Greetings fellow iGEM members and enthusiasts, hope you’re all having a great summer! This week has been a busy week for the summer intern-team back over here, but we’re getting close to finally conducting our tests!
Monday, June 1st
On Monday we all worked as a team to develop our Microbial Fuel Cell (MFC) project as much as we could before we presented our ideas to the iGEM members and faculty advisors still located on campus on Tuesday. We developed presentations for the MFC project and the Lignin Project and ensured that both were as equally developed as one another by the end of the day.
Tuesday, June 2nd
On Tuesday we presented our project ideas to our advisors and other members located on campus. After receiving feedback on both projects we came to the conclusion that we would be the most successful working on the lignin project, so long we ensured that our work was accurate and thorough. We put the MFC project on the shelf for next year’s jamboree because we would have more time to work and develop the project than if we worked on it this summer.
For the rest of the day we continued to work on the lignin project and split into three teams. An assay team, killswitch team, and enzyme team. The assay team researched assays we would use to collect data for our project. The killswitch team found promoters and killswitches we would use on our engineered yeast strains, and the enzyme team collected and organized the enzymes we would test. We decided to test four different enzymes, two from termites and two from fungi, and two different helper enzymes.
Wednesday, June 3rd
On Wednesday we have concluded that we’d test the enzymes/helper enzymes in combination and estimated about 120 tests to be conducted. We met with our graduate advisor, Sam Lee, and worked with her to develop our plasmids and G-Blocks. Originally, we assumed we could finish designing our plasmids and blocks by the end of Wednesday, but ran into some obstacles. We continued to work on developing our plasmids and had to continue working on them through Thursday and Friday.
Thursday, June 4th
On Thursday we continued working on our plasmids and blocks and found “errors” on NCBI, the website we used to collect the sequences for our enzymes, and found R’s and S’s in the DNA of our termite enzymes. After emailing Dr. Scharf, our Termite Guru, he cleared up the reasons for the R’s and K’s and gave us the correct nucleotide sequences.
Friday, June 5th
After three days of grueling work we finally finished designing our genetic constructs and believe that we can finally order our DNA on Monday the 8th, of next week.
Apologies for the late report, these should come out on Fridays in the future, but welcome to the first weekly report for iGEM Summer 2015! Our goal with these reports is to keep everyone in iGEM in the loop on the development of the project this summer.
So, starting things off with last week. On Tuesday, after getting our desk space and lab approval to Bindley, we dug into the biodigester project, starting with researching the enzymes we would need to do all of the breakdown in our preprocess. Things were looking good when on Wednesday, we met with Dr. Mosier (ABE professor who does research on biodigester pretreatment) to ask about how our solution would compare to current practices.
Dr. Mosier informed us that current industrial pretreatments essentially pressure cook the plant matter, exposing it to high temperature and high pressure. This melts the lignin, because lignin is hydrophobic, it wants to reduce its surface area as much as possible, so it clumps into small spheres. This allows the other enzymes (cellulases and hemicellulases) to go in and breakdown those polysaccharides (which happens in the biodigester). It turns out that lignin monomers actually inhibit one type of cellulose activity so our solution of just breaking apart the lignin may have a counter-productive effect on the efficiency of the biodigester. Dismayed with this news, we felt as though we had hit a dead end Wednesday afternoon. On Thursday, we resurrected the microbial desalination cell project as a back-up and began looking at details pertaining to that one. We found some great potential for a project.
On Friday, Arren discovered a paper in which a group of synthetic biologists had engineered a yeast cell to perform all of the biodigester processes except pretreatment. Suddenly, our lignin-breakdown idea was relevant again because we would breakdown the lignin but it would not inhibit the cellulase activity because the cellulases are only present inside the cell while the lignin is only outside of the cell. We also continued to research background on the fuel cell project and found a number of different areas we could focus on, including the production of electron conducting filaments called nanowires, focusing on increased electron shuttling between cells, and the application of this to a desalinating fuel cell (which would be new for iGEM).
A lot has happened over the past few months, and we’re closing in our final project idea for this year’s jamboree. The time between Spring Break and the end of Spring semester a lot will be happening, but starting now to the jamboree, we (me and the rest of the executive board) will be keeping you updated.
Thanks very much!!
-Sean (Director of PR)
After four weeks of work this summer, we have made some substantial progress on our project. Here’s what’s going on:
1. Project Name
After a brainstorming session, we have settled on “Minecrobe” as our project theme. Minecrobe combines the power of microbes in soil with a Minecraft twist, relating to the way in which mine carts shuttle ore from one location to another, as our bacteria will release phytosiderophores that will shuttle iron from the soil into plant roots. Expect all of our deliverables to have a Minecraft element to them.
This week we obtained the supplies necessary to begin our first round of plants. We are planting 102 plants, both corn and rice, in ideal growth conditions with the exception of iron availability. We are going to create a gradient of applied Sprint 330, which contains an iron-chelating compound called DTPA, which will enable us to assess numerical values for iron deficiency, sufficiency, and toxicity for both species of plant. We are scheduled to plant on Monday of next week.
While the first round of plants are growing, we will be shifting our focus to growing our bacteria. Our orders of three different strains of Bacillus subtilis have come in from the Bacillus stock center at Ohio State University and just today we have cultured them on LB plates. We are also in the process of determining the exact sequence of DNA base pairs we are going to send in for synthesis. Today, we ran our desired genes through an optimizing program to raise their level of success once the plasmids are transformed into the bacteria.
This year the iGEM Team is tackling the problem of global malnutrition! More than 870 million people are malnourished, according to the United Nations World Food Program. We plan to utilize the realm of synthetic biology to combat this problem by engineering a microbe, Bacillus Subtillus, to increase plants’ ability to uptake nutrients from the soil. Essentially we are optimizing bacteria that naturally live around plants to help plant take in more nutrients from the soil. If the plants take in more nutrients, their nutritional value increases, ultimately leading to more nourished plants into the global food chain. With diligent science and human practices committees, we plan to execute a project that is bigger and better than ever!
The time has well passed since our team competed in the iGEM jamborees. Since then, we have been busy eagerly preparing the team for the upcoming year, but don’t worry, we haven’t forgotten about the great successes that occurred during the jamborees and are excited to share those successes with you!
The regional jamboree, consisting of the North American iGEM teams, took place at the University of Toronto (which looked unbelievably like Hogwarts). At this competition we were named finalists, ranking third in the undergraduate division! This honor granted us the opportunity to present in front of all 64 teams that attended the event. Beyond this, we also received the award for Best New Natural BioBrick Part and advanced to the World Championship at MIT.
Although we didn’t win any additional awards at the international competition, we were more than satisfied with our performance and had an unforgettable experience in Boston, which included attending the Red Sox victory parade!
We are harnessing our enthusiasm from the previous competition to continue this success and reach for even greater heights!
The Purdue Biomakers have been working hard this week to fill out and finish our iGEM wiki! It’s still a work in progress, but if you haven’t checked it out yet go look at it here: http://2013.igem.org/Team:Purdue