Team:Paris Saclay/Project

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=Project=
=Project=
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==Countdown==
 
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This page is under '''Marie''''s responsibility
 
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* Deadline: 08/oct.
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In the beginning of our reflection to choose a project, we had a lot of ideas in health, water treatment, and anti-fouling but for each we always raised the same issue: Can we do whatever with genetically modified organisms?
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** General introduction of the project.
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These recurring issues '''get us to think about deeper ethical questions'''. In effect, synthetic biologists modify living organisms in order to perform specific functions like a machine, as illustrated in the word "iGEM." But we wonder if these modified organisms are really machines. So our main interrogation was to '''know how synthetic biology blurs the limits of living beings or if synthetic biology can change our definition of natural/artificial life'''. Would everybody have the same limit or criteria to define if a life is artificial or not? It would definitely depend on the perception that people will have of this unconventional form of life. To rise all our issues, we choose an artistic approach and in particular a '''Bio-Art approach'''. As art is accessible to everybody, we believe that this is the best way to reach the general public and allow them to introspect. Our piece will play with the perception of things by '''recreating a living lemon''' tree. We use synthetic biology to design a lemon, a bacterial lemon, but that will look like a real one: same smell, same shape and color, and that will slowly change from green to yellow, like a lemon when it ripens. Would you consider our lemon as a fake? Another kind of lemon? This brings us back to our first question on the definition of life, an aspect that we have developed in our Ethics part.
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** Introduction text of each part of the project
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** Sean's video (bettencourt)
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* Deadline: 12/oct
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** Final review par Maher.
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As we use living beings to make art, it raised a lot of other questions: can we modify and/or use living organisms to create a piece of art work? In fact, every time that we debate on this question, within the team or with other iGEMers, scientists or artists, we always arrived at the same critical questions: what is our definition of the living? Do we accept to use every kind of living to do Bio-Art? Is using bacteria the same that as rabbits or humans? And finally the use of Bio-Art nourished our ethical questioning. Art, Science and Ethics are so intricately intertwined.
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==[https://2014.igem.org/Team:Paris_Saclay/Project/Inspirations Inspirations]==
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Food is essential to our lives and is filled with symbolism. With our lemon, we wish that the public will '''think about future food''' consumption habits. Is synthetic food the future? Will this lemon be found in your fridge one day?
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==Video==
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In a collaboration with iGEM Paris-Bettencourt team in our [https://2014.igem.org/Team:Paris_Saclay/Project/Workshop iGEM French Meeting], we made a video to introduce the project.
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<html><div style="width:560px; margin:0 auto;"><iframe width="560" height="315" src="//www.youtube.com/embed/oYY6H_yvft0" frameborder="0" allowfullscreen></iframe></div></html>
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==[https://2014.igem.org/Team:Paris_Saclay/Project/Inspirations Inspirations]==
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==[https://2014.igem.org/Team:Paris_Saclay/Project/Odor-free_ecoli A - The ''E. coli'' odor free chassis]==
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The question of living-being's representation reminded us Magritte's work. But our inspirations came from others artistic works. Indeed, the idea of our project is fully referenced. In this section we described how these artists and their concepts help us to build and design our project.
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''Escherichia coli'' stinks because of the ''tnaA'' gene which produces an enzyme that transforms the L-tryptophan into indole, responsible for the stench. If we want our lemon to smell like one, we have to delete this gene.
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In the lab, we already had a strain in which the tnaA was replaced by a kanamycin resistance, but this strain was too modified to be used for our project. So we switched the tnaA sequence with the kanamycin resistance in our bacterium by phage transduction. After the recombination, we used a flipase to delete the kanamycin resistance. The remaining bacterium doesn't smell at all.
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== Scientific part==
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Our project is based on the construction of a bacterial lemon that will look like lemon but made only of ''Escherichia coli'' modified to produce a lemon scent and to change colour from green to yellow. We will achieve our project by genetically modifying ''Escherichia coli'' to be devoid of any unpleasant odour by deleting the genes involved in ''E. coli'''s odor, by introducing  genes for the production of the lemon scent and finally by adding a yellow-blue chromoprotein whose expression is controlled by a tRNA suppressor for the colour switching.
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==[https://2014.igem.org/Team:Paris_Saclay/Project/Lemon_Scent B - The Lemon Scent]==
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===[https://2014.igem.org/Team:Paris_Saclay/Project/Odor-free_ecoli  Remove the bad smell of ''E. coli'']===
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The aim is to make three different populations of ''E.coli''.
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Our lemon should smell like a lemon. Our chassis is ''Escherichia coli'' , a bacterium known to have a foul odor. We thus have to remove the genes involved in this particular phenotype. The ''tnaA'' gene is required for the degradation of tryptophan into indole, the main molecule at the origin of ''E. coli'' smell. We use a phage transduction method to reach our goal.
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# The first is transformed with a plasmid that contains the limonene synthase gene
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===[https://2014.igem.org/Team:Paris_Saclay/Project/Lemon_Scent Lemon Scent]===
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# The second is transformed with a plasmid that contains the β-pinene synthase gene
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The particular odor of lemon is mainly due to 3 monoterpenes: limonene, beta-pinene and geranial. We will clone the 3 monoterpene synthases responsible for the production of these 3 molecules into our bacteria to allow them to produce this fragrance. We will also improve the production of the GPP precursor using a synthetic mevalonate pathway using the construction of the team of T. S. Lee.
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# The third is transformed with a plasmid that contains the geraniol synthase gene and the CAD gene to increase citral A and B production by the bacteria
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We could thus play with the density of these populations for a better lemon scent, like cooking, putting the right quantity of each ingredient.
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===[https://2014.igem.org/Team:Paris_Saclay/Project/Salicylate_Inducible_System Lemon appearance and Ripening]===
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Since vision is one of the most important senses in humans, we want the lemon to look as real as possible. To achieve this, we plan to make our lemon look green or yellow, like a real one. Furthermore, we also want to simulate the ripening process of the lemon by changing its color gradually from green to yellow.
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Don't worry more explanation will be there soon (melanie)
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==Artistic Part==
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===[https://2014.igem.org/Team:Paris_Saclay/Project/Lemon_Shaping Lemon Shaping]===
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The lemon fragrance contains mainly three different monoterpene components as citral (also called geraniol), limonene and pinene. These components come from the common precursor geranyldiphosphate (GPP). In E.coli, we would like to produce these monoterpene improving the GPP level by an additional plasmid containing a MVA-pathway from others species. Finally, we would cloned the enzyme required to generate monoterpene as limonene synthase, pinene synthase and geraniol synthase.
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1st  idea
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==[https://2014.igem.org/Team:Paris_Saclay/Project/Salicylate_Inducible_System C - Lemon Appearance and Ripening]==
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We basically wanted to build up a lemon tree in which one we would have put lemons we had made. As lemons pass from green to yellow, we would have simulated the season’s cycle.
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In nature, a lemon is firstly green and becomes yellow after some month. We would like to follow this ripeness transforming our lemon from green to yellow. In order to make our lemon looks green and having reported that there is no green chromoprotein in the RFC, we would like to fuse a yellow chromoprotein with a blue one separated by a linker containing two amber stop codon. Thus, the expression of a tRNA suppressor would suppress amber stop codon and allow the translation of the yellow and blue fusion chromoprotein, hopefully resulting in a green chromoprotein. Then, in the absence of the tRNA suppressor, only the yellow chromoprotein would be translated, allowing our lemon to switch from green to yellow.
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===Boston Installation===
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The aim of this section is to simulate appearance of a lemon and its ripening process by:
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2nd  idea
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1- making bacteria display a green color. This part required the design of a green chromoprotein.
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The idea was to project the shadow of a little sculpture in a screen or a wall: the positioning of the light with respect to the sculpture would have enabled the creation of shadow ten times bigger than the sculpture itself. The aim of this structure would have been to show the gap between a object and its image, between real things and decoys.
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2- making bacteria change its color gradually from green to yellow through time. This part required the design of a color switch system.
 
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==[https://2014.igem.org/Team:Paris_Saclay/Project/Lemon_Shaping D - The Lemon Shaping]==
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3rd  idea (chosen for Boston)
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==[https://2014.igem.org/Team:Paris_Saclay/Project/Workshop The Workshop]==
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Finally we decided to modify the second idea (for logistic reasons). The element which could this time reveal the gap between an object and its image, between real things and decoys, would be a mirror …
{{Team:Paris_Saclay/default_footer}}
{{Team:Paris_Saclay/default_footer}}

Latest revision as of 03:51, 18 October 2014

Contents

Project

In the beginning of our reflection to choose a project, we had a lot of ideas in health, water treatment, and anti-fouling but for each we always raised the same issue: Can we do whatever with genetically modified organisms? These recurring issues get us to think about deeper ethical questions. In effect, synthetic biologists modify living organisms in order to perform specific functions like a machine, as illustrated in the word "iGEM." But we wonder if these modified organisms are really machines. So our main interrogation was to know how synthetic biology blurs the limits of living beings or if synthetic biology can change our definition of natural/artificial life. Would everybody have the same limit or criteria to define if a life is artificial or not? It would definitely depend on the perception that people will have of this unconventional form of life. To rise all our issues, we choose an artistic approach and in particular a Bio-Art approach. As art is accessible to everybody, we believe that this is the best way to reach the general public and allow them to introspect. Our piece will play with the perception of things by recreating a living lemon tree. We use synthetic biology to design a lemon, a bacterial lemon, but that will look like a real one: same smell, same shape and color, and that will slowly change from green to yellow, like a lemon when it ripens. Would you consider our lemon as a fake? Another kind of lemon? This brings us back to our first question on the definition of life, an aspect that we have developed in our Ethics part.

As we use living beings to make art, it raised a lot of other questions: can we modify and/or use living organisms to create a piece of art work? In fact, every time that we debate on this question, within the team or with other iGEMers, scientists or artists, we always arrived at the same critical questions: what is our definition of the living? Do we accept to use every kind of living to do Bio-Art? Is using bacteria the same that as rabbits or humans? And finally the use of Bio-Art nourished our ethical questioning. Art, Science and Ethics are so intricately intertwined.

Food is essential to our lives and is filled with symbolism. With our lemon, we wish that the public will think about future food consumption habits. Is synthetic food the future? Will this lemon be found in your fridge one day?

Video

In a collaboration with iGEM Paris-Bettencourt team in our iGEM French Meeting, we made a video to introduce the project.

Inspirations

The question of living-being's representation reminded us Magritte's work. But our inspirations came from others artistic works. Indeed, the idea of our project is fully referenced. In this section we described how these artists and their concepts help us to build and design our project.

Scientific part

Our project is based on the construction of a bacterial lemon that will look like lemon but made only of Escherichia coli modified to produce a lemon scent and to change colour from green to yellow. We will achieve our project by genetically modifying Escherichia coli to be devoid of any unpleasant odour by deleting the genes involved in E. coli's odor, by introducing genes for the production of the lemon scent and finally by adding a yellow-blue chromoprotein whose expression is controlled by a tRNA suppressor for the colour switching.

Remove the bad smell of E. coli

Our lemon should smell like a lemon. Our chassis is Escherichia coli , a bacterium known to have a foul odor. We thus have to remove the genes involved in this particular phenotype. The tnaA gene is required for the degradation of tryptophan into indole, the main molecule at the origin of E. coli smell. We use a phage transduction method to reach our goal.

Lemon Scent

The particular odor of lemon is mainly due to 3 monoterpenes: limonene, beta-pinene and geranial. We will clone the 3 monoterpene synthases responsible for the production of these 3 molecules into our bacteria to allow them to produce this fragrance. We will also improve the production of the GPP precursor using a synthetic mevalonate pathway using the construction of the team of T. S. Lee.

Lemon appearance and Ripening

Since vision is one of the most important senses in humans, we want the lemon to look as real as possible. To achieve this, we plan to make our lemon look green or yellow, like a real one. Furthermore, we also want to simulate the ripening process of the lemon by changing its color gradually from green to yellow.

Artistic Part

Lemon Shaping

1st idea

We basically wanted to build up a lemon tree in which one we would have put lemons we had made. As lemons pass from green to yellow, we would have simulated the season’s cycle.

Boston Installation

2nd idea

The idea was to project the shadow of a little sculpture in a screen or a wall: the positioning of the light with respect to the sculpture would have enabled the creation of shadow ten times bigger than the sculpture itself. The aim of this structure would have been to show the gap between a object and its image, between real things and decoys.


3rd idea (chosen for Boston)

Finally we decided to modify the second idea (for logistic reasons). The element which could this time reveal the gap between an object and its image, between real things and decoys, would be a mirror …