World Championship Jamboree/blog2

From 2011.igem.org

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iGEM 2011 World Championship Finals!!!!

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This will be a blow-by-blow account of the iGEM 2011 World Championship Finals!!

Tom Richard is our speaker yet again, and all the teams are anxiously awaiting the announcement of special awards and the 4 finalists!

Tom is explaining the judging process-how to compare kumquats and oranges or something along those lines.

Here are the top 16 teams with the most votes!

CommunityBricks: bridging science and society

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Hey everyone!

 

CommunityBricks is an open source collection of human practices activities and lesson plans that will stimulate deeper, more engaging experiences for both iGEMers and the public. The site will serve as the human practices version of the Parts Registry, where many “tools” that iGEM teams create to present synthetic biology and biosafety are catalogued so future teams can utilize and improve them. Example “tools” include fun synbio-inspired games that engage the public, a series of lesson plans that introduce high school students to synbio, and thoughtful considerations of bioethics and the roles it should play in our future.
By collaborating on human practices (instead of working alone), iGEM teams can come up with creative ways to reach out to and educate the public more effectively and globally, vs. being limited to their local community or to the segment of the population that has access to museums, computers, and smartphones.

 

To help promote a sense of community among iGEMers, consider having synbio slams (like Words Like Fire, which was organized by alumni and current iGEMers) at iGEM Jamborees! Synbio slams are a great opportunity for everyone–alumni and current iGEMers alike–to share their views and passions about synthetic biology through poetry, talks, speeches, and other variants on the spoken word. (See the post on Words Like Fire for more info.) Let’s make synbio slams an annual tradition at iGEM jamborees!

 

Also, iGEM teams are constantly in search of more money and lab equipment to support their projects. In addition to cataloging human practices and outreach projects, there have been requests for a guide–fundraising tips from iGEM teams–that will help iGEMers obtain funding in general. Let’s brainstorm ways to get iGEM teams the support they need to complete their summer projects.

 

What can your iGEM team and you do to help? Go to the CommunityBricks website on OpenWetWare and share your human practices and fundraising ideas!

http://openwetware.org/wiki/IGEM_Outreach

(The site is on OpenWetWare for now. With the help of iGEM HQ, it will become part of iGEM.org soon.)

 

***To clarify, the AlumniGEM team is also running the CommunityBricks website. We hope to get many of you involved in organizing the alumni association and advancing human practices in 2012 and beyond. Many of you did projects on foundational advances for synthetic biology. Think of AlumniGEM and CommunityBricks as complementary, foundational advances for iGEM!

 

If you would like to join the alumni association and advance biosafety, human practices, and iGEM lab support, please join the alumni association mailing list

and email us at this address:

alumni@igem.org

 

 

Workshops, part III: WORDS LIKE FIRE!

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Words Like Fire was a synbio slam, the iGEM Championship Jamboree edition! Speakers–”Word Wizards”–had 3 minutes to divulge their passion for synbio in the form of poetry, short talks, music videos, and live songs. Yes, there was singing and guitars involved, and it was AWESOME.

 

There will be a video posted on iGEM.org sometime soon; stay tuned!

In the meantime, you can check out Calgary’s hilarious music video, “Last Project Night,” on their Youtube channel!

 

Cambridge iGEM 2010, look what you’ve started, haha…

 

If the judges are still deliberating the grand prize winner after we all come back from the “iGEM from above” photo shoot, teams are welcome to show their videos and animations. I’m sure Calgary iGEM would love to show their music video. And the AlumniGEM/ CommunityBricks team will perform their live song, “iGEMers Rockin’ in the Free World.” With everyone joining in on the chorus!

Workshops, part II: AlumniGEM

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Hey, iGEMers!

Starting on Monday, you will all be iGEM alumni!

Do you love synthetic biology? Of course you do. Here is how you can stay involved in the iGEM/ synbio community:

Join the mailing list, igem_alumni@igem.org.

–There is a link to the AlumniGEM website on the bottom of the igem.org home page.

–When you click on it, you’ll be led to the AlumniGEM website, which is undergoing construction: http://igem.org/Alumni

–Click on the “sign up here!” link to join the mailing list.

 

What did we discuss at the workshop?

What you can do, as alumni:

–Coordinate the iGEMer’s Prize, a prize awarded by iGEMers, for iGEMers. iGEMers vote for their favorite iGEM teams/ projects. (Let’s make this an annual tradition!)

–Contact your favorite high school teachers and start a high iGEM team!

–Mentor an iGEM team

–Post job opportunities (once the website is fully up and running)

–Help coordinate reunions/ regional meetups

 

AlumniGEM’s leadership structure (a few ideas):

1. The entire organization will be headed by 2 co-chairs.

From Randy (in an earlier conversation): there will be an iGEM Council in each region, where all the councils form the iGEM Government. AlumniGEM will be an organization under the iGEM umbrella, so to speak, and the co-chairs will be part of the overall iGEM government.

 

2. At first, we thought that each region would have 1 chair and a social chair. But, after breaking down into groups by region–Americas, Asia, and Europe–to discuss each region’s needs, we realized that

–The Americas should exist as several sub-regions. For example: western Canada, eastern Canada, northern CA/bay area/Pacific Northwest, and the East Coast.

–Europe: workshop attendees suggested that it remain as one overall region

–Asia: should also be divided into subregions; not sure what those would be yet.

We are considering having region/subregion co-chairs.

 

3. Each iGEM team will have an AlumniGEM representative, who will be responsible for contacting as many of his/her school’s iGEM alums from pre-2011 as possible. We are thinking of offering a prize at regional/ world championship jamborees to the teams who put forth the most effort in getting their school’s iGEM alumni to join AlumniGEM and remain active in the synbio community.

Regional reps and the AlumniGEM co-chairs will be voted on by all the alumni who join the association (via the mailing list). Team reps will work with regional reps to organize reunions and such. For now, workshop attendees will serve as regional reps.

We (the AlumniGEM team) are in constant discussion with iGEM HQ about AlumniGEM’s future steps. Additionally, we look forward to hearing what you have to say about (a) what services you would like AlumniGEM to provide, and how those services might be provided; and (b) AlumniGEM’s organizational structure.

 

Questions? Comments? Suggestions?

Email the AlumniGEM team at alumni@igem.org

 

Workshops! Entrepreneurial Division and the latest news for North America

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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

uOttawa: A platform for robust quantification of transcriptional regulators and promoters and Brick Mason

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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:

http://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?

 

UNITS Trieste: SynBiome

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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:

http://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?

 

UC Davis: Mutant Libraries for BioBrick Circuit Synthesis

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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):

http://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:

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

 

 

Paris Bettencourt: TuBe or not TuBe? Cell-cell communication with nanotubes

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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?

 

 

 

 

 

 

 

 

ENSPS-Strasbourg

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ENSPS-Strasbourg is last, but not least, in the software track.

They want to create automatic system design software for synthetic biology, by applying concepts from microelectronics.

They demoed their software, called “BioBricks model generator for electronic simulator”. You can add different species and different interactions, and it gives an output to the system.

AWWW! The system output looks like low and high discretized voltage curves or waveforms. It tickles the electrical engineer in me (though it is a very small electrical engineer).

Their team is very new to synthetic biology field. I approve the exploratory attitude.

Good job.

Their wiki: link

High School Division Winner – Greenfield-Central High School

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As the last talk, the Greenfield High school will present their grand prize project from the high school division.

Teamphoto: Nice ties guys!

The team consists of three pupils who did not know anything about iGEM. So first, do research and brainstorming for ideas. They come up with a toxic metal water tester, because it is needed in every part of the world – even in the USA!. Further the already used ones are truly expensive, especially in third world countries. The team used a yeast as a cadmium biosensor. Cadmium is known to be present in Mineral mining, landfills and industrial waste. So cadmium pollution is an international problem and a major health issue.

The Greenfield team used the Cup-1 promoter coupled with a mCherry translation unit. So the heavy metal is detected and directly transformed into an output. The high school team tested their system with copper, hence they did not get in contact with cadmium. Therefore they changed their project goal a little bit and built up a heavy metal detector. The molecular biological methods were DNA extracted, PCR and Gelelectrophoreses. The cup-1 was not on the partsregistry. So they had to extract it out of the yeast, transformed it into a BioBrick and submitted it to the registry. The team uses Gibson Assembly in order to create the BioBrick.

The team managed all this work in only three weeks. Very nice Work!

 

USTC-Software

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University of Science and Technology of China presented their software, Lachesis (named after the second of the Three Fates in Greek mythology).

They want to create a network of the interactions from BioBrick parts and simulate behaviors of different parts of the network.

They have an assembler,where you can drag and drop components, and the assembler will solve the corresponding differential equations modeling the system, using MoDeL.

They have a very cool looking parameter fitting tool for fitting data. They collaborated with USTC wetware team, to model and simulate the behavior of the wetware team’s system.

They did a lot. A lot more on their wiki

Hmm…the MoDeL link seems to be dead on the wiki. Guess we’ll have to ask the team for more information on it.