# Team:Colombia/Modeling/Ecological Model

(Difference between revisions)
 Revision as of 22:52, 26 October 2012 (view source)Ksk 89 (Talk | contribs)← Older edit Revision as of 23:14, 26 October 2012 (view source)Ksk 89 (Talk | contribs) (→Implementation Model)Newer edit → Line 9: Line 9: =Implementation Model= =Implementation Model= - - The following is a short preview of the ecological model we are currently working on. '''General objective''' '''General objective''' - To generate a computational model that simulates the most relevant ecological relationships between our engineered system and the plant pathogens inside the appropriate habitat. + To generate a computational model that simulates the most relevant relationships between our engineered system and the plant pathogens inside the appropriate habitat for the Rust control. '''Specific Objectives''' '''Specific Objectives''' Line 20: Line 18: - To limit the multifactorial ecological problem in a way that a simple mathematical model may be proposed. Such model should be able to answer relevant questions regarding the problem. - To limit the multifactorial ecological problem in a way that a simple mathematical model may be proposed. Such model should be able to answer relevant questions regarding the problem. - - To find the populational proportions between our organism, pathogens, and the host plants that optimize our biological control. + - To find the populational proportions between our organism and the plant pathogens that optimize our biological control. - To generate hypotheses for future experimental confirmations. - To generate hypotheses for future experimental confirmations. - ==Graphical Model== + ==Biological Panorama== - + - [[File:ecological.jpg|600px|thumb|center]] + - + - The idea is to treat the population number as boxes with inflows and outflows. Each arrow represents the formula by which the different boxes are connected. Arrows that do not point to another box represent organisms that die. + - + - - I stand for bacteria that are asleep. + - + - - A stand for bacteria that are awake and active (+) or inactive (-). + - + - - R stands for the coffee rust fungus. + - - N stands for A + I + Coffee Rust dispersion is based on the generation of uredospores. These are dispersed by wind and water predominantly, as well as by active animal or human dispersion. These spores require about 24 to 48 hours of free continuous humidity, so the infection process usually occur only during rainy seasons. The fungus grows as a mycelium on the leaves of the plant, and the generation of new spores takes about 10 to 14 days. Since leaves drop prematurely, this effectively removes important quantities of epidemic potential inoculum; nevertheless, a few green leaves will survive through the dry season. Dry uredospores may live for about 6 weeks. In this way, there is always a viable inoculum capable of infecting new leaves ath the beginning of the next rainy season. - ''We plan to hand in a complete version of the model for the world championship if we classify!'' + In this year's iGEM, our main goal is to significatively reduce the mycelial form of the fungus in order to control inocula from a season to the next. The way this works is by spraying bacteria on top of the leaves of the plants, however, the amount and concentration of bacteria are not necessarily known. Thanks to a population control system by toxin-antitoxin modules, a small fraction (near 15%) of the bacterial population will live in a persistant state. Persister cells have very low metabolic rates. Non-persister active cells, even though more sensitive to environmental hazards, readily detect fungal infections. If a determined chitin profile (based on our molecular mathematical models) is detected, active bacteria are stimulated in a way that they are capable of secreting a plant hormone to induce its natural defense responses.

# Implementation Model

General objective

To generate a computational model that simulates the most relevant relationships between our engineered system and the plant pathogens inside the appropriate habitat for the Rust control.

Specific Objectives

- To limit the multifactorial ecological problem in a way that a simple mathematical model may be proposed. Such model should be able to answer relevant questions regarding the problem.

- To find the populational proportions between our organism and the plant pathogens that optimize our biological control.

- To generate hypotheses for future experimental confirmations.

## Biological Panorama

Coffee Rust dispersion is based on the generation of uredospores. These are dispersed by wind and water predominantly, as well as by active animal or human dispersion. These spores require about 24 to 48 hours of free continuous humidity, so the infection process usually occur only during rainy seasons. The fungus grows as a mycelium on the leaves of the plant, and the generation of new spores takes about 10 to 14 days. Since leaves drop prematurely, this effectively removes important quantities of epidemic potential inoculum; nevertheless, a few green leaves will survive through the dry season. Dry uredospores may live for about 6 weeks. In this way, there is always a viable inoculum capable of infecting new leaves ath the beginning of the next rainy season.

In this year's iGEM, our main goal is to significatively reduce the mycelial form of the fungus in order to control inocula from a season to the next. The way this works is by spraying bacteria on top of the leaves of the plants, however, the amount and concentration of bacteria are not necessarily known. Thanks to a population control system by toxin-antitoxin modules, a small fraction (near 15%) of the bacterial population will live in a persistant state. Persister cells have very low metabolic rates. Non-persister active cells, even though more sensitive to environmental hazards, readily detect fungal infections. If a determined chitin profile (based on our molecular mathematical models) is detected, active bacteria are stimulated in a way that they are capable of secreting a plant hormone to induce its natural defense responses.