Microbiology for the Masses

One of the biggest problems with biology is that it requires a lab. Culturing bacteria, something that grows everywhere and over every surface on this planet, requires a great deal of complex incubation steps and manipulating it requires a shaker, 2 temperature specific water baths set to hot and cold, expensive pipettes and reagents, and various autoclaved sterile equipment. In order words, if you wanted to do this at home, you are looking at an investment of thousands of dollars and the loss of an entire room of your house.

That is now looking to change as there is a growing market of synthetic biology platforms- dubbed “garage biology”- that can enable people to do sophisticated biological research in their own home without the need for the expensive and space consuming equipment. Last month, I travelled up to Montreal to try one such platform and  felt that I held the future of science in my hands.

 

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In a robotics makerspace in the hip area of Saint Viateur, I experienced the Amino, an all in one platform for the growth, transformation and genetic manipulation, and propagation of bacteria that combines the rigor and specificity of a full scale lab with the convenience of a device that takes up little more space than a personal computer. As I was doing a bacterial transformation (the implantation of DNA into a bacterial target), I felt as if I knew how the mindset of those who tested the first PCs. After all, before the first PC, navigating a computer required a morass of complex and/or convoluted systems of commands. The PC simplified all that by taking away the levels of complexity and creating a user-friendly interface that all could enjoy. In other words, these are the same theoretical gains a budding scientist would experience by using the Amino platform.

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Performing a bacterial transfection sounds daunting but in theory, is a very simple concept. One simply starts by growing bacteria-usually a strain of Ecoli that is harmless to humans-in a small 37C dome located on the top of the amino. 37C translates to roughly 98.6F, or human body temperature. The process really commences when the bacteria is transferred via a simple plastic inoculating loop to a nutrient broth that is then placed in a tube well that has been pre-cooled to 19C. This puts an environmental stress on the bacteria causing it to release a set of proteins that allow it to adapt to the new temperature. Just when it equilibrates to the changes, the bacterial tube is transferred to a second well that has been heated to 42C at which point foreign DNA can be added. This part of the transformation is called heat shock and this sudden change of temperature causes the bacterial to open its cell walls allowing to take in material from the surrounding environment. After this, the transformed bacteria is injected in a growth tube by something as simple as a plastic transfer pipette.

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The heart of this whole experiment is the DNA that is added to this bacterial mixture. With the right DNA, it is possible to have a tube of microbes begin to produce a variety of things from flavor extracts to paint to simply growing more of a certain sequence for use in other experiments. There are a few additional steps to get it to this form but the removal of the bacteria and purification of the product is mostly built into the Amino. Adding in some basic PCR and molecular biology equipment can enable users to generate their own sequences to insert and really do sophisticated biology in their own home. Even further, these “cDNA” libraries can be shared with others to allow an open source biology platform across all Amino users.

The software for the Amino is based on Arduino which allows a number of external apps to interface and allow all manners of experimental readouts, many of which have not quite been explored yet but the potential is virtually limitless. The base unit does have it’s own very useful readout features and all of them can be viewed its own website where users can monitor the colony number, pH, and temperature of the reacting mixture. As the bacteria grows, there will be changes in all of these that denote colony health and there are countless experiments that can be designed to simply test how certain things affect microbial growth so adding cDNA isn’t even necessary to begin to exploring the magical tiny world of bacterial cells.

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Science teachers are often seen as gatekeepers of content but that is changing. Tools like the Amino will allow curious users to begin their own deep dives into microbiology and similar platforms are being developed that will allow individuals to explore concepts in biochemistry, organic chemistry, and even particle physics all using the garage technology platform! Until then, my students will be working to beta test the Amino and do their own investigations. They will have their own ideas, projects, and experiments to test and most certainly will have a multitude of questions regarding controls, methodologies, interpretations, and troubleshooting. So my role is less as a science “teacher” and more a “principle investigator.” Rather than opening the doors for students to learn, I remove the blockades that will help students learn and gain valuable experience so that in a few years, they can solve their own problems and help others with theirs.

Much ink has been spilled over the importance of student driven inquiry based models of learning and innovations like the Amino will help drive the science end of this. The creators of the Amino have had requests for the machine from all over the world. North America, China, France, and even schools in the Amazon Basin want it and from personal experience, I can see why!  As a research scientist, the idea that an elementary student can study biology the same way I did when I was in the tech realm is thrilling. After all, personal commuting got really exciting when it hit the garage so perhaps the same can be said for biology.

For more information on the Amino and how to contact them check out http://www.amino.bio!

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