Team:KU Leuven/Notebook/Newsfeed

main

Research

Interlab

Modeling

Outreach

Future

Team

Notebook

main

Research

Interlab

Modeling

Outreach

Future

Team

Notebook

Show all

Newsfeed

Week 9: the 24^th-28^th of August

hide

-Ordered hoodies & T-shirts
-Collaboration: Skype with NAIT_Edmonton, Canada
-Contacting sponsors (new sponsor: Imec) & driving to sponsors for giving the sponsoring brochure

hide

-We finished the lab safety form

hide

-Because two colony of the devices containing the promoter J23117 did not give the expected bands after restriction mapping, we repeated our fluorescence and absorbance measurements with other colonies. In the end, all the selected colonies for the data analysis were confirmed by restriction mapping.
-Last week, we constructed the biobricks LuxI, LuxR and IlvE by performing a phusion high-fidelity tail-PCR on our gBlocks. This week, we digested our biobricks LuxI, LuxR and IlvE with BcuI and EcoRI and purified this with help of a GeneJET PCR Purification Kit of Thermo Fisher Scientific. We ligated this with cutted pSB1C3 by use of T4 ligase. The ligated plasmid was electroporated in E. cloni. After performing a colony PCR and restriction mapping, we concluded that the biobricks LuxR and IlvE were correct. So, we still need to repeat the construction of the LuxI biobrick.
-We transformed Ag43 originating from the iGEM 2015 kit in E. cloni. Thereafter, we made a liquid culture and mini prepped this.
-This Friday the Gibson Assembly was repeated, but this time a pUC19 vector was added. This vector was first modified by tail PCR in this way that the overhangs would match those of the gBlocks. This DNA was electroporated in E. cloni.

hide

-Meeting with PhD students from the lab of Jan Michiels
-Meeting with VSC (Vlaams Supercomputer centrum)
-First step in adding internal model to hybrid model
-Extending hybrid model with interaction

hide

-Organizing symposium
-Mailing schools to give a playful course about synthetic biology
-Inviting people for symposium
-Contacting possible panel members + moderator of the debate of the symposium

hide

-Adapting pages

hide

-Design the card game about synthetic biology
-Finishing touch of the bacteria-stickers for use in schools and as gadget
-Making funny images for our secret page on our wiki
-Design T-shirt & hoody images

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

hide

-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.

hide

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

hide

-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.

hide

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

hide

-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

hide

-Adapting pages
-Putting ‘Symposium’ page online

hide

-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

hide

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

hide

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

hide

-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

hide

-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

hide

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

hide

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

hide

-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

hide

-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

hide

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

hide

-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.

hide

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

hide

-Contact potential keynote speakers for the symposium

hide

-The History-page is online!

hide

-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

hide

-Plane tickets to Boston are booked
-Hotels Boston are booked
-We have two new sponsors: Eppendorf & LRD!

hide

-Make protocol for plasmid assembly
-Make protocol for leucine detection
-Make protocol for AHL detection
-Design & order primers for the Gibson Assembly Method

hide

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

hide

-The 2D models on 100 by 100 grid are working

hide

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

hide

-Modeling page online
-Adjust the description of the project

hide

-Making images for wiki team presentation
-Making images for wiki icons for subsections of the Newsfeed
-Making animation that represents our pattern forming bacteria

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

hide

-Meeting Toulouse team at 07/21/15 in Brussels

hide

-Search parameters necessary in mathematical model
-Design and order the designed plasmid gBlocks

hide

-Performing a PCR and gel electrophoresis to confirm that the kanamycin cassette has successfully been removed from ΔTar and make a stock of this new strain.
-Preparations for phage P1 lysate for making the double knock-out strains

hide

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

hide

-Looking for potential keynote speakers for the symposium
-Design flyer

hide

-Team page is added

hide

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

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

hide

-Construct plasmid
-Design & order primers for controlling the knock-out processes
-Research to an alternative knock-out technique for double knockouts

hide

-Calculation of transformation efficiency of competent cells (E. cloni)
-Order 3 knock-out strains (ΔTar, ΔTsr and ΔCheZ) & prepare a stock
-Order Chromobacterium violaceum CV026 transposon mutant for use in AHL detection & prepare a stock
-Removing the kanamycin resistance gene of the ΔTar by transforming a plasmid with recombinase gene

hide

-Making and adapting the 1D hybrid and continuous model to the conditions of the wet lab
-Making a simple 2D continuous model
-Thinking about true parameters
-Making a 1D model with pdepe in Matlab -Explore symbiology
-Making a 2D model with PDE toolbox in Matlab (not ready yet)

hide

-Preparing e-mail for symposium and contact possible key speaker

hide

-The description of our project is online

hide

-Make images for wiki

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

hide

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

hide

-Prepare LB agar medium
-Prepare competent cells (E. cloni) and test competency

hide

-Literature research into hybrid models
-Further work on single cell agent-based model
-Implemented simple one-dimensional hybrid model
-Explore PDE Toolbox
-Work on an implicit continuous model
-Try if it’s possible to simulate pattern formation of bacteria in COMSOL

hide

-Thinking of school projects for primary school and secondary school
-Thinking of symposium

hide

-Helping with images and layout of wiki
-Helping with images and brochure for sponsors

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

hide

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

hide

-Searching for strains and biobricks for our circuit

hide

-Set up GitHub
-Constructed simple single cell agent-based model
-Worked on an explicit discretization of a continuous model