公开(公告)号：US20120185226A1

公开(公告)日：2012-07-19

申请号：US13203470

申请日：2010-02-26

Applicant: Imandohkt Famili ,  Christophe H. Schilling

Inventor： Imandohkt Famili ,  Christophe H. Schilling

IPC: G06G7/60

CPC classification number: G06F19/12 ,  G06F19/26

Abstract: The invention provides models and methods useful for optimizing cell lines. The invention provides methods and computer readable medium or media containing such methods. Such a computer readable medium or media can comprise commands for carrying out a method of the invention. The methods of the invention can be utilized to model improved characteristics of a cell line, for example, improved product production, improved growth, improved culture characteristics, and the like.

Abstract translation: 本发明提供了用于优化细胞系的模型和方法。 本发明提供了包含这些方法的方法和计算机可读介质或介质。 这样的计算机可读介质或介质可以包括用于执行本发明的方法的命令。 本发明的方法可用于模拟细胞系的改进特征，例如，改进的产物生产，改善的生长，改善的培养特征等。

公开(公告)号：US08216814B2

公开(公告)日：2012-07-10

申请号：US13288699

申请日：2011-11-03

Applicant: Anthony P. Burgard ,  Priti Pharkya ,  Robin E. Osterhout

Inventor： Anthony P. Burgard ,  Priti Pharkya ,  Robin E. Osterhout

IPC: C12P7/40 ,  C12N1/20

CPC classification number: C12N15/52 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/001 ,  C12N9/1029 ,  C12N9/1096 ,  C12N9/80 ,  C12N9/88 ,  C12P7/44 ,  C12P7/46 ,  C12P7/62 ,  C12P13/001 ,  C12P13/005 ,  C12P13/02 ,  C12P17/10 ,  C12Y101/01035 ,  C12Y102/0101 ,  C12Y103/01031 ,  C12Y206/01 ,  C12Y402/01

Abstract: The invention provides a non-naturally occurring microbial organism having an adipate, 6-aminocaproic acid or caprolactam pathway. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in the respective adipate, 6-aminocaproic acid or caprolactam pathway. The invention additionally provides a method for producing adipate, 6-aminocaproic acid or caprolactam. The method can include culturing an adipate, 6-aminocaproic acid or caprolactam producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an adipate, 6-aminocaproic acid or caprolactam pathway enzyme in a sufficient amount to produce the respective product, under conditions and for a sufficient period of time to produce adipate, 6-aminocaproic acid or caprolactam.

公开(公告)号：US20120122171A1

公开(公告)日：2012-05-17

申请号：US13348564

申请日：2012-01-11

Applicant: Mark J. Burk ,  Stephen J. Van Dien ,  Anthony P. Burgard ,  Wei Niu

Inventor： Mark J. Burk ,  Stephen J. Van Dien ,  Anthony P. Burgard ,  Wei Niu

IPC: C12P7/18 ,  C12N1/19 ,  C12N1/15 ,  C12N1/21

CPC classification number: C12N15/52 ,  B01D3/002 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/88 ,  C12N9/93 ,  C12N15/70 ,  C12N15/81 ,  C12P7/18 ,  C12P7/42 ,  C12P7/52 ,  C12P17/04 ,  C12Y101/01061 ,  C12Y102/01076 ,  C12Y401/01071 ,  C12Y602/01004 ,  Y02P20/52

Abstract: The invention provides a non-naturally occurring microbial biocatalyst including a microbial organism having a 4-hydroxybutanoic acid (4-HB) biosynthetic pathway having at least one exogenous nucleic acid encoding 4-hydroxybutanoate dehydrogenase, succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase, or α-ketoglutarate decarboxylase, wherein the exogenous nucleic acid is expressed in sufficient amounts to produce monomeric 4-hydroxybutanoic acid (4-HB). Also provided is a non-naturally occurring microbial biocatalyst including a microbial organism having 4-hydroxybutanoic acid (4-HB) and 1,4-butanediol (BDO) biosynthetic pathways, the pathways include at least one exogenous nucleic acid encoding 4-hydroxybutanoate dehydrogenase, succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase, 4-hydroxybutyrate:CoA transferase, 4-butyrate kinase, phosphotransbutyrylase, α-ketoglutarate decarboxylase, aldehyde dehydrogenase, alcohol dehydrogenase or an aldehyde/alcohol dehydrogenase, wherein the exogenous nucleic acid is expressed in sufficient amounts to produce 1,4-butanediol (BDO). Additionally provided is a method are methods for the production of 4-HB and BDO.

Abstract translation: 本发明提供了一种非天然存在的微生物生物催化剂，其包括具有4-羟基丁酸（4-HB）生物合成途径的微生物生物，其具有至少一种编码4-羟基丁酸脱氢酶的外源核酸，琥珀酰辅酶A合成酶，CoA依赖性琥珀酸半醛 脱氢酶或α-酮戊二酸脱羧酶，其中外源核酸以足够的量表达以产生单体4-羟基丁酸（4-HB）。 还提供了非天然存在的微生物生物催化剂，其包括具有4-羟基丁酸（4-HB）和1,4-丁二醇（BDO）生物合成途径的微生物生物，该途径包括至少一种编码4-羟基丁酸脱氢酶的外源核酸 ，琥珀酰辅酶A合成酶，CoA依赖性琥珀酸半醛脱氢酶，4-羟基丁酸酯：CoA转移酶，4-丁酸酯激酶，磷酸转移酶，α-酮戊二酸脱羧酶，醛脱氢酶，醇脱氢酶或醛/醇脱氢酶，其中外源核酸为 以足够的量表示产生1,4-丁二醇（BDO）。 另外提供了一种生产4-HB和BDO的方法。

公开(公告)号：US08129169B2

公开(公告)日：2012-03-06

申请号：US12794700

申请日：2010-06-04

Applicant: Stephen J. Van Dien ,  Anthony P. Burgard ,  Robert Haselbeck ,  Catherine J. Pujol-Baxley ,  Wei Niu ,  John D. Trawick ,  Harry Yim ,  Mark J. Burk ,  Robin E. Osterhout ,  Jun Sun

Inventor： Stephen J. Van Dien ,  Anthony P. Burgard ,  Robert Haselbeck ,  Catherine J. Pujol-Baxley ,  Wei Niu ,  John D. Trawick ,  Harry Yim ,  Mark J. Burk ,  Robin E. Osterhout ,  Jun Sun

IPC: C12N1/21

CPC classification number: C12P7/18 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/001 ,  C12N9/13 ,  C12N9/16 ,  C12N9/88 ,  C12N9/93 ,  C12N15/52

Abstract: The invention provides non-naturally occurring microbial organisms comprising a 1,4-butanediol (BDO) pathway comprising at least one exogenous nucleic acid encoding a BDO pathway enzyme expressed in a sufficient amount to produce BDO and further optimized for expression of BDO. The invention additionally provides methods of using such microbial organisms to produce BDO.

Abstract translation: 本发明提供了包含1,4-丁二醇（BDO）途径的非天然存在的微生物生物，其包含至少一种编码足够量的BDO途径酶的外源核酸以产生BDO并进一步优化用于BDO的表达。 本发明还提供了使用这种微生物生产BDO的方法。

公开(公告)号：US08088607B2

公开(公告)日：2012-01-03

申请号：US12875084

申请日：2010-09-02

Applicant: Anthony P. Burgard ,  Priti Pharkya ,  Robin E. Osterhout

Inventor： Anthony P. Burgard ,  Priti Pharkya ,  Robin E. Osterhout

IPC: C12P13/00 ,  C12P7/44 ,  C12P7/00 ,  C12N1/20

CPC classification number: C12N15/52 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/001 ,  C12N9/1029 ,  C12N9/1096 ,  C12N9/80 ,  C12N9/88 ,  C12P7/44 ,  C12P7/46 ,  C12P7/62 ,  C12P13/001 ,  C12P13/005 ,  C12P13/02 ,  C12P17/10 ,  C12Y101/01035 ,  C12Y102/0101 ,  C12Y103/01031 ,  C12Y206/01 ,  C12Y402/01

Abstract: The invention provides a non-naturally occurring microbial organism having an adipate, 6-aminocaproic acid or caprolactam pathway. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in the respective adipate, 6-aminocaproic acid or caprolactam pathway. The invention additionally provides a method for producing adipate, 6-aminocaproic acid or caprolactam. The method can include culturing an adipate, 6-aminocaproic acid or caprolactam producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an adipate, 6-aminocaproic acid or caprolactam pathway enzyme in a sufficient amount to produce the respective product, under conditions and for a sufficient period of time to produce adipate, 6-aminocaproic acid or caprolactam.

Abstract translation: 本发明提供了具有己二酸，6-氨基己酸或己内酰胺途径的非天然存在的微生物。 微生物生物体含有至少一种编码相应己二酸，6-氨基己酸或己内酰胺途径中的酶的外源核酸。 本发明另外提供了生产己二酸，6-氨基己酸或己内酰胺的方法。 该方法可以包括培养己二酸，6-氨基己酸或己内酰胺生产微生物，其中微生物生物体表达至少一种编码己二酸，6-氨基己酸或己内酰胺途径酶的外源核酸，其量足以产生相应的产物 在条件下和足够的时间内生产己二酸，6-氨基己酸或己内酰胺。

公开(公告)号：US20110229946A1

公开(公告)日：2011-09-22

申请号：US13109732

申请日：2011-05-17

Applicant: Robert Haselbeck ,  John D. Trawick ,  Wei Niu ,  Anthony P. Burgard

Inventor： Robert Haselbeck ,  John D. Trawick ,  Wei Niu ,  Anthony P. Burgard

IPC: C12P7/24 ,  C12N1/00

CPC classification number: C12P7/18 ,  C12P7/24 ,  C12P7/42 ,  C12P13/001 ,  C12P19/40

Abstract: The invention provides non-naturally occurring microbial organisms comprising a 1,4-butanediol (BDO), 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine pathway comprising at least one exogenous nucleic acid encoding a BDO, 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine pathway enzyme expressed in a sufficient amount to produce BDO, 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine and further optimized for expression of BDO. The invention additionally provides methods of using such microbial organisms to produce BDO, 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine.

公开(公告)号：US07947483B2

公开(公告)日：2011-05-24

申请号：US11891602

申请日：2007-08-10

Applicant: Anthony P. Burgard ,  Stephen J. Van Dien ,  Mark Burk

Inventor： Anthony P. Burgard ,  Stephen J. Van Dien ,  Mark Burk

IPC: C12N1/20 ,  C12N1/21 ,  C12Q1/68 ,  C12P7/18

CPC classification number: C12P7/18 ,  B01D3/002 ,  C12N9/0006

Abstract: The invention provides a non-naturally occurring microorganism comprising one or more gene disruptions, the one or more gene disruptions occurring in genes encoding an enzyme obligatory to coupling 1,4-butanediol production to growth of the microorganism when the gene disruption reduces an activity of the enzyme, whereby the one or more gene disruptions confers stable growth-coupled production of 1,4-butanediol onto the non-naturally occurring microorganism. The microorganism can further comprise a gene encoding an enzyme in a 1,4-butanediol (BDO) biosynthetic pathway. The invention additionally relates to methods of using microorganisms to produce BDO.

Abstract translation: 本发明提供了包含一种或多种基因破坏的非天然存在的微生物，所述一个或多个基因破坏发生在编码需要将1,4-丁二醇生产偶联以生产微生物的酶的基因发生在基因破坏时降低活性 该酶，其中一个或多个基因破坏赋予非天然存在的微生物上1,4-丁二醇稳定的生长偶联产生。 微生物还可以包含编码1,4-丁二醇（BDO）生物合成途径中的酶的基因。 本发明还涉及使用微生物来生产BDO的方法。

公开(公告)号：US20100330626A1

公开(公告)日：2010-12-30

申请号：US12875084

申请日：2010-09-02

Applicant: Anthony P. Burgard ,  Priti Pharkya ,  Robin E. Osterhout

Inventor： Anthony P. Burgard ,  Priti Pharkya ,  Robin E. Osterhout

IPC: C12P17/10 ,  C12N1/00 ,  C12P7/46

CPC classification number: C12N15/52 ,  C12N9/0006 ,  C12N9/0008 ,  C12N9/001 ,  C12N9/1029 ,  C12N9/1096 ,  C12N9/80 ,  C12N9/88 ,  C12P7/44 ,  C12P7/46 ,  C12P7/62 ,  C12P13/001 ,  C12P13/005 ,  C12P13/02 ,  C12P17/10 ,  C12Y101/01035 ,  C12Y102/0101 ,  C12Y103/01031 ,  C12Y206/01 ,  C12Y402/01

Abstract: The invention provides a non-naturally occurring microbial organism having an adipate, 6-aminocaproic acid or caprolactam pathway. The microbial organism contains at least one exogenous nucleic acid encoding an enzyme in the respective adipate, 6-aminocaproic acid or caprolactam pathway. The invention additionally provides a method for producing adipate, 6-aminocaproic acid or caprolactam. The method can include culturing an adipate, 6-aminocaproic acid or caprolactam producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an adipate, 6-aminocaproic acid or caprolactam pathway enzyme in a sufficient amount to produce the respective product, under conditions and for a sufficient period of time to produce adipate, 6-aminocaproic acid or caprolactam.

Abstract translation: 本发明提供了具有己二酸，6-氨基己酸或己内酰胺途径的非天然存在的微生物。 微生物生物体含有至少一种编码相应己二酸，6-氨基己酸或己内酰胺途径中的酶的外源核酸。 本发明另外提供了生产己二酸，6-氨基己酸或己内酰胺的方法。 该方法可以包括培养己二酸，6-氨基己酸或己内酰胺生产微生物，其中微生物生物体表达至少一种编码己二酸，6-氨基己酸或己内酰胺途径酶的外源核酸，其量足以产生相应的产物 在条件下和足够的时间内生产己二酸，6-氨基己酸或己内酰胺。

公开(公告)号：US07856317B2

公开(公告)日：2010-12-21

申请号：US10173547

申请日：2002-06-14

Applicant: Christophe H. Schilling

Inventor： Christophe H. Schilling

IPC: G01N33/48

CPC classification number: G06F19/12

Abstract: The invention provides a computer implemented process for constructing a scalable output network model of a bioparticle. The process includes computer implemented steps of: (a) accessing a database of network gene components including an annotated network set of open reading frames (ORFs) of a bioparticle genome; (b) forming a data structure associating the network gene components with network reaction components, the data structure establishing a data set specifying a network model of connectivity and flow of the network reaction components, and (c) transforming the data set into a mathematical description of reactant fluxes defining the network model of connectivity and flow, wherein the mathematical description defines a scalable output network model of a bioparticle.

Abstract translation: 本发明提供了一种用于构建生物颗粒的可伸缩输出网络模型的计算机实现过程。 该过程包括计算机实现的步骤：（a）访问网络基因组件的数据库，包括生物颗粒基因组的开放阅读框（ORF）的注释网络集合; （b）形成将网络基因组件与网络反应组件相关联的数据结构，数据结构建立指定网络反应组件的连通性和流程的网络模型的数据集，以及（c）将数据集变换为数学描述 反应物通量定义了连通性和流量的网络模型，其中数学描述定义了生物颗粒的可伸缩输出网络模型。

公开(公告)号：US20100304453A1

公开(公告)日：2010-12-02

申请号：US12639977

申请日：2009-12-16

Applicant: John D. Trawick ,  Mark J. Burk ,  Anthony P. Burgard

Inventor： John D. Trawick ,  Mark J. Burk ,  Anthony P. Burgard

IPC: C12P7/42 ,  C12N1/00 ,  C12P7/04

CPC classification number: C12P7/18 ,  C12N9/0006 ,  C12N9/10 ,  C12N9/1029 ,  C12N9/88 ,  C12N15/52 ,  C12P7/04 ,  C12P7/42

Abstract: A non-naturally occurring microbial organism having an isopropanol, 4-hydroxybutryate, or 1,4-butanediol pathway includes at least one exogenous nucleic acid encoding an isopropanol, 4-hydroxybutryate, or 1,4-butanediol pathway enzyme expressed in a sufficient amount to produce isopropanol, 4-hydroxybutryate, or 1,4-butanediol. The aforementioned organisms are cultured to produce isopropanol, 4-hydroxybutryate, or 1,4-butanediol.

Abstract translation: 具有异丙醇，4-羟基丁酸酯或1,4-丁二醇途径的非天然存在的微生物包括至少一种编码以足够量表达的异丙醇，4-羟基丁酸酯或1,4-丁二醇途径酶的外源核酸 产生异丙醇，4-羟基丁酸酯或1,4-丁二醇。 培养上述生物体以产生异丙醇，4-羟基丁酸酯或1,4-丁二醇。