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61. 发明申请

WO03068910A2 GLYCOSIDASES, NUCLEIC ACIDS ENCODING THEM AND METHODS OF MAKING AND USING THEM 审中-公开
标题翻译：糖苷酸，编码它们的核酸及其制备和使用方法
公开(公告)号：WO03068910A2
公开(公告)日：2003-08-21
申请号：PCT/US0223550
申请日：2002-07-22
申请人： DIVERSA CORP , SHORT JAY M , SWANSON RONALD V , BYLINA EDWARD , MATHUR ERIC J , LAM DAVID E
发明人： SHORT JAY M , SWANSON RONALD V , BYLINA EDWARD , MATHUR ERIC J , LAM DAVID E
IPC分类号： C12N9/24 , C12N9/38 , C12N9/46 , C12N
CPC分类号： C12N9/2468 , C12N9/2402 , C12N9/2437 , C12N9/2454 , C12N9/2457 , C12N9/2465 , C12N9/2494 , C12Y302/01004 , C12Y302/01022 , C12Y302/01025 , C12Y302/01041 , C12Y302/01078
摘要： The invention is directed to enzymes having a glycosidase activity, including thermostable and thermotolerant glycosidase activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The glycosidase activities of the enzymes of the invention include the hydrolysis of any glycosidic linkages. For example, a glycosidase activity of an enzyme of the invention includes hydrolysis of a beta-anomeric configuration of a glycosidic linkage, such as the hydrolysis of beta-glucosides, beta-fucosides and beta-galactosides. Another glycosidase activity of an enzyme of the invention includes alpha-galactosidase activity, e.g., catalysis of the hydrolysis of galactose groups on a polysaccharide backbone or catalyzing the hydrolysis of the cleavage of di- or oligosaccharides comprising galactose. Another glycosidase activity of an enzyme of the invention includes catalysis of the hydrolysis of mannose groups internally on a polysaccharide backbone or hydrolysis of the cleavage of di-or oligosaccharides comprising mannose groups. Beta-mannosidases of the invention can hydrolyze non-reducing, terminal mannose residues on a mannose-containing polysaccharide and catalyze the cleavage of di- or oligosaccharides comprising mannose groups.
摘要翻译：本发明涉及具有糖苷酶活性的酶，包括耐热和耐热糖苷酶活性，以及编码这些酶的多核苷酸，以及制备和使用这些多核苷酸和多肽。本发明的酶的糖苷酶活性包括任何糖苷键的水解。例如，本发明的酶的糖苷酶活性包括糖苷键的β-端基异构构型的水解，例如β-葡糖苷，β-岩藻糖苷和β-半乳糖苷的水解。本发明的酶的另一种糖苷酶活性包括α-半乳糖苷酶活性，例如催化多糖主链上的半乳糖基团的水解或催化水解包含半乳糖的二糖或寡糖的裂解。本发明的酶的另一种糖苷酶活性包括在多糖骨架内部水解甘露糖基团或水解包含甘露糖基团的二糖或寡糖的水解。本发明的β-甘露糖苷酶可以在含甘露糖的多糖上水解非还原性末端甘露糖残基，并催化包含甘露糖基团的二糖或寡糖的切割。

62. 发明申请

WO03029425A3 WHOLE CELL ENGINEERING USING REAL-TIME METABOLIC FLUX ANALYSIS 审中-公开
标题翻译：使用实时代谢流量分析的全细胞工程
公开(公告)号：WO03029425A3
公开(公告)日：2003-08-21
申请号：PCT/US0231380
申请日：2002-10-01
申请人： DIVERSA CORP , FU PENCHENG , SHORT JAY M
发明人： FU PENCHENG , SHORT JAY M
IPC分类号： C12N20060101 , C12N15/85 , C12P21/00 , G01N33/48
CPC分类号： C12N15/85
摘要： The invention provides methods for whole cell engineering of new and modified phenotypes by using "on-line" or "real-time" metabolic flux analysis. The invention provides a method for whole cell engineering of new or modified phenotypes by using real-time metabolic flux analysis by making a modified cell by modifying the genetic composition of a cell and culturing the modified cell to generate a plurality of modified cells and measuring at least one metabolic parameter of the cell by monitoring the cell culture of in real time. The invention also provides articles comprising machine-readable medium including machine-executable instructions and systems, e.g., computer systems, to practice the methods of the invention.
摘要翻译：本发明通过使用“在线”或“实时”代谢流分析提供了新细胞和修饰表型的全细胞工程方法。本发明提供了一种通过使用实时代谢流分析通过修饰细胞的遗传组成来修饰细胞并培养修饰细胞以产生多个修饰细胞并在通过实时监测细胞培养物的细胞的至少一个代谢参数。本发明还提供包括机器可读介质的物品，所述机器可读介质包括机器可执行指令和系统（例如计算机系统）以实践本发明的方法。

63. 发明申请

WO2003048329A2 CHROMOSOMAL SATURATION MUTAGENESIS 审中-公开
标题翻译：染色体饱和诱变
公开(公告)号：WO2003048329A2
公开(公告)日：2003-06-12
申请号：PCT/US2002/038587
申请日：2002-12-03
申请人： DIVERSA CORPORATION , SHORT, Jay, M. , CAYOUETTE, Michelle
发明人： SHORT, Jay, M. , CAYOUETTE, Michelle
IPC分类号： C12N
CPC分类号： C12N15/102
摘要： In One aspect, the invention provides methods for Chromosomal Saturation Mutagenesis (CSM) comprising generating randomly mutated, overlapping segments for an entire chromosome using error-prone PCR or other techniques, and libraries of nucleic acids made by these methods.
摘要翻译：在一个方面，本发明提供了用于染色体饱和突变（CSM）的方法，所述方法包括使用易错PCR或其他技术为整个染色体产生随机突变的重叠区段，以及由这些方法。

64. 发明申请

WO2003031928A3 CELLULAR ENGINEERING, PROTEIN EXPRESSION PROFILING, DIFFERENTIAL LABELING OF PEPTIDES, AND NOVEL REAGENTS THEREFOR 审中-公开
公开(公告)号：WO2003031928A3
公开(公告)日：2003-04-17
申请号：PCT/US2002/023549
申请日：2002-07-22
申请人： DIVERSA CORPORATION , SHORT, Jay, M. , LATTERICH, Martin , WEI, Jing , LEVIN, Michael
发明人： SHORT, Jay, M. , LATTERICH, Martin , WEI, Jing , LEVIN, Michael
IPC分类号： G01N33/48
摘要： The invention provides cellular transformation, directed evolution, and screening methods for creating novel transgenic organisms having desirable properties. Thus in one aspect, this invention relates to a method of generating a transgenic organism, such as a microbe or a plant, having a plurality of traits that are differentially activatable. Also, a method of retooling genes and gene pathways by the introduction of regulatory sequences, such as promoters, that are operable in an intended host, thus conferring operability to a novel gene pathway when it is introduced into an intended host. For example a novel man-made gene pathway, generated based on microbially-derived progenitor templates, that is operable in a plant cell. Furthermore, a method of generating novel host organisms having increased expression of desirable traits, recombinant genes, and gene products. Additionally, the invention provides novel methods for determining polypeptide profiles, and protein expression variations, which methods of simultaneously identifying and quantifying individual proteins in complex protein mixtures. Protein expression levels can be globally quantified.

65. 发明申请

WO2003029425A2 WHOLE CELL ENGINEERING USING REAL-TIME METABOLIC FLUX ANALYSIS 审中-公开
标题翻译：使用实时代谢通量分析的全细胞工程
公开(公告)号：WO2003029425A2
公开(公告)日：2003-04-10
申请号：PCT/US2002/031380
申请日：2002-10-01
申请人： DIVERSA CORPORATION , FU, Pencheng , SHORT, Jay, M.
发明人： FU, Pencheng , SHORT, Jay, M.
IPC分类号： C12N
CPC分类号： C12N15/85
摘要： The invention provides methods for whole cell engineering of new and modified phenotypes by using "on-line" or "real-time" metabolic flux analysis. The invention provides a method for whole cell engineering of new or modified phenotypes by using real-time metabolic flux analysis by making a modified cell by modifying the genetic composition of a cell and culturing the modified cell to generate a plurality of modified cells and measuring at least one metabolic parameter of the cell by monitoring the cell culture of in real time. The invention also provides articles comprising machine-readable medium including machine-executable instructions and systems, e.g., computer systems, to practice the methods of the invention.
摘要翻译：本发明通过使用“在线”或“实时”代谢通量分析提供新的和修饰的表型的全细胞工程的方法。本发明提供了一种通过使用实时代谢通量分析通过改变细胞的遗传组成并培养修饰的细胞以产生多个修饰的细胞并通过在通过实时监测细胞培养物，细胞的至少一种代谢参数。本发明还提供包括机器可读介质的文章，其包括机器可执行指令和用于实施本发明的方法的系统，例如计算机系统。

66. 发明申请

WO0222810A3 COMBINATORIAL SCREENING OF MIXED POPULATIONS OF ORGANISMS 审中-公开
标题翻译：混合人口组织的组合筛选
公开(公告)号：WO0222810A3
公开(公告)日：2003-02-27
申请号：PCT/US0129712
申请日：2001-09-17
申请人： DIVERSA CORP , SHORT JAY M
发明人： SHORT JAY M
IPC分类号： C12N15/09 , C12N15/10 , C12Q1/68 , C12N15/00
CPC分类号： C12N15/1058 , C12N15/1027 , C12N15/1093
摘要： Provided is a method of screening gene libraries derived from a mixed population of organisms for a bioactivity of biomolecule of interest. The mixed population of organisms can be a cultured population or an uncultured population from, for example, the environment. Also provided are methods of screening isolates or enriched populations of organisms, which isolates include a population that is spatially, temporally, or hierarchical, for example, of a particular species, genus family, or class of organisms. Identified clones containing a biomolecule or bioactivity of interest can be further variegated or the DNA contained in the clone can be variegated to create novel biomolecules or bioactivities of interest.
摘要翻译：提供了筛选源自生物体的混合群体的基因文库的方法，用于感兴趣的生物分子的生物活性。生物的混合群体可以是来自例如环境的培养人口或未培养的群体。还提供了筛选分离物或富集的生物群体的方法，所述分离物包括空间上，时间上或等级的，例如特定物种，属或类生物体的群体。包含生物分子或感兴趣的生物活性的鉴定的克隆可以进一步杂色，或者克隆中包含的DNA可以杂色以产生新的生物分子或感兴趣的生物活性。

67. 发明申请

WO2003000840A3 NITRILASES 审中-公开
公开(公告)号：WO2003000840A3
公开(公告)日：2003-01-03
申请号：PCT/US2002/015983
申请日：2002-05-15
申请人： DIVERSA CORPORATION , MADDEN, Darcy , DESANTIS, Grace , CHAPLIN, Jennifer, Ann , WEINER, David, Paul , MILAN, Aileen , CHI, Ellen , SHORT, Jay, M. , BURK, Mark
发明人： DESANTIS, Grace , CHAPLIN, Jennifer, Ann , WEINER, David, Paul , MILAN, Aileen , CHI, Ellen , SHORT, Jay, M. , BURK, Mark
IPC分类号： C12N9/00 , C12N9/78 , C12N1/20 , C12N15/00 , C07H21/02 , C12P1/00 , C12P7/00 , C12P7/62 , C07K1/00
摘要： The invention relates to nitrilases and to nucleic acids encoding the nitrilases. In addition methods of designing new nitrilases and method of use thereof are also provided. The nitrilases have increased activity and stability at increased pH and temperature.

68. 发明申请

WO0077262A9 SYNTHETIC LIGATION REASSEMBLY IN DIRECTED EVOLUTION 审中-公开
标题翻译：合成发射在指导演进中重组
公开(公告)号：WO0077262A9
公开(公告)日：2002-06-13
申请号：PCT/US0016838
申请日：2000-06-14
申请人： DIVERSA CORP , SHORT JAY M
发明人： SHORT JAY M
IPC分类号： C12N15/09 , A61K38/00 , A61K39/00 , A61K39/39 , A61K48/00 , A61P33/06 , C07K14/445 , C12N20060101 , C12N1/15 , C12N1/19 , C12N1/21 , C12N5/10 , C12N9/14 , C12N15/01 , C12N15/10 , C12P21/02 , C12Q1/02 , C12Q1/68 , C40B30/00 , C40B40/02 , C40B50/06 , C40B60/12 , G01N33/15 , G01N33/50 , G01N33/53 , G01N33/566
CPC分类号： C12N15/1058 , A61K39/00 , A61K2039/53 , C07K14/445 , C12N9/14 , C12N15/102 , C12N15/1027 , C12N15/1034
摘要： The invention is directed to a process of preparing nucleic acid and poly nucleotide libraries by cloning non-randomly generated nucleotide fragments having ligatable ends into an expression vector. The expression of the polynucleotide provides an indirect means by which to screen the polynucleotide library.
摘要翻译：本发明涉及通过将具有可连接末端的非随机产生的核苷酸片段克隆到表达载体中来制备核酸和多核苷酸文库的方法。多核苷酸的表达提供了筛选多核苷酸文库的间接方法。

69. 发明申请

WO2002029032A3 WHOLE CELL ENGINEERING BY MUTAGENIZING A SUBSTANTIAL PORTION OF A STARTING GENOME, COMBINING MUTATIONS, AND OPTIONALLY REPEATING 审中-公开
公开(公告)号：WO2002029032A3
公开(公告)日：2002-04-11
申请号：PCT/US2001/031004
申请日：2001-10-01
申请人： DIVERSA CORPORATION , SHORT, Jay, M. , FU, Pengcheng , LATTERICH, Martin , WEI, Jing , LEVIN, Michael
发明人： SHORT, Jay, M. , FU, Pengcheng , LATTERICH, Martin , WEI, Jing , LEVIN, Michael
IPC分类号： G01N33/68
摘要： An invention comprising cellular transformation, directed evolution, and screening methods for creating novel transgenic organisms having desirable properties. In one embodiment, this invention provides a method of generating a transgenic organism, such as a microbe or a plant, having a plurality of traits that are differentially activatable. This invention also provides a method of retooling genes and gene pathways by the introduction of regulatory sequences, such as promoters, that are operable in an intended host, this conferring operability to a novel gene pathway when it is introduced into an intended host. For example a novel man-made gene pathway, generated based on microbially-derived progenitor templates, that is operable in a plant cell. This invention also provides a method of generating novel host organisms having increased expression of desirable traits, recombinant genes, and gene products. This invention provides novel methods for determining polypeptide profiles, and protein expression variations, which methods are applicable to all sample types disclosed herein. The present invention provides methods of simultaneously identifying and quantifying individual proteins in complex protein mixtures. Additionally this invention provides methods for cellular and metabolic engineering of new and modified phenotypes by using "on-line" or "real-time" metabolic flux analysis.

70. 发明申请

WO9962847A3 CONSTRUCTION AND USE OF CATALOGUED NUCLEIC ACID LIBRARIES THAT CONTAIN ADVANTAGEOUSLY ADJUSTED REPRESENTATIONS OF DEFINED COMPONENTS 审中-公开
标题翻译：包含定义成分的有效调节表示的目标核酸图像的构造和使用
公开(公告)号：WO9962847A3
公开(公告)日：2000-03-23
申请号：PCT/US9912496
申请日：1999-06-03
申请人： DIVERSA CORP , SHORT JAY M
发明人： SHORT JAY M
IPC分类号： C12N15/09 , C07B61/00 , C07H21/00 , C12Q1/68 , C12N1/00 , C12N9/00 , C12N11/00 , C12N15/10 , C12Q1/00
CPC分类号： C07H21/00 , C12N15/1093 , C40B40/00 , C40B40/08
摘要： A process for constructing a catalogued nucleic acid library in which the proportional representation of the constituents is adjusted to advantage through the use of disclosed technologies for positive and negative selection. The resultant benefit is that significantly fewer library constituents will need to be screened in order to identify a potentially desired constituent. Moreover, library constituents that previously would have been essentially "lost" are now recoverable. Preferred embodiments of this invention include the cataloguing, normalization, and enrichment of library constituents. By way of example, but not limitation, this technology is serviceable for constructing a library that contains an adequate representation of desirable constituents that (1) are initially found in low-copy numbers within a sample source or (2) originate from an organism that is problematic to culture. Applicable uses of this invention include any library-screening endeavor previously hindered by logistical impediments. By expanding previous logistical frontiers this invention allows for a novel generation of previously unattainable molecules - particularly molecules that are "unclonable" from conventional, unadjusted libraries - to now be detected, cloned, manipulated, expressed, studied, and used. By disclosing the construction and screening of high yielding nucleic acid libraries from mixed and uncultivated organisms, the instant technology eclipses former boundaries in the area of biological discovery and enables the full breadth of biological diversity to be accessed in the search for previously undiscovered genes and gene products. The benefits of the present invention are seen to extend to areas of diagnosis, medicine, agriculture, manufacturing, and academia.
摘要翻译：用于构建编目的核酸文库的方法，其中通过使用所公开的用于阳性和阴性选择的技术来调整成分的比例表示。最终的好处是，需要筛选的图书馆成分要少得多才能识别潜在的所需成分。此外，以前基本上“迷失”的图书馆成员现在可以收回。本发明的优选实施例包括图书馆成分的编目，归一化和丰富。作为示例而非限制，该技术可用于构建包含所需成分的适当表示的文库，（1）最初以样品源中的低拷贝数发现，或（2）源于生物体对文化有问题。本发明的适用用途包括以前受后勤障碍阻碍的任何图书馆筛选工作。通过扩展以前的后勤领域，本发明允许以前不可实现的分子的新一代，特别是来自常规的未调整的文库的“不可克隆”的分子 - 现在被检测，克隆，操纵，表达，研究和使用。通过披露来自混合和未培养生物体的高产核酸文库的构建和筛选，即时技术在生物学发现领域中脱颖而出，可以在寻找先前未发现的基因和基因的过程中获得全面的生物多样性产品。本发明的好处被看作延伸到诊断，医学，农业，制造和学术领域。

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