Difference between revisions of "Welcome to the In-Silico Model of Cutaneous Lipids Wiki"
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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. | 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. | 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. | ||
| + | |||
| + | == Reactions == | ||
| + | The reactions per compartment are the following: | ||
| + | |||
| + | {|width ="80%" | ||
| + | | | ||
| + | |||
| + | * [[Transformation of PL to AA |Transformation of PL to AA]] | ||
| + | |||
| + | '''''Prostanoids''''' | ||
| + | * [[Transformation of AA to PGH2 |Transformation of AA to PGH2]] | ||
| + | * [[Transformation of PGH2 to PGF2α |Transformation of PGH2 to PGF2α]] | ||
| + | * [[Transformation of PGH2 to TXA2 |Transformation of PGH2 to TXA2]] | ||
| + | * [[Transformation of PGH2 to PGI2 |Transformation of PGH2 to PGI2]] | ||
| + | * [[Transformation of PGH2 to PGD2 |Transformation of PGH2 to PGD2]] | ||
| + | * [[Transformation of PGH2 to PGE2 |Transformation of PGH2 to PGE2]] | ||
| + | * [[Transformation of TXA2 to TXB2 |Transformation of TXA2 to TXB2]] | ||
| + | * [[Transformation of PGI2 to 6-K-PGF1α |Transformation of PGI2 to 6-K-PGF1α]] | ||
| + | * [[Transformation of PGD2 to PGJ2 |Transformation of PGD2 to PGJ2]] | ||
| + | * [[Transformation of PGJ2 to 15-D-PGJ2 |Transformation of PGJ2 to 15-D-PGJ2]] | ||
| + | |||
| + | '''''Mono and Poly Hydroxy Fatty Acids''''' | ||
| + | * [[Transformation of AA to 5-HPETE |Transformation of AA to 5-HPETE]] | ||
| + | * [[Transformation of AA to 12-HPETE |Transformation of AA to 12-HPETE]] | ||
| + | * [[Transformation of AA to 15-HPETE |Transformation of AA to 15-HPETE]] | ||
| + | * [[Transformation of 5-HPETE to 5-HETE|Transformation of 5-HPETE to 5-HETE]] | ||
| + | * [[Transformation of 12-HPETE to 12-HETE|Transformation of 12-HPETE to 12-HETE]] | ||
| + | * [[Transformation of 15-HPETE to 15-HETE|Transformation of 15-HPETE to 15-HETE]] | ||
| + | * [[Transformation of 5-HETE to 5-OXO-ETE|Transformation of 5-HETE to 5-OXO-ETE]] | ||
| + | * [[Transformation of 5-HPETE to LTA4|Transformation of 5-HPETE to LTA4]] | ||
| + | * [[Transformation of LTA4 to LTB4|Transformation of LTA4 to LTB4]] | ||
| + | * [[Transformation of LTA4 to LTC4|Transformation of LTA4 to LTC4]] | ||
| + | |} | ||
== Species == | == Species == | ||
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Information on the initial concentrations of all species can be found [[Overview of Model#Initial concentrations of species|'''here''']]. | Information on the initial concentrations of all species can be found [[Overview of Model#Initial concentrations of species|'''here''']]. | ||
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== Experimental Data == | == Experimental Data == | ||
Revision as of 14:11, 8 April 2016
Contents
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.
Reactions
The reactions per compartment are the following:
Species
| Acronym | Name | Species Type |
|---|---|---|
| 12-LOX | 12-Lipoxygenase | Enzyme |
| 15-D-PGJ2 | 15-Deoxy-Cyclopentenone Prostaglandin | Chemical |
| 15-LOX | 15-Lipoxygenase | Enzyme |
| 5-LOX | 5-Lipoxygenase | Enzyme |
| 6-K-PGF2α | 6-Keto-Prostaglandin F2α | Chemical |
| AA | Arachidonic Acid | Chemical |
| COX-1 | Cycloxygenase-1 | Enzyme |
| COX-2 | Cycloxygenase-2 | Enzyme |
| FA | Fatty Acid | Chemical |
| PGD2 | Prostaglandin D2 | Chemical |
| PGDS | Prostaglandin D Synthase | Enzyme |
| PGE2 | Prostaglandin E2 | Chemical |
| PGES | Prostaglandin E Synthase | Enzyme |
| PGF2α | Prostaglandin F2α | Chemical |
| PGFS | Prostaglandin F Synthase | Enzyme |
| PGH2 | Prostaglandin H2 | Chemical |
| PGI2 | Prostaglandin I2 | Chemical |
| PGJ2 | Cyclopentenone Prostaglandin J2 | Chemical |
| PLA2 | Phospholipase A2 | Enzyme |
| TXA2 | Thromboxane A2 | Chemical |
| TXB2 | Thromboxane B2 | Chemical |
| TXAS | Thromboxane A Synthase | Enzyme |
Information on the initial concentrations of all species can be found here.
