Team:KULeuven/13 July 2009

From 2009.igem.org

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{{Team:KULeuven/Common/SubMenu_Notebook}}
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{{Team:KULeuven/Notebook/DayNavigator}}
{{Team:KULeuven/Notebook/DayNavigator}}
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= Project progress =
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==A & B (comparator), ideas==
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Key/lock system, see [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain Riboregulators (Berkeley 2006)]
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==Odor synthesis/sensor==
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* Vanillin synthesis: DNA not yet complete/in library [http://partsregistry.org/wiki/index.php/Part:BBa_I742140]
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**Combination of 5 genes; 3 are available
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***[https://2007.igem.org/Edinburgh/Yoghurt/Design#Vanilla_Flavour_Production Edinburgh Vanilla production] (Synthesis pathway by Edinburgh igem 2007)
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** [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17437627#id538997 Vanillin production using metabolically engineered Escherichia coli under non-growing conditions], Ferrulic accid --> Vanillin, 5k bp
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==Light sensor==
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*''YcgF'' Gene, natural available in [http://ecoliwiki.net/colipedia/index.php/ycgF:Gene 3 E. Coli strains]. Can use the promotor of ''YcgF'' gene for expression
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*Probable strain K12
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* Primer of YcgF Promotor:
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**AACAATCCAGGGTAATGGGTGAGGCGAGAGTAAGACGGTAACAGACATATCTTCTTG TGTCTTTCTTTTAATACCAAAACATAACCGTTTCTTTACATTGATAAAAAATGGAAAAAG TTGAACACTAGTTGGCGAAAAATCTTGTATAGATTGTCAGTTAAATGATGCAATATGTT TTATCATAACACATTGTTTTATATGCATTAGCACTAATTGCAAAAAATTAATTTATCATT CTGTACACATATTTCGTACAAGTTTGCTATTGTTACTTCACTTAACATTGATTAACATTTTTAACAGAGGCGTAGC'''ATG''' (bron: [www.ncbi.nlm.nih.gov])
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==Odourless strain of ''E.coli''==
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* [http://openwetware.org/wiki/IGEM:MIT/2006 MIT 2006] used an indoline deficient strain of E.coli: [http://cgsc.biology.yale.edu/Strain.php?ID=64826 YYC912].
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* Knockout of [http://cgsc.biology.yale.edu/Mutation.php?ID=6240 TNAa5-] gene (tryptophanase) in various strains and selected the least 'smelly.'
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=To do=
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* Blue light receptor
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** Decide on ''E.Coli'' strain
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***Try with K12
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***Vector in neural scent (indole knockout)
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**Decide on primers (!Pre + suffix!)
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**PCR of promotor
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**Couple promotor to GFP --> Standard iGEM plasmid
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**Test!
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**Obtain regulation site
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*Vanillin synthesis
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**Send mail to University of Tuscia
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*Presentations
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*Order receptor biobrick
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** {{kulpart|BBa_J58105}}
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** Trg - Env2 {{kulpart|BBa_J58104}}
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**PBP
= Drylab =
= Drylab =
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[http://www.kuleuven.be/rega/mvr/bookmarktsdl.html BioInformatics bookmarks]
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== Wiki ==
== Wiki ==
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* create [[Team:KULeuven/Ideas|Ideas]] page
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* Create [[Team:KULeuven/Ideas|Ideas]] page
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= Wetlab =
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* Some idiot replaced the example logo [[:Image:Example_logo.png]] with his own logo, so all references to it were removed from our wiki
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[[Category:Team:KULeuven/Notebook/Wiki]]
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[[Category:Team:KULeuven/Notebook/Links]]
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<div class='experiment'>
 
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== Experiment Name ==
 
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=== Description ===
 
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=== Elaboration ===
 
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=== Results and conclusions ===
 
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</div>
 
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= Remarks =
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<!-- Don't edit below this line -->
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__NOEDITSECTION__
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= Progress of parts =
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{{Team:KULeuven/EditableTemplateH3|Blue Light Receptor|{{PAGENAME}}/BlueLightReceptor}}
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{{Team:KULeuven/EditableTemplateH3|Vanillin Production|{{PAGENAME}}/VanillinProduction}}
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{{Team:KULeuven/EditableTemplateH3|Vanillin Receptor|{{PAGENAME}}/VanillinReceptor}}
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{{Team:KULeuven/EditableTemplateH3|Key/Lock/Anti-Key|{{PAGENAME}}/KeyLockAntiKey}}
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{{Team:KULeuven/Common2/PageFooter}}

Latest revision as of 08:36, 10 September 2009

Contents

Project progress

A & B (comparator), ideas

Key/lock system, see [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain Riboregulators (Berkeley 2006)]

Odor synthesis/sensor

  • Vanillin synthesis: DNA not yet complete/in library [http://partsregistry.org/wiki/index.php/Part:BBa_I742140]
    • Combination of 5 genes; 3 are available
    • [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17437627#id538997 Vanillin production using metabolically engineered Escherichia coli under non-growing conditions], Ferrulic accid --> Vanillin, 5k bp

Light sensor

  • YcgF Gene, natural available in [http://ecoliwiki.net/colipedia/index.php/ycgF:Gene 3 E. Coli strains]. Can use the promotor of YcgF gene for expression
  • Probable strain K12
  • Primer of YcgF Promotor:
    • AACAATCCAGGGTAATGGGTGAGGCGAGAGTAAGACGGTAACAGACATATCTTCTTG TGTCTTTCTTTTAATACCAAAACATAACCGTTTCTTTACATTGATAAAAAATGGAAAAAG TTGAACACTAGTTGGCGAAAAATCTTGTATAGATTGTCAGTTAAATGATGCAATATGTT TTATCATAACACATTGTTTTATATGCATTAGCACTAATTGCAAAAAATTAATTTATCATT CTGTACACATATTTCGTACAAGTTTGCTATTGTTACTTCACTTAACATTGATTAACATTTTTAACAGAGGCGTAGCATG (bron: [www.ncbi.nlm.nih.gov])

Odourless strain of E.coli

  • [http://openwetware.org/wiki/IGEM:MIT/2006 MIT 2006] used an indoline deficient strain of E.coli: [http://cgsc.biology.yale.edu/Strain.php?ID=64826 YYC912].
  • Knockout of [http://cgsc.biology.yale.edu/Mutation.php?ID=6240 TNAa5-] gene (tryptophanase) in various strains and selected the least 'smelly.'

To do

  • Blue light receptor
    • Decide on E.Coli strain
      • Try with K12
      • Vector in neural scent (indole knockout)
    • Decide on primers (!Pre + suffix!)
    • PCR of promotor
    • Couple promotor to GFP --> Standard iGEM plasmid
    • Test!
    • Obtain regulation site
  • Vanillin synthesis
    • Send mail to University of Tuscia
  • Presentations
  • Order receptor biobrick
    • Trg - Env2
    • PBP

Drylab

[http://www.kuleuven.be/rega/mvr/bookmarktsdl.html BioInformatics bookmarks]

Wiki

  • Create Ideas page
  • Some idiot replaced the example logo Image:Example_logo.png with his own logo, so all references to it were removed from our wiki


Progress of parts

[edit] Blue Light Receptor

  • YcgF Gene, naturally available in [http://ecoliwiki.net/colipedia/index.php/ycgF:Gene 3 E. Coli strains]. Can use the promotor of Ycgf gene for expression
  • Probable strain K12
  • Promotor voor YcgF gene:
    • AACAATCCAGGGTAATGGGTGAGGCGAGAGTAAGACGGTAACAGACATATCTTCTTG TGTCTTTCTTTTAATACCAAAACATAACCGTTTCTTTACATTGATAAAAAATGGAAAAAG TTGAACACTAGTTGGCGAAAAATCTTGTATAGATTGTCAGTTAAATGATGCAATATGTT TTATCATAACACATTGTTTTATATGCATTAGCACTAATTGCAAAAAATTAATTTATCATT CTGTACACATATTTCGTACAAGTTTGCTATTGTTACTTCACTTAACATTGATTAACATTTTTAACAGAGGCGTAGCATG
      (source: [http://www.ncbi.nlm.nih.gov])

[edit] Vanillin Production

  • Vanillin synthesis: DNA not yet complete/in library [http://partsregistry.org/wiki/index.php/Part:BBa_I742140]
    • Combination of 5 genes; 3 are available
    • [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17437627#id538997 Vanillin production using metabolically engineered Escherichia coli under non-growing conditions], Ferulic accid --> Vanillin, 5k bp

[edit] Vanillin Receptor

[edit] Key/Lock/Anti-Key

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