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1. 发明授权

US09109861B1 System for assembling a derived nucleotide sequence 有权
标题翻译：用于组装衍生的核苷酸序列的系统
公开(公告)号：US09109861B1
公开(公告)日：2015-08-18
申请号：US12720638
申请日：2010-03-09
申请人： Frederick R. Blattner , Schuyler F. Baldwin , Timothy J. Durfee , Daniel A. Nash , Kenneth C. Dullea , Richard D. Nelson
发明人： Frederick R. Blattner , Schuyler F. Baldwin , Timothy J. Durfee , Daniel A. Nash , Kenneth C. Dullea , Richard D. Nelson
IPC分类号： G06F19/00 , F41H13/00
CPC分类号： F41H13/0056 , G06F19/22
摘要： Systems and methods automatically assemble a set of read sequences into one or more larger nucleotide sequences using a set of comparing sequences as a template. The sequences of each set are divided into smaller mer sequences and sorted to arrange the mer sequences in order, and the sets of mers originating from the read sequence set and the comparing sequence set are compared pairwise to determine matching regions between the sequences of the read sequence set and the sequences of the comparing set. The sorting of the sequence sets prior to the pairwise comparison reduces the amount of volatile memory required to assemble the read sequence set and also reduces the overall time to assemble the read sequence set into one or more larger nucleotide sequences.
摘要翻译：系统和方法使用一组比较序列作为模板，将一组读序列自动组装成一个或多个较大的核苷酸序列。将每组的序列划分成较小的序列，并将其排序以顺序排列mer序列，并且将从读序列集合和比较序列集合起源的集合成对比较，以确定读取的序列之间的匹配区域序列集和比较集的序列。在成对比较之前对序列集的排序减少了组装读取序列集所需的易失性存储器的量，并且还减少了将读取序列组合成一个或多个较大核苷酸序列的总体时间。

2. 发明授权

US08039243B2 Insertion sequence-free bacteria 有权
标题翻译：插入无序细菌
公开(公告)号：US08039243B2
公开(公告)日：2011-10-18
申请号：US11275094
申请日：2005-12-09
申请人： Frederick R. Blattner
发明人： Frederick R. Blattner
IPC分类号： C12N1/20 , C07H21/04
CPC分类号： C12N15/70
摘要： The present invention provides a bacterium having a genome that is genetically engineered to be smaller than the genome of its native parent strain. A bacterium with a smaller genome can produce a commercial product more efficiently. The present invention also provides methods for deleting genes and other DNA sequences from a bacterial genome. The methods provide precise deletions and seldom introduces mutations to the genomic DNA sequences around the deletion sites. Thus, the methods can be used to generate a series of deletions in a bacterium without increasing the possibility of undesired homologous recombination within the genome. In addition, some of the methods provided by the present invention can also be used for replacing a region of a bacterial genome with a desired DNA sequence.
摘要翻译：本发明提供了一种具有遗传工程化以小于其天然亲本菌株的基因组的基因组的细菌。具有较小基因组的细菌可以更有效地产生商业产品。本发明还提供从细菌基因组中删除基因和其他DNA序列的方法。该方法提供精确的缺失，很少引入缺失位点周围基因组DNA序列的突变。因此，该方法可用于在细菌中产生一系列缺失，而不增加基因组内不希望的同源重组的可能性。此外，本发明提供的一些方法也可用于用期望的DNA序列替代细菌基因组的区域。

3. 发明授权

US06855814B2 Sequences of E. coli O157 有权
标题翻译：大肠杆菌O157的序列
公开(公告)号：US06855814B2
公开(公告)日：2005-02-15
申请号：US10114170
申请日：2002-04-01
申请人： Frederick R. Blattner , Valerie Burland , Nicole T. Perna , Guy Plunkett , Rod Welch
发明人： Frederick R. Blattner , Valerie Burland , Nicole T. Perna , Guy Plunkett , Rod Welch
IPC分类号： C07K14/245 , C12Q1/68 , C07H21/02
CPC分类号： C07K14/245
摘要： The entire genome of pathogenic E. coli strain 0157:H7 has been sequenced. All of the genomic DNA sequences present in 0157 and absent in the previously sequenced laboratory strain K12 are presented here.
摘要翻译：病原性大肠杆菌菌株0157：H7的整个基因组已被测序。存在于0157中的所有基因组DNA序列和在先前测序的实验室菌株K12中不存在。

4. 发明授权

US06649402B2 Microfabricated microbial growth assay method and apparatus 有权
公开(公告)号：US06649402B2
公开(公告)日：2003-11-18
申请号：US09887647
申请日：2001-06-22
申请人： Daniel W. Van der Weide , Frederick R. Blattner
发明人： Daniel W. Van der Weide , Frederick R. Blattner
IPC分类号： C12M134
CPC分类号： C12M23/12 , C12M23/20 , C12M23/22 , C12M41/36
摘要： Microbial growth assays are carried out utilizing assay apparatus having a base plate with a plurality of microbial growth assay wells, each well having a liquid content of 30 &mgr;l or less. Electrodes are coupled together through the wells and electrical connectors are connected to the electrodes to allow the effect of the content of the wells to be measured by measuring the capacitance or resistance or both between the electrodes at each well, with the change in the capacitance or resistance in each well over time being correlated with the extent of growth of a bacterium introduced into the well with a growth medium. The small size of the microwells causes the growth of bacteria in the well to quickly show a change in the electrical properties of the well, particularly in the capacitance or resistance between the electrodes at each well, with growth to saturation occurring for common bacteria such as E. coli in a few hours or less. High density base plates may be tested with a large variety of substances that may have an effect on the growth of the bacteria in the well over a relatively short period of time, allowing high throughput while maintaining the accuracy of the test.

5. 发明授权

US06223128B1 DNA sequence assembly system 失效
标题翻译： DNA序列组装系统
公开(公告)号：US06223128B1
公开(公告)日：2001-04-24
申请号：US09106370
申请日：1998-06-29
申请人： Carolyn F. Allex , Jude W Shavlik , Frederick R. Blattner
发明人： Carolyn F. Allex , Jude W Shavlik , Frederick R. Blattner
IPC分类号： G01N3348
CPC分类号： G06F19/22
摘要： A computerized method is described for assembling DNA sequence determined for small DNA fragments, called fragment reads, into larger fragments of DNA sequence called contigs. The method used makes a table of occurrences or counts for each mer appearing in any of the fragment reads and then picks from among those mers specific mers to use as mer tags. Following checking, the mer tags are used to assemble fragment reads into contigs. A feature of this method is that the processing time necessary to perform this process on a computer varies linearly with the number of fragment reads rather than with the square or cube of the number of fragment reads.
摘要翻译：描述了一种计算机化方法，用于将针对称为片段读取的小DNA片段确定的DNA序列组装成称为重叠群的DNA序列的更大片段。所使用的方法使得在每个片段读取中出现的每个词典的出现或计数表，然后从这些特定的词典中选择用作mer标签。检查之后，mer标签用于将片段读取组合到重叠群中。该方法的一个特点是在计算机上执行此过程所需的处理时间与片段读取次数呈线性关系，而不是片段读取次数的平方或立方。

6. 发明授权

US5525515A Process of handling liquids in an automated liquid handling apparatus 失效
标题翻译：在自动化液体处理设备中处理液体的过程
公开(公告)号：US5525515A
公开(公告)日：1996-06-11
申请号：US284018
申请日：1994-08-01
申请人： Frederick R. Blattner
发明人： Frederick R. Blattner
IPC分类号： B01L3/02 , G01N35/10 , G01N35/02
CPC分类号： B01L3/0241 , G01N35/1004 , B01L2400/021 , Y10T436/114998 , Y10T436/119163 , Y10T436/2575
摘要： A fluid delivery device which delivers microliter and sub-microliter volumes by means of a reciprocating force mechanism requires no capillary contact between the delivery system and work surface. Furthermore, a built-in vacuum-based rinse station permits the user to dispense a variety of fluids while avoiding complex and time consuming changes to the fluid delivery system.
摘要翻译：通过往复力机构传送微升和亚微升体积的流体输送装置不需要输送系统和工作表面之间的毛细管接触。此外，内置的基于真空的冲洗台允许用户分配各种流体，同时避免流体输送系统的复杂和耗时的变化。

7. 发明授权

US4771384A System and method for fragmentation mapping 失效
标题翻译：碎片映射的系统和方法
公开(公告)号：US4771384A
公开(公告)日：1988-09-13
申请号：US889981
申请日：1986-07-24
申请人： Donna L. Daniels , John L. Schroeder , Frederick R. Blattner , Michael Waterman
发明人： Donna L. Daniels , John L. Schroeder , Frederick R. Blattner , Michael Waterman
IPC分类号： C12Q1/68 , G01N27/447 , G06G7/58
CPC分类号： C12Q1/683 , G01N27/44717
摘要： A system and method for the construction of one-dimensional maps from fragmentation data is disclosed. Particularly useful for construction of restriction maps of DNA, the system and method completely permutes sites, single digest fragments, and any available multiple digest fragments, and displays maps in rank-order according to a quality factor. Display of constructed maps includes information about relative ordering of all fragments, sites, and particularly about closely-spaced sites and fragments.
摘要翻译：公开了一种从碎片数据构建一维地图的系统和方法。特别适用于DNA限制图的构建，系统和方法完全排列位点，单个摘要片段和任何可用的多个摘要片段，并根据品质因子按等级顺序显示地图。显示构造的地图包括有关所有片段，站点的相关顺序的信息，特别是关于紧密间隔的站点和碎片的信息。

8. 发明授权

US08178339B2 Reduced genome E. coli 有权
标题翻译：减少基因组大肠杆菌
公开(公告)号：US08178339B2
公开(公告)日：2012-05-15
申请号：US12064332
申请日：2006-08-18
申请人： John W Campbell , Frederick R. Blattner , Guy Plunkett , Gyorgy Posfai
发明人： John W Campbell , Frederick R. Blattner , Guy Plunkett , Gyorgy Posfai
IPC分类号： C12P21/04 , C12P19/34 , C12N1/20
CPC分类号： C12N1/20 , C12P19/34 , C12P21/00 , C12R1/19
摘要： Reduced genome strains of E. coli MG1655 are described. In various embodiments, the strains have one or more of equal or improved growth rate, transformation efficiency, protein expression, DNA production, DNA yield and/or DNA quality compared to the parental strain and commercially available strains.
摘要翻译：描述了大肠杆菌MG1655的减少的基因组菌株。在各种实施方案中，与亲本菌株和市售菌株相比，菌株具有相同或改善的生长速率，转化效率，蛋白质表达，DNA产生，DNA产量和/或DNA质量的一种或多种。

9. 发明授权

US07989181B2 Methods and compositions for producing recombinant proteins using a gene for TRNA 有权
标题翻译：使用TRNA基因生产重组蛋白的方法和组合物
公开(公告)号：US07989181B2
公开(公告)日：2011-08-02
申请号：US12294369
申请日：2007-04-23
申请人： Frederick R. Blattner , John Walter Campbell , Guy Plunkett
发明人： Frederick R. Blattner , John Walter Campbell , Guy Plunkett
IPC分类号： C12P21/04 , C12N5/10 , C12N1/20 , C12N1/19
CPC分类号： C12P21/02 , C12N15/11
摘要： The invention relates to host cells with improved protein expressed properties. The host cells comprise rare tRNA genes within the one or more rRNA operons.
摘要翻译：本发明涉及具有改进的蛋白质表达特性的宿主细胞。宿主细胞在一个或多个rRNA操纵子内包含罕见的tRNA基因。

10. 发明申请

US20110165680A1 CLEAN GENOME BACTOFECTION 审中-公开
标题翻译：清洁基因组细菌
公开(公告)号：US20110165680A1
公开(公告)日：2011-07-07
申请号：US13063450
申请日：2009-09-14
申请人： Frederick R. Blattner , Val Burland , Charles Landy , Nian-Qing Shi , Buffy Stahl
发明人： Frederick R. Blattner , Val Burland , Charles Landy , Nian-Qing Shi , Buffy Stahl
IPC分类号： C12N15/85 , C12N1/21 , C07H21/04 , C12N15/63 , C07K14/00
CPC分类号： C12N15/70 , A61K39/00 , C12N15/79 , Y02A50/403 , Y02A50/476
摘要： Methods for introducing and expressing genes in animal cells are provided comprising infecting the animal cells with live invasive reduced-genome bacteria comprising a eukaryotic expression cassette comprising said gene. Also provided are methods for producing a pluripotent stem (iPS) cell from a mammalian somatic cell comprising infecting the somatic cell with live invasive reduced-genome bacteria comprising one or more eukaryotic expression cassettes comprising at least a gene encoding the transcription factor Oct3/4 and a gene encoding a member of the SRY-related HMG-box (Sox) transcription factor family.
摘要翻译：提供了用于在动物细胞中引入和表达基因的方法，包括用包含所述基因的真核表达盒的活侵入性还原基因组细菌感染动物细胞。还提供了用于从哺乳动物体细胞产生多能茎（iPS）细胞的方法，包括用活侵入性减少基因组细菌感染体细胞，所述活体减少基因组细菌包含至少包含编码转录因子Oct3 / 4的基因的一个或多个真核表达盒，编码SRY相关HMG盒（Sox）转录因子家族成员的基因。

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