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51. 发明申请

WO2018071072A1 CHEMICAL SUBSTRUCTURE SEARCH QUERY BUILDING AND EXECUTION 审中-公开
标题翻译：化学结构搜索查询建立与执行
公开(公告)号：WO2018071072A1
公开(公告)日：2018-04-19
申请号：PCT/US2017/040751
申请日：2017-07-05
申请人： ZYMERGEN INC.
发明人： DEAN, Erik, Jed , SAFIR, Adam , WERNER, Gregory
IPC分类号： G06F17/30
CPC分类号： G06F16/2428 , G06F16/2246 , G06F16/2282 , G06F16/2456 , G06F16/248 , G16C20/40 , G16C20/90
摘要： Systems and methods for enabling construction of a complex Boolean chemical substructure query in a structured graphical user interface are provided. The chemical substructures (molecules) may be represented graphically in standard molecular notation, and may be arranged horizontally and vertically on the interface, along with Boolean logical operators. Boolean logical operators of a first type may logically associate molecules arranged in horizontal fashion to form row queries, whereas Boolean logical operators of a different, second type may logically associate the row queries to form a composite query to be applied to a database of molecules. The operators of the first type may comprise disjunctive operators, whereas the operators of the second type may comprise conjunctive operators.
摘要翻译：提供了用于在结构化图形用户界面中构建复杂布尔化学子结构查询的系统和方法。化学子结构（分子）可以以标准分子符号的图形表示，并且可以与布尔逻辑运算符一起在界面上水平和垂直排列。第一类型的布尔逻辑运算符可以逻辑地关联以水平方式排列的分子以形成行查询，而不同的第二类型的布尔逻辑运算符可以逻辑地关联行查询以形成将被应用于分子数据库的组合查询。第一类运营商可能包括分离运营商，而第二类运营商可能包括合并运营商。

52. 发明申请

WO2018013990A1 SCARLESS DNA ASSEMBLY AND GENOME EDITING USING CRISPR/CPF1 AND DNA LIGASE 审中-公开
标题翻译：使用CRISPR / CPF1和DNA Ligase无血清DNA组装和基因组编辑
公开(公告)号：WO2018013990A1
公开(公告)日：2018-01-18
申请号：PCT/US2017/042245
申请日：2017-07-14
申请人： ZYMERGEN INC.
发明人： DELOACHE, William C. , MARINUS VAN ROSSUM, Hendrik , PATEL, Kedar Gautam
IPC分类号： C12N15/09 , C12N15/11 , C12N15/113 , C12N15/63 , C12N15/66
摘要： The disclosure describes a scarless DNA assembly and genome editing methodology termed "CLIC" (CRISPR and Ligase Cloning), which utilizes a CRISPR/Cpfl complex and DNA ligase to perform programmable gene editing and nucleotide assembly. The CLIC process is highly amenable to applications in vitro for the scarless assembly of a plurality of DNA parts simultaneously or in vivo for the site-specific insertion of one or more DNA molecules into the host genome.
摘要翻译：本公开描述了称为“CLIC”的无瘢痕DNA组装和基因组编辑方法。（CRISPR和连接酶克隆），其利用CRISPR / Cpfl复合物和DNA连接酶进行可编程基因编辑和核苷酸装配。 CLIC方法非常适合体外应用，用于多个DNA部分无痕组装同时或体内用于位点特异性插入一个或多个DNA分子进入宿主基因组。

53. 发明申请

WO2018005793A1 METHODS FOR GENERATING A GLUCOSE PERMEASE LIBRARY AND USES THEREOF 审中-公开
标题翻译：产生葡萄糖渗透酶库的方法及其用途
公开(公告)号：WO2018005793A1
公开(公告)日：2018-01-04
申请号：PCT/US2017/039997
申请日：2017-06-29
申请人： ZYMERGEN INC.
发明人： MANCHESTER, Shawn , MELLIN, Jeffrey
IPC分类号： C12N15/70 , C12P19/02
摘要： The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial glucose permease gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial glucose permease gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial glucose permease genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum .
摘要翻译：本公开描述了产生表达产生目标生物分子的异源细菌葡萄糖通透酶基因的微生物菌株的方法。在一些方面，本公开提供了新的细菌菌株，其表达异源细菌葡萄糖通透酶基因，其表达受天然棒状谷氨酸棒状杆菌启动子或由其衍生的突变启动子控制。本文还提供了使用包含多个来源于谷氨酸棒状杆菌的启动子的启动子梯产生细菌葡萄糖通透酶基因文库的方法。

54. 发明申请

WO2018005655A3 METHODS FOR GENERATING A BACTERIAL HEMOGLOBIN LIBRARY AND USES THEREOF 审中-公开
公开(公告)号：WO2018005655A3
公开(公告)日：2018-01-04
申请号：PCT/US2017/039772
申请日：2017-06-28
申请人： ZYMERGEN INC.
发明人： MANCHESTER, Shawn , NECKELMANN, Alexander
IPC分类号： C12N15/09 , C12N15/67 , C12N15/52 , C12N15/70 , C12N15/10 , C12N15/77 , C12N15/82 , C12P21/02 , C12P19/34
摘要： The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial hemoglobin gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial hemoglobin gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial hemoglobin genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.

55. 发明申请

WO2017189784A1 METHODS AND SYSTEMS FOR GENERATING FACTORY ORDER FORMS TO CONTROL PRODUCTION OF NUCLEOTIDE SEQUENCES 审中-公开
标题翻译：用于生成工厂订单表格以控制核苷酸序列生成的方法和系统
公开(公告)号：WO2017189784A1
公开(公告)日：2017-11-02
申请号：PCT/US2017/029725
申请日：2017-04-26
申请人： ZYMERGEN INC.
发明人： FREWEN, Barbara , KIMBALL, Aaron , ZACHARY, Palchick
IPC分类号： G06F19/10 , G06Q10/06
CPC分类号： G06Q10/0633 , G05B15/00 , G06Q10/0631 , G16B50/00 , G16B99/00
摘要： 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.
摘要翻译：控制基因制造系统产生核苷酸序列的工厂顺序的产生包括接收指示对序列操作数进行操作的表达式，每个操作数表示至少一个核苷酸序列部分，将表达式评估为序列规范，其中所述序列规范包括数据结构，所述数据结构包括一个或多个第一级操作和一个或多个第二级操作，并且基于所述一个或多个第一级操作的执行生成所述工厂订单，并且所述一个或多个二级操作。以递归方式，一个或多个第一级操作对至少一个第一级序列操作数进行操作，通过执行一个或多个第二级操作来解决其值。然后可以将工厂订单提供给基因制造系统以将序列部分组装成序列说明所表示的核苷酸序列。

56. 发明申请

WO2017100377A1 MICROBIAL STRAIN IMPROVEMENT BY A HTP GENOMIC ENGINEERING PLATFORM 审中-公开
标题翻译：用HTP基因工程平台改进微生物菌株
公开(公告)号：WO2017100377A1
公开(公告)日：2017-06-15
申请号：PCT/US2016/065465
申请日：2016-12-07
申请人： ZYMERGEN, INC.
发明人： SERBER, Zach , DEAN, Erik Jed , MANCHESTER, Shawn , GORA, Kasia , FLASHMAN, Michael , SHELLMAN, Erin , KIMBALL, Aaron , SZYJKA, Shawn , FREWEN, Barbara , TREYNOR, Thomas
IPC分类号： G06F19/22 , G06F19/28 , C12N15/10
CPC分类号： G06F19/22 , C12N15/10 , C12N15/1093
摘要： 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.
摘要翻译：本公开提供了一种HTP微生物基因组工程平台，其被计算驱动并且集成了分子生物学，自动化和先进的机器学习协议。该综合平台利用一套HTP分子工具集来创建HTP基因设计库，这些库来源于科学洞察力和迭代模式识别。本文描述的HTP基因组工程平台是微生物菌株宿主不可知的，因此可以跨分类群实施。此外，可以实施所公开的平台以调节或改善任何感兴趣的微生物宿主参数。

57. 发明申请

WO2017100376A9 PROMOTERS FROM CORYNEBACTERIUM GLUTAMICUM 审中-公开
公开(公告)号：WO2017100376A9
公开(公告)日：2017-06-15
申请号：PCT/US2016/065464
申请日：2016-12-07
申请人： ZYMERGEN, INC.
发明人： SERBER, Zach , GORA, Katherine G. , MANCHESTER, Shawn P.
IPC分类号： C12N15/77
摘要： Provided are native promoters comprising polynucleotides isolated from Corynebacterium glutamicum , and mutant promoters derived therefrom, which may be used to regulate, i.e., either increase or decrease, gene expression. Also provided are promoter ladders comprising a plurality of the promoters having incrementally increasing promoter activity. Also provided are host cells and recombinant vectors comprising the promoters, and methods of expressing genes of interest and producing biomolecules using the host cells.

58. 发明申请

WO2017100376A2 PROMOTERS FROM CORYNEBACTERIUM GLUTAMICUM 审中-公开
公开(公告)号：WO2017100376A2
公开(公告)日：2017-06-15
申请号：PCT/US2016/065464
申请日：2016-12-07
申请人： ZYMERGEN, INC.
发明人： SERBER, Zach , GORA, Katherine G. , MANCHESTER, Shawn P.
IPC分类号： C12N15/77
CPC分类号： C12N15/77
摘要： Provided are native promoters comprising polynucleotides isolated from Corynebacterium glutamicum , and mutant promoters derived therefrom, which may be used to regulate, i.e., either increase or decrease, gene expression. Also provided are promoter ladders comprising a plurality of the promoters having incrementally increasing promoter activity. Also provided are host cells and recombinant vectors comprising the promoters, and methods of expressing genes of interest and producing biomolecules using the host cells.

59. 发明申请

WO2023081764A1 HEXADEPSIPEPTIDE COMPOUNDS AND METHODS OF USING THE SAME 审中-公开
公开(公告)号：WO2023081764A1
公开(公告)日：2023-05-11
申请号：PCT/US2022/079230
申请日：2022-11-03
申请人： ZYMERGEN INC.
发明人： TIANERO-MCINTOSH, Ma Diarey , RAMOS ALVARENGA, Rene Francisco , HOVER, Bradley Morgan , COLLETTI, Stephen L.
IPC分类号： C12N15/52 , C07K7/64 , A61K38/12 , C07K7/06 , C12N15/86
摘要： The present disclosure provides compounds of Formula (I) or a pharmaceutically acceptable salt, solvate, or tautomer thereof, and uses of the same in treating a disease or disorder (e.g., cancer or fibrosis).

60. 发明申请

WO2023283413A1 ENERGY STORAGE APPLICATION ELECTROLYTES AND ELECTRODE COMPOSITIONS COMPRISED OF HETEROCYCLES 审中-公开
公开(公告)号：WO2023283413A1
公开(公告)日：2023-01-12
申请号：PCT/US2022/036474
申请日：2022-07-08
申请人： ZYMERGEN INC.
发明人： MCNAMARA, John , INIESTA-CIVERA, Luis Matias
IPC分类号： G06F30/18
摘要： The present disclosure relates to polymers and additives that may be used in energy storage applications, and, more specifically, in liquid and solid state electrolytes. The present disclosure further relates to batteries and capacitors containing the electrolytes.

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