Difference between revisions of "Team:KU Leuven/Notebook/Newsfeed"

  <div class="showall"><img src="https://static.igem.org/mediawiki/2015/a/a2/KU_Leuven_Wiki_Button_-_Show_all2.png" width="100%"></div>

     <div class="circle"></div> <h2>Week 12: the 14^th-18^th of September</h2>

<p>-Writing and constructing wiki pages. </br>

-Our sweaters and T-shirts arrived!</p>

 

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<p>-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!<br/>

-Assembling the biobrick CheZ-GFP behind a strong promoter and RBS in order to characterize this biobrick. <br/>

-Performing the OHHL quantification method and the leucine quantification method.</p>

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<p>-Making new continuous model simulation videos simulating each part of the model separately.</p>

 

 

 

 

 

 

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<p>- Constructing the BioBricks LuxI-His, RBS-LuxI-His and CheZ-GFP, RBS-CheZ-GFP by high fidelity tail-PCR, digestion and ligation in pSB1C3<br/>

- Transforming these BioBricks in <i>E. cloni</i>, testing colonies by PCR and preparing for sequencing. The high fidelity PCR and cloning of other potential BioBricks was repeated. <br/>

- Making our strains Δ<i>tar</i>Δ<i>tsr</i> and Δ<i>tar</i>Δ<i>cheZ</i> electrocompetent<br/>

- 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. <br/>

- 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. </p>

<p>- Hybrid model: implementing periodic boundary conditions <br/>

- Hybrid model: incorporating the first draft of the internal model into hybrid model <br/>

- Attendeding MATLAB webinar: Optimizing and Accelerating your MATLAB Code

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<p>- Updating Facebook & Twitter<br/>

- Adapting text of interview with Jo De Wachter</p>

<p>- Preparing games and presentations for school visits<br/>

- Visiting schools to teach children about DNA and synthetic biology<br/>

- Analyzing the results of our survey</p>

<p>- Writing texts for the Wiki<br/>

<p>- Working on the design of the sweaters

<p>- We are in the track ‘New applications’<br/>

- Receiving offers for sweaters, stickers and tattoos <br/>

- Collaboration: Skype session with TU Delft <br/>

- Collaboration: Measuring pH of tap water and river water & sending samples to the iGEM team of York <br/>

- Collaboration: Interviewing people on the street for chewing-gum survey of the iGEM team of Aix-Marseille Université <br/>

- Translating our survey in French for further distribution in Wallonie.

<p>- Searching more information about lab safety <br/>

- Analyzing the results of the InterLab Measurement Study</p>

<p>- Preparing electrocompetent cells<br/>

- Optimizing the tail PCR to make Biobricks <br/>

- Cloning the PCR products into pSB1C3, transforming the plasmids and screening of colonies to find the correct insert <br/>

- Transforming the devices for the Interlab Measurement Study <br/>

- Preparation of the standard curve based on fluorescein and measuring the fluorescence of the new devices <br/>

- Assembling the gBlocks using NEBuilder® HiFi DNA Assembly Master Mix and transforming the checked pcr products in electrocompetent <i>E. cloni</i> </p>

<p>- Meeting with Tim Odenthal <br/>

- Optimization of hybrid model code <br/>

- Implementation of cell-cell interactions, including repulsion as well as attraction</p>

<p>- Updating Facebook & Twitter <br/>

- Spreading the survey on social media & informing people about the symposium <br/>

- Appointment with Ilse Frederickx for KU Leuven press </p>

<p>- Contacting keynote speakers for the Symposium<br/>

- Organizing symposium <br/>

- Mailing schools to give a playful course about synthetic biology <br/>

- Deciding on the rules for a nice card game about synthetic biology </p>

<p>- Adapting pages <br/>

- Putting ‘Symposium’-page online</p>

<p>- Making informative images for the Research-page <br/>

- Making buttons for the wiki <br/>

- Designing bacteria-stickers for use in schools and as gadgets <br/>

- Continuing with the design of our sweaters <br/>

- Designing funny images for our secret page on the wiki </p>

<p>- Our flyers and sponsor brochures arrived!<br/>

- Conducting a survey about synthetic biology interviewing people on the street <br/>

- Working on a team song

<p>- Making a protocol for leucine detection <br/>

- Researching lab safety</p>

<p>- Switching from transformation of chemocompetent cells to electroporation due to low efficiency for the Interlab Measurement Study <br/>

- Checking the intactness of other genes in the tar-tap-cheRBYZ operon by PCR <br/>

- Ordering NEBuilder to repeat the failed Gibson Assembly <br/>

- Making three BioBricks starting from our gBlocks by tail PCR and restriction digestion <br/>

- Ordering materials for leucine and AHL detection </p>

<p>- Finishing implementation of the hybrid model I in 2D, including ADI scheme for PDE part <br/>

- Extending hybrid model II to 2D <br/>

- Running hybrid model simulations <br/>

- Finishing report Simbiology <br/>

- Contacting Toulouse team for collaboration <br/>

- Contacting professors for possible collaboration</p>

<p>- Updating Facebook & Twitter </p>

<p>- Brainstorming about educational games </p>

<p>- Putting our ‘Newsfeed’ & ‘Research’-page online! <br/>

- Implementing an EasySwitch button and a Lightbox</p>

<p>- Making informative images for the ‘Research’-page <br/>

- Starting the design of sweaters <br/>

- Photoshopping funny images for our secret page </p>

<p>- We received lab material kindly provided by KOLO Instruments - Paulussen Freddy <br/>

- Searching hotels in Bordeaux for the iGEM Meetup France 2015 <br/>

- Ordering folders and brochures</p>

<p>- Writing protocols for AHL detection <br/>

- Writing abstract about literature on Wiki</p>

<p>- Confirming the double knock-outs and checking the intactness <br/>

- Performing a motility test to verify the phenotypical change of knocking out <i>cheZ</i> <br/>

- Assembling the gBlocks using the Gibson Assembly Method <br/>

- Transforming <i>E. cloni</i> with the BioBricks J23101, I12504, J23106 and J23117 to participate in the iGEM 2015 Measurement Interlab Study.</p>

<p>- Writing a report about Simbiology <br/>

- Extending the Hybrid Model to 2D </p>

<p>- Updating Facebook & Twitter </p>

<p>- Contacting potential keynote speakers for the symposium  </p>

<p>- Putting the History-page online</p>

<p>- Making images for wiki-icons for subsections of the Newsfeed <br/>

- Making tattoo-images to use as gadgets </p>

<p>- Booking plane tickets to Boston<br/>

- Booking hotels Boston <br/>

- Two new companies are sponsoring: Eppendorf & LRD!</p>

<p>- Preparing the protocol for plasmid assembly <br/>

- Making the protocol for leucine detection <br/>

- Making protocol for AHL detection <br/>

- Designing & ordering primers for the Gibson Assembly Method</p>

<p>- Making double knock-out strains by P1 transduction <br/>

- Performing PCR and gel electrophoresis to confirm correct double knock-outs</p>

<p>- Finishing the 2D models on a 100 by 100 grid </p>

<p>- Updating Facebook & Twitter <br/>

- Mailing library for putting the iGEM display in the library</p>

<p>- Contacting potential keynote speakers for the symposium<br/>

- Making a survey about public perception of synthetic biology <br/>

- Mailing the Bordeaux iGEM team for the France Meetup 2015</p>

<p>- Putting the Modeling page online <br/>

- Adjusting the description of the project</p>

<p>- Designing images for wiki team presentation <br/>

- Designing images for wiki icons for subsections of the Newsfeed <br/>

- Designing animations that represent our pattern forming bacteria </p>

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

<p>- Searching parameters necessary in mathematical model <br/>

- Designing and ordering the designed plasmid in gBlocks</p>

<p>- Checking the removal of the kanamycin cassette in the Δ<i>tar</i> strain and make a stock of our successful knockout <br/>

- Preparing phage P1 lysate to make the double knock-out strains</p>

<p>- Simulating cell A and cell B in SymBiology<br/>

- Looking for usable constants<br/>

- Adapting the 2D continuous model </p>

<p>- Updating Facebook & Twitter <br/>

- Making understandable mail about our project for family and friends in English and Dutch<br/>

- Mailing for a possible collaboration with SVCE (Indian iGEM team) </p>

<p>- Inviting potential keynote speakers for the symposium</p>

<p>- Adding the Team page</p>

<p>- Making images for wiki team presentation <br/>

- Designing the flyer <br/>

- Making images of animals with new patterns for the wiki</p>

<p>- Constructing the plasmids <br/>

- Designing & ordering primers for controlling the knock-out proces <br/>

- Researching an alternative knock-out technique for double knockouts</p>

<p>- Calculating the transformation efficiency of competent <i>E. cloni</i> cells <br/>

- Ordering 3 knock-out strains (Δ<i>tar</i>, Δ<i>tsr</i> and Δ<i>cheZ</i>) & preparing a stock <br/>

- Ordering <i>Chromobacterium violaceum</i> CV026 transposon mutant for usage in AHL detection & preparing a stock <br/>

- Removing the kanamycin resistance gene of the Δ<i>tar</i> strain by transforming a plasmid with recombinase gene</p>

<p>- Making and adapting the 1D hybrid and continuous model to the conditions of the wet lab<br/>

- Making a simple 2D continuous model<br/>

- Implementing biologically relevant parameters <br/>

- Making a 1D model with pdepe in Matlab <br/>

- Exploring symbiology <br/>

- Making a 2D model with the PDE toolbox in Matlab (not ready yet)</p>

<p>- Updating Facebook & Twitter <br/>

- Contacting responsible people for adding a text of our iGEM project to the websites of our faculties<br/>

- Contacting the Toulouse 2015 iGEM team for a meetup at ESI (Expo Science International), Brussels on 07/21/2015 <br/>

- Interview with Jo De Wachter from the Science department</p>

<p>- Preparing e-mail for symposium and contacting possible keynote speakers</p>

<p>- Putting the description of our project online</p>

<p>- Making images for the wiki</p>

<p>- Discussion with modeling team: which parameters do they need?<br/>

- Searching experiments for quantification of specific proteins, small molecules and amino acids<br/>

- Deciding on promoters of the plasmid<br/>

- Constructing the plasmids<br/>

- Making a working scheme (strategy)</p>

<p>- Preparing LB agar medium <br/>

- Preparing competent cells (<i>E. cloni</i>) and testing their competency</p>

<p>- Researching literature about hybrid models<br/>

- Further working on single cell agent-based model<br/>

- Implementing a simple one-dimensional hybrid model<br/>

- Exploring PDE Toolbox<br/>

- Working on an implicit continuous model<br/>

- Trying to simulate pattern formation of bacteria in COMSOL</p>

<p>- Updating Facebook & Twitter with pictures and text of every individual team member <br/>

- Contacting responsible people for adding a text of our iGEM project to the websites of our faculties

<p>- First meeting about school projects <br/>

- Brainstorming about a symposium</p>

<p>- Designing images and layout of wiki <br/>

- Designing images and brochure for sponsors</p>

<p>- Lab safety training<br/>

- Discussing tasks and practical arrangements (tickets Boston)<br/>

- Taking photos to use in the brochure, on the wiki and for social media <br/>

- Taking a tour through our high tech bio laboratory <br/>

- Meeting with potential sponsor</p>

<p>- Searching for strains and BioBricks for our circuit</p>

<p>- Setting up GitHub <br/>

- Constructing a simple single cell agent-based model</br>

- Working on an explicit discretization of a continuous model</p>

<p>- Linking Facebook and Twitter</p>

<p> - 'Coming soon' page is online</p>

<p> - Designing images and layout of wiki <br/>

- Designing images and brochure for sponsors</p>

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