Team:Amsterdam

From 2012.igem.org

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<h1>The Cellular Logbook</h1>
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{| style="color: black; background-color: #004083;" width="100%" class="wikitable" | colspan="1" |
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<p>A Prokaryotes have been selected through evolutionary processes for accurate sensing
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| <font color=black size=5><center>Abstract</center></font>
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and acting upon their living environments. This bacterial versatility can be used by
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| style="width: 100%;"| <font color=black size=5><center>Medal requirements</center></font>
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us, humans, to sense the environments in places we have trouble reaching. Maybe we
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would want to measure the conditions (e.g. nutrient availability, toxicity, pathogen
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| style="width: 50%; background-color: white; text-align: justify;"|
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presence, light) somewhere deep under the ground, perhaps we would want to noninvasively
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Meet '''The Cellular Logbook''', a methylation based memory module which uses the naturally occurring phenomenon
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scan for biomarkers in diseased tissue in our bodies. The classical way
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of '''DNA methylation''' to robustly store signals it has sensed in its environment. The
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to make a bacteria tell us whether a certain event has happened is to link it to the
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transcription of fluorescent proteins. This however requires constant monitoring and
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maintenance in order to get an idea of the time-variation of the studied system. Could
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we make the cell ‘remember’ what it has sensed and when so we can leave it alone for a
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while and make it report back to us later?</p>
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<p>Meet E. memo, a ‘cellular logbook’, which uses the naturally occurring phenomenon
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of <b>DNA methylation</b> to robustly store signals it has sensed in its environment. The
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Amsterdam iGEM 2012 team, consisting of six students, will dedicate the summer to
Amsterdam iGEM 2012 team, consisting of six students, will dedicate the summer to
the realization of this innovative and ambitious plan. This novel storage mechanism,
the realization of this innovative and ambitious plan. This novel storage mechanism,
redesignating an evolutionarly designed tested and proven principle for novel purposes,
redesignating an evolutionarly designed tested and proven principle for novel purposes,
could be linked to any of the many biological sensors that are available in the DNA
could be linked to any of the many biological sensors that are available in the DNA
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parts registry. E. memo therefore holds great promise as a detect & store–system for
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parts registry. The Cellular Logbook therefore holds great promise as a detect & store–system for
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experimental and industrial purposes.</p>
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experimental and industrial purposes.
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<p>Just storing whether certain signals have been sensed by the cell is only half of the story
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however. The proposed memory mechanism would be a form of volatile memory,
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[[File:Amsterdam_thumbs_up.gif|20px]] <font color="#8C7853">[https://igem.org/Team.cgi?id=874 <font color="#8C7853">Team registration</font>]<br\>
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of which the traces slowly dissappear as the E. memo-population keeps proliferating.
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[[File:Amsterdam_thumbs_down.jpg|20px]] Complete judging form <br\>
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This is because methylation-patterns are not transferred to the progeny in eukaryotes.
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[[File:Amsterdam_thumbs_up.gif|20px]] [https://2012.igem.org/Team:Amsterdam <font color="#8C7853">Team Wiki</font>]<br\>
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We can use this our advantage. The most exciting part of our project would be to infer
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[[File:Amsterdam_thumbs_down.jpg|20px]] Present a poster and a talk at the iGEM Jamboree <br\>
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when a signal has been sensed from the percentage of bits that is methylated, which
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[[File:Amsterdam_thumbs_down.jpg|20px]] New biobrick <br\></font>
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slowly decreases as the cells keep proliferating. This way, we won’t just store whether
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<font color="#C0C0C0">[[File:Amsterdam_thumbs_down.jpg|20px]] Working biobrick <br\>
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a certain signal has occured; we will also know when it happened.</p>
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[[File:Amsterdam_thumbs_down.jpg|20px]] Biobrick characterization <br\> </font>
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</div>
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<font color="#FFD700">[[File:Amsterdam_thumbs_down.jpg|20px]] Improve an existing biobrick <br\>
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[[File:Amsterdam_thumbs_down.jpg|20px]] Collaboration <br\>
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<div class="content-block">
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[[File:Amsterdam_thumbs_down.jpg|20px]] Human outreach <br\></font>
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<h2>Molecular mechanism</h2>
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In short, we will introduce a site-specific methyltransferase into the iGEM default
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| style="width:50%;"| <font color=black size=5><center>Project</center></font>
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chassis organism E. coli, that will only be active/transcribed when the measured signal
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| style="width:50%;"| <font color=black size=5><center>Modeling</center></font>
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is encountered by the logbook-cell. The activated methyltransferase will then move
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over to a plasmid region we’ve termed the bit and append a methyl-group to it. By
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1
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<font color=black>
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linking the methyltransferase to a Zinc-Finger, its site-specificity is greatly increased,
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[https://2012.igem.org/Team:Amsterdam/project/description Project description]<br\>
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reducing the amount of undesired background methylation events to a minimum.
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[https://2012.igem.org/Team:Amsterdam/project/applications/ Applications]<br\>
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Furthermore, by slowing down the cell replication cycle of the cells, we can increase
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[https://2012.igem.org/Team:Amsterdam/project/FAQ/ Frequently Asked Questions]<br\>
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the span of time we can use to do measurements on.</p>
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[https://2012.igem.org/Team:Amsterdam/project/diary/ Diary]<br\>
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[https://2012.igem.org/Team:Amsterdam/project/protocols/ Protocols]<br\>
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[https://2012.igem.org/Team:Amsterdam/project/flashPOC1 Flash Animation for the Proof of Concept]<br\>
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</font>
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There are no models online yet<br\>
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| style="width:50%;"| <font color=black size=5><center>Tools</center></font>
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| style="width:50%;"| <font color=black size=5><center>Outreach</center></font>
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Plasmid Design Tool: Under production<br\>
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Wiki Editting Tool: Under production<br\>
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[https://2012.igem.org/Team:Amsterdam/safety/questions Safety: questions]<br\>
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[https://2012.igem.org/Team:Amsterdam/safety/components Safety: components]<br\>
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Revision as of 09:55, 14 September 2012

{| style="color: black; background-color: #004083;" width="100%" class="wikitable" | colspan="1" | |
Abstract
 | style="width: 100%;"|
Medal requirements
 |- | style="width: 50%; background-color: white; text-align: justify;"| Meet '''The Cellular Logbook''', a methylation based memory module which uses the naturally occurring phenomenon of '''DNA methylation''' to robustly store signals it has sensed in its environment. The Amsterdam iGEM 2012 team, consisting of six students, will dedicate the summer to the realization of this innovative and ambitious plan. This novel storage mechanism, redesignating an evolutionarly designed tested and proven principle for novel purposes, could be linked to any of the many biological sensors that are available in the DNA parts registry. The Cellular Logbook therefore holds great promise as a detect & store–system for experimental and industrial purposes. | style="width: 50%; background-color: white;"| [[File:Amsterdam_thumbs_up.gif|20px]] [https://igem.org/Team.cgi?id=874 Team registration] [[File:Amsterdam_thumbs_down.jpg|20px]] Complete judging form [[File:Amsterdam_thumbs_up.gif|20px]] [https://2012.igem.org/Team:Amsterdam Team Wiki] [[File:Amsterdam_thumbs_down.jpg|20px]] Present a poster and a talk at the iGEM Jamboree [[File:Amsterdam_thumbs_down.jpg|20px]] New biobrick [[File:Amsterdam_thumbs_down.jpg|20px]] Working biobrick [[File:Amsterdam_thumbs_down.jpg|20px]] Biobrick characterization [[File:Amsterdam_thumbs_down.jpg|20px]] Improve an existing biobrick [[File:Amsterdam_thumbs_down.jpg|20px]] Collaboration [[File:Amsterdam_thumbs_down.jpg|20px]] Human outreach |- | style="width:50%;"|
Project
 | style="width:50%;"|
Modeling
 |- | style="width:50; background-color:white;"| [https://2012.igem.org/Team:Amsterdam/project/description Project description] [https://2012.igem.org/Team:Amsterdam/project/applications/ Applications] [https://2012.igem.org/Team:Amsterdam/project/FAQ/ Frequently Asked Questions] [https://2012.igem.org/Team:Amsterdam/project/diary/ Diary] [https://2012.igem.org/Team:Amsterdam/project/protocols/ Protocols] [https://2012.igem.org/Team:Amsterdam/project/flashPOC1 Flash Animation for the Proof of Concept] | style="width:50; background-color:white;"| There are no models online yet |- | style="width:50%;"|
Tools
 | style="width:50%;"|
Outreach
 |- | style="width:50; background-color:white;"| Plasmid Design Tool: Under production Wiki Editting Tool: Under production | style="width:50; background-color:white;"| [https://2012.igem.org/Team:Amsterdam/safety/questions Safety: questions] [https://2012.igem.org/Team:Amsterdam/safety/components Safety: components] |}

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