Team:Amsterdam

From 2012.igem.org

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{{Team:Amsterdam/Sidebar1}}
{{Team:Amsterdam/Sidebar1}}
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<p><b>Introduction</b><br>
 
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Prokaryotes have been selected through evolutionary processes for accurate sensing
 
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and acting upon their living environments. This bacterial versatility can be used by
 
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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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presence, light) somewhere deep under the ground, perhaps we would want to noninvasively
 
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scan for biomarkers in diseased tissue in our bodies. The classical way
 
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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?<br><br>
 
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Meet <b>'Me C0l1'</b>, a methylation based celullar log, which uses the naturally occurring phenomenon
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{| style="color: black; background-color: #004083;" width="100%" class="wikitable" | colspan="1" |
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of <b>DNA methylation</b> to robustly store signals it has sensed in its environment. The
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| <font color=black size=5><center>Abstract</center></font>
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| style="width: 100%;"| <font color=black size=5><center>Medal requirements</center></font>
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| style="width: 50%; background-color: white; text-align: justify;"|
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Meet '''The Cellular Logbook''', a methylation based memory module which uses the naturally occurring phenomenon
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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
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.<br><br>
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experimental and industrial purposes.
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| style="width: 50%; background-color: white;"|
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Just storing whether certain signals have been sensed by the cell is only half of the story
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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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however. The proposed memory mechanism would be a form of volatile memory,
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[[File:Amsterdam_thumbs_down.jpg|20px]] Complete judging form <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_up.gif|20px]] [https://2012.igem.org/Team:Amsterdam <font color="#8C7853">Team Wiki</font>]<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_down.jpg|20px]] Present a poster and a talk at the iGEM Jamboree <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]] New biobrick <br\></font>
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when a signal has been sensed from the percentage of bits that is methylated, which
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<font color="#C0C0C0">[[File:Amsterdam_thumbs_down.jpg|20px]] Working biobrick <br\>
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slowly decreases as the cells keep proliferating. This way, we won’t just store whether
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[[File:Amsterdam_thumbs_down.jpg|20px]] Biobrick characterization <br\> </font>
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a certain signal has occured; we will also know when it happened.<br><br>
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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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<b>Molecular mechanism</b><br>
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[[File:Amsterdam_thumbs_down.jpg|20px]] Human outreach <br\></font>
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In short, we will introduce a site-specific methyltransferase into the iGEM default
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|-
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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>Project</center></font>
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is encountered by the logbook-cell. The activated methyltransferase will then move
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| style="width:50%;"| <font color=black size=5><center>Modeling</center></font>
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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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| style="width:50; background-color:white;"|
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linking the methyltransferase to a Zinc-Finger, its site-specificity is greatly increased,
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<font color=black>
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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/description Project description]<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/applications/ Applications]<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/FAQ/ Frequently Asked Questions]<br\>
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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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</font>
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There are no models online yet<br\>
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|-
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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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|}
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{{Team:Amsterdam/Foot}}
{{Team:Amsterdam/Foot}}

Revision as of 11:46, 9 August 2012

Abstract
Medal requirements

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.

Amsterdam thumbs up.gif Team registration
Amsterdam thumbs down.jpg Complete judging form
Amsterdam thumbs up.gif Team Wiki
Amsterdam thumbs down.jpg Present a poster and a talk at the iGEM Jamboree
Amsterdam thumbs down.jpg New biobrick
Amsterdam thumbs down.jpg Working biobrick
Amsterdam thumbs down.jpg Biobrick characterization
Amsterdam thumbs down.jpg Improve an existing biobrick
Amsterdam thumbs down.jpg Collaboration
Amsterdam thumbs down.jpg Human outreach

Project
Modeling

Project description
Applications
Frequently Asked Questions
Diary
Protocols

There are no models online yet

Tools
Outreach

Plasmid Design Tool: Under production
Wiki Editting Tool: Under production

Safety: questions
Safety: components

Retrieved from "http://2012.igem.org/Team:Amsterdam"