IGEM:UNAM Genomics Mexico/2009/Notebook/Wifi coli/2010/05/25

From OpenWetWare
Jump to: navigation, search
Igem-logo-150px.png iGEM Project name 1 Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png

25th May 2010

Represilator

A brief review to compare

  • What?.

A loop negative system.

  • Parameters?.

Degradation of the mRNA, protein and the rate of transcription.

Perspectives for our system

  • Goes to a stable state.

Limitants -> lifespan of E. coli?, luciferin?.

"If is all on, we expect, that stuck there, but if one system turn off, maybe there is a stochastic component".

LOVTAP System

May-25-1-UNAM-Genomics-2010.png

Lifespan TetR

  • We need a tag for increase the degradation of our repressor.

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle δTetR= β - αTetRο}

We require a formula:

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle F([TetR]) = Pops}

But what happen with the production of endougenos TetR?, exists?.

  • No... haha, it seems to be in a RESISTANCE plasmid.

Green emission

May-25-2-UNAM-Genomics-2010.png

Input Pops -> Photons.

τ → ∞ -> Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle [14-CHO]=k}

  • This because the action of deg. and the production of CDE by M. acid tend to stabilize

Again we need to propose a formula:

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle [LuxAB]=Pops=N*f(Promoter force)}

Pathway

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle LuxAB-FMNH} 2Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle -O} 2Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle -R-CHO -> LuxAB + FMN + R-COOH + H} 2Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle O + Light}

And the enzymes work in this form (Daniela has the references in German :S):

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle Acid M. -} LuxDFailed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle > C} 13Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle H} 27Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle -COOH -} LuxEFailed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle >C} 13Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle H} 27Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle Co-Amp -} LuxCFailed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle > 14-CHO}

Here we see:

  • It appears that the product of the aldehyde can enter in the recicle pathway of LuxC and LuxE
  • We assume that C & E enzymes will be ocuppied with more substrate than the D, that only receives the membrane acid to form R-COOH. This mean, we need a major concentration of LuxCE than LuxD

Modelling with a Michael-Menten paradigm

May-25-3-UNAM-Genomics-2010.png

Perspectives

It is relevant?:

  • Formation of the dimer A|B
  • Formation of the complex FMN-AB
  • Formation of the complex R-CHO-FMN-AB
  • Temperature

Can we assume Micahel-Menten equation?

To find list

  • Rate of deg. 14-CHO
  • Distribution of the acid trough the membrane
  • Size of the cell
  • Rates of transcription
  • Kcat´s and Km´s
  • Parameters that affects the emission.