Team:Paris Liliane Bettencourt

From 2010.igem.org

(Difference between revisions)
(→Major achievements)
 
(55 intermediate revisions not shown)
Line 1: Line 1:
-
<span/ id="bottom">[https://2010.igem.org/ iGEM ] > [[Team:Paris_Liliane_Bettencourt#top | Paris]] > [[Team:Paris_Liliane_Bettencourt#top | Home]] > [[Team:Paris_Liliane_Bettencourts#bottom | Synopsis]]
+
{{Template:paris2010_2}}
-
{{Template:Paris2010}}
+
-
{{Template:Paris2010_menu}}
+
-
 
+
-
==Memo-Cell==
+
 +
==Summary==
<html>
<html>
-
<style type="text/css">
+
<p style="display:block;">
-
a.bloc {
+
-
    display:block;  
+
-
    height:100%
+
-
}
+
-
}
+
-
</style>
+
-
</html>
+
-
===Abstract===
+
<br>''Counting'' is the action of finding the number of elements in a set.  Past attempts at developing counters in cells have mostly attempted to mimic the binary methods that computers use to count. Our first counter takes a new approach to counting in cells, essentially using a mechanical rotary counter implemented on a micro scale.  Each time the counter detects an input, it performs an excision and an integration directly down-stream of the active site, turning on a reporter and rotating over one "notch" on the counter.
 +
<br /><br />
 +
Our second counter operates on the wholly different principle that the statistical occurrence of a rare event in a large population can be modeled and experimentally verified.  Each cell in our population harbors a construct that when stimulated has a small chance of excising a terminator and expressing a reporter gene which creates cells with a distinctive phenotype.  The number of these cells is thus an accurate count of the number of input stimuli. <br>
-
<br>Counting is the action of finding the number of elements in a set.  Counting is a basic operation in electronic circuitry accomplished by the use of flip-flops, which are a type of digital device that has two stable states and can act as a single “bit” of memory for a counter.
+
<center>
-
<br><br>Early efforts by synthetic biologists have shown that implementing this type of counter in cells is not easy.  Since components in a cell are not strictly sequestered in the manner of electronic circuits, and since the cell signalling channels often interfere with each other in ways that are difficult to predict, digital methods seem like a problematic way to count in cells.
+
<br><a href="https://2010.igem.org/Team:Paris_Liliane_Bettencourt/Project/Memo-cell"><img src="https://static.igem.org/mediawiki/2010/a/aa/Memo_cell-01.jpg" width="129" height="107" title="Memo-Cell"></a><a href="https://2010.igem.org/Team:Paris_Liliane_Bettencourt/Project/Population_counter"><img src="https://static.igem.org/mediawiki/2010/9/93/Pop_counter_logo-01.jpg" width="129" height="107" title="Population Counter"><br></a></center>
-
<br><br>When looking to nature for inspiration, one finds mostly circuits that don’t actually count in a strict sense, but instead act as “threshold detectors” that cause something to happen after a certain threshold has been reached. Cell aggregation, telomere length regulation, and quorum sensing all fall under this category of device.
+
-
<br>The method of counting in our project is capable both of true counting and of threshold detection, and is more similar to the mechanical counters invented in the late 19th century than to any digital circuit.
+
-
<br><br>Our main project is designed to count on a cellular level. The cells include plasmids in their genome in a such way that the integration is sequential and controlled by a pulse of an input molecule. One pulse induces one integration. The integration is performed by an integrase which permits to integrate the whole plasmid in the genome. The plasmid carries one transposition site and one half of the integration site. The other half of the integration site and the second transposition site are present in the genome in multiple copies. When the plasmid is integrated both transposition sites are on the chromosome and the transposase cans excise the sequence in between. This creates a new full integration site and another plasmid can be integrated in response to the next input. The number of integrated sequences corresponds to the number of inductions and this number can be checked by PCR, which creates a counter.
+
-
This event recorder can also play the role of a timer thanks to a reporter gene placed after a predetermined number of integration sites. A screening system permits to kill the cells that don’t count correctly.
+
-
<br><br>Our second project is based on the capacity to make rare events happen in a number of cells of a population and the possibility to communicate. At each induction a few cells excise a terminator thanks to an integron. This excision provokes the expression of an antibiotic resistance downstream of a constitutive promoter. The proportion of resistant cells in the population reflects the number of induction pulses, which creates an event counter. At the same time, the induced cells express LuxI downstream of the constitutive promoter. When the proportion of induced cells reaches a certain level and the concentration of AHL exceeds a threshold the whole population starts expressing GFP, which creates a timer. To be able to count correctly, we have to control the conditions and wash away AHL from previous induction to produce a step function of its concentration. So we decided to use a microfluidic chemostat.
+
-
[[Image:populationcounter.pdf]]
+
<br>
-
[https://igem.org/Team.cgi?year=2010&team_name=Paris_Liliane_Bettencourt Team official Page]
+
As part of the joy of the iGEM competition is actually winning, we have worked out an algorithm based on semantic analysis of past years' wikis that selects and visualises automatically keywords unique to each team. This can be extended in the future to aid in automated analysis of past winners, as well as many other metrics about a given team.
-
{{Template:Paris2010_guided2|#prev|#next}}
+
-
<!-- You can open a new frame, with adding this "header"
+
<br><br> Last but not least... We made major contributions to the nascent SynBioWorld collaborative web platform that aims at building a universal site for  the synthetic biology community as a place to meet, talk, share data and resources, and stay abreast of new developments in the field. <br><br>
-
<html>
+
<center>
-
</div>
+
<a href="https://2010.igem.org/Team:Paris_Liliane_Bettencourt/Project/Synbioworld">
-
<div id="paris_content">
+
<img src="https://static.igem.org/mediawiki/2010/2/25/SBW.jpg" width="129" height="107"  title="SynBioWorld">
 +
</a>
 +
<a href="https://2010.igem.org/Team:Paris_Liliane_Bettencourt/Project/SIP">
 +
<img src="https://static.igem.org/mediawiki/2010/4/4c/SIP.png" width="132" height="107"  title="SIP">
 +
</a></center></html><br>
 +
==Major achievements==
 +
<html><p style="display:block;">
 +
<br><u>These are our major achievements</u>
</html>
</html>
-
== A second Frame ==
+
* We designed two different types of counter and timer.
 +
* We managed to go beyond the concept and genetically constructed systems that let us test these devices and make a proof of concept.
 +
<br>Specifically:
 +
* <b>Our bacteria count to 2! Nothing stops them from counting more.</b>
 +
* We have shown that the IntI1 integrase can perform specific excision of a site flanked by two attC sites in response to an arabinose pulse down to 120 minutes.
 +
* We have shown that our mutated designed IntLambda/IntHK022 system is able to integrate DNA fragments into the chromosome in a sequential way with high efficiency (74%-100%).
 +
* We designed, cloned and proved the efficiency of the Tn916 transposase.
 +
* We designed and cloned the smallest bacterial death gene, microcinA (8 amino acids) that serves as a new way of negatively selecting clones.
 +
<br>* We modeled the population counter that demonstrates the feasibility of our counter and timer approach.
 +
* We fabricated and tested a microfluidic chemostat.
 +
* We contributed to the birth of the first online community of synthetic biology lead by students (with collaborators from UCSF and PKU teams)
 +
* We've made the first steps of using automated semantic analysis algorithm to analyse objectively iGEM wikis.
 +
* We have learned a lot during iGEM
 +
</p>
-
=== Hello World ! ===
 
-
Nice frame, isn't it ?
+
</p>
-
 
+
-
-- Just in example -->
+
<html>
<html>
 +
</div>
</div>
</div>
</html>
</html>

Latest revision as of 03:58, 28 October 2010


Summary


''Counting'' is the action of finding the number of elements in a set. Past attempts at developing counters in cells have mostly attempted to mimic the binary methods that computers use to count. Our first counter takes a new approach to counting in cells, essentially using a mechanical rotary counter implemented on a micro scale. Each time the counter detects an input, it performs an excision and an integration directly down-stream of the active site, turning on a reporter and rotating over one "notch" on the counter.

Our second counter operates on the wholly different principle that the statistical occurrence of a rare event in a large population can be modeled and experimentally verified. Each cell in our population harbors a construct that when stimulated has a small chance of excising a terminator and expressing a reporter gene which creates cells with a distinctive phenotype. The number of these cells is thus an accurate count of the number of input stimuli.




As part of the joy of the iGEM competition is actually winning, we have worked out an algorithm based on semantic analysis of past years' wikis that selects and visualises automatically keywords unique to each team. This can be extended in the future to aid in automated analysis of past winners, as well as many other metrics about a given team.

Last but not least... We made major contributions to the nascent SynBioWorld collaborative web platform that aims at building a universal site for the synthetic biology community as a place to meet, talk, share data and resources, and stay abreast of new developments in the field.


Major achievements


These are our major achievements

  • We designed two different types of counter and timer.
  • We managed to go beyond the concept and genetically constructed systems that let us test these devices and make a proof of concept.


Specifically:

  • Our bacteria count to 2! Nothing stops them from counting more.
  • We have shown that the IntI1 integrase can perform specific excision of a site flanked by two attC sites in response to an arabinose pulse down to 120 minutes.
  • We have shown that our mutated designed IntLambda/IntHK022 system is able to integrate DNA fragments into the chromosome in a sequential way with high efficiency (74%-100%).
  • We designed, cloned and proved the efficiency of the Tn916 transposase.
  • We designed and cloned the smallest bacterial death gene, microcinA (8 amino acids) that serves as a new way of negatively selecting clones.


* We modeled the population counter that demonstrates the feasibility of our counter and timer approach.

  • We fabricated and tested a microfluidic chemostat.
  • We contributed to the birth of the first online community of synthetic biology lead by students (with collaborators from UCSF and PKU teams)
  • We've made the first steps of using automated semantic analysis algorithm to analyse objectively iGEM wikis.
  • We have learned a lot during iGEM

</p>


</p>

Retrieved from "http://2010.igem.org/Team:Paris_Liliane_Bettencourt"