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Week 11: the 7^th-11^th of September

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-On Monday, we had our ‘iGEM Symposium Day on Synthetic Biology, Cell Systems and Ethics in Biochemistry’.

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-We are constructing the BioBricks LuxI-His, RBS-LuxI-His, cheZ-GFP, RBS-cheZ-GFP, RBS-cheZ-GFP-RBS-PenI-Term-PpenI-RBS-RFP-Term by high fidelity tail-PCRn digestion and ligation in pSB1C3. We transformed these BioBricks in E. cloni and tested these colonies by PCR. The BioBrick RBS-cheZ-GFP-RBS-PenI-Term-PpenI-RBS-RFP-Term was confirmed by PCR and prepared for sequencing. The high fidelity PCR and cloning of other potential BioBricks was repeated.
-This week, we made our strains ΔtarΔtsr and ΔtarΔcheZ electrocompetent.
-Further, we would like to characterise a BioBrick. Therefore, we pasted RBS-cheZ-GFP after the promoter J23101. The idea is to test this BioBrick in a cheZ knock-out strain and to prove the presence of GFP.
-Our colonies containing the assembled gBlocks were checked by restriction mapping. The presence of the pUC vector in our samples made the restriction mapping complicated. This is why we chose to also investigate different samples who were treated with DpnI after the Gibson Assembly. The DpnI only cuts methylated DNA and thus only the original pUC. Unfortunately, the restriction mapping did not give the expected result.
-To have a backup plan, we also repeated the Gibson Assembly with pUC and the enzyme DpnI. After cloning and restriction mapping, we concluded that our sample contains only pUC.
-Our fourth gBlock is more or less 600 bp. To increase the amount and concentration of this gBlock, we performed a Phusion high fidelity PCR.

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-Hybrid model: implemented periodic boundary conditions
-Hybrid model: first draft of internal model incorporation into hybrid model
-Attended MATLAB webinar: Optimizing and Accelerating your MATLAB Code

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-Preparing games and presentations for school visits
-Visit the schools to teach children about synthetic biology
-Analyzing the results of our survey

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-Writing texts for on Wiki
-Our secret page is online!

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-Working on the design of the hoodies

Week 10: the 31^thAugust-6^th of September

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-We have new sponsors: Gips Mineral, Genzyme and VWR !
-We kindly received gadgets of our sponsors for use in our goody bag.
-Our bacteria-stickers are ordered

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-We obtained assembled gBlocks 1-2-3 and 5-6 in mini prepped form. On gel, we discovered that we have assembled gBlocks in pUC, but also a band at the height of pUC. We cut out the correct band, did a gel purification and transformed again.
-In parallel, we further tried to assemble gBlocks 1+2+3 with gBlock 4 by using two colonies who did not contain pUC. Later, we noticed by PCR that the assembly was not correct.
-We also tried to assemble gBlocks 1+2+3 with 5+6, this would give us the total plasmid for cell B. On gel, we saw that the restriction did not work. Probably, there was a problem with the restriction enzyme.

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-Collaboration with Toulouse: diffusion in Comsol
-Implementation of cells algorithm for nearest neighbor search
-Code optimization
-Meeting with Dirk Roose
-Examine effects of different contributions to cell movement in hybrid mode

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-Making presentation, scenario for our symposium.
-Practical arrangements for our symposium.
-Working on an educational game about synthetic biology

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-Adapting the team page: our mentors and advisors are online!
-Adapting our website for mobiles.
-Making a game for our secret pag.

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-Designing our iGEM banner
-Designing the print of our hoodies
-Adapting buttons of the wiki
-Designing the bacteria version of our promoter and supervisor
-Graphical design for the secret page

Week 8: the 17^th-21^th of August

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-We are in the track ‘New applications’
-Received offers for hoodies, stickers and tattoos
-Collaboration: Skype session with TU Delft
-Collaboration: Measure pH of tap water and river water & sending samples to the iGEM team of York
-Collaboration: Interviewed people on the street for chewing-gum survey of the iGEM team of Aix-Marseille Université
-We translated our survey in French for further distribution in Wallonie.

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-We searched more information about lab safety.
-We utilized literature to prepare our experiment of the InterLab Measurement Study.

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-This week we made electrocompetent cells. Their transformation efficiency is higher than that of chemocompetent cells, so they could be useful in making BioBricks and transforming our assembled gBlocks.
-We repeated the tail PCR of luxR. This time we performed a touchdown PCR in order to become more specific results.
-Our three BioBricks were purified by using a gel extraction kit. After this, we inserted our BioBricks in pSB1C3. The next step is screening colonies by PCR to find plasmids with the right insert.
-We made our devices for the InterLab Measurement Study by using the BioBrick Assembly Method. After this we transformed electrocompetent E. cloni with our devices. First we grew our cells under the recommended conditions of iGEM on plates and afterwards we made a liquid culture. On Friday, we made our standard curve based on fluorescein and we measured our devices.
-We used the NEBuilder® HiFi DNA Assembly Master Mix to assemble our gBlocks. After doing a PCR, we visualised our results on a gel. We obtained a positive result for gBlocks 5 and 6. So we transformed these assembled gBlocks in electrocompetent E. cloni. We checked our transformed gBlocks on PCR, but a confirmation by restriction mapping is still needed.

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-Meeting with Tim Odenthal
-Optimization of hybrid model code
-Implementation of cell-cell interactions, including repulsion as well as attraction

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-Contacting speakers for symposium
-Organizing symposium
-Mailing schools to give a playful course about synthetic biology
-We decided on rules for a nice card game about synthetic biology

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-Adapting pages
-Putting ‘Symposium’ page online

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-Making informative images for the Research-page
-Making buttons for the wiki
-Design bacteria-stickers for use in schools and as gadget
-Continue with the design of our hoodies
-Making funny images for our secret page on our wiki

Week 7: the 10^th-14^th of August

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-Our flyers and sponsor brochures arrived!
-Survey about synthetic biology with people in the street
-Working on a team song

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-Making a protocol for leucine detection
-Research about lab safety

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-The transformation of chemocompetent cells for the Interlab Measurement Study was not efficient, therefore we repeat this with electrocompetent cells. We grew the transformed cells overnight and performed a miniprep.
-To check if the operon of ΔtarΔcheZ is OK, we used a PCR to confirm that all the genes are present.
-After performing a PCR, there were no bands visible of the assembled gBlocks, probably we didn’t use enough Gibson Assembly Master Mix
-We started making three BioBricks starting from our gBlocks. We performed a high fidelity tail PCR to include the prefix and suffix in our BioBrick. The parts were digested and purified on a gel.
-We ordered materials for leucine and AHL detection

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-Finish implementing hybrid model I in 2D, including ADI scheme for PDE part
-Extend hybrid model II to 2D
-Run hybrid model simulations
-Finishing report Simbiology
-Contacting Toulouse team for collaboration
-Contacting professors for possible collaboration

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-Thinking of educational games
-Outreach: Put popular message about our project on Facebook and Twitter

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-Our ‘Newsfeed’ & ‘Research’-page are online!
-Implemented Lightbox and EasySwitch button

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-Making informative images for the ‘Research’-page
-Start with the design of hoodies
-Making funny images for our secret page

Week 6: the 3^th-7^th of August

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-We received lab material kindly given by KOLO Instruments - Paulussen Freddy
-Searching hotels in Bordeaux for the iGEM Meetup France 2015
-Folders and brochures are ordered

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-Writing protocol for AHL detection
-Writing abstract about literature on Wiki

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-Perform gel electrophoresis to confirm double knock-outs: 2 colonies of Δtar ΔcheZ and 4 colonies of Δtar Δtsr still had Δtar. This means we have our double mutants! We still need to check Δtar ΔcheZ to be sure the rest of the operon is still intact.
-We performed a motility test to verify the phenotypical change of knocking out cheZ
-Assembly of gBlocks by using the Gibson Assembly Method
-We decided to participate at the iGEM 2015 Measurement Interlab Study. Therefore we transformed E. cloni with the BioBricks J23101, I12504, J23106 and J23117.

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-Write report about Simbiology
-Extending Hybrid Model to 2D

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-Contact potential keynote speakers for the symposium

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-The History-page is online!

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-Making images for wiki-icons for subsections of the Newsfeed
-Making tattoo-images to use as gadget

Week 5: the 27^th-31^th of July

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- Booking plane tickets to Boston
- Booking hotels Boston
- Two new companies are sponsoring: Eppendorf & LRD!

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- Making the protocol for plasmid assembly
- Making the protocol for leucine detection
- Making protocol for AHL detection
- Designing & ordering primers for the Gibson Assembly Method

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- Making double knock-out strains by P1 transduction
- Performing PCR and gel electrophoresis to confirm correct double knock-outs

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- Finishing the 2D models on a 100 by 100 grid

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- Contacting potential keynote speakers for the symposium
- Making a survey about public perception of synthetic biology
- Mailing the Bordeaux iGEM team for the France Meetup 2015

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- Putting the Modeling page online
- Adjusting the description of the project

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- Designing images for wiki team presentation
- Designing images for wiki icons for subsections of the Newsfeed
- Designing animations that represent our pattern forming bacteria

Week 4: the 20^th-24^th of July

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- Meeting the Toulouse iGEM team on 07/21/2015 at ESI (Expo Science International) in Brussels

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- Searching parameters necessary in mathematical model
- Designing and ordering the designed plasmid in gBlocks

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- Checking the removal of the kanamycin cassette in the Δtar strain and make a stock of our successful knockout
- Preparing phage P1 lysate to make the double knock-out strains

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- Simulating cell A and cell B in SymBiology
- Looking for usable constants
- Adapting the 2D continuous model

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- Inviting potential keynote speakers for the symposium

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- Adding the Team page

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- Making images for wiki team presentation
- Designing the flyer
- Making images of animals with new patterns for the wiki

Week 3: the 13^th-17^th of July

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- Constructing the plasmids
- Designing & ordering primers for controlling the knock-out proces
- Researching an alternative knock-out technique for double knockouts

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- Calculating the transformation efficiency of competent E. cloni cells
- Ordering 3 knock-out strains (Δtar, Δtsr and ΔcheZ) & preparing a stock
- Ordering Chromobacterium violaceum CV026 transposon mutant for usage in AHL detection & preparing a stock
- Removing the kanamycin resistance gene of the Δtar strain by transforming a plasmid with recombinase gene

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- Making and adapting the 1D hybrid and continuous model to the conditions of the wet lab
- Making a simple 2D continuous model
- Implementing biologically relevant parameters
- Making a 1D model with pdepe in Matlab
- Exploring symbiology
- Making a 2D model with the PDE toolbox in Matlab (not ready yet)

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- Preparing e-mail for symposium and contacting possible keynote speakers

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- Putting the description of our project online

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- Making images for the wiki

Week 2: the 6^th-10^th of July

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- Discussion with modeling team: which parameters do they need?
- Searching experiments for quantification of specific proteins, small molecules and amino acids
- Deciding on promoters of the plasmid
- Constructing the plasmids
- Making a working scheme (strategy)

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- Preparing LB agar medium
- Preparing competent cells (E. cloni) and testing their competency

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- Researching literature about hybrid models
- Further working on single cell agent-based model
- Implementing a simple one-dimensional hybrid model
- Exploring PDE Toolbox
- Working on an implicit continuous model
- Trying to simulate pattern formation of bacteria in COMSOL

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- First meeting about school projects
- Brainstorming about a symposium

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- Designing images and layout of wiki
- Designing images and brochure for sponsors

Week 1: the 1^st-3^th of July

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- Lab safety training
- Discussing tasks and practical arrangements (tickets Boston)
- Taking photos to use in the brochure, on the wiki and for social media
- Taking a tour through our high tech bio laboratory
- Meeting with potential sponsor

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- Searching for strains and BioBricks for our circuit

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- Setting up GitHub
- Constructing a simple single cell agent-based model
- Working on an explicit discretization of a continuous model