Patents Assigned to Zymergen, Inc.
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Patent number: 11189362Abstract: The present disclosure provides methods and systems for identifying natural product-encoding multi-gene clusters (MGCs). In some embodiments, the present disclosure also teaches methods for producing sequenced and assembled metagenomic libraries that are amenable to MGC search bionformatic tools and techniques.Type: GrantFiled: February 16, 2021Date of Patent: November 30, 2021Assignee: Zymergen Inc.Inventors: Oliver Liu, Eyal Akiva, Tom Hayon Eyles, Ute Galm, Sangita Ganesh, Stephanie Leanne Brown Hendrix, William W. Hwang, Jeffrey Hoon Kim, Alexander Neckelmann, Samuel Oteng-Pabi, Claus Pelikan, Devin Scannell, Zachariah Serber, Jennifer Shock, Michael Sneddon, Xiao Yang
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Patent number: 11180753Abstract: HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods can be carried out within optofluidic devices.Type: GrantFiled: December 20, 2019Date of Patent: November 23, 2021Assignee: Zymergen Inc.Inventors: Vytas SunSpiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir Fong, III
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Patent number: 11155808Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.Type: GrantFiled: March 22, 2021Date of Patent: October 26, 2021Assignee: Zymergen Inc.Inventors: Zachariah Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
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Patent number: 11155807Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.Type: GrantFiled: December 18, 2020Date of Patent: October 26, 2021Assignee: Zymergen Inc.Inventors: Zachariah Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
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Patent number: 11151497Abstract: The generation of a factory order to control production of nucleotide sequences by a gene manufacturing system includes receiving an expression indicating an operation on sequence operands, each representing at least one nucleotide sequence part, evaluating the expression to a sequence specification, wherein the sequence specification comprises a data structure including one or more first-level operations and one or more second-level operations, and generating the factory order based upon execution of the one or more first-level operations and the one or more second-level operations. In a recursive manner, the one or more first-level operations operate on at least one first-level sequence operand, the value of which is resolved by execution of one or more of the second-level operations. The factory order may then be provided to the gene manufacturing system to assemble the sequence parts into nucleotide sequences represented by the sequence specification.Type: GrantFiled: April 27, 2016Date of Patent: October 19, 2021Assignee: Zymergen Inc.Inventors: Barbara Frewen, Aaron Kimball
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Publication number: 20210317269Abstract: A polymer film comprising at least two properties selected from (i) a thickness of not greater than 100 ?m; (ii) a tensile modulus according to ASTM D882 of at least 5 GPa; (iii) a first optical transparency according to ASTM D1746-15 at 380 nm of less than 50%; (iii) a Yellowing Index according to ASTM E313-15e1 of not greater than 2.5; (iv) a haze as determined according to ASTM D1003-13 of not greater than 1.5%; (v) a pencil hardness of greater than 1H; (vi) a coefficient of moisture expansion (‘CME’) as determined according to ASTM D5229/D5229M-14 of not greater than 50 ppm; (vii) an elongation at break as determined according to ASTM D5034-09 (2017) of at least 10%; or (viii) a folding endurance as determined according to ASTM D2176-16 at a radius of 1 mm of at least 10,000 folds.Type: ApplicationFiled: August 6, 2019Publication date: October 14, 2021Applicant: Zymergen Inc.Inventors: Arjan Zoombelt, Steven M. Edgar, Alejandra Alvarez Albarran
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Patent number: 11130955Abstract: Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations. High throughput methods of CRISPRi and CRISPRa.Type: GrantFiled: August 15, 2019Date of Patent: September 28, 2021Assignee: Zymergen Inc.Inventors: Brian Chaikind, Hendrik M. Van Rossum, Aaron Miller, Paul Perkovich, Shawn Szyjka, Kedar Patel
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Patent number: 11111507Abstract: The present disclosure is directed to methods of scarless genomic engineering in microorganisms, such as Bacillus, and provides for new molecular tools and methods which enable scarless genetic editing using at least one counterselectable marker that has been codon optimized for the microorganism. The disclosure allows for the high-throughput introduction of stable genetic edits to a genome using either plasmid or linear DNA constructs for genetic engineering.Type: GrantFiled: September 23, 2020Date of Patent: September 7, 2021Assignee: Zymergen Inc.Inventors: Tara F. Mahoney, Amanda Renae Reider Apel, Paloma Rueda Romero
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Publication number: 20210261721Abstract: An epoxy resin composition comprises about 70 wt % to about 95 wt % by weight of the composition of an epoxy component; and a curing component comprising about 5 wt % to about 30 wt % by weight of the composition, wherein the curing component is includes an imidazole; wherein the epoxy component and the curing component react together at a temperature of about 100 C to about 130 C to form a substantially cured reaction product in about 10 minutes or less and the cured product shows high tensile and flexural strength.Type: ApplicationFiled: June 14, 2019Publication date: August 26, 2021Applicant: Zymergen Inc.Inventors: Szymon Kosinski, Stephen Lo, Timothy Mauldin, Shilpa Naresh Raja, Nicole G. Ricapito, Adam Safir
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Patent number: 11098279Abstract: Aspects of this disclosure relate to liquid-based workflows for strain engineering. In strain engineering, cells undergo a modification process to acquire a desired change or changes in the cells. Some of the cells accept the change or changes and some do not. Provided herein are liquid-based methods for selecting the population of cells that have accepted the change or changes. Also provided herein are liquid-based methods for removing markers from transformed cells and liquid-based methods for isolating clonally pure populations of cells.Type: GrantFiled: July 2, 2019Date of Patent: August 24, 2021Assignee: ZYMERGEN INC.Inventors: Sean Poust, Vytas SunSpiral, William Serber, Matthew Jonathan Myers, Sara da Luz Areosa Cleto, Philip Weyman
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Patent number: 11098305Abstract: Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations.Type: GrantFiled: August 8, 2019Date of Patent: August 24, 2021Assignee: Zymergen Inc.Inventors: Brian Chaikind, Hendrik Marinus van Rossum
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Patent number: 11085040Abstract: The present disclosure provides systems and methods for host cell improvement utilizing epistatic effects. The systems and methods described herein are host cell agnostic and therefore can be implemented across taxa. Furthermore, the disclosed systems and methods can be implemented to modulate or improve any host cell parameter of interest.Type: GrantFiled: October 28, 2019Date of Patent: August 10, 2021Assignee: Zymergen Inc.Inventors: Zachariah Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
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Publication number: 20210225455Abstract: Systems, methods and non-transitory computer-readable media identify a candidate biological sequence for enabling a function in a host cell. Embodiments access a predictive model that associates a plurality of biological sequences, such as enzymes, with one or more functions, such as reaction catalysis; predict, using the predictive model, that one or more candidate sequences of the plurality of biological sequences enable a desired function; and classify using a processor, candidate sequences that satisfy a confidence threshold as filtered candidate sequences.Type: ApplicationFiled: August 14, 2019Publication date: July 22, 2021Applicant: Zymergen Inc.Inventors: Anupam Chowdhury, Alexander Glennon Shearer, Stepan Tymoshenko, Michelle L. Wynn, Erik Jedediah Dean
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Patent number: 11066663Abstract: The present disclosure relates to methods of joining three or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro or in vivo. The method allows the joining of a large number of DNA fragments, in a deterministic fashion. It can be used to rapidly generate nucleic acid libraries that can be subsequently used in a variety of applications that include, for example, genome editing and pathway assembly. Kits for performing the method are also disclosed.Type: GrantFiled: October 31, 2019Date of Patent: July 20, 2021Assignee: Zymergen Inc.Inventors: Erik Jedediah Dean, Kedar Patel, Aaron Miller, Kunal Mehta, Philip Weyman
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Patent number: 11053506Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.Type: GrantFiled: March 20, 2020Date of Patent: July 6, 2021Assignee: Zymergen Inc.Inventors: Stephen Blaskowski, Sara da Luz Areosa Cleto, Cameron Coates, Aaron Miller, Sharon Nademanee, Melissa Netwal, Kedar Patel, Shawn Szyjka, Philip Weyman, Solomon Henry Stonebloom, Colin Scott Maxwell, Elizabeth Lauren Meier
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Patent number: 11053515Abstract: The present invention relates to methods for editing the genome of a microbial host cell in one or more rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in a pooled and/or iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Compositions and kits for performing the methods are also disclosed.Type: GrantFiled: March 20, 2020Date of Patent: July 6, 2021Assignee: Zymergen Inc.Inventors: Stephen Blaskowski, Sara da Luz Areosa Cleto, Cameron Coates, Aaron Miller, Sharon Nademanee, Melissa Netwal, Kedar Patel, Shawn Szyjka, Philip Weyman, Solomon Henry Stonebloom, Colin Scott Maxwell, Elizabeth Lauren Meier
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Patent number: 11046974Abstract: The disclosure presents a platform for discovering novel insecticidal proteins from highly heterogeneous environmental sources. The methodology utilizes metagenomic enrichment procedures and unique genetic amplification techniques, which enables access to a broad class of unknown microbial diversity and their resultant proteome. The disclosed insecticidal protein discovery platform (IPDP) can be computationally driven and is able to integrate molecular biology, automation, and advanced machine learning protocols. The platform will enable researchers to rapidly and accurately access the vast repertoire of untapped insecticidal proteins produced by uncharacterized and complex microbial environmental samples. Also presented herein are a group of newly discovered pore-forming toxins (PFT) from a rare class of insecticidal proteins, which were discovered utilizing the insecticidal protein discovery platform.Type: GrantFiled: September 1, 2020Date of Patent: June 29, 2021Assignee: Zymergen Inc.Inventors: William W. Hwang, Jeffrey Kim, Oliver Liu, Jennifer Shock
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Publication number: 20210180096Abstract: The present disclosure describes the engineering of microbial cells for fermentative production of histamine and provides novel engineered microbial cells and cultures, as well as related histamine production methods.Type: ApplicationFiled: April 19, 2019Publication date: June 17, 2021Applicant: Zymergen Inc.Inventors: Cara Ann Tracewell, Alexander Glennon Shearer, Michael Shareef Siddiqui, Steven M. Edgar, Nicolaus Herman, Murtaza Shabbir Hussain
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Patent number: 11028401Abstract: The present disclosure provides a microbial genomic engineering method and system for transforming, screening, and selecting filamentous fungal cells that have altered morphology and/or growth under specific growth conditions. The method and system utilize high-throughput (HTP) methods to produce filamentous fungal production strains with a desired morphological phenotype.Type: GrantFiled: June 6, 2019Date of Patent: June 8, 2021Assignee: Zymergen Inc.Inventors: Kenneth S. Bruno, Sachin Jain, Brandon Pfannenstiel, Edyta Szewczyk
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Patent number: 11028416Abstract: The present disclosure describes the engineering of microbial cells for fermentative production of tyramine and provides novel engineered microbial cells and cultures, as well as related tyramine production methods.Type: GrantFiled: June 26, 2019Date of Patent: June 8, 2021Assignee: ZYMERGEN INC.Inventors: Michael Shareef Siddiqui, Stefan de Kok, Alexander Glennon Shearer, Franklin Lu, Cara Ann Tracewell, Steven M. Edgar