World Championship Jamboree/blog

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World Champions of iGEM 2011

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Walking home with the platinum football, the metallic award, the traveling biobrick.
THE
UNIVERSITY
OF
WASHINGTON!

First Runner Up- iGEM World Champions

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Imperial College London!!!

First Runner UP

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Imperial College Londonnnnnn

2nd Runner Up World Champion

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ZJU CHINA! Congratulationssssss

iGEMer’s Prize!!

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Joint Winners!:

Tokyo Tech!!!
Imperial College London!!!

Software- Best Use of Registry

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METU-BIN Ankara!!

Best Software Division Winner

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Made foundational advances that could also be applied to wetware.
Thirty-two interviews later: BU Wellesley Software!!!

Best Poster!!

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There are too many good posters out there:

University of Washington!!
Imperial College London!!

Best Human Practice

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Notable mentions:
Harvard- IP
Community Bricks

Award:
Edinburgh!
Art Science Bangalore!

Best Information Processing

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ETH Zurich!!!

Best Foundational Advance

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UC- DAVIS!!!

Best New Application!

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Joint Award- Brown-Stanford and ZJU-China!!!
WOOOOO.

Best Manufacturing team

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Awarded to the incredibly talented team of Cornell University! Loved your suspenseful trailers!

Best Health or Medicine Project

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Awarded by Carmella:

Extensive modeling, and then actualization. Congratulations to the MIT Team!

,

Best Food or Energy

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Joint Prize between Washington and Yale!

Best Environment Project!

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Calgary!!!!!!!!

ZJU Finalist Presentation

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The previous post for ZJU can be found here!

Visit their wiki!


WHY ZJU ROCKS OUR RAINBOWS!

1. Although the conventional perception of biofilms is negative they made

it colorful based on the natural gradients in biofilms! They went on to create

biofilms that can produce sugar or glue in a strategic step by step process as

well as biofilms that can serve as multi-functional biosensors in adverse

environmental conditions.

2. They have a really diverse human practices project: novels, app games,

funding studies… I played that app game! It’s tough :P


 

Imperial College of London Finalist Presentation

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For your reference, previous posts for Imperial College of London’s presentation can be found HERE, HeRe, and hErE.

Visit their wiki!

This entry will be purely focused on WHY THEY ARE AWESOME (top 2 reasons).

 

1. They are delivering a synthetic biology solution to the crucial problem of desertification. Briefly, make E. coli that (i) move toward roots, (ii) enhance lateral root formation when absorbed and (iii) possess a mechanism against horizontal gene transfer.

2. They interviewed a panel of experts to extensively inform their project and produce a compelling proof-of-concept.

 

More details to be found on their achievements slide!

Finalists!!!

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The 4 finalists are…

Imperial College London!

MIT!

University of Washington!

ZJU China!

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.

Peking_R

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Fine-tuning Biological Circuit Using Genetic Rheostat

Genetic rheostats are truly modular ligand-responsive riboswitches, while the RBS calculator is software for both translation of ligand concentration into quantified translation strength and automated design of synthetic ribosome binding sites (RBS) with customized strength.

Long story short: Team Peking is going to present a new way of finetuning biological circuits. Riboswitches shall give control of gene expression dependent of TPP.

Showing the characterization of their rheostat, they show that higher TPP results in lower reporter (GFP) expression. It also seems to be robust and independent enough for lots of promoter-gene combinations. That team loves thermodynamics.

They show how they optimized Sali’s model for quantification of translation strengths using a Thermodynamic Scoring Matrix. Their optimization seems to have worked pretty well, comparing before/after results.

From Ligand concentration to RBS Sequence: Converting any given TPP concentration into a RBS sequence using their RBS calculator.

A picture of their stochastic model explains, how they bring translation strengths to different color signal outputs (RFP, GFP) and how they fine tune the outcome using different TPP concentrations. There is a centered area though, where the whole system is bistable.

In the next part of the talk, Peking presents Biosynthetic pathways, they want to fine tune in terms of translation strength. In their example it’s Violacein production.

Human Practice consisting of high school visits and an investigation of antibiotics use plus awareness of biosafety issues in labs.

That was the last iGEM team of the Championships. Highschool teams are coming up, though.

UPO- Sevilla: Flashbacter

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USB technology has been around for a while, and the members of UPO Sevilla have decided to take it to the next level with thier project.

They are a 10-student team using a method called Flip flop in order to store information in a binary format (0 and 1).

They did a lot of amazing things in their project like made a tool kit software and create 10 new plasmids constructed for the registry.

There are a lot of more achievements shown in the images below!

For their Human Practices, they went to many high schools to talk about SynBio. There was a lot of excitement from the students and a lot of quetions too, which are answered in their wiki. They also did a Science fair, posted 73 articles in the blog that they created called Tornillos y Genes and many many more.

To summarize they submitted 31 new BioBricks to the registry including 10 new plasmids.

 

 

 

 

 

 

METU-BIN iGEM Software team

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Next team is from Turkey.

They wanted an easier way to search though the parts registry.
so they created m4b (mining for biobricks), a web-based search tool.

They created their own search algorithm and a scoring algorithm to return the results.

Pretty interesting project.

More on their wiki

Tokyo Tech

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Now, a team that probably most of you already have seen. First, they all are wearing “traditional” japanese clothes with a BLACK BELT (BAMM!) and secondly, because probably the team members have approached you and gave you some flyers.

Cool Down in Summer with our Rock-Paper-Scissors Game

Urea cooler as a prize for winning a game against E. coli? Meh not sure if want… but okay.

Three signaling molecules for the human, three for E.coli. The judges will be bacteria with end gate promoter. AND gates seem to be one of the hot topics! In summary 6 signaling molecules and 9 judge configurations. The judge receives an input and gives out an output. At the beginning E. coli had some trouble…

For the Simpsons fans out there….Bart Simpson: “The good ol’ rock”

The team tried and achieved to improve and help E.coli to have and use the other two remaining options by giving him “hands”.

After that, let’s get to the judging. First, the team presents a single colony isolation strategy utilizing Colicin. They also modeled their approach. Sadly, the rock strain cannot survive in the old model. :( But: In their new model the outcome is random and every strain can survive. Also, the Cre-lox randomizer design of the team succeed. Concludingly, also this part of their project worked.

Now to the prize for winning. ”Make it rain!” WHAT THE F#@$ JUST HAPPENED? Raining cats and dogs and thunder struck? What kind of prize is that? The team determined the carbon and nitrogen sources for the urea production and thus enabled the winner to gain a prize of cooling.

The team showed all the working subparts. I would have loved to see them play some rounds against their bacteria.

 

 

BU Wellesley Software

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Software time!

First up is the BU Wellesley Software team. They want to help solve problems the scientists face in laboratory settings.
They made a lot of different software tools, to address issues such as data management and design.

They created 5 different tools such as:

  • G-nome Surfer Pro: a genome browsing tool that allows users to browse GenBank, and some articles from PubMed, on the Microsoft Surface.
  • Optimus Primer: a primer designer.
  • Trumpet: a tool that finds the permutations of the genes flanked with invertase, using pancake sort and link sort
  • Puppetshow: created Puppeteer, a language for lab protocols that can be compiled into robot instruction sets

For each tool, a video demo was played (I think all the videos are on their wiki).

They also have a wetlab team and study study TB. Great way to test out your tools.

More on their wiki

WITS-CSIR South Africa: BioTweet

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WITS-CSIR South Africa in room 34-101.

I love their opening slide!

Chemotaxis:

Riboswitches (here’s atrazine):

Send and receive module: analyte A and B, with key thresholds of concentrations triggering chemotaxis. Put send and receive module on one construct, governed by a constitutive promoter.

Also had a Cre recombinase system to switch off A and switch on B (so it responds to analyte B) and travel back to Analyte A.

They set out to create riboswitch-induced motility: to control chemotaxis so bacteria would be attracted to analyte A and then travel back to analyte B after an IPTG inducible toggle switch was activated.

Used two riboswitches to control the bacteria: theophylline and atrazine.

Cute video of bacterial motility. Check it out on their wiki!

http://2011.igem.org/Team:WITS-CSIR_SA

Characterization: epifluorescence microscopy, fluorometry. Observed a 46-fold activation! Submitted as a BBrick part (BB_K537012).

Created a chemotaxis test device (parafilm involved in its construction).

 

Outreach:

–Workshops at Sci-bono Discovery Centre during national science week.

–Helped present bacteria to the community as “superheros” that can perform functions that you instruct them to do. For example, have bacteria turn black in the presence of cholera in water.

 

Submitted 11 parts to the registry, characterized 2 theophylline riboswitches

 

Ending slide: they thanked their advisors, who were with them from the beginning of the competition to the end. =)

 

Great job, team! They had a lot of fun and helped develop synbio in Africa. Awesome!

 

Questions:

–What risks would you raise by releasing these bacteria into the environment? Will they truly swim back to their start location?

–Did you talk about disadvantages as well as advantages of synthetic biology, when talking to the public?

 

 

Uppsala_Sweden – Setting the colour with lights

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Last session of the day and of the iGEM Championship Jamboree this year: track new applications.

Before the presentation starts they formed a motivation team huddle. So, Go Uppsala!

The team wants to create bacteria, which will be produce a color output (chromoproteins, fluorescence protein), triggered with a light signal = a bacterial photo copier. So the gene expression will be controlled by the use of light. Further it is possible to exchange the color-protein-genes with other GOI, which will be triggered by light. The swedish team is inspired by Jeff Tabor and his collogues, who published a multi chromatic control system for gene expression. They presented their ideas in really nice overview slides/ assembly plans. Check these on their wiki.

They implemented different light sensors (red and blue light) into E.coli. The blue light sensor works as follows. In darkness he triggers the expression of a protein. This expression is suppressed under blue light. The team coupled the sensor signal with colored proteins (blue ight => blue color, green light => yellow color, red light => red color). On the basis of these three colors an output of a lot of different colors is possible. Further they worked with a so called lambda red recombination plan, in order to get more stability (chromosome based), more control and to avoid crosstalk. So, how does this work? First of all you amplify your sequence by PCR. Here you create new flanking tags off your DNA part. These flanking parts should be homologue to the sequence inside the chromosome. The construct gets transformed into your bacterial chassis and afterwards you do a selection.

They talk about their favorite parts. Looks pretty colorful. And sure they characterize their parts as well as their used promoters. And sure there is a human practice part. Visiting schools, being in the newspaper and in the radio. Nice work guys.

Somebody fell asleep a few rows in front of me and woke up snoring loudly. Shame on you dude. Get yourself together. This project is definitely worth being awake.

Penn State – Radicoli

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With Osaka, Penn State is another team coping with radiation detection. Radicoli – the bacterial dosimeter. Fukushima was the initiator of that idea, again.

Their activator RecA polymerizes on ssDNA to form an activated filament, which is responsible for the cleavage of CI repressor dimer & repair of damaged dsDNA. They replaced the DNA repair function of the RecA protein with a reporting function… or rather making it connect to a reporter. They submitted both, the original RecA and their mutated version.

To further process that signal, they use a lambda phage switch, which (in short) leads to the production of the TEV-protease, when ssDNA binds. That one will later be used, to cleave a GFP, C230 fusion protein, allowing unbound C230 to form tetramers and convert the colorless substrate catechol into a yellow product. Signal output, here we are.

They show models of their sensing system as well as of DNA damage occurence over time.

Some tests with various RBS strength show, that they might be able to tune the whole construct.

They also designed a bacterial dosimeter device and evaluated its cost effectiveness.

A video designed to explain synthetic biology in an understandable way for a general audience as well as other surveys form their human practice efforts.

 

Even though the dosimeter idea came twice, we found pretty different approaches here. Many ways to Rome.

UTP-Panama – Thermogenic Response Nutrient Biosensor

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To develop flexible and better sensors for environmental, agricultural and engineering applications are the aims of the UTP-Panama Team “SynBio Engineering Tool Kit”. In this way we work with Nitrate Biosensor (PyeaR – GFP composite) developed by Team BCCS-Bristol 2010, which expresses fluorescent signals upon nutrient detection, producing a high-resolution map of arable land. To achieve this goal we use the collateral effect of the AOX enzyme (Alternative oxidase) mainly designed to generate heat in response to a cold-shock, using the hybB promoter. This effect increases the bacteria growth at temperatures below 20°C. Finally we design a prototype device with a better cold shock promoter (CspA promoter) developed by UNAM-CINVESTAV Team in 2010, in order to give our E. coli a “Intelligent Coat”, which means that not to only survive a cold-shock but to also still been able to keep up with his duties due to improve their expression mechanism at low temperature.

*****

The UTP-Panama team seeks to create more robust sensors that function at low temperatures. They chose the Nitrate Biosensor (PyeaR – composite GFP developed by BCCS-Bristol 2010) that has agricultural applications—if this sensor can be made to work at lower temperatures (than 37oC), it will have be more agriculturally relevant!

Their THErmogenic REsponse Nutrient BiOsensor (THE RENBO) construct puts this biosensor under control of a cold shock-sensitive promoter. The team used this construct to assess the activity of the biosensor under different cold shock conditions and found that it could sense nitrate at lower temperatures…

For their human practices, UTP-Panama looked at the diversity of human practices projects across all iGEM teams and developed an outreach campaign that educates and then examines their target audience. Exam results were on average a B grade! Please find their software on their wiki HERE. They have also contributed significantly to CommunityBricks in hopes of spreading the word about synthetic biology all over the world!

Osaka 2011

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The team that accidentally started crazy music while the ITESM Mexico was presenting. Face palm.

An introduction concerning the earthquake that led to the Fukushima nuclear crisis, the most severe nuclear crisis in Japan. Negative biological effects of radiation are shown. A human practices survey is shown where most the people associate negative terms with “radiation”. Seems like no huge surprise to me.

Main idea of the team is to design a bio-dosimeter which has some advantages to common dosimeters. Two main aspects of the design plan are presented: Damage tolerance and detection of DNA damage. Since Deniococcus radiodurans has a very high resistance towards radiation and a very effective DNA repair mechanism, it shall be used. The team cloned various DNA repair genes from Deniococcus radiodurans. Afterwards, different tolerance assays were performed. They could show that the IPTG induced expressed of these genes led to an increased tolerance/viability. When combing the parts PprM and RecA, they showed the effects are additive.

Thereafter, the DNA damage detection, which is focused on the OS response, is shown. A damage detection device using the SOS promoter and a reporter gene lycopene is used. The cells are damaged with UV radiation and the OD measured. They could show that the SOS promoter could be induced by UV radiation.

For the future, the team has a lot of promising plans.

 

 

Yale – Nature’s Antifreeze

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Antifreeze proteins have applications in cryopreservation of food, cells, and organs, as well as in cryosurgery and agriculture. The purpose of this study was to express, purify, characterize, and optimize a novel, hyperactive antifreeze protein recently isolated from the Siberian beetle, Rhagium inquisitor (RiAFP). Large scale (150mg/L), stable production of RiAFP and a RiAFP-GFP fusion protein was achieved in E. coli. Proteins were purified by Ni-NTA affinity chromatography. E. coli expressing RiAFP exhibited increased survival post-freezing. RiAFP inhibited ice recrystallization in a dose-dependent manner. RiAFP also improved tissue morphology of rat livers post-freezing. Preliminary results indicate that RiAFP may have a cryoprotective effect in C. elegans. To optimize the activity of the hypothesized RiAFP binding site, we used directed evolution through multiplex automated genome engineering and are currently screening for mutants with enhanced properties. Finally, to better understand the structure-function relationship, we have generated promising crystals of RiAFP for x-ray crystallography and are now optimizing crystallization conditions.

*****

On a cold february day in New Haven, the Yale iGEM team decided to study antifreeze proteins (AFPs)…

AFPs can be found in organisms dwelling in cold environments such as insects and fish. AFPs are conventionally characterised by how they affect the melting point of water… but more interestingly, AFPs are used in various industries, particularly in ice cream production!!

Ice cream today uses fish AFPs which are much less effective than insect AFPs that are limited to laboratory use. The Yale team looks at the RiAFP, a novel hyperactive AFP from the Rhagium inquisitor beetle. They have successfully characterized this as well as 2 other AFP biobricks through measurement of expression of the eGFP-AFP fusion proteins.

These AFPs were purified via cold finger; sticking a cold metal tube seeded within a thin layer of ice that AFPs bind (their natural property). This is comparatively cheaper than conventional purification methods and is specific to AFPs.

With Yale’s infrastructure for structural characterization, the team obtained X-ray crystallography diffraction patterns of their RiAFP.

They demonstrated RiAFP’s ability to improve freezing tolerance in different organisms: E. coli (bacteria) and rat liver tissue (rat work performed by licensed personnel).

To take their project to another level, the Yale team embarked on multiplex automated genome engineering (MAGE) optimization of AFP activity. To date, they have generated four hundred and thirty four million predicted genomic variants that will be tested via multiple freeze-thaw cycles.

ITESM-Mexico- SensE.coli

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Second session, first talk, environmental track

The speakers suited up and they got a very nice mascot – the biobrickcoatl! The mexican team shares a dream, bringing technological ideas into biology – taaadaaa iGEM! So they applied for the competition. After refusing different ideas, they want to work with a biosensor. Hence, they reviewed different projects from other iGEM Team (Monterrey iGEM, Cambridge, Tokyo etc..). Finally they called their project SensE.coli. SensE.coli The project consist of a standardized Biosensor, which can be used in different applications. They chose to build an arabinose biosensor. The project can be divided into two big sub-projects; A photoreceptor, which is activated by the receptor and the promoter,which produces the RecA protein.

Under green light and low arabinose concentration conditions, the low conc. promoter is induced. This leads to the production of the key for the GFP production and GFP is produced. In high concentration conditions, the anti-key for the GFP-key is produced and suppresses GFP-production. Hence CFP is produced. So the Biosensor is able to differentiate between low and high concentrations of arabinose. The user gets a different color-output for different concentrations. I am wondering at which concentration the switch might be and how sensitive this kind of biosensor is…

The first, which pointed out that iGEM is fun and fun should be in the results part. You are damn right! Concerning the wetlab work, they were not able to test their whole system. So they broke it down and created a express test system. They manage to find some of their DNA via gelelectrophoreses, but they pointed out that the PCR primers, necessary to proof the principle of the mechanism, are still under construction at the DNA synthase factory (it seems that it takes about 4-5 weeks in mexico. unbelievable.)

The judges are concerned about the strict regulation in mexico, which seems to block the success of the team (sequencing and ordering of parts). It seems that every mexican team deals with this kind of problem. The judges suggest to do some human practice projects on this problems. So all in all, these guys did a good job concerning their struggling with the mexican government.

EPF-Lausanne – Transcription Factor Development

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We have developed a pipeline for selection and characterization of new transcription factors (TFs), specifically:

  1. in vivo selection offunctional mutants from a large library of variants using a “survival of the weakest” strategy;
  2. in vitro characterization of affinity and specificity of mutants with MITOMI;
  3. in vivo characterization of selected mutants using reporter plasmids.

 

*****

The EPF-Lausanne team aims to derive more transcription factors (TFs) since there are few well-characterized ones on the registry! Their strategy is to mutagenize to create and characterize orthogonal TFs using existing TFs

Their protocol selects for TFs (their teenage mutant ninja turtles) with high binding affinity by

1. in vivo by lysis selection

- Using lysis cassette (Berkeley 08) to lyse cells with effective TFs and release TF-encoding DNA

- They controlled for lysis rates by comparing the amount of plasmid in supernatant in their desired strain versus control

2. in vitro by microfluidics (in vitro findings were later confirmed in vivo)

- Measure TF-DNA interaction over 5 hours

- Focus on TetR repressor mutants and their binding affinity to the promoter using RFP reporter

For teams interested in incorporating microfluidics into their project, the EPF-Lausanne team (which built their own accessible microfluidics setup) recommends ordering your chip from existing foundries to avoid dressing up like an astronaut and making your own ;)

Northwestern

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1.7 million hospital acquired infections, from that 170000 caused by pseudomonas aeruginosa. The team from Northwestern University wants to create an detector (E. coli biosensor) for that bacteria, using quorum sensing signals from P. aeruginosa to induce their reporter.

Their detection system based on LasR is explained and tested. You clearly see the effect of the autoinducer in comparison to the negative control. Unfortunately, there is no distinct differentiation between different concentrations of the inducer. Or in other words: It’s a binary outcome.

Rhl Based Detection System, now.
This time, the output fluorescence is clearly dependent of the autoinducer concentration. They show two different versions of this system – both seem to work pretty well.

They could nicely model their system, showing predicted GFP concentrations over time for different inducing concentrations of LasR or RhlR respectively. Their model builds upon hill equations. The critical parameters for that model are the degradation rate of the R protein and the degradation of the dimer of LasR and PIA-1, RhlR PIA-2 respectively.

They imply that they can optimize their construct to “tune” its sensitivity.

Applications: We see pictures of a possible stick to use for P. aeruginosa sample pick-up and a LED-box to detect the resulting fluorescence.

The team submitted 38 parts, 19 of them fully characterized.

 

A content-packed presentation finds it end. Find more information on what they did on their wiki: http://2011.igem.org/Team:Northwestern

Potsdam Bioware

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Second time, I am listening to Potsdam. This time they have left their youngsters at home. ;)

First an introduction, presenting how protease activity is involved in many diseases. Afterwards the potential of cyclic peptides for protease inhibition is presented. Their main focus lies on a group of cyclic peptides called microvidins which originate form Mycrocystis aeruginosa. The team wants to analyzed and optimize a member of this group, but their first aim is to express microviridins in E.coli. With the major aim being to modify the microviridin mdnA so that protease inhibiting activity is enhanced. For this mdnA libraries are generated which have to be characterized with selection systems. Different systems are present, such as Phage Display and a novel in vivo display system. Both system were set up successfully and they also modeled their in vivo selection system. The team was able to fit their model to their data. Also, a protease detector is presented. They conducted studies with the libararies to find new microviridins. Sadly, cut to human practice, would have like to hear more about their novel protease inhibitors.

Human practice and Xtras. Survey within the German parlament. Sadly, only ten people from over 600 answered. No t-test is needed for this data. ;)

Again, their adroid application (BioLog App), a in silico lab journal with a huge variety of functions. You can get it, if you visit their poster. Probably, you can also download it from their wiki. They have absolutely everything covered: “There is a feature for that.” For total madness, you should put that video on repeat and listen until the end of time.

MTT: Still congrats on your wiki. I like it! Also, who speaks in your video and why this time no Plug’nPlay approach?

Unicamp-EMSE-Brasil – Stress War

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Second Day, first session, second talk, track medicine

The brazilian team took some kind of a yoda coli along: Very nice artwork. I am excited. The presentation is designed in the star wars look. Nice.

The team wants to deal with pathogenic stress, which everybody suffers from time to time or constantly. Like me, blogging all the day :) They describe the interplay between the naive t-lymphocytes and the t-helper class 1 (Th1) or 2 (Th2). In a pressure situation, stress hormones are released, which lead to a shift in th2 (th1 suppression) and low cellular immune response. The low immune response can promote an infection caused by microorganisms. They want to create the JEDI coli that can sense stress and drive the naive t-cell differentiation.

They use oxidative stress system and a quorum sensing system to sense the immune imbalance (NO-sensing) in stress situations. The application of the project might be the modulation of vaccine response or treatment of diseases caused by immune in-balance. They introduce two different systems, which in stress situations battle against each other. This is done by the production of different molecules (cathelolamines), which can trigger the th1 or th2 concentration respectivly (Interleukin 12 and 10). The two systems interact which each other. This is done in the following way. If one systems gets triggered by a stress symptome it will start the production of its interleukin, in order to trigger th1 or th2. This mechanism works vice versa. The brazilian team characterized their producing systems with gfp.Unfortunately their system is a little bit too complex to explain it here in detail respectively to blog and hear it at the same time. Or I am just too tired. Check their wiki for full information. It is definitely worth it. C’mon they got YODA!:

http://2011.igem.org/Team:UNICAMP-EMSE_Brazil/Project

 

 

 

MIT

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Morning session, first talk. For 9 AM the room is quite crowded. Let’s see what the local team has done the last months.

Programmed Mammalian Tissue Engineering - Local interactions to global patterns

A short introduction to their main topic: The need for tissues which is a global problem since the current approach is solely based on human donors (18 deaths per day waiting for organs). The team wants to use the synthetic biology approach for tissue engineering and has focused on pattern formation. They present their system design where two phenotypes are possible – a sender and a receiver phenotype – and where three main modules are implemented. These modules are: cell-cell signaling, internal logic processing, and cadherin output.

A nice 3D animation showing how the final system should look like, is presented. The first component of their genetic circuit is a Notch-Gal4 which finally leads to the expression of cadherin and Delta-mCherry. The presented system is tunable with IPTG. Through cis-inhibition the expressed Delta-mCherry can shut down its own notch or activate other cells.

They also used a computational design tool to see what other interesting genetic circuits can be created. A simulation is shown how a group of cells forms a pattern after 24 h. They used their tools to simulate other designs and parameters.

Now to the experimental results. They started characterizing their parts one by one starting with UAS-Gal4. Afterwards the lacI repressor is tested. Gal4 connected to an inverter and a tunable amplifier are checked. Finally all the parts are put together (Inverter/Amplifier/Sender) and the mCherry fluorescence is measured. They can show that both, the sender and the receiver module works. This is underlined by some nice confocal microscopy pictures. It’s always cool to have something visualized. ;) Nice presentation.

Dundee: Sphereactor

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Abstract:

Bacterial microcompartments are proteinaceous reaction chambers designed to ‘cage in’ metabolic pathways and increase efficiency. Potentially, these could be engineered to house any chemical reaction imaginable; to sequester toxic material; or to confer new physical properties to a host. Here, a synthetic microcompartment (“The Sphereactor”) was designed and built. This was assisted by the creation of new mobile apps and web-based tools for DNA analysis. A synthetic operon was constructed, based on the pduABJKNTU genes from Salmonella, that assembled into the empty Sphereactor, which was also affinity-tagged to allow its isolation for downstream applications. A new targeting sequence comprising 20 residues of PduD was shown to target GFP into The Sphereactor. Attempts were made to pack the Sphereactor with many other proteins. Together, the Sphereactor and its new targeting sequence is a foundational advance that could influence the design of new metabolic pathways or inspire new bioremediation or biomedical projects.

Applications:

–arsenic binding

–bacterial lemonade!

 

To see if proteins are inside the sphereactor, they had a cool video with dramatic music. Intense!

Human Practices:

–Debate and discussion w/ the public

–SynBin: online safety database: sharing accidents, or “syns,” in the lab

–Software: Gene Synthesizer

–Apps: The Lazy Scientist and Gene Cutter (free at Apple app store and Android Market)

Future Plans:

–Futher develop synthetic BMC as a tool to allow cell-free system

–Magnetism

–Flavorings and bioproducts

 

One of the questions asked: why used ordinary diff eq’s instead of a stochastic model?

 

 

 

 

Poster session!

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There were many great posters in the Stata Center and Lobby 13! Here are some of the fun things I came across:

1. A Microsoft Surface by BU Wellesley Software’s poster, just outside 32-123. It looked like a small table with a gigantic iPad for its surface–a tabletop computer! Tony Stark probably has one for a nightstand, haha. A team member told me that they downloaded the apps that they made onto it. Awesome! The app I was shown was G-Nome Surfer Pro, which one can use to look up genomic data for numerous organisms and a list of relevant Pubmed publications. Like with an iPad, you can physically move objects around onscreen with your fingers.

Their future work: develop a Microsoft Surface the size of a conference table so you can gather your entire iGEM team + advisors around it and have the most awesome brainstorming sessions ever! :D

 

2. A novel by ZJU-China about synthetic biology called In the Name of God. Here’s an excerpt:

“The man with a serious look thanked the other and put on the badge: bronze, equilateral triangular shape badge with black gothic letters “Gel” on the lower side and “Bob Savage” engraved with a smaller letter. He picked his name from “the Brave New World” when he decided to join this biology research group. They didn’t even ask for his real name because everything they care about is talent. If one has never had any scientific education in his entire life but has unbounded creativity, he would still be taken as a part of the mission.”

Interesting… A definite must-read!

 

3. Washington iGEM: purple and yellow M&M’s with BBrick part numbers on them. The joke? One of their projects involves developing a therapeutic for gluten intolerance (celiac disease) in pill form.

4. Imperial College iGEMers in green jumpsuits handing out Auxin pins. I think I’ll put one on my backpack.

5. Tokyo Tech’s Human-Bacteria rock-paper-scissors game

6. USTC-China’s self-organizing bacteria, guided by a theophylline gradient, riboswitches, and toggle switches

7. NYMU Taipei’s “optomagnetic” project, inspired by James Cameron’s Avatar movie and optogenetics. After seeing Sam Worthington connect to his avatar in that link unit, they wondered how synthetic biology can be used to enable Avatar-esque technology.

Logging out for tonight,

Alyssa

SYSU-China: Nuclear Leakage Rescuers

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SYSU China has many adorable E. coli illustrations in their presentation!

Inspired by nuclear disaster (Fukushima). Cs137: 30-yr half life, huge injury, spreads into water, many source sites. ”We need something that is easy to control, senses radiation, and DEALS WITH IT!” =)

Project summary (as a cute video!):

–migration towards radiation: recA promoter with CheZ downstream

–absorption of Cs: recN promoter

–Aggregation of Ecoli: recN promoter with trkD and ag43 downstream.

Bacteria capture: PrecA with cheZand egfp downstrream. Also constitutively expressed mRFP to test whether bacteria were live/dead.

–13 BBricks submitted to registry

 

Some of their BBricks:

1. RecA promoter powers SOS repair system. Project uses flagellar motor system, where CheZ encodes the motor. Put both together; bacteria moves to radiation source.

–The closer the bacteria get to the radiation source, the faster they go

2. Ion channel TrkD. Low affinity transport of K into cell, high affinity transport of Cs. Attached w/ GFP downstream of Plac.

4. RecN promoter: can be triggered by higher radiation than recA promoter.

5. BBrick: aggregation, using antigen 43 (it sure is a popular brick!)

Constructed PrecN with trkD and ag43 downstream. Goal: E. coli cells absorb Cs and aggregate, making them removable.

6. Bacteria capture: PrecA with cheZ and eGFP downstrream. Also constitutively expressed mRFP to test whether bacteria were alive/dead.

 

Human practices projects: iOS app and board game, as well as a workshop.

 

Future work:

1. Part measurement

2. Protection system

3. Parameter optimization

 

A few of the questions asked were:

Do your bacteria survive in seawater without media?

There is much K in seawater. Would that affect how TrkD responds to Cs, when there’s so much K in the water?

Your project = chemotaxis against the current. Will that work? Also, how can you detect fluorescence in seawater, which has many substances in it?

 

Great job, SYSU China! Way to apply synbio to tackle a significant environmental issue.

 

 

Imperial College: When Auxin Met Root II

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4PM: Cool, a preview video! It looks like Imperial took the time to answer questions from the iGEM Europe jamboree in a creative way. The music sounds very Tron-ish; Daft Punk?

Motivation: Desertification–more than the area of Boston is lost in one day!

Solution:

–Improve lateral root growth, get bacteria to localize around roots to increase root growth.

–Why engineer bacteria instead of the plant? Because engineering bacteria = a modular approach; can theoretically use engineered bacteria to affect many different plants.

–New research states that plant roots actively break down their cell walls and take up microbes; good way to get GE’d bacteria to go into the roots = delivery mechanism of compounds of interest.

–Get bacteria to secret auxin.

–And they “faced HP head-on:” consulted several experts about their project. Elephant in the room (pic of elephant with glasses, LOL) = horizontal gene transfer; hazard of GMOs in the environment. Kill switch doesn’t answer teh issue and it’s not robust ==> so a need for GeneGuard, a novel containment device. HGT impacted chassis choice. B.sub not the best–hard to contain in nature?–so went w/ E.coli. Looked at survivability of GFP expression in soil; K12 E.coli stayed alive for over 7 weeks and retained the plasmid of interest w/o antibiotics present. Great!

Modules:

1. Phyto-route: EC move to roots

2. AuxinExpress: auxin secretion

3. GeneGuard

 

A) Module 1:

–Rewired chemotaxis to induce movement to roots. Overexpressed PA2652 ==> Alter flagellar motor = alter chemotactic behavior. (Express foreign chemoreceptor in EC = influence chemotaxis.) Construct = pJ23100 Anderson promoter + rbs + PA2652.

–GE’d EC to be attracted to malate (compound in roots). Used capillary assay, each capillary = a different [auxin]. Optimal time for expression = 60min. EC responds to a uM – mM range of malate = biologically relevant levels. Good!

–Bacteria at root: great pic showing superfolded GFP in root, + confocal image showing bacteria actively taken up by root.

B) Module 2:

–Team gardener grew Arabidopsis in different concentrations to see effect of auxin on root growth; 0.1nM best.

–COOL MODEL: input [IAA], get root morphology output.

–Another lab provided seeds that respond to IAA by producing YFP. IC found YFP expr. in roots.

–Bacteria still viable after time passes: tested w/ Dendra2-expressing EC. (D2 tracks cell viability, new platform for imaging gene expr. in roots.)

C) Module 3: Geneguard==> prevents HGT, keeps construct in chassis. When plasmid moves out, cells lyse.

–Best promoter/rbs strength ratio = 300. Went for 400 to play it safe.

–Made antiholin construct, troubleshooting toxin construct.

 

Future Applications: spoke w/ companies. ”use a seed coat!”

–Incotec = working on incorporaing GEed microbes

–met w/ Berkeley reforestation trust; provide tech to promote revegetation, perhaps apply in agricultural sector.

 

Outreach/Human Practices: Natural history museum, Radio iGEM, art by college intern, additional help from HS interns.

 

 

 

 

 

British Columbia – iSynthase Terpene Production in Yeast

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In nature, monoterpenes are synthesized and secreted by trees as a defense against invading beetles and fungi. The bluestain fungus and mountain pine beetle are in a symbiotic relationship where the fungus deactivates toxic terpenoids and enables the survival of the beetle, which in turn facilitates the spread of the fungus from tree to tree. Meanwhile, from an industrial point of view, various monoterpenes are involved in the production of pharmaceuticals, flavours/fragrances and biofuels. The 2011 UBC iGEM team aims to optimize production of terpenes in Saccharomyces cerevisiae yeast by constructing the biosynthetic pathways necessary to synthesize these compounds. To simulate the system, we are developing models of (i) monoterpene synthase structure, (ii) monoterpene production in yeast and (iii) the dynamics of the mountain pine beetle populations in British Columbia under the influence of our synthetic yeast. A new human practices approach we have pursued this year involves interviewing experts across various fields to obtain their opinions on the release of synthetic organisms into the wild.

*****

The UBC iGEM team aims to tackle the pine beetle epidemic in North America by constructing a proof-of-concept terpene-producing yeast. Beetles have invaded 17.5 million hectares of pine forests to date, resulting in devastating economic, environmental and social consequences. Trees are normally able to fend off beetles by producing terpenes. However, the blue stain fungus that lives symbiotically with the beetle is able to degrade these terpenes.

Producing terpenes would serve a dual purpose: one, to assist pine in fending off the fungus and two, for industrial purposes.

The team created 2 models. One to simulate monoterpene production in a metabolically optimized yeast. The other to predict the beetle epidemic and identify strategic sub-population sites for dispersing the synthetic yeast.

Human Practices: interviewed experts, made word clouds from undergrad, wrote a dialogue about releasing synthetic organisms into the wild, made a guide for how to start a high school iGEM team, mentored high school students.

Harvard: Massively Multiplexed Zinc Finger Protein Engineering.

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Foundational Advance: a system to make and test biological parts.

What they want is to create zinc finger proteins that bind to DNA tripletsfor which no zinc finger protein currently exists.

So.. Harvard, exciting presentation it was. They stated how motivated the became by the fact that designing new interactions is difficult.

So far… You can make educated guesses using structural and biochemical information

The Harvard guys decided to combine advantages of the existing approaches and produce their method

The two features it is meant to inclulde are 1)Test many interactions and 2) Higher probability of succes

 

The steps for their methodology are:

  1. Design
  2. Synthesize
  3. Test

 

Zinc Finger Proteins are naturally evolved DNA-binding protein which can be cuztomized to target DNA sequences.

Their structure comprises 3 elements:

Helix, Backbone, and Finger (binds to a dna triplet).

Their project

 

1 DESIGN: used bioinformatics, predicted 55,000 zing finger sequences (Targeted against 5 dn sequences for 3 diseases)

Lots of possibilities with 7 binding aminoacids.
They created an algorithm that generates zinc fingers with high probability of binding target sequences, the algorithm used information from previous studies and known models: predictions. They also expanded the pool of zinc fingers including homologous backbones, as well as including randomness “to consider sequences that nature and previous studies might have missed”.

2 SYNTHESIZE: Chip Synthesis (new tech) synthesizes DNA sequences on a microarray chip, it is cheaper than traditional methods (I think it was 10,000 dollars), and 55,000 fit in one chip.

The most common problems with Chip synthesis were frameshift, 2+ point mutations. 1 point mutations. About 60% is perfect squence.

They used a genomic-metabolic (Histidine) selection system to obtain the zinc fingers successfully binding to DNA. When grown in media without histidine, the cells can only survive if a zinc finger-omega subunit of RNA polymerase (also knocked out in the strain) fusion protein binds successfully and initiates creation of histidine .

Human Practices:

they claim that they want to make a difference in the world

How do we bring technology to the world?

-Commercialization

-iGem enterpreneurial division

Case study of their own project, explored the impact of their project in the open community vs the commercial path.

They thought about the pros an cons of Open Source Technology and Intellectual Property rights

Proposal: Research Exemption. Allows academic research without high licensng costs. *They were reminded, though, that Research Exemption is not as simple as it reads on paper.

They were also asked about their brainstorming process, the supportment of their advisors, the timing of their work.

BYU Provo – E. colinoscopy

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Last talk in this session, last talk for the track information processing and the last talk for today.

The complete team is at the front. The topic is the construction of a molecular AND gate in E. coli that may be used for example in the detection of early onset of colorectal cancer. Since two features, heat and reactive-oxygen species are the two hallmarks of colon cancer, an AND gate will be a great way to detect these cells.

A nice stop-motion video is presented.

Now, modeling. The team used various differential equations and shows some nice figures, but it is not possible to describe these figures in words…you have to be a robot/transformer.

A thermosensor from Listeria monocytogenes that is used for infection will be used in the project. The problem is that the team needs a thermosensor with a narrow temperature range, but details concerning that will follow later.

They used the thermosenor for proof of concept experiments. A pSox promoter is also used and proofs that the AND gate is functional and that parts are interchangeable.

They tried to rationally design a thermosensor with a narrower temperature range. Also random mutagenesis was tested. A huge screening was performed (“100s of thousands”). The team was able to find novel 30-37° C thermosensors and also thermosensors with a really narrow temp range…35-37 °C. Congrats. After designing the new thermosensors, they started characterizing them so that they could go back and do a rational design again. For this, they started with some folding software.

Community outreach. DNA extraction from strawberries at a local elementary school. “Is that really DNA? – Yeah.”

 

Groningen – Count Coli

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It’s the “Information Processing” session and Groningen counts on E.coli. They want to make use of synthetic biology to count and control cell cycle, to control cell differentiation and to record environmental events.

In their cell models they show the modularity, the extensibility, read outs and control of their system.

They use their input inducing a 1st memory to… well… memorize and finally to give an output. An AND-gate follows, combining the initial signal and the first memory to induce the 2nd memory and so on… They made use of several promoters and different degradation rates of gene products for that and also implemented a reset mechanism. See a complete explanation here: http://2011.igem.org/Team:Groningen/project or take this picture for explanation:

Coming to the math. The speaker talks about really difficult equations he had to solve, and I totally believe him. At that point I’ld kindly refer to the teams wiki page, once again ;) With Cumulus they developed a platform for data input, model creation/processing, evaluation, selection and sharing of solutions. He talks about a genetic algorithm, about random mutations in the parameter set of his models. Evolutionary optimization of models in collaborative cloud computing. nice! He doesn’t stop dropping buzz words that I love to hear when it comes to software (Flexibility, General availability, Scalability, …)