Team:CIDEB-UANL Mexico/Software-Machine'sOverview

Our project’s aim is to develop a system or tool that can automate the process of experimentation with our project. A machine which would enable the user to regulate the temperature of E-Coli, in order to produce the Vip3Ca3 and transport it in different containers while keeping the rate of the bacterium’s population controlled.

In an enclosed system the Bacterium’s rate of growth reaches its peak point approximately after a time lapse of 16 hours, after that, the growth rate will remain constant. After this event bacteria will start to die, and we don’t want that… yet. In order to avoid the death of the population, several procedures are taken. One of them is freezing and maintaining the population at a temperature ranging along 4˚C, which stops the bacteria’s production and growth process, while keeping them ‘alive’.

We've been working on the design of another method, with automation in mind as a one of the main objectives. Many other ideas have been thought of, but only 1 of them will be developed. The goal is to make it real and work. It's not another method to control or prevent the death of E.Coli, since it's rather a machine that helps us to grow E.Coli and produce Vip3Ca3, before our bacteria die.

Growth and Production Regulator Project, VIP-OMatic Machine:

This project has the aim as described before, to produce Vip3Ca3 while regulating the growth and production of the bacteria’s population. It's machine that helps with experiments. This is achieved using the following designed system:

The system consists of 2 containers. The one on the left is a normal container which allows heat to be transferred with ease. We will denominate this container, the growth controller. Below the growth controller, there's a heat sink, whose function consists in dissipating the heat in the container. There’s a resistor whose function consists on providing heat and increasing the temperature of the medium, or solution placed in the container.

The box on the right is a heat sink, and the one below is the resistor, though their positions in the real project are alternated. The heat sink just cools the system and the resistor heats it. Since the system doesn't need to be frozen, a PC fan should do the work. The growth controller, uses more heat than cooling.

The container on the right will be denominated the production controller. The material of this container is the same as the other one; it’s in fact, a simple beaker. It has a heat sink which transfers heat away from the container, in order to ‘cool’ a little bit more the solution or medium. The heat sink has a fan, which acts along with its iron linings in order to maintain heat away from the medium.

Its function is to maintain the water below room temperature, along 20˚C. The resistor below, is used if the temperature decreases a lot, which is unlikely but still inside a margin of possibility. In summary, this container uses more cooling than heating, so the resistor is unlikely to be used.

Both containers are connected by a transparent tube which has a water pump. This allows water to be pumped from the left container to the right container. The pump is necessary to compare results between both containers. The system has 2 waterproof sensors, which are in their respective containers. This allows us to tell the temperature of the containers and receive data from them. The water pump is handmade, and small enough to transfer a fair amount of water.

It's to be noted, that this is all controlled with electricity. This is because the system will be controlled and powered by a board with a micro-controller. Thus you could call this a robot, because this system is automatic and smart! Though not all times, since we intend to make it interactive too.

The interactivity will be achieved, using a simple LCD display, and some buttons. We can control and add some extra functions to the machine with this, like for example controlling the pump or the heat and cooling ourselves.

We already described the how, but we certainly haven’t explained the why though. Since our goal is to produce Vip3Ca3 while controlling the growth of the bacteria and their production, we need to manipulate their temperature!

Look at the following graph.


Source: http://www.ugr.es/~eianez/Microbiologia/12crecimiento.htm

Yet, this doesn't tell us how we are controlling the temperature. Even with sensors and outputs (resistors and heat sinks) we can’t do much. We need something that can manipulate all the data, and that’s where the micro-controller comes into play.

The micro-controller used in this project, isn't rather just the micro-controller itself, but a board with it. In other words, we are talking about an built open source board, with an Atmel micro-controller. The Arduino board, in this case, the Mega ADK to be more specific.

The main option was using an Arduino UNO itself, but since the Mega was already at our reach, we decided to go with it.

This allows us to connect in a prototype like way, all of the output devices, or inputs, and manipulate them trough the means of code! The code used to program Arduino, Is based on Processing and is written in Java. It has functionality similar to C/C++.

With this in mind, we can program our board in order to control the whole system by receiving and responding to the environment, that is. We will also add interactivity to this board, through the means of an interface.

Next comes into play an array of UV LEDs. We know that our E. coli population will be producing Vip3Ca3 at temperatures ranging along 20˚C or low. It’s in these moments when the GFP reporter is produced alongside with Vip3Ca3. The GFP reporter when exposed to ultraviolet radiation emits a green glow. Thus logically, if the glow is there, we can infer that Vip3Ca3 is being produced, and the experiment is a success.

In other words, we need to expose the solution to a wavelength similar of ultraviolet rays. The UV LEDs we mentioned before, emit a wavelength of an approximate 400 nm which should be enough, to expose the green glow in the solution.

But in case the wavelength wasn't enough to expose the glow, and it wasn't fully observable from the eye. Then it would mean trouble for us. That’s where the spectrometer comes into play. This device is simple and handmade, using a simple box and a CD. We should observe differences in the spectrometer, by comparing and observing both containers with it. One without Vip3Ca3, and the other one with it.