01Oct
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If you’re strapped for time here’s a little help. In our humble opinion these are todays best posts/presentations:
Sadly, due to wifi problems, not all of our posts on these teams are complete. Please look up the presentation videos of the teams once they’re up.
01Oct
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The team pushes themselves with pushing their clenched fist together. I will call this a bro fist, regarding to Barney Stinson. Like it. Unfortunately the sound check was misunderstood as their presentation. So there were some seconds of confusion. I will use these last minutes before I am going to hear the final presentation today, to thank my man on the camera => Niko. Without his help, managing all the technical stuff, i would not be able to write this live blog and provide you with “hot topics of synthetic biology”. So you as a reader might applaud if you wanna.
Now it is on and they started like a rocket. More words per second than in the last session as a whole. The idea of the project is to create synergy outside of the cell. They want to use a cellosome and hopefully use this as a bio-refinery one day. Very nice animations to explain their phage display. Manufacturing in E.coli and use the phage as a carrier. The next thing really happens to fast for me. I am truly sorry. But nice eating sounds =)
The model system contains of endoglucanase, exoglucanase and beta-glucosidase for glucose degradation. They want to use the synergy system, which means triplets of enzymes, in order to achieve a higher efficiency of degradation. Their model is easy to understand and to extend. Which is a nice idea. The model shows that the synergy system should work in real life applications with real life data. Let”s see.
HP:
they performed a feasibility study (will it work, how could it be applied and what role will it play). Nice idea and i guess one of the few teams who really presented this stuff today. Maybe more teams did this, but they do not presented it in this way. Investigating the real life application regarding technical aspect in industrial standards and economic views. Like this. Further they interviewed different discussion makers. Like it. Now the bell is ringing. Let op! But they stay calm and would not let them be distracted by an automated announcement! Even if the building will be closed in 15 minutes, we will stay for science! Interesting last session.
Conclusion: They selled me a new approach of assembly protocol, which was invented by their supervisor. mmH. Further i did not get how many BioBricks and what kind of Biobricks were made. Might be me. Nevertheless this is definitely a nice and good performed project. Keep an eye on this team.
01Oct
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Explosions in coal mines cost 50 workers their life every year. Methane gases contribute to global warming.
Methane monoxygenase converts methane to methanol. After conversion, the LUSH protein is used to entrap the methanol. To ensure safety of the project the team has included a temperature sensitive kill switch.
The team has submitted a new methane monooxygenase. To characterize their construct the team used SDS-Page.
Funnel methanol into a water tank, add MethanE.COLIc, receive methanol.
This was not a long post, have a cute Coli as a pickme-up, courtesy of the METU-Ankara team.
01Oct
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Live blog from the presentation of the team Paris Bettencourt:
15.55 I personally apologize to the Paris-Bettencpourt team, I had written up a long post about your great, great presentation, but sadly due to connectivity issues it was lost in the depths of the internet.
I therefore encourage everyone to check out the poster of the team Paris-Bettencourt and thereby try to answer the question TuBe or not TuBe?
01Oct
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They really got a romantic emblem on their start slide. It is a bird chirping out flowers, which surrond their team name. They come from the heart of europe. So they were committed to such an emblem, aren’t they? Back to work. The project will be about a lipid driven genetically engineered machine.
Lipids can be use to regulate a machine, because they are able to mediate gene expression. The machine has to consist of a lipid sensing element, regulator, effect and a switch for switching the genetically machine. They built up their project by using Zn-fingers used by the last team Debrecen. Further they implemented a new input signal (lipids, i guess) and a switch off system by programmed cell death (that seems to be a little harsh, to shut down a system by destroying it?!). Zn-fingers are transcriptional factors and hence can be used to regulate gene expression. For activating the cell death they introduce the bax genes to the host cells.
There is a cute little devil on the slides. So special points for design. As a result of their project they managed to built up a two-hybrid mammalian system. So they proved that their Zn-finger works. The system was trained on oil sand samples, provided by the oil sands leadership foundation and cheese. The lipid extracts out of these things worked with their system. Further the apoptosis inducement work nicely 24h after transfection.
It was a long day full of presentations. So i did not get the last part of their presentations with the real water samples. I have to apologize. Check their wiki for the lacking information. It seems that you have to confront high school students with your project to be a good iGEM team. Nearly every team did it. So put this on your to do list, if you – yeah you, the reader of this blog – will start a team next year.
Q & A
Design of the transcriptional factors. Are there linkers? Design guidelines which were followed?
They put together the ligand binding domain and the DNA binding domain, which both were designed by them and synthesized by a company.
The judges were wondering if they did any modelling?!
They will do this in the future.
Is the apoptosis system in the Partsregistry?
No, they are currently designing it.
01Oct
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If you thought flip-flops are things you wear on your feet, you thought wrong! This year’s UPO Sevilla team gave a whole new meaning to this word: a molecular switching device. Dressed all green they sure make a fresh impression.
Many teams tried this before, rather unsuccessful, but the Sevilla team outsmarts them all. By making the behavior of the construct more robust, it became more useful. This is why they envision a broad use of this part, just like flip-flops are a general part in electrical engineering.
 - UPO Sevilla team wearing their flashy green shirts
Furthermore they introduce the MiniTn7 toolkit. This toolkit is a set of plasmids with transposition capabilities. Teams can use this kit to introduce biobricks into the bacterial genome.
It is cool to see that multiple iGEM teams find different solutions for integrating parts in the genome. Now that teams are getting more and more ambitious, the amount of altered DNA they want to transform seems to be increasing rapidly. Both UPO Sevilla and Uppsala Sweden now added posible solutions for this to the Registry.
Spanish SynBio Blog
Last but certainly not least I would like to highlight the fact that the Sevilla team has set up the first blog completely devoded to SynBio in Spanish. Please take a look at it: http://tornillosygenes.com/.
01Oct
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Team Bilkent starting out on a serious note, with an aim to fix the problems of the earth. The team of 7 devised a project to degrade TNT in the environment.
They restrained themselves to the problem of TNT contamination, which can be found throughout the world, often in the form of unexploded landmines. TNT can contaminate soil and water, water turns pink, if the waterstream is for drinking water, it may be hazardous to human life.
In order to degrade TNT the team grabbed a gene from E. Cloacae, codon-optimised it for algae and transfected Chlamydomonas reinhardtii. Apparently the team had to wait two months to receive the gene to build their construct. Apparently waiting for their DNA has had a negative impact on the scope of the project.
Sadly, the team doesn’t yet have any data to support the hypothesis that their construct has been succesfully transfected into their host. They have growth, but no characterization.
In conclusion, the team encountered large problems with delivery of DNA synthesis,
Q: Why did you work in plants instead of bacteria and
A: Algae can grow in toxic environments, it grows fast, and it would be a sustainable solution.
Q: How does the TNT enter the cell, so that it can be degraded?
A: We haven’t tested it yet.
Q: Have you considered the environmental impact of introducing algae into the environment.
A: We expect algae will biodegrade TNT.
01Oct
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Liveblog from the team Amsterdam presentation:
15.19 The team’s own conclusion: Our bacteria are cool!
15.17 The Amsterdam team starts out with welcoming everyone to their city. Their project icE.Coli is based on the so-called cryobricks, biobricks optimizing E.coli for growing and surviving at lower temperature.
A lot of things can be done with cold-optimized bacteria, for example could it be used to optimize biofuel production in cold environments. Cryobricks could also be used as a selection mechanisms (fx if you do not want to use antiobiotics at all) and then using cold as the selection agent.
How are the cryobricks supposed to work? One cryobrick is a specialized chaperone which helps to correctly form proteins at low temperatures. This chaperone originally come from the organism O. antarctica. E.coli normally lose a lot of their normal function at lower temperatures, because of the inactivation of certain proteins. The protein SheDnak from an antarctic salmonella species prohibitis this and keeps the proteins working.
Antifreeze protein cryobricks were also added to the coli from Amsterdam, which are originally present in bacteria of the kind Polariibacter.
The results show that the growth rate of E.coli was not enhanced, even though all the cryobricks were added. Contrary to that, the survival rate over continuous freeze/thaw cycles has been significantly improved through the use of cryobricks.
Amsterdam’s human practice efforts were focused on creating a cardgame, which is about creating different genetic constructs for use in synthetic biology. This game will be presented at the night of the nerds on the 8th of october.
On top of that the team also collaborated with the iGEM team from Wageningen and the Rathenau institute.
Overall the team has submitted three novel biobricks, characterized two of them and shown that one of them works as expected.
01Oct
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A bacterial photocopy machine? They must be out of their mind. It must have something to do with light sensors and color expression. Judging by the Uppsala teams colorful t-shirts they sure know what they are talking about!
They presentation introduction is like a ceremony taking place. The presenter introduces the topic and principle goals as if he is announcing a dramatic news item. It is clear and crisps what the Uppsala team wants to achieve.
A blue light sensor (YF1) is shown on the screen after a rapid animation that triggers a mild laugh in the room. The blue light sensor is a new addition to the already existing red and green light sensors in the Registry. All three sensors are proposed to be transformed into the same cell, coupled to their own expression cassette for the production of the associated color.
All together the team wanted to insert a great amount of basepairs they chose to incorporate the genes into the bacterial genome. For this they used the Lamba red assembly system. Despite a nice full overview of the technique, this approach has not been fully characterized yet. Future teams can pick up this task, because the Lamba red plasmid is now available in the Registry.
Btw, contrarily to using the red light sensor from the registry, the team got the sensor from the authors of the original paper. They succesfully removed the illegal restriction sites as well. So, for those of you ever planning to use this sensor: please contact Uppsala.
Summarizing, it was a colorful presentation with an interesting Q&A session afterwards. A bacterial photocopier still seems to be a bridge to far, but to say the least this is a proper foundation.
01Oct
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Intracellular Protegrin-1 Production and its Potential Applications
Introduction to an Antimicrobial peptide (APM) kill-switch for E.coli which potentially by pore creation kills the cells. The tested APM is protegrin-1, an 18 amino acid residue peptide. This peptide has high microbicidal activity against E. coli (gram-negative), N. gonorrheae (gram-positive), and HIV-1 (lipid-coated virus), amongst several other bacterial and virion species. Wet-work, modelling as well as pros and cons of the application is delivered. In particular latter is quite interesting since most teams show a critical relefection towards the applicability. Since time is always a critical matter they used fluorescent dyes to distinguish between live and dead cells. For this, a the LIVE/DEAD Baclight Bacterial Viability kit, which functions via a mixture of two dyes, was purchased.
Meta-team, a statistical analysis on the iGEM competition: “Is iGEM fair?” For this 33 variables have been selected and analysed, e.g. the no. of adivisors and the no. of BioBricks created. Criticical view on both aspects. Very interesting. Nice work.
01Oct
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The second software development team of the day. Before they start, they had to fought against the awkward silence, while the minutes to the kick off are melting away. Passed confident!
They asked if I am ready for the presentation. Nice introduction. I am ready, go!
Problems with the iGEM competition regarding increasing team numbers, increasing wet lab use and hence increasing use of the Partsregistry. The team wants to improve the starting point of every wetlab team, the BioBricks, by creating a BioBrick data mining software. Find easy and simple your BioBricks respctivly the Biobricks you need. They need a GUI, a search algorithm…. They created a Parts connection database, in order to increase the good feeling of biologist, finding the stuff they liked to find. They faced problems by data storage in their new database. therefore they had to define some rules for systems and devices in the Parts registry (and hopefully future stored in their database). Their rules:
- Minimal functional device (Promoter, GOI,Terminator)
- Inputs according to promoters
- Outputs according to genes (they even had to search NCBI and the Team wikis)
- Combination between devices (output of one gene, will be the input of the other)
- Simplification of devices
- Accessories (Tags, RNA,DNA)
The software packages used are JAVA based (Swing, Applet) and MySQL Database and yfiles for graphics. Further they used two different algorithms; one for searching and one for scoring (makes sense, i guess). The search algorithm is explained by jumping colored dots. That is something even I get. Thanks for that.
Seems that i can built up my own devices in silico as well. Will check wiki after the presentation, if this is true. I definetly can compare my findings and creations with other scientists.
Despite a little oxygen supply problem during the presentation (breath easy guys), I think this application might help a lot of iGEMers in the next years. Let us give it a try.
Q & A
Concerns about the ranking systems => did they take into account how often a part is counted, in order to create the ranking score?
Seems as if.
01Oct
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Liveblog from the Cambridge team’s presentation:
14.52 The 2011 team from cambridge i working on a quite novel class of proteins, reflectins. This class of proteins is commonly only found in squids, but this team has set their minds on changing that.
The teams approach has been to turn reflectins from the most popular papers on this clkass of protein into biobricks. From here on the team histagged one of their protein generator bricks and purified the reflectin protein from their bacteria. The protein was afterwards turned into thin films, which have a colorful, rainbow-like appearance. The special feature of these films, and thereby proteins, is that the color changed depending on the viewing angle.
Part of the presentation are videos with reflectin films changing colors, looking a little like an acid trip. Their in vitro characterization seems like a total success, showing multiple graphs of the change in wavelength of light reflected by the protein films.
This working outside of bacteria is nice and all, but what about reflectin directly in E.coli? What does that look like? This is where it gets a little more tricky, the results from this are not as clear-cut anymore. The team wanted to experiment with other organisms (fx onions), but could not do that because of time constraints.
Gibson assembly has become the focus of the talk by now, it’s advantages are that there is no use of restriction enzymes needed and that no scars will be created. The only downside is that the primer design for this kind of assembly is time consuming. This is where Gibthon comes in, a python based tool that will assist you in creating primers for gibson assembly that fit your desired sequence.
The application is quite user friendly for abioinformatics tool, with drag nad drop support and automatic checking for misprimings and correct annealing temperatures.
Overall the team has created three novel reflectin biobricks and a bunch of others and the software tool gibthon.
01Oct
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In few minutes Potsdam is kicking off the Health track. Potsdam has probably the youngest iGEM team members. Look-out for the kids in magenta colored shirts.
In many diseases protease activity is involved. Potential of cyclic peptides for protease inhibition, in particular a group called microvidins form Mycrocystis aeruginosa, shall be analyzed. First aim is to express microviridins in E.coli. With the major aim being to modify 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. Future plan is to conduct studies with the libararies to find new microviridins.
Plug’nPlay approach again. This is one of the hot topics of this meeting.
Human practice and Xtras. Survey within the German parlament. Oh…an adroid application (BioLog App), a in silico lab journal with additional functions. They have everything covered: “There is a feature for that.”
MTT: Congrats on your wiki. I like it!
01Oct
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The Groningen team takes the stage with great enthusiasm. Now only presenting in their own country they are even more eager to make it to the final 18 teams that can go to Boston. Being the first fundamental “logics” project I have seen so far today, with strong modeling efforts, surely gives them some upper hand.
The first part of the presentation covered their wet lab work. Characterizing a number of promoters and novel memory units, this part is strong and convincing. However, they did not show that much data. We will have to check out their wiki for that probably.
In the second part the audience was impressed with their modeling skills. A new software tool was developed for specific parameter fitting using a genetic algorithm. What really made the tool special was the implementation of cloud computing, which enables sharing the data and thereby improving its predicting capabilities. The call for changing the Registry of Standard Biological Parts into a Registry of Standard Biological Parts AND Models was a really great suggestion. Megan, Randy, are you listening to this as well?
Last but not least I definitely need to mention that the presentation was the smoothest and most engaging I have seen so far today. Really involving the audience in the presentation is always a bit of a gamble, but in the way Groningen did it, it turned out really well.
The final discussion on a question popped by the judges on patenting these kinds of logic systems was also handled fair and honest.
Overall this was a great contribution to the Regional Jamboree and the iGEM community.
01Oct
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There is slightly confusion about who should judge a team, which is already qualified. Both matters are really astonishing in a competition. Nevertheless the second session today ends with the strasbourg team.
They are physics and technological informatics. They deal with a idea to create an automated BioBrick software tool, which will be used to create BioBricks, characterize them and do a model. The problem is, that computer system get difficult and more complex over the years. So you need optimized automation to handle the complexity. The idea of the project is an analogie between computer/informatics and biology. So they are talking about gates and devices and deferential equations. The software should enable an non-electrician person -might be me or any other biologist. nobody called me non-electrician before. guess they are right – reliable modells for BioBricks. And now it is about boolean algebra and if you are interested you should visit their wiki. if I am in trouble with computers, i checked for my IT-crowd, so I am no help here.
Seems to be a proper and well done project. I am sorry for my weak coverage of their project. Go out and check their wiki.
01Oct
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Here with an all girl team is DTU-Denmark-2, they’ve been working on a new assembly standard, plug’n'play with DNA.
Since this talk is going to be about Assembly standards, let’s start with a table from the teams wiki comparing their standard with other assembly standards.
| Assembly system |
Speed |
Scars |
Res. digestion |
Multiple part assembly |
Ease of use |
| Standard BioBrick |
Slow |
Yes |
Yes |
No, two |
low/medium |
| 3 A |
Slow |
Yes |
Yes |
No, two |
low/medium |
| Gibson |
Medium-Fast |
No |
No |
Yes |
medium |
| Gateway |
Slow-Medium |
No |
No |
Yes |
low |
| In fusion |
Fast |
Yes/No |
No |
Yes |
high |
| Plug’n Play |
Fast |
Yes/No |
No |
Yes |
high |
The standard assembly is getting old. So the DTU-2 team decided that they would improve on the technique.
You can assemble many parts in one reaction without restrictions on which parts can be used. Their standard is based on USER cloning. The USER enzyme modifies a PCR product to give each brick sticky ends, the bricks then autoassemble.
One advantage of the plug’n'play approach is that there is no “illegal sequences” as in the standard assembly. The Copenhagen team used the standard and found it superior to the standard assembly.
To show that the standard works in fungi and mammalian cells as well as bacteria, the girls designed a reporter construct expressing GFP and transfected mammalian cells with their constructs. They showed expression of GFP, YFP, RFP and CFP in mammalian cells, also they showed RFP expression in fungi.
—-
Some of this post were lost in an unfortunate wifi-accident. Please take a look at the teams wiki, this is a very worthy project and they’ve provided a great deal of material for this standard to disseminate including a guide.
In conclusion, im very excited about this project, the girls have created a very nice assembly standard and provided good documentation.
01Oct
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Yeah, another heavy metal. I wonder if anyone here has been to the mercury fountain in the Miró museum in Barcelona. Looks great. Now, back to topic. (^_^)
20 minutes delay due to technical problems. C’est la vie. ;)
AV on it’s best. Again problems with the mic. Man, I am feeling really sorry for them. So much distraction.
First timers grenoble have done a pretty good job. And again, an extremely sophisticated model. So many variables.
01Oct
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Liveblog from Fatih Turkey’s presentation:
13.02 Q & A:
Q: How many slides were in your presentation?
A: At the beginning we had 90, but now only (!) 70-80.
Q: What application do you see for your project?
A: It could be applied as an antibiotic, working as a broad-spectrum gram-negative antibiotic.
Q: Would You like to comment on the fact that you are all standing here in labcoats?
A: We are all medical students, so we really like our labcoats!
12.55 Fatih Turkey aims to synthesize a protein from a special crab’s blueblood, so that these animals won’t have to be harmed for the accumulation of this protein. So what does this protein (LALF) do?s
The desired protein inhibits growth of gram-negative bacteria like the pathogen EHEC, through attacking the LPS layer of gram-negative bacteria.
This means that the team would have to stray away from the usual iGEM convention to use E.Coli for the projects and instead use a gram-positive bacteria, in this case B. subtilis. To test if the LALF works, there would have to ba an easy indicator if E.coli is dead or alive. For this cause the team introduced reflectin “the rainbow protein” into E.coli, which only will lights in certain wavelengths in living bacteria, therefore helping to determine if the LALF from B.subtilis kills the E.coli or not.
(Sorry for the brief coverage, but these guys are talking FAST making it really hard to blog and understand their quite complex project)
So did the team achieve these promises and eradicate gram-negative growth? To find out this they tried to grow RFP expressing E.coli on LALF biofilm and biofilm without LALF. The results were that both LALF containing and non-LALF containing biofilm could inhibit E.coli growth, but the biofilm containing LALF did a better job (less E.coli) growth than the non-LALF biofilm.
This experiment was repeated with B.subtilis supernatant instead of the biofilm, which showed no gram-negative growth in LALF supernatant and gram-negative grwoth in non-LALF supernatant.
The Fatih iGEM team has been very thorough with these experiments and have done them in many different variations, most of them pointing in the direction of LALF killing gram-negative bacteria.
The last bit of characterization was done on the reflectin expression in E.coli, they show some light microscopy pictures which do not really tell all that much without a detailed explanation.
(Wow, the last girl presenting is talking at lightspeed – ZOOOOOOOOOM!)
The humas practice sapproach of this team was focused around creating a board game related to the team’s project and iGEM, making the subject accessible to all age groups.
They apparently also created a cartoon, titled Gang-O-Bang! (No, I won’t comment further on that.)
01Oct
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Disco-Stu likes that!
They are dealing with Biofilm formation coupled with light-induced 3D sculpting of the Biofilm and light-induced promoters for gene of interest, hence for product formation.
Biofilms curse pipe corrusion. Therefore they are a pain to the oil companies. Which is a shame. These poor guys. Biofilms are cell attaching to one another into 3D-structures. They are a characteristic of pseudomonas aeruginosa, which is known to be an oppurtunistic pathogen. Hence they used an alternative, which is able to form biofilms quickly, transformable and can produce products. So they use a new E Coli, which was made competend and transformed. Something which was not done before inside the iGem competition. Next problem, they need a new reporter gene, because biofilms are provide only anaerobic conditions. Hence the often use reporter genes are no help in this case. The choose the LOV-domain & provided it to the BioBrick database.
So the second part is the 3D sculpturing of the 3D Biofilm. They use light dependent promoters, in order to achieve remote Biofilm structures. Further they need a dispersal mechanism. Altering the behavior directly, surfactant or lyse the cells. They used a secondary messenger to dispersal Biofilms by altering the concentration of the second messenger. Surfacting proteins can disrupt a Biofilm as well. So they isolated the protein of the horse sweat. So stay away from horses if you are a Biofilm. The lysis topic was done by parts taken out of the Partsregistry.
They did a quite nice physical modell, which I am not able to explain. Again there are equations.
The last step is the synthesis of products. They need a trigger light signal to activate their genes. They use some genes of the carotine pathway. A application will be any pathway, which needs a single-precorsur. For example the opium pathwaz, which needs morphine, to gain some therapeutics. No really doc, I need this morphine for my BioBrick =).
HP:
They did videologs on Youtube, doing a blog about their experiments on iGEM and showed a project to high school students. They keept hence a public record of the lab. Like a lab in a glashouse. Nice idea, because a lot of people in the public are concerned about scientists hiding stuff. Further they checked at companies (BP) and institutes (NASA) wether or not they might use such an invention. And they did a manual.
Conclusion:
They were able to successfully solve all three sub projects. They show different applications, which make defnetitly sense. The question, like in Bielefeld is, will it work, when fused together?
Q & A
Did they do the genetic engineering of LOV?
No they made a BioBrick out of it and characterize it.
Question about bleaching and the physical model regarding the bleaching?!
It recovers so quickly that the degradation can not be measured in a better way
Question on HP: Did the companies answered their request?
No answers yet, but maybe when they reached Boston
Same question regarding HP like the Bielefeld team faced: What does your project contributes to good human practice and mankind?
They exchange their chassis from a opp. pathogen to an apathogenic one (E.Coli).
01Oct
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Alright, here we go again. This time with the team from Dundee, who are presenting a project named The Sphereactor. It’s Dundees first time in iGEM and they’ve done an admirable job. They’re students from biomedical studies, mathematics and computer sciences.
Microcompartments have many uses in biology, they’re naturally expressed in Salmonella. In salmonella it keeps toxic metabolic products from interfering with cytosolic processes. The team leveraged the Pdu operon from salmonella to produce microcompartments in E. Coli
Without a way to target a protein to the microcompartment theres very little use for a microcompartment. So they used a tailing sequence from Pdu, and fused it into the targeted protein.
To prove that the spherereactor worked and proteins could be targeted to it the team used HIS-tagged spherereactors and targeted GFP to the compartment. Microscopy showed a definite change in flourescence patterns. SDS-Page confirmed the production of the involved proteins.
In conclusion, Dundee designed and produced microcompartments and deviced a way for proteins to be targeted into the compartments.
Human practices: The SynBin – A repository for lab mistakes and sins (or should i write syns?), so that others won’t repeat your mistake.
Q: Limits of the bioreactor, how many can you produce in a cell.
A: It’s not limited by cell size, but we do not have much data.
Q: What makes you sure that the proteins actually enter the reactor opposed to attaching to it?
A: the protein purification steps would wash attached proteins off. This was not observed
01Oct
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Heavy metal sounds always good. ;)
An introduction to the topic, concerning the regional as well as the worldwide frame is given.
The team is working with protein-based systems and different reporter genes…again usual suspects appear. GFP, lacZ, lux genes. A promotor-based nickel system is presented. Altough a strategy for the use of different bacterial sensors are presented. Sketchy!
Primer designer. Everybody needs good tools! But: On what algorithms/code is this tool based?
Human practice workshop in München with DNA isolation and glowing bacteria, school project….and suddenly.
“Let’s rock?!” WTF is happing the LMU is dancing and rocking…. (@thevideo: the girl fits in a fridge…wow).
My two pennies: No debate on the importance of heavy metal detection. Although a lot of aspects are covered, the whole project is a little bit sketchy.
01Oct
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Liveblog from NTNU Trondheim’s presentation:
12.30 Q & A
Q: Did you use pSB1C3 (the plasmid all biobricks have to be submitted in) for your charachterization?
A: No, the characterization was done in pSB1A2.
Q: How have you improved another team’s biobrick?
A: We changed the pprnB1 promoter from the BBb biobrick standard to the BBa biobrick standard. This makes the promoter much more widely available to other iGEM teams, in that way improving it.
12.20 The first norwegian team in the iGEM competition has created”the red fluorescent stress sensor”. The original idea was to use alarmones (small intracellular signaling molecules) to detect stress in E.coli, this would make it possible to differentiate between stressed and non-stressed cells. Coloring stressed bacteria red was chosen as thesubject, since it would be easy to grasp for the public and seemed well suited to the constrained timeframe the Trondheim was working in.
The signaling molecule ppGpp is expressed when E.coli are stressed. This molecule changes the expressional pattern from grwoth and proliferation to the expression of survival genes. The stress sensor itself is the prrnbP1 promoter, which is inhibited by ppGpp.
The team’s construct works like this:
pprnbP1 activates the transcription of Lacl, which inhibits the pLac promoter that otherwise would express mCherry (RFP). If ppGpp is present it inhibits the pprnbP1 promoter, thereby removing the lac inhibition and leading to the transcription of mCherry. In short form:
ppGpp present -> mCherry expression -> Red cells
no ppGpp present -> no mCherry expression -> Normally colored cells.
So did this work? The results were not as clear cut as the team had hoped for but with the help of a fluorometer they could detect an increased RFP expression and differences in the expression levels of the lac inhibitor. This means the system works, but the output is just not as clear as stressed cells being recognizably red.
The norwegian team also created a working model of their system, which further confirmed the viability of their system and aligned with the wetlab results.
There are a lot of possible extensions for the project, which include proting it to other organisms or have a GFP read-out for cells that are not stressed.
Overall the team created 4 biobricks which they added to the partsregistry.
01Oct
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The presentation will be given by Mr. T-imo (Wolf as last name, like the animal). The team dealt over the summer with a cell-free biosensor. As a target they choose Bisphenol A (BPA). You are getting in daily contact with BPA in cans, baby bottles, and nearly all other plastic containing stuff. BPA mimics estrogen and is hence harmfull to humans, especially in growth phases and development. It is banned in the EU and Canada in the production of baby bottles since this year.
The Biosensor is divided into three subparts. First there is the BPA degradation step, the coupled color output (NAD+)and the immobilization of S-layer proteins onto beads. By coupling all the subparts, you get a biosensor, which is easy to applicate in daily use.
They showed that they are able to degrade BPA in E.coli. Further they improved an existing BioBrick and they build up the missing third enzyme for the cell-free approach.The light output by using a NAD+ dependent molecular beacon works as well. S-Layer fusion proteins were used for the cell-free construction of the biosensor. These are proteins, which form a structure on cell boundaries or surfaces by self-assemble. There are different proteins with different 3D-structures. They managed to coupled the proteins onto a silica bead.
Human Practices:
They build up a beacon box – which is quite self-made – to reach out to the public, telling people about synthetic biology. They visited a lot of public discussions to spread the german public about the biological news.
Conclusion:
They were able to successfully realize alle their three subprojects. So we have to wait, if the fusion of these parts will get us a new biosensor. Although nobody of the team members really fits to my old heros from the A-team (where is face? where is Mr. T?), they achieved a lot and presented a nice project. They love it, when a plan comes together.
Q&A
First question concerning the model parameters?!
Literature found, no experimental data.
What concentration is getting loose from a baby bottle ?!
If they found something, it is enough. so it does not matter how many BPA is in your bottle.
Question about the cell free approach. How many enzyme do you need, what kind of fusion protein was done?
You need all three enzymes. They build up a fusion protein, which was tested in e.coli, where the third enzyme is not needed.
Human practice. How does your project improve mankind, environment etc..?
cell- free approach. So no GMOs are needed outside the lab
01Oct
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The freiburg team opened their presentation with a reading of the synbio oath, that they’ve written. The synbio oath is inspired by the hippocratic oath, why shouldn’t scientists use a similar oath to garner trust from non-scientists?
Being a scientist can be very expensive, the lab in a cell project aims to reduce these costs and increase stability.
In total the team wanted to utilize 16 genes, since thats a bit much for a plasmid, a bacterial artificial chromosome was used. Colored (Red, green and blue) light-sensors induce production of various components.
The team produced a fusion protein between a polysterene binding protein and GFP and showed that the resultant protein indeed bound to polysterene.
The temperature sensitive lysis depends on a constitutive repressor that denatures at 42 degress Celsius. Holin forms intramembrane protein complexes. Fuses inner and outher membrane, allowing the cell to lyse.
Q: Data on the precipitator
A: Assembled, not tested beyond plastic binding.
Q: Would there be any legal ramifications if i took the oath and failed to adhere to it?
A: No, the oath is a tool for the community and a guideline for conduct.
Q: Why do you speak of local law, instead of international law in the oath.
A: International law is included in local law. Wording could be changed, feedback is welcome.
01Oct
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The ETH Zurich was inspired by the magnificent hosting country of the iGEM Regional Jamboree: The Netherlands. Thinking of Holland they came up with the idea to create a bacterial smoke detector, being able to indicate whether a typical Dutch party gets out of hand.
As target component of smoke they choose Acetylaldehyde. Creating a circuit that has a sensitivity range and a threshold value for a “alarm mode”, they took a great syn bio approach. As a basis of their experiments they modeled the system taking into account 36 parameters.
The experiments itself have a solid setup. Taking the right positive and negative controls into account they could unfortunately not express their sensor. The codon optimized synthesis of the construct was delayed by more than a month. Which is why they continued using a xylene sensor from the biobrick library. let’s hope they will get a chance to complete their cloning and present it in Boston next month!
ETH Zurich showed that they are not easily defeated when facing difficulty, which is without any doubt the result of their terrific team spirit.
01Oct
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Liveblog from Team TU-Delft’s presentation:
12.01 Q & A:
Q: Do the cells expressing your construct actually stick together?
A: Yes. (The other part of the answer was lost to me)
Q: Did you create a novel biobrick?
A: We achieved a lot with the characterization and working in a team is very hard, which made the whole process complicated. In the end we did not send in any biobrick to the partsregistry.
11.52 The team from the TU-Delft has worked on biofilm formation this year. They thought that biofilm formation is not as controllable as it should be, yet. The team set out to change this, with the ultimate goal of controllable single cell adhesion. If this was made possible it could be used for biosensing, cell-communication and biomass retention.
Imagine a situation where a lot of bactera are suspended in a liquid and producing a desired product. Now You can give them a signal that makes them stick to each other, forming a cluster. Now it would be easy to remove/recycle the biomass for a clean product and/or reuse of the biomass.
The girls doing the presentation are explaining a lot about their modeling and the algorithms used for the math. All I see are a lot of spheres clashing with each other, weird how something like this makes a lot of sense to some persons and little to others, but that’s most certainly my fault.
To make the aforementioned applications possible an inducing system had to be established, the adhesive proteins had to be located to the outer membrane and they should not have any adhesive effect inside the cell.
But what is this magic protein that makes E.coli adhesive? The answer is MFP-5, a mussel protein used by mussels to attach to surfaces.
A biobrick for the expression of this protein has been created by the Berkeley wetlab 2009 team, which the Delft team has modified for their purposes. This ensures the production of the protein, but how does it get into the outer membrane? This question has not been answered by the presentation, but they have shown that the protein locates itself in the outer membrane by a GFP-assay.
BUT: Mfp5 does not stick without a tyrosinase that hydroxylates the protein. Luckily the team from TokyoTech2009 has created such a tyrosinase brick, this brick was then incorporated into Delft’s system and hopefully made the bacteria stick.
Somehow they have not shown the coli sticking to anything yet, so did their system work or not? I really do not know right now.
Apparently the other teams biobricks were characterized, but with what results sadly is still unclear.
01Oct
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Now, Environment track starts..
iGEM team from Lyon addressing the issue on the presence of cobalt from radioactive water, making a tiny bug as a cobolt BUSTERR
Well, let’s start(the show begins): first they succeeded in creating constitutive biofilm from the bugs in response to the presence of cobalt, induced by the consititutive promoter,
[...]
Author notice: Since connection blows the rest of this post was deleted. Awesome…
01Oct
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They are a very interdisziplinary team. Their topic deals with the biological computer. The problem is that you are not able to use just one cell, because of the limit of information processing. Hence they use different strains. They split everything up into modules with different, specific functions. Further you need to build up a system, in which the modules can communciate with each other. They got a new approach towards a hierarchy in such a system.
The hierarchy consists of:
cell level
community level (Moduls). They used “BioBits”, which are substances, which can be exchanged between the bacteria. They made this word up, but I guess it really fits. They defined different cells, featured with different genetic characteristics, in order to build up their communciating system.
Population level
It is based on the communication among the modules. The communication needs to be standardized, that the system will not lead into chaos. They called their standard UBBIT, an acronyme for universal BioBits.
So they build up an example system connecting modules with one another. To be honest I am not quite sure about the structure of these modules. They used for sure adding modules. For more information check their wiki. I do understand their example, which is quorum sensing. This means they use the the system which bacteria normally use to communicate with one another. They build up a model and compared it with the experimental data using GFP, X-GAL and ONPG. So they validate their module with reporter genes. Some parts worked. I can see it on a nice purple plate.
The experimental work seems to be a little bit underestimated in their project. Further they were facing a lot of different wet labs problems. Nevertheless they managed to build up some of the modules and wires. Moreover they created a BioBit open source database. Like a brother of the partsregistry for computer stuff.
All in all this topic is quite a tricky one, which was solved on a theoretically level in nice way. So with more time they might be able to validate their theory.
Q & A
How many wires do you created?
Seems about three. The other wires were impossible to build up by same regarding the nightmare wet lab experience. Welcome to my world guys =)
The judges are aware of the wet lab problems , so how would they advise future iGEM teams?
Order early, start early with the wet lab. They seem really exhausted. Must have been a hell of a cloning trip.
My advise would be to ask somebody, who is currently working in a wet lab. They will tell you, where, how and when you should order your stuff. We are all a Band of Brothers regarding wet lab cloning problems.
01Oct
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The UCL team worked on supercoiling DNA using gyrases. The team consists of 9 students from very diverse backgrounds.
DNA vaccines using plasmids. H1N1 showed how very out of date our production of vaccines is. In E. Coli we could produce a vaccine in 3 weeks with increased.
Supercoiled DNA transfects cells better, transcription better and makes the cells more resistant to forces like shear stress. Quality and purity is important.
Supercoilogy. By overexpressing DNA Gyrase the amount of supercoiled target plasmids would increase. Magneto-sites. By introducing a binding site for DNA gyrase on the target plasmid the team achieved a 35 % increase in coil quality.
Extractery. By raising the temperature endolysin is produced. Endonuclease digests uncoiled plasmids. Holin enables lysis of the cell by endolysin. by inducing these systems in concert the team aims to extract product from the cells.
Stresslights 2.0. Based on last years UCL teams work, detects stress conditions as defined by O2 avaibility and glucose. Cells flouresce when the stress is on. Supercoilometer is a promoter designed to detect the level of supercoiling in the cell. Together Stesslights and supercoilometer are proposed as a way to optimize production.
E. Coili combines the above concepts.
Modelling showed a increase in Purity by 1% and a 20 % yield increase.
I’m still unsure how much is this enormous project the team actually succeded in constructing.
Wow, this is probably the best presentation i’ve ever seen, well done UCL! In
01Oct
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The final presentation held in the first session this morning was by the Norwich team, introducing us to photosynthetic organisms in iGEM. This is a whole new playing field in the competition, so the members can be regarded as true pioneers.
Compared to normal E. Coli transformation, injecting foreign DNA in algae is not an easy task. The team designed a new algae specific biobrick and explored several parameters for successful transformation.
But just algae was not enough for the team. Their next challenge was to use Moss as a model organism. An established model organism in plant research, but completely new to the synthetic biology community. Their overall aim was to show effective transformation methods.
Overall, the team paved the way for a future iGEM teams to dig further into plants. Based on their lessons learned, future teams will get a head start!
Hosting the UK team meet up, they had a lot of fun, interesting talks and eat a lot of pizza. Requirement “have fun”: check!
01Oct
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“Swimming lessons for bacteria”. The South Africa team had a mind blowing concept: directing bacteria from one point to another. Simple idea, but quite difficult to get. They needed to construct a regulatory circuit that would first influence the motility in such a way that it would move to point A, and after reaching it, it should move to point B.
As a regulatory mechanism they used riboswitches. Using several assays they show that the riboswitches are able to regulate motility. A superb result! They even created their own software that models the motility. Even more impressive!
As an outreach they presented the concepts of SynBio to less fortunate children in South Africa. Some of them came up with the idea to create a cholera detecting organism, indicating the team did a great job in making them understand the potentials of iGEM and SynBio in general.
After presenting at the first national symposium on SynBio in South Africa they are sure that they motivated more universities in their country to join iGEM. So we can expect more exciting subscribing teams from the far South in the future!
01Oct
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The Trieste team competes in iGEM for the first time this year. They focused on cellular communication, based on the principle of quorem sensing. This system is a general way of controlling many processes in cells. Trieste investigated the quorum sensing between multiple species, even between several kingdoms. The goal was to create a full communication system between eukaryotics and bacteria: SynBiome consortium.
They used a nice range of methods to detect the communication molecules: chromatography, lactamase assays, western blotting and GFP detection. The induction of expression of their reporter in the HeLa cells, induced by the bacterial product, looks most impressive. The measurements even don’t show any cross talk.
The three presenters were very proud to show there nice results. They had a lot of fun, “like babies, playing with synthetic biology”. The project was truly set up by the students and execute by them from end-to-end. Their passion for SynBio was clearly expressed. Although they were just rookies in iGEM they already covered all aspects: blunt ideas, lots of fun, cooperation with other iGEM teams and reach out to society. We will surely hear more from them in future!
01Oct
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Liveblog from the Valencia team’s presentation:
10.53 Q & A:
Q: How does your method compare to classical water cleaning mechanisms?
A: Our mechanism does not make use of chemical compounds and has very high or low specificity as need for the task.
Q: Do you fear that if we use bacteriocins for water cleaning that we will provoke resistance against them, so that we won’t be able to use them for more important applications?
A: The bacteriocins only kill bacteria with a certain receptor and won’t affect the ones not being killed. Therefore the team does not think that their project could induce resistance against bacteriocins.
10.46 The last team in this session is the Valencia iGEM team. Over this summer they developed the project “Water Colicin Cleaner”.
The presentation starts out with a scientific play, quite creative.
The project involves killing microbial pathogens in water by the means of antimicrobial proteins, the team’s AMP of choice is colicin, which forms holes in the bacterias’ membranes, effectively killing them.
We suddenly went over to results already, the team has achieved to kill E.Coli contaminating waste water through the colicin peptide. But this is not enough yet, they wanted to control the AMPs activity by a biological pH-stat. Adjustment of pH will make it possible to increase the antimicrobial activity of the proteins.
I am sorry if this post is a little confusing, but the team is going thorugh all this really fast.
Wow, now there is a whole lab setup right in the presentation room, The team has built a dialysis-like machine: It takes contaminated water, kills the pathogens in it and transport the cleaned water to a new flask. This really is a biological MACHINE!
The team has achieved:
Producing Colicin in bacteria.
Designed and developed a low-cost disinfection system for waste water.
01Oct
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They entered the stage with about 14 students and presented their insertion system to improve cloning.
They modelled a 30 to 50% collusion rate regarding the transcriptional level of the polymerase. To established the model they need a whole lot of equations, flying towards the auditorium. Scary, good we got some mathematics, who can deal with it. In the end they compared their model to the wet lab experiments and it worked out nearly fine. Hence the model works.
Human Practice:
They were able to remove the antibiotic selection marker, after the cloning steps. Most people are scared that scientists might pollute or modify the bacteria respectively the environment by using to much and to strong antibiotics. You have to take into account that you need antibiotic as a selection marker in cloning steps. Hence this is a nice attempt to get rid of undesired effects caused by antibiotics.
Further they went out into the public and asked for their opinion of synthetic biology. Like we learned yesterday at the meeting of minds. It is necessary to go out and teach about synth. biology.
Q & A
What would you have done differently if you had more time?
They would provide more BioBricks and characterize their existing ones more in detail. They provide that the system works with the iGEM BioBricks.
How do you selecte without a selection marker after the flip recombinase?
They performed a parallel picking, which means that you use the same clone on two different plates. One with LB-media and one with LB supplemented with the antibiotic chloramphenicol. So they can just choose the clone by growth comparison.
Although they had to face same criticism for their screening system, the presentation was quite nice and filled with content. So stay tuned with this team.
01Oct
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The Synchroscillator.
As if someone was reading my posts….the team starts of with Human practices. MiniGem, a project at three different schools is presented. Also, drawing competitio, high school visit, radio and newspapers ( the usual suspects).
Now, to the project. So what is the Synchroscillator. “Controlling and visualizing synchronized oscillations in real-time.” Main work areas are outline oscillation, synchronity, visualization and real time.
Introduction to biological oscillators and bridge to syn bio. Their presented circuit consists of elements from Vibrio fischeri lux quorum sensing system. To have a oscillating system, the components needed to be interconnected in positive and negative feedback loops, which regulate expression of GFP.
To provide the right environment required for oscillation, the team has designed and manufactured a custom flow-chamber.
Again, a quite comprehensive mathematical model. Good job (as far as I can understand modeling)
01Oct
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The team consists of 14 students. Their projects is a a 3D printer based on optogenetics. Bacteria produce pigment when hit by 2 different color lasers, which can be mounted on orthogonal axes.
The team utilizes 2 different plasmids, one is a optogenetical AND-gate and the other is a Reporter plasmid. Red light induces one of the signals necessary for induction of the second construct which outputs a black pigment. The second signal is blue light.
In order for the second laser to not induce pigment production the team produced an impressive amount of modelling to figure out the timing of laser inputs.
Testing on the red light sensor were inconclusive. Cells incubated under blue light succeeded in inducing a downstream expression measured by GFP.
The output of a 3D printer of this type could easily be exchanged to produce some other product instead of pigment, for example collagen could be used in battling osteoporosis.
Human practices: Childrens book describing the discovery of GFP. A bacteria learns how to glow after reading a scroll that originally belonged to a jellyfish. Please tell me where i can get this !
In conclusion, the team presented a very well modelled idea, some solid positive results and a very interesting idea. 3D printing biological materials would be an incredible technology.
Q: How is modelling data reflected in the lab data?
A: We don’t actually know yet, since the system is not ready for 3D printing.
Q: Did modelling influence the design
A: It influenced our experimental timeframes.
Q: Have you included any positive / negative control in your characterisations?
A: A negative control. No positive control.
Q: What is the link to a collagen scaffold. What is the resolution of the cell printer?
A: It is a link to build a collagen scaffold. Depends on the laser and the cell density.
Q:
01Oct
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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.
Q&A
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.
01Oct
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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.
01Oct
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Liveblog from the ICL presentation:
10.27 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.
10.22 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:
Phyto-Route
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).
GeneGuard
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.
01Oct
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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.
01Oct
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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:
09.17 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!
09.16 New branches: Entrepenurial divisiom, high school division, maybe a software tool division.
09.16 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.
09.13 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.
09.08 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?
09.07 I’d like to give you some background on iGEM history and what’s happening in iGEM right now.
09.05 iGEM – international genetically engineered machine competition or collaboration? In this competition we’re competing in collaboration. Collaboration against ignorance and competition against each other.
09.05 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!
09.01 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.
08.59 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!
08.57 Synthetic biology is the best way to test our knowledge of systems biology.
08.56 “Usual rational drug design focuses on targeting individual molecules. But for network diseases we need to apply a network approach.”
08.55 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.
08.54 “Partly because we have cured many infectious diseases, we’re entering an age of multifactorial diseases or systems diseases.”
08.52 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.
08.22 Opening session starts 08:45. Check back in 25 minutes for the live coverage.
Meeting of Young Minds
We are now reporting live from the “Meeting of the Young Minds”, we are going to present it in a pros and cons form. Rd will designate pro-synthetic biology viewpoints and green viewpoints against synthetic biology:
21.52 Everyone has one final sentence. Only few keep it to one.
MOYM is over, I hope You enjoyed our coverage! Tune back in tomorrow for the iGEM presentations.
21.47 What is important is that we need good education and publicity about new technologies like synthetic biology. Mr Expert, iGEM HQ has said that for quite some time (years).
21.43 OOhh, expert analysis coming up!
21.40 I’m not necessarily against changes genes in humans.
21.38 Yeah, animals without nervous systems would be acceptable for food production.
21.35 Would you feel that it is okay to breed pigs without brains for use in research, so that they won’t feel pain.
21.31 If You look at the effects of these technologies, changing nature is not new. Synthetic biology is not different from traditional breeding for example – it is optimizing the fruits of nature.
How You can interprete that into wanting to modify the human genome is a bit beyond me.
21.26 Would you say that is it fair that a drug, discovered in the USA using synbio, curing HIV falls under american patent law and as such many african countries can’t afford it. [Bad wording by me, sorry]
21.26 The Dodo was said to be very tasteful, especially with southern pepper… We have come quite far with the discussion, now that we are discussing the resurrection of the Dodo.
21.22 Statement: By definition the assumption that the status quo is the safest is flawed, so why cling to it?
21.19 Statement: Synthetic biology is a wonderful technology, but going too fast. We do NOT need SynBio to solve our problems like world hunger, fuel problems and others.
21.18 Statement: Nature does not need improvement through synthetic biology. First improve humans.
21.14 Life itself does not carry specific moral weight, but when the cells come together in a form that feels pain things change. If we banish research on animals, where should we stop? It is too easy to say that they are nothing more than a machine.
21.13 Life in itself has not a special moral state deviating from other machines. Life does not differentiate bacterial machines from other stuff like nanomachines. The question is can we patenting life? The young democrats don’t think there are any problems with that.
21.12 Stetement: A cell is nothing more than a machine, which we are allowed to modify and create.
21.09 Break is over. Next up is Ownership. Is there a difference between manipulating plants, birds and man?
20.42 The politicians ask the Freiburg team how they want to enforce their synthetic biology oath. They have to admit that many countries would not agree to it and that even a lot of labs have expressed their disagreement. For the first time in the debate the scientists are on the defensive.
20.42 We’re gonna have a break of half an hour. After the break we’re gonna talk about Ownership.
20.33 iGEMers point out that the balance of nature is already destroyed, with phenomenons like desertification. Rebecca from ICL says that the chances are much greater to undo this imbalance through synthetic biology instead of making it worse.
20.31 We have to treat this technology with respect, and there should be regulation, what we need right now is a framework.
20.25 i Agree we should do a case by case study, but why not let scientists do the evaluation?
20.22 Altering one or two genes of an organism doesn’t change an organism much.
20.19 Currently 8 people are waiting for their turn to speak in response to the demand for examples.
20.18 Examples of “going too far” are being demanded. None are given.
20.18 Statement: Synbio and GMO should be regulated as one and the same.
20.15 Right now one of the politicians is comparing the potential risks of synthetic biology to the risks of nuclear energy. The argument is that when something goes wrong the fallout will be huge. [Comment: Really?]
20.13 Introducing new species into the environment may alter the natural balance more than we can foresee, we feel we should regulate via ban and exception. Exceptions being granted on a project to project basis. Labs should be properly isolated from the environment.
20.11 Alfred from UCL points out that the views presented here are very extreme, why not take a more moderate approach and consider both sides? It is important to inform the public about our field, so that they can from an own opinion instead of being forcefed one by a pseudo authority. He also points out that scientists doubt themselves all the way through a project, so they definitely are not careless. [Comment: This man is a great speaker!]
20.10 Round 2: Regulation. How much risk are we willing to take, will too much innovation hamper further development of a promising field?
20.04 Transparancy towards the outer public might have its own risks, like dictators wanting to weaponize synbio.
20.03 If you trust doctors with your life, why dont you trust scientists? Therefore we made a synbio oath inspired by the hippocratic oath to inspire trust in scientists.
20.02 The potential benefits should notmake us careless, we should still be aware of the possible risks of synthetic biology.
19.59 I want to comfort you, you seem very afraid of synbio in general. We believe that the scientists are very open for discussions.
19.56 The question is not if we want to accept this (SynBio) happening, since we are already funding this research. So we should not just sit back and watch what is going to happen, but take influence on the evolution of the field. (regulations)
19.54 This cannot be stopped, it should not be stopped, because of its possibilities. There is however a sense of danger, we need to find a way to adress those. The best defence against synbio being used for evil is transparency.
19.52 We’re extremely reluctant to let any synbio into the environment.
19.50 At some point we will lose the ability to estimate the effect of new technologies – so new technologies are frightening since the general public could lose track of the implications and the effects SynBio will have.
19.50 It is far to cheap to only talk about how to use synbio, we should discuss whether we want to use this technology, even with potentially frightening consequences.
19.47 It is irrelevant to discuss if humans should interfere in nature, since new technologies like synthetic biology are unstoppable. It is more important to handle them responsibly.
19.45 Statement 1: Synthetic biology developments cannot be stopped. The question should not be if we want to use synthetic biology, but in what way.
How far are we, as humankind, willing to interfere in nature. How far is it our responsibility to go?
19.42 Dutch politics are confusing for most of the audience, one guy is representing two parties at the same time? How, does that even work?
19.42 Debate round 1 is starting now: PROMISE! Will we solve the energy crisis, improving health or creating monsters?
19.41 The biotec expert congratulates the ladies for being well represented in the life sciences, he is definitely charming the ladies right now.
19.39 The scientists and politicians sit across from each other, separated. But the politics representative that is up now, does not believe in this separation.
19.39 We’ll be having three rounds of debates, monitored by two experts. The debate is about to start.
19.37 The Rathenau institute is hosting this discussion. Their goal is to prepare scientists and society for the new technologies like synthetic biology and raising public awareness.
19.35 This meeting brings together a new generation of scientists and a new generation of politicians. Hoping to gain a better understanding of each other.
19.32 Subjects for tonight: Promises, regulations, who owns synthetic biology
22Sep
Filed in 2011 | iGEM | Statistics
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 Preliminary investigations point to this man being the culprit who froze your wikis! Since 11:59 PM Boston time the European wikis have been frozen. This means that the teams cannot update their wikis in the next two weeks. This gives us time to take a look at the big picture instead of focusing on single teams.
In this post we will look at some numbers and graphs from all the European teams and compare them with the other regions later. For an overview we start out with a map, “The World according to iGEM”, where the different countries’ area has been distorted according to the number of teams participating in the iGEM 2011 competition (a so-called cartogram):
 The World according to iGEM As You can see, rather small countries with many teams participating, like the Netherlands, suddenly take up a whole lot of the world map. Sadly only one African team made it through in the end and as a result the African continent has been shrunk a lot in comparison to it’s normal size. Japan and the UK suddenly turn into islands of Greenland-like size because of the high density of iGEM teams there. Let us focus on Europe for now and take a look at where the European teams hail from:
| Country |
Teams participating |
| Germany |
5 |
| England |
5 |
| France |
4 |
| Netherlands |
4 |
| Turkey |
4 |
| Denmark |
3 |
| Spain |
3 |
| Scotland |
3 |
| Belgium |
2 |
| Switzerland |
2 |
| Italy |
2 |
| Hungary |
1 |
| Norway |
1 |
| Poland |
1 |
| Sweden |
1 |
| South Africa |
1 |
| Total: |
42 |
(We excluded teams that did not pay the registration fee and / or did not submit any parts.)
These 42 teams consist of 410 students from vastly different fields of study ranging from ecoonomics and psychology, telematics (?!), theoretical physics to microbiology. The average team size for Europe is 9,76 students per team with the biggest team being TU-Munich with 19 students and the smallest team being ENSPS-Strasburg with 2 team members.
Overall 638 biobricks were submitted to the partsregistry, which is a mean of 15,19 parts / team. DTU-Denmark 2 has submitted 70 biobricks and wins the title for spamming the partsregistry, while Bilkent UNAM-Turkey, St Andrews,ULB Brussel and Lyon INSA-ENS all share the spot for fewest parts submitted with two.
But what is the relation between parts submitted and the amount of members of each team? Let us find out via a chart:
From this chart we can see that DTU-Denmark 2 has created a whopping 14 parts per team member, they must have spent day and night in the lab the last year!
So what about the tracks? Well, let’s just answer that one with a pie-chart, where You can see how the European teams are distributed in the different tracks. It is not unexpected that “New Application” and “Foundational Advance” are popular tracks, still almost half the European teams this year are competing in these two categories. It’s also interesting to note that “Health and Medicine” has become the smallest category, which is somewhat unexpected given the amount of past contributions in this track. Finally software tools is interesting, not because it is small, but because we aren’t seeing any of the old software teams, both contributions being from rookie teams this year.
Out of the 42 teams participating in the European regionals, 15 are competing for the first time. So how did the “old” teams fare in the past years? This graph tells us all about that:
 Medal results of the "old" teams from Europe competing in 2011: Gold represents that the team received a gold medal, silver a silver medal, bronze a bronze medal. White means that the team did not participate that year and black means that results are not available yet.
We hope You enjoyed our little detour into statistics today – tomorrow we will return to our more standard writing style and post short (!) reviews of the 15 rookie teams that are going to the regionals in Amsterdam.
Disclaimer: The statistics that form the basis for our statistical analysis have been personally mined from the teams’ wikis and iGEM homepage and therefore are prone to personal error and misjudgement. The raw data can be found here.
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