Difference between revisions of "Welcome to the In-Silico Model of Cutaneous Lipids Wiki"

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== Species ==
 
== Species ==
 +
 +
{|class="wikitable" style="text-align:center"
 +
|-
 +
! Acronym
 +
! Name
 +
! Species Type
 +
|-
 +
| AA
 +
| Arachidonic Acid
 +
| Chemical
 +
|-
 +
|
 +
|
 +
|
 +
|-
 +
| PGH2
 +
| Prostaglandin H2
 +
| Chemical
 +
|-
 +
| PGF2α
 +
| Prostaglandin F2α
 +
| Chemical
 +
|-
 +
| O<sub>R</sub>-R<sub>2</sub>
 +
| Complex of R protein and operator site upstream ''scbR'' promoter
 +
| Cell
 +
|-
 +
| O<sub>A</sub>-R<sub>2</sub>
 +
| Complex of R protein and operator site within ''scbA'' promoter
 +
| Cell
 +
|-
 +
| O<sub>A</sub>'-AR<sub>2</sub>
 +
| Putative operator site presumed to activate ''scbA'' gene by the AR<sub>2</sub> complex
 +
| Cell
 +
|-
 +
| r
 +
| mRNA transcript of ''scbR'' gene
 +
| Cell
 +
|-
 +
| a
 +
| mRNA transcript of ''scbA'' gene
 +
| Cell
 +
|-
 +
| r-a
 +
| complex of full length ''scbR'' and ''scbA'' mRNAs due to antisense effect
 +
| Cell
 +
|-
 +
| R
 +
| ScbR protein
 +
| Cell
 +
|-
 +
| R<sub>2</sub>
 +
| ScbR homo-dimer
 +
| Cell
 +
|-
 +
| A
 +
| ScbA protein
 +
| Cell
 +
|-
 +
| C
 +
| SCBs (γ-butyrolactones)
 +
| Cell
 +
|-
 +
| AR<sub>2</sub>
 +
| ScbA-ScbR complex
 +
| Cell
 +
|-
 +
| S
 +
| Glycerol derivative and β-keto acid derivative precursors
 +
| Cell
 +
|-
 +
| C<sub>2</sub>-R<sub>2</sub>
 +
| SCBs-ScbR complex
 +
| Cell
 +
|-
 +
| C<sub>e</sub>
 +
| Extracellular SCBs (γ-butyrolactones)
 +
| Environment
 +
|}
 +
 +
Information on the initial concentrations of all species can be found [[Model Overview#Initial concentrations of species|'''here''']].
  
 
== Reactions ==
 
== Reactions ==

Revision as of 15:36, 11 January 2016

About the Project

The skin is the largest structure in the body and acts as the ultimate barrier to our environment. The aim of this project is to comprehend how the lipid network within the skin responds in physiopathological states such as inflammation (sunburn, atopic dermatitis, psoriasis). Little is known about the regulatory relationships within the cutaneous lipid signalling networks, and there is a distinct lack of information about how these networks interact between compartments (the different layers of the skin).

Description of the Model

We aim to create a quantitative computational model of the cutaneous lipid signalling networks, including variables such as multiple lipid substrates and enzyme isoforms. Model construction will be guided by literature studies, combined with new experimental lipidomics data collected in this project. In order to analyse model properties, experimental studies such as altering the systemic availability of fatty acids and the effect upon the anti-inflammatory milieu will be measured. This information will be integrated into the model to obtain estimated kinetic parameter values and also to validate and refine the overall model topology. The resulting mathematical model will be testable and predictive of the lipid responses during inflammation. The insights obtained will allow for more targeted experiments to be designed in order to better understand skin lipid biology and to aid in the mapping of lipid networks contributing to inflammation. This will ultimately support the design of interventional studies to combat skin disease.

Species

Acronym Name Species Type
AA Arachidonic Acid Chemical
PGH2 Prostaglandin H2 Chemical
PGF2α Prostaglandin F2α Chemical
OR-R2 Complex of R protein and operator site upstream scbR promoter Cell
OA-R2 Complex of R protein and operator site within scbA promoter Cell
OA'-AR2 Putative operator site presumed to activate scbA gene by the AR2 complex Cell
r mRNA transcript of scbR gene Cell
a mRNA transcript of scbA gene Cell
r-a complex of full length scbR and scbA mRNAs due to antisense effect Cell
R ScbR protein Cell
R2 ScbR homo-dimer Cell
A ScbA protein Cell
C SCBs (γ-butyrolactones) Cell
AR2 ScbA-ScbR complex Cell
S Glycerol derivative and β-keto acid derivative precursors Cell
C2-R2 SCBs-ScbR complex Cell
Ce Extracellular SCBs (γ-butyrolactones) Environment

Information on the initial concentrations of all species can be found here.

Reactions

Parameter Overview

References

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