iGEM 2013 — Team TU-Eindhoven

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# Team:TU-Eindhoven/Notebook

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* [Home](/Team%3ATU-Eindhoven)
* [Team](/Team%3ATU-Eindhoven/Team)
* Project
  + [Abstract](/Team%3ATU-Eindhoven/Project)
  + [Project Description](/Team%3ATU-Eindhoven/Description)
  + [Background](/Team%3ATU-Eindhoven/Background)
  + [The Chassis](/Team%3ATU-Eindhoven/Chasis)
  + [Potential Contrast Agents](/Team%3ATU-Eindhoven/Production)
  + [Kill Switch](/Team%3ATU-Eindhoven/KillingMechanism)
  + [Applications](/Team%3ATU-Eindhoven/Applications)
  + Results
  + [Main Results](/Team%3ATU-Eindhoven/Results)
  + [Parts Submitted](/Team%3ATU-Eindhoven/Parts)
  + Outlook
  + [Future Steps](/Team%3ATU-Eindhoven/FutureProspects)
  + Others
  + [Attributions](/Team%3ATU-Eindhoven/Attributions)
  + [Collaboration](/Team%3ATU-Eindhoven/Collaboration)
  + [Achievements](/Team%3ATU-Eindhoven/Achievements)
* Wetlab
  + [Overview](/Team%3ATU-Eindhoven/Wetlab)
  + [Preparation](/Team%3ATU-Eindhoven/Preparation)
  + Lab Reports
  + [MRI Data Processing](/Team%3ATU-Eindhoven/MRIProcessing)
  + [Anaerobic FNR Testing](/Team%3ATU-Eindhoven/AnearobicTesting)
  + [CEST Agent Testing](/Team%3ATU-Eindhoven/CESTAgentTesting)
  + [Lab Journal](/Team%3ATU-Eindhoven/LabJournal)
* Drylab
  + [Summary](/Team%3ATU-Eindhoven/Modeling)
  + [Protein Selection](/Team%3ATU-Eindhoven/ProteinSelection)
  + Contrast Mechanism
  + [Decoy Sites](/Team%3ATU-Eindhoven/StochasticModel)
  + [FNR Dynamics](/Team%3ATU-Eindhoven/ODEModel)
  + [FNR Promotor](/Team%3ATU-Eindhoven/FNRPromotor)
  + [Integral Model](/Team%3ATU-Eindhoven/IntegralModel)
  + Bacteria in the Body
  + [Ganciclovir Distribution](/Team%3ATU-Eindhoven/PBPK)
  + [Time-kill Behavior](/Team%3ATU-Eindhoven/TimeKill)
* Safety
  + [Overview](/Team%3ATU-Eindhoven/Safety)
  + [Lab Safety](/Team%3ATU-Eindhoven/LabSafety)
  + [Public and Environmental Safety](/Team%3ATU-Eindhoven/PublicSafety)
  + [Biosafety Within iGEM](/Team%3ATU-Eindhoven/SafetyiGEM)
* Society
  + [Outreach](/Team%3ATU-Eindhoven/Outreach)
  + [Human Practice](/Team%3ATU-Eindhoven/Society)
* [Notebook](/Team%3ATU-Eindhoven/Notebook)

In this section you can find a small description of all the work we have done so far organized by the category it belongs to. For the journal of the wet lab, see our  [Lab Journal page](/Team%3ATU-Eindhoven/LabJournal "Team:TU-Eindhoven/LabJournal").

* [Feb-Apr](#Feb-Apr)
* [May](#May)
* [June](#June)
* [July](#July)
* [August](#August)
* [September](#September)
* [October](#October)

## Feb-Apr

Feb-Mar

* Background research

Mar-Apr

* Selection of topic
* Further research
* Selection of project

Apr-May

* Further research

## May

1-5 May

*General Activities*

* Regular team meeting
* Looking for sponsors
* Month planning

*Wetlab*

* Researching about the promoters
* Researching about the possible proteins for CEST imaging

*Drylab*

* Defining what needs to be modeled and what type of model is the most appropriate for it

6-12 May

*General Activities*

* Regular team meeting
* Looking for sponsors

*Wetlab*

* Researching and defining the killing mechanism

*Drylab*

* Starting the Molecular Dynamics model for the proteins selection.

13-19 May

*General Activities*

* Regular team meeting
* Looking for sponsors

*Wetlab*

* Defining the needed materials
* Defining the needed equipment

*Drylab*

* Continuing the Molecular Dynamics model for the proteins selection.

20-26 May

*General Activities*

* Regular team meeting
* Looking for sponsors

*Wetlab*

* Locating, booking and learning how to use the necessary equipment

*Drylab*

* Analyzing the results from the Molecular Dynamics model for the proteins selection and identifying the most useful proteins for CEST imaging
* Researching and defining the needed parameters for the analysis of the decoy sites through a stochastic simulations model

*Human Practices*

* Selecting a main project

27-31 May

*General Activities*

* Regular team meeting
* Looking for sponsors

*Wetlab*

* Locating, booking and learning how to use the necessary equipment

*Drylab*

* Starting the stochastic simulations for the analysis of the decoy sites

*Human Practices*

* Selecting a main project

## June

3-9 June

*General Activities*

* Regular team meeting
* Looking for sponsors
* Collaborating with Purdue iGEM team
* Planning month activities

*Wetlab*

* General construct design

*Drylab*

* Continuing the stochastic simulations for the analysis of the decoy sites

*Human Practices*

* Defining the structure of the fact checker project

10-16 June

*General Activities*

* Regular team meeting
* Looking for sponsors

*Wetlab*

* Protein design

*Drylab*

* Continuing the stochastic simulations for the analysis of the decoy sites

*Human Practices*

* Redacting the preliminary description and survey for collaborators of the fact checker project

17-23 June

*General Activities*

* Regular team meeting
* Looking for sponsors

*Wetlab*

* Final design of the constructs

*Drylab*

* Continuing the stochastic simulations for the analysis of the decoy sites

*Human Practices*

* Revising the preliminary description and survey for collaborators of the fact checker project

24-30 June

*General Activities*

* Regular team meeting
* Looking for sponsors

*Wetlab*

* Ordering the constructs
* Working on the protocols

*Drylab*

* Analyzing the results from the stochastic simulations for the analysis of the decoy sites

*Human Practices*

* Researching for facts and myths related to Synthetic Biology to be checked

## July

1-7 July

*General Activities*

* Regular team meeting
* Looking for sponsors
* Planning month activities

*Wetlab*

* Finalizing the protocols
* Planning lab schedule

*Drylab*

* Starting the ODE model for the analysis of the FNR promoter

*Human Practices*

* Researching for facts and myths related to Synthetic Biology to be checked

8-14 July

*General Activities*

* Regular team meeting
* Looking for sponsors
* Collaborating with Purdue iGEM team

*Drylab*

* Continuing the ODE model for the analysis of the FNR promoter

*Human Practices*

* Researching for facts and myths related to Synthetic Biology to be checked

15-21 July

22-28 July

*General Activities*

* Regular team meetings
* Looking for sponsors
* Collaborating with Purdue iGEM team

*Wetlab*

* Creating agar plates
* Transforming DNA
* Plating bacteria
* Making LB medium
* Creating small cultures
* DNA retention from cultures
* Nano-drop tests

*Drylab*

* Analyzing the results from the ODE model for the analysis of the FNR promoter

*Human Practices*

* Researching for facts and myths related to Synthetic Biology to be checked
* Sending the survey to collaborators

29-31 July

*General Activities*

* Regular team meetings
* Looking for sponsors

*Wetlab*

* Creating agar plates
* Transforming DNA
* Plating bacteria
* Making LB medium
* Creating small cultures
* DNA retention from cultures
* Nano-drop tests

*Drylab*

* Merging the stochastic simulations model for the decoy sites with the ODE model for the FNR promoter

*Human Practices*

* Researching for facts and myths related to Synthetic Biology to be checked

## August

1-4 August

*General Activities*

* Regular team meetings
* Looking for sponsors
* Working on outreach ideas

*Wetlab*

* Creating the Cultures
* Retaining the DNA
* Nanodrop Test

*Drylab*

* Merging the stochastic simulations model for the decoy sites with the ODE model for the FNR promoter
* Working on the pharmacokynetics model

*Human Practices*

* Researching for facts and myths related to Synthetic Biology to be checked
* Working on the fact checker web platform
* Redacting the first facts to be added on our fact checker platform

5-11 August

*General Activities*

* Regular team meetings
* Looking for sponsors
* Working on outreach ideas

*Wetlab*

* Creating the cultures
* Retaining the DNA
* Nanodrop test

*Drylab*

* Improving the merged model
* Making an ODE model of the decoy sites
* Working on the pharmacokynetics model

*Human Practices*

* Working on the fact checker web platform
* Preparing the instructions and example files for collaborating teams

12-18 August

*General Activities*

* Regular team meetings
* Looking for sponsors
* Working on outreach ideas
* Sharing our project with colleagues and faculty members

*Wetlab*

* Digestion
* Construct digestion
* Vector digestion
* PCR purification for the constructs
* PCR puricfication for the vectors
* Nanodrop results
* Continuing with the purification
* Vector purification
* Construct purification
* Ligation
* Preparing agar plates
* Transformation
* Plating
* Colony picking and PCR
* Culturing the ligation products

*Drylab*

* Sensitivity analysis of the merged model
* Estimating promoter rates
* Working on the pharmacokynetics model

*Human Practices*

* Working on the fact checker web platform

19-25 August

*General Activities*

* Regular team meetings
* Looking for sponsors
* Working on outreach ideas

*Wetlab*

* Colony picking and PCR
* Small cultures and preparation for protein expression
* Miniprepping new constructs
* Sequencing
* Trnasformation and plating
* Expressing samples
* Protein purification
* Determining protein concentration
* SDS analysis
* Performing the protein expression in an anaerobic environment
* MRI experiments

*Drylab*

* Working on the pharmacokynetics model

*Human Practices*

* Fact checker platform is up and running

26-31 August

*General Activities*

* Regular team meetings
* Looking for sponsors
* Contacting the media for outreach purposes
* Editing and sending our *Brick of knowledge* to the Copenhagen iGEM team for our collaboration with them.

*Wetlab*

* Expression cultures
* Anaerobic expression
* Protein expression
* Making the BioBricks
* SDS analysis
* BugBuster protocol
* SDS PAGE gel

*Drylab*

* Working on the pharmacokynetics model

*Human Practices*

* Editing the newly arrived revised "facts"

## September

2-8 Sept

*General Activities*

* Regular team meetings
* Looking for sponsors
* Contacting the media for outreach purposes
* Designing our team t-shirts

*Wetlab*

* Digesting samples
* Gel extraction purification
* PCR purification
* Nanodrop test
* Ligation
* Transformation
* Plating
* Colony picking and PCR
* Gel analysis

*Drylab*

* Working on the pharmacokynetics model last details

*Human Practices*

* Editing the newly arrived revised "facts"
* Designing promotional goodies for the *Synthetic Facts* website

9-15 Sept

*General Activities*

* Regular team meetings
* Looking for sponsors
* Contacting the media for outreach purposes

*Wetlab*

* Preparation for protein expression
* Preparation of LB medium
* Protein expression
* Making more BioBricks
* Preparation for CEST measurements
* Miniprepping
* PCR and PCR purification
* Gel extraction
* Re-digesting 1G70
* Ligation

*Drylab*

* Working on the update of the models on the wiki

*Human Practices*

* Editing the newly arrived revised "facts"
* Getting promotional goodies for the *Synthetic Facts* website

16-22 Sept

*General Activities*

* Regular team meetings
* Looking for sponsors
* Contacting the media for outreach purposes
* Designing the poster and the presentation

*Wetlab*

* Transformation and plating
* Colony picking and PCR
* Small cultures
* Miniprepping
* Preparing the BioBricks for shipment to Boston
* Making of samples for sequencing

*Drylab*

* Working on the update of the models on the wiki

*Human Practices*

* Editing the newly arrived revised "facts"

23-30 Sept

*General Activities*

* Regular team meetings
* Looking for sponsors
* Contacting the media for outreach purposes
* Designing the poster and the presentation

*Wetlab*

* Preparing the BioBricks for shipment once more due to an external issue with the shipment of the BioBricks
* Culturing bacteria
* Prepare bacteria for electroporation and perform electroporation
* Creating small samples
* Preparing LB medium

*Drylab*

* Working on the update of the models on the wiki

*Human Practices*

* Editing the newly arrived revised "facts"

## October

1-4 Oct

*General Activities*

* Regular team meetings
* Contacting the media for outreach purposes
* Adding the final touches to the poster and the presentation
* Adding final details to the wiki
* Adding last details on the judging form

*Wetlab*

* Protein purification
* SDS analysis
* Fluorescence analysis
* Filling in the characterization forms from our BioBricks on the registry

*Drylab*

* Double checking modeling content on the wiki

*Human Practices*

* Editing the newly arrived revised "facts"
* Making sure all the goodies for the Jamboree are good to go

7-13 Oct

*General Activities*

* Get ready for the European Jamboree!
* Have fun at the European Jamboree

14-20 Oct

*General Activities*

* Regular team meetings
* Looking for more sponsors
* Contacting the media for outreach purposes
* Improving the poster, presentation and wiki

*Wetlab*

* Preparing the anaerobic vessel
* Anaerobic Expression
* Sample Storage

*Drylab*

* Improving the model based on experimental data

*Human Practices*

* Analyzing and adding to the wiki the results from the poll we did during the European Jamboree.

21-27 Oct

*General Activities*

* Regular team meetings
* Adding final touches to the poster, presentation and wiki

*Wetlab*

* Preparing the Anaerobic Vessel
* Preparing for Aerobic Expression
* Semi-Anaerobic Expression
* Sample Analysis
* Purification
* Fluorescence Measurements
* SDS Gel and Western Blot Preparation
* Aerobic Expression
* Preparing MRI samples
* Sample purification
* EGFP Protein Analysis
* Running the SDS Gels
* Coomaaise Analysis
* Western Blot

*Drylab*

* Improving the model based on experimental data

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