Patents by Inventor Mark A. Emalfarb

Mark A. Emalfarb 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).

  • Publication number: 20230346913
    Abstract: Recombinant expression of influenza virus surface proteins in the fungus Myceliophthora thermophila strain C1 is provided. The recombinant proteins are for use in influenza vaccine compositions.
    Type: Application
    Filed: July 11, 2023
    Publication date: November 2, 2023
    Applicant: DYADIC INTERNATIONAL INC.
    Inventors: Mark EMALFARB, Teunis Cornelis Verwoerd, Mark R. Alfenito, Mark Baer, Isabelle Legastelois, Marie-Pierre Kazek, Marie-Clotilde Bernard, Jean Dubayle, Richard Kensinger
  • Patent number: 11738080
    Abstract: Recombinant expression of influenza virus surface proteins in the fungus Myceliophthora thermophila strain C1 is provided. The recombinant proteins are for use in influenza vaccine compositions.
    Type: Grant
    Filed: August 9, 2018
    Date of Patent: August 29, 2023
    Assignee: DYADIC INTERNATIONAL INC.
    Inventors: Mark Emalfarb, Teunis Cornelis Verwoerd, Mark R. Alfenito, Mark Baer, Isabelle Legastelois, Marie-Pierre Kazek, Marie-Clotilde Bernard, Jean Dubayle, Richard Kensinger
  • Publication number: 20200215183
    Abstract: Recombinant expression of influenza vims surface proteins in the fungus Myceliophthora thermophila strain Cl is provided. The recombinant proteins are for use in influenza vaccine compositions.
    Type: Application
    Filed: August 9, 2018
    Publication date: July 9, 2020
    Inventors: Mark EMALFARB, Teunis Cornelis VERWOERD, Mark R. ALFENITO, Mark BAER, Isabelle LEGASTELOIS, Marie-Pierre KAZEK, Marie-Clotilde BERNARD, Jean DUBAYLE, Richard KENSINGER
  • Patent number: 10415045
    Abstract: The present invention provides a new fungal production system comprising a fungal host strain of Chrysosporium lucknowense wherein the endogenous cellulase secretion is less than 20% of the endogenous cellulase secretion of Chrysosporium lucknowense strain UV 18-25. Preferably, also the secretion of endogenous protease, endogenous ?-glucanase and endogenous cellobiohydrolase is less than 20% of the secretion of Chrysosporium lucknowense strain UV 18-25. Furthermore, fungal host strains are provided wherein several genes have been disrupted. According to another aspect of the invention a method for homologous and/or heterologous production of a pure protein with a purity of higher than 75%, comprising expressing a gene encoding said protein in the strains according to the invention have been described. Furthermore, a method for production of artificial protein mixes comprising expressing a gene encoding each of said proteins in a strain according to the invention have been disclosed.
    Type: Grant
    Filed: September 9, 2015
    Date of Patent: September 17, 2019
    Assignee: DANISCO US INC
    Inventors: Peter J. Punt, Richard Paul Burlingame, Christine M. Pynnonen, Phillip T. Olson, Jan Wery, Johannes Heinrich Visser, Mark A. Emalfarb, Jacob Visser, Jan Cornelis Verdoes
  • Patent number: 9862956
    Abstract: The invention is generally directed to modified filamentous fungal host cells comprising one or more nucleic acids encoding one or more polypeptides under the control of one or more promoters that are functional in said cells. Methods of using the modified cells to express one or more polypeptides are also disclosed, including methods of screening cells transformed with one or more expression vectors comprising nucleic acids derived from synthetic or genomic nucleic acids including, cDNAs. Methods of purifying one or more polypeptides or complexes comprising one or more polypeptides expressed in the modified cells, intended for use as substrates in structure/function studies, as therapeutic agents, as diagnostic reagents, or as human or animal vaccines, are also disclosed.
    Type: Grant
    Filed: January 29, 2014
    Date of Patent: January 9, 2018
    Assignee: DANISCO US INC.
    Inventors: Mark A. Emalfarb, Peter J. Punt, Cornelia Van Zeijl, Cornelius Van den Hondel, Jan Cornelis Verdoes, Richard P. Burlingame
  • Publication number: 20170037417
    Abstract: The invention is generally directed to modified filamentous fungal host cells comprising one or more nucleic acids encoding one or more polypeptides under the control of one or more promoters that are functional in said cells. Methods of using the modified cells to express one or more polypeptides are also disclosed, including methods of screening cells transformed with one or more expression vectors comprising nucleic acids derived from synthetic or genomic nucleic acids including, cDNAs. Methods of purifying one or more polypeptides or complexes comprising one or more polypeptides expressed in the modified cells, intended for use as substrates in structure/function studies, as therapeutic agents, as diagnostic reagents, or as human or animal vaccines, are also disclosed.
    Type: Application
    Filed: January 29, 2014
    Publication date: February 9, 2017
    Applicant: Dyadic International, Inc.
    Inventors: Mark A. EMALFARB, Peter J. PUNT, Cornelia VAN ZEIJL, Cornelius VAN DEN HONDEL, Jan Cornelis VERDOES, Richard P. BURLINGAME
  • Publication number: 20150376629
    Abstract: The present invention provides a new fungal production system comprising a fungal host strain of Chrysosporium lucknowense wherein the endogenous cellulase secretion is less than 20% of the endogenous cellulase secretion of Chrysosporium lucknowense strain UV 18-25. Preferably, also the secretion of endogenous protease, endogenous ?-glucanase and endogenous cellobiohydrolase is less than 20% of the secretion of Chrysosporium lucknowense strain UV 18-25. Furthermore, fungal host strains are provided wherein several genes have been disrupted. According to another aspect of the invention a method for homologous and/or heterologous production of a pure protein with a purity of higher than 75%, comprising expressing a gene encoding said protein in the strains according to the invention have been described. Furthermore, a method for production of artificial protein mixes comprising expressing a gene encoding each of said proteins in a strain according to the invention have been disclosed.
    Type: Application
    Filed: September 9, 2015
    Publication date: December 31, 2015
    Inventors: Peter J. PUNT, Richard Paul BURLINGAME, Christine M. PYNNONEN, Phillip T. OLSON, Jan WERY, Johannes Heinrich VISSER, Mark A. EMALFARB, Jacob VISSER, Jan Cornelis VERDOES, Jacoba VERDOES
  • Patent number: 9175296
    Abstract: The present invention provides a new fungal production system comprising a fungal host strain of Chrysosporium lucknowense wherein the endogenous cellulase secretion is less than 20% of the endogenous cellulase secretion of Chrysosporium lucknowense strain UV 18-25. Preferably, also the secretion of endogenous protease, endogenous ?-glucanase and endogenous cellobiohydrolase is less than 20% of the secretion of Chrysosporium lucknowense strain UV 18-25. Furthermore, fungal host strains are provided wherein several genes have been disrupted. According to another aspect of the invention a method for homologous and/or heterologous production of a pure protein with a purity of higher than 75%, comprising expressing a gene encoding said protein in the strains according to the invention have been described. Furthermore, a method for production of artificial protein mixes comprising expressing a gene encoding each of said proteins in a strain according to the invention have been disclosed.
    Type: Grant
    Filed: March 16, 2010
    Date of Patent: November 3, 2015
    Assignee: DYADIC NEDERLAND B.V.
    Inventors: Peter J. Punt, Richard Paul Burlingame, Christine M. Pynnonen, Phillip T. Olson, Jan Wery, Johannes Heinrich Visser, Mark A. Emalfarb, Jacob Visser, Jan Cornelis Verdoes, Jacoba Verdoes
  • Publication number: 20150211013
    Abstract: The invention is generally directed to modified filamentous fungal host cells comprising one or more nucleic acids encoding one or more polypeptides under the control of one or more promoters that are functional in said cells. Methods of using the modified cells to express one or more polypeptides are also disclosed, including methods of screening cells transformed with one or more expression vectors comprising nucleic acids derived from synthetic or genomic nucleic acids including, cDNAs. Methods of purifying one or more polypeptides or complexes comprising one or more polypeptides expressed in the modified cells, intended for use as substrates in structure/function studies, as therapeutic agents, as diagnostic reagents, or as human or animal vaccines, are also disclosed.
    Type: Application
    Filed: January 29, 2014
    Publication date: July 30, 2015
    Applicant: Dyadic International, Inc.
    Inventors: Mark A. EMALFARB, Peter J. PUNT, Cornelia VAN ZEIJL, Cornelius VAN DEN HONDEL, Jan Cornelis VERDOES, Richard P. BURLINGAME
  • Patent number: 8916363
    Abstract: This invention provides novel enzyme compositions using newly identified and isolated C. lucknowense enzymes, including CBH Ib CBH IIb, EG II, EG VI, ?-glucosidase, and xylanase II in conjunction with previously identified enzymes CBH Ia, CBH IIa (previously described as Endo 43), and EG V. These enzyme compositions demonstrate an extremely high ability to convert lignocellulosic biomass (e.g., Avicel, cotton, Douglas fir wood pretreated by organosolv) to glucose. CBH Ia and IIb, which both have a cellulose-binding module (CBM) displayed a pronounced synergism with three major endoglucanases (EG II, EG V, EG VI) from the same fungus in hydrolysis of cotton as well as a strong synergy with each other. The enzyme compositions are effective in hydrolysis of the lignocellulosic biomass.
    Type: Grant
    Filed: October 20, 2010
    Date of Patent: December 23, 2014
    Assignee: Dyadic International (USA), Inc.
    Inventors: Alexander V. Gusakov, Tatyana N. Salanovich, Alexey I. Antonov, Boris B. Ustinov, Oleg N. Okunev, Richard P. Burlingame, Mark A. Emalfarb, Marco A. Baez, Arkady P. Sinitsyn
  • Patent number: 8680252
    Abstract: The invention provides a method for the expression and subsequent screening of DNA libraries, particularly synthetic, genomic, and cDNA libraries, in filamentous fungal hosts. In particular, the invention provides vectors, host strains, and a method for the expression and screening of complex DNA libraries, including, but not limited to, combinatory (combinatorial) libraries expressing one, two or more variable constituents and/or prepared from two or more sublibraries (e.g., for the expression and screening of immunoglobulin (including fragments and derivatives of whole immunoglobulin proteins) and other receptor or complex DNA libraries or libraries of libraries). The invention is useful for the expression and screening for a large variety of proteins and protein complexes, including human proteins. The present invention also relates to novel fungal protease sequences.
    Type: Grant
    Filed: December 10, 2007
    Date of Patent: March 25, 2014
    Assignee: Dyadic International (USA), Inc.
    Inventors: Mark A. Emalfarb, Peter J. Punt, Cornelia Van Zeijl, Cornelius Van Den Hondel, Jan Verdoes, Richard P. Burlingame
  • Patent number: 8673618
    Abstract: This invention provides novel enzyme compositions using newly identified and isolated C. lucknowense enzymes, including CBH Ib CBH IIb, EG II, EG VI, ?-glucosidase, and xylanase II in conjunction with previously identified enzymes CBH Ia, CBH IIa (previously described as Endo 43), and EG V. These enzyme compositions demonstrate an extremely high ability to convert lignocellulosic biomass (e.g., Avicel, cotton, Douglas fir wood pretreated by organosolv) to glucose. CBH Ia and IIb, which both have a cellulose-binding module (CBM) displayed a pronounced synergism with three major endoglucanases (EG II, EG V, EG VI) from the same fungus in hydrolysis of cotton as well as a strong synergy with each other. The enzyme compositions are effective in hydrolysis of the lignocellulosic biomass.
    Type: Grant
    Filed: October 20, 2010
    Date of Patent: March 18, 2014
    Assignee: Dyadic International (USA), Inc.
    Inventors: Alexander V. Gusakov, Tatyana N. Salanovich, Alexey I. Antonov, Boris B. Ustinov, Oleg N. Okunev, Richard P. Burlingame, Mark A. Emalfarb, Marco A. Baez, Arkady P. Sinitsyn
  • Publication number: 20130280764
    Abstract: The present invention relates to modified filamentous fungal organisms having improved activity profiles with respect to the conversion of complex carbohydrates into simple sugars from cellulosic materials, including fungal organisms belonging to a genus selected from the group consisting of: Chrysosporium, Thielavia, Talaromyces, Thermomyces, Thermoascus, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryplococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, Trichoderma, and Talaromyces, plus anamorphs and teleomorphs thereof.
    Type: Application
    Filed: April 19, 2013
    Publication date: October 24, 2013
    Applicant: DYADIC INTERNATIONAL (USA) LTD.
    Inventors: Mark EMALFARB, Arkady SINITSYN, Richard JUNDZIL, Jan WERY, Jacob VISSER, Rob JOOSTEN, Martijn KOETSIER
  • Patent number: 8551751
    Abstract: This invention relates to novel enzymes and novel methods for producing the same. More specifically this invention relates to a variety of fungal enzymes. Nucleic acid molecules encoding such enzymes, compositions, recombinant and genetically modified host cells, and methods of use are described. The invention also relates to a method to convert lignocellulosic biomass to fermentable sugars with enzymes that degrade the lignocellulosic material and novel combinations of enzymes, including those that provide a synergistic release of sugars from plant biomass. The invention also relates to a method to release cellular content by degradation of cell walls. The invention also relates to methods to use the novel enzymes and compositions of such enzymes in a variety of other processes, including washing of clothing, detergent processes, biorefining, deinking and biobleaching of paper and pulp, and treatment of waste streams.
    Type: Grant
    Filed: September 5, 2008
    Date of Patent: October 8, 2013
    Assignee: Dyadic International, Inc.
    Inventors: Mark A. Emalfarb, Alexander Vasilievich Gusakov, Peter J. Punt, Jan Cornelis Verdoes, Arkady Panteleimonovich Sinitsyn, Elena Vlasenko, Sandra Wihelmina Agnes Hinz, Mark Gosink, Zhijie Jiang, Jacoba Van der Meij
  • Publication number: 20120107856
    Abstract: The present invention provides a new fungal production system comprising a fungal host strain of Chrysosporium lucknowense wherein the endogenous cellulase secretion is less than 20% of the endogenous cellulase secretion of Chrysosporium lucknowense strain UV 18-25. Preferably, also the secretion of endogenous protease, endogenous ?-glucanase and endogenous cellobiohydrolase is less than 20% of the secretion of Chrysosporium lucknowense strain UV 18-25. Furthermore, fungal host strains are provided wherein several genes have been disrupted. According to another aspect of the invention a method for homologous and/or heterologous production of a pure protein with a purity of higher than 75%, comprising expressing a gene encoding said protein in the strains according to the invention have been described. Furthermore, a method for production of artificial protein mixes comprising expressing a gene encoding each of said proteins in a strain according to the invention have been disclosed.
    Type: Application
    Filed: March 16, 2010
    Publication date: May 3, 2012
    Inventors: Peter J. Punt, Richard Paul Burlingame, Christine M. Pynnonen, Phillip T. Olson, Jan Wery, Johannes Heinrich Visser, Mark A. Emalfarb, Jacob Visser, Jan Cormelis Verdoes, Jacoba Verdoes
  • Publication number: 20120030839
    Abstract: The invention provides a method for the expression and subsequent screening of DNA libraries, particularly synthetic, genomic, and cDNA libraries, in filamentous fungal hosts. In particular, the invention provides vectors, host strains, and a method for the expression and screening of complex DNA libraries, including, but not limited to, combinatory (combinatorial) libraries expressing one, two or more variable constituents and/or prepared from two or more sublibraries (e.g., for the expression and screening of immunoglobulin (including fragments and derivatives of whole immunoglobulin proteins) and other receptor or complex DNA libraries or libraries of libraries). The invention is useful for the expression and screening for a large variety of proteins and protein complexes, including human proteins. The present invention also relates to novel fungal protease sequences.
    Type: Application
    Filed: December 10, 2007
    Publication date: February 2, 2012
    Applicant: DYADIC INTERNATIONAL, INC.
    Inventors: Mark A. Emalfarb, Peter J. Punt, Cornelia Van Zeijl, Cornelius Van Den Hondel, Jan Verdoes, Richard P. Burlingame
  • Publication number: 20110047656
    Abstract: This invention provides novel enzyme compositions using newly identified and isolated C. lucknowense enzymes, including CBH Ib CBH IIb, EG II, EG VI, ?-glucosidase, and xylanase II in conjunction with previously identified enzymes CBH Ia, CBH IIa (previously described as Endo 43), and EG V. These enzyme compositions demonstrate an extremely high ability to convert lignocellulosic biomass (e.g., Avicel, cotton, Douglas fir wood pretreated by organosolv) to glucose. CBH Ia and IIb, which both have a cellulose-binding module (CBM) displayed a pronounced synergism with three major endoglucanases (EG II, EG V, EG VI) from the same fungus in hydrolysis of cotton as well as a strong synergy with each other. The enzyme compositions are effective in hydrolysis of the lignocellulosic biomass.
    Type: Application
    Filed: October 20, 2010
    Publication date: February 24, 2011
    Inventors: ALEXANDER V. GUSAKOV, TATYANA N. SALANOVICH, ALEXEY I. ANTONOV, BORIS B. USTINOV, OLEG N. OKUNEV, RICHARD P. BURLINGAME, MARK A. EMALFARB, MARCO A. BAEZ, ARKADY P. SINITSYN
  • Publication number: 20110045546
    Abstract: This invention provides novel enzyme compositions using newly identified and isolated C. lucknowense enzymes, including CBH Ib CBH IIb, EG II, EG VI, ?-glucosidase, and xylanase II in conjunction with previously identified enzymes CBH Ia, CBH IIa (previously described as Endo 43), and EG V. These enzyme compositions demonstrate an extremely high ability to convert lignocellulosic biomass (e.g., Avicel, cotton, Douglas fir wood pretreated by organosolv) to glucose. CBH Ia and IIb, which both have a cellulose-binding module (CBM) displayed a pronounced synergism with three major endoglucanases (EG II, EG V, EG VI) from the same fungus in hydrolysis of cotton as well as a strong synergy with each other. The enzyme compositions are effective in hydrolysis of the lignocellulosic biomass.
    Type: Application
    Filed: October 20, 2010
    Publication date: February 24, 2011
    Inventors: ALEXANDER V. GUSAKOV, TATYANA N. SALANOVICH, ALEXEY I. ANTONOV, BORIS B. USTINOV, OLEG N. OKUNEV, RICHARD P. BURLINGAME, MARK A. EMALFARB, MARCO A. BAEZ, ARKADY P. SINITSYN
  • Patent number: 7883872
    Abstract: This invention provides novel enzyme compositions using newly identified and isolated C. lucknowense enzymes, including CBH Ib CBH IIb, EG II, EG VI, ?-glucosidase, and xylanase II in conjunction with previously identified enzymes CBH Ia, CBH IIa (previously described as Endo 43), and EG V. These enzyme compositions demonstrate an extremely high ability to convert lignocellulosic biomass (e.g., Avicel, cotton, Douglas fir wood pretreated by organosolv) to glucose. CBH Ia and IIb, which both have a cellulose-binding module (CBM) displayed a pronounced synergism with three major endoglucanases (EG II, EG V, EG VI) from the same fungus in hydrolysis of cotton as well as a strong synergy with each other. The enzyme compositions are effective in hydrolysis of the lignocellulosic biomass.
    Type: Grant
    Filed: July 13, 2006
    Date of Patent: February 8, 2011
    Assignee: Dyadic International (USA), Inc.
    Inventors: Alexander V. Gusakov, Tatyana N. Salanovich, Alexey I. Antonov, Boris B. Ustinov, Oleg N. Okunev, Richard P. Burlingame, Mark A. Emalfarb, Marco A. Baez, Arkady P. Sinitsyn
  • Patent number: 7794962
    Abstract: The invention provides a method for the expression of exogenous DNA libraries in filamentous fungi. The fungi are capable of processing intron-containing eukaryotic genes, and also can carry out post-translational processing steps such as glyclosylation and protein folding. The invention provides for the use of fungi with altered morphology, which permits high-throughput screening and directed molecular evolution of expressed proteins. The same transformed fungi may be used to produce larger quantities of protein for isolation, characterization, and application testing, and may be suitable for commercial production of the protein as well.
    Type: Grant
    Filed: July 21, 2006
    Date of Patent: September 14, 2010
    Assignee: Dyadic International (USA), Inc.
    Inventors: Mark A. Emalfarb, Peter J. Punt, Cornelia van Zeijl, Cornelius van den Hondel