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91. 发明授权

US07078035B2 Phytases, nucleic acids encoding them and methods for making and using them 失效
公开(公告)号：US07078035B2
公开(公告)日：2006-07-18
申请号：US10156660
申请日：2002-05-24
申请人： Jay M. Short , Kevin A. Gray , Nelson R. Barton , James B. Garrett , Eileen O'Donoghue
发明人： Jay M. Short , Kevin A. Gray , Nelson R. Barton , James B. Garrett , Eileen O'Donoghue
IPC分类号： C12N9/06 , C07K1/00 , C07H21/04 , A23J1/00 , A61K38/46
CPC分类号： A21D8/042 , A01K2217/05 , A23J3/14 , A23K10/30 , A23K20/189 , A23L5/25 , A23L7/107 , A23L11/33 , A23L29/06 , A23V2002/00 , A61K38/00 , C12N9/16 , C12Y301/03008 , C12Y301/03026 , A23V2300/21
摘要： The invention provides isolated and recombinant phytase enzymes. In one aspect, the phytases are produced by modification of the wild type appA of E. coli. The enzyme can be produced from recombinant host cells. The phytases of the invention can be used to aid in the digestion of phytate where desired. In particular, the phytases of the invention can be used in foodstuffs to improve the feeding value of phytate rich ingredients. The phytases of the invention can be thermotolerant and/or thermostable. Also provided are methods for obtaining a variant polynucleotide encoding a phytase and for obtaining a phytase with thermostability or thermotolerant at high or low temperatures.

92. 发明授权

US06939689B2 Exonuclease-mediated nucleic acid reassembly in directed evolution 失效
标题翻译：定向进化中核酸外切酶介导的核酸重组
公开(公告)号：US06939689B2
公开(公告)日：2005-09-06
申请号：US10029221
申请日：2001-12-21
申请人： Jay M. Short , Tsotne David Djavakhishvili , Gerhard Johann Frey
发明人： Jay M. Short , Tsotne David Djavakhishvili , Gerhard Johann Frey
IPC分类号： A61K39/00 , C07K14/445 , C12N9/00 , C12N9/14 , C12N9/16 , C12N9/24 , C12N9/38 , C12N15/10 , C12Q1/68 , C12P21/06 , C07H21/04 , C07K17/00
CPC分类号： C07K14/445 , A61K39/00 , A61K2039/53 , C12N9/00 , C12N9/14 , C12N9/16 , C12N15/102 , C12N15/1034 , C12Q1/6811
摘要： This invention provides methods of obtaining novel polynucleotides and encoded polypeptides by the use of non-stochastic methods of directed evolution (DirectEvolution™). A particular advantage of exonuclease-mediated reassembly methods is the ability to reassemble nucleic acid strands that would otherwise be problematic to chimerize. Exonuclease-mediated reassembly methods can be used in combination with other mutagenesis methods provided herein. These methods include non-stochastic polynucleotide site-saturation mutagenesis (Gene Site Saturation Mutagenesis™) and non-stochastic polynucleotide reassembly (GeneReassembly™). This invention provides methods of obtaining novel enzymes that have optimized physical &/or biological properties. Through use of the claimed methods, genetic vaccines, enzymes, small molecules, and other desirable molecules can be evolved towards desirable properties. For example, vaccine vectors can be obtained that exhibit increased efficacy for use as genetic vaccines. Vectors obtained by using the methods can have, for example, enhanced antigen expression, increased uptake into a cell, increased stability in a cell, ability to tailor an immune response, and the like. Furthermore, this invention provides methods of obtaining a variety of novel biologically active molecules, in the fields of antibiotics, pharmacotherapeutics, and transgenic traits.
摘要翻译：本发明提供了通过使用定向进化（DirectEvolution TM）的非随机方法获得新的多核苷酸和编码的多肽的方法。外切核酸酶介导的重组方法的一个特别优点是重新组装核酸链的能力，否则这些核酸链将成为嵌合的问题。外切核酸酶介导的重组方法可以与本文提供的其它诱变方法组合使用。这些方法包括非随机多核苷酸位点饱和诱变（Gene Site Saturation Mutagenesis TM）和非随机多核苷酸重组（GeneReassembly TM）。本发明提供获得具有优化的物理和/或生物学特性的新型酶的方法。通过使用所要求保护的方法，可以将遗传疫苗，酶，小分子和其它所需分子演变成期望的性质。例如，可以获得表现出增加用作基因疫苗的功效的疫苗载体。通过使用该方法获得的载体可具有例如增强的抗原表达，增加的细胞摄取，增加细胞的稳定性，定制免疫应答的能力等。此外，本发明提供了在抗生素，药物治疗剂和转基因性状领域中获得各种新型生物活性分子的方法。

93. 发明授权

US06849395B2 Gene cluster screening of clones having DNA from mixed populations of organisms 失效
标题翻译：对来自混合生物群体的DNA的克隆进行基因簇筛选
公开(公告)号：US06849395B2
公开(公告)日：2005-02-01
申请号：US09407525
申请日：1999-09-28
申请人： Jay M. Short
发明人： Jay M. Short
IPC分类号： C12N15/09 , C12N1/21 , C12N9/00 , C12N15/10 , C12N15/52 , C12Q1/00 , C12Q1/25 , C12Q1/68
CPC分类号： C12N15/1086 , C12N15/1034 , C12N15/1079 , C12N15/1093 , C12N15/52 , C12Q1/00
摘要： Disclosed is a process of screening clones having DNA from an uncultivated microorganism for a specified protein, e.g. enzyme, activity by screening for a specified protein, e.g. enzyme, activity in a library of clones prepared by (i) recovering DNA from a DNA population derived from at least one uncultivated microorganism; and (ii) transforming a host with recovered DNA to produce a library of clones which is screened for the specified protein, e.g. enzyme, activity.
摘要翻译：公开了一种筛选具有来自未培养的微生物的DNA的克隆用于特定蛋白质的方法，例如，酶，通过筛选特定蛋白质的活性，例如酶，通过（i）从源自至少一种未培养微生物的DNA群体回收DNA的克隆文库中的活性; 和（ii）用回收的DNA转化宿主以产生筛选特定蛋白质的克隆文库，例如。酶，活性。

94. 发明授权

US06846627B2 Screening for novel compounds which regulate biological interactions 失效
标题翻译：筛选调节生物相互作用的新型化合物
公开(公告)号：US06846627B2
公开(公告)日：2005-01-25
申请号：US09529458
申请日：1998-10-15
申请人： Jay M. Short
发明人： Jay M. Short
IPC分类号： G01N33/50 , C12N15/09 , C12N15/10 , C12P7/26 , C12Q1/02 , C12Q1/26 , C12Q1/34 , C12Q1/48 , C12Q1/68 , C12R1/01 , G01N33/15 , G01N33/53
CPC分类号： C12N15/1055 , C12Q1/6897 , G01N2333/195 , G01N2333/39
摘要： Disclosed is a process for identifying compounds having a specified activity of interest, which process comprises (i) introducing interacting molecules into a host cell under conditions to generate or repress a detectable signal; and (ii) introducing a third compound or gene or genes encoding a third compound into the host cell from (i); and (iii) screening said host cell utilizing a method for detecting the inhibition or enhancement of interaction of proteins or other molecules in an in vivo or in vitro system. Another aspect of the present invention provides a process for identifying compounds of interest, which process comprises (i) generating one or more expression libraries derived from nucleic acid directly isolated from the environment; and (ii) screening said libraries utilizing a method for detecting the inhibition or enhancement of interaction of proteins or other molecules in an in vivo or in vitro system.
摘要翻译：公开了用于鉴定具有特定目的活性的化合物的方法，该方法包括（i）在产生或抑制可检测信号的条件下将相互作用的分子引入宿主细胞; 和（ii）从（i）引入第三化合物或基因或编码第三化合物的基因到宿主细胞中; 和（iii）利用在体内或体外系统中检测蛋白质或其他分子的相互作用的抑制或增强的方法筛选所述宿主细胞。本发明的另一方面提供了鉴定目的化合物的方法，该方法包括（i）产生一种或多种源自直接从环境中分离的核酸的表达文库; 和（ii）利用检测体内或体外系统中蛋白质或其他分子的相互作用的抑制或增强的方法筛选所述文库。

95. 发明授权

US06794127B1 Capillary array-based sample screening 有权
标题翻译：基于毛细管阵列的样品筛选
公开(公告)号：US06794127B1
公开(公告)日：2004-09-21
申请号：US09687219
申请日：2000-10-12
申请人： William Michael Lafferty , Jay M. Short , Martin Keller
发明人： William Michael Lafferty , Jay M. Short , Martin Keller
IPC分类号： C12Q100
CPC分类号： C40B40/02 , B01J19/0046 , B01J2219/00351 , B01J2219/00367 , B01J2219/00416 , B01J2219/00479 , B01J2219/00481 , B01J2219/00522 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/0061 , B01J2219/00612 , B01J2219/00619 , B01J2219/00621 , B01J2219/00626 , B01J2219/0063 , B01J2219/00637 , B01J2219/00659 , B01J2219/00677 , B01J2219/00686 , B01J2219/00689 , B01J2219/00702 , B01J2219/00722 , B01J2219/0074 , B01J2219/00743 , B01L3/5085 , B01L3/50857 , B82Y30/00 , C12N15/1037 , C12N15/1055 , C12Q1/6811 , C12Q1/6837 , C40B40/06 , C40B60/14
摘要： Provided are methods of screening and identification of bio activities and bioactive molecules of interest using a capillary array system. More specifically, disclosed are methods of using optical detection and capillary array-based techniques for screening libraries and recovering bioactive molecules having a desired activity or a nucleic acid sequence encoding such bioactive molecules.
摘要翻译：提供了使用毛细管阵列系统筛选和鉴定生物活性和生物活性分子的方法。更具体地，公开了使用光学检测和毛细管阵列技术来筛选文库和回收具有所需活性的生物活性分子或编码这种生物活性分子的核酸序列的方法。

96. 发明授权

US06790605B1 Methods for obtaining a desired bioactivity or biomolecule using DNA libraries from an environmental source 有权
标题翻译：使用来自环境来源的DNA文库获得所需生物活性或生物分子的方法
公开(公告)号：US06790605B1
公开(公告)日：2004-09-14
申请号：US09375605
申请日：1999-08-17
申请人： Jay M. Short
发明人： Jay M. Short
IPC分类号： C12Q100
CPC分类号： C12N9/00 , C12N9/16 , C12N9/2445 , C12N15/102 , C12N15/1034 , C12Y301/03001 , C12Y302/01021
摘要： Disclosed is a process for obtaining an enzyme having a specified enzyme activity derived from a heterogeneous DNA population by screening, for the specified enzyme activity, a library of clones containing DNA from the heterogeneous DNA population which have been exposed to directed mutagenesis towards production of the specified enzyme activity. Also disclosed is a process for obtaining an enzyme having a specified enzyme activity by screening, for the specified enzyme activity, a library of clones containing DNA from a pool of DNA populations which have been exposed to directed mutagenesis in an attempt to produce in the library of clones DNA encoding an enzyme having one or more desired characteristics which can be the same or different from the specified enzyme activity.
摘要翻译：公开了一种获得具有来自异质DNA群体的特定酶活性的酶的方法，对于规定的酶活性，筛选含有已经暴露于定向诱变的异源DNA群体的DNA的克隆的文库，指定的酶活性。还公开了获得具有特定酶活性的酶的方法，通过筛选已经暴露于定向诱变的DNA群体中含有DNA的克隆的特定酶活性文库，试图在文库中产生的克隆DNA，其编码具有一个或多个可以与指定酶活性相同或不同的所需特征的酶。

97. 发明授权

US06713282B2 End selection in directed evolution 有权
公开(公告)号：US06713282B2
公开(公告)日：2004-03-30
申请号：US10099816
申请日：2002-03-14
申请人： Jay M. Short , Gerhard Johann Frey
发明人： Jay M. Short , Gerhard Johann Frey
IPC分类号： C12P2106
CPC分类号： C07K14/445 , A61K39/00 , A61K2039/53 , C12N9/00 , C12N9/14 , C12N9/16 , C12N9/88 , C12N15/102 , C12N15/1027 , C12N15/1034 , C12Q1/6811 , C12Y301/11002
摘要： This invention provides methods of obtaining novel polynucleotides and encoded polypeptides by the use of non-stochastic methods of directed evolution (DirectEvolution™). A particular advantage of end-selection-based methods is the ability to recover full-length polynucleotides from a library of progeny molecules generated by mutagenesis methods. These methods include non-stochastic polynucleotide site-saturation mutagenesis (Gene Site Saturation Mutagenesis™) and non-stochastic polynucleotide reassembly (GeneReassembly™). This invention provides methods of obtaining novel enzymes that have optimized physical &/or biological properties. Through use of the claimed methods, genetic vaccines, enzymes, small molecules, and other desirable molecules can be evolved towards desirable properties. For example, vaccine vectors can be obtained that exhibit increased efficacy for use as genetic vaccines. Vectors obtained by using the methods can have, for example, enhanced antigen expression, increased uptake into a cell, increased stability in a cell, ability to tailor an immune response, and the like. Furthermore, this invention provides methods of obtaining a variety of novel biologically active molecules, in the fields of antibiotics, pharmacotherapeutics, and transgenic traits.

98. 发明授权

US06635449B2 Exonuclease-mediated nucleic acid reassembly in directed evolution 有权
公开(公告)号：US06635449B2
公开(公告)日：2003-10-21
申请号：US10108077
申请日：2002-03-26
申请人： Jay M. Short
发明人： Jay M. Short
IPC分类号： C12P2106
CPC分类号： C07K14/445 , A61K39/00 , A61K2039/53 , C12N9/00 , C12N9/16 , C12N15/102 , C12N15/1027 , C12N15/1034 , C12Q1/6811 , C12Y301/11002
摘要： This invention provides methods of obtaining novel polynucleotides and encoded polypeptides by the use of non-stochastic methods of directed evolution (DirectEvolution™). A particular advantage of exonuclease-mediated reassembly methods is the ability to reassemble nucleic acid strands that would otherwise be problematic to chimerize. Exonuclease-mediated reassembly methods can be used in combination with other mutagenesis methods provided herein. These methods include non-stochastic polynucleotide site-saturation mutagenesis (Gene Site Saturation Mutagenesis™) and non-stochastic polynucleotide reassembly (GeneReassembly™). This invention provides methods of obtaining novel enzymes that have optimized physical &/or biological properties. Through use of the claimed methods, genetic vaccines, enzymes, small molecules, and other desirable molecules can be evolved towards desirable properties. For example, vaccine vectors can be obtained that exhibit increased efficacy for use as genetic vaccines. Vectors obtained by using the methods can have, for example, enhanced antigen expression, increased uptake into a cell, increased stability in a cell, ability to tailor an immune response, and the like. Furthermore, this invention provides methods of obtaining a variety of novel biologically active molecules, in the fields of antibiotics, pharmacotherapeutics, and transgenic traits.

99. 发明授权

US06579704B2 Modified nucleotides and methods useful for nucleic acid sequencing 失效
公开(公告)号：US06579704B2
公开(公告)日：2003-06-17
申请号：US09851542
申请日：2001-05-08
申请人： Jay M. Short
发明人： Jay M. Short
IPC分类号： C12P1934
CPC分类号： C12Q1/6869 , C12Q2527/125
摘要： The present invention relates to a method for sequencing nucleic acids. In particular, such method includes incorporating certain modified nucleotides referred to as Simtides into nucleic acid strands. These Simtides are complexes comprising a nucleotide base (or analog thereof), a linker, and a label capable of generating a detectable signal for sequencing. A Simtide may be incorporated into a sequencing fragment as a primer component, as a chain elongator, or as a chain terminator.

100. 发明授权

US06489145B1 Method of DNA shuffling 失效
标题翻译： DNA洗牌方法
公开(公告)号：US06489145B1
公开(公告)日：2002-12-03
申请号：US08962504
申请日：1997-10-31
申请人： Jay M. Short
发明人： Jay M. Short
IPC分类号： C12P1934
CPC分类号： C12Q1/6811 , C12N15/1027
摘要： Disclosed is a method of producing random polynucleotides by introducing two or more related polynucleotides into a suitable host cell such that a hybrid polynucleotide is generated by recombination and reductive reassortment. Also provided are vector and expression vehicles including such polynucleotides, polypeptides expressed by the hybrid polynucleotides and a method for screening for hybrid polypeptides.
摘要翻译：公开了通过将两个或更多个相关多核苷酸引入合适的宿主细胞中产生随机多核苷酸的方法，使得通过重组和还原重配产生杂交多核苷酸。还提供了载体和表达载体，包括这样的多核苷酸，由杂交多核苷酸表达的多肽和杂交多肽的筛选方法。

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