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Team:Groningen/Template/MODULE/project/MBD
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Revision as of 10:51, 16 October 2014
Project
>
Model-based design
Why modeling?
Modeling is an important tool used for understanding the behavior of variables without testing it in real time. From designing small genetic circuits to space shuttles, modeling plays a pivotal role. In our case, modeling is the backbone of our project.
The main focus of the modeling in this project lies in aiding the development of the actual prototype. The results from modeling should help the design of a bandage that detects pathogens in burnwounds and secretes molecules that either kill- or inhibit growth of these pathogens. Key here is the ability to produce nisin, DspB and AHLase upon sensing quorum molecules from the pathogens. In order to provide useful information to the ‘material’-people in our team, we made a first model that shows how nisin, DspB and AHLase are produced by L. lactis and diffuse through the bandage. By using this model, we can estimate which of six possible designs (LINK) is the best.
Awesome! The ‘why modeling’-question has been answered, let’s show its actual use!
Staphylococcus aureus and Pseudomonas aeruginosa are the two pathogens that cause most infections in burn wounds. The aim of our project is to design a smart bandage that can produce Infection Prevention Molecules (IPMs) only in the presence of these two pathogens. This kind of bandage will reduce the problem of antibiotic resistance by reducing the amount of antibiotics applied to the wound. The IPMs are produced by our genetically modified Lactococcus lactis. These bacteria are fixed in the hydrogel. It is key that the molecules produced by L. lactis reach the infected wound. Understanding the nuances that are associated with the diffusion of IPMs is therefore important for us.
To start with actual modeling, we will first give an overview of the parameters involved in the modeling.
Bandage modeling
Our main goal for this project is to design a bandage prototype or burn wounds. Burn wounds are usually infected with Staphylococcus aureus and Pseudomonas aeruginosa. The quorum molecules produced by these two pathogens should diffuse through the bandage and activate the production of Nisin, Aiia and DspB proteins. These three proteins should diffuse out of the bandage and act on the pathogens. There were different possible bandage designs considering our bandage specifications. We’ve made six, to get a rough estimation of the best design.
You’ve probably seen our design on the front page of our wiki. If not, here is a link that describes the different components of the bandage in a more precise way (LINK TO 3D MODEL). We are mainly interested in how fast and how much our three Infection Preventing Molecules (IPM’s) are diffusing into the wound. That makes our to-obtain-results clear:
1. Amount of nisin that diffuses from the bandage into the wound over time.
2. Amount of DspB that diffuses from the bandage into the the wound over time.
3. Amount of AiiA that diffuses from the bandage into the the wound over time.
These amounts can be found by modeling. We made six designs with different distributions of our L. lactis throughout the gel. These designs and their modeled diffusion results are displayed below.
You’ve probably seen our design on the front page of our wiki. If not, here is a link that describes the different components of the bandage in a more precise way (LINK TO 3D MODEL). We are mainly interested in how fast and how much our three Infection Preventing Molecules (IPM’s) are diffusing into the wound. That makes our to-obtain-results clear:
1. Amount of nisin that diffuses from the bandage into the wound over time.
2. Amount of DspB that diffuses from the bandage into the the wound over time.
3. Amount of AiiA that diffuses from the bandage into the the wound over time.
These amounts can be found by modeling. We made six designs with different distributions of our L. lactis throughout the gel. These designs and their modeled diffusion results are displayed below.
