Difference between revisions of "Team:Czech Republic/Goals"

 
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'''Module 1 builds synthetic haploid strains with refactored mating loci that are conjugated to make a functional IOD. These strains have the wild-type mating phenotype and differentially express a reprogrammed signalling pathway in their diploid state proving the feasibility of the clone-free assembly concept.'''
 
'''Module 1 builds synthetic haploid strains with refactored mating loci that are conjugated to make a functional IOD. These strains have the wild-type mating phenotype and differentially express a reprogrammed signalling pathway in their diploid state proving the feasibility of the clone-free assembly concept.'''
  
−
* Constructed a set of reporter promoters for yeast cells
+
:<span style="color:#00ff00;">✓</span> Construct a set of reporter promoters for yeast cells
−
* Characterized reporter promoters in all mating types
+
:<span style="color:#00ff00;">✓</span> Characterize reporter promoters in all mating types
−
* Designed and materialized synthetic MATa and MATx strains
+
:<span style="color:#00ff00;">✓</span> Design and materialized synthetic MATa and MATx strains
−
* Built a synthetic diploid strain with a functional yeast pheromone pathway
+
:<span style="color:#00ff00;">✓</span> Build a synthetic diploid strain with a functional yeast pheromone pathway
−
* Demonstrated the correct functionality of yeast pheromone pathway in synthetic diploids
+
:<span style="color:#00ff00;">✓</span> Demonstrate the correct functionality of yeast pheromone pathway in synthetic diploids
  
 
'''Module 2 builds a set of orthogonal pheromones and receptors. These pheromone-receptor pairs enable specific localized signalling proving the feasibility of multichannel signal transmission underlying logic operations necessary for reliable diagnosis.'''
 
'''Module 2 builds a set of orthogonal pheromones and receptors. These pheromone-receptor pairs enable specific localized signalling proving the feasibility of multichannel signal transmission underlying logic operations necessary for reliable diagnosis.'''
  
−
* Constructed a set of yeast plasmids with different mating pheromones and their receptors and contributed to the Registry with 6 BioBricks
+
:<span style="color:#00ff00;">✓</span> Construct a set of yeast plasmids with different mating pheromones and their receptors and contribute to the Registry with BioBricks
−
* Verified the correct coupling of the receptors to the yeast pheromone mating pathway
+
:<span style="color:#00ff00;">✓</span> Verify the correct coupling of the receptors to the yeast pheromone mating pathway
−
* Verified the correct expression and secretion of the different pheromones
+
:<span style="color:#00ff00;">✓</span> Verify the correct expression and secretion of the different pheromones
−
* Showed the orthogonality of the used receptors and pheromones  
+
:<span style="color:#00ff00;">✓</span> Show the orthogonality of the used receptors and pheromones
  
 
'''Module 3 builds a set of location tags that recognize common tumor surface markers and agglutinate cell populations. Location tags displayed in the correct conformation strengthen cell-cell interactions to enable localization of signal transmission.'''
 
'''Module 3 builds a set of location tags that recognize common tumor surface markers and agglutinate cell populations. Location tags displayed in the correct conformation strengthen cell-cell interactions to enable localization of signal transmission.'''
−
* Expressed streptavidin, EpCAM, Anti-EpCAM scFv, c-Myc scFv and anti-HuA scFv on the surface of yeasts
+
:<span style="color:#00ff00;">✓</span> Express streptavidin, EpCAM, Anti-EpCAM scFv, c-Myc scFv and anti-HuA scFv on the surface of yeasts
−
* Demonstrated the ability of our receptors to bind chosen markers
+
:<span style="color:#00ff00;">✓</span> Monitor the dynamic binding of the displayed fragments of antibodies and corresponding markers
−
* Monitored the dynamic binding of our receptors and their corresponding markers
+
:<span style="color:#00ff00;">✓</span> Demonstrate compatibility of our yeast system and blood and functionality of the location tags in plasma
  
−
'''Module 4 provided modeling and simulation support for other modules.'''
+
'''Module 4 provides modeling and simulation support for other modules.'''
−
* Developed a simulation environment CeCe to capture the complexity of cell-cell signal transmission
+
:<span style="color:#00ff00;">✓</span> Develop a simulation environment CeCe to capture the complexity of cell-cell signal transmission
−
* Designed an IOD chemical reaction network model
+
:<span style="color:#00ff00;">✓</span> Design an IOD chemical reaction network model
−
* Developed a schematic architecture for conceptual modeling of signal transmission networks
+
:<span style="color:#00ff00;">✓</span> Develop a schematic architecture for conceptual modeling of signal transmission networks
−
* Designed a two IOD signal transmission network suitable for the IOD band
+
:<span style="color:#00ff00;">✓</span> Design a two IOD signal transmission network suitable for the IOD band
−
* Illustrated the robustness and efficiency of the IOD band design in CeCe simulations
+
:<span style="color:#00ff00;">✓</span> Illustrate the robustness and efficiency of the IOD band design in CeCe simulations
 +
 
 +
'''Module 5 allows other modules to use microfluidics devices for their experiments.'''
 +
:<span style="color:#00ff00;">✓</span> Set of microfluidic devices fabricated by PDMS soft-lithography.
 +
:<span style="color:#00ff00;">✓</span> Characterization of signal transmission range between wildtype MATa and MATx Saccharomyces cerevisiae cells.
 +
:<span style="color:#00ff00;">✓</span> Dynamic characterisation of signal transmission between synthetic MATa and MATx Saccharomyces cerevisiae cells.
 +
:<span style="color:#00ff00;">✓</span> Comparison with mathematical model of signal transmission mechanism and estimation of the activation threshold for different cell concentrations.
 +
:<span style="color:#00ff00;">✓</span> Demonstrate yeast induced blood agglutination on-chip by human antigen A displayed on cell surface by Yeast Surface Display.
  
−
'''Module 5 allowed other modules to use microfluidics devices for their experiments.'''
 
−
* Set of microfluidic devices fabricated by PDMS soft-lithography.
 
−
* Characterization of signal transmission range between wildtype MATa and MATx Saccharomyces cerevisiae cells.
 
−
* Dynamic characterisation of signal transmission between synthetic MATa and MATx Saccharomyces cerevisiae cells.
 
−
* Comparison with mathematical model of signal transmission mechanism and estimation of the activation threshold for different cell concentrations.
 
−
* Demonstrated yeast induced blood agglutination on-chip by human antigen A displayed on cell surface by Yeast Surface Display.
 
 
{{:Team:Czech_Republic/Template:Bottom}}
 
{{:Team:Czech_Republic/Template:Bottom}}

Latest revision as of 20:35, 18 September 2015

Goals


Module 1 builds synthetic haploid strains with refactored mating loci that are conjugated to make a functional IOD. These strains have the wild-type mating phenotype and differentially express a reprogrammed signalling pathway in their diploid state proving the feasibility of the clone-free assembly concept.

✓ Construct a set of reporter promoters for yeast cells
✓ Characterize reporter promoters in all mating types
✓ Design and materialized synthetic MATa and MATx strains
✓ Build a synthetic diploid strain with a functional yeast pheromone pathway
✓ Demonstrate the correct functionality of yeast pheromone pathway in synthetic diploids

Module 2 builds a set of orthogonal pheromones and receptors. These pheromone-receptor pairs enable specific localized signalling proving the feasibility of multichannel signal transmission underlying logic operations necessary for reliable diagnosis.

✓ Construct a set of yeast plasmids with different mating pheromones and their receptors and contribute to the Registry with BioBricks
✓ Verify the correct coupling of the receptors to the yeast pheromone mating pathway
✓ Verify the correct expression and secretion of the different pheromones
✓ Show the orthogonality of the used receptors and pheromones

Module 3 builds a set of location tags that recognize common tumor surface markers and agglutinate cell populations. Location tags displayed in the correct conformation strengthen cell-cell interactions to enable localization of signal transmission.

✓ Express streptavidin, EpCAM, Anti-EpCAM scFv, c-Myc scFv and anti-HuA scFv on the surface of yeasts
✓ Monitor the dynamic binding of the displayed fragments of antibodies and corresponding markers
✓ Demonstrate compatibility of our yeast system and blood and functionality of the location tags in plasma

Module 4 provides modeling and simulation support for other modules.

✓ Develop a simulation environment CeCe to capture the complexity of cell-cell signal transmission
✓ Design an IOD chemical reaction network model
✓ Develop a schematic architecture for conceptual modeling of signal transmission networks
✓ Design a two IOD signal transmission network suitable for the IOD band
✓ Illustrate the robustness and efficiency of the IOD band design in CeCe simulations

Module 5 allows other modules to use microfluidics devices for their experiments.

✓ Set of microfluidic devices fabricated by PDMS soft-lithography.
✓ Characterization of signal transmission range between wildtype MATa and MATx Saccharomyces cerevisiae cells.
✓ Dynamic characterisation of signal transmission between synthetic MATa and MATx Saccharomyces cerevisiae cells.
✓ Comparison with mathematical model of signal transmission mechanism and estimation of the activation threshold for different cell concentrations.
✓ Demonstrate yeast induced blood agglutination on-chip by human antigen A displayed on cell surface by Yeast Surface Display.