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.
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