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Warsaw – Synthetic cloning and expression control

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Five students from Warsaw come up with a double-project. First, they want to bring regulation in expression levels via expression adapters: This will allow better control on how much gene product is product in time. Second, they present a novel method to get your BioBrick DNA ready for cloning in just two hours (well, … virtually – but still faster!).

The first part of the project deals with expression adapters. They created 5 expression adapters leading to different expression levels and committed their BioBricks. Use of RBS calculator to check your perfect expression adapters. Their created model worked fine.


algorithm data line for expression adapter modelling:

Starting population

RBS calc

best seque -> pop data -> order seq

beset survive

Mutate recombine

new populations


The second part deals with problems with cloning. Often the gene of interest might be toxic to your host cells. The solution they provide is a synthetic cloning step with the phi 29 polymerase (Rolling circle amplification). Hence you do not deal with GMOs unless the last step of cloning => the transformation. This might increase Biosafety.

Human practices

Synthetic cloning can be seen as a new safety standard, because of the lack of bacteria escaping out of the laboratory.. They co-operated with the BioCen team-up, which provides innovative bioscience education in Warsaw. They keep contact with their friends via their facebook homepage.


Cells still involved in cloning at the end, but process can be used for cell-free expression. phi29 is able to work with high fidelty, hence there will not be any failures introduced by the polymerase. Further the system is very cheap, you have to calculate one euro per cloning pcr.They faced problems regarding public awareness in Poland. there is a no GMO to students opinion. Hence they choose to do the synthetic cloning.

EPF-Lausanna: Transcription Factor Development Pipeline

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Raphael, Donatello Leonardo and Michelangelo. They are all here. Yeah, dressed as ninja turtles. This brings back memories….I miss the nineties.

Some problems with the MacBook and projector. 1/5 of the presentation is not visible, but now they have to start anyway.

Idea: A tool box with a lot of transcription factors (TFs). For this, a TF development pipeline consiting of a selecetion and characterization system is needed.

A negative selection system based on lysis is presented. Also, they were able to recover plasmid DNA coding for the functional variant.

In vitro and in vivo characterization systems were set up successfully. So this part of the project also worked and they were able to characterize differnt TFs with a changed specificity.

Vivid presentation.

Strange. Neither the DTU Denmark nor the EPF Lausanne presented PR work.

Imperial College London: When Auxin met Root

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Liveblog from the ICL presentation:


Q & A:

Q: How does the auxin get out of the cell?

A: There is no active transport needed, auxin diffuses out of the cell.


Q: Will your modified plants have an advantage over the naturally occuring plants?

A: The plants would have an edge over the normal vegetation, since the longer roots would allow them to absorb water more easily.


Q: How long do the plants retain E.Coli in their roots?

A: Arabidopsis retain bacteria for ~10days in their roots.


Nickie and Chris are going to present the project AuxIn, starting out with a video showcasing their most important results – Really good idea!

Nicky is giving an introduction to their project, explaining what they want to do with their project: fighting desertification. They want to engineer plant roots to keep the soil layers together and thereby fertile. The team engineered bacteria instead of plants, since it would be a more modular and versatile approach.

The first module of the project is making the bacteria migrate (chemotaxis) toward the plant roots. It’s called Phyto-Route.

The second module of the project encompasses the bacteria secreting the plant growth hormone auxin in plant roots, Auxin Xpress.

The third part of the project is called GeneGuard, which is acontainment device instead of the usually used kill swicth mechanisms. This is supposed to improve the safety of the project and make GMO release in the environment less dangerous.

Chris is now going into detail with the project’s modules:


First up, the chemotaxis. For this the team introduced a malate receptor into the bacterial chemotaxis pathway, so that malate acts as a chemoattractant.When they compared the velocity of the chemotaxis modified bacteria and their controls in a medium saturated with malate, it showed that the malatesensing bacteria traveled at higher velocities, which indicates the stimulation of the chemotaxis pathway.

Auxin expression

This module started out with modeling to find out how much production of auxin by the bacteria was need to achieve enhanced plant growth. The construct for this consists of the PVeg2 promoter, the IaaM gene and the IaaH gene which are involved in the biosynthesis of Auxin. The results they achieved: The bacteria succesfully produce auxin and enhance the growth of arabidopsis compared to normal arabidopsis (without bacteria).


This module introduces holin (a toxin) and anti-holin (the anti-toxin), to contain the growth of their bacteria. If this actually works the team has not had a chance to test yet, since they have only created the anti-holin construct so far, while the holin construct is still being constructed.

The way the described system would work in the future would be to create a bacterial seedcoat for the plant seeds.

On top of this the team also did various outreach projects, like a radioplay and the radio iGEM show.

ICL’s achievements list is so long that I can not list it here. The most important part is probably that they submitted 6 novel biobricks and fulfilled almost all their goals they set out to achieve.



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Copenhagen is a rookie team, composed of 7 students, from 3 different lines of study. They’ve been collaborating with DTU-2 over the summer. Their project is called Cyperman.

Through the use of aromatic aminoacids, the cyperman creates oxime bombs, that are toxic to fungi. Applications for the cyperman include woodprotection and plant protection. Usually fungicides for wood protection is produced by chemical synthesis. The cyperman should produce oxime bombs cheaper and cleaner. Alternatively the cyperman could be sprayed directly on to the woodwork. Plants could produce oxime bombs in response to a specific signal from a inviading fungus, maybe in a tissue specific way, increasing expression in leafs.

The cytochrome P450, CYP79, is the key part for this team, when seperated from the normal metabolome it will produce oximes from aromatic aminoacids. Oximes kill fungi by inducing mitochondrial dysfunction leading to cell death.

The team ran into troubles using the standard assembly model, by using the new “Plug’n'play” standard proposed by DTU-Denmark-2 this year they we’re able to finish their construct.

To characterise their construct the team used Thin layer chromatography, from the results of this analysis they believe they’ve had succes in coaxing their Coli’s to produce Oximes.

In conclusion, the team managed to create a construct for producing oximes and cloning the construct into E. Coli.


Q: Please elaborate on problems with the standard assembly.

A: Basically problems in all areas, the DTU method was much easier and had no need to reduce illegal restriction sites.


Q: Regarding the ethical forum, could you distill some points from there

A: A lot of science-students feel that life and machines are more alike than students from other areas of research.


Q: Could you say more about how considerations for human practice affected your project

A: At first we considered spraying our bacteria all over farms, but after finding out we might harm beneficial fungi we decided to put our construct under inducible promotion and introduced considerations for tissue-specific expression.

DTU Denmark: The Universal Tool For Gene Silencing

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Liveblogging from the DTU Denmark presentation


DTU kicked off the Foundational Advance track. Starting of giving a introduction on the study and design of regulation as well as the limitations of the often used direct gene editing.

Basis of their project is the use of sRNA for post-transcriptional regulation. For this they choose a system inspired by chitobiose regulation in E. coli.

The team is working on a system to target and repress any gene of interest (GOI). They were able to show that the system in general works fine, but unfortunately time was not enough to perform the experiments needed for the repression of GOIs.

Instead, a comprehensive and sophisticated model was presented. Also, I love heat maps. ;)

Also a rationally designed arabinose promoters library was created and characterized.

All in all, a quite interesting project even though there was not enough time for achieving all aims set. Probably most teams know this problem.

Now, for Q&A

The DTU is prepared. They have a additional slides prepared. One of these already answers the first question. Clever.

Opening Ceremony

Here is our coverage from the opening session of the Europen iGEM regionals 2011:



If any of you want to come work at iGEM headquarters, pay attention, we’ll be putting out announcements for job opportunities at the iGEM foundation!


New branches: Entrepenurial divisiom, high school division, maybe a software tool division.


iGEM has evolved from being something happening in Randy’s lab to being too big for all of MIT. That is why iGEm is moving out of MIT and being based on the iGEM foundation. The competition is also branching out, with the addition of a highschool branch that will schedule a separate competition for these teams.


Up until the industrial revolution your potential was determined by your muscles, your slaves’ muscles and the muscles of your critters. In the industrial revolution we discovered that energy is a fundamental entity in the world, and got good at applying it. Later, in a discovery analogous to that of energy, we discovered that information too is a fundamental entity. The industrial revolution did energy, the computer revolution information and synthetic biology will do matter.

Biology deals with molecules with precision and grace, synbio is about utilizing these properties.


Randy Rettberg now takes the stage. Everybody remember to set your posters up this morning, the judges will go around all day, not only at the poster session.

Randy gives a little history lesson, from the greeks to the romans, to religion as being the answer for everything. Is he going to suggest synthetic biology as the latest stage of this evolution of mankinds intellectual progress?


I’d like to give you some background on iGEM history and what’s happening in iGEM right now.


iGEM – international genetically engineered machine competition or collaboration? In this competition we’re competing in collaboration. Collaboration against ignorance and competition against each other.


The speaker now moves on from “In silico” in synbio to “In vivo”. He mentions iGEM as one of the main arms of the research happening in in vivo synthetic biology. There are alot of controversies around our field and the speakers draws comparisons to all the controversies in Amsterdam – you can’t get coffee in a coffee shop for example. Afterwards he describes the iGEM competition as a a collaboration towards performance so that everyone is a winner in the end!


In silico systems biology: modelling cells by using characteristics of their metabolism, such as enzyme kinetics, and predicting what will happen if a particular characteristic is modified.


For the development of drugs and systems biology we need a good understanding of networks. Synthetic biology gives us a chance to test our understanding of this subject, a chance we have at iGEM.

From here he carries on with a short history of synthetic biology, one of the milestones:

2005 – The creation of the partsregistry, Megan Lizarazo.

2011 – The iGEM Regional Jamboree in the Netherlands, Douw Molenaar.

Interesting take on the evolution of SynBio!


Synthetic biology is the best way to test our knowledge of systems biology.


“Usual rational drug design focuses on targeting individual molecules. But for network diseases we need to apply a network approach.”


We are starting out with a discussion of systems biology and it’s relation to curing diseases. A rather unusual way to start the jamboree which is normally opened by Randy, let’s see where this goes.


“Partly because we have cured many infectious diseases, we’re entering an age of multifactorial diseases or systems diseases.”


Hans V. Westerhoff opens this session. He is the chair of microbial physiology at the VU Amsterdam and professor of systems biology at at the University of Amsterdam.


Opening session starts 08:45. Check back in 25 minutes for the live coverage.