From 2007.igem.org

Revision as of 01:20, 27 October 2007

• Home
  • Site Map
  • Meet the Team
  • Fun with iGEM
  • IcGEMs@OpenWetware
  • Acknowledgements
• Infector Detector
  • Introduction
  • Specification
  • Design
  • Modelling
  • Implementation
  • Testing/Validation
  • F2620 Comparison
  • Conclusion
• Cell by Date
  • Introduction
  • Specification
  • Design
  • Modelling
  • Implementation
  • Testing/Validation
  • Conclusion
• Cell-Free
  • What is Cell-Free?
  • Cell-Free Vs. Cell
  • Our Contributions
  • Characterisation
  • Applications
• Wet Lab
  • Lab Notebook
  • Protocols & Results
  • DNA Constructs
• Dry Lab
  • Modelling
  • Data Analysis
  • Software

Cell by Date: Testing

Summary

Key results of our experiments are :

1.Operating Range : Our System Operates between 8-37 Degrees
2.Activation Energy : The activation energy of our system is 1.5kJ/mol
3.Optimum DNA Concentration : The optimum DNA concentration for our system is 2-4ug DNA

Aims

Having determined that our system worked at a basic level in our implementation phase we set out to ascertain a clearer picture of the performance of our system to ultimately reveal whether our design had realised our specifications.

Results

Investigating properties of system under isothermal scenarios

To estimate the properties of our system we looked at the evolution of the Fluorescence with time for experiments where temperature is carefully kept constant. (Figure 1).
General Behaviour:

• In all experiment we can observe a linear growth of fluorescence corresponding to a steady rate of protein production.
• This matches the claims of the manufacturer of the cell-free extract that the extract is optimised so that protein degradation is negligible.
  

Figr 1:Isothermal Data - Averages GFPmut3b molecules synthesised for pTet-GFPmut3b construct at different temperatures

Operating Range:

• Our system seems to 'turn off' at around 4 degrees C.
  
• At 8 degrees with have minimal expression which then increases to a substantial expression at 37 degrees.
  

Synthesis rate vs Temperature

• Over the range of temperature considered here the rate increases with temperature.
  
• To investigate the relation between synthesis rate and temperature we extracted the rate of synthesis of GFP for each experiment and plotted it against 1/T (Figure 2).
  
• A strong linear correlation in the log plot supports an arrhenius type dependence on temperature with an activation energy of 1.5kJ/mol.
  

Fig 2: Arrhenius Plot

Other practical considerations:

• Unfortunetly we have not been able to use a visible reporter and so have no idea whether the construct can in fact produce a visible signal.
  
• In terms of lifespan we have had major problems with evaporation meaning that the lifespan of our system is limited to a few days as discussed in our packaging experiment below.
  

Investigating properties of system under dynamic temperature scenarios

Fig 3:Moelcules of GFPmut3b produced on average over time for two samples at constant temperatures of 4&degC and 20°C and two with a temperature step (4-20°C and 20-4°C)

qualitative analysis:

20-4 slow down as per meat model -> Good sign

4-20 gets going quickly as per meat -> Good sign

Hard to quantify response time due to lack of data points would like to look into this

Other Experiments

1. DNA Concentration

2. Packaging