I Love Viruses! (and other things I never thought I'd say)

This past few weeks in 20.020, I've come to a startling realization:

I love viruses!

Note: that should not be read as "I love experiencing viruses." A clear distinction must be made here. Regardless, recently my job in Team Human Health/Cancer/Turtle has been to look into viral vectors and their human implications, and I am finding that I actually really enjoy it. I have been able to research many different kinds of viruses that are widely used in clinical applications and what makes them unique and effective. The virus we decided on is the EBV/PAC viral vector, which has been widely used in medicine and can hold an insane amount of genetic material. It was recently used to construct a human genomic library. In other words, it can pack a lot of information into a small space. Most people have already had EBV, so they are immune to the wild-type virus. This means that clinical trials have been pretty successful and low on side-effects.

Because of the fact that most people have already had EBV, one concern of ours was that the immune system would recognize and target the host virus and destroy it using existing antibodies. However, further research showed that the immune response to the virus is dependent on the presence of helper viruses found in the wild-type infection. Without these viruses (which are not present in the manufactured vector), EBV can successfully inundate its target cell.

The research on viruses is pretty much complete at this point, so I'll be moving on to helping the team with other aspects of the system; but the EBV vector will always have a special place in my heart (another thing I never thought I would say). I'm excited to see what other interesting things come up as we move on with the project!

We're Makin' It

In the past two weeks, I've seen our decomposition project grow from hand-wavey ideas and concepts to something concrete, with detailed parts specifications and a plan of action to bring it all together. It is very exciting, being a part of this process of creation and seeing how your personal contribution plays just as important a role as everyone else's.

I think it's hilarious how, despite our thoroughness in designing the system, we entirely overlooked the method by which the e. coli would receive their sustenance! As it currently stands, our chassis wouldn't have lasted much time at all, when you consider the amount of energy required to pump salt out and build decomposition enzymes, all while being starved in the middle of the salty ocean.

Wednesday's inventor/investor activity was highly illuminating in terms of just how much capitalism gets in the way of advancing the current states of science and medicine. I voluntarily hindered another team's progress just so I can sign an exclusive deal and rake in the dough, and while the stakes were significantly lower in our little social experiment, I can't help but to think how much these things happen in real life, on a large scale.

Post Tech Spec Thoughts

The feedback we received after the tech spec was very useful: to either switch our chassis or our target location, and to simplify our system. Looking back on it, it seems like it should have been obvious that we should use an ocean organism to solve an ocean problem, but I think we were drowning in our many devices to the point where we forgot to even think of what our system would look like as we deployed it. Our E. coli wouldn’t have had a carbon source or even a native salt water survival system and wouldn’t have lasted very long in the sea. Right now, we have agreed to switch to a cyanobacterial chassis but are still deciding what strain to use- a common strain that floats, or a less-well-researched species that can adhere to plastics and other hydrophobic objects.

As for the device list, we are narrowing down our focus from four targets (PET, polyethylene, polystyrene, and phthalates) to just one, polystyrene. (We will add in others later if we have the time.) We’ll also have to remove my favorite part, the OmpW salt pump, as cyanobacteria naturally thrive in the salty ocean water. We are not sure now whether to even include a similar cell death mechanism, because how much damage could these cyanobacteria really do if they got loose?

The cell death question is now one of a large number of open questions on this project, and it’s kind of difficult to know how to proceed in answering them. I’m almost wishing for another Tech Spec—another chance to regroup, reassess, and move us forward in the best direction possible. This project is also making me realize just how challenging the different aspects of an open-ended project are: narrowing down research so the problem does not seem overwhelming, planning out a timeline for discussing certain aspects of the problem, and balancing higher-level thinking with detail specification. They are all super hard! Hopefully by the end of the semester I’ll have gotten at least a little better at these skills, even if we don’t have a design that would really work.

After reviewing our feedback and planning out a new direction of research, our group is going strong.  Go Team 99 Bottles!

Coloring With Cancer

I really enjoy brainstorming. The process of developing ideas under the assumption that everything is perfect and nothing can go wrong is fun. Actually fleshing out an idea is a much harder process involving some serious reality checking, and that is exactly what I discovered this week. Our project is to develop a biological mechanism to tag GI cancer. Ideally this would replace the current, highly-invasive methods implemented in hospitals today. Most widely used are endoscopies, which involve sticking a long tube with a camera down the patient's throat-- a less-than-pleasant sounding procedure. Hopefully our project would allow patients to physically see something in their excrement that would alert them to the presence of cancer cells. 

This sounds like a simple enough concept. I thought so too, until we actually began looking into how cancer environments actually work. Many of the surface proteins that we had intended to tag are found on normal healthy cells, which increases the possibility of a false-positive. In addendum, the high turgidity and low pH of tumor microenvironments make them nearly indelible to drug access. Our method will need to be able to detect cells on a very nominal level, before that microenvironment establishes. However, this creates a problem, as then the surface proteins will be in similar concentrations to the surrounding cells. 

Despite these obstacles, the team managed to conduct some stellar research and find surface tags that are specific to GI cancer cells. We're still settling on which receptor we are going to use, but at least now we have options that can latch onto our target cells. Furthermore, we found a high-capacity adenoviral vector into which we could transform our desired gene sequence. Our plan involves a large amount of recombinant DNA, so the high storage capacity of the virus is a major draw. It also is highly effective at accessing target cells, so breaking into the tumor microenvironment should be much easier. While the term "adenovirus" may raise some red flags, all of the clinical trials involving its use in other cancer studies saw minimal side effects. 

As I said, brainstorming with no consequences is fun, but I am finding that I definitely prefer the actual design process of a real idea. Sure, it's harder and there are plenty of obstacles, but our project is beginning to come to life, and I'm really excited to see what challenges we overcome next and how our design continues to grow from here.

The Devil's in the Details

      The last two weeks (aside from the much need interlude that was spring break) have largely been spent investigating at ever increasing levels of specificity the projects we have chosen.  It's very easy to see why curing cancer is the subject of such a large amount of research; there are seemingly infinite possible mutations that can lead to the disease making it difficult (if not impossible, at least for the moment) for any one detection or treatment method to work on all possible cancerous phenotypes.  As such we've decided to narrow our primary goal to detecting gastrointestinal (GI) cancers, as that is an area of the body that is fairly accessible.  You can ingest a pill, put something in a piece of food or just straight up use a scope to get things into the GI tract; much easier than something like the brain which has that messy blood-brain barrier to contend with.
      Our decision to narrow the scope of our project has made our job of detection (at least a little) easier.  Since GI cancers are in the same areas and involve many of the same kinds of cells, they tend to have more in common than any two generic cancer cells from other forms of cancer, making it easier to avoid false positives on our test.  The job of finding a reliable marker was still in no way trivial.  We investigated a variety of surface proteins that are common on cancer cells but ruled them out because most were also upregulated in several other non-cancerous diseases.  In the end we decided to focus in measuring an activity within the cells that we are screening for cancer.  According to research we found, one of the most common mutations in GI cancers is loss of function in the APC gene.  We'll go into more detail about how we plan to check for that mutation in our tech spec review this week but I'm pretty excited about what we've come up with thus far.  Overall, I think we have a pretty solid system planned for checking for APC mutation and while I hope we can find a more generalized solution (perhaps something involving the common loss of DNA repair mechanisms), things are looking pretty good.

APC, Our Little Friend

When we first sat down and discussed our project ideas, everything seemed like it would be a breeze. We were able to come up with tons of ideas and it seemed like we could solve them all right then and there. And I’m now coming to realize, just like the rest of my group, why cancer sucks.  Since a cancerous cell is essentially a regular cell that divides more than usual, it makes sense detecting the differences between healthy and cancerous cells would be very difficult—the task seemed insurmountable a few days ago. I found it hard to believe that a couple of college freshman were going to be able to produce anything that billions of dollars of research wasn’t able to produce. It seemed like every time we found a potential avenue for detection, we found article saying, “two-billion dollars went into discovering this detection method could never work.” It was pretty discouraging until we stumbled upon a nifty little protein we like to call APC. It seemed like in the sea of proteins in the cytoplasm, this one just might have been overlooked earlier in cancer research. While it’s possible there’s someone out there researching this protein right now, we were at least able to begin to exploit this. APC is the most commonly different protein in colon cancers, and it seems to have a lot of potential for success with this project. I’m looking forward to everything coming together just in time for the tech-spec review. One small matter that could be an issue is that our method relies on the viral delivery of mRNA. This could be a huge bioethical barrier because the FDA would likely not approve the viral infection of humans for the purpose of only checking if someone has cancer or not. If it were a cure to cancer, perhaps the FDA could reconsider. For this project, however, I’m sure it’s fine to ignore the bioethical side of things for now.  

Signalling spectrum regulation?

It's the end of week 8 of 20.020, and we're finally starting to see what our projects will be looking like! The plastics decomposition projects is progressing well: we've found our enzymes and we have a general idea of how we would like to regulate the system. Now we just have to hammer out some details for the Tech Spec. I shudder to think about how much debugging we would have to do if we were building it for real.

In one of the classes, I was thinking about our signal molecules (TetR, AlcR, ...). All the signal molecules we are using are popular, and probably will be used in other projects. What would happen if our project came into contact with another, and they started messing with the internal signaling in each other's cells? Worst case, this could lead to almost completely unregulated behavior, like the complete shutdown of a feedback loop, which could be fatal if in a larger organism. Best case, both projects shut down and disable.

So I started to think about how biological engineers should negotiate to not interfere with each other's signaling. Electrical and mechanical engineers don't really think about this, because things they don't attach generally don't interact. But when they do, really bad things can happen (see: Fukushima, Challenger). Maybe they need to think about it some more.

The people who have most experience with this, however, is radio communications. Companies sign up to use a specific wavelength for each specific application, so no two companies every have interference. Maybe biological engineers can register a certain class of signals just for them. Preferably ones that don't occur in nature, so nature can use its own domain of signals.

However, this scheme disproportionately hurts small laboratories and tinkerers, who can't afford the fees and are therefore blocked from the market. I don't have a solution, but I think this issue will become increasingly important for biological engineering as more and more projects are put out into the world.