So these past two weeks have been a whirlwind of research and feasibility questions. After our post-translational modification project was deemed overly complex and not feasible, we started brainstorming other ideas for the main project.
Like we said in the first research update, we first looked at quality control mechanisms of the registry, and how robust parts are. Currently there's no way to tell how parts will function in other systems besides the one it was designed in. This is a big limitation of synthetic biology, as it doesn't allow for easy part implementation. So we thought about designing a way to test and quantify how robust a part is in relation to variables such as temperature, pH, and salinity. Unfortunately when we presented this to our advisers they offered many drawbacks and limitations to this project, not to mention how incredibly hard it would be to pinpoint one variable and make the system more robust for that specific variable. There are just too many factors to control. So we still kept thinking about quality control, but not for robustness.
That quality control perspective lead us to look at the registry and think about the overall shortcomings of it. One of the major ones we realized was how un-standardized the characterization data for the parts are. Each year, teams upload parts with little to no characterization. And even if there is a good deal of characterization, there's no way to compare two parts because they did completely different tests! So that lead us to one of our current side projects, which is to develop a standardized characterization protocol system that all teams would use when submitting parts to the registry. But every year teams create protocols that never get adopted or used. That's why we started contacting every iGEM team we could to get a massive collaboration across the board to know that the protocol was worked on by a multitude of teams.
So we've gotten feedback from over 30 teams that want to collaborate, and we have many plans in the works to develop this standard. (For more on this project, read the post below or email us at PurdueBiomakers@gmail.com)
As for our main project, we had two main ideas that we focused on this week. The first one was a way to retrieve toxic metal ions from contaminated water sources, and the second was to look at recreating steps towards multicellularity in a laboratory setting. We researched both ideas thoroughly, and determined as a team that the multicellularity project was a better one, because it's much more novel even though it's more complex. We looked at some of the initial steps that single celled organisms take to evolve into multicellular ones, and found that polarization of cells relative to a surface is a pretty important step, and also doable within our limited time frame. We are now researching ways to first grow cells in a single layer biofilm, and then how to get those cells to recognize their attachment to a surface.
That's what we've been working on the past two weeks, hopefully we'll start posting weekly research updates on Fridays to keep everyone in the loop.
One of the things we're looking at this year is collaborating with as many schools as possible to create a definitive characterization standard for the parts registry. Because we all know how annoying it is when you go looking for parts and you can't find any characterization data, or characterization that was done poorly. We are trying to write a standard protocol that all teams need to follow before they submit a part to the registry. This will help future teams find high quality parts easier and faster.
Unfortunately, every year teams write protocols that they think everyone should follow, and nothing ever gets done. We think this is because it's written from one team's perspective, and not reviewed by multiple parties.
That's where you guys come in!
We're looking for teams that are willing to at least look at the protocol we write and make suggestions on how to improve it. And maybe if we do it well enough, we'd like to have teams actually use the protocol to characterize their parts for this year's competition.
This will not only help iGEM be better characterized, each team that collaborates with us will be able to use that for completing the requirements for a gold medal in the competition.
But we haven't written the protocol yet, we're just fielding interest and seeing who's willing to collaborate. We're hoping we get a large number of teams to help, because the more teams that help and approve it, the more likely an actual protocol will be put in place by iGEM HQ.
So if you and the rest of your team could each take this short, 10 question survey, it would help us immensely and be the first step to creating this standard!
Here's an update on what we've done this week and what we're doing with the project.
Our initial idea was to create a tool kit for the registry that allows iGEM teams to easily implement post translational modifications (PTMs) to complex proteins that they want to produce. Many eukaryotic cells have these PTMs to make the proteins they need, but prokaryotic organisms like E.coli have a much smaller selection of PTMs. So iGEM teams are limited in what proteins they can produce in E.coli. Our idea was to create a toolkit of devices and enzymes that other teams could put in their device to allow for the needed PTMs to work. So that's what we spent most of this week researching.
Unfortunately, after researching this idea we decided that PTMs weren't really a good project direction and that there isn't much we could do with it that would really be new or impressive. We can't create a toolkit like we originally planned because each type of PTM is radically different, even when it's two cases of the same modification. So since we can't create a useful toolkit, all we would be doing is putting coding regions in E.coli and seeing if it worked, which isn't really a good project.
So we started talking about quality control after Dr. Rickus mentioned it to us. We realized that there's no real standard for robustness of a part in the registry. People just put parts in one situation and test it in that specific set of variables, which doesn't help other teams if they want to use it in a different strain of microbe or under different conditions. So we read a paper that just came out that talked about creating a quality control number for genetic parts that shows how robust a part is to change. One of our focuses will be to adapt their method to iGEM parts and create a new system for measuring robustness of parts in the registry so teams can easily see how well a part can be used in different situations. It will add a level of characterization to the registry that is sorely needs. We are also talking about creating a number of devices or even a toolkit that teams can use to control robustness of a part. So let's say we create one device that keeps the output of a circuit steady in temperature changes, one that keeps steady in pH changes, and one that keeps it steady when the host species is changed. Then teams could use our quality control devices to better build and characterize their parts.
That's the direction we'll be focusing on for the last bit of this week and all of next week, and hopefully we'll have a working project outline by the end of next week.