Team:Amsterdam/practices/results

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<h1>Human Practices: Results</h1>
<h1>Human Practices: Results</h1>
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<h4>Social scientist</h4>
<h4>Social scientist</h4>
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We started working on our human practice through a ‘crash course’ on SB and iGEM organized by the supervisors of the Amsterdam and Delft 2012 iGEM teams. One of our advisors, Wieke Betten, gave a lecture about the importance of ‘good’ incorporation of the societal context in the development of SB and embedding of SB in society. The key word from this presentation was valorization. The only way this can be achieved, she stated, was by early involvement of stakeholders and public in the design of a new scientific project. This lecture inspired us to outline a generic approach in human practice that could be applied not only to our present iGEM topics, the Cellular Logbook, but also to all future iGEM teams. Such a generic approach in human practice would reflect on the ethical, societal, safety and security issues concerning each specific project. Our Interactive iGEM research approach was born.
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We started working on our human practice through a ‘crash course’ on SB and iGEM organized by the supervisors of the Amsterdam and Delft 2012 iGEM teams. One of our advisors, [https://2012.igem.org/Team:Amsterdam/team/advisors#Wieke_Betten ''Wieke Betten''], gave a lecture about the importance of ‘good’ incorporation of the societal context in the development of SB and embedding of SB in society. The key word from this presentation was [https://2012.igem.org/Team:Amsterdam/practices/methods#Key_Concepts ''valorization'']. The only way this can be achieved, she stated, was by early involvement of stakeholders and public in the design of a new scientific project. This lecture inspired us to outline a generic approach in human practice that could be applied not only to our present iGEM topics, the Cellular Logbook, but also to all future iGEM teams. Such a generic approach in human practice would reflect on the ethical, societal, safety and security issues concerning each specific project. Our Interactive iGEM research approach was born.
<h4>Experts in biotechnology</h4>
<h4>Experts in biotechnology</h4>
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[[File:Amsterdam_practices_1.jpg|300px|right|thumb|Figure 1: Presenting our project in an early stage to the experts at the UvA]]
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[[File:Amsterdam_practices_1.jpg|300px|right|thumb|Presenting our project in an early stage to the experts at the UvA]]
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In the first month of our project we organized presentations at both universities (UvA and VU) and invited scientists from the departments of Molecular Cell Biology and the Swammerdam Institute for Life Sciences (SILS). During these presentations we explained how we wanted to realize our project, the Cellular Logbook. We proposed our designed molecular mechanisms of the Cellular Logbook to these experts. Although most feedback confirmed the neatness of our project design, we received some relevant feedback:
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In the first month of our project we organized presentations at both universities (UvA and VU) and invited scientists from the departments of [http://www.falw.vu.nl/nl/onderzoek/molecular-cell-biology/ ''Molecular Cell Biology''] and the [http://sils.uva.nl/ ''Swammerdam Institute for Life Sciences (SILS)'']. During these presentations we explained how we wanted to realize our project, the Cellular Logbook. We proposed our designed [https://2012.igem.org/Team:Amsterdam/project/molecular_design ''molecular mechanisms''] of the Cellular Logbook to these experts. Although most feedback confirmed the neatness of our project design, we received some relevant feedback:
* Low concentrations of IPTG may (1-100 µM) not enter the cell, because of the phenomenon called ‘inducer exclusion’. In this case, glucose transport leads to phosphorylation of a compound of the phosphotransferase system (PTS), which in turn blocks the lacY transporter of IPTG. During our experiments we prevented this from happening by using higher concentrations of IPTG.
* Low concentrations of IPTG may (1-100 µM) not enter the cell, because of the phenomenon called ‘inducer exclusion’. In this case, glucose transport leads to phosphorylation of a compound of the phosphotransferase system (PTS), which in turn blocks the lacY transporter of IPTG. During our experiments we prevented this from happening by using higher concentrations of IPTG.
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* The basal activity of the envisioned LacH promotor might result in background noise because of leaky expression of the methyltransferase.
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* The basal activity of the envisioned LacH promotor might result in background noise because of leaky expression of the methyltransferase. We tried to solve this problem by doing experiments with the [https://2012.igem.org/Team:Amsterdam/data/experimental#Reducing_basal_activity_of_the_LacH_promoter_using_LacIQ_E._Coli_strain: ''LacIQ strain of E.coli and by using the pBAD promotor.'']
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We tried to solve this problem by doing experiments with the LacIQ strain of E.coli and by using the pBAD promotor. (link to data page: ‘reducing basal activity…’)
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<h4>Innovation manager & Business developer</h4>
<h4>Innovation manager & Business developer</h4>
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Early in the stage of our project we realized that the Cellular Logbook had the potential to become a platform technology for synthetic biology. Although we could think of numerous different applications for our system in the future, none of these applications were really evident at the moment; our main focus was to get the proof of concept that our multi-signal sensing system would work. We did realize though, that we needed to have a clear story on how to present our project to all kinds of audiences.
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Early in the stage of our project we realized that the Cellular Logbook had the potential to become a [https://2012.igem.org/Team:Amsterdam/practices/methods#Key_Concepts ''platform technology''] for synthetic biology. Although we could think of numerous different applications for our system in the future, none of these applications were really evident at the moment; our main focus was to get the proof of concept that our multi-signal sensing system would work. We did realize though, that we needed to have a clear story on how to present our project to all kinds of audiences.
In order to get some advice on this, we went to talk to Willem Fokkema, innovation manager and business developer at the UvA Technology Transfer Office. Willem Fokkema is specialized in the applicability of knowledge and aiding life scientists to find commercial partners. We started of with an explanation of our project, after which he gave us some tips:
In order to get some advice on this, we went to talk to Willem Fokkema, innovation manager and business developer at the UvA Technology Transfer Office. Willem Fokkema is specialized in the applicability of knowledge and aiding life scientists to find commercial partners. We started of with an explanation of our project, after which he gave us some tips:
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* Concerning legal issues: he stated that we shouldn’t think about patenting until we would have a clear ‘product and application’ in mind. He proposed he would give us advice regarding patenting at a later stage of our project.
* Concerning legal issues: he stated that we shouldn’t think about patenting until we would have a clear ‘product and application’ in mind. He proposed he would give us advice regarding patenting at a later stage of our project.
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* In thinking of applications for your project, consider going through the list of Global Grand Challenges.
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* In thinking of applications for your project, consider going through the list of [http://www.millennium-project.org/millennium/challeng.html ''Global Grand Challenges''].
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We went through the list of 15 Global Grand Challenges and figured out for which points our Cellular Logbook system could provide a solution. Click here to see the results.
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We went through the list of 15 Global Grand Challenges and figured out for which points our Cellular Logbook system could provide a solution. Click [https://2012.igem.org/Team:Amsterdam/project/features_and_applications#Global_Challenges ''here''] to see the results.
<h4>Stakeholders in potential fields</h4>
<h4>Stakeholders in potential fields</h4>
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<h5>BioDetection Systems B.V (Amsterdam, The Netherlands)</h5>
<h5>BioDetection Systems B.V (Amsterdam, The Netherlands)</h5>
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We tried to further investigate the future potential of our system as a multi-sensor that could register different signals in the environment. In the light of this, we consulted BioDetection Systems b.v. (BDS). We spoke with dr. Bart van der Burg, Chief Scientific Officer at BDS b.v.
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We tried to further investigate the future potential of our system as a multi-sensor that could register different signals in the environment. In the light of this, we consulted [http://www.biodetectionsystems.com/ ''BioDetection Systems b.v. (BDS)'']. We spoke with dr. Bart van der Burg, Chief Scientific Officer at BDS b.v.
'''Bioassays'''<br\>
'''Bioassays'''<br\>
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BDS uses human and animal cells to detect compounds in samples, as a cheaper alternative to existing chemical screening methods. This is done by measuring the acute toxic effects of the compound on the cell instead of directly measuring the presence of the compound. Measured substances are: (I) aromatic carbon-hydroxides (dioxins) and (II) hormones. Dioxins are very stable and not metabolized by the cells that measure their toxic effects, hence easily measurable
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BDS uses human and animal cells to detect compounds in samples, as a cheaper alternative to existing chemical screening methods. This is done by measuring the acute toxic effects of the compound on the cell instead of directly measuring the presence of the compound. Measured substances are: (I) aromatic carbon-hydroxides (dioxins) and (II) hormones. Dioxins are very stable and not metabolized by the cells that measure their toxic effects, hence easily measurable using this technique. Hormones are sometimes metabolized by the chassis cells used, which affects the outcome of the measurement. European and international legislation concerning analytical chemistry is mostly directed at chemical measurements of dioxins, not the biological measurement.
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using this technique. Hormones are sometimes metabolized by the chassis cells used, which affects the outcome of the measurement. European and international legislation concerning analytical chemistry is mostly directed at chemical measurements of dioxins, not the biological measurement.
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'''Cons to bioassays'''<br\>
'''Cons to bioassays'''<br\>
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We summarized the molecular mechanism of the Cellular Logbook for Bart van der Burg and asked him if he could see advantages of a memory module in a multi-sensor system. Applications he could think of on the spot:
We summarized the molecular mechanism of the Cellular Logbook for Bart van der Burg and asked him if he could see advantages of a memory module in a multi-sensor system. Applications he could think of on the spot:
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* Forensics: Intrigued by the facet of time indication that is inherent to the Cellular Logbook, he thought of bacteria that would solve a crime, by inferring the time on which the criminal was at the crime scene. One major bottleneck would be that the crime scene would have to be supplied with bacteria containing the Cellular Logbook beforehand.
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* Forensics: Intrigued by the facet of [https://2012.igem.org/Team:Amsterdam/project/features_and_applications#Time_Indicator ''time indication''] that is inherent to the Cellular Logbook, he thought of bacteria that would solve a crime, by inferring the time on which the criminal was at the crime scene. One major bottleneck would be that the crime scene would have to be supplied with bacteria containing the Cellular Logbook beforehand.
* Control of compound emission at industrial sites (e.g. factory): he envisioned to place the bacteria at multiple locations around a factory site to get an idea where and when chemicals were released.
* Control of compound emission at industrial sites (e.g. factory): he envisioned to place the bacteria at multiple locations around a factory site to get an idea where and when chemicals were released.
'''Problems envisioned'''<br\>
'''Problems envisioned'''<br\>
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* Release of GMOs into the environment
* Release of GMOs into the environment
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<h5>Waternet (Amsterdam, the Netherlands)</h5>
<h5>Waternet (Amsterdam, the Netherlands)</h5>
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Ron van der Oost is a toxicologist at a Dutch water company, named Waternet. He is specialized in research on risks, effects and behavior of emerging substances in the water cycle. Waternet is the only company in the Netherlands that focuses on the whole water cycle. Waternet is responsible for cleaning wastewater, making water drinkable and monitor and clean surface water.
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Ron van der Oost is a toxicologist at a Dutch water company, named [https://www.waternet.nl/ ''Waternet'']. He is specialized in research on risks, effects and behavior of emerging substances in the water cycle. Waternet is the only company in the Netherlands that focuses on the whole water cycle. Waternet is responsible for cleaning wastewater, making water drinkable and monitor and clean surface water.
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[[File:Amsterdam_practices_2.jpg|300px|right|thumbs|Figure 2: Ron van Oost from waternet discussing possible project applications]]
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[[File:Amsterdam_practices_2.jpg|300px|right|thumbs|Ron van Oost from waternet discussing possible project applications]]
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Ron van der Oost was really interested in our multi-sensor idea. Right now they use 20 different sensors for different groups of compounds. These bioassays are not optimal. They are really expensive and it is hard to normalize the data (at what point does a certain concentration become toxic?). Therefore it is often
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Ron van der Oost was really interested in our multi-sensor idea. Right now they use 20 different sensors for different groups of compounds. These bioassays are not optimal. They are really expensive and it is hard to normalize the data (at what point does a certain concentration become toxic?). Therefore it is often necessary to get a toxicologist to look at the data from bioassays, what makes it even more expensive. He pointed out some crucial issues regarding the potential use of our Cellular Logbook:
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necessary to get a toxicologist to look at the data from bioassays, what makes it even more expensive. He pointed out some crucial issues regarding the potential use of our Cellular Logbook:
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* The output of our system would have to be easy to interpret.
* The output of our system would have to be easy to interpret.
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* He also put emphasis on the possibility to register concentrations of compounds, using our system. What concentrations can we measure?
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* He also put emphasis on the possibility to register concentrations of compounds, using our system. What [https://2012.igem.org/Team:Amsterdam/project/features_and_applications#Concentration_Indicator ''concentrations''] can we measure?
* The sensitivity of the multi-sensor has to be good; you don’t want the system to register the presence of a toxic compound only when the concentration of this toxin is already high.
* The sensitivity of the multi-sensor has to be good; you don’t want the system to register the presence of a toxic compound only when the concentration of this toxin is already high.
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* The sensor should be able to monitor it’s environment for quit some time; the system needs to be ‘up and running’; a lot of systems they use now can be in the water for weeks/months. The time-indicator is an interesting feature -> let the system be in the water for 4 weeks and register when a certain compound was registered.
* The sensor should be able to monitor it’s environment for quit some time; the system needs to be ‘up and running’; a lot of systems they use now can be in the water for weeks/months. The time-indicator is an interesting feature -> let the system be in the water for 4 weeks and register when a certain compound was registered.
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* What (groups of) compounds can we measure?
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* What groups of compounds can we measure?
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* Maybe most important: how do you want to put the GMO’s in the water? By using some sort of filter/membrane, where the bacteria can’t escape from, but can sense their environment. He mentioned passive sampling/samplers.
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* Maybe most important: how do you want to put the GMO’s in the water? By using some sort of filter, where the bacteria can’t escape from, but can sense their environment. He mentioned passive sampling.
'''Points of action'''
'''Points of action'''
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* Check which (20) compounds we could detect
* Check which (20) compounds we could detect
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<h4>Biosafety Officer</h4>
<h4>Biosafety Officer</h4>
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Some safety and security questions were already addressed during our talks with scientist and companies. But for a more extensive and fundamental way of addressing these kinds of issues, we contacted dr. Cécile van der Vlugt, from the National Institute of Public Health and the Environment (RIVM). She is specialized in the risk assessment of Genetically Modified Organisms (GMOs). We were interested in what she would think about a possible application and thereby controlled release of our Cellular Logbook into the environment.
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Some safety and security questions were already addressed during our talks with scientist and companies. But for a more extensive and fundamental way of addressing these kinds of issues, we contacted dr. Cécile van der Vlugt, from the [http://www.rivm.nl/ ''National Institute of Public Health and the Environment (RIVM)'']. She is specialized in the risk assessment of Genetically Modified Organisms (GMOs). We were interested in what she would think about a possible application and thereby controlled release of our Cellular Logbook into the environment.
'''Biosafety'''<br\>
'''Biosafety'''<br\>
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'''Points of action'''<br\>
'''Points of action'''<br\>
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Since our Cellular Logbook system contains genes of which there products have a role in genome rearrangements (the M.ScaI methyltranserase and a Zinc Finger), we included a little risk assessment (link to 2nd question in safety) in the design process of our Cellular Logbook.
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Since our Cellular Logbook system contains genes of which there products have a role in genome rearrangements (the M.ScaI methyltranserase and a Zinc Finger), we included a little [https://2012.igem.org/Team:Amsterdam/safety/questions ''risk assessment''] in the design process of our Cellular Logbook.
<h4>Human Outreach</h4>
<h4>Human Outreach</h4>
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We had two main goals concerning public engagement and human outreach:
We had two main goals concerning public engagement and human outreach:
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'''1. Introducing SB to the general public and engaging in a dialogue.'''
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'''1. Introducing SB to the general public and engaging in a dialogue.'''<br\>
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We approached a broad audience by:
We approached a broad audience by:
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* Featuring in a documentary that will be broadcasted next year in Germany, Belgium and the Netherlands.
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* Featuring in a [https://2012.igem.org/Team:Amsterdam/practices/results#Documentary ''documentary''] that will be broadcasted next year in Germany, Belgium and the Netherlands.
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* Participating on a national art, music and science festival, named Discovery Festival.
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* Participating on a national art, music and science festival, named [https://2012.igem.org/Team:Amsterdam/practices/results#Discovery_Festival ''Discovery Festival''].
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'''2. Creating awareness amongst students of the two universities of Amsterdam (UvA and VU).'''
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'''2. Creating awareness amongst students of the two universities of Amsterdam (UvA and VU).'''<br\>
Young, bright minded scientist earn to get acquainted with the exciting and promising field of SB. Especially, since we have noticed that only a little group of students in Amsterdam ever heard about SB and iGEM, we felt called upon to change this. We decided to do this in two ways:
Young, bright minded scientist earn to get acquainted with the exciting and promising field of SB. Especially, since we have noticed that only a little group of students in Amsterdam ever heard about SB and iGEM, we felt called upon to change this. We decided to do this in two ways:
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<h5>National iGEM Collaboration</h5>
<h5>National iGEM Collaboration</h5>
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[[File:Amsterdam_practices_3.jpg|300px|right|thumb|Meeting with the other Dutch teams to discuss the program of the Discovery Festival]]
We collaborated with the iGEM teams from Eindhoven, Wageningen and Groningen to make iGEM and SB feature in the program of Discovery Festival. During the summer we had several meetings with representatives from each collaborating iGEM team. During these sessions we discussed, together with the organization of the event, on how to incorporate SB into the program. All teams took their responsibility by providing and preparing part of the program. In addition, we divided all participating teams over the three locations, so that iGEM would be represented on all locations. Because of the excellent teamwork and effort, we were able to realize the following program:
We collaborated with the iGEM teams from Eindhoven, Wageningen and Groningen to make iGEM and SB feature in the program of Discovery Festival. During the summer we had several meetings with representatives from each collaborating iGEM team. During these sessions we discussed, together with the organization of the event, on how to incorporate SB into the program. All teams took their responsibility by providing and preparing part of the program. In addition, we divided all participating teams over the three locations, so that iGEM would be represented on all locations. Because of the excellent teamwork and effort, we were able to realize the following program:
'''The program'''
'''The program'''
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[[File:Amsterdam_practices_4.jpg|300px|thumb|Flyer for the Discovery Festival]]
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'''1. The SB-experience'''<br\>
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As main part of the program, people will experience the process of genetically modifying bacteria by following a 7-step workshop in an improvised laboratorial setting: From ordering DNA online, to implementing the perceivable characteristic into bacteria and showing the resulting bacteria on agar plate. Safety is of course a priority: no actual GMOs or E.coli will be used.
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'''1. The SB-experience'''
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'''2. The posters'''<br\>
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As main part of the program, people will experience the process of
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genetically modifying bacteria by following a 7-step workshop in an improvised laboratorial setting: From ordering DNA online, to implementing the perceivable characteristic into bacteria and showing the resulting bacteria on agar plate. Safety is of course a priority: no actual GMOs or E.coli will be used.
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'''2. The posters'''
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We have made a wall full of posters, on which several fictional and non-fictional iGEM-projects are shown. The goal of this is to give the people an idea of the potential of SB, but also to inspire them and see how they will react on this.
We have made a wall full of posters, on which several fictional and non-fictional iGEM-projects are shown. The goal of this is to give the people an idea of the potential of SB, but also to inspire them and see how they will react on this.
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'''3. What would you do with your own iGEM project?'''
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'''3. What would you do with your own iGEM project?'''<br\>
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After the experience, people are asked what they would do if they could start their own iGEM project. All these ideas are recorded on a video guestbook.
After the experience, people are asked what they would do if they could start their own iGEM project. All these ideas are recorded on a video guestbook.
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'''4. Tuur van Balen'''
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'''4. Tuur van Balen'''<br\>
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We invited [http://www.tuurvanbalen.com/ ''Tuur van Balen''], an artist who got heavily inspired by SB, to the Discovery Festival in Amsterdam. His work will prove to be a stimulus in introducing SB to the public.
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We invited Tuur van Balen, an artist who got heavily inspired by SB, to the Discovery Festival in Amsterdam. His work will prove to be a stimulus in introducing SB to the public.
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Because the event will take place after the wiki-freeze we are unable to show the results. Click [http://www.facebook.com/IgemAmsterdam2012 ''here''] to see a report of the festival!
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Because the event will take place after the wiki-freeze we are unable to show the results. On this link (link to discovery facebook?) you can see a report of the festival!
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<h5>Documentary</h5>
<h5>Documentary</h5>
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Together with the iGEM team from Delft, the Netherlands Institute for Neuroscience (NIN) and the Advanced Nano Characterization Center (ANCC) from Japan, we will feature in a documentary called Lab Life, by Belgian documentary maker Frank Theys. The documentary will show a portrait of the daily life around innovative scientific research projects. Moreover, the documentary will focus on responsible innovation by showing the projects through the perspective of a social scientist that follows these projects. By highlighting the aspects of CTA and MM, this documentary is the perfect extension of our Interactive iGEM research approach. Lab Life will be broadcasted next year on German, Belgian and Dutch television.
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[[File:Amsterdam_practices_5.jpg|300px|right|thumb|Frank Theys, the documentary maker]]
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Together with the iGEM team from Delft, the Netherlands Institute for Neuroscience (NIN) and the Advanced Nano Characterization Center (ANCC) from Japan, we will feature in a documentary called [http://www.savagefilm.be/documentary/LAB-LIFE ''Lab Life''], by Belgian documentary maker Frank Theys. The documentary will show a portrait of the daily life around innovative scientific research projects. Moreover, the documentary will focus on responsible innovation by showing the projects through the perspective of a social scientist that follows these projects. By highlighting the aspects of CTA and MM, this documentary is the perfect extension of our Interactive iGEM research approach. Lab Life will be broadcasted next year on German, Belgian and Dutch television.
<h5>Press releases</h5>
<h5>Press releases</h5>
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Press releases in magazines from UvA and VU: VU: http://www.advalvas.vu.nl/nieuws/op-naar-het-wk-synthetische-biologie
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'''Press releases in magazines from UvA and VU'''
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VU: [http://www.advalvas.vu.nl/nieuws/op-naar-het-wk-synthetische-biologie ''Ad Valvas'']
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UvA: Unfortunately not published yet.
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UvA: Folia. Unfortunately not published yet.
<h1>References</h1>
<h1>References</h1>

Latest revision as of 03:55, 27 September 2012