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1. 发明申请

US20150038348A1 MICROBIAL BIOINDICATORS OF HYDROCARBONS IN WATER AND IN MARINE SEDIMENTS AND METHODS FOR MAKING AND USING THEM 审中-公开
标题翻译：水中海水和海水中微生物生物降解剂及其制备和使用方法
公开(公告)号：US20150038348A1
公开(公告)日：2015-02-05
申请号：US13696954
申请日：2011-07-29
申请人： Matthew Ashby , Dago Dimster-Denk , Ulrika Elisa Lidstrom
发明人： Matthew Ashby , Dago Dimster-Denk , Ulrika Elisa Lidstrom
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6888 , C07H21/04 , C12Q1/689 , C12Q2600/16
摘要： In alternative embodiments, the invention provides products of manufacture and compositions, e.g., nucleic acid probes, for use as identifying agents or indicators to detect the presence of a hydrocarbon in a sample, e.g., in marine sediments, muds, sands and the like, or in a solution, e.g., an aqueous solution, such as a production water, fresh water, underground water or seawater. In alternative embodiments, the invention provides compositions, e.g., nucleic acid probes or primers or primer pairs, for use as sensors and/or identifying agents to detect the presence of a hydrocarbon in a sample (e.g., in fresh water, underground water or seawater, or a marine mud, sand or sediment), where the presence of the hydrocarbon indicates e.g., the presence of a subsurface oil, petroleum or gas accumulation or deposit. In alternative embodiments, the invention provides compositions and methods for use as tools for offshore oil exploration activities.
摘要翻译：在替代实施方案中，本发明提供制造产品和组合物，例如核酸探针，用作识别剂或指示剂，以检测样品中例如海洋沉积物，泥浆，沙子等中的烃的存在，或在溶液中，例如水溶液，例如生产水，淡水，地下水或海水。在替代实施方案中，本发明提供组合物，例如核酸探针或引物或引物对，用作传感器和/或识别试剂以检测样品中烃的存在（例如，在淡水，地下水或海水中，或海洋泥沙，沙子或沉积物），其中烃的存在表示例如存在地下油，石油或气体积聚或沉积物。在替代实施例中，本发明提供了用作海上石油勘探活动的工具的组合物和方法。

2. 发明申请

US20130116126A1 COMPOSITIONS AND METHODS FOR IDENTIFYING AND MODIFYING CARBONACEOUS COMPOSITIONS 有权
标题翻译：用于鉴定和改性碳组合物的组合物和方法
公开(公告)号：US20130116126A1
公开(公告)日：2013-05-09
申请号：US13504120
申请日：2011-06-16
申请人： Matthew Ashby , Ladonna Wood , Ulrika Lidstrom , Christine Clarke , Alison Gould , Dariusz Strapoc , Adewale J. Lambo , Bradley James Huizinga
发明人： Matthew Ashby , Ladonna Wood , Ulrika Lidstrom , Christine Clarke , Alison Gould , Dariusz Strapoc , Adewale J. Lambo , Bradley James Huizinga
IPC分类号： E21B43/295 , C12P5/02 , C12Q1/04
CPC分类号： C12P5/023 , C09K8/582 , C12N1/20 , C12Q1/04 , E21B43/16 , E21B43/295 , Y02E50/343 , Y02P20/128
摘要： This invention generally relates to natural gas and methylotrophic energy generation, bio-generated fuels and microbiology. In alternative embodiments, the invention provides nutrient amendments and microbial compositions, e.g., consortia, that are both specifically optimized to stimulate methanogenesis, or for “methylotrophic” or other conversions. In alternative embodiments, the invention provides methods to develop nutrient amendments and microbial compositions that are both specifically optimized to stimulate methanogenesis in a given reservoir. The invention also provides methods for the evaluation of potentially damaging biomass formation and scale precipitation resulting from the addition of nutrient amendments. In other embodiments, the invention provides methods for simulating biogas in sub-surface conditions using a computational model.
摘要翻译：本发明一般涉及天然气和甲基营养能量的产生，生物燃料和微生物学。在替代实施方案中，本发明提供营养物修饰物和微生物组合物，例如联合体，其都被特别优化以刺激产甲烷生成，或用于“甲基营养”或其它转化。在替代实施方案中，本发明提供了开发营养物修饰物和微生物组合物的方法，所述营养物质修饰物和微生物组合物都被特别优化以刺激给定储存器中的产甲烷生成。本发明还提供了用于评估由添加营养物修饰导致的潜在的破坏性生物质形成和水垢沉淀的方法。在其他实施方案中，本发明提供了使用计算模型来模拟在亚表面条件下的沼气的方法。

3. 发明申请

US20130030714A1 METHODS FOR THE SURVEY AND GENETIC ANALYSIS OF POPULATIONS 审中-公开
公开(公告)号：US20130030714A1
公开(公告)日：2013-01-31
申请号：US13566945
申请日：2012-08-03
申请人： Matthew Ashby
发明人： Matthew Ashby
IPC分类号： G06F19/18
CPC分类号： G16B30/00 , C12Q1/6809 , C12Q1/683 , C12Q1/6869 , C12Q1/6888 , C12Q2600/156 , G16B20/00 , Y10T436/21 , C12Q2525/191 , C12Q2525/151 , C12Q2521/313 , C12Q2525/131
摘要： The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

4. 发明申请

US20110251983A1 METHODS FOR THE SURVEY AND GENETIC ANALYSIS OF POPULATIONS 有权
标题翻译：人口调查与遗传分析方法
公开(公告)号：US20110251983A1
公开(公告)日：2011-10-13
申请号：US13019045
申请日：2011-02-01
申请人： Matthew Ashby
发明人： Matthew Ashby
IPC分类号： G06N3/12
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/683 , C12Q1/6869 , C12Q1/6888 , C12Q2600/156 , G06F19/18 , Y10T436/21 , C12Q2525/191 , C12Q2525/151 , C12Q2521/313 , C12Q2525/131
摘要： The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.
摘要翻译：本发明涉及进行群体遗传多样性调查的方法。本发明还涉及用于进行群体遗传分析的方法。本发明还涉及用于创建数据库的方法，该数据库包括调查信息和由这些方法创建的数据库。本发明还涉及用于分析信息以将核酸标记物的存在与样品中的期望参数相关联的方法。这些方法适用于地球化学勘探，农业，生物修复，环境分析，临床微生物学，法医学和医学领域。

5. 发明授权

US06574568B2 Systems for generating and analyzing stimulus-response output signal matrices 有权
公开(公告)号：US06574568B2
公开(公告)日：2003-06-03
申请号：US09826474
申请日：2001-04-04
申请人： Jasper Rine , Matthew Ashby
发明人： Jasper Rine , Matthew Ashby
IPC分类号： G06F1900
CPC分类号： G06F19/24 , G06F19/18 , G06F19/20
摘要： Stimulus-response patterns are analyzed using deduction protocols applied through AI systems such as expert systems and neural networks. Generating an output signal matrix database involves: (i) constructing a stimulated physical matrix; (ii) detecting a physical signal at each unit of the physical matrix; (iii) transducing each physical signal to generate an electrical output signal; (iv) storing each output signal in an output signal matrix data structure; and (v) repeating steps (i)-(iv) to iteratively store output signal matrix data structures for a plurality of stimuli to form an output signal matrix database. Individual output signal matrices are compared to such output signal matrix databases according for qualitative analysis. The stimulated physical matrices comprise an ordered array of units, each confining (1) either a different responder of a living thing or a probe corresponding to such a different responder and, (2) an identifier for the responder or probe. The living thing is provided a stimulus capable of repressing the responders of a plurality of the units and the identifier provides a physical signal corresponding to the repression of such different responder.

6. 发明授权

US5569588A Methods for drug screening 失效
标题翻译：药物筛选方法
公开(公告)号：US5569588A
公开(公告)日：1996-10-29
申请号：US512811
申请日：1995-08-09
申请人： Matthew Ashby , Jasper Rine
发明人： Matthew Ashby , Jasper Rine
IPC分类号： G01N33/15 , C12N1/19 , C12N1/21 , C12N5/10 , C12N9/04 , C12N15/09 , C12Q1/68 , C12R1/91 , G01N33/566 , C07H21/04 , C12N15/00
CPC分类号： C12N9/0006 , C12Q1/6897
摘要： Methods and compositions for modeling the transcriptional responsiveness of an organism to a candidate drug involve (a) detecting reporter gene product signals from each of a plurality of different, separately isolated cells of a target organism, wherein each cell contains a recombinant construct comprising a reporter gene operatively linked to a different endogenous transcriptional regulatory element of the target organism such that the transcriptional regulatory element regulates the expression of the reporter gene, and the sum of the cells comprises an ensemble of the transcriptional regulatory elements of the organism sufficient to model the transcriptional responsiveness of said organism to a drug; (b) contacting each cell with a candidate drug; (c) detecting reporter gene product signals from each cell; (d) comparing reporter gene product signals from each cell before and after contacting the cell with the candidate drug to obtain a drug response profile which provides a model of the transcriptional responsiveness of said organism to the candidate drug.
摘要翻译：用于对生物体对候选药物的转录反应性进行建模的方法和组合物包括（a）从靶生物的多个不同的，单独分离的细胞中的每一个检测报告基因产物信号，其中每个细胞含有包含报道分子基因可操作地连接到靶生物的不同内源性转录调节元件，使得转录调节元件调节报告基因的表达，并且细胞总数包含足以模拟转录的生物体的转录调节元件的整体所述生物体对药物的反应性; （b）使每个细胞与候选药物接触; （c）检测来自每个细胞的报道基因产物信号; （d）比较将细胞与候选药物接触之前和之后每个细胞的报道基因产物信号，以获得药物应答谱，其提供所述生物体对候选药物的转录反应性的模型。

7. 发明授权

US08476016B2 Databases for rRNA gene profiling of microbial communities 有权
标题翻译：微生物群落rRNA基因谱分析数据库
公开(公告)号：US08476016B2
公开(公告)日：2013-07-02
申请号：US13019045
申请日：2011-02-01
申请人： Matthew Ashby
发明人： Matthew Ashby
IPC分类号： C12Q1/68 , C12Q1/64 , C12P19/34 , C07H21/02 , C07H21/04
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/683 , C12Q1/6869 , C12Q1/6888 , C12Q2600/156 , G06F19/18 , Y10T436/21 , C12Q2525/191 , C12Q2525/151 , C12Q2521/313 , C12Q2525/131
摘要： The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.
摘要翻译：本发明涉及进行群体遗传多样性调查的方法。本发明还涉及用于进行群体遗传分析的方法。本发明还涉及用于创建数据库的方法，该数据库包括调查信息和由这些方法创建的数据库。本发明还涉及用于分析信息以将核酸标记物的存在与样品中的期望参数相关联的方法。这些方法适用于地球化学勘探，农业，生物修复，环境分析，临床微生物学，法医学和医学领域。

8. 发明授权

US07078169B2 Methods for the identification of inhibitors of an isoprenoid metabolic pathway 失效
标题翻译：用于鉴定类异戊二烯代谢途径抑制剂的方法
公开(公告)号：US07078169B2
公开(公告)日：2006-07-18
申请号：US10205841
申请日：2002-07-26
申请人： Matthew Ashby , Stewart Scherer , John W. Phillips , Michael Ziman , Nicholas Marini
发明人： Matthew Ashby , Stewart Scherer , John W. Phillips , Michael Ziman , Nicholas Marini
IPC分类号： C12Q1/68 , C12Q1/02 , G01N33/53 , C12N15/63 , C07H21/02
CPC分类号： G06F19/22 , G06F19/20
摘要： The present invention relates to methods of identifying genes whose expression is indicative of activation of a particular biochemical or metabolic pathway or a common set of biological reactions or functions in a cell (“regulon indicator genes”) The present invention provides an example of such an indicator gene. The present invention also relates to methods of partially characterizing a gene of unknown function by determining which biological pathways, reactions or functions its expression is associated with, thereby placing the gene within a functional genetic group or “regulon”. These partially characterized genes may be used to identify desirable therapeutic targets of biological pathways of interest (“regulon target genes”) The present invention provides examples of such target genes. Methods for identifying effectors (activators and inhibitors) of regulon target genes are provided. The present invention also provides examples of regulon target gene inhibitors.
摘要翻译：本发明涉及鉴定其表达指示特定生物化学或代谢途径的激活或细胞中的一组共同的生物反应或功能的基因的方法（“调节子指示基因”）。本发明提供了这样一种实例指标基因。本发明还涉及通过确定其表达与哪些生物学途径，反应或功能相关联来部分表征未知功能基因的方法，由此将基因置于功能性遗传组或“调节子”内。这些部分表征的基因可用于鉴定感兴趣的生物学途径的所需治疗靶标（“调节基因靶基因”）本发明提供了这些靶基因的实例。提供了用于鉴定调节子靶基因的作用剂（活化剂和抑制剂）的方法。本发明还提供了调节基因靶基因抑制剂的实例。

9. 发明授权

US06613520B2 Methods for the survey and genetic analysis of populations 有权
公开(公告)号：US06613520B2
公开(公告)日：2003-09-02
申请号：US09829855
申请日：2001-04-10
申请人： Matthew Ashby
发明人： Matthew Ashby
IPC分类号： C12Q168
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/683 , C12Q1/6869 , C12Q1/6888 , C12Q2600/156 , G06F19/18 , Y10T436/21 , C12Q2525/191 , C12Q2525/151 , C12Q2521/313 , C12Q2525/131
摘要： The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

10. 发明授权

US09206680B2 Compositions and methods for identifying and modifying carbonaceous compositions 有权
标题翻译：用于鉴定和改性碳质组合物的组合物和方法
公开(公告)号：US09206680B2
公开(公告)日：2015-12-08
申请号：US13504120
申请日：2011-06-16
申请人： Matthew Ashby , Ladonna Wood , Ulrika Lidström , Christine Clarke , Alison Gould , Dariusz Strapoc , Adewale J. Lambo , Bradley James Huizinga
发明人： Matthew Ashby , Ladonna Wood , Ulrika Lidström , Christine Clarke , Alison Gould , Dariusz Strapoc , Adewale J. Lambo , Bradley James Huizinga
IPC分类号： C12Q1/04 , E21B43/295 , C09K8/582 , C12P5/02 , E21B43/16
CPC分类号： C12P5/023 , C09K8/582 , C12N1/20 , C12Q1/04 , E21B43/16 , E21B43/295 , Y02E50/343 , Y02P20/128
摘要： This invention generally relates to natural gas and methylotrophic energy generation, bio-generated fuels and microbiology. In alternative embodiments, the invention provides nutrient amendments and microbial compositions, e.g., consortia, that are both specifically optimized to stimulate methanogenesis, or for “methylotrophic” or other conversions. In alternative embodiments, the invention provides methods to develop nutrient amendments and microbial compositions that are both specifically optimized to stimulate methanogenesis in a given reservoir. The invention also provides methods for the evaluation of potentially damaging biomass formation and scale precipitation resulting from the addition of nutrient amendments. In other embodiments, the invention provides methods for simulating biogas in sub-surface conditions using a computational model.
摘要翻译：本发明一般涉及天然气和甲基营养能量的产生，生物燃料和微生物学。在替代实施方案中，本发明提供营养物修饰物和微生物组合物，例如联合体，其都被特别优化以刺激产甲烷生成，或用于“甲基营养”或其它转化。在替代实施方案中，本发明提供了开发营养物修饰物和微生物组合物的方法，所述营养物质修饰物和微生物组合物都被特别优化以刺激给定储存器中的产甲烷生成。本发明还提供了用于评估由添加营养物修饰导致的潜在的破坏性生物质形成和水垢沉淀的方法。在其他实施方案中，本发明提供了使用计算模型来模拟在亚表面条件下的沼气的方法。

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