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Team:Paris Bettencourt/Results
From 2013.igem.org
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| - | <h2> | + | <h2><a href="">Modelling</h2> |
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| - | <h2><a href="">Structural analysis of SirA</h2> | + | <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Structural analysis of SirA</h2> |
<ul> | <ul> | ||
<p>Using Swiss pdb we demonstrated the superimposed 3D structures of Mycobacterium tuberculosis SirA and Escherichia coli CysI highlighting their similarities and differences. Both proteins are important in their respective sulphite reduction pathways. We then predicted the effect of a small drug target based on SirA's structure. </p> | <p>Using Swiss pdb we demonstrated the superimposed 3D structures of Mycobacterium tuberculosis SirA and Escherichia coli CysI highlighting their similarities and differences. Both proteins are important in their respective sulphite reduction pathways. We then predicted the effect of a small drug target based on SirA's structure. </p> | ||
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<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Flux Balance Analysis</h2> | <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Flux Balance Analysis</h2> | ||
<ul> | <ul> | ||
| - | <p></p> | + | <p>We used an E. coli model iJR904 obtained from BiGG database as a starting model and obtained a growth rate represented by the f value of 0.9129. We then deleted the reaction ‘SULR’ which encodes for the sulphite reduction pathway involving cysI and obtained a f value of -8.63596783409936e-13 indicating that the sulphite reduction pathway is required for growth. Finally we introduced two new reactions for sirA and fprA and a new species fdxA. We found that growth was restored with the mycobacteria pathway resulting in a f value of 0.9105</p> |
Revision as of 03:49, 5 October 2013
Detect
Background
CRISPR/Cas systems generate site-specific double strand breaks and have recently be used for genome editing.
Results
- Successfully cloned gRNA anti-KAN, crRNA anti-KAN, tracrRNA-Cas9 and pRecA-LacZ into Biobrick backbones and therefore generated four new BioBricks.
- Testing the new assembly standard for our cloning.
Assembly Standard
We offer a new assembly standard. It enables keeping the BioBrick standard while providing the needed tools to perform assembly of several parts in one step. BBG is a fusion of the BioBrick standard cloning and Gibson isothermal assembly.
BioBricks
Aims
Building a genotype sensor based on CRISPR/Cas that reports existance of an antibiotic resistance gene.
Target
Background
SirA is an essential gene in latent tuberculosis infections
Results
- Produced an E. coli strain which relies upon mycobacterial sirA, fprA and fdxA genes to survive in M9 minimal media
- Demonstrated that E. coli can survive with mycobacterial sulfite reduction pathway with Flux Balance Analysis
- Located drug target sites on sirA as well as identified high structural similarity between cysI and sirA through structural anaylsis
Aims
To perform an drug screen targeted at the sirA gene from mycobacteria
Infiltrate
Background
Latent tuberculosis persists inside macrophages of the lungs, where it is partially protected from both the host immune system and conventional antibiotics.
Results
- We expressed the enzyme Trehalose Dimycolate Hydrolase (TDMH) in E.coli and showed that it is highly toxic to mycobacteria in culture.
- We expressed the lysteriolyin O (LLO) gene in E. coli and showed that it is capable of entering the macrophage cytosol.
- We co-infected macrophages with both mycobacteria and our engineered E. coli to characterize the resulting phagocytosis and killing.
BioBricks
Aim
To create an E. coli strain capable of entering the macrophage cytosol and delivering a lytic enzyme to kill mycobacteria.
Sabotage
Background
One of the main concern about tuberculosis today is the emergence of antibiotic resistant strain
Results
- Construction and characterization of phagemids coding for small RNA targeting antibiotic resistance proteins
- successful conversion of antibiotic resistant population of E. coli to a sensitive state
BioBricks
Aims
Our objective is to make an antibiotic-resistant bacterial population sensitive again to those same antibiotics.
Human Practice
Technology Transfer
An essay that addresses the issue of designing a technology aimed at "developing" countries, rather than at “developed” ones: a typical case of technology transfer.
Gender Study
A comprehensive and quantitative study of gender equality(equality) in iGEM and synthetic biology. A database was gathered to depict sex ratio in teams' students and supervisors in all iGEM teams as well as other available information. This was statistically analysed to investigate gender in(equality) in iGEM, as well as SB conferences and synthetic biology labs.
TB gallery
A gallery of famous historic figures who had tuberculosis, made to raise awareness to its prevalence of in the past and present .
TB facts
Infographics page containing TB data and facts that captures all you need to know at a glance.
TB in France
An analysis of the social and political aspects of the management of Tuberculosis in France.
Collaboration
Sensigem
SensiGEM is the iGEM Biosensor database generated by the teams Paris Bettencourt 2013 and Calgary 2013. In this database you can find fast and easy what biosensor projects were already done by past iGEM Teams. To be able to select the projects that fit into the database, we also collaborated to compose a joint definition a biosensor.
Braunschweig iGEM Team
Idea, bibliography, and beer sharing!
BGU iGEM Team from Israel
A mutual part characterization. We characterize the promoter units produced by the lac/ara-1 promoter of cI, a repressor of their constructed kill switch. In return, BGU characterizes our TDMH biobrick protein expression levels by Western Blot.
Modelling
Population Dynamics Model
This model investigates the effects of the fitness-cost of a genetic element on it's spread in a bacterial population, based on a phagemid helper system
Structural analysis of SirA
Using Swiss pdb we demonstrated the superimposed 3D structures of Mycobacterium tuberculosis SirA and Escherichia coli CysI highlighting their similarities and differences. Both proteins are important in their respective sulphite reduction pathways. We then predicted the effect of a small drug target based on SirA's structure.
Flux Balance Analysis
We used an E. coli model iJR904 obtained from BiGG database as a starting model and obtained a growth rate represented by the f value of 0.9129. We then deleted the reaction ‘SULR’ which encodes for the sulphite reduction pathway involving cysI and obtained a f value of -8.63596783409936e-13 indicating that the sulphite reduction pathway is required for growth. Finally we introduced two new reactions for sirA and fprA and a new species fdxA. We found that growth was restored with the mycobacteria pathway resulting in a f value of 0.9105
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