Team:KU Leuven/Notebook/Newsfeed

Show all

Show all

Newsfeed

Week 12: the 14th-18th of September

team

hide

-Writing and constructing wiki pages.
-Our sweaters and T-shirts arrived!

team

hide

-Cloning our biobricks by use of the plasmid backbone originating from the InterLab Measurement Study. As a result,the biobricks CheZ-GFP, LuxI-His, LuxR-E and Ag43-YFP were obtained!
-Assembling the biobrick CheZ-GFP behind a strong promoter and RBS in order to characterize this biobrick.
-Assembling a strong promoter with GFP in order to compare the fluorescence to our library of promoters generated during the InterLab Measurement Study. Unfortunately the strong promoter was not green which indicates that the ligation did not work.
-Performing the OHHL quantification method and the leucine quantification method.

team

hide

-Making new continuous model simulation videos simulating each part of the model separately.

team

hide

-Working further on our educational card game about synthetic biology.

team

hide

-Our wiki game is online!

team

hide

-Graphical design of our wiki
-Design of our poster

Week 11: the 7th-11th of September

team

hide

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

team

hide

- Constructing the BioBricks LuxI-His, RBS-LuxI-His and CheZ-GFP, RBS-CheZ-GFP by high fidelity tail-PCR, digestion and ligation in pSB1C3
- Transforming these BioBricks in E. cloni, testing colonies by PCR and preparing for sequencing. The high fidelity PCR and cloning of other potential BioBricks was repeated.
- Making our strains ΔtarΔtsr and ΔtarΔcheZ electrocompetent
- Checking our colonies containing the assembled gBlocks by restriction mapping showed the presence of the original pUC19 vector in our samples. Treating the assembled gBlocks with DpnI should circumvent this since DpnI only cuts the methylated DNA.
- Digesting with DpnI eliminated the original pUC19 and not a single colony grew on the control plate transformed with plasmid only. Analysing the positive colonies showed presence of pUC19.

team

hide

- Hybrid model: implementing periodic boundary conditions
- Hybrid model: incorporating the first draft of the internal model into hybrid model
- Attendeding MATLAB webinar: Optimizing and Accelerating your MATLAB Code

team

hide

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

team

hide

- Writing texts for the Wiki
- Putting our 'Secret'-page online!

team

hide

- Working on the design of the sweaters

Week 10: the 31thAugust-6th of September

team

hide

- We have new sponsors: Gips Mineral, Genzyme and VWR!
- We kindly received gadgets from our sponsors to distribute in our goody bags for the Symposium
- Ordering our self-designed bacteria stickers

team

hide

- Miniprepping and analyzing the assembled gBlocks is showing the assembled plasmid, but also the presence of pUC19 used as template. Transformation of the gel-purified correct plasmid was done in E. Cloni
- In parallel, assembling LuxI with gBlocks 1+2+3 and gBlocks 5+6 with gBlocks 1+2+3 was conducted with colonies that did not contain any pUC. Analysis of the gel was not showing any sign of digestion.

team

hide

- Collaboration with Toulouse: diffusion in Comsol
- Implementation of cells algorithm for nearest neighbor search
- Optimization of the code
- Meeting with Dirk Roose
- Examining effects of different contributions to cell movement in hybrid mode

team

hide

- Making a presentation and writing the scenario for our symposium
- Arranging our symposium
- Working on an educational game about synthetic biology

team

hide

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

team

hide

- Designing our iGEM banner
- Designing our sweaters
- Adapting buttons of the wiki
- Designing the bacterium stickers of our promoter and supervisor
- Designing funny pictures for the secret page

Week 8: the 17th-21th of August

team

hide

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

team

hide

- Searching more information about lab safety
- Analyzing the results of the InterLab Measurement Study

team

hide

- Preparing electrocompetent cells
- Optimizing the tail PCR to make Biobricks
- Cloning the PCR products into pSB1C3, transforming the plasmids and screening of colonies to find the correct insert
- Transforming the devices for the Interlab Measurement Study
- Preparation of the standard curve based on fluorescein and measuring the fluorescence of the new devices
- Assembling the gBlocks using NEBuilder® HiFi DNA Assembly Master Mix and transforming the checked pcr products in electrocompetent E. cloni

team

hide

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

team

hide

- Contacting keynote speakers for the Symposium
- Organizing symposium
- Mailing schools to give a playful course about synthetic biology
- Deciding on the rules for a nice card game about synthetic biology

team

hide

- Adapting pages
- Putting ‘Symposium’-page online

team

hide

- Making informative images for the Research-page
- Making buttons for the wiki
- Designing bacteria-stickers for use in schools and as gadgets
- Continuing with the design of our sweaters
- Designing funny images for our secret page on the wiki

Week 7: the 10th-14th of August

team

hide

- Our flyers and sponsor brochures arrived!
- Conducting a survey about synthetic biology interviewing people on the street
- Working on a team song

team

hide

- Making a protocol for leucine detection
- Researching lab safety

team

hide

- Switching from transformation of chemocompetent cells to electroporation due to low efficiency for the Interlab Measurement Study
- Checking the intactness of other genes in the tar-tap-cheRBYZ operon by PCR
- Ordering NEBuilder to repeat the failed Gibson Assembly
- Making three BioBricks starting from our gBlocks by tail PCR and restriction digestion
- Ordering materials for leucine and AHL detection

team

hide

- Finishing implementation of the hybrid model I in 2D, including ADI scheme for PDE part
- Extending hybrid model II to 2D
- Running hybrid model simulations
- Finishing report Simbiology
- Contacting Toulouse team for collaboration
- Contacting professors for possible collaboration

team

hide

- Brainstorming about educational games

team

hide

- Putting our ‘Newsfeed’ & ‘Research’-page online!
- Implementing an EasySwitch button and a Lightbox

team

hide

- Making informative images for the ‘Research’-page
- Starting the design of sweaters
- Photoshopping funny images for our secret page

Week 6: the 3th-7th of August

team

hide

- We received lab material kindly provided by KOLO Instruments - Paulussen Freddy
- Searching hotels in Bordeaux for the iGEM Meetup France 2015
- Ordering folders and brochures

team

hide

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

team

hide

- Confirming the double knock-outs and checking the intactness
- Performing a motility test to verify the phenotypical change of knocking out cheZ
- Assembling the gBlocks using the Gibson Assembly Method
- Transforming E. cloni with the BioBricks J23101, I12504, J23106 and J23117 to participate in the iGEM 2015 Measurement Interlab Study.

team

hide

- Writing a report about Simbiology
- Extending the Hybrid Model to 2D

team

hide

- Contacting potential keynote speakers for the symposium

team

hide

- Putting the History-page online

team

hide

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

Week 5: the 27th-31th of July

team

hide

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

team

hide

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

team

hide

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

team

hide

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

team

hide

- 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

team

hide

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

team

hide

- 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 20th-24th of July

team

hide

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

team

hide

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

team

hide

- 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

team

hide

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

team

hide

- Inviting potential keynote speakers for the symposium

team

hide

- Adding the Team page

team

hide

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

Week 3: the 13th-17th of July

team

hide

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

team

hide

- 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

team

hide

- 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)

team

hide

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

team

hide

- Putting the description of our project online

team

hide

- Making images for the wiki

Week 2: the 6th-10th of July

team

hide

- 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)

team

hide

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

team

hide

- 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

team

hide

- First meeting about school projects
- Brainstorming about a symposium

team

hide

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

Week 1: the 1st-3th of July

team

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
- Taking a tour through our high tech bio laboratory
- Meeting with potential sponsor

team

hide

- Searching for strains and BioBricks for our circuit

team

hide

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

team

hide

- 'Coming soon' page is online

team

hide

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

Contact

Address: Celestijnenlaan 200G room 00.08 - 3001 Heverlee
Telephone: +32(0)16 32 73 19
Email: igem@chem.kuleuven.be