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<title>Test page</title>
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<title>iGEM Amsterdam: Cell Logbook</title>
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<p>Bacterial populations in their natural form are very capable of storing, processing and acting on stimuli in their environment. Why not exploit these properties in the pursuit of massively parallel computation? The first thing one needs when constructing a computing device is memory to store the results onto. In order to meet this demand we present the cellular logbook which is usable to reliably store whether a signal was detected in E. coli's environment for a time span of its life duration. Expanding this straightforward molecular mechanism, multiple signals can be stored with the prospective of storing up to 64 bits on a single plasmid. Complex cellular behaviour can then be programmed according to the memory status of the cell by way of introducing additional modules transcriptionally controlled by the introduced memory plasmid.</p>
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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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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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Latest revision as of 20:23, 27 June 2012

Test page

iGEM Amsterdam: Cell Logbook

1  Introduction

Prokaryotes have been selected through evolutionary processes for accurate sensing and acting upon their living environments. This bacterial versatility can be used by us, humans, to sense the environments in places we have trouble reaching. 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. 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. This however requires constant monitoring and maintenance in order to get an idea of the time-variation of the studied system. Could we make the cell ‘remember’ what it has sensed and when so we can leave it alone for a while and make it report back to us later?

Meet E. memo, a ‘cellular logbook’, 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. E. memo therefore holds great promise as a detect & store–system for experimental and industrial purposes.

Just storing whether certain signals have been sensed by the cell is only half of the story however. The proposed memory mechanism would be a form of volatile memory, of which the traces slowly dissappear as the E. memo-population keeps proliferating. This is because methylation-patterns are not transferred to the progeny in eukaryotes. We can use this our advantage. 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. This way, we won’t just store whether a certain signal has occured; we will also know when it happened.

2  Molecular mechanism

In short, we will introduce a site-specific methyltransferase into the iGEM default chassis organism E. coli, that will only be active/transcribed when the measured signal is encountered by the logbook-cell. The activated methyltransferase will then move over to a plasmid region we’ve termed the bit and append a methyl-group to it. 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. 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.




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