Amsterdam is our most significant collaboration. We skyped together early in the summer and realized that both of our projects had an important connection. The Amsterdam iGEM team worked on making E. coli to produce fumarate, which reduces methane emissions in cattle when fed in certain doses. As a result, the UNebraska-Lincoln iGEM team and the Amsterdam iGEM team joined forces to come up with a way to reduce methane emissions. Methane emissions have a huge impact on climate change. UNL and Amsterdam explored the possibilities of feeding fumarate to cattle in order to reduce methane emissions. We can conclude that fumarate is a promising molecule for this application. The result of our collaboration is shown below.
On top of this, Amsterdam was also able to give us comments on our safety case page. Using their suggestions, we further modified our information. Their comments are found below.
The introduction is actually very clear, it is well written and raises ‘the need’ very well.
Safety Case Units and Structure:
This part is clear as well, except for the actual meaning of a diamond. I don’t see a diamond anywhere. Also the last line of this part could use an extra figure, in which you can see the standard form of what every safety case must have. Actually this is figure 4. I might place it a bit up.
Modularity of Safety Cases for iGEM:
Smart idea. However did you consider the statement: ‘could help change the views of those still skeptical of the safety involved in synthetic biology’ This makes it sound like the safety case is meant to change people's mind instead of making synthetic biology safer. Implicitly saying that the concerns of these people are invalid, I don’t think you want to go into this, since it is quite sensitive. Maybe just leave this sentence out.”
Above is a picture showcasing our successful skype session with the Amsterdam iGEM team.
We collaborated with Methungeny about safety cases and general research questions. They posed us a question about their experiment, and we gave them suggestions on how they could solve their problem. Methungeny’s project aim is to develop a methane biosensor medium which consists of methane-utilizing bacteria and an enzymatic assay. When methane is present in the environment of the bacteria, they will produce lactate which will be converted to a colorful substance by the assay kit. The bacterium they chose to perform the methane to lactate conversion is the Methylococcus capsulatus. Normally, it does not produce lactate and that's why they are going to insert a gene of the lactate-dehydrogenase (LDH) enzyme in it, which is able to transform pyruvate to lactate. Since this bacterium is a thermotolerant organism, they thought it would be worth using the LDH of another thermotolerant bacterium, so the LDH gene is originated from Bacillus coagulans. They will put this gene into a vector designed especially for Methylococcus capsulatus, but at this point they faced an issue.
They were searching for an appropriate constitutive promoter which would be able to drive the LDH gene, but they had not found an exact promoter sequence. They asked us if we could help them find a promoter which could be used in Methylococcus capsulatus. The UNebraska-Lincoln iGEM team did some research and gave them some suggestions on which promoter they could use. We suggested that Methylococcus capsulatus's primary sigma factor for exponential growth (RpoD) is very similar to E. coli's RpoD, especially the DNA binding region. So we believe an Anderson promoter will be sufficient for their purpose. In the spirit of iGEM, we sent them a link to Anderson promoters already cataloged in the registry: http://parts.igem.org/Promoters/Catalog/Anderson.
In return, they helped us with our safety page section. Our team has designed a new idea called safety cases to help with safety in the iGEM world. We asked them for help critiquing our explanation of the safety cases and also our general safety information. They promptly responded with many helpful suggestions seen below.
“We missed a "Safety measures in a molecular biology laboratory" part what describes the biosafety dress code (the need of wearing gloves, goggles, lab coats etc.). In our opinion, it would be also essential to mention the separate collection of disposable materials (e.g.: pipette tips, Eppendorf tubes and inoculating loops connecting with microorganisms). Writing about the chemicals’ material safety data sheet (MSDS) and important safety pictograms found on the bottles and flasks would be also very useful because they are a basic part of biosafety and so that everybody not just biologists can understand the meaning of the figures found on each material in a laboratory. We also recommend to write about the biosafety risk group of the used bacteria before and after the genetic modification (BSL1 and S1). You should write some sentences about the biosafety laws of your country and institution and mention that your team meet all the requirements. They may seem very basic aspects but we think you had better write about them to make sure about nothing will miss from the safety cases. In conclusion, we think, your safety part is a well-written, comprehensive, professional work. Congratulate!”
Using our safety case, Hungary also developed their own. We are very excited another iGEM team has tried safety cases!
This is our collaboration badge that we presented to all the teams that participated in our survey (results found HERE). Here is a map marking all the teams!
We completed a survey for Waterloo iGEM team to assist them in their investigation of using 3D printing as a partial solution to expensive lab equipment.
BostonU Hardware survey
We completed a survey for BostonU Hardware iGEM team regarding the synthetic biology and microfluidics.
We completed a survey for Dalhousie iGEM team to aid in their understanding of the conception of science literacy. Later a brochure will be created to raise awareness of science literacy, the distribution of scientific information, and the validity of such sources.
University of Washington survey
We completed a survey for the University of Washington in order to help them create a global iGEM server for easier communication among the teams.
We completed a survey for the University of Ottawa. The purpose of their survey was to gather information on how much people know about what genetic engineering is and what their opinions are on the type of research that's going on in their community. Genetic engineering technology has implications for more people than just those affected by diseases; it has the potential to revolutionize our way of life. However, misconceptions on how its used and misinformation spread much quicker than facts. This is largely due to the lack of communication between the scientific and nonscientific community, leaving the media to bridge that gap.
In addition to filling out surveys and collaborating with Amsterdam and Hungary, we also skyped several other teams to talk about our projects, GMO policies, and modeling.
We skyped with a high school team and presented our idea of safety cases. They provided us with great feedback which we followed and used to revise our page. In return, we helped mentor them because they are a high school team.