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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