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Team:ETH Zurich/blog
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Revision as of 15:01, 28 August 2014
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Blog
- For the agar-design we filled the chamber and channels with LB-agar or in a second attempt with agarose only. Subsequently, we punched a cylindric hole in each chamber. The capacities were filled with regulator/sensor strain culture or AHL/AHL producer strain culture, respectively. After 3 to 4 h at 37 °C we could observe an increase in the sfGFP signal. Since we used comparably high concentration of AHL in our first attempts, we could not detect a delayed sfGFP signal for chambers connected by a longer channel. The experiment will be repeated using lower concentrations. However, conducting the experiment using the agar-design, we encountered a problem: after some hours the LB-agar/agarose started to shrink and dried out. Thus, the agar-design cannot be used without modifications for experiments of longer duration.
- In an attempt we only left a small agar fragment in each channel and filled the rest with liquid medium, so as to decrease chance of it drying out, while avoiding at the same time that bacteria from one chamber reach the other chamber.
- The bead-design consists of an alginate bead for each chamber and liquid medium in between. The beads either contained regulator/sensor-bacteria or AHL.
- We carried diffusion experiment with different designs : punched PDMS, liquid, beads. For every design we added high concentrations of pure AHL in the sender well, so cells are glowing a lot. However because of this high concentration, diffusion is very high and at a given AHL concentration, receiving cells are glowing at the same time for all 4 channel lengths. Check the corresponding article for more details.
- We have a Comsol simulation for these experiments that explains why at this concentration of AHL (1mM), all 4 wells glow at the same time irrespectively of channel length. Check this article for more details.
- We could fit degradation rates of external, internal AHL and GFP thanks to quorum sensing dynamic curves.
- Our first diffusion try with highlighter ink !
- We have been fitting quorum sensing experiments at steady state to a Hill function and found some quorum sensing parameters.
- We wrote a survey in English, in French and in German on complexity for our human practice project. We expect 500 responses.
- We have a lot of results for cross-talk experiments. Check the corresponding article for more details. For the moment lux promoter doesn't respon to other AHLs. This is a good step towards orthogonality.
- Current challenges :
- AHL producer strains are not producing enough. We have to improve the RBS.
- GenScript has problems to produce our Las sensor with riboregulator RR42.
- We have a project description !
- We have a first draft of our abstract.
- We have results for our first quorum sensing experiment .
- We have now a proper PDMS chip for diffusion experiments.
- We have a simple GFP production model for simulation of these quorum sensing experiments.
- In the next weeks we will fit quorum sensing parameters thanks to the first quorum sensing experiments and our simple GFP production model, refine this Comsol diffusion model with the right quorum sensing parameters and then fit this diffusion model to diffusion experiments to find the diffusion constant.
- We designed two possibilities for the chip: either cells laying on agar or punched cylinders in the agar.
- 8 out of 21 plasmids were positively sequenced. 7 further plasmids are sent for sequencing.
- We will start cross-talk experiments this week. It should help us choose an orthogonal AHL pair among three different quorum sensing systems.
- We have started to learn bead production.
- We started to simulate diffusion experiments on a Comsol model. We consider cells will lay on agar for the moment.
- Our first mold didn't enable us to peal the PDMS correctly. We have to make it less deep.
- 5 of 8 regulator plasmids are done. We have to repeat construction of producer plasmids.
- Parameter estimation for integrases is not working at the moment.
- We skyped with Paris Bettencourt for human practice collaboration and are participating to their newsletter project.
- Our first Gibson assemblies worked well. Regulator plasmids piG0040, piG0041 and piG0042 have been constructed :
- We printed our first mold for millifluidic chip :
- We simulated the whole model with and without riboswitch in Matlab with random parameters for integrases. We are still trying to estimate integrase parameters from the literature but it is very difficult.
- REDIRECT Team:ETH Zurich/labblog/20140829mod
- We have a logo !
- In the lab, we did some :
- Plasmid preparation
- Sequencing
- Digests
- Purification of backbone fragments needed for GA
- On the modeling side, we tried to estimate integrase parameters from the paper from Bonnet et al. [9], more particularly with the figure S4 :
- We have a precise plan for our human practice project. We would like to study the emergence of complexity in many different fields and investigate how people deal with it. We will do this with interviews of experts in different fields, and with a survey for a wider outreach. We will also reach younger people by organizing talks in schools. We will finally give our own advice on the question by writing an essay on the subject and linking it to our experience with Mosaicoli.
- We have a clear organization of the different experiments we would like to perform.
- We have also clear plans for the Gibson assemblies to perform. As an example, here is the plan for regulator plasmids :
- We have a facebook page !
- We simulated quorum sensing without leakiness on Matlab, with parameters from the literature.
- We will use Gibson assembly to assemble our constructs, and have now a construct assembly strategy. We know the list of experiments we want to carry (cross-talk between quorum sensing molecules, quorum sensing leakiness with or without riboswitch, cross-talk between integrases, integrase activity and logic gate behaviour) and the exact sequences of base units we will assemble (lux, rhl, las promoter and repressor units, reporter units, logic units with 3 different integrases, constitutive AHL production units for diffusion test, backbone units).
- From the modeling side, we calculated analytically the steady state of the integrase and terminator modules, and it appears that the deterministic model gives a binary steady state corresponding to an XOR gate. This is what we expected, it confirms that deterministic model in our case is interesting for the study of dynamics of the whole system, and not for steady state calculations. So we are now moving to dynamic studies.
- We improved a little bit the plasmid design, determined which parts will be taken from the iGEM registry, and which parts we have to synthesize.
- From the modeling side, the whole model has been modularized and we have calculated and simulated steady state for the quorum sensing module.
- GeneScript, Microsynth, EraSynbio are willing to support us !
- We started plasmid design :
- We tried to print our first agar millifluidic chip : we printed it too small, and the printer had resolution problems.
- We wrote all reactions and found parameters from the literature for our model.
- diffusion,
- parameter fitting,
- modeling of the genetic circuit itself, which comprises
- a deterministic model
- a stochastic model.
- find orthogonal quorum sensing molecules and orthogonal integrases
- discuss with microfluidics experts to check if using microfluidics is possible and presents advantages in our case
- find possible parts in the registry for integrases, and design plasmids
Diffusion Experiments
Monday, 25th August
Now that we tested the different constructs for leakiness, dose response and cross talk, we are investigating in the diffusion rate of AHL. Therefore we designed a chip with chambers connected by channels of different length (see figure). In one chamber we added a strain containing a regulator and a sensor plasmid, to the second chamber we added AHL or an AHL producer strain. As soon as AHL is diffused to the former chamber it induces sfGFP production on the sensor plasmid. The time it takes until we can measure the sfGFP signal and the length of the channel gives us information about the velocity of AHL diffusion.
Three main experiment designs were tested and modified: the agar-design, the liquid-design and the beads-design.
Week 14 : Diffusion experiments started, simulated with Comsol, and fitting of quorum sensing dynamics
Monday, August 25th
Check the corresponding article for more details.
Week 13 : Steady state quorum sensing fitted and human practice survey launched !
Wednesday, August 20th
The design of punched agar doesn't seem to be the best but at least we can see something. Diffusion experiments with different designs are running now.
Week 12 : Nice cross-talk results, problems with producer strains, and with synthesis of our Las riboregulated sensor
Wednesday, August 13th
First cross talk experiments
Friday, 11th August
After having constructed the necessary regulator and sensor plasmids we were able to start first cross talk experiments. Therefore we transformed competent cells with different combinations of regulator and sensor plasmids. One example would be the strain siG0024 which contains the regulator plasmid piG0041 producing LuxR under a constitutive promoter and the sensor plasmid piG0051 that encodes for sfGFP. The latter is under control of a pluxR promoter, hence it will be transcribed in the presence of LuxR and Lux. To assess crosstalk and leakiness we conducted multiple experiments: after adding one of the three AHLs to the cultures we analyzed the raise in sfGFP production using a microtiterplate reader. In a first step we measured the dose response of constructs with different ribosomal binding sites (RBSs) and with or without riboregulator. We could observe differences not only in sensitivity, but also in leakiness; some strains expressed GFP even without AHL induction. To give an example: we evaluated the sensitivity of the siG0024 strain to different concentrations of 3OC6-HSL (LuxI product) and compared its characteristics to those of other constructs. Additionally, we measured the sensitivity of siG0024 to 3OC12-HSL (LasI product) and C4-HSL (RhlI product). Indeed, we could observe the induction of sfGFP transcription by comparably low levels of 3OC12-HSL. Crosstalk can be observed between the Las and the Lux system. To simulate a situation most similar to the final experiment, we added the diluted supernatant of AHL producer cells to the test cultures. However, we could not detect any GFP production as reaction to the supernatant. We assume that the AHL concentration is not high enough to induce transcription. By constructing stronger RBSs on the producer plasmids we aim at increasing the AHL production. All these informations we will use to design a system tailored to our plans.
The figure shows the dose response of xxx to 3OC12-HSL, 3OC6-HSL and C4-HSL. Both 3OC12-HSL and 3OC6-HSL induce production of GFP, although at different concentrations. This is an example for cross talk between the lux and the las system.
Week 11 : PDMS chip built, First quorum sensing experiment
Wednesday, August 6th
Week 10: Chip design, Plasmid assembly, Bead production
Wednesday, July 30th
Week 9: First simulations, Skype with Paris Bettencourt, Chip fail
Wednesday, July 23rd
We will have a chip with these four different channels 1 to 4 mm long. The model still has to be refined because at the moment it doesn't take into account internal/external concentrations of AHL.
Week 8 : Plasmdis assembly, First mold 3D printed
Wednesday, July 16th
Week 7: Human practice planning, Plasmid assembly running, Logo design
Wednesday, July 9th
We are trying several strategies : minimization of the error function and Markov Chain Monte Carlo.
Construction of the regulator plasmids
Thursday, July 5th
Construction of the lasR regulator plasmid (piG0040)
Competent cells were transformed with piG0028 (K553003, lasR) and selected on chloramphenicol-LB-plates. Plasmid DNA was extracted by performing a miniprep. The relevant plasmid sequence was sequenced by Microsynth using the primers oiG0001 and oiG0002. Amplification of lasR by PCR using oiG0003 and oiG0004 resulted in the fragment fiG0004 (1.0 kb). The vector piG0034 (pSEVA 181) was digested with the restriction enzymes HindIII and PacI to fiG0001 (3.0 kb). The two fragments, fiG0001 and fiG0004, were assembled using Gibbson assembly. Thus we used the plasmid backbone of piG0034 and lasR of piG0028 to construct the lasR regulator plasmid piG0040. Competent cells were transformed with piG0040 and selected on ampicillin-LB-plates. Colony PCR using the primers oiG0035 and oiG0036 was conducted to check the size of the inserted fragment (expected bands at 1.0 and 1.2 kb). The sequence was verified by Microsynth using the same primers.
Construction of the luxR regulator plasmid (piG0041)
Competent cells were transformed with piG0008 (F2620, luxR) and selected on chloramphenicol-LB-plates. Plasmid DNA was extracted by performing a miniprep. The relevant plasmid sequence was sequenced by Microsynth using the primers oiG0001 and oiG0002. Amplification of luxR by PCR using oiG0005 and oiG0006 resulted in the fragment fiG0005 (0.8 kb). The backbone of the vector piG0040 (lasR in pSEVA 181) was amplified by PCR using oiG0007 and oiG0008. This fragment, fiG0011 (3.2 kb), and fiG0005 were assembled using Gibbson assembly. Thus we formally replaced lasR by luxR to construct the luxR regulator plasmid piG0041. Competent cells were transformed with piG0041 and selected on ampicillin-LB-plates. Colony PCR using the primers oiG0035 and oiG0036 was conducted to check the size of the inserted fragment (expected bands at 1.1 and 1.2 kb). The sequence was verified by Microsynth using the same primers.
Construction of the rhlR regulator plasmid (piG0042)
Competent cells were transformed with piG0023 (C0171, rhlR) and selected on chloramphenicol-LB-plates. Plasmid DNA was extracted by performing a miniprep. The relevant plasmid sequence was sequenced by Microsynth using the primers oiG0001 and oiG0002. Amplification of rhlR by PCR using oiG0009 and oiG0010 resulted in the fragment fiG0006 (0.8 kb). The backbone of the vector piG0040 (lasR in pSEVA 181) was amplified by PCR using oiG0011 and oiG0012. This fragment, fiG0012 (3.2 kb), and fiG0006 were assembled using Gibbson assembly. Thus we formally replaced lasR by rhlR to construct the rhlR regulator plasmid piG0042. Competent cells were transformed with piG0042 and selected on ampicillin-LB-plates. Colony PCR using the primers oiG0035 and oiG0036 was conducted to check the size of the inserted fragment (expected bands at 1.1 and 1.2 kb). The sequence was verified by Microsynth using the same primers.
Construction of the luxR regulator plasmids with alternative constitutive promoters (piG0046 and piG0047)
The promoter site of the luxR regulator plasmid piG0041 was mutated by QuikChange site-specific mutagenesis to produce promoters of different strength. The primers oiG0031 and oiG0032 were used to establish piG0047, a plasmid with a promoter of intermediate strength (J23111). Analoguos the primers oiG0033 and oiG0034 were used to construct piG0046, a plasmid with a weak promoter (J23109). Competent cells were transformed with piG0046 and piG0047 and selected on ampicillin-LB-plates. The sequence was verified by Microsynth using the primers oig0035 and oiG0036.
Week 6: Project planning, Gibson assemblies planning, First Matlab simulations
Wednesday, July 2nd
We want to optimize quorum sensing to have non-leaky non-cross-talking constructs. We want to prevent cross-talk between integrases and check their dynamics with different quorum sensing promoters. Then we will test the XOR gate without production of LuxI, to check how it works without the loop, and we will finally test our final construct with the loop, hoping that the delay between GFP production and the possible second switching due to AHL production is long enough to have enough fluorescence.
The red line is our critical timeline. Numbers of days are very optimistic,therefore we multiply the whole timeline by 2. The stars stand for modeling inputs.
Week 5: Assembly strategy and steady states derivation
Wednesday, June 25th
Week 4: Improving plasmid design, Modularization of the whole model
Wednesday, June 18th
Sensor plasmids will be approx. 9.3kb long, and logic plasmids will be approx. 5,2kb long.
Week 3: Plasmid design started, Modeling started
Wednesday, June 11th
ΦC31 and Bxb1 are integrases. LuxR an RhlR are quorum sensing repressors. A riboswitch construct is placed around quorum sensing constructs to prevent leakiness of lux and rhl promoters. Type p colonies produce AHL by expressing the enzyme LuxI. Type q colonies produce Rhl by expressing the enzyme RhlI. In fact, we don't know yet which quorum sensing systems we will use. We will have to perform cross-talk experimetns in order to choose the ones that are the most orthogonal.
Week 2: Investigating microfluidics, Writing a modeling pipeline
Wednesday, June 4th
This week, we have talked with people from the microfluidics group and it came out that we should be able to use beads to encapsulate our cells and use a microfluidic chip. Therefore we will try to develop this possibility in parallel with the 3D-printed agar chip.
We have set up a modeling pipeline. We divided the modeling project into 3 parts :
We know that the modeling challenges will be to model how integrases work, and to model the delay between reception of a quorum sensing signal and production of a quorum sensing signal by the receiver cell. Indeed, a colony could switch itself OFF when it should be ON, if it receives QS1 and produces QS2, for example. If a delay is present between reception of QS1 and production of QS2, the colony will produce GFP before it is switched OFF, and as GFP is stable enough, it will stay visible during a long time and the self-switching OFF won't be observed. This delay should be modeled.
Week 1 : Project selected
Wednesday, May 28th
After more than one month of endless meetings and passionate debates, we finally chose the project that will keep us occupied in the next five months. From the beautiful pattern made by the Sierpinski triangles, we will focus on cellular automata and try to implement one.
Sierpinski triangles appear when the rule 90 is followed by every cell on the grid :
Ideally we will use a microfluidic chip. We could also use a 3D printed agar plate like this one to load the colonies. On this grid we can implement the rule 6, which is the simplification of rule 90 considered as a rule with 2 inputs : each cell computes a simple XOR gate of its two parents.
The logic part will be built with integrases and the colony-to-colony communication will use quorum sensing.
Every colony will receive two quorum sensing signals (QSp and QSq) from the two cells above it. These two signals trigger the production of two different integrases r and s in the colony. Integrases enable to build biological XOR logic gates by switching twice a terminator. Indeed, every integrase can switch the terminator only once. Thus if the colony produces only r or only s, the terminator is switched only once, so the terminator is OFF, and GFP and QS1 or QS2 are produced (depending on the colony). If the colony produces r and s, the terminator is switched twice, so it is ON and it blocks expression of GFP and of the quorum sensing molecule.
We need to :
BSSE Openhouse Day
Saturday, May 10th
Sharing our iGEM and synthetic biology interest with the public
On May 10th the public in Basel had the unique chance to get an insight into many different scientific laboratories and the work done there. It was the joint open house day of D-BSSE of ETH (Department of Biosystems Science and Engineering) and the Biozentrum of the University of Basel. The many different labs opened their doors to the public and many scientists were present to give interested people some details about their daily work. So did the ETH iGEM team 2014. The team was present with a poster showing the history of iGEM, the previous ETH iGEM teams with their projects and general information about synthetic biology. Additionally there was a slideshow giving a best-of photo collection of last years jamboree. The goal of this day was to inform the public about synthetic biology in general and specifically about the spirit and the many different projects of iGEM. Many people showed strong interest in truly student driven projects and are curious to follow our team wiki for the next months.
