Team:Edinburgh/Modelling/Genomic

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Overview: Modelling genomic BRIDGEs

Unlike the modelling of genetic regulation networks or metabolic pathways, modelling a generic protocol does not achieve much in light of the ultimate goal of being able to understand and answer questions regarding biological processes. On the other hand, we did wish to have a model corresponding to the BRIDGE protocol, and such a model would be useful to demonstrate an ability of Kappa that has not been touched upon yet: perturbations. These are described in further detail below, but in short allow for certain effects (such as activation or inhibition of rules) to be enacted at certain times within simulation of the model.

The sections below describe, in turn: the agents and rules that are present in the model, the perturbations that govern time-dependent behaviour, the results of running the simulation, and analysis of the results obtained.

The Model

The genomic BRIDGE model, focused as it is on interactions the BRIDGE protocol, requires only one basic agent - the DNA agent presented previously in the introduction to Kappa. Each DNA agent has two lateral sites to bind other DNA agents both upstream and downstream, one to hold the type of the agent (usually materialised either as a descriptive acronym or as a reference number from the BioBrick Registry), and one to bind proteins interacting with the DNA agent (typically transcription factors or RNA polymerase, omitted in this model ). This basic agent, chained together as shown in Figure 1, can then be used to construct larger composite agents that represent different sequences in the BRIDGE protocol - for example, the cat-sacB construct or the insert.

The rules involved in the BRIDGE protocol can be roughly divided into three distinct groups, or chapters. The first chapter involves the introduction of fresh agents to the protocol, and consists of a single rule in which the desired insert (i.e., the DNA that we wish to insert into the target vector during the second stage of BRIDGE recombination) is created. This rule has an unmodified rate of 0, since we do not want this to occur without our express permission.

The second chapter involves the degradation of various composite agents under the influence of antibiotics or growth on sucrose, as per the selection methods employed by the BRIDGE protocol. For example, applying antibiotic selection will result in all composite agents not containing a DNA agent with type cat to degrade; similarly, applying growth on sucrose will cause all composite agents containing a DNA agent with type sacB to degrade. Again, this will only occur at certain time-points within the model, and thus the rate of the rules are set at zero.

The third and final chapter of rules describe the two stages of recombination as previously outlined in Figure 1 on the introduction to the BRIDGE protocol here. They involve the exchange of the relevant DNA agents between their respective composites, an example of which is shown in Figure 2 below.

The initial conditions of the simulation are set such that it contains both the cat-sacB construct and the vector into which the final insert needs to be placed. The remaining DNA required for the protocol - the insert itself - will be added to the simulation at a predetermined point in time, as described by the perturbations to follow.

For details of the rules themselves, readers are directed to browse the actual Kappa file.

Perturbations

Perturbations in the Kappa modelling language are simply timed alterations to the rates of particular rules, simulating the effect of external influences upon the modelled environment. In the context of modelling genomic BRIDGEs, the perturbations describe the effect caused by various stages of the protocol - selection over antibiotic resistance, introduction of the insert, and selection over sucrose. Hence, there are again three sets of perturbations included in the model.

The first set of perturbations deal with antibiotic selection, regulating at predetermined time points within the simulation the two relevant rules described previously. Four separate perturbations are required in total - two to activate the rules (i.e. set their reaction rate to a value greater than 0), and two more to deactivate them again (i.e. reset their reaction rate to 0). Similarly the second set of two perturbations activate and deactivate the introduction of the insert, and the third set of six perturbations do the same thing regarding selection over sucrose.

Again, for the perturbations themselves, readers are directed to browse the actual Kappa file.

Results

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Analysis

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