A CRISPR way of editing genes (still working on the crispness though...)

Genetic engineering is something that has long fascinated us. It holds the secret to eradicating genetic disorders, studying the function of almost anything in biological systems, and creating “perfect” organisms (where organism is a loose term that could refer to anything from plants in agricultural practice to humans in the 1997 movie Gattaca). So of course, the development of CRISPR created quite a stir the world over. And with good reason, I think. 

It’s still quite unbelievable that in Mod 2 we were able to sit at a lab bench, order some oligos from a company, mix some things together (alright, this may be a tad oversimplified) and cause a lasting change in E. Coli. A change they pass down to their daughter cells, which those daughter cells will pass to their daughter cells and then their daughter… Well anyway, the point is that we are doing some amazing, cutting-edge stuff. 

At my UROP, I’ve been working on using CRISPR to mediate homology-directed repair to convert GFP in HeLa cells to BFP, effectively allowing the cells to express blue fluorescence rather than green. The first time we visualized our transfected cells, we disappointedly scrolled through the sea of green in our plate until we saw EXACTLY ONE bright blue spot. Yes, it seems we had exactly one cell do what we wanted our hundreds of thousands of cells to do. Either way, it was beyond exciting to see that it actually worked. So when I analyzed the ethanol production in our CRISPR-modified (and very stinky) E. Coli in Mod 2, I was awed that our experimental samples had a SEVERAL fold increase in ethanol production over the control ones. 

Truthfully, I was pretty skeptical that our experiments would work. SO many things could have gone wrong: bad oligo design, ineffective plasmid transformation, dCas9 not preventing transcription well enough. And I mean, there’s always something that goes mysteriously wrong. But our experiments, for the most part, worked! While there are definitely some kinks that need to be worked out of the CRISPR-Cas9 system, the possibilities this technology opens up are incredibly exciting. 

“The miracle of life”: some truth in advertising

It’s everywhere: articles on recent research to find a cure, stories of people battling it, public service announcements to get tested for it. It’s cancer and somewhat ironically, this topic is taking over the medical field and people’s lives just as fast as the disease manifests itself. And yet, I believe that many people have yet to grasp the full extent of this disease or how it comes about. To begin with, I was fully flabbergasted to discover – while I was reading up on DNA repair for Mod 1, of course – that simple cellular activities and just everyday exposure to radiation can cause between 10,000 and 1 million DNA lesions in EVERY CELL of our body in just one day! Lesions that could lead to mutations, if not fixed. And we all know what mutations can lead to.

How are any of us even alive, you ask? Precisely my thoughts! Turns out cells are these superiorly sophisticated, MIT-level engineers because they’ve already got this all figured out. In 20.109, we spent a lot of time learning about base excision repair, this fantastic and evidently accurate method of fixing those thousands of lesions before they become mutations and lead to something like cancer. So we can all let out that collective sigh of relief. But still, I continue to marvel at just how intricate and delicate the body is and how truly lucky the vast majority of people are to not have some life-altering mutation. I know that wasn’t at all what the CometChip experiments were about, but this might be my biggest take-away from Mod 1. Learning about CometChip honestly just made me reflect on the huge importance of cancer prevention and the fact that mutations aren’t just something we can get if we ingest carcinogens or sun-tan too long.

On a related note, I think it’s so cool that there are these emerging tools to easily test our DNA repair capability. It turns out that this might be THE ultimate factor in how likely we are to get cancer.  So regardless of how healthy we think we are, why not test our body’s DNA repair potential early and prepare ourselves best against mutagens? I definitely hope things like CometChip become more commercially available and accessible to people. Cancer preventions seems to be piquing the interest of researchers lately and rightfully so, because we want to stop cancer in its tracks, way before it can even THINK of metastasizing.

20.10byee

I walked into 109 with zero wetlab experience. Apart from this, I can’t cook for the life of me. If I could burn water, I would. This potentially disastrous combination had me imagining all sorts of scenarios on the first day of lab. Now, four months later, I can honestly say 109 has been the class that taught me the most. I no longer feel completely incompetent in a lab setting. I don’t have to keep asking my lab partner what pipette to use. 109 also exposed many of us to our first real technical writing and everything this entails: reading numerous papers and being able to understand their main findings and identifying potential areas of future research, writing clear and concise methods, creating intuitive and instructional figures and captions, knowing when and where to include interpretations, exactly how to interpret data, and discovering the real meaning of ‘significance’.

Having the class split into 3 different modules allows us to become exposed to different areas of the field by scientists who are working on the cutting edge. All three modules were exciting and interesting, with fun lab components that allowed us to get comfortable with different techniques and research practices important in bioengineering. Although they were very challenging, the assignments also helped us improve our scientific writing and oral communication, which will become vital in our futures regardless of what we decide to do.

The open, safe, and enriching environment of 109 made this challenging class extremely enjoyable. I loved our small lab section, where we got to work close together while learning and collaborating. Despite the long hours spent on the assignments, I always felt like I was writing about something new I was learning, and I was fortunate enough to see it in action. The amount of time and dedication the 109 staff put into this class in order to make it such an invaluable experience is incredible, and I think it shows. Not many people can say they enjoy their lab classes, but thanks to you, I can J.

Thank you for a great semester!

All the gold I've ever wanted

Mod 3 was by far the most relaxed module of the year. I really appreciated this because, since so many of us are in 20.320, it was a stressful time in a lot of other classes. I really enjoyed learning about how biology can be used to make materials usually not made with biology. Although the other two modules were cool as well, this was the first module that really made me feel like a bioengineer.

Everything we did to prepare was pretty simple, since we didn't do the phage screening to find the best mutant, which would have taken more time. We prepared our phage in the gold solutions. May I just say, I did not expect gold nanoparticles to be a purple/reddish color. It was pretty cool to be able to tell my friends I was working with gold in my bio lab.

After our nanowires dried for a couple of days, we were able to image them with TEM. When we went into the room, Professor Belcher and Jifa were imaging the no-gold control. We saw what the Fe(III)PO4 were supposed to look like. Then, Jifa began imaging our nanowires. ALL WE SAW WAS GOLD.

 Although, since Professor Belcher told us we had more Fe(III)PO4 than most other groups, we weren't as worried. Then came the moment of truth. We charged our battery with the 9volt battery for around 10 seconds. Then we put the LED light on and we were SHOCKED when it turned on. Our battery worked, and I was ecstatic. Even though we have to charge it everytime we wanted to use it, this was one of the coolest things I've ever built.

For the last part of the year, we had to come up with our research proposal. This was probably the hardest thing we'd done all semester. Coming up with an idea took days. Additionally, after we had our idea, we had to polish it, which took even longer. While we were making our slides, we ran into many questions and problems with our idea. However, we finally finished and didn't die while presenting. It felt great to be done with this module and the semester. It may have been stressful, but the research proposal was a great experience and is a useful skill to have for our future.

Rolling Along

I really enjoyed Mod3 because it had a nice balance of hands on lab time, researching topics that interested us, making us practice our oral presentation skills, and we ended up with a neat little battery we can show off at home.

I never thought having too much gold could be a problem, but when we visualized our nanowires using TEM, our results looked nothing like what Professor Belcher showed us in class. I was scared that we had somehow managed to mess up the experiment (again), and was a little relieved when I heard it had happened to all other teams as well. Thankfully, we all got working batteries, so I guess too much of a good thing isn’t such a bad thing?

I didn’t anticipate one of the hardest parts of this module to be the rolling of the batteries (we’ve all rolled pizza dough before, right?), or the manipulation of lithium inside the glove box to prevent it from reacting with oxygen and exploding. Attempting to do this ourselves showed me how it is often not the biology or chemistry of experiments that cause them to fail, but other external factors play a huge role as well. Thankfully we had the magic hands of Jifa to help us out.

Although I don’t particularly enjoy speaking in public, practicing this is a very useful skill, and doing so on a topic of our choosing and in a welcoming environment like 109 is a great way to practice. Despite feeling like I learned a lot this semester, I didnt believe I knew enough to come up with a reasonable, interesting and viable research proposal. Nicole and Apekshya really impressed me with their knowledge and we ended up having a proposal I am quite proud of. 

When I grow up I wanna be a bioengineer...

...well really I wanna be a doctor, but at least now I have a better understanding of what bioengineering is. 

When I applied to MIT, one of the admissions questions was "Which department or program appeals to you and why?" I had already known I absolutely loved biology, specifically human and cellular physiology, so it was then that I had my mini Course 7 vs Course 20 crisis. Of course as this was only the application I was not expected to stick to the Course I wrote about, but I still knew that I would come across with a lot more passion if I chose the department I felt suited my interests more clearly.

I chose Course 20 because I want to invent more than just learn. I want to design and fix more than just experiment. And I want to solve more than just ask. Biology is the study of life and the molecules that make it up. Bioengineering is the study of how to use life to solve awesome challenges. That's what stuck out to me. I want to solve -- or at least begin to solve -- problems that inflict the lives and well-being of people all around the world.

20.109 has really been a transformative class for me. When I was in high school I worked in a lab for a while, but I didn't have a great deal of knowledge under my belt. My freshman and sophomore years here I worked in a lab again, except the premise of my work was in organic chemistry, an area I am not as passionate about. Then I got the opportunity to study DNA damage and repair. I got to optimize and utilize a new technology that is likely to revolutionize this research sphere. Then I got to genetically modify bacteria to produce more ethanol. I got to use cutting edge CRISPRi molecular biology that too is likely to change the course of humanity for the better. Then I got to build and test a battery with a cathode made out of viruses. I got to implement the same incredible protocol that even President Obama was privileged to witness first hand.

I feel so fortunate to have had these opportunities. Thinking about the amount of work the 109 staff put into this class, it puts a smile on my face knowing you all care so much about our education and our development as biologists and engineers. Lab classes are often boring. We often have to follow a protocol to a tee without really understanding why we're mixing A with B, etc., etc. and it really can feel like mind-numbing work. This class was very different. The prelab lectures put everything into perspective. The prelab presentations helped form the basis for the work we would do that day, and I never felt like I was working on a protocol I didn't understand. The work itself was absolutely remarkable. I am sure this is the only class in the world that gives undergrads the opportunity to work on these three specific areas all in one semester. 

The best part about this class was the confidence it instilled in me as I move forward in my bioengineering education. Not only did the labs teach me the biology, chemistry, and engineering I'll need as I advance, but all of the assignments have made me a much more informed student and aspiring scientist. We worked in groups to write a research paper. We worked independently on an extensive research report. And we worked in groups again to design a potentially game-changing biotechnology or protocol.  Looking back on this class, we did so much it really is hard to believe we squeezed it all into three months of work. 

I think the reason I love this discipline so much is because it so beautifully combines a passion to directly and personally change lives with the cutting edge science necessary to do so. 20.109 put that into perspective for me. I am forever thankful because of that. 

I really want to again thank the 109 staff (Noreen, Leslie, Maxine, Angela, Sean, Emily, and Bevin). Your dedication to us made this class so enjoyable and so fulfilling. I hope you know how much all of us appreciate the hard work you all did for us. You all are what is great about MIT and about Course 20.



With appreciation always,
David

P.S. These beaker DNA mugs are amazing!! I use it all the time now. 

Thoughts on Module 3

We looked. We looked again. Why was there so much gold?

My heart started beating faster. Did we screw something up? Was it our fault?

I really enjoyed Mod 3 despite the, let’s call it, “Gold Conundrum.” While all the modules were incredibly exciting, this module stood out to me the most because of how obvious and straightforward the real-world applications of phage-batteries were. (It also helped that I could take my phage-battery baby home with me) I wish we could have done more experiments and in general focused a little more on this project instead of the research proposals. I felt like we weren’t exploring this topic as deeply as topics in the previous modules.

When I realized that we would be presenting our own research idea, I was terrified. None of my previous classes had given us so much leeway to create something original. To be honest, I didn’t think I had the knowledge and experience to propose a novel project. But, after I read some CRISPR papers, ideas came on their own, so much so that I felt surprised by myself. For the
first time I can really envision myself as a future researcher.

On that note, I'ma leave you with a parting meme: