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Liveblog from the iGEM European regionals’ final session. We’re going to colourcode our entries, so entries by Marc are in green and entries by Christian are in dark blue.
11.02
Finalist Nr. 3 is taking the stage, WITS-CSIR South Africa and their project BioTweet!
Their project is chemotaxis focused and the idea is that bacteria will be able to “mark a spot”, migrating out to somewhere and finding it’s way back again, as if programmed to do so.
To achieve this behavior, the team chose to use riboswitches (which make it possible to turn the transcription of genes on and off) and a normally non-motile bacterial strain, where the team has restored motility through expression of the chemotactic factor CheZ.
To achieve the up and down movement, they wanted to engineer a system of overlapping gradients which would have the highest concentration of attractant at a certain endpoint, which when reached would turn riboswitch and render the bacteria immobile. Afterwards the riboswitch would be able to be turned again and the bacteria would follow the other chemoattractant gradient “back home”.
(This probably sounds very cnfusing, so I encourage everyone to check out the team’s slideshow and their figures for a better understanding)
Riboswitches are nothing new in iGEM. Teams from Taipei and Lethbridge have created riboswitches before, but always with a 6-11 nucleotide scar between the switch and coding sequence. The South African team has therefore created a riboswitch without the scar, which can be easily combined with any desired coding sequence. They also added the venus gene for read-out.
When testing the switch itself, they found a 4xincrease in fluorescence intensity of their read-out when induced, pointing towards a very well functioning riboswitch. This was also recreated with CheZ, showing increased motility when induced with theophylline.
The overlapping gradient experiment has only been modeled so far, according to the presentation you can check it out on the team’s wiki and play around with it, so I encourage you to do so.
The team achieved the following in the course of this year:
-Submitted 11 biobricks, including two novel theophylline riboswitches
- Introduced a broad audience to synthetic biology.
The riboswitches created in this project are really cool and I would guess that we will see them used in future projects.
10.44
Pictures from Paris Bettencourts presentation. The order is a little jumbled.
10.35
The parisian team’s project is based on the discovery of bacterial nanotubes in cell-to-cell communication in early 2011. They asked themselves if they could characterize these tubes and make them work for synthetic biology.
These nanotubes can be found between B.subtilis/B.subtilis and B.subtilis/E.coli. These are only observed in exponential phase and only in solid growth media. The original characterization was done through GFP transport via diffusion through the nanotubes. The other experiment that showed the presence of these nanotubes was the transfer of antibiotic resistance from one cell to the other.
Paris Bettencourt started out with modeling the diffusion through the nanotubes and thereby see if the diffusion really is enough to explain the transfer of molecules through nanotubes. The model seemed plausible, but the team wanted concrete evidence, so to the wetlab they went.
They recreated the GFP project and confirmed the transfer of GFP in their bacteria. But when they tried to recreate the experiment with the transfer of antibiotic resistance, they could not recreate the original articles’ findings. So the question TuBE or not TuBe still was not answered.
Therefore they decided to create their own experiments and prove the existence of the nanotubes themselves. Their experiment design for this is have a emitter cell and a receiver cell with an amplifier, that amplifies a molecule, if successfully transferred. They designed 3 possible ways to do this:
1. A concentrator
2. A positive feedback loop
3. Bistable switches
The concentrator system works like this: The emitter cell expresses TetR-YFP and the receiver does not, instead it expresses a TetR-Array, which will concentrate the YFP. When testing the system through by fluorescence microscopy, there can be seen protein aggregates of YFP, pointing towards the existence of the nanotubes.
Model nr 2 is working with a T7 polymerase positive feedback loop, called an autoloop. First of all they tested their loop in cells expressing T7 polymerase and cells not expressing T7. The conclusion from this experiment was that the positive feedback loop works, ergo it can be used in the emitter-receiver experiment. The emitter cell produces T7 polymerase, and the receiver express the positive feedback loop with GFP as a read-out. If T7 polymerase is transferred via nanotubes, the coli not producing T7 polymerase should light-up on fluorescence microscopy, since the autoloop has been induced. Before they conducted the experiment they modeled it and the model suggested that the experiment should theoretically work if the nanotubes exist. The actual wetlab work on this experiment has not been concluded yet, so there is no final result yet, only that all the biobricks needed for it work.
Overall the team has achieved the following:
- reproduced and proved the original article’s hypothesis
- Designed 6 emitters/receivers and modeled their behavior
- Provided proof of principle of 5 emitter/receiver systems
Still, one question remains TuBe or not TuBE?
10.22
10.14
Slides from the ICL presentation
Slides from the ICL presentation
10.12
Finalist Nr.2 is up! Paris Bettencourt’s liveblog yesterday was lost in the depths of the net, but we luckily have a second chance to create a write up of their project. Letø’s see if we can answer the question “TuBe or not TuBe?”
10.11
ICL presenting
10.08
Next up is Paris Bettencourt
10.07
Everyone just sang happy birthday to Rebecca from ICL who’s turning 21 today. She seems to be having a great birthday so far :)
10.04
ICL has one huge achievements list, no wonder they are one of the finalists!
10.03
The final implementation of ICLs system would be to create a bacterial seed coat, to maximize the bacteria’s effect on the plants.
10.01
The third part of the project, GeneGuard, is supposed to hinder horizontal gene transfer. Once again, the modeling looks great and they are presenting quite a few nice graphs, ut I honestly wonder how many people in the audience really understand the complex equations being presented here.
Before introducing Holin into bacteria, you will have to introduce Anti-Holin else your cells will just lyse (holin is bacteriocidal). Right now the team has introduced holin into their bacteria, but the construct for holin has not been completed yet.
09.58
So the bacteria can get into the roots, but what are they supposed to do there? ICL engineered their bacteria to secrete the growth hormone, turbocharging root growth. They are presenting quite a few fancy models of root growth, I have no idea how the model works, but it looks nice.
The bacterias ability to secrete auxin was determined via a salkowsky assay, where cultures containing auxin producing E.coli will look more red compared to normal bacteria.
09.54
Chris from ICL apologizes for being a bit slow this morning, but he is still presenting well. Still he presents fine and shows us “the world’s most boring graph”. (Picture follows later)
The chemotaxis module of the project focused on making E.coli swim towards malate (malate acts as a chemoattractant), which is a byproduct of plant root growth. Once there, the model plants (arabidopsis) take up the bacteria into their roots, where the bacteria stay for 10 days. All of this is shown with nice and flashy videos of fluorescence microscopy, delivering quite the light show.
09.48
Just a short summary if You have not checked out the ICL project yet. The team has created bacteria that are able to migrate towards plant roots and secrete the growth hormone auxin in the roots, making them grow faster. This will anchor the top layer of soil to the bottom layer and thereby making it harder for wind and rain to sweep away the fertile top soil, thereby fighting desertification.
09.45
ICL playing electronica in their results summary video, that’s the right music for hungover iGEMers this morning, some almost started dancing again.
09.43
Imperial College London is going to first up presenting. If You want to know all about their project check our spotlight and liveblog from yesterday. Technical difficulties delay the beginning of the presentation.
09.39
The three finalists are:
Imperial College London
Paris Bettencourt and
WITS-CSIR SA!
09.38
Finalists are about to be announced!
09.18
The opening remarks start at 09:30 check back by then for the liveblog.
