TrCel6a cellulase are also provided. The modified TrCel6A cellulase of the invention display at least a 15% decrease in inactivation by lignin relative to a parental TrCel6A cellulase from which the modified TrCel6A is derived. Such cellulases find use in a variety of applications in industry requiring enzymatic hydrolysis of cellulose in the presence of lignin, e.g., the hydrolysis of pretreated lignocellulosic feedstocks for the production of fermentable sugars, sugar alcohols and fuel alcohols.Type: GrantFiled: July 30, 2009Date of Patent: February 7, 2012Assignee: Iogen Energy CorporationInventors: James A. Lavigne, Brian R. Scott, Martine Whissel, John J. Tomashek