User:Maiko Furubayashi/jp

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(おてがるクローニング)
(べんりリンク)
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*[http://www.genscript.com/tools.html Bioinformatics Tools - GenScript]
*[http://www.genscript.com/tools.html Bioinformatics Tools - GenScript]
*[http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Tool&SubPageType=ToolOverview&PageID=11 Agilent Tech Tools and Calculators]
*[http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Tool&SubPageType=ToolOverview&PageID=11 Agilent Tech Tools and Calculators]
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====DNA====
 
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*promoter prediction
 
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**[http://www.fruitfly.org/seq_tools/promoter.html BDGP: Neural Network Promoter Prediction]
 
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**[http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb BPROM: prediction of bacterial promoters]
 
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*[https://salis.psu.edu/software/ RBS calculator v1.1 from Salis Lab]
 
====たんぱく====
====たんぱく====
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*[http://www16.plala.or.jp/x-tomo/ OSX Freewares]
*[http://www16.plala.or.jp/x-tomo/ OSX Freewares]
*DNA配列編集等
*DNA配列編集等
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**[http://www.geneious.com/ Geneious]
+
**'''[http://www.geneious.com/ Geneious]'''
**[http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE: A plasmid Editor]
**[http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE: A plasmid Editor]
**[http://www.mekentosj.com/ mekentosj] : EnzymeX, 4Peaks
**[http://www.mekentosj.com/ mekentosj] : EnzymeX, 4Peaks
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*http://mkweb.bcgsc.ca/
*http://mkweb.bcgsc.ca/
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===文献管理/SBM===
 
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*[http://www.readcube.com/ readcube] freeware!
 
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*[http://www.mekentosj.com/ mekentosj] Papers (shareware)
 
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*[http://www.mendeley.com Mendeley] (freeware)
 
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*[http://www.citeulike.org/ CiteULike]
 
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*[http://www.connotea.org/ Connotea]
 
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*[http://www.zotero.org/ Zotero] (Firefox plugin)
 
| <!-- ################## 右 ################## -->
| <!-- ################## 右 ################## -->
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*[http://www.keckfutures.org/conferences/synthetic-biology.html National Academies Keck Futures Initiative - synthetic biology]
*[http://www.keckfutures.org/conferences/synthetic-biology.html National Academies Keck Futures Initiative - synthetic biology]
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===いきたい===
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===文献管理/SBM===
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*[http://www.grc.org/programs.aspx?year=2012&program=enzymes GRC - Enzymes, Coenzymes & Metabolic Pathways]
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*[http://www.mekentosj.com/ mekentosj] Papers (shareware)
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*[http://www.engconfintl.org/12ay.html ECI - Metabolic Engineering IX]
+
*[http://www.readcube.com/ readcube] freeware
-
 
+
*[http://www.mendeley.com Mendeley] (freeware)
 +
*[http://www.citeulike.org/ CiteULike]
 +
*[http://www.connotea.org/ Connotea]  
 +
*[http://www.zotero.org/ Zotero] (Firefox plugin)
|}
|}
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 +
==Useful tips/links for DNA construct design==
 +
====Promoter====
 +
*promoter prediction
 +
**[http://www.fruitfly.org/seq_tools/promoter.html BDGP: Neural Network Promoter Prediction]
 +
**[http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb BPROM: prediction of bacterial promoters]
 +
*constitutive promoters
 +
**[http://partsregistry.org/wiki/index.php/Part:BBa_J23100 BBa_J23100-119] from iGEM berkeley 2006 biobricks: -35 to +1 (35bp). minimal and portable
 +
**[http://www.ncbi.nlm.nih.gov/pubmed/20843779 Davis JH 2010 NAR] 15 different e.coli promoters. -105 to +55 (160bp) avoiding UP element affection/promoter escape.
 +
*measuring method: [http://www.jbioleng.org/content/3/1/4 Kelly 2009 JBE]
 +
*natural inducible regulators
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====RBS====
 +
*[https://salis.psu.edu/software/ RBS calculator v1.1 from Salis Lab]
==実験tips==
==実験tips==

Revision as of 09:57, 30 May 2012

English/日本語

古林 真衣子

  • 千葉大学大学院 工学研究科 共生応用化学専攻 博士後期課程1年
  • バイオマテリアル研究室 梅野太輔グループ
  • 日本学術振興会 特別研究員 (DC1)

Contact

  • maiko.furubayashi *at* gmail.com
  • 263-8522 千葉市稲毛区弥生町1-33 千葉大学工学部1号棟313号室


業績

論文・総説

  1. 古林真衣子, 梅野太輔, 代謝ネットワーク建設のための進化分子工学―進化的デザインによる非天然代謝経路の創出―, 植田充美(監修)合成生物工学の隆起 ―有用物質の新たな生産法構築をめざして―, シーエムシー出版 (2012) link
  2. Furubayashi M, Umeno D, Directed Evolution of Carotenoid Synthases for the Production of Unnatural Carotenoids. Methods Mol Biol 892 (2012) link
  3. 古林真衣子, 田代洋平, 梅野太輔, 材料科学のための合成生物学, 未来材料, 10, 2-7 (2010) link
  4. 梅野太輔, 古林真衣子, 三沢典彦, 第3章・カロテノイドの生合成, 宮下和夫(監修)カロテノイドの科学と最新応用技術, シーエムシー出版, pp.27-37 (2009) link
  5. 梅野太輔, 田代洋平, 古林真衣子, 細胞のプログラム死と合成生物学. 極限環境微生物学会誌, 7, 31-35 (2008) link
  6. Tashiro Y, Furubayashi M, Morijiri T, Suzuki K, Yasuno K, Matsuno S, Katabami A, Saito K, Umeno D, Escherichia coli robots that freeze, smell, swell, and time-keep. Synthetic Biology, IET., 1, 41-43 (2007)

特許

  1. 梅野太輔,古林真衣子,三沢典彦,高市真一「炭素数50のカロテノイドの製造方法」特願2011-130326 (2011/6/10)
  2. 梅野太輔,生悦住茉友,古林真衣子,方波見彰仁,斎藤恭一「テルペン合成酵素遺伝子のスクリーニング方法」特願 2009‐264294 (2009/11) / 特開2011-125334 (2011/6/30)

受賞

  1. ○古林真衣子,生悦住茉友,高市真一,斎藤恭一,梅野太輔「人工代謝経路によるC50-β-Caroteneの生合成」日本農芸化学会関東支部 2011年度大会,若手奨励賞(口頭発表・学生部門)
  2. iGEM Chiba,千葉大学 平成18年度課外活動等による学長表彰(コンペ部門)(2007)

べんりリンク

bioinformatics tools

リンク集

たんぱく

フリーソフト


database

よみもの

文献管理/SBM

Useful tips/links for DNA construct design

Promoter

RBS

実験tips


おてがるクローニング

  1. ligation independent cloning (LIC) by T4 dnapol
    1. LIC: C Aslanidis 1990 NAR
    2. SLIC: Li MZ 2007 Nat Meth
  2. ligation independent cloning (LIC) by PCR
    1. Overlap extension PCR cloning: Bryksin AV 2010 BioTechniques
    2. Self-assembly cloning: Matsumoto A 2011 BioTechniques
  3. Type IIS 制限酵素を使って同時に digestion & ligation.
  4. Gibson Assembly

ほか

Personal tools