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Cornell – Biofactory

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Visit their wiki!

Cornell’s 2011 iGEM team has designed a new, scalable, and cell-free method to produce complex biomolecules. Current methods for purification from cellular lysate are expensive and time consuming. BioFactory utilizes modified enzymes, capable of being attached to surfaces, in the creation of a modular microfluidic chip for each enzyme. The surface bonding is performed by the well-characterized biotin-avidin mechanism. When combined in series, these chips operate as a linear biochemical pathway for continuous flow reactions. Additionally, we plan to engineer E. coli with the mechanism for light-induced apoptosis to easily lyse cultures producing the necessary enzymes. The resulting lysate is flowed through the microfluidic channels, coating them with the desired enzyme. We believe this chemical synthesis method will reduce unwanted side reactions and lower the costs of producing bio-pharmaceuticals in the future.

*****

Nice opening animation; cue dramatic music. They are SUPER excited to be here today.

Cornell’s project involves designing, building and testing a new method of manufacturing biochemicals outside of cells. The problem with biochemical synthesis in cells is that there’s a ton of problems involved, including hard-to-control conditions (pH), toxic or unusable side products and sometimes long purification steps.

Isolate enzymes and use a microfluidic device to optimize a compelx reaction. For a POC they looked at a 3-enzyme pathway involving L-tryptophan. They wanted a high surface area, modular and scalable microfluidic system with enzyme-studded channels. To get the enzymes first they lyse the cells, which could be costly with huge bioreactor-sized cultures. So they looked at light-inducible lysis.

They get enzymes to stick with the avidin-biotin reaction, tagging their enzymes with an “AviTag”. They found no negligible effects of flowing cell lysate through their channel. Enzymes will get knocked off from the fluidic flow, so they need to be refreshed every 15 hrs.

Cute animation. Future application – using a large pipe with enzyme-coated beads, kind of like Caltech’s biofilm for endocrine remediation.

Human Practices: science experiments with kids, teaching high school girls molecular biology, Community Bricks.

Wuhan University (WHU)-China

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Wuhan University (WHU)

After working really hard on convincing their university, this team managed to participate in the 2011 iGem competition with the supportment they seeked.

This team found inspiration in an exciting feature of a traditional chinese dance: “Face changing”. It’s a very rapid movement made by the dancer where she changes the mask she’s wearing. But it’s so fast that you have to pay attention to notice the exact change.

They showed us then the picture of a tree and how it changes with each season focusing on a point. This color-changing over time inspired an Oscillator.

A strain of E.coli that works as an oscillator and can yield different kinds of pigment periodically.

Another branch of this team’s project is the “E film”, they aim to build three E coli strains which can produce and secrete colours, the three primary colours, in the presence of different light wavelengths.

The key players of their gene circuit are LsrR and LsrK alternating their expression. At the beginning LsrR is expressed and inhibits LsrK. When concentration builds up, LsrR inhibits its own expression, eventually conentration drops and LsrK has a chance to express. Then, LsrK induces expression of LsrR and there we go again.

They talked about two methodologies, used when attempting to build their system:

a) Golden gate method

Some systems require too many biobricks in the assembly, which lead to tedious experimental process and increasing demand of time.

What they did was digest their Biobricks with Xbal and Pstl, then ligated them to ten “module plasmids” (Previously designed). They mixed these plasmids and an array plasmid in a single reaction and added a Bsal and ligase. By using BsaI theywe provided their biobricks with cohensive end

and in the same reaction, assembled them in order into the array plasmid. The array plasmid has lacZ flanked by Bsal recognition site, and under the effect of Bsal, it will be able to produce sticky ends complementary to the first and tenth module plasmids. This saved them days.

b) Reverse assembly

Facing thee need of one BioBrick that was in a composite they got from Edinburgh, they needed to break down these assembled BioBricks and their only chance was a costly (time and moneywise) PCR.

So what they think is, the backbone standard should include HindIII sites flanking BioBricks for their recovery.

After working really hard on convincing their university, this team managed to participate in the 2011 iGem competition with the supportment they seeked.

This team found inspiration in an exciting feature of a traditional chinese dance: “Face changing”. It’s a very rapid movement made by the dancer where she changes the mask she’s wearing. But it’s so fast that you have to pay attention to notice the exact change.

They showed us then the picture of a tree and how it changes with each season focusing on a point. This color-changing over time inspired an Oscillator.

A strain of E.coli that works as an oscillator and can yield different kinds of pigment periodically.

Another branch of this team’s project is the “E film”, they aim to build three E coli strains which can produce and secrete colours, the three primary colours, in the presence of different light wavelengths.

The key players of their gene circuit are LsrR and LsrK alternating their expression. At the beginning LsrR is expressed and inhibits LsrK. When concentration builds up, LsrR inhibits its own expression, eventually conentration drops and LsrK has a chance to express. Then, LsrK induces expression of LsrR and there we go again.

They talked about two methodologies, new standards they used when attempting to build their system:

a) Golden gate method

Some systems require too many biobricksin the assembly, which lead to tedious experimental process and increasing demand of time.

What they did was digest their Biobricks with Xbal and Pstl, then ligated them to ten “module plasmids” (Previously designed). They mixed these plasmids and an array plasmid in a single reaction and added a Bsal and ligase. By using BsaI theywe provided their biobricks with cohensive end

and in the same reaction, assembled them in order into the array plasmid. The array plasmid has lacZ flanked by Bsal recognition site, and under the effect of Bsal, it will be able to produce sticky ends complementary to the first and tenth module plasmids. This saved them days.

b) Reverse assembly

Facing thee need of one BioBrick that was in a composite they got from Edinburgh, they needed to break down these assembled BioBricks and their only chance was a costly (time and moneywise) PCR.

So what they think is, the backbone standard should include HindIII sites flanking BioBricks for their recovery.

Washington – Make it or Break it

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Last talk in this session.

The team deals with diesel production and gluten destruction. Two very similar topics. First they focused on the diesel production. They want to use Biofuels, because these are renewable sources of energy and mix them with petroleum to get the right mixture of good fuel. The alkane production should be managed by using fatty acid as a starter substrate. This pathway was implemented , expressed it in E.coli , analyzed it via GC/MC and calculated a model. They achieved a production of C13, C14,C15 and C17 Alkanes and Alkenes respectively. So they can convert sugar into diesel, as they expected! They called it the PetroBrick, which is able to produce alkanes of different chain length.

The second topic is the gluten degradation. Some people suffer under gluten side effects. The only treatment is, a total dietary change. Gluten peptides trigger a immune response. So they want to digest these peptides. There is a protein already in test trail, unfortunately this protein is not able to work at a low pH. So they choose kumamolisin, which can work under low pH conditions. They used computational tools to redesign kumamolisin for their purpose. The team developed a whole cell lysate assay, in order to test their mutations. The top mutants were purified and characterized. These could be increase to a 100-fold improvement of breaking down these bad gluten peptides.

 

Further the Washington Team achieved to create a iGEM toolkit box, which can be used by the iGEM community. I like toolkits. Nice work.

I do not really understand, why they choose three totally different topics. However, I have to say that they did a really nice work on all of their subprojects.

Just a quick side comment. The last girl can speak with the speed of light or like a automatic gun. 1000 words per seconds. Literally. And counting. I am blown away.

Q&A

Why do you choose such different topics?

Because they were soooo many people, they did different topics. The connection between the topics seems to be making the world a better place with the help of synthetic biology.

What about your application concerning the biofuels

Just a proof of principle. There is a need for more work in order to get the best yields.

 

UC Berkeley: DetectR

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DetectR

We were given an introduction to Biosensing. The question is: How do we detect molecules?

We have organisms that detect specific protein/molecules of interest, we also have that many molecules have no known receptor.

Traditional Biosensors creation is time-consuming, and not that efficient.

They wanted a system where they can take a ligand binding domain (natural or synthetic)

Things to pay attention to: where the biosenser is going to sense, where it is going to respond. Because you need to know about permeability, if it senses in the periplasm, if it expresses in the citoplasm.

The ToxR system.

ToxR is transcriptionally inactive as a monomer. ToxS interacts with cytoplasm domain of ToxR, brings them together promoting transcription (ctx promoter). So they saw a potential to link ToxR dimerization (and gene expression) to the presence of specific ligands

They replaced the periplasm domain of ToxR with another domain aiming to create a biosensor. By using a GFP after the ctx promoter, they can detect if it is activated.

First attempt, they truncated the periplasmic domain of ToxR, then built a translational fusion of IILK (constitutively dimerizing leucine zipper protein IILK) and the ToxR truncation driven by a Pbad promoter. This means that the periplasmic domain IILK should dimerize and cause the ToxR dimerization, thus activating transcription from the ctx promoter.

High toxicity and low cell growth were seen.

ToxR-IILK high expression causes stress. They wanted to replace the promoter of the chimera with a promoter reacting to stress and downregulating ToxR-ILLK… how to find the regulatory elements?

They looked into the E coli genome for stressed-based regulatory elements they could use as a self-regulating system.

They checked microarray data (Moen, et. al. 2009) and identified 35 potential promoters. Then isolated ORF upstream region through PCR and placed the resulting pool in front of GFP, then measured looked for decreased fluorescence.

The promoters with the desired behaviour were incorporated into the ToxR system. The ToxR-IILK expression went to a nonlethal level.

The fact that they looked for a way to solve the problem (which was not small) they encounterd is very important, something everyone should do.

Edinburgh – “Synergy”

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A biorefinery is a special type of refinery in which biomass, such as plant cellulose, is converted by microorganisms into useful products. Edinburgh’s 2011 iGEM project is a feasibility study into the creation of biorefineries using E. coli, the workhorse of synthetic biology; and whether biorefineries can be improved by arranging for the different enzymes involved to be in close proximity to each other, so as to create synergy between them. We investigated two methods of bringing the enzymes close together: cell surface display via Ice Nucleation Protein, and phage display via M13′s major coat protein. We attempted a new DNA assembly protocol, provisionally named “BioSandwich”. We constructed computer models of synergy to assess whether it is a feasible option. Finally, we considered the broader economic and social questions surrounding the construction of a biorefinery: can it be done, and should it be done?

The team presents the concept of synergy – within their team and within nature. Afterwards, they transfer this concept to two different strategies – cell surface display and phage display.

The first presented system uses E. coli as a scaffold and displays proteins on its outer membrane. To achieve high expression levels, they attempted to use Ice Nucleation Protein as a carrier for enzymes. They show promising results where they could degrade cellulose and also starch. Nearly not necessary to mention, but the team did some modeling and even though they say it’s quite simple, they have lost me. They also compare stochastic and deterministic models.

A new protocol named BioSandwich, a method for the assembly of multiple BioBricks in a single reaction is presented. The protocol seems pretty simple and consists of only five steps. You can find a lot of details on this in their wiki.

They performed a feasibility study. I suppose this is the only team that has been doing such an extensive study to see if their project is applicable and how one could realize it. Furthermore, they have performed interviews with various persons from politics, academics and even a member of the Church of Scotland. This is probably the most outstanding part of the Edinburgh teams project. I suppose very few iGEM teams before have been covering so many outreach and human practices aspects. Really impressive.

 

 

Imperial college London

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IMPERIAL COLLEGE LONDON which their project is called AUXIN….
there will be more information provided soon. we are sorry for any inconvenience.

Johns Hopkins – Vita yeast

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Third session. First talk of the Food or Energy track

Before the talk starts, somebody has some really serious problems with the light switch. It’s on, off, on, off again. Gives me the disco feeling.

So, back to serious topics. The team is dealing with the big problem of worlds hunger and malnutrition! They pointed out that is not only a problem of quantity, but also quality. You need your vitamins! Infant and maternal care as well as sustainability are the two other main issues. The JHU team focused on vitamin A and C. The project consists of a theoretical, modeling, toolkit and a deployment part. As a chassis they choose yeast, because it is already evaluated in the scientific community and has been used for centuries. The main aim is to create a vitamin A and vitamin C producing Yeast. The Vitamin A should be produced from the beta-carotine pathway. They transformed the used genes in different Biobricks, transformed it into the yeast and viola you get orange yeast (do not try at home). For the Vitamin C pathway they choose GDP-D-Mannose as a precoursur to produce L-ascorbate. They transformed all the used genes into BioBricks. For purification a his-tag was used and enzyme assays performed. And of course, there is a model. Unfortunately, it is math, so I am out. Sorry guys! But it seems pretty nice. They calculated a Pareto Frontier, which seems to be the calculation of the turning point of the system. At which time point do I have to supply to much nitrogen, without getting more product. Interesting and well performed project. But the questions is, what do they think about golden rice, which solves the same problem like their Vita-Yeast.

Further they supply a yeast toolkit, containing promoters, UTRs vectors and reporters. Toolkits are always a great idea, because they can really help other teams out. Nice work!

Finally they liked to baked bread by using their optimized yeast. So people can get more vitamins by eating their bread. The prototype bread is not orange, but looks like real bread! They measured their beta-carotine amount by HPLC. So there is beta-carotine in their bread. With this idea they went out of the laboratory for their Human Practice part. So finally they mantioned the golden rice, and claimed that their bread will be better, because it is not orange. Further they say, because their bread only contains 1% of GMOs, instead of the golden rice, which is a complete GMO itself….

Let’s check the Q&A part.

What about the instability of your vitamins?

They did consider that the vitamins can be degraded under heat. So they want to produce more than required and they claime that the compounts are stable under baking conditions

2 questions I did not get not acoustically.

SYSU-China

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Following we have this ASIA´s Team which have worked on a NUCLEAR LEAKAGE rescuers…
as they are explaing they separeted their project in two process

First MIGRATION, they´re using two promoters to make E. coli able to sense the radiation of Cs-137 and move toward the radiant….

Second they are explaing ABSORTION, here the explained that by expressing a protein, and a ion channel with high afinity to Cs.

WAO: they also are using a system to avoid E. coli to be eating by fishes…..

Now they are showing a video…pretty cool!
To see this video remember visit their wiki by using this link: http://2011.igem.org/Team:SYSU-China/main_page_project

now are talking about their Human Practice…..
they developed only with workshop, survey…judges will not like this!!!…..

Question time!
Problems answering!…
judges want to know how much will the E. coli collect….
uhh….there is not question yet..

People question:
one audience is asking about quantity of Pottasium will be on environment, and how to avoid collecting this metal when is needed in seawater….GOOD QUESTION no?
Answered: they didnt apply this,…could a sensor for potasium be add in their bacteria in order to avoid collecting it….

Tokyo-NokoGen

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It’s 2:55, and the team is uploading their presentation onto the screen…

3PM: Game time! Tokyo-NokoGen–EcoLion: collecting heavy metals

Apparently, they won the mascot fun run at iGEM Asia: pikachu with a yellow lion’s mane/ wig. =)

Problem: heavy metal pollution; heavy metals for making iPads expensive, need to recycle.

Idea: E coli collecting heavy metal ions

4 devices in a closed system to keep people and the environment safe.

 

A) Metal ion uptake

1. Inducible auto-lysis (for environmental considerations). Red-light induced?

a) Metal ion uptake: harmful to E coli and harmful if leaked.

–Capture: metallothionein: SmtA and fMT. SmtA under low and high copy promoter. Metallotheionein will bind to Cd and prevent toxicity.

–Localize: tag (PduP)

Results: high metallothionein + high tag expression = growth at high [Cd]

b) Store: bacterial microcompartment (BMC): PduBMC

–Brick: pduP-GFP, pduBMC

–PduP-GFP works

–pduP-GFP expressed in pduBMC? Still needs characterization

c) phototaxis: Combine chemotaxis machinery with blue light induction.

–Light = tumbling

–Dark = smooth swimming (bigger colonies)

d) Antigen 43 = aggregation

BBrick: Plac with antigen 43 coding region. Expect aggregated bacteria to settle on bottom of test tube = less crowded medium = drop in optical density. That result was achieved.

e) Environmental Considerations; control of EcoLion

–EcoLion dies under red light. Lysis under light.

–Under Plac promoter, induced by IPTG. When induced by IPTG, lysis occurred, OD decreased significantly.

 

Summary: EcoLion reduces heavy metal waste and enables recycling of rare heavy metals

–Capture: metallothionein

–localized in BMC

–Blue light causes Ecolion to swim from big tank into a small tank

–Green light = aggregation (via antigen 43)

–Drop to bottom of tank

–Harvest Ecolion to collect heavy metal ions easily.

–Drain water, induce lysis with red light

 

Questions:

1. Did you test metalliothionein with other heavy metals? (Specific to Cd?) Did you consider using metal-eating bacteria?

Answer: although Metallothionein responds to copper and manganese, we didn’t encounter any problems. No, we didn’t look at other kinds of bacteria.

2. Safety in terms of lysing. And did you talk with the public about biosafety (to get feedback) and did you use that to make a safety protocol?

Answer: They worked on the iGEM project and didn’t have time to reach out to the public

3. So… Lysis under IPTG is not at zero CFU/mL… Any ideas for how to make that go to zero?

Answer: We’ll increase promoter strength.

 

Back to Presentations!

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Tokyo-NokoGen Team is presenting now…
they have working on building a biobrick that makes capable E. coli to collect heavy metals from the environment!…Cool!
They called EcoLion, cool name!….
What is really interesting on this project is that E coli that has stored heavy metals will be conveniently collected by light….but how?….well they are using the phototaxis process or also they can made this possible by self-aggregation (they said).

They want to used this for collecting a different toxic molecules by using specific proteins…
They also want this bacteria to collect the metal from water and then will be put into a small tank…and here they induced segregation cells and collect the metals molecules which can be recycleable!…cool!….for more information about this team´s project click this link: http://2011.igem.org/Team:Tokyo-NoKoGen.

They have done a good project but seem like there is not Human Practice work, = (
….Now questions time…
they are having hard answering question….one of the judges asked them if they try the system in a different bacteria than E. coli, but they said they have´nt try…so will their E. coli work in all environment?…

Bad answer….one of the judges asked them what they did to show their project to their society, but answer was..”we focussed on lab-work”…..which is the more important part, but nowdays working on Human Practices is important as well!….

Brown-Stanford: conquering space

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Brown-Stanford Team: Synthetic Biology for Space exploration.

Space exploration is now difficult and expensive. Brown-Stanford thinks that we need a new toolset.

Biological tools has advantages such as: self replicating, self repairng, programmable. They can be applied in all sorts of useful ways:

But first… the source of energy: “Powercell”. It’s a cyanobacteria energy generator

Selected Chassis: Anabaena PCC7120.

*Photosintetic

*Freshwater organism (when placed in hypertocin solution produces sucrose as osmotic buffer), *Nitrogen fixation.

 

The nutrient secretion:

They placed a sucrose symporter gene, cscB, behind the Anabaena psaC promoter in order to confine sucrose secretion to only vegetative cells.

-They had to see if their organisms could actually survive on this sucrose. Bacteria was grown on minimal media and different sucroce concentration. It was concluded that they can power their cells with this sucrose.

-DNA transformation was hard, anabena has 3 restricton enzymes. They epigenetically protected their DNA (helper plasmid carrying methyltransferases).

 

So the next question… What can we power now?

RegoBricks. The team aimed to modularize the well studied process of biocementation. The obvious application: habitat building.

Biocementation goes as it follows, urease cleaves urea into ammonia and carbon dioxide, ammonia raises pH causing divalent carbonate anions formation. The anions meet with calcium cations to form calcium carbonate crystals.

 

They were really interested in the urease cassette, the aviable one was at least 7 genes, no full sequence existed. They realised that PBU11 contains urease genes from S pasteurii. They cloned it and transformed the cassete into their own E coli.

The functionallity was tested on urease test plates: phenol red signal indicates raising pH.

They sent a couple of balloons into the stratosphere (near-space). Conditions mimic those found on mars.

 

Update since Regionals:

They asked yale for their anti-freeze proteins ==> increase biocimentation process (contends with space lower temperature).

 

Human Practices

*The team went to NASA to discuss the usage of Synthetic Biology for space exploration.

*It is really important to mention the Outreach activity of Brown-Stanford. It includes an analysis on the future of the public image of synthetic biology, thus describing the need for new and creative approaches to taking-SynBio-to-society. The need for a Synthetic Biology community is also stressed.

*Community Bricks: a place (internet) to share creative, reproducible Human Practices activities.

 

ZJU-China! The Asia Jamboree winners.

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So this is ZJU-China! The Asia Jamboree winners.

We have 10 presentators, they are dressed in coloured T-shirts, matching their Rainbofilm concept.

The presentation is starting with a video as a trailler or their project, pretty well coordinated presentation, they don’t even look at the slides.

 

Introducing Biofilms:

The team developed three different Biofilm formation methods. It’s a DIY!

1) Bubbling Method

Inoculated overnight cultured E.coli DH5α in LB, a glass slide inside the tube was placed, the bubble supply system was built with a common air pump for aquarium, an ultrafilter membrane and rubber tubes. The formation can take place at about 27℃. Biofilm was generally formed in 72 hours.

2)Rubber Tube Method

3)Cell Culture Plate Method

(see details at their wiki)

 

*The BioFilm formation modeling considered:

-Growth

-Thickness

-Oxygen Gradient

These features are all related and modeling aimed to simulating biofilm formation and the stratification of concentration of oxygen.

 

RAINBOFILM

This year the tem focused on the tissue level; the goal was to make cells differentiated within a natural bacteria “tissue” biofilm.

Their Rainbofilm was constructed with three different sub-devices, the expressio is controlled by three different promoters, each under aerobic, micro-aerobic, and anaerobic conditons. They managed to use oxygen concentration gradients within the biofilm as signals to induce the expression of different proteins.

The film was formed made using different plasmid constructions (The rainbow part comes with the different layers, using different reporters, hence colours).

The interesting thing is, they wanted to improve the input signals of the rainbofilm system by

  1. Fine-tuning the stratification pattern

    They used vgb promoter to regulate middle layer behaviour. Trying to change the the distribution of the layer they made a promoter library to screen the promoters with peaks in different oxygen concentration. They managed to see that three transcription factors coordinate the vgb regulation, but the mechanism is not clear.

  2. Changing the differentiation signal

    They want to use something more controllable as input signal(differentiation with oxygen as input signal is sort of spontaneous). The idea is to build a biosensor with Hg2+ and Pb2+ as signals. They also screened for ideal-sensing mutated promoters.

 

On the Human Practices:

 

They…

-Funded a Synthetic Biology club at their university

-Wrote an original novel on Biosafety issues

-Developed an iphone app which is about building a path through solving tasks and advancing levels . It’s a game that lets you learn synbio concepts through playing.

 

 

Lyon-INSA-ENS – Cobalt Busters

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Last presentation before lunch break – The cobalt busters from Lyon. I hope no growling stomachs will interrupt the presentation. ;)

How to remove cobalt from radioactive water?

Another tribute to one of my favorite childhood series. Humming the title track, I keep following the presentation.

They demonstrate how radioactive cobalt is formed in French nuclear power plants, originating from the steel pipes. The cobalt is part of the radioactive waste which has to be stored. Since space for storage is expansive and a problematic issue, the team has come up with a new way to threat with the waste.

As already heard in the Grinnell presentation earlier this morning, biofilms are involved. But surprisingly, this time the advantageous aspects and the potential of biofilms in bioremediation are pointed out. Since they want to use a modified E. coli chassis which is accumulating cobalt, a separation of the bacteria and the waste is beneficial and for this they want to use biofilm formation. Two different options are presented: A synthetic culi operon and by activation of cryptic curli genes. Results for the characterization of both ways are presented. They can show that their device employing the first option works as desired and displays increasing adherence with increasing cobalt concentrations. Also, they show that their rcn promotor is the reason for that behavior. After comparing both possible ways, the first option is selected.

Now, for the actual implementation of their bacteria. The team presents a figure how a filter carrying their bacteria would be used in the bioremediation of contaminated water. Also, further applications such as air filters are presented. Like nearly all of the iGEM teams, they have been heavily working on the iGEM outreach.

I hope that you all are as hungry as your designated bloggers are.

 

USTC-China´s Presentation

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Here we continue with the World Championship Jamboree, now with this team from ASIA!…

their project is called SELF-organizing Bacteria…sounds interesting no?…they based their project on Stochastic Switch and Chemotaxis…mmm!, lets see what is this about but if you want to know more about get into this link: http://2011.igem.org/Team:USTC-China/Project
They have constructed a novel system in which bacterial colonies will automatically divide into two parts after certain time….but for this they needed to assembling ribowitches which were finely tuned by small molecules…interesting, no!…

The application is very nice, since they want to used their bacteria as a nice functional weapon to destroy the pathogens which invade the intestinal mucosal system. This is very usefully cause proteins expressed by their bacteria at the infection site will kill pathogens by self-destruction…Cool!

Now they are talking about their Human Practice…where basically their worked with a survey applied to students about Biosafety…but also they made some activities with community!…

Well done…now lets go to lunch and we will continue with more presentation in this World Championship Competition for iGEM!

Grenoble: Mercuro-Coli

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Find the mercury in water! Mercury is a problem for water-quality all over the world. That’s why the Grenoble team started a partnership with an industrial partner from chemistry to establish a detection and quantitation device for mercury, based on our friend E.coli.

They use a plate with constant mercury concentration and an IPTG gradient to start expression in either sending (mercury > IPTG) or receiving (IPTG > mercury) bacteria. For that, they created a 2-way switch, which allows to distinguish between higher Hg or IPTG concentrations and will cause quorum sensing from receiving bacteria to sending bacteria. As a result, the receiving bacteria will accumulate at the equilibrium of Hg and IPTG and create a coloration, there. That again, allows to read the mercury concentration according to the IPTG concentration gradient. They additionally implemented a power button for the whole system. See their wiki for a way better explanation and helpful images :)

They show some models, to make clear how they expect the results to look like. They modeled predictive outcomes.

As Grenoble is a pretty interdisciplinary team they aim to improve the interaction between biologists and modelers. For that they created two info flyers “Modeling for Biologists” and “Biology for Modelers”. They tested their flyers in a collaboration with Paris, where they had two test groups – one using the flyers, the others not – and a quiz for evaluation. The results proof the usefulness of their attempt. And finally somebody can explain modeling to me. Nice!

In the human practice part, they show some actions in science communication, including conferences, newspapers and radio.

All in all they could make 3 proofs of principle (2-way switch, power button and quorum sensing), committed 19 BioBricks and MOST IMPORTANT they will be back in 2012 with the next Grenoble iGEM team :)

 

Time for questions:

Didn’t understand the question..
They showed, that their systems works for Hg and tetracycline.

Couldn’t understand the question…
But the answer is, that you need 10^4 bacteria to achieve a 10% precision in the system.

Please repeat the questions :) …
For creating the information flyers for modeling and biology, they switched the roles in the team, to make sure to hit the important questions that arise, when a biologist tries modeling and vice versa. Their goal was to bring the basic knowledge of both worlds to every team member in order to allow an efficient team work.

What is the response time of the system?
It is about 1 hour.

Does their system work for other substrates?
It should be easy to use other sensors for the same basic concept.

Are their requirements (37 degree, 1 hour response time) realistic for real world applications?
They seem to use only bacteria in exponential growth for their test, making it independent of such limitations.

Tsinghua-A Team´s Presentation

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Next presentation on this World Championship Jamboree at MIT, Boston….is by Tsinghua-A Team….

they have constructed a biological oscillator, which they called ECHO, which means: E. coli Homochronous Oscillator.

This Oscillator works basically when a cell, called CELL-B induced CELL-A, and

this one will restrict CELL-B.

If you are interesting in learning more from this team´s project, acces

this link, http://2011.igem.org/Team:Tsinghua-A/Project

and it will show you how this team work on this interesting project!…

Good job have done this team, they establish a mathematical model to analyze

the dynamics of the system and also they introduced a computer simulation

software into the process….COOL!


ArtScienceBangalore – UGEM

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Second session – first talk, environment track

The team dressed up in traditional clothes. Nice impression. Although they are artists and designers, they take part in the iGEM competition – Which, in my opinion, is very fresh and different from all the other team jerseys. The team is dealing with ubiquitous BioBricks, so they call their project UGEM – ubiquitous GEM. One can divide their project into three different parts: Speculations about BioBricks, an alternative for BioBricks and the Community outreach.

Speculate:

The check for mankinds impacts on the environment. So they collect soil samples from all over the world – even from Denver!! Further they collect soil samples from all over India, with the help of the local farmers. The purpose is to check if tou can fingerprints of genes, which are containing in BioBricks. They created an experimental briefcase, which they used for sampling and investigation of the samples.

Alternative uses of BioBricks:

They extracted DNA from the soil and check via PCR – Preffix, Suffix- for BioBricks, E.Coli containing BioBricks and Plasmids. They found no BioBricks, but E.Colis with Plasmid by using the BioBrick primers. They put the Plasmids they found into the E.Colis. Hopefully i get that right.

Community

In India a lot of people are driven towards science. Nevertheless the most people can not afford the money to get deeper into science. So the team decided to create laboratory material out of every day life materials. So they invented a community lab, where the all the people can work under supervision in the scientific field. More over they used balloons and a camera for “balloon mapping” over India. Some kind of DIY google maps. Definetly a nice idea and colourful cause of the balloons.

Further they created a handbook, in order to reach kids with scientific questions.

 

What method do you use to extract DNA

Alcohol-Detergent extraction

What was the cost to build the DIY lab?

Each item of the lab is about 20-40$

Did they have a negativ control? Did they check for the sensitivity of their assay?

They did several Nanodrop samples.

How much time it takes to create the soil-sampling briefcase?

The modelling about a week, the prototype a few month

 

 

 

Second Presentations Sessions

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Hey!…now after a short break we had, we continue with the presentations sessions… and is Waterloo Team´s opportunity to show in the First World Championship Jamboree what they have done…

Their projet its called: In Vivo Protein Fusion Assembly Using Self Excising Ribozyme this is about implementing self-excising ribozymes (introns) as BIOBRICKS, cool not?…

if you´re interesting knowing more about their project you can click on this link http://2011.igem.org/Team:Waterloo

and it will show what amazing project have done this TEAM!!!….

their used a model as Cambridge in 2009…

The team is doing a good presentation….but now the fearful is coming on…

..so lets see in few minutes what Judges think about their projetc?…

WAO!!!….their made a commercialization toolkit…

this is pretty cool, the team worked with Juniors Grades and show then how important is to wash hands…by cultivating bacteria´s

from a washed hands and not washed hands!…. nice!!!

Now finally we are in the questions…..

There are a lot of questions…the team is giving a good answer to each one….

Bielefeld – The Bisphenol A Team

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“Check one, two” and the presentation starts.

The iGEM Bielefeld-Germany team deals with a cellfree biosensor this year, used to detect the possible toxic and polluting substance bisphenol A (BPA). Reminds me of my old 80ties heroes.

BPA is used polycarbonate plastics, hence we get in contact with this substance every day (DVD,CD, baby bottles). There are concerns that BPA, because of mimicing estrogen, is bad for your health. Hence it is forbidden in the EU and Canada for the production of baby bottles (Never let your baby suck on a number 7).

They checked for advise by the project manager of synthetic biology of the federal agency of technology assessment. The project manager adivised: Go cellfree, where ever it is possible. In a small animated video the team explained their project. They fused three, BPA degrading, enzymes to a silica bead by using S-layer proteins. The visual light signal was established by detecting the NAD+, which is created during the enzymatic BPA degradation steps, with the help of a molecular beacon. So the detected amount of NAD+ correlates with the degraded BPA. SO the project can be divided into three subparts : BPA degradation, NAD+ detection and S-Layer.

They showed that the BPA degradation works fine by creating a double and a triple fusion protein out of the three enzymes. Further the NAD+ detection works as expected and can be checked by the naked eye. This kind of detection can be used by every future iGEM teams => nice.

The S-layer proteins were used to couple the enzyme reaction onto the silica beads. S-layers proteins self-assemble in solution or on surfaces. Further they have the big advantage that the coupled enzymes are ordered in a defined orientation. They created a DIY-Nanotech Guide, so that every other team can use this guide to build up their own S-layer based systems. Seems as if it works fine.

The Human Practice part consists of high school visiting, debating their project with the industry and public discussion. So it seems that they love it when a plan comes together and I will now check for my cigar.

Questions:

The judges like the idea of going cell free, but they are wondering about the NAD+ detection. Might there be any interference with this kind of bio-assay, especially by applying a complex matrix.

In the case of their study, there is no complex matrix, but if you use a complex matrix there might be interference.

Did they do the microscope image by themselves?

No, they took the photo out of their working group, not enough time to establish an atom force microscope-strategy.

Did you try any other substrate than silica beads?

Just silica beads and silica weavers. But they observe that their S-layer could stuck on the bacterial membran and the literature sugest that they might stick to gold particles

Why use your biosensor and not just ban the BPA?

They are scientists, no politicians.

Caltech – Bioremediation of Endocrine-Disrupting Chemicals

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Visit their wiki!

Endocrine-disrupting chemicals are substances which detrimentally effect the development and reproduction of wild organisms. These chemicals mimic natural biological estrogen in their interaction with animal estrogen receptors. This interaction has negative effects for reproductive processes of several species of fish and birds. To remedy that, the Caltech iGEM team hopes to engineer bacteria which can degrade DDT, synthetic estrogen (17a-ethynylestradiol), bisphenol A, and nonylphenol to less toxic forms. Compared to traditional forms of pollution removal, bioremediation is relatively cheaper and less disruptive to the environment. However, a successful project must make sure that the bacteria used for remediation do not act as pollutants or introduce toxic byproducts into the environment.

*****

Investigated BPA, DDT, Estradiol, Nonylphenol. Proposed system passes contaminated water through purification column with biofilm- coated beads.

Looking for a degradation pathway:

  1. Gene Fishing – looked for microorganisms in the LA river. As it is heavily polluted, organisms which can metabolize compounds of interest might already exist. Grew water samples up with minimal media and one of 4 compounds to screen for relevant microorganisms.
  2. BisdA and BisdB
  3. DDT Dehydrochlorinase
  4. Cytochrome p450 analysis

Feasibility Analysis:

  1. Biofilm construction – verified that E.coli would grow as a biofilm on the glass beads.
  2. Water plant integration analysis – looked at 3 existing water treatment plants.
Accomplishments:
  1. Determined enzymes for BPA and DDT
  2. Showed biofilms are a possible method of deploying bioremediation systems, but expressing genes in e.coli interferes with biofilm formation.

 

Questions:
  1. Any reason you think inserting a gene caused your biofilm formation to stop working? They don’t know; they tried a few different strains but got the same results each time.
  2. You show that big compounds like BPA and DDT can be degraded, but into what? How toxic are the degradation products? There’s research showing that degradation products are less toxic, but that’s something that they will look into for the future. They are only aiming to be able to demonstrate the beginnings of degradation.
  3. Are biofilms the best way to get your product implemented – for example, industrial plants use large tanks with the microorganisms swiming around. They used the biofilm bead method because it was easy to implement under lab conditions; had they more time they would look at more traditional methods.
  4. Did any of the plant managers have questions about the introduction of a synthetic organism? They had limited time and knowledge regarding this topic. Basically, the plants should be able to self-remediate the problems caused by genetically engineered bacteria.

 

Future directions - The team would like to continue by extracting whole DNA from river samples, insert into plasmids, transform and see if these bacteria are viable to identify genes for survival.