World Championship Jamboree/blog6

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Lethbridge – Tailings Pond Clean Up Kit

 

Visit their wiki!

Managing byproducts of the extraction and refinement processes is a common problem in harvesting natural resources, such as oil. In most cases, tailings ponds are used for storing the toxic water byproducts, which not only have severe negative environmental impacts but also by using current methods can take decades before they can be reclaimed. The current remediation methods need to be improved to provide economical, effective and efficient processes to decrease the negative environmental impact of the tailings ponds. We will produce a tailings pond clean up kit that uses environmentally safe methods to accelerate the decontamination of toxic organic molecules, heavy metals, and settle the fine clay particles at an increased rate.

*****

Tailings ponds store mining waste including toxic organic compounds. Project stages: look at reducing fine clay particles, toxic organic compounds and ensuring cell viability.

  1. Reducing fine clay particles: strategy involves inducing e.coli to bind to clay particles and expressing Antigen43 so that they bind to each other and precipitate out of solution.
  2. Ensuring viability: Found that “nothing in tailings ponds that will kill e.coli outright”. Clashes with iGEMCalgary team’s similar experiment, who experienced a much slower growth rate as compared to LB broth.
  3. Toxic degradation: co-localizing metabolic enzymes in a micro-compartment to facilitate metabolic process using Lumazine synthase from Auifex aeolicus. Utilized mutant to generate negatively charged microcompartments.

Ethics – focussed on public awareness. Made a movie, “BioSpirits” about teams competing to win a contract from from a beer-brewing company. Protagonist uses water purified from tailings ponds to grow synthetic beer-producing trees. A movie provides accessibility ot public and the movie gives a context for technological and scientific innovation.

Accomplishments:

  1. Addressed safety issues with chassis (e.coli) using 2007 Berkeley iGEM’s killswitch part.
  2. Confirmed functionality of their sedimentation parts – took longer than expected, but it worked.
  3. Ensured viability of chassis in tailings pond water – found that there was not a a significant difference in growth with tailings pond water and LB broth.
  4. Created charged microcompartments which can localize positively charged molecules, characterized with electron and fluorescent microscopy.

 

Judge Questions:
  1. Where did the Lumizine synthase come from?
    This was not engineered by the team, but we produced a biobrick from published research.
  2. When you get the system working, then what?
    One method we could use is removing water from the tailings pond and putting it in a controlled bioreactor, so that saftey issues are better addressed.
  3. Can the toxic compounds enter the microcompartment?
    Yes, the microcompartments are porous and allow for movement in and out by organic compounds.
  4. What kind of % kill rate do you want with your killswitch?
    We don’t think we should accept anything less than 100%. Even beyond that, safety measures can be added on top of that.
  5. Is there a lower temperature threshold for your Lumizine synthase?
    We don’t know yet; our experiments were run at 37 deg C and we haven’t looked at the lower limits yet


Team Grinnell – suit up

So, second team in the manufacturing track. The team Grinnell – in dark suits – deals with biofilms, a common problem in health, food and ecology. Like in every problem in the biological world, there are two options to solve it. Kill or degrade it!

Let’s get into details. They want to use Caulobacter cresentus RsaA protein and it’s signal sequence for the type I secretion system. Two proteins that can degrade biofilms were chosen to be tested with the presented system. Esp from Staphlyococcus and DspB from a mouth bacterium.

So, what are biofilms? Cells attach themselves to surfaces, other cells join and after some time you have a biofilm consisting of many cells from different bacteria. Biofilms are a problem of industrial scale!

To find out if there products where expressed, they performed cultivations and checked for their proteins with silver-stained gels. For the activity of the proteins, their performed a “biofilm assay” in which S. aureus was cultivated for several days so it could build a biofilm. After it was stained with crystal violet and checked for relative biofilm growth. They have some promising results, but also display that still some improvements can be done in the future. Also for the future, they would like to see Caulobacter as a secretion chassis, further optimize their secretion proteins and add a cleave site between the signal and coding region.

By the way. Wow, that’s a really small team. Only 3 members and one supervisor. Respect to that.

 

Calgary – Naphthenic Acid Biosensor

Visit their wiki!

This year, the University of Calgary iGEM team aims to build a biosensor for naphthenic acids (NAs). NAs are organic acids that are toxic to terrestrial and aquatic wildlife. Because they are waste products of the bitumen extraction process that mines petroleum from the Alberta oil sands, the accumulation of NAs in the on-site settling ponds (tailings ponds) is an environmental concern requiring constant monitoring and eventual remediation. In addition to harming the environment, NAs also contribute to refinery equipment corrosion, directly increasing maintenance and replacement costs. Currently, sophisticated and expensive procedures, such as Fourier Transform Infrared Spectrometer (FTIR) or gas chromatography-mass spectrometry, are needed to identify and assess NA concentrations in the environment. A bacterial sensor, if developed, could greatly improve the cost- and time-efficiency of NA detection, and facilitate a workable approach for remediation.

*****

Naphthenic acids (NAs) are toxins found in tailings ponds as a result of oil extraction. NAs are a group of very diverse and difficult to detect acids that are harmful to wildlife.

Current technology for detection is inaccessible; large machinery tucked far away in labs. The Calgary team’s vision is to create a biosensing organism that will report NAs based on a biotinylation/immunoprecipitation sensory promoter:

The biosensing organism can be lysed and immunoprecipitation can be performed using strepavidin “fishing hooks” with biotinylated NA “bait” that can fish for promoters and proteins that interact with NAs. Click here for more details.

The progress to date for their search for promoters is

1. designing a protocol to identify small molecule interactors

2. identifying a gene that is responsive to NA exposure

Additionally, Calgary chose Pseudomonas or microalgae as their chassis as these organisms are capable of naturally surviving a tailings pond environment and may contain necessary regulatory elements required for a response to NAs. To help future iGEM teams work with these chassis, they have created tools to aid the conjugation of E. coli and Pseudomonas.

The Calgary team also performed a market analysis for their biosensing system and found that it could cost approx. $40 per sensor prototype, which is 5-10x less than what current companies are charging today for the analysis of NAs in tailing pond samples.

TU Munich

First session, first talk: The TU Munich Team starts with a conversation of two of their members, talking about their experience with iGEM. They introduce themselves and their project just like small-talk. Unconventional, but it seems to work.

Their project is about an optogenetical AND-gate that can be triggered via the output of reporter plasmids => e.g. GFP fluorescence signal. Combine e.g. red light and blue light to fulfill the AND-condition.

Testing their reporter plasmids, they found, that their LacZ and GFP reporters induced with several IPTG concentration worked just like expected. Red light seemed to make problems though – mysterious things had to have happened with the formerly working part between 2004 and 2007. They found a bug in the DNA sequence and want to make sure no-one else will run into the same trouble. Check their wiki for further information.

For their blue light assay, they constructed some LED-box matching the light-sensor absorbance spectra, allowing them to easily test their system.

They are still doing that “Small-Talk-Conversational-Style” of presentation, now presenting their models. They show a model of localizing cells according to the AND-gate, being in a blue beam AND a perpendicular red beam -> thats a coordinate.

Human Practice: Communicating synthetic biology to kids of different ages, they contacted both kinder gardens and high schools. They also collaborated with a crowd-funding network to create a portal for iGEM teams to raise funds. As the other german teams, they were invited to the German Council in Boston, which was a nice meeting of the German finalist teams and the Scientific Liaison Officer – who is in the audience right now – and the Principal Officer.

Their conversation, err… presentation comes to an end: time for questions.

 

The judges are concerned about the whole laser thing. The team pointed out that they were working with LED-lights, cause laser are really expensive!

Further they feed their model with literature parameters.

Opening Ceremony_pt2

And there is the kickoff for the championship.

Let the games begin.

Randy is ready and starts the opening ceremony. He greets all the teams, who made it to the MIT. And you can not mention it often enough, big thanks to Meagan for the organisation.

Randy likes that Obama knows and concerns about synthetic biology. Obama had an ethical report done about synthetic biology, which points out that synthetic biology is one of the brightest new fields of biology. Further Randy likes that even the iGEM competition is mentioned in this report. We made it guys. Obama knows about us!

Randy thanks the sponsors and judges. But, bigger news, he tells the audience, that the iGEM HQ is leaving the MIT, in order to move into their new offices. The new HQ is very close to the MIT Stata Center. But, nevertheless, they “graduated” from the MIT. The iGEM competition expands every year, hence the HQ divided the competition this year in regionals with their own semi-finals.

Why is iGEM so successful?

=> it is all about the iGEM philosophy of get and give. Get and give BioBricks.

2700 people are participating on the competition this year, divided into 165 teams. But the competion is still growing, so the HQ decided to do 5 regionals in 2011, called:

Europe (probably in Amsterdam), Asia (probably in Hong Kong), Latin America, East and West North America.

But there is more work to do, in order to improve iGEM every year. Improvements will be made for :

iGEM Techniques (shipping of parts etc..)

High School Divisions (hopefully there will be more teams next year)

Entrepreneur Division (Developing synthetic biology Industry / business plans / iGEM Alumni and university focus / Championship scheduled around the iGEM Championship)

Software Division (unique aspect of iGEM with its own culture and identity)

iGEM Alumni (stay in touch with iGEM, be volunteer, alumni@igem.org, live blog, words like fire, iGEMers Prize, CommunityBricks)

Opening Speech!

Randy Rettman gives the opening speech, highlighting Obama’s Bioethics Commission and iGEM’s history of success.

This year, 165 teams worldwide participated! The estimate for next year is 205 teams (25% growth)… the number of regionals will increase as well to include West, East, South America, Europe and Asia.

Important announcements: iGEM is graduating from MIT and starting high school, entrepreneurial and software sections! Above are the persons-in-charge.

We are also pleased to hear about iGEM community initiatives such as AlumniGEM and Community Bricks.

*****

In the Kresge Auditorium… The British Columbia team! :P (Alina and Sam are liveblogging)

Opening ceremony_pt 1

The Kresge Auditorium is slowly getting crowded for the opening ceremony. The tension is rising, soon the iGEM 2011 World Championship will begin.

 

Setting up for the opening ceremony

Good morning fellows, wash your face, check your hair, grab your best team shirt:

IT’S iGEM TIME !

The next two days will be live-blogged by the igemwatch.net team. We will provide you with short summaries and comments about the team’s projects, presentations as well as the whole iGEM event at the MIT. So stay tuned and check for updates in the next days.

We will start in a few minutes with the live blogging from the opening ceremony.