World Championship Jamboree/blog2

Hello everyone!

I was able to attend most of the iGEM Entrepreneurial Division (ED) workshop and part of the North America workshop, so here are tidbits of info that I picked up.

A) News from Jose of iGEM HQ about how you can become rich and famous with your latest synbio ideas:

1. The ED competition (in November right before or after the World Championship Jamboree) is very similar to the competition held at MIT. Your business team must have at least 1 iGEMer to participate, to ensure that your team/ business plan will be in sync with the iGEM culture.

2. Judges will consist of “mentors,” company reps and other people who can fund startup companies.

3. There will be 4 tracks.

4. Jose is expecting ~14 teams to participate, so regional competitions might not be necessary. (Let’s exceed his expectations!)

5. To encourage participation, there will be no registration fee! All the more reason to put your best foot forward. =)

More details are in the pics below:

Questions? Email Jose.

B) The scoop on North America (and regions in general)

While I was running in and out of 32-123 prepping for the AlumniGEM workshop, I overheard Dr. Tom Richard saying that North America will be 2 regions next year: West Coast and East Coast. Because they have a different school schedule, Latin America will be its own division.

It’s very likely that both North American iGEM Jamborees will take place on the same weekend; Tom was not sure about Latin America, since it’s on a different schedule.

I also think I heard Dr. Richard say that the jamboree locations will be Berkeley and Pittsburgh, but I could be wrong.

Regarding how Canada fits into all of this, I will ask Tom and update this post tomorrow. ;)

–Alyssa

They used a Prezi presentation. Two contributions they made were:

1. BioBrick assembly made easier.

–Get rid of the need for cut sites and scars. Seamless construction.

2. Characterization and parts measurement: built a new dual color detection device

And outreach: modern educational tool. Wanted to reach a wide number of people with an online game to teach others the basic of synthetic biology.

For more info about their Brick Mason assembly method, please go here:

https://2011.igem.org/Team:uOttawa/NewAssemblyProtocol

(Nice animations!)

Their educational synbio game, Gears of Evolution:

Haha, they’re having a judge play their game! :D

The judge is in the center of the front row, waiting with anticipation to thwart nefarious Dr. Power’s next move so EC (E. coli) can live to see another day.

Questions asked: how does Brick Mason work, and how many parts went into the mix? Did you use a HF polymerase? How many cycles of PCR total had to occur for any given construct to be made? What about the error rate? How can we decrease the error rate as the length of your construct increases? How many levels are there in your smartphone game? (10) How will you use this game as an educational tool? How does Gibson Assembly compare to BrickMason?

Note: the pics of their friendly cartoon bacteria are so cute, my smartphone is refusing to share them! Will update this post with pictures as soon as I get my phone to behave. In the meantime, please check out their wiki:

https://2011.igem.org/Team:UNITS_Trieste

Symbiosis and quorum sensing (using AHLs for gram negative bacteria).

Question: can you use quorum sensing in eukaryotes? Parasitism, infection, mutualism.

Goal: use synbio to construct a consortium where one uses QS to engineer a dialogue between 3 different chassis.

Abstract:

The synbiome project exploits synthetic biology to obtain a synthetic stable community of eukaryotic and prokaryotic cells. Two different bacterial strains ‘A’, ‘B’ and one eukaryotic cell type ‘C’ will be engineered to establish mutualism: ‘A’ produces a N-acyl homoserine lactone (AHL) sensed by ‘B’, which in turn produces a different AHL sensed by ‘A’. In addition, both bacterial cells activate, through AHL, an enzyme necessary to convert cellobiose to glucose, which represents the only energy source for the whole consortium. The eukaryotic cell ‘C’ responds to AHL through a hybrid protein, thereby producing a secreted beta-lactamase, which allows the bacterial cells to grow in the presence of ampicillin. The creation of a consortium of inter-dependent cells from different kingdoms is expected to pave the way to multiple applications, since different cells might cooperate and, for instance, better produce complex molecules.

Potential Applications:

–Libraries and complex molecule screening

Human practices

–Researcher’s night

–Science Cafe

–Wiki theme = friendly with cartoons and bright colors

Their abstract was accepted to the 4th ASM Conference on Cell-cell communication in Bacteria in Miami! Wooo!

Love their Questions slide.

Questions included:

–What about expanding your community to 4 or 6 organisms? What’s the potential feedback there?

–If you move from a closed system to an open system, have you thought about how you might shut the communication down?

Thoughts from UC Davis:

1. If an electrical engineer wants to build an oscillator: diagram, make mathematical model, define parameters, find parts with those parameters,and build and test it. Synbio is very much the same.

2. Goal: make this process easier to do in biology! Most important part: finding parts with the desired parameters.

3. Parts registry is meant to allow this. parts family = group of parts w/ unified function, but different parameters. Ex: the Anderson promoter library.

==> Developed a process by which basic BBricks can be expanded into a parts family.

Making a part family: need time, funding, manpower, more funding…

1. Target part

2. Mutagenesis

3. Screening

4. Characterization

Prototyped their mutagenesis process using GFP

Used error-prone PCR for mutagenesis. Mutation rate of 1 – 7 bp changes per kb.

Screening: used a plate reader. 3-step process: visually screen (with GFP fluorescence), primary screen (plate reader, 84 colonies per plate). found mutants that differed from control by at least 1.5STD’s.

Characterization: plate reader. Strategy dependent on part and parameters testing for. They tested two parameters, 1 parameter per plate, tested 2 plates per day if someone was willing to come in during the middle of the night. ;)

–pBAD regulated repressor transcription, with lac repressor.

Chose to work with repressible promoters.

Data was provided in relative promoter units (RPUs).

Modeling parameters (in ODEs): basal transcription, promoter strength, binding constant, and bound fraction.

Have KO3D software tool: their own 3D plotting library software (can see on their wiki and on GitHub):

https://2011.igem.org/Team:UC_Davis/KO3D

Proposed improvements to the parts registry:

1. Data on the front page of every part so we can see if the part = useful for our projects (YES!)

2. A “variants” section (of other parts from the part’s part family)

Future goals:

1. Encourage other teams to make part families

2. They made a song… It’s on this blog!

3. Formalization of mutant libraries into parts families (RFC draft in progress)

4. Future characterization of LacI promoter mutants

See their wiki for more info:

https://2011.igem.org/Team:UC_Davis

Early 2011: discovery of bacterial nanotubes: interspecies communication! Two Q’s: Can they characterize them, and what can synbio bring to the table? 2, or not 2?

Imagine: a biofactory

Now, instead of just looking like Mike and Ike candy, with nanotubes, B. subtilis bacteria probably look like this:

iGEM collaboration map (connections at the human level, haha):

Where synbio comes in: their general scheme:

Future work: microfluidic device for nanotube formation.

Created 49 BBricks and characterized 25

Conclusion: nanotubes–no evidence, but perhaps they’re a rare event. They have faith in them, and they’ll continue to study this phenomenon with the following considerations:

The question remains: TuBe, or not TuBe?