Difference between revisions of "Team:Grenoble-Alpes/Hardware"

What if your Cell phone became a portable lab ?

What if you could use your cell phone as a laboratory ? It might sound weird and difficult, but using 3D printing technique, basic electronics components and programming, your phone may become a very efficient tool. This is what we aimed to do with SnapLab, our portable kit that detects cholerae. SnapLab is the combination of a user-friendly application with a 3D printed device, in which smartly designed plasmids are used to detect particular DNA sequences.

SnapLab is the result of the collaboration between biology and engineering students. We designed an all-in-one kit, which integrates own-made lab instruments. Not only a measurement tool, SnapLab is also able to complete the entire analysis. After extracting the DNA sequence of interest from feces or water, the plasmid that we designed hybridizes with this particular DNA sequence. The plasmid is then internalised by the bacteria through a process of bacterial transformation, that once again occurs within the kit. Thus, bacteria are able to emit fluorescence that the smartphone captures by taking a photograph. All these steps are made possible by the 3D printed kit and the Arduino card connected to the smartphone. Here is an exploded view of the kit.

SnapLab has entirely been created in 3D with Onshape, a full-cloud and public online software. All 3D models are available for those who have a free account on Onshape. Use the keyword “iGEM Grenoble-Alpes” with the research tool. All parts are given in the following table. Weight, time of printing and the approximate price of the material are pointed out, for a layer height of 0.3mm in ABS.

Our project is part of the Do It Yourself (DIY) approach. It is to say that the kit is designed to be easily editable and reproduced. To do so, we decided to use 3D printing as much as we could. It has two major advantages. First, 3D printing allows to create parts with very specific dimensions, thus minimizing the number of parts as to favor a better insulation between the different compartments. Second, mechanical properties of the material used in 3D printing, Acrylonitrile butadiene styrene (ABS), are interesting to ensure the solidity of the structure.

Moreover, ABS is also heat resistant. SnapLab needs temperature from 0°C up to 75°C and ABS reaches its transition state at 125°C, so this is the perfect material in every aspects. We are also aware of the potential danger that represent genetically modified bacteria, especially if there are any kinds of leak. The impermeability of the device is ensured by the parameters of the 3D printing, using a shell thickness of 3mm.

The kit is divided into two different parts : the DNA extraction column and the detection part SnapLab. The DNA extraction device is entirely disposable. It is electronic free and it is designed to ease the DNA extraction protocol, making it accessible to anyone. This device is designed in multiple layers independent of the others. Each layer is filled with different reagents that will be used for the extraction. Each step of the extraction protocol is then realised by a mechanical rotation of a layer in relation to another one. This rotation allows reagents to drop in the right compartment, waiting for the reaction to occur.

This part raises multiple challenges. The device has to be as small as possible, but it has to include objects essential for DNA extraction (reagents, silica membrane…). Having this in mind, a cylindrical device including every necessary material was imagined. Each compartment is designed to take the right volume of reagent. Reagents are confined in their compartment until the user decides to rotate the appropriate layer, to make it work. When he does, the reagents are mixed together.

When dealing with fluids, it is important to pay attention to impermeability, especially since liquids have to be transferred between the different layers of the device. This is why each layer is isolated from the others with four O-rings custom made. By doing so, liquids are contained and cannot leak through the column. The different compartments are filled with reagents through catheters, that are only open when decided by the user.

When all the biological steps are over, a mix of DNA sequences and enzymes is obtained in the last compartment (see section Emline et Nico). DNA still needs to be cut and denatured so the sequence is able to fit to the probe (see section Clément et Romy). The enzymatic cut is made in the second part of the device. The last compartment of the extraction part is designed to be integrated into the temperature control compartment of SnapLab. The support is made to ease the interlocking of the two parts.

The DNA sequence of interest is now ready to integrate the probe. The first syringe-pump is activated to collect the product of the DNA extraction process. The DNA extraction column has fulfilled its job and can now be washed. Every removable parts can be changed (filter, silica membrane…). The whole device can be disassembled and plunged into bleach before other uses.

The SnapLab kit is at the heart of our project. It is designed to lead the analysis anywhere, as if you were in a laboratory. To do so, the whole kit is controlled by an application we have developed for android phones. We have designed a specific shell to integrate the phone. The entire kit has then been designed around the phone. In fact, the phone is both used as the sensor of our detection system and as image processing tool. The phone is connected via Bluetooth to the Arduino Card which controls the different steps of the analysis. The application also guides the user through the phone’s screen (see more information on the app page).

SnapLab is divided into two parts; a permanent part and a removable part. The removable part contains an Eppendorf tube of 0.5mL in which the dried plasmids are placed (see section Jusuf/Dam ou Clément/Romy). Once the DNA extraction has occurred, this tube is inserted in SnapLab and the analysis begins. The tube has to be perfectly closed before entering in the kit. This is done using four elastics that hold a lid on the top of the Eppendorf. These elastics are strong enough to keep the tube closed in the outside of the kit, but once the removable part is inserted, the lid gets pushed by the stop. The Eppendorf is opened for the rest of the analysis. When it is over, the removable part can be removed, the elastics pull the lid back, and bacteria that have integrated the plasmid are confined in the Eppendorf.

In our prototype, the permanent part is composed of several parts, previously listed before (in green). Printing the kit into several parts allowed us to easily modify any parts when needed. That being said, the whole structure could have been printed in a single part. It would have ensured solidity of the kit as well as impermeability between the different compartments.

The interesting part when designing SnapLab was to combine the very different areas we had been working on in the smallest device possible. The cell phone was the cornerstone of our kit. Since it is our light detector, it was necessary to design an optical system in front of the camera. To avoid moving the Eppendorf, we also had to think about a way to both controlling the tube’s temperature and transferring the different reagents needed at a given moment.

Parts that are used in the detection system are highlighted in red in the previous inventory. Our optical system is inspired by epifluorescence microscopes. More information can be found on the following link (section detection). The idea is to use a white source and a green filter to excite the sample. This excitation source is controlled by an Arduino card, allowing the application to control the sample’s excitation. Then, a photograph is taken by the camera of the cell phone. The photo is taken through a red filter and a magnifying lens. Thanks to an image processing program, the application turns the photo into a numerical value which represents the amount of fluorescence. After comparing this value to a threshold, diagnosis can be done. More information on the detection system can be found on the detection page. (lien vers la page detection)

Parts that are used for the temperature control are highlighted in green in the inventory. Our project requires several temperatures. Denaturation for instance happens at 74°C. Thermal shock, necessary for the bacterial transformation, oscillates between 0 and 42°C. This implies the following constraint: the temperature control system has to be related to the application, so the temperature can change when needed. Given that the kit had to both heat up and cool down, using a Peltier device was our best option (see more information on section temperature control). The temperature control system uses an instrumentation amplifier with the following electrical circuit that uses CMS components, that are smaller than the classical ones.

To lead the analysis, different reagents need to be incorporated in SnapLab. Those reagents are mixed in a particular order to have a final solution that expresses or not fluorescence. To do so, SnapLab contains a 3D printed syringe pump. This pump is designed to work with a specific syringe that the user will prepare in advance, and change when needed. This syringe pump is controlled by the same Arduino card previously mentioned, which means that once again the application can activate the pump when needed, to deliver the precise amount of reagent (see more information on section Fluid Transfer)

SnapLab has been an ambitious project especially considering the short amount of time we had. Each part has been designed and tested separately, but the whole kit has not been tested in real life conditions. The project can be improved in many ways. Using other material for example could improve the insulation of the different compartments, thus providing a better safety for the device. It could also be possible to facilitate the temperature control, by using good thermal insulating materials. Other designs could also be considered. A major improvement would be to tilt the screen of the phone when inserted in SnapLab to make it more convenient for the user. More interactions between the cell phone and the kit could also improve the efficiency of the different parts.

If you have your own ideas about how we could add additional functionalities to SnapLab, feel free to contact us via Facebook or LinkedIn. We would love to discuss with you any of your ideas.