Difference between revisions of "Team:Evry Paris-Saclay/Human Practices"
m |
m |
||
| Line 114: | Line 114: | ||
<p style="font-size:15px;">Bacteria communicate through quorum sensing (QS) systems that can be classified into two kinds based on the signalling molecule used: small molecule (AHL) based QS and peptide based QS [1]. When we met Jérôme Bonnet (<font style="color:red;">link to Human Practices</font>), he explained to us that it would be very useful to characterise a number of different orthogonal communication molecules. Since peptides are easier to engineer than small molecules, we decided to focus on a peptide based QS. After we had engineered the system for our chassis of choice (<em>E. coli</em>), we expected to be able to generate several variants of it through directed evolution. | <p style="font-size:15px;">Bacteria communicate through quorum sensing (QS) systems that can be classified into two kinds based on the signalling molecule used: small molecule (AHL) based QS and peptide based QS [1]. When we met Jérôme Bonnet (<font style="color:red;">link to Human Practices</font>), he explained to us that it would be very useful to characterise a number of different orthogonal communication molecules. Since peptides are easier to engineer than small molecules, we decided to focus on a peptide based QS. After we had engineered the system for our chassis of choice (<em>E. coli</em>), we expected to be able to generate several variants of it through directed evolution. | ||
</p> | </p> | ||
| − | <p style="font-size:15px;">In addition, our communication system had to be as orthogonal as possible to avoid crosstalk with other variants of this communication system as well as with other natural | + | <p style="font-size:15px;">In addition, our communication system had to be as orthogonal as possible to avoid crosstalk with other variants of this communication system as well as with other natural communication systems inside the cell. Therefore, we found the “Arbitrium” bacteriophage QS [2] to be a good candidate, since the orthogonality would be better using a bacteriophage system non-native to our bacterium.</p> |
<p style="font-size:15px;">Finally, while using the original “Arbitrium” system, we get a promoter which respond to an activator and a deactivator. Since the activator can be produced constitutively, the system finally looks like a promoter with an inhibitor. This kind of promoter can be really useful for logic gates construction. However, many labs and companies are used to work with promoters which can be activated to induce the production of some compounds, such as LacI/IPTG, pBad/Ara, TetR/tetracycline and LasR/Acyl-homoserine-lactone. Therefore, we decided to switch the system, using the original promoter as a operator for an E. coli promoter. Thus, we developed a promoter which respond to a constitutive inhibitor and a “de-inhibitor”.</p> | <p style="font-size:15px;">Finally, while using the original “Arbitrium” system, we get a promoter which respond to an activator and a deactivator. Since the activator can be produced constitutively, the system finally looks like a promoter with an inhibitor. This kind of promoter can be really useful for logic gates construction. However, many labs and companies are used to work with promoters which can be activated to induce the production of some compounds, such as LacI/IPTG, pBad/Ara, TetR/tetracycline and LasR/Acyl-homoserine-lactone. Therefore, we decided to switch the system, using the original promoter as a operator for an E. coli promoter. Thus, we developed a promoter which respond to a constitutive inhibitor and a “de-inhibitor”.</p> | ||
<h3 style="font-weight:800;">Choosing the chassis</h3> | <h3 style="font-weight:800;">Choosing the chassis</h3> | ||
| − | <p style="font-size:15px;">After we | + | <p style="font-size:15px;">After we identified the “Arbitrium” system, a decision had to be made: which chassis should we use? We initially thought of using <em>B. subtilis</em>, which is the host of the SPbeta bacteriophage group, to characterise a library of orthogonal QS signals. However, our Human Practices research revealed that most labs and companies are working with <em>E. coli</em>. So, we decided to adapt the “Arbitrium” system to fit the <em>E. coli</em> chassis, which as a Gram-negative bacterium does not naturally use a peptide based QS. Once we are able to establish a peptide based QS in <em>E. coli</em>, the characterisation of a library of new QS peptides would become possible.</p> |
<h3 style="font-weight:800;">Popularising the project</h3> | <h3 style="font-weight:800;">Popularising the project</h3> | ||
Revision as of 20:21, 15 October 2018
HUMAN PRACTICES
MEETING WITH PROFESSIONALS
APPLICATIONS
EDUCATION & PUBLIC ENGAGEMENT
https://2018.igem.org/Team:Evry_Paris-Saclay/Public_Engagement
INTEGRATED HUMAN PRACTICES
During our Human Practices research, we quickly realised two things. First, there is a real and pressing need for new bacterial communication systems for researchers. According to this assessment, we have investigated in detail what kind of communication system would fit the most to current research needs and interests. Second, the general public has limited knowledge about biology, which makes it really hard for them to understand a foundational advance project such as ours. Therefore, we decided to make great efforts in educating people about biology and synthetic biology.
Choosing the communication system
Bacteria communicate through quorum sensing (QS) systems that can be classified into two kinds based on the signalling molecule used: small molecule (AHL) based QS and peptide based QS [1]. When we met Jérôme Bonnet (link to Human Practices), he explained to us that it would be very useful to characterise a number of different orthogonal communication molecules. Since peptides are easier to engineer than small molecules, we decided to focus on a peptide based QS. After we had engineered the system for our chassis of choice (E. coli), we expected to be able to generate several variants of it through directed evolution.
In addition, our communication system had to be as orthogonal as possible to avoid crosstalk with other variants of this communication system as well as with other natural communication systems inside the cell. Therefore, we found the “Arbitrium” bacteriophage QS [2] to be a good candidate, since the orthogonality would be better using a bacteriophage system non-native to our bacterium.
Finally, while using the original “Arbitrium” system, we get a promoter which respond to an activator and a deactivator. Since the activator can be produced constitutively, the system finally looks like a promoter with an inhibitor. This kind of promoter can be really useful for logic gates construction. However, many labs and companies are used to work with promoters which can be activated to induce the production of some compounds, such as LacI/IPTG, pBad/Ara, TetR/tetracycline and LasR/Acyl-homoserine-lactone. Therefore, we decided to switch the system, using the original promoter as a operator for an E. coli promoter. Thus, we developed a promoter which respond to a constitutive inhibitor and a “de-inhibitor”.
Choosing the chassis
After we identified the “Arbitrium” system, a decision had to be made: which chassis should we use? We initially thought of using B. subtilis, which is the host of the SPbeta bacteriophage group, to characterise a library of orthogonal QS signals. However, our Human Practices research revealed that most labs and companies are working with E. coli. So, we decided to adapt the “Arbitrium” system to fit the E. coli chassis, which as a Gram-negative bacterium does not naturally use a peptide based QS. Once we are able to establish a peptide based QS in E. coli, the characterisation of a library of new QS peptides would become possible.
Popularising the project
Through our Human Practices research, we realised that it was not possible to explain our project to the general public and make people interested about it because it was very abstract for them. So we managed to do two things. First, we have searched for a lot of applications (link to Applications) which can be reached with our new communication system, such as distributed logic gates, sensitive biosensors or gene regulation. Then, we have created many different media to educate the public about each of these applications. The orthogonality of a communication system is described through our video game (link), distributed logic gates are explained through our interactive rug (link) and other applications were described through many events we were involved in (link).
COLLABORATIONS
https://2018.igem.org/Team:Evry_Paris-Saclay/Collaborations
REFERENCES
[1] Federle MJ, Bassler BL. Interspecies communication in bacteria. J Clin Invest (2003) 112, 1291-1299.
[2] Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R. Communication between viruses guides lysis-lysogeny decisions. Nature (2017) 541, 488-493.