I was determined to get "hand's on" with my genome editing bioethics research, so I enrolled in a four-day lab course that was being offered at a community lab in Brooklyn, NY.
What is a "community" lab? A lab that anyone can join to work on their own projects. Much like a gym membership, becoming a member gives you access to the lab, the equipment, and some supplies to get you started. This particular lab is called Genspace, and is “a nonprofit organization dedicated to promoting citizen science and access to biotechnology. . . providing educational outreach, cultural events, and a platform for science innovation at the grassroots level.” (1)
I signed up for the "Biohacker Boot Camp" course, which promised to teach me how to "extract our own DNA, analyze ancestry through bioinformatics, splice genes into bacteria, and learn all the standard techniques such as using pipettors, gel electrophoresis, amplifying DNA with PCR reactions, working with restriction enzymes to build plasmids, and growing and transforming bacteria." (2)
Day 1: Pipettes, isolating DNA, and "polymerase chain reaction"
On the first day, I met my instructor, Dr. Mike Flanagan, and the fellow students I would be working with for the next four days. It was interesting to see that we all came from different backgrounds (even my instructor revealed he had a Ph.D. in electrical engineering!) and some, like me, had no prior experience in a lab. I also learned that some of the current members of Genspace got started with the same class I was taking, and went on to join the lab to pursue projects as biotech entrepreneurs, synthetic biology hobbyists, and artists.
We started with an hour-long introduction to some of the basic concepts in molecular biology, and while the content was robust, the explanations were designed for learners with limited biology knowledge, so I was able to learn quite a bit. The big goal for the class was to test our mitochondrial DNA; a small portion of DNA that we inherit from our mothers. We were also instructed on how to use a pipette (a tool used to transfer tiny and precise amounts of liquid) which we would be using a lot in the next four days. Then, the hands-on work began.
We swabbed the inside of our cheeks with a Q-tip and then inserted it into a small test tube filled with saline. For the next two hours, we were in the lab spinning, pipetting, shaking, and boiling our small sample. Our instructor guided us through each movement, and told us what each step was supposed to accomplish to help us learn more about the structure of cells at the molecular level.
For instance, since most DNA is inside the nucleus of the cell, the cells need to be ruptured to free the DNA. And because rupturing the cell also frees enzymes that will destroy the DNA, these enzymes need to be neutralized by an additive.
By the end of the process, I was staring at a tiny test tube that had my DNA strands floating freely inside. The more I looked, the more I felt an odd feeling creep over me— I was holding my DNA, my genetic code, isolated from my cells, in a test tube. . . It can only be described as the strangest feeling of vulnerability I've ever experienced.
The final step we covered was "polymerase chain reaction" (PCR) where a chosen segment of DNA is replicated exponentially. By replicating the specific segment of DNA we want tested (in our case, a small portion of the mitochondrial DNA), we get a rich sample to send off for testing.
PCR requires adding “primers” to the sample; short DNA molecules that will guide an enzyme that copies DNA to exactly the right spot in the 3 billion letters that make up the human genome. If DNA can be thought of like a book, the primers are the bookmarks that show the pages in the book where a photocopy is supposed to begin and end. The PCR starts after putting the sample in a thermocycler (a machine that raises and lowers the temperature over and over) and turning it on to the correct setting. The temperature changes create a reaction where the DNA strands separate into two halves, and build new halves onto all the old halves.
Day 2: Gel electrophroesis
On day two, we were introduced to “gel electrophroesis”: using a slab of thick gel submerged in a salt solution connected to an electrical power supply to check the quality of our DNA sample.
We learned the recipe for making and molding the gel, and made one of our own together in the lab. We also learned which additives we needed to pipette into our sample to prepare it for the gel, and where to put our DNA sample in the gel once it was set.
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The glowing clusters of each of our DNA,
suspended in gel.
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Once the gel was set, positioned in its salt bath, and the DNA had been added, we were ready to safely apply an electric current to the gel using electrodes at both ends of the gel connected to the power supply. Because DNA is negatively charged, it migrates towards the positive electrode, with short strands moving faster, and long strands moving slower as they tangle in the molecular obstacle course that is part of the structure of the gel.
After letting the gel sit for awhile in the magnetic field, we turned off the electricity, removed the gel, and put it under UV light, where the DNA and its additives started to glow inside the gel.
Under the UV light, we were able to see the concentration of different sizes of DNA from our sample, which allowed us to assess its quality. The heavily concentrated clusters of DNA glowed brightest, and the less concentrated clusters glowed dimmest. And depending on how far the clusters had advanced through the gel, we were able to determine the length of the DNA within that cluster. According to our instructor, all of our samples appeared to be good.
Day 3: Plasmids, restriction enzymes, and transforming bacteria
On day three, we learned about plasmids and restriction enzymes in preparation for an experiment with bacteria. This was a completely new topic for me, so it was a lot to learn, but I was able to grasp the basics: plasmids are circular forms of DNA, and restriction enzymes are proteins inside cells that evolved in bacteria to search and destroy any DNA that doesn’t belong. Because restriction enzymes “search and destroy” DNA in a very targeted way, they can be used like molecular scissors to cut and paste DNA to literally ‘build’ a plasmid.
This introduction prepared us for our experiment: modifying E. coli plasmids to produce E. coli colonies that were bright red. We learned about the structure of the particular plasmid we were targeting and how introducing the restriction enzymes would change the plasmid. We returned to the lab and were guided through introducing the restriction enzymes, plasmids, and bacteria together in the right order before putting it all on a petri dish and placing it in our incubator to grow overnight.
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The positive control is the only petri dish
glowing bright red under UV light, but a
closer look shows that my team’s dish has
a few colonies going strong!
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By the end of this experiment, I had officially genetically modified my first organism!
Day 4: Bioinformatics and analyzing ancestry
On our final day together, our first activity was to examine the petri dishes we had left in the incubator. The results? Bright red colonies of E.coli bacteria that glowed under a UV light! The experiment was a success.
Our next activity was to sit together to review the results of having our mitochondrial DNA sequenced. Before viewing our results, we learned a bit about bioinformatics—the task of taking the DNA sample and sequencing it into a string of letters that can be analyzed.
At last, it was time to view our results, and I was first to be put on the spot. Our instructor pulled up a Word document containing a string of 329 letters. A portion of my mitochondrial DNA sequence was displayed on the projector.
If I thought holding my DNA in a test tube was a surreal experience, seeing a piece of my mitochondrial DNA that connected me to my maternal ancestors was equally so. What did each letter on that Word document determine about my body? How did this string of letters connect me to my mother, grandmother, great-grandmother, and beyond?
The thought about my great-grandmother made me remember a story that was told at the family dinner table only a few weeks before: how as a young, unmarried woman in the 1920s, my great-grandmother made the unthinkable journey of traveling from Minnesota to New York City alone by car. And here I was, sitting in a lab in Brooklyn after my own first-ever solo road trip to New York City. Musing on our shared experience while staring at our shared DNA created a sense of oneness and connection to my maternal heritage that I had never felt before.
Next, we looked at my maternal "haplogroup.” A haplogroup is an ancestral group based on a common line of lineage. Our maternal haplogroup is our ancestry line traced through the mitochondrial DNA we inherit from our mothers.
Each student had their turn to look at their maternal haplogroup, and together we researched the geographic areas in the world that are associated with our particular maternal haplogroup to get a picture of where in the world our maternal ancestors may have come from. And while we were all from different haplogroups, I learned that human mitochondrial DNA is incredibly similar; in the approximately 200 base pairs of mitochondrial DNA that we looked at, between the eight of us there were only about 6 total differences.
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| A DIY thermocycler |
To finish, we learned that some of the lab equipment we used, such as a thermocycler and a centrifuge (used for spinning test tubes really fast) can actually be made by hand for a DIY lab. We looked at a few examples of DIY lab equipment, and while they still required some complex assembly, anyone with the motivation to learn how to assemble this equipment could possibly create a decent makeshift lab on a limited budget.
2 months later. . .
This four-day class gave me an incredible introduction to molecular biology and working in a lab. I picked up new skills like pipetting, using various pieces of lab equipment, and how to be safe, organized, and sterile while working with different lab materials. The lab has become a less-intimidating place for me as a non-scientist, and I feel ready to try any other lab-based experiences when given an opportunity in the future.
I also felt like this class helped me commit more biological concepts to memory than any textbook I had ever studied. My instructor gets part of the credit for being a great presenter, but a lot of the educational magic was being able to “see” firsthand how each concept tied into our experiments as we were performing them. (Its hard to forget what a restrictive enzyme is after it featured in two lab projects you performed yourself!)
And finally, I felt inspired to become a “citizen scientist.” I don’t know if I will be building a DIY lab in a basement or joining a community lab just yet, but I do have a new desire to continue experiencing and learning science first-hand.
And as for bioethics, through this experience I've become very intrigued by the idea of "citizen scientists" or amateur biologists working on independent biology projects. Where will DIY biology take the future of biotechnology? How will it impact society? Is a humble entrepreneur capable of creating the next great invention to cure the ills of humanity, or unknowingly unleashing devastation on the human race? I’m interested in hearing more from the biohackers and citizen-scientists themselves to hear their thoughts.
Special thanks to Dr. Ellen Jorgensen of Genspace for editing help!
SOURCES
(1) Genspace. (n.d.). About. Available at: http://genspace.org/page/About
(2) Genspace. (n.d.) Biohacker Boot Camp. Available at: http://genspace.org/event/20150706/1800/Biohacker%20Boot%20Camp.
