Team:CIDEB-UANL Mexico/tupapa1

Overview

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

The Bacterium’s rate of growth reaches its peak point approximately after a time lapse of 16h*(?), 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 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 3 of them will be developed, and the goal is to make one of them physical. They are not just other methods to control this, but rather, they give us an overview of the applications.

Growth and Production Regulator Project:

This project has the aim as described before, to regulate the growth and production of the bacteria’s population, and to automate the 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 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 disperser, whose function is to cool the system. The system doesn't need to be frozen, so this part complies perfectly with our necessities.

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 disperser which transfers heat away from the container, in order to ‘cool’ a little bit more the solution or medium. The heat disperser 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.

Both containers are connected by tubes which have 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.

Reading this would probably make you notice, ‘this is all electrically manipulated’. This is because the system will be controlled and powered with a micro-controller. Thus you could call this a robot, because this system is smart!

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

Look at the following graph. (Subject to change, please note it isn't exact)

You may notice the growth line going down when time extends too much. This is the 16h time lapse, we mentioned at the beginning. Bacteria’s will die after a 16h time lapse, we need to prevent this!

That’s where the resistors and heat dispersers come in. We power the resistors to produce heat, and we power the fans, or heat dispersers to disperse heat. But, a curious thought may arise from this. If you turn them on, how do you know when to turn them off? How are we going to control that?

This is achieved using temperatures sensor probes, which are waterproof thus protecting them from water and allowing us to receive a sharper and more precise lecture. The data received from this sensors, is related to temperature.

Yet, this doesn't tell us how we are controlling the temperature. Even with sensors and outputs (resistors and heat dispersers) we can’t do much. We need something to manipulate that data, that’s where the micro-controller comes in 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 a 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 UNO itself, but since this 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 input sensors, 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.

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 the case this wasn't enough, and the glow wasn't fully observable from the eye. Then it would mean trouble. 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 both containers with it.