Team:FDR-HB Peru/Hardware

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Here at hardware we initially created a bioassay as a means to incubate the bacteria to detect Cadmium in fishmeal products that have been diluted into the bacterial liquid on a boat. However, after discussions with TASA we shifted ideas and decided to use a cell free system instead as it’s easier to educate the fishermen about its use and it does not require the maintenance of living organisms. Since we have changed our focus, the our bioassay is no longer necessary for the implementation of our solution, which is why we have decided to turn our bioassay into a shaking incubator for the use of iGEM teams around the world who don’t have direct access to a lab. This will inspire and abilitate more people as well as teams to explore the field of synthetic biology.

Design of the Orbital Shaker

We based our orbital shaker in a design we found online ( We used this design as a base and started modifying it to suit our needs.

We introduced a self-regulating heater to keep bacteria at an optimal temperature (37°C). The temperature regulator will turn off the heater when the temperature surpasses this temperature, and it will turn the heater on when the temperature drops below it. At first, we decided that the heater was going to go in the middle of the upper part of the orbital shaker, but we realized that it wouldn’t heat the bacteria high enough and it took a long time to heat up, so we have been brainstorming different possible solutions for this problem. Unfortunately, we cannot test these ideas because under our current situations we cannot access the shaker which is in our lab.

For the test tube holder we made five holders so the user can have multiple sets of bacteria. Also, to keep light from entering the bioassay we decided to encapsulate the upper part of the bioassay.

Last but not least, we decided to power the orbital shaker by using a 12V battery. This way the shaker can be taken on boat trips by fishermen.

The motor is used to shake the upper part of the bioassay in order to make sure the bacteria are able to obtain enough oxygen to work properly. The battery is just supplying power to the motor and heater which is connected to an arduino chip that has an lm35 temperature addition in order to monitor the temperature and keep the heater from heating the inside up past 37º C. The tubes merely contain the bacteria in the medium inside. There will be 5 tubes in order to allow multiple sets of bacteria.

The motor shakes a part of the container, which is heated to 37 degrees. This ensures a quick, optimal breeding environment for the bacteria.

Most recent prototype of our bioassay.

Shaking Incubator Manual

When realizing that Africa and South America accounted for less than 4% of the teams, we couldn't help but question the financial aspect of the situation. To bridge this gap, we have worked on making open-source instructions for the construction of the shaking incubator to help other institutions have an easy and cheap way of growing bacteria. What makes this even better is that it can help people all over the world practice synthetic biology as long as they have $40 (reduced from common $900). This way several institutions (not just iGEM teams) can engage in world-changing projects. The manual will be finalized when specific measurements are obtained upon the return to our technology department.

Shaking Incubator Instructions (In Progress)

Hardware Component of the Cell-Free System

As previously stated we are looking into applying our bioassay as a low-cost shaking incubator for iGEM teams that don’t have incubators in the labs of their facilities and cannot afford a more expensive one. Currently, we are in the process of creating an instructional manual so teams are able to build their own shaking incubator from scratch, however, due to the COVID-19 pandemic, we don’t have direct access to our lab. For that reason, we are going to be collaborating with the Tübingen iGEM team, who would 3D print and laser cut our shaking incubator and test it by conducting a growth curve with E.Coli to then give us feedback on the model. As well as providing us with knowledge for the creation and testing of our new alternative; a cell-free “DipStick”.

We are hoping that through their testing and feedback we can continue to improve on our design as well as the instructions we have made along with it to inform other teams and science groups interested in synthetic biology on how to build the shaking incubator. When we have finalized the design and instructions we will make them public and aim to help people all around the world find a cheaper way of incubating bacteria.

Freeze-Drying the Cell-Free Test

As explained in the integrated human practices section, we wish to lyophilize our construct onto paper in order to reduce maintenance costs and make the test easier to use. According to our research and interactions with Arbor Biosciences, this should be possible. If we are not able to do this, alternative liquid methods will be pursued.

We intend to use the protocol developed by professor Keith Pardee from Harvard University written in his paper "paper-based gene networks." (Link)

Given the current circumstances, we are unable to run any tests (no lab access). However, TASA, our sponsor, is willing to run the freeze-drying tests for us. At the moment we have attempted to set up experiments to test the ability to freeze-dry. The master mix has a GFP control and therefore experiments ensuring its expression would be set up.

Pipets capable of pipetting 0 –100 μL
Phosphate-buffered saline
Sterile and nuclease-free 1.5 or 2.0-mL Eppendorftubes
Water bath
Nuclease-free, barrier tips
PCR tubes or multi-well plates
Nuclease-free, molecular biology-grade water
Filter Paper

Tuebingen Team Collaboration

Throughout the pandemic, we established a collaboration with the Tubingen igem German team. Being a High School team in a third world nation that will most likely open schools in late 2021, we realized that to execute our plans next season, we needed all the support we could get from other teams to avoid any possible setbacks. For that reason, we are extremely grateful for Tubingen’s mentorship in the process. Their help regarding our freeze-drying protocol and their guidance through certain obstacles and possible issues makes us feel confident that our project will be done correctly when the opportunity arises. Furthermore, the Tubingen team, having access to a lab and tech department, has agreed to build our shaking incubator with the manual our hardware team has set up. Their feedback will be very helpful and their attempts to run growth curves using the device will let us know how to better improve certain design aspects. So far, we have had three meetings to check in and troubleshoot possible problems.