Team:Amsterdam

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<title>iGEM Amsterdam: Cell Logbook</title>
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<h2>Cellular Logbook - A methylation-based reporter system</h2>
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'''Multi-sensing genetic devices''' offer great future perspectives for biotechnology, environmental monitoring and medical diagnostics. In light of this we have created an innovative '''epigenetic DNA-methylation''' based '''detection system''' in <i>E. coli</i>, named '''Cellular Logbook''', that has the potential of simultaneously reporting on significantly more signals than current fluorescence-based systems (eg. GFP). The Cellular Logbook can be used to '''detect (Sensor module) and store (Writer module)''' the presence of '''any compound''' linked to a transcriptional regulator. This system allows for '''offline monitoring''' by functioning as a '''memory module (Writer module)'''. Assessment of the memory status is performed by digesting with restriction endonucleases followed by gel electrophoresis '''(Reader Module)'''. Furthermore, the Cellular Logbook is able to infer the '''time of signal-onset''' or '''signal-intensity''' using the natural dilution of the registered signal’s due to cell division. In shourt our novel epigenetic memory module system could potentially be utilized as a '''mulit-sensor/time indicating platform''' for many groundbreaking technologies and applications (eg. to measure environmental changes such as toxic compounds).
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<H2 CLASS="section"><!--SEC ANCHOR --><A NAME="htoc1">1</A>&#XA0;&#XA0;Introduction</H2><!--SEC END --><P>
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Prokaryotes have been selected through evolutionary processes for accurate sensing and acting upon their living environments.  
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This bacterial versatility can be used by us, humans, to sense the environments in places we have trouble reaching.
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Maybe we would want to measure the conditions (e.g. nutrient availability, toxicity, pathogen presence, light) somewhere deep under the ground, perhaps we would want to non-invasively scan for biomarkers in diseased tissue in our bodies.
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The classical way to make a bacteria tell us whether a certain event has happened is to link it to the transcription of fluorescent proteins.
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This however requires constant monitoring and maintenance in order to get an idea of the time-variation of the studied system.
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Could we make the cell &#X2018;remember&#X2019; <EM>what</EM> it has sensed and <EM>when</EM> so we can leave it alone for a while and make it report back to us later?</P><P>Meet <EM>E. memo</EM>, a &#X2018;cellular logbook&#X2019;, which uses the naturally occurring phenomenon of <B>DNA methylation</B> 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.  
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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.  
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E. memo therefore holds great promise as a detect &amp; store&#X2013;system for experimental and industrial purposes. </P><P>Just storing whether certain signals have been sensed by the cell is only half of the story however.
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The proposed memory mechanism would be a form of <EM>volatile</EM> memory, of which the traces slowly dissappear as the <EM>E. memo</EM>-population keeps proliferating.
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This is because methylation-patterns are not transferred to the progeny in eukaryotes.
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We <EM>can</EM> use this our advantage.
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The most exciting part of our project would be to infer when a signal has been sensed from the percentage of bits that is methylated, which slowly decreases as the cells keep proliferating.
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This way, we won&#X2019;t just store <EM>whether</EM> a certain signal has occured; we will also know <EM>when</EM> it happened.</P><!--TOC section Molecular mechanism-->
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<H2 CLASS="section"><!--SEC ANCHOR --><A NAME="htoc2">2</A>&#XA0;&#XA0;Molecular mechanism</H2><!--SEC END --><P>
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In short, we will introduce a site-specific methyltransferase into the iGEM default <EM>chassis</EM> organism E. coli, that will only be active/transcribed when the measured signal is encountered by the logbook-cell.  
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The activated methyltransferase will then move over to a plasmid region we&#X2019;ve termed the <EM>bit</EM> and append a methyl-group to it.
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By linking the methyltransferase to a Zinc-Finger, its site-specificity is greatly increased, reducing the amount of undesired background methylation events to a minimum.
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Furthermore, by slowing down the cell replication cycle of the cells, we can increase the span of time we can use to do measurements on.</P>
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<h2>Sponsors</h2>
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<a href="http://www.aimms.vu.nl/en/index.asp"><img src="https://static.igem.org/mediawiki/2012/1/12/Amsterdam_Logo_AIMMS.png" height="35" align="left" style="padding:10px; padding-top:20px;"></a>
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<a href="http://www.genscript.com/"><img src="https://static.igem.org/mediawiki/2012/6/6e/Amsterdam_Logo_Genscript.jpeg" height="35" align="left" style="padding:10px; padding-top:20px;"></a>
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<a href="http://nbv.kncv.nl/"><img src="https://static.igem.org/mediawiki/2012/8/8e/Amsterdam_Logo_nbv.gif" height="35" align="left" style="padding:10px; padding-top:20px;"></a>
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<a href="http://www.sysbio.nl/"><img src="https://static.igem.org/mediawiki/2012/0/01/Amsterdam_Logo_NISB.png" height="35" align="left" style="padding:10px; padding-top:20px;"></a>
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<a href="http://www.uva-alumni.nl/page.aspx?pid=460"><img src="https://static.igem.org/mediawiki/2012/3/3f/Amsterdam_Logo_universiteitfonds.png" height="35" align="left" style="padding:10px; padding-top:20px;"></a>
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<a href="http://eu.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/c/c4/Xxidt.png" height="35" align="left" style="padding:10px; padding-top:20px;"></a>
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<a href="http://www.vu.nl/nl/index.asp"><img src="https://static.igem.org/mediawiki/2012/8/81/Amsterdam2012VuLogoHeader.png" height="35" align="left" style="padding:10px; padding-top:20px;"></a>
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Latest revision as of 03:56, 27 September 2012

Cellular Logbook - A methylation-based reporter system

Multi-sensing genetic devices offer great future perspectives for biotechnology, environmental monitoring and medical diagnostics. In light of this we have created an innovative epigenetic DNA-methylation based detection system in E. coli, named Cellular Logbook, that has the potential of simultaneously reporting on significantly more signals than current fluorescence-based systems (eg. GFP). The Cellular Logbook can be used to detect (Sensor module) and store (Writer module) the presence of any compound linked to a transcriptional regulator. This system allows for offline monitoring by functioning as a memory module (Writer module). Assessment of the memory status is performed by digesting with restriction endonucleases followed by gel electrophoresis (Reader Module). Furthermore, the Cellular Logbook is able to infer the time of signal-onset or signal-intensity using the natural dilution of the registered signal’s due to cell division. In shourt our novel epigenetic memory module system could potentially be utilized as a mulit-sensor/time indicating platform for many groundbreaking technologies and applications (eg. to measure environmental changes such as toxic compounds).

Sponsors

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