http://2014.igem.org/wiki/index.php?title=Special:Contributions/Meistefa&feed=atom&limit=50&target=Meistefa&year=&month=2014.igem.org - User contributions [en]2024-03-28T17:39:28ZFrom 2014.igem.orgMediaWiki 1.16.5http://2014.igem.org/Team:ETH_Zurich/teamTeam:ETH Zurich/team2015-04-12T20:41:12Z<p>Meistefa: </p>
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<div>{{:Team:ETH Zurich/tpl/head|Our Team}}<br />
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<center> <b> Welcome to our team page. We are a bunch of seven crazy and enthusiastic master students from Biology, Biotechnology, Bioinformatics, and Bioengineering backgrounds. Here, you'll find more information about each of us. <br />
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<grouppicture id="crazy"></grouppicture><br />
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<h4>That's us in the infamous BSSE Science Lounge.</h4><br />
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<article class="4u special"><br />
<claude></claude><br />
<header><br />
<h4><a href="#">Claude</a></h4><br />
</header><br />
<p><br />
<font size="3">Biomedical Engineering</font><br />
</p><br />
<p><br />
"I am addicted to COMSOL!"<br />
</p><br />
</article><br />
<article class="4u special"><br />
<elise></elise><br />
<header><br />
<h4><a href="#">Elise</a></h4><br />
</header><br />
<p><br />
<font size="3">Computational Biology and Bioinformatics</font><br />
</p><br />
<p><br />
"Life is beautiful!"<br />
</p><br />
</article><br />
<article class="4u special"><br />
<sumana></sumana><br />
<header><br />
<h4><a href="#">Sumana</a></h4><br />
</header><br />
<p><br />
<font size="3">Computational Biology and Bioinformatics</font><br />
</p><br />
<p><br />
"I hate parameters."<br />
</p><br />
</article><br />
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<div class="row"><br />
<article class="4u special" style="margin-left:13%"><br />
<maximilian></maximilian><br />
<header><br />
<h4><a href="#">Maximilian</a></h4><br />
</header><br />
<p><br />
<font size="3">Biotechnology</font><br />
</p><br />
<p><br />
"I want my bed and just to let you know: Hill functions are always wrong."<br />
</p><br />
</article><br />
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<article class="4u special" style="margin-left:4%"><br />
<daniel></daniel><br />
<header><br />
<h4><a href="#">Daniel</a></h4><br />
</header><br />
<p><br />
<font size="3">Biotechnology</font><br />
</p><br />
<p><br />
"It's slowly becoming urgent."<br />
</p><br />
</article><br />
</div><br />
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<div class="row"><br />
<article class="4u special" style="margin-left:13%"><br />
<nadine></nadine><br />
<header><br />
<h4><a href="#">Nadine</a></h4><br />
</header><br />
<p><br />
<font size="3">Biotechnology</font><br />
</p><br />
<p><br />
"Let's watch a unicorn <a href="http://www.youtube.com/watch?v=Sm368W0OsHo" style="color:#FF69B4"> video</a>!"<br />
</p><br />
</article><br />
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<article class="4u special" style="margin-left:4%"><br />
<stefanie></stefanie><br />
<header><br />
<h4><a href="#">Stefanie</a></h4><br />
</header><br />
<p><br />
<font size="3">Microbiology and Immunology</font><br />
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<p><br />
"I need some chocolate! Or cookies"<br />
</p><br />
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{{:Team:ETH_Zurich/team/end}}<br />
{{:Team:ETH Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:48:17Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article id='Reflection'></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This questions splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider as of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, sharing and thinking. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity and its emergence. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. A feature of living beings might be that they have emerging properties. This is what we experience as complex. 70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way. This fact may indicate cultural variation. The survey has taught us how complexity is perceived in the public. From our survey we can conclude that in our sample population an interest in complexity exists. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. Albeit we are surrounded by complexity, it is not easy for us to name and define it. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. This enabled us to broaden our horizons away from the complexity we are facing in our project to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners as their approaches to complexity were very diverse. Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. From the talk with the priest [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 J. Fuisz] we learnt that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and despair. According to [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 K. Chikkadi], a scientist working with mikro- and nano systems, and Mr. Veress, a philosophy teacher, complexity arises from simple phenomena. From [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 D. Garcia] we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“ We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
<br />
Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. In our [https://2014.igem.org/Team:ETH_Zurich/human/outreach outreach] part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:47:47Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article id='Reflection'></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This questions splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider as of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, sharing and thinking. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity and its emergence. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. A feature of living beings might be that they have emerging properties. This is what we experience as complex. 70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way. This fact may indicate cultural variation. The survey has taught us how complexity is perceived in the public. From our survey we can conclude that in our sample population an interest in complexity exists. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. Albeit we are surrounded by complexity, it is not easy for us to name and define it. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. This enabled us to broaden our horizons away from the complexity we are facing in our project to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners as their approaches to complexity were very diverse. Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. From the talk with the priest [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 J. Fuisz] we learnt that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and despair. According to [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 K. Chikkadi], a scientist working with mikro- and nano systems, and Mr. Veress, a philosophy teacher, complexity arises from simple phenomena. From [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 D. Garcia] we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“ We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. In our [https://2014.igem.org/Team:ETH_Zurich/human/outreach outreach] part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:46:30Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article id='Reflection'></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This questions splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider as of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, sharing and thinking. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity and its emergence. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. A feature of living beings might be that they have emerging properties. This is what we experience as complex.<br />
<br />
70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way. This fact may indicate cultural variation. <br />
<br />
The survey has taught us how complexity is perceived in the public. From our survey we can conclude that in our sample population an interest in complexity exists. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. Albeit we are surrounded by complexity, it is not easy for us to name and define it. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. This enabled us to broaden our horizons away from the complexity we are facing in our project to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners as their approaches to complexity were very diverse. Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. From the talk with the priest [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 J. Fuisz] we learnt that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and despair. According to [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 K. Chikkadi], a scientist working with mikro- and nano systems, and Mr. Veress, a philosophy teacher, complexity arises from simple phenomena. <br />
<br />
From [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 D. Garcia] we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“<br />
<br />
We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. <br />
In our [https://2014.igem.org/Team:ETH_Zurich/human/outreach outreach] part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:45:09Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article id='Reflection'></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This questions splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider as of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, sharing and thinking. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity and its emergence. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. A feature of living beings might be that they have emerging properties. This is what we experience as complex.<br />
<br />
70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way. This fact may indicate cultural variation. <br />
<br />
The survey has taught us how complexity is perceived in the public. From our survey we can conclude that in our sample population an interest in complexity exists. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. Albeit we are surrounded by complexity, it is not easy for us to name and define it. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. This enabled us to broaden our horizons away from the complexity we are facing in our project to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners as their approaches to complexity were very diverse. <br />
<br />
<br />
Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. <br />
<br />
<br />
Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. From the talk with the priest [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 J. Fuisz] we learnt that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and despair. According to [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 K. Chikkadi], a scientist working with mikro- and nano systems, and Mr. Veress, a philosophy teacher, complexity arises from simple phenomena. <br />
<br />
From [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 D. Garcia] we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“<br />
<br />
We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
In our [https://2014.igem.org/Team:ETH_Zurich/human/outreach outreach] part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:44:15Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article id='Reflection'></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This questions splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider as of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, sharing and thinking. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity and its emergence. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. A feature of living beings might be that they have emerging properties. This is what we experience as complex.<br />
<br />
70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way. This fact may indicate cultural variation. <br />
<br />
The survey has taught us how complexity is perceived in the public. From our survey we can conclude that in our sample population an interest in complexity exists. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. Albeit we are surrounded by complexity, it is not easy for us to name and define it. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. This enabled us to broaden our horizons away from the complexity we are facing in our project to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners as their approaches to complexity were very diverse. <br />
<br />
<br />
Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. <br />
<br />
<br />
Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. From the talk with the priest [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 J. Fuisz] we learnt that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and despair. According to [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 K. Chikkadi], a scientist working with mikro- and nano systems, and Mr. Veress, a philosophy teacher, complexity arises from simple phenomena. <br />
<br />
From [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 D. Garcia] we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“<br />
<br />
We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
In our outreach part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:30:20Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This questions splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider as of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, sharing and thinking. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity and its emergence. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. A feature of living beings might be that they have emerging properties. This is what we experience as complex.<br />
<br />
<br />
70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way. This fact may indicate cultural variation. <br />
<br />
<br />
The survey has taught us how complexity is perceived in the public. From our survey we can conclude that in our sample population an interest in complexity exists. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. Albeit we are surrounded by complexity, it is not easy for us to name and define it. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. This enabled us to broaden our horizons away from the complexity we are facing in our project to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners as their approaches to complexity were very diverse. <br />
<br />
<br />
The knowledge gained from our survey, the interviews and the thoughts about them in combination we wanted to share. Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. <br />
<br />
<br />
<br />
Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. From the talk with the priest we learnt that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and despair. <br />
From Dr. Chikkadi and also from Mr. Veress the philosophy teacher we learned that in their point of view complexity arises from simple phenomena. <br />
<br />
From Dr. Garcia we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“<br />
<br />
We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
In our outreach part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/adaptationTeam:ETH Zurich/human/essay/adaptation2014-10-18T03:16:34Z<p>Meistefa: /* Going further */</p>
<hr />
<div><html><article></html><br />
<br />
== Going further ==<br />
<br />
In this part, we analyze the methods we used to answer our human practice question. We hope that this analysis will provide iGEMers material to think about their policy and practice project. <br />
<br/><br />
<br/><br />
;'''Survey'''<br />
:The internet as a media allowed us to reach more than 800 persons willing to participate in our survey. We thank each participant for its support! We are also grateful for all the people that provided us with additional comments; no matter whether these were suggestions for publications to read, complaints about the complexity of the survey or encouraging words. <br />
<br />
<br />
:We called for other iGEM team's solidarity for the survey. The idea of winning a badge for the wiki was appealing to many of them. The teams were motivated to participate as often as time allowed, since we introduced a two badge system (a colorful badge for 20 answers and a golden badge for 50 answers). In fact, two teams, namely the [https://2014.igem.org/Team:Hannover iGEM team Hannover] and the [https://2014.igem.org/Team:SDU-Denmark iGEM team SDU Denmark], handed in more than 50 filled in surveys. We are impressed and grateful!<br />
<br />
:We did not define a target population, as we were too ambitious and wanted to cover all subgroups of society. However, the data set we collected is strongly biased towards students. It could be interesting to particularly design a survey concerning this part of the population.<br />
<br />
:Our goal was to learn more about the people's understanding of complexity and emergence. Even though our survey included spaces for own answers, most people chose one of the preformed answers. It would be interesting to encourage people to express themselves, so as to receive more individual answers. One option could be to ask people on the streets to answer one question, e.g.: "what is complexity for you?". Audio or video records of the interviews could be used to supplement the survey study. It would be strongly dependent on the country of investigation but it could give some unexpected insights on the topic. Moreover, it would give an occasion to increase awareness of the public on synthetic biology.<br />
<br />
;'''Interviews'''<br />
:First, we would like to thank every person that accepted to answer our questions.<br />
<br />
:As one of our goals was to investigate how complexity is taken into account in different fields, interviews seemed to be the best way to get a broad overview of different fields. We achieved to get seven personal and professional points of view about complexity. It was highly interesting to explore in details different conceptions of complexity in scientific and non-scientific fields.<br />
<br />
:An interesting interview is not self-evident. It is advisable to practice the dialogue before the real interview so as to make full use of the meeting with the interviewee. Recording the interviews could provide raw material of interest.<br />
<br />
;'''Outreach'''<br />
:We managed to have diverse outreach projects targeting several population groups, from high school students to elder people.<br />
<br />
:If outreach is an interesting task in itself, it could be advisable to stick to a more strictly defined theme or topic to be more consistent. For instance, focusing on activities for a certain age group or on media outreach through television, audio and newsletter could give a coherent whole and give rise to multiple interpretations.<br />
<br />
;'''Literature Work'''<br />
:Defining a question to answer is a difficult starting point. One has to screen literature hoping to find interesting, promising hints. Being mentored in the first part could avoid a team to go into a dead end.<br />
<br />
:As many iGEM teams we were extremely busy with our project. Reading of scientific literature on the topic of human practice is probably one of the first things to be missed out. Doing a weekly journal club on human practice could broaden the horizon of all team members and allow them to discover interesting new points of view.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:14:56Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This questions splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider as of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, sharing and thinking. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity and its emergence. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. A feature of living beings might be that they have emerging properties. This is what we experience as complex.<br />
<br />
<br />
70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way. This fact may indicate cultural variation. <br />
<br />
<br />
This survey has taught us how complexity is perceived in the public. From our survey we experienced that in our sample population interest in complexity exists. <br />
<br />
From our results we mainly got an indication of complexity in nature. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. This means the topic is present but not easily formulated. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. The discussions with experts enabled us to broaden our horizons away from the complexity we are facing in our daily life to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners were very diverse. <br />
<br />
<br />
The knowledge gained from our survey, the interviews and the thoughts about the two previous ones in combination we wanted to share. Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. <br />
<br />
<br />
<br />
Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. The interviews have especially made this point clear e.g. from the talk with the priest we found out that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and desperate. <br />
From Dr. Chikkadi and also from Mr. Veress the philosophy teacher we learned that in their point of view complexity arises from simple phenomena. <br />
<br />
From Dr. Garcia we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“<br />
<br />
We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
In our outreach part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:09:10Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How do people experience complexity? Which approaches do exist to approach complexity? How does complexity arise? Should people, scientists in particular, consider that subparts of a complex entity are mixed in a both ordered and unorganized way, and accept uncertainty? If yes, how can the uncertainty be taken into account? Or are simple parts strictly ordered, and complexity arises when these simple parts follow rules?”'''<br />
<br />
<br />
This question splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider and of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, thinking and sharing. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. <br />
<br />
<br />
70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way, which may indicate cultural variation. <br />
<br />
We are grateful for all the people that provided us comments in addition to the questions to answer. No matter whether these were suggestions for publications to read, complaints about the complexity of the survey or encouraging words. <br />
<br />
This survey has taught us how complexity is perceived in the public. From our survey we experienced that in our sample population interest in complexity exists. <br />
<br />
From our results we mainly got an indication of complexity in nature. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. This means the topic is present but not easily formulated. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. The discussions with experts enabled us to broaden our horizons away from the complexity we are facing in our daily life to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners were very diverse. <br />
<br />
<br />
The knowledge gained from our survey, the interviews and the thoughts about the two previous ones in combination we wanted to share. Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. <br />
<br />
<br />
<br />
Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. The interviews have especially made this point clear e.g. from the talk with the priest we found out that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and desperate. <br />
From Dr. Chikkadi and also from Mr. Veress the philosophy teacher we learned that in their point of view complexity arises from simple phenomena. <br />
<br />
From Dr. Garcia we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“<br />
<br />
We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
In our outreach part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/answerTeam:ETH Zurich/human/essay/answer2014-10-18T03:00:06Z<p>Meistefa: /* Our reflections */</p>
<hr />
<div><html><article></html><br />
== Our reflections ==<br />
This essay is the third of four pillars towards a better understanding of complexity. It brings elements from the survey, from the interviews, the outreach and from further reading together. Here, we reflect on how our project and science, in general, relate to these topics. <br />
<br />
<br />
Our human practice project was guided by the following questions:<br />
<br />
<br />
'''“How is complexity Should scientists consider that subparts of a complex entity are mixed in a both ordered and unorganized way, accept uncertainty, and try to take it into account? Or should they consider that parts are strictly ordered, and that complexity arises from simple parts by following rules?”'''<br />
<br />
<br />
This question splits up into two approaches. The first approach is needed to take into account uncertainty of intrinsic complexity of the parts we consider and of the environment. The second approach is necessary to understand the parts better in order to be able to predict results.<br />
<br />
<br />
On our way of answering the questions coming along with complexity we focused on four different components: Listening, discussing, thinking and sharing. <br />
<br />
<br />
The first component of listening was covered by a survey regarding complexity. We listened to the public and learned about the existing ideas of complexity and how people relate to it. Something that we have observed is a trend of increasing complexity when going from non-living objects to living beings. <br />
<br />
<br />
70% of the participants of our survey have shown an interest to simplify and try to understand complexity instead of avoiding it. Another phenomenon observed was the deviation between languages. Depending on the language spoken, complexity was judged in a different way, which may indicate cultural variation. <br />
<br />
We are grateful for all the people that provided us comments in addition to the questions to answer. No matter whether these were suggestions for publications to read, complaints about the complexity of the survey or encouraging words. <br />
<br />
This survey has taught us how complexity is perceived in the public. From our survey we experienced that in our sample population interest in complexity exists. <br />
<br />
From our results we mainly got an indication of complexity in nature. A point to consider is that often people are not forced to deal with complexity directly. A cell, a dog and a computer exist as items in our daily lives but most of us do not think about their complexity in relation to other items on a daily basis. This means the topic is present but not easily formulated. <br />
<br />
<br />
Our second component involved interviews with experts from different backgrounds. The discussions with experts enabled us to broaden our horizons away from the complexity we are facing in our daily life to the complexity faced by people of other backgrounds. This exchange has enriched our project, as the professional fields of the interview partners were very diverse. <br />
<br />
<br />
The knowledge gained from our survey, the interviews and the thoughts about the two previous ones in combination we wanted to share. Sharing as our fourth pillar was done in lectures at a high school where we aimed at explaining the fundamentals of synthetic biology and how it can be a way of approaching complexity. A science slam is defined as a scientific presentation competition where scientists present their topics in a predefined timeslot and in a funny, accessible way for the open public. <br />
<br />
<br />
<br />
Our human practice has shown us the diversity of approaches of addressing complexity in our daily lives, in our professional fields, in science and when encountering complex situations. The interviews have especially made this point clear e.g. from the talk with the priest we found out that in his opinion religion and believe help us to find a way away from complexity and towards God. Thus we can live a life in trust instead of confusion and desperate. <br />
From Dr. Chikkadi and also from Mr. Veress the philosophy teacher we learned that in their point of view complexity arises from simple phenomena. <br />
<br />
From Dr. Garcia we got the following input on the perception of complexity. „Complexity is a property of a system and it can be measured. It can be shown whether a system is complex or not: for a complex system, the sum of its elements is higher than each one of them independently in superposition.“<br />
<br />
We learned that it is often useful to simplify the complexity to obtain a more accessible approach. In the process of simplification we should not forget the relationship to reality. <br />
<br />
In our outreach part we experienced how important it is to break the complexity of the own down to make it accessible for a broader public. On our way of spreading the word of synthetic biology we had many enriching encounters. We met many different people and encountered the phenomenon already described in our survey. The people we met all showed interest in trying to simplify complex problems and a will to understand what seems complex in first place. <br />
<br />
<br />
We did not find a universal answer to the question guiding our human practice project. What we found are many different approaches to address complexity arising in many different fields. This project helped us to improve our understanding of complexity as a whole and how we could profit from this profound, interdisciplinary knowledge. <br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/adaptationTeam:ETH Zurich/human/essay/adaptation2014-10-18T02:55:21Z<p>Meistefa: /* Going further */</p>
<hr />
<div><html><article></html><br />
<br />
== Going further ==<br />
<br />
In this part, we analyze the methods we used to answer our human practice question. We hope that this analysis will provide iGEMers material to think about their policy and practice project. <br />
<br/><br />
<br/><br />
;'''Survey'''<br />
:The internet as a media allowed us to reach more than 800 persons willing to participate in our survey. We thank each participant for its support! <br />
<br />
:We called for other iGEM team's solidarity for the survey. The idea of winning a badge for the wiki was appealing to many of them. The teams were motivated to participate as often as time allowed, since we introduced a two badge system (a colorful badge for 20 answers and a golden badge for 50 answers). In fact, two teams, namely the [https://2014.igem.org/Team:Hannover iGEM team Hannover] and the [https://2014.igem.org/Team:SDU-Denmark iGEM team SDU Denmark], handed in more than 50 filled in surveys. We are impressed and grateful!<br />
<br />
:We did not define a target population, as we were too ambitious and wanted to cover all subgroups of society. However, the data set we collected is strongly biased towards students. It could be interesting to particularly design a survey concerning this part of the population.<br />
<br />
:Our goal was to learn more about the people's understanding of complexity and emergence. Even though our survey included spaces for own answers, most people chose one of the preformed answers. It would be interesting to encourage people to express themselves, so as to receive more individual answers. One option could be to ask people on the streets to answer one question, e.g.: "what is complexity for you?". Audio or video records of the interviews could be used to supplement the survey study. It would be strongly dependent on the country of investigation but it could give some unexpected insights on the topic. Moreover, it would give an occasion to increase awareness of the public on synthetic biology.<br />
<br />
;'''Interviews'''<br />
:First, we would like to thank every person that accepted to answer our questions.<br />
<br />
:As one of our goals was to investigate how complexity is taken into account in different fields, interviews seemed to be the best way to get a broad overview of different fields. We achieved to get seven personal and professional points of view about complexity. It was highly interesting to explore in details different conceptions of complexity in scientific and non-scientific fields.<br />
<br />
:An interesting interview is not self-evident. It is advisable to practice the dialogue before the real interview so as to make full use of the meeting with the interviewee. Recording the interviews could provide raw material of interest.<br />
<br />
;'''Outreach'''<br />
:We managed to have diverse outreach projects targeting several population groups, from high school students to elder people.<br />
<br />
:If outreach is an interesting task in itself, it could be advisable to stick to a more strictly defined theme or topic to be more consistent. For instance, focusing on activities for a certain age group or on media outreach through television, audio and newsletter could give a coherent whole and give rise to multiple interpretations.<br />
<br />
;'''Literature Work'''<br />
:Defining a question to answer is a difficult starting point. One has to screen literature hoping to find interesting, promising hints. Being mentored in the first part could avoid a team to go into a dead end.<br />
<br />
:As many iGEM teams we were extremely busy with our project. Reading of scientific literature on the topic of human practice is probably one of the first things to be missed out. Doing a weekly journal club on human practice could broaden the horizon of all team members and allow them to discover interesting new points of view.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/adaptationTeam:ETH Zurich/human/essay/adaptation2014-10-18T02:39:46Z<p>Meistefa: /* Going further */</p>
<hr />
<div><html><article></html><br />
<br />
== Going further ==<br />
<br />
In this part, we analyze the methods we used to answer our human practice question. We hope that this analysis will provide iGEMers material to think about their policy and practice project. <br />
<br/><br />
<br/><br />
;'''Survey'''<br />
:The internet as a media allowed us to reach more than 800 persons willing to participate in our survey. We thank each participant for its support! <br />
<br />
:We called for other iGEM team's solidarity for the survey. The idea of winning a badge for the wiki was appealing to many of them. The teams were motivated to participate as often as time allowed, since we introduced a two badge system (a colorful badge for 20 answers and a golden badge for 50 answers). In fact, two teams, namely the [https://2014.igem.org/Team:Hannover iGEM team Hannover] and the [https://2014.igem.org/Team:SDU-Denmark iGEM team SDU Denmark], handed in more than 50 filled in surveys. We are impressed and grateful!<br />
<br />
:We did not define a target population, as we were too ambitious and wanted to cover all subgroups of society. However, the data set we collected is strongly biased towards students. It could be interesting to particularly design a survey concerning this part of the population.<br />
<br />
:Our goal was to learn more about the people's understanding of complexity and emergence. Even though our survey included spaces for own answers, most people chose one of the preformed answers. It would be interesting to encourage people to express themselves, so as to receive more individual answers. One option could be to ask people on the streets to answer one question, e.g.: "what is complexity for you?". Audio or video records of the interviews could be used to supplement the survey study. It would be strongly dependent on the country of investigation but it could give some unexpected insights on the topic. Moreover, it would give an occasion to increase awareness of the public on synthetic biology.<br />
<br />
;'''Interviews'''<br />
:First, we would like to thank every person that accepted to answer our questions.<br />
<br />
:As one of our goal was to investigate how complexity is taken into account in different fields, interviews seemed to be the best way to get a broad overview on different fields. We achieved to get seven personal and professional points of view about complexity. It was interesting to explore in details different conceptions of complexity in scientific and non-scientific field.<br />
<br />
:A training to be a good interviewer could be an option to improve our method. Recording the interviews would provide raw material of interest.<br />
<br />
;'''Outreach'''<br />
:We managed to have diverse outreach projects targeting several population groups, from high school students to elder people.<br />
<br />
:If outreach is an interesting task in itself, it could be wise to add a global theme or topic to be more consistent. For instance, focusing on activities for a certain age group or on media outreach through television, audio and newsletter could give a coherent whole and give rise to multiple interpretations.<br />
<br />
;'''Literature Work'''<br />
:Defining a question to answer is a difficult starting point. One has to look through literature for pieces of information. Being mentored in the first part could avoid a team to go into a dead end.<br />
<br />
:As most of teams, we were overloaded with work, scientific literature reading. Doing one weekly journal club on human practice could broaden our visions and allow us to discover interesting points of view.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/adaptationTeam:ETH Zurich/human/essay/adaptation2014-10-18T02:33:38Z<p>Meistefa: /* Going further */</p>
<hr />
<div><html><article></html><br />
<br />
== Going further ==<br />
<br />
In this part, we analyze the methods we used to answer our human practice question. We hope that this analysis will provide iGEMers material to think about their policy and practice project. <br />
<br/><br />
<br/><br />
;'''Survey'''<br />
:The internet as a media allowed us to reach more than 800 persons willing to participate in our survey.<br />
<br />
:We called for other iGEM team's solidarity for the survey. The idea of winning a badge for the wiki was appealing to many of them. The teams were motivated to participate as often as time allowed, since we introduced a two badge system (a colorful badge for 20 answers and a golden badge for 50 answers).<br />
<br />
:We did not define a target population, as we were too ambitious and wanted to cover all subgroups of society. However, the data set we collected is strongly biased towards students. It could be interesting to particularly design a survey concerning this part of the population.<br />
<br />
:Our goal was to learn more about the people's understanding of complexity and emergence. Even though our survey included spaces for own answers, most people chose one of the preformed answers. It would be interesting to encourage people to express themselves, so as to receive more individual answers. One option could be to ask people on the streets to answer one question, e.g.: "what is complexity for you?". Audio or video records of the interviews could be used to supplement the survey study. It would be strongly dependent on the country of investigation but it could give some unexpected insights on the topic. Moreover, it would give an occasion to increase awareness of the public on synthetic biology.<br />
<br />
;'''Interviews'''<br />
:First, we would like to thank every person that accepted to answer our questions.<br />
<br />
:As one of our goal was to investigate how complexity is taken into account in different fields, interviews seemed to be the best way to get a broad overview on different fields. We achieved to get seven personal and professional points of view about complexity. It was interesting to explore in details different conceptions of complexity in scientific and non-scientific field.<br />
<br />
:A training to be a good interviewer could be an option to improve our method. Recording the interviews would provide raw material of interest.<br />
<br />
;'''Outreach'''<br />
:We managed to have diverse outreach projects targeting several population groups, from high school students to elder people.<br />
<br />
:If outreach is an interesting task in itself, it could be wise to add a global theme or topic to be more consistent. For instance, focusing on activities for a certain age group or on media outreach through television, audio and newsletter could give a coherent whole and give rise to multiple interpretations.<br />
<br />
;'''Literature Work'''<br />
:Defining a question to answer is a difficult starting point. One has to look through literature for pieces of information. Being mentored in the first part could avoid a team to go into a dead end.<br />
<br />
:As most of teams, we were overloaded with work, scientific literature reading. Doing one weekly journal club on human practice could broaden our visions and allow us to discover interesting points of view.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T02:19:03Z<p>Meistefa: /* Influence of human practice on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence of human practice on our scientific project ==<br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br />
<br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
<br />
<br />
In [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert2 town planning] it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia, a member of the research team of [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 Systems Design]. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
<br />
<br />
Unexplainable noise is jointly responsible for complexity. There might be ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi who studies [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 micro- and nanosystems] expressed this fact in a scientific context, while J. Fuisz highlighted the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 religious aspect] of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
<br />
<br />
To not get lost while interpreting experimental data, we followed the advice of the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert6 physicist and philosopher] E. Klein: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress, the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert1 philosophy teacher]. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
<br />
<br />
While [https://2014.igem.org/Team:ETH_Zurich/human/outreach/ spreading the word about synthetic biology] we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
<br />
<br />
Many participants of our [https://2014.igem.org/Team:ETH_Zurich/human/survey survey on emergence on complexity] encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T02:18:29Z<p>Meistefa: /* Influence of human practice on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence of human practice on our scientific project ==<br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
<br />
In [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert2 town planning] it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia, a member of the research team of [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 Systems Design]. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
<br />
Unexplainable noise is jointly responsible for complexity. There might be ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi who studies [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 micro- and nanosystems] expressed this fact in a scientific context, while J. Fuisz highlighted the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 religious aspect] of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
<br />
To not get lost while interpreting experimental data, we followed the advice of the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert6 physicist and philosopher] E. Klein: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress, the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert1 philosophy teacher]. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
<br />
While [https://2014.igem.org/Team:ETH_Zurich/human/outreach/ spreading the word about synthetic biology] we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
<br />
Many participants of our [https://2014.igem.org/Team:ETH_Zurich/human/survey survey on emergence on complexity] encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T02:18:03Z<p>Meistefa: /* Influence of human practice on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence of human practice on our scientific project ==<br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
<br />
In [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert2 town planning] it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia, a member of the research team of [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert3 Systems Design]. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
<br />
Unexplainable noise is jointly responsible for complexity. There might be ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi who studies [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert5 micro- and nanosystems] expressed this fact in a scientific context, while J. Fuisz highlighted the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert4 religious aspect] of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
<br />
To not get lost while interpreting experimental data, we followed the advice of the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert6 physicist and philosopher] E. Klein: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress, the [https://2014.igem.org/Team:ETH_Zurich/human/interviews/expert1 philosophy teacher]. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While [https://2014.igem.org/Team:ETH_Zurich/human/outreach/ spreading the word about synthetic biology] we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
<br />
Many participants of our [https://2014.igem.org/Team:ETH_Zurich/human/survey survey on emergence on complexity] encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T02:08:58Z<p>Meistefa: /* Influence on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence of human practice on our scientific project ==<br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
<br />
Unexplainable noise is jointly responsible for complexity. There might be ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
<br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T02:08:17Z<p>Meistefa: /* Influence on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence on our scientific project ==<br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
<br />
Unexplainable noise is jointly responsible for complexity. There might be ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
<br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T02:07:32Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the [https://2014.igem.org/Team:ETH_Zurich/expresults cross-talk]. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and 3D-printing followed by PDMS molding allowed us to use custom-designed [https://2014.igem.org/Team:ETH_Zurich/lab/chip millifluidic chips]. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As this [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, a reductionist approach was indispensable. Thus we tried to legitimate every assumption in a biological way. <br />
<br />
: Our modeling part focuses on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We used a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: The fact that randomness is a property of complex systems motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena.<br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]), thus to divide our systems into simpler submodules seemed obvious. We took the fact into account that the different levels of description can give several insights on how the systems work. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to explain the complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:57:30Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the [https://2014.igem.org/Team:ETH_Zurich/expresults cross-talk]. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and 3D-printing followed by PDMS molding allowed us to use custom-designed [https://2014.igem.org/Team:ETH_Zurich/lab/chip millifluidic chips]. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As this [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:56:49Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the [https://2014.igem.org/Team:ETH_Zurich/expresults cross-talk]. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and 3D-printing followed by PDMS molding allowed us to use custom-designed [https://2014.igem.org/Team:ETH_Zurich/lab/chip millifluidic chips]. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As this [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:55:52Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the [https://2014.igem.org/Team:ETH_Zurich/expresults cross-talk]. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and 3D-printing followed by PDMS molding allowed us to use custom-designed [https://2014.igem.org/Team:ETH_Zurich/lab/chip millifluidic chips]. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:55:20Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the cross-talk. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and 3D-printing followed by PDMS molding allowed us to use custom-designed [https://2014.igem.org/Team:ETH_Zurich/lab/chip millifluidic chips]. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:54:34Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the cross-talk. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and [https://2014.igem.org/Team:ETH_Zurich/lab/chip 3D-printing followed by PDMS molding] allowed us to use custom-designed millifluidic chips. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:54:16Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the cross-talk. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and [[https://2014.igem.org/Team:ETH_Zurich/lab/chip | 3D-printing followed by PDMS molding]] allowed us to use custom-designed millifluidic chips. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:53:51Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the cross-talk. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
<br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and [[https://2014.igem.org/Team:ETH_Zurich/lab/chip|3D-printing followed by PDMS molding]] allowed us to use custom-designed millifluidic chips. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:52:25Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
:At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments we could observe cross-talk between the different quorum sensing molecules. In a next step we focused on quantifying the cross-talk. We found interactions between the subparts (AHLs, AHL binding molecules and promoters) on different levels. The various ways of crosstalk are characteristics of a complex system with emerging features. The whole is more than the sum of its parts; living beings, even if not multicellular have various naturally emergent properties. <br />
:In fact the observation of emergence was one of the central topics of our project. The techniques of rapid prototyping and 3D-printing followed by PDMS molding allowed us to use custom-designed millifluidic chips. The chip with the alginate bead grid on it enabled us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. The design of our experiments aimed at the consideration of different interactive factors rather than a complete reduction of complexity. Since the knowledge of biological systems is limited such an approach seems to be nearby.<br />
:During our project we experienced that many times biological systems are not behaving as expected. While in some cases mistakes of the person planning or conducting the experiment were discovered, we could many times not localize a causation for the unexpected behavior. This taught us about the influence of parameters that have a priori not been taken into account or that are beyond our control. A cell is an open system that interacts with its environment; it is possible to reduce the number of factors influencing the system, but is not possible to eradicate them all.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:20:47Z<p>Meistefa: /* Complexity in our project */</p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
;'''Wet lab'''<br />
<br />
At the very beginning the work in the wet lab seemed straightforward. The way we planed our time was ambitious, but soon after the start we faced first problems. In different experiments cross-talk between our different quorum sensing molecules was observed. The next steps focused on quantifying this cross-talk, this was never achieved completely. Identifying interactions on the subparts (molecules) level of the cell in order to understand the whole system behavior.<br />
One of the central questions in our project was the observation of emergence. The techniques of rapid prototyping and 3D-printing followed by PDMS molding allowed us to use custom-designed millifluidic chips. The chip with the grid on it allowed us to observe the phenomenon of guided emergence. In this case we do not have a simplification but a contextualisation. In the design of our experiments, we took into account the different factors.<br />
Living beings, even if not multicellular have naturally emergent properties.<br />
While facing problems with our own constructs, especially to mention the integrases, we decided to attempt a reproduction of the logic XOR implemented in Bonnet paper.[9]. We faced many problems and on the way of trying to reproduce the experiments they did. On this way our team had many interesting discussions concerning the reproducibility of data in general and in this specific case.<br />
Another important lesson we have learned in the lab is the debugging constructs. Many times the biology did at first glance not work as expected. Further examination has then shown mistakes in the design, mistakes of the person conducting the experiment and also taught us about the influence of parameters that have a priori not been taken into account. The cell as open system which interacts with its environment.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T01:18:01Z<p>Meistefa: </p>
<hr />
<div><html><article></html><br />
== Influence on our scientific project ==<br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br/><br />
<br/><br />
<br/><br />
'''Wet Lab'''<br />
<br/><br />
<br/><br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
<br />
Unexplainable noise is jointly responsible for complexity. There might ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
<br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:17:01Z<p>Meistefa: </p>
<hr />
<div><html><article></html><br />
== Complexity in our project ==<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/projectTeam:ETH Zurich/human/essay/project2014-10-18T01:16:07Z<p>Meistefa: Created page with "<html><article></html> == Complexity in our project == <html><article></html>"</p>
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<div><html><article></html><br />
== Complexity in our project ==<br />
<br />
<html><article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essayTeam:ETH Zurich/human/essay2014-10-18T01:14:58Z<p>Meistefa: </p>
<hr />
<div>{{:Team:ETH Zurich/tpl/head|Our insights}}<br />
<br />
{{:Team:ETH_Zurich/human/essay/answer}}<br />
<br />
{{:Team:ETH_Zurich/human/essay/project}}<br />
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{{:Team:ETH_Zurich/human/essay/influence}}<br />
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{{:Team:ETH_Zurich/human/essay/adaptation}}<br />
<br />
{{:Team:ETH Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T01:11:30Z<p>Meistefa: /* Influence on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence on our scientific project ==<br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br/><br />
<br/><br />
<br/><br />
'''Wet Lab'''<br />
<br/><br />
<br/><br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
Unexplainable noise is jointly responsible for complexity. There might ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T01:11:08Z<p>Meistefa: /* Influence on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence on our scientific project ==<br />
<br/><br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br/><br />
<br/><br />
<br/><br />
'''Wet Lab'''<br />
<br/><br />
<br/><br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
Unexplainable noise is jointly responsible for complexity. There might ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T01:10:43Z<p>Meistefa: /* Influence on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence on our scientific project ==<br />
<br/><br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br/><br />
<br/><br />
<br/><br />
<br/><br />
'''Wet Lab'''<br />
<br/><br />
<br/><br />
<br/><br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
Unexplainable noise is jointly responsible for complexity. There might ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T01:10:24Z<p>Meistefa: /* Influence on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence on our scientific project ==<br />
<br/><br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br/><br />
<br/><br />
'''Wet Lab'''<br />
<br/><br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
Unexplainable noise is jointly responsible for complexity. There might ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/essay/influenceTeam:ETH Zurich/human/essay/influence2014-10-18T01:09:56Z<p>Meistefa: /* Influence on our scientific project */</p>
<hr />
<div><html><article></html><br />
== Influence on our scientific project ==<br />
<br/><br />
<br/><br />
As soon as we agreed on a subject for our iGEM project, we started to observe patterns and complexity all among us. Our awareness of structures and compositions, as well as exchange and interaction between subunits, continuously increased. It quickly became a running gag among us to say: "Anyway, it is too complex". <br />
<br />
Here we aim at describing the influence human practice had on our scientific project. Our human practice part is intricately linked to our scientific project, since we investigated in a philosophical and sociological way the concepts we tried to reproduce biologically: The emergence of a complex pattern from simple rules. By analyzing complexity and pattern formation in depth, we learned new strategies to approach them. Our human practice project allowed us to consider our scientific project from different points of view. <br />
<br />
'''Wet Lab'''<br />
In our human practice project we interviewed experts of different fields, conducted a survey and sought to outreach our experience and knowledge. Thereby we learnt new strategies of how to approach complexity, but also ways to handle it. Furthermore, we found a source of motivation and reinforcement in our human practice project.<br />
In town planning it is crucial to not reduce a problem too much. Otherwise, the architectural intervention will be an isolated and foreign object in its surrounding. Such interventions have a high risk to fail, explained D. Übelhör. As urban systems, biological systems are highly complex. In order to understand them we tend to reduce them to single subunits. However, reductionist approaches run the risk of neglecting important information, especially when transferring behavior of subunits to the behavior of the whole. That is also what we learnt from D. Garcia. He pointed out that in some situations reductionism is not only an unsuitable strategy but also unnecessary at the same time. Why should one struggle with details if they cannot explain the entity? <br />
Unexplainable noise is jointly responsible for complexity. There might ways to reduce the noise and thus increase the predictability of systems, however, we have to accept that we do not know everything. K. Chikkadi expressed this fact in a scientific context, while J. Fuisz highlighted the religious aspect of acceptance. The trust in a higher power helps to overcome complexity. Of course, this cannot be transferred to a research project literally. Anyhow, to accept that there is no human omnipotence can protect from frustration. We cannot - but we also do not have to - solve all complexity. <br />
To not get lost while interpreting experimental data, we followed E. Klein’s advice: we limited our ambitions in order to become efficient. Many times it is advisable to proceed in small steps rather than aiming at the full monty immediately. However, pedantic planning is always highly important especially when dealing with complexity, emphasized C. Veress. Looking back on the past weeks and months we can only agree with that. Spending time with planning instead of rushing quite often saves time, money and work.<br />
While spreading the word about synthetic biology we experienced the importance of a simple, comprehensible language. In fact, good communication and articulation is crucial for functional teamwork. Explaining concepts to high school students, interested visitors at the open house or during a science slam increased our awareness of the importance of communication and trained our skills at the same time.<br />
Many participants of our survey encouraged us in our research project. They agreed on the importance of analyzing complexity and the emergence of patterns. We were very happy to get such a positive feedback and motivated to continue our studies.<br />
<br />
<br />
;'''Modeling'''<br />
: A model is always a simplistic representation of reality. It contains assumptions. Using standard descriptions, like chemical reactions and mass action, we analytically derived each formula we wanted to fit. This derivation was only possible thanks to some assumptions. As these [https://2014.igem.org/Team:ETH_Zurich/modeling/int page] shows, every assumption was carefully made and thought about. The process of simplification was put into question because our human practice project tends to investigate why simplification is powerful but not enough to understand the surrounding world. In our case, simplifying was necessary. That's why we tried to understand what every assumptions could make sense in a biological way. <br />
<br />
: Our modeling part is focused on parameter fitting (see our [https://2014.igem.org/Team:ETH_Zurich/modeling/parameters parameter page]). We use a classical deterministic model and tried to fit it to the experiments. Matching the reality level with the description level is a complicated task, as there is no optimal match. Differences and similarities between experiments and simulations give insights on where emergent phenomena could happen.<br />
<br />
: As randomness is a property of complex systems, it motivated us to derive a stochastic model. Some biological events, like binding, are typically stochastic phenomena. The human practice part inspired us in a certain sense. <br />
<br />
: We opted for an engineered representation (see the [https://2014.igem.org/Team:ETH_Zurich/project/infopro information processing page]). It was natural to divide our systems into submodules. Thus, we took into account the fact that different levels of description can give several insights on the system works. The decomposition into interacting submodules (see the [https://2014.igem.org/Team:ETH_Zurich/modeling/overview modeling overview page]) was crucial to face this complex problem.<br />
<br />
<html></article></html></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/human/interviews/expert7Team:ETH Zurich/human/interviews/expert72014-10-17T23:09:40Z<p>Meistefa: /* Is complexity linked to Emergence? */</p>
<hr />
<div>{{:Team:ETH_Zurich/tpl/head|Interview with PD Dr. Harald Atmanspacher}}<br />
<br />
<html><article></html><br />
<br />
''Harald Atmanspacher is an associate fellow at Collegium Helveticum. His fields of research are theory of nonlinear dynamical systems and complex systems, conceptual and theoretical aspects of (algebraic) quantum theory and mind-matter relations from interdisciplinary perspectives.''<br />
<br />
===There are various definitions of complexity. Most of the time, the notion of system is mentioned in those definitions. Would you say that complexity is a property of a system? ===<br />
<br />
I would say that complexity is not a property, but a characterization of a system. The next question is what could be the defining criterion for this characterization. At some point, people tried to come up with formal definitions of what complexity could actually be and how it can be measured quantitatively. Before that happened, for a long time, for decades actually, people were talking about complex systems in a colloquial sense. What you’ll find in literature is criteria like, for instance: “The coupling of a system with its environment is important for the behavior of the system” (open systems), “Many complex systems have a lot of constituents” (Nevertheless, we can find complex systems with a small number of degrees of freedom, for example in deterministic chaos). What you need for complexity is non-linear behavior, non-linear feedback. Another criterion that some people use is that you are dealing with systems far from thermal equilibrium. In biology, you are typically far from the thermal equilibrium. Another feature of complex systems is their intrinsic instability, which makes it difficult or impossible to treat their behavior as stationary. <br />
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=== Can one measure complexity quantitatively? ===<br />
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The first attempt to really define complexity in more rigorous way was already happening in the 1960s, it was done not by physicists but by mathematicians. Kolmogorov and others had a definition of complexity that has later been called “algorithmic complexity”. When you have a pattern and want to measure its complexity, their approach was the following: if you construct an algorithm that you can run on a computer, then the length of the shortest algorithm that is capable of reproducing the pattern is the algorithmic complexity of the pattern. If you have a completely regular pattern, like a period 2 process, this is a short algorithm and the complexity is low. On the other hand, if you construct your pattern as a random sequence of black and white pixels, then the shortest algorithm to reproduce that is the sequence of pixels. So that is the longest algorithm in relation to the pattern itself that you can imagine. It will be the pattern with the highest complexity score. There was a point of criticism that was quickly raised: in this sense, complexity is indeed nothing else than randomness. Then, the question is: why do we need two different names for the same phenomenon? In the 1980s, people came up with a different view point. The intuition was: if you have a completely regular behavior, that is not complex anyway but, if you only have a completely random behavior, this should also not be called complex. What should be called complex is an intricate mixture between random and regular elements in your pattern. <br />
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This is a basic distinction between two different general categories of complexity measures: one of them just being a measure of randomness, the other one characterizing the mixture between order and randomness. <br />
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In a review paper back in the 1990s, we reviewed all the complexity measures that existed at that time(more than 40). We tried to identify to which class they belong and how they behave on the basis of a very simple example, an artificial example: the so-called logistic map. The logistic map is a discrete recursive map. That means that you have a starting value x. The value of x at the next step is given by rx(1-x). It is a very simple map. It is a nice example because it is very simple on the one side and on the other side; it exhibits quite a lot of complicated, complex if you prefer, dynamics. <br />
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=== What were the results of your review? ===<br />
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First of all, we had a distinction between monotonic and convex measures. Then, within these categories, there are multiple different definitions of complexity and they all react to different features of the logistic map in different ways. <br />
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For instance, take the epsilon-machine complexity. That is a very sophisticated and powerful measure. That’s worth knowing. So far as I know, it is the only measure of complexity that is embedded in a very comprehensive theoretical background. The person who originally developed this was Jim Crutchfield. He was one of the pioneers in chaos theory in the 1980s. <br />
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In a way, all the other people including ourselves, just tried to identify certain measures of complexity that we thought would be interesting for a particular purpose but we did not care about a theoretical framework for them. Finally, if you are interested in identifying certain kinds of instabilities in a system, particular measures serve this purpose best but they are maybe not very sensitive to other features, like identifying periods. <br />
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===Is complexity linked to Emergence? ===<br />
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Yes, because that’s another one of these colloquial features of complexity. Complex systems often have a hierarchical structure. So you have levels of description. For instance, you can describe complex systems in terms of individual constituents, like individual neurons in the brain. Then, you also have other levels of description: for instance, the level at which neural assemblies are formed. Then, these neural assemblies often have properties, some people call them emergent properties, which you cannot simply derive from their constituents unless you know something about the collective level. In physics, when you study the relationship of individual molecules in a box of gas and the thermodynamic behavior, temperature is, of course, not a property of single molecules. In this sense, it is also an emergent property and much has been written about that example. <br />
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Emergence is very intensely discussed in the context of complex systems. Another issue that is more and more discussed in the context of complex systems is the issue of reproducibility of certain results or experiments.<br />
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=== Why are complex systems most of time not reproducible? Is it due to the subjectivity of the observer that has to be taken into account? ===<br />
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That is one issue but I think even more basic is the intrinsic instability of complex systems. When you have unstable behavior, what usually happens is that systems search their sample space in such a way that they end up relaxing into stable attractors. But in complex systems, this can take an enormously long time. There are lots of studies which started in 1990s about these super-transients. The behavior of your complex system can remain transient. This means that your complex system does not reach the stationary regime for an extremely long time. Whenever you are still in the transient phase and you try to reproduce something, you fail, because of the instability. If you know a little bit more about your system then you may be able to calculate with certain tools the time that it takes for the system to become stationary and that helps you. Then you can say: “To achieve reproducible results, I have to wait that much time”. But if you don’t have this knowledge, then you are completely lost. <br />
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Most of the research results we are talking about are a few decades old. Was there an evolution in the field of complexity this past few years or has the research on complexity attained a bottleneck? <br />
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I think there was a very decisive point in time in the study of complexity. That was when people could buy for not so much money high-power computing system. The reason is obvious. You cannot analytically solve complex systems in most cases and if you really want to study them, you have to run them in simulation studies. Everything that happened before the late 1970s was more or less heuristic: mathematicians had analytical examples for complex systems. Those examples were the simplest ones. After powerful computers came up, everything could be simulated. Then, the whole field exploded.<br />
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===You just talked about simple complex systems. Does an antagonist notion of complexity like simplicity exist?===<br />
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Of course. The notion of simplicity has not become such a buzz word in science. Using the complexity measures we talked about before, one possibility would be: if the complexity is low, then the system will be simple. There is an interesting book on complexity. The final chapter of this book says something about Simplexity and Complicity, as opposed to Simplicity and Complexity. This word game tends to say that it is not that easy to tear complex behaviors and simple behaviors apart from another. <br />
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===You described diverse measures for complexity. Would it be possible to build a universality theory of complex systems? ===<br />
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There are differences in the notion of universality classes on the way from regular to chaotic behavior. I am not saying that complexity lacks completely of a kind of universal behavior. But what we do not have is a compact set of equations that describes everything, like Maxwell’s equations. Maxwell’s equations resulted from the attempt of physicists to create a fundamental universal law for electromagnetism. In complex systems research, something like this has simply never happened. My intuition is that it is a fundamental problem in complex system theory and it is not simply that we have to work harder or to work for a longer time. Considering universality as a methodological pillar on scientific work, Peter Grassberger had an intuitive argument about this issue. He brings in the issue of meaning. For him, complexity is nothing else than the “difficulty of a meaningful task”. Thus, meaning implies subjectivity, which implies uniqueness, which is opposed to universality. That created some real controversy at that time in the study of complex systems because people realized that when you try to import meaning as an explicit object of study in physics, then you are really not doing physics anymore. At that time, a lot of people considered this as a no-go in physics. But Grassberger was courageous, he did it. I think this is interesting because it opens up a whole new level of discussion and deliberation. My favorite notion in this kind of discussion is contextuality. I would not contrast universality with the subjective but with the contextual. <br />
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=== What do you mean by contextuality?===<br />
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For instance, measures of complexity are not universal but they have to be applied in a way that respects the context of the question that you have. What do you want to know? What do you look for? If your answer would be independent of the context, then it would be universal. <br />
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=== It seems to be a vain quest to have a global wrap up of complexity. However, could meta-models give new insights on this issue?===<br />
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I cannot rule this out. That would change the whole methodology of theory building. What you usually do is considering experimental results, facts or data and then you try to find a model that more or less fits your data. With a meta-model, you would presuppose the data and the model that you have and try to see the relationship between them. It may be a possible path to come up with something more universal than present-day models of complex systems.<br />
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<br />
<br />
== To learn more ==<br />
<br />
*[http://www.sciencedirect.com/science/article/pii/096007799490023X Wackerbauer, Renate, et al. "A comparative classification of complexity measures." Chaos, Solitons & Fractals 4.1 (1994): 133-173.]<br />
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*[https://ejournals.library.ualberta.ca/index.php/complicity/article/viewFile/8764/7084 Complicity and Simplexity, Ian Stewart]<br />
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*[http://link.springer.com/article/10.1007/BF00668821 Grassberger, Peter. "Toward a quantitative theory of self-generated complexity."International Journal of Theoretical Physics 25.9 (1986): 907-938. ] <br />
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<html></article></html><br />
{{:Team:ETH_Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/File:ETH_Escher.jpgFile:ETH Escher.jpg2014-10-17T22:59:09Z<p>Meistefa: uploaded a new version of &quot;File:ETH Escher.jpg&quot;</p>
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<div></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/lab/sequencesTeam:ETH Zurich/lab/sequences2014-10-17T21:20:08Z<p>Meistefa: </p>
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<div>{{:Team:ETH_Zurich/tpl/head|Sequences}}<br />
<html><article></html><br />
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The plasmid sequences can be accessed by clicking on the plasmid name (e.g. [https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]) or the plasmid picture.<br />
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Construct types:<br />
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[[Team:ETH_Zurich/lab/sequences#Regulator_Constructs|Regulator Constructs]]<br />
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[[Team:ETH_Zurich/lab/sequences#Producer_Constructs|Producer Constructs]]<br />
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[[Team:ETH_Zurich/lab/sequences#Sensor Constructs|Sensor Constructs]]<br />
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[[Team:ETH_Zurich/lab/sequences#BUFFER_Gate_Construct|BUFFER Gate Construct]]<br />
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[[Team:ETH_Zurich/lab/sequences#Signal_Propagation_Construct|Signal Propagation Construct]]<br />
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[[Team:ETH_Zurich/lab/sequences#Combined_Sensor_and_Producer_Constructs|Combined Sensor and Producer Constructs]]<br />
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==Regulator Constructs==<br />
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[https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]<br />
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LasR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasR bound to 3OC12-HSL induces the expression of genes under the control of pLasR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
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[[File:ETH2014_piG0040_Map.png|link=https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt]]<br />
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[https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt piG0041]<br />
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LuxR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
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[[File:ETH2014_piG0041_Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt]]<br />
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[https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt piG0042]<br />
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RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
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[[File:ETH2014_piG0042_Map.png|link=https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt]]<br />
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[https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt piG0042max]<br />
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RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by an RBS optimised for RhlR ([https://salis.psu.edu/software/forward RBS calculator]). RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
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[[File:ETH2014_piG0042max_Map.png|link=https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt]]<br />
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[https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt piG0046]<br />
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LuxR is expressed under the weak constitutive promoter [http://parts.igem.org/Part:BBa_J23109 BBa_J23109] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
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[[File:ETH2014_piG0046_Map.png|link=https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt]] <br />
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[https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt piG0047]<br />
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LuxR is expressed under the medium strong constitutive promoter [http://parts.igem.org/Part:BBa_J23111 BBa_J23111 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
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[[File:ETH2014_piG0047_Map.png|link=https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt]]<br />
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==Producer Constructs==<br />
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[https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt piG0049]<br />
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LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
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[[File:ETH2014_piG0049_Map.png|link=https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt]]<br />
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<br />
[https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt piG0049max]<br />
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LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LasI ([https://salis.psu.edu/software/forward RBS calculator]). LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
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<br />
[[File:ETH2014_piG0049max_Map.png|link=https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt]]<br />
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[https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt piG0050]<br />
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LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
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[[File:ETH2014_piG0050_Map.png|link=https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt]]<br />
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<br />
[https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt piG0050max]<br />
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LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
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<br />
[[File:ETH2014_piG0050max_Map.png|link=https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt]]<br />
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[https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt piG0051]<br />
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RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
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[[File:ETH2014_piG0051_Map.png|link=https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt]]<br />
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<br />
[https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt piG0051max]<br />
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RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for RhlI ([https://salis.psu.edu/software/forward RBS calculator]). RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051max_Map.png|link=https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt]]<br />
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==Sensor Constructs==<br />
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[https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt piG0058]<br />
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Expression of sfGFP is induced when LasR bound to 3OC12-HSL bind to pLasR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
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[[File:ETH2014 piG0058 sensor plasRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt]]<br />
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[https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt piG0059]<br />
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Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
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[[File:ETH2014 piG0059 sensor pluxRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt]]<br />
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[https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt piG0060]<br />
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Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
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[[File:ETH2014 piG0060 sensor prhlRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt]]<br />
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[https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt piG0062]<br />
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Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
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[[File:ETH2014 piG0062 sensor pluxRcr12yRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt]]<br />
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[https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt piG0065]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0065 sensor pluxRRR12y-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt piG0066]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0066 sensor prhlRRR12-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt]]<br />
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[https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt piG0109]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0109 is a derivate of piG0065 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0109 pluxRRR12y-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt piG0110]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0110 is a derivate of piG0066 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0110 prhlRRR12-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
==BUFFER Gate Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt piG0067]<br />
<br />
The directional terminator [http://parts.igem.org/Part:BBa_B0015 BBa_B0015] blocks transcription of sfGFP under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100]. Only if the integrase Bxb1 flips B0015 between the attP and the attB sites, transcription of sfGFP is possible. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup><br />
<br />
<br />
[[File:ETH2014 piG0067 logic bxb1 BUFFER-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt]]<br />
<br />
<br />
<br />
<br />
==Signal Propagation Construct==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt piG0071]<br />
<br />
Expression of the integrase Bxb1 and the fluorophore mCherry is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of Bxb1 and mCherry, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0071 sensor pluxRRR12y bxb1 mCherry Map.png|link=https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt]]<br />
<br />
<br />
<br />
<br />
==Combined Sensor and Producer Constructs==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt piG0096]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0096 pluxRRR12y-sfGFP-maxRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt piG0097]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt piG0099]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The expression level of sfGFP and LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.png|link=https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt]]<br />
<br />
<br />
<html></article></html><br />
{{:Team:ETH_Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/lab/sequencesTeam:ETH Zurich/lab/sequences2014-10-17T21:18:45Z<p>Meistefa: /* Combined Sensor and Producer Constructs */</p>
<hr />
<div>{{:Team:ETH_Zurich/tpl/head|Sequences}}<br />
<html><article></html><br />
<br />
The plasmid sequences can be accessed by clicking on the plasmid name (e.g. [https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]) or the plasmid picture.<br />
<br />
Construct types:<br />
<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Regulator_Constructs|Regulator Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Producer_Constructs|Producer Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Sensor Constructs|Sensor Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#BUFFER_Gate_Construct|BUFFER Gate Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Signal_Propagation_Construct|Signal Propagation Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Combined_Sensor_and_Producer_Constructs|Combined Sensor and Producer Constructs]]<br />
<br />
<br />
==Regulator Constructs==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]<br />
<br />
LasR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasR bound to 3OC12-HSL induces the expression of genes under the control of pLasR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
[[File:ETH2014_piG0040_Map.png|link=https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt piG0041]<br />
<br />
LuxR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0041_Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt piG0042]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042_Map.png|link=https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt piG0042max]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by an RBS optimised for RhlR ([https://salis.psu.edu/software/forward RBS calculator]). RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042max_Map.png|link=https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt piG0046]<br />
<br />
LuxR is expressed under the weak constitutive promoter [http://parts.igem.org/Part:BBa_J23109 BBa_J23109] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0046_Map.png|link=https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt]] <br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt piG0047]<br />
<br />
LuxR is expressed under the medium strong constitutive promoter [http://parts.igem.org/Part:BBa_J23111 BBa_J23111 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0047_Map.png|link=https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt]]<br />
<br />
==Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt piG0049]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049_Map.png|link=https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt piG0049max]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LasI ([https://salis.psu.edu/software/forward RBS calculator]). LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049max_Map.png|link=https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt piG0050]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0050_Map.png|link=https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt piG0050max]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0050max_Map.png|link=https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt piG0051]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051_Map.png|link=https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt piG0051max]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for RhlI ([https://salis.psu.edu/software/forward RBS calculator]). RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051max_Map.png|link=https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt]]<br />
<br />
==Sensor Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt piG0058]<br />
<br />
Expression of sfGFP is induced when LasR bound to 3OC12-HSL bind to pLasR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0058 sensor plasRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt piG0059]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0059 sensor pluxRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt piG0060]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0060 sensor prhlRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt piG0062]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0062 sensor pluxRcr12yRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt piG0065]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0065 sensor pluxRRR12y-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt piG0066]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0066 sensor prhlRRR12-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt piG0109]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0109 is a derivate of piG0065 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0109 pluxRRR12y-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt piG0110]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0110 is a derivate of piG0066 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0110 prhlRRR12-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
==BUFFER Gate Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt piG0067]<br />
<br />
The directional terminator [http://parts.igem.org/Part:BBa_B0015 BBa_B0015] blocks transcription of sfGFP under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100]. Only if the integrase Bxb1 flips B0015 between the attP and the attB sites, transcription of sfGFP is possible. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup><br />
<br />
<br />
[[File:ETH2014 piG0067 logic bxb1 BUFFER-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt]]<br />
<br />
==Signal Propagation Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt piG0071]<br />
<br />
Expression of the integrase Bxb1 and the fluorophore mCherry is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of Bxb1 and mCherry, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0071 sensor pluxRRR12y bxb1 mCherry Map.png|link=https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt]]<br />
<br />
==Combined Sensor and Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt piG0096]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0096 pluxRRR12y-sfGFP-maxRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt piG0097]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt piG0099]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The expression level of sfGFP and LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.png|link=https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt]]<br />
<br />
<br />
<html></article></html><br />
{{:Team:ETH_Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/lab/sequencesTeam:ETH Zurich/lab/sequences2014-10-17T21:17:56Z<p>Meistefa: /* Signal Propagation Construct */</p>
<hr />
<div>{{:Team:ETH_Zurich/tpl/head|Sequences}}<br />
<html><article></html><br />
<br />
The plasmid sequences can be accessed by clicking on the plasmid name (e.g. [https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]) or the plasmid picture.<br />
<br />
Construct types:<br />
<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Regulator_Constructs|Regulator Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Producer_Constructs|Producer Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Sensor Constructs|Sensor Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#BUFFER_Gate_Construct|BUFFER Gate Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Signal_Propagation_Construct|Signal Propagation Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Combined_Sensor_and_Producer_Constructs|Combined Sensor and Producer Constructs]]<br />
<br />
<br />
==Regulator Constructs==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]<br />
<br />
LasR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasR bound to 3OC12-HSL induces the expression of genes under the control of pLasR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
[[File:ETH2014_piG0040_Map.png|link=https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt piG0041]<br />
<br />
LuxR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0041_Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt piG0042]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042_Map.png|link=https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt piG0042max]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by an RBS optimised for RhlR ([https://salis.psu.edu/software/forward RBS calculator]). RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042max_Map.png|link=https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt piG0046]<br />
<br />
LuxR is expressed under the weak constitutive promoter [http://parts.igem.org/Part:BBa_J23109 BBa_J23109] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0046_Map.png|link=https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt]] <br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt piG0047]<br />
<br />
LuxR is expressed under the medium strong constitutive promoter [http://parts.igem.org/Part:BBa_J23111 BBa_J23111 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0047_Map.png|link=https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt]]<br />
<br />
==Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt piG0049]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049_Map.png|link=https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt piG0049max]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LasI ([https://salis.psu.edu/software/forward RBS calculator]). LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049max_Map.png|link=https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt piG0050]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0050_Map.png|link=https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt piG0050max]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0050max_Map.png|link=https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt piG0051]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051_Map.png|link=https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt piG0051max]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for RhlI ([https://salis.psu.edu/software/forward RBS calculator]). RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051max_Map.png|link=https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt]]<br />
<br />
==Sensor Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt piG0058]<br />
<br />
Expression of sfGFP is induced when LasR bound to 3OC12-HSL bind to pLasR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0058 sensor plasRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt piG0059]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0059 sensor pluxRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt piG0060]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0060 sensor prhlRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt piG0062]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0062 sensor pluxRcr12yRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt piG0065]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0065 sensor pluxRRR12y-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt piG0066]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0066 sensor prhlRRR12-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt piG0109]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0109 is a derivate of piG0065 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0109 pluxRRR12y-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt piG0110]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0110 is a derivate of piG0066 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0110 prhlRRR12-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
==BUFFER Gate Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt piG0067]<br />
<br />
The directional terminator [http://parts.igem.org/Part:BBa_B0015 BBa_B0015] blocks transcription of sfGFP under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100]. Only if the integrase Bxb1 flips B0015 between the attP and the attB sites, transcription of sfGFP is possible. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup><br />
<br />
<br />
[[File:ETH2014 piG0067 logic bxb1 BUFFER-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt]]<br />
<br />
==Signal Propagation Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt piG0071]<br />
<br />
Expression of the integrase Bxb1 and the fluorophore mCherry is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of Bxb1 and mCherry, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0071 sensor pluxRRR12y bxb1 mCherry Map.png|link=https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt]]<br />
<br />
==Combined Sensor and Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt piG0096]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]).The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0096 pluxRRR12y-sfGFP-maxRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt piG0097]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt piG0099]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The expression level of sfGFP and LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.png|link=https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt]]<br />
<br />
<br />
<html></article></html><br />
{{:Team:ETH_Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/lab/sequencesTeam:ETH Zurich/lab/sequences2014-10-17T21:16:50Z<p>Meistefa: /* Sensor Constructs */</p>
<hr />
<div>{{:Team:ETH_Zurich/tpl/head|Sequences}}<br />
<html><article></html><br />
<br />
The plasmid sequences can be accessed by clicking on the plasmid name (e.g. [https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]) or the plasmid picture.<br />
<br />
Construct types:<br />
<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Regulator_Constructs|Regulator Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Producer_Constructs|Producer Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Sensor Constructs|Sensor Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#BUFFER_Gate_Construct|BUFFER Gate Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Signal_Propagation_Construct|Signal Propagation Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Combined_Sensor_and_Producer_Constructs|Combined Sensor and Producer Constructs]]<br />
<br />
<br />
==Regulator Constructs==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]<br />
<br />
LasR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasR bound to 3OC12-HSL induces the expression of genes under the control of pLasR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
[[File:ETH2014_piG0040_Map.png|link=https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt piG0041]<br />
<br />
LuxR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0041_Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt piG0042]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042_Map.png|link=https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt piG0042max]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by an RBS optimised for RhlR ([https://salis.psu.edu/software/forward RBS calculator]). RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042max_Map.png|link=https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt piG0046]<br />
<br />
LuxR is expressed under the weak constitutive promoter [http://parts.igem.org/Part:BBa_J23109 BBa_J23109] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0046_Map.png|link=https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt]] <br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt piG0047]<br />
<br />
LuxR is expressed under the medium strong constitutive promoter [http://parts.igem.org/Part:BBa_J23111 BBa_J23111 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0047_Map.png|link=https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt]]<br />
<br />
==Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt piG0049]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049_Map.png|link=https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt piG0049max]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LasI ([https://salis.psu.edu/software/forward RBS calculator]). LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049max_Map.png|link=https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt piG0050]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0050_Map.png|link=https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt piG0050max]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0050max_Map.png|link=https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt piG0051]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051_Map.png|link=https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt piG0051max]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for RhlI ([https://salis.psu.edu/software/forward RBS calculator]). RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051max_Map.png|link=https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt]]<br />
<br />
==Sensor Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt piG0058]<br />
<br />
Expression of sfGFP is induced when LasR bound to 3OC12-HSL bind to pLasR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0058 sensor plasRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt piG0059]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0059 sensor pluxRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt piG0060]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0060 sensor prhlRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt piG0062]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0062 sensor pluxRcr12yRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt piG0065]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0065 sensor pluxRRR12y-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt piG0066]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0066 sensor prhlRRR12-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt piG0109]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0109 is a derivate of piG0065 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0109 pluxRRR12y-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt piG0110]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. A biologically neutral spacer sequence was designed using the web application R2oDNA<sup>[[Team:ETH_Zurich/project/references#refR2oDNA|[34]]]</sup>. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0110 is a derivate of piG0066 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0110 prhlRRR12-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
==BUFFER Gate Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt piG0067]<br />
<br />
The directional terminator [http://parts.igem.org/Part:BBa_B0015 BBa_B0015] blocks transcription of sfGFP under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100]. Only if the integrase Bxb1 flips B0015 between the attP and the attB sites, transcription of sfGFP is possible. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup><br />
<br />
<br />
[[File:ETH2014 piG0067 logic bxb1 BUFFER-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt]]<br />
<br />
==Signal Propagation Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt piG0071]<br />
<br />
Expression of the integrase Bxb1 and the fluorophore mCherry is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of Bxb1 and mCherry, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0071 sensor pluxRRR12y bxb1 mCherry Map.png|link=https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt]]<br />
<br />
==Combined Sensor and Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt piG0096]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]).The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0096 pluxRRR12y-sfGFP-maxRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt piG0097]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt piG0099]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The expression level of sfGFP and LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.png|link=https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt]]<br />
<br />
<br />
<html></article></html><br />
{{:Team:ETH_Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.pngFile:ETH2014 piG0099 pluxstRBS-sfGFP-stRBS-luxI Map.png2014-10-17T21:10:14Z<p>Meistefa: uploaded a new version of &quot;File:ETH2014 piG0099 pluxstRBS-sfGFP-stRBS-luxI Map.png&quot;</p>
<hr />
<div></div>Meistefahttp://2014.igem.org/File:ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI_Map.pngFile:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png2014-10-17T21:09:55Z<p>Meistefa: uploaded a new version of &quot;File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png&quot;</p>
<hr />
<div></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/lab/sequencesTeam:ETH Zurich/lab/sequences2014-10-17T21:04:40Z<p>Meistefa: /* Combined Sensor and Producer Constructs */</p>
<hr />
<div>{{:Team:ETH_Zurich/tpl/head|Sequences}}<br />
<html><article></html><br />
<br />
The plasmid sequences can be accessed by clicking on the plasmid name (e.g. [https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]) or the plasmid picture.<br />
<br />
Construct types:<br />
<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Regulator_Constructs|Regulator Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Producer_Constructs|Producer Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Sensor Constructs|Sensor Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#BUFFER_Gate_Construct|BUFFER Gate Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Signal_Propagation_Construct|Signal Propagation Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Combined_Sensor_and_Producer_Constructs|Combined Sensor and Producer Constructs]]<br />
<br />
<br />
==Regulator Constructs==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]<br />
<br />
LasR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasR bound to 3OC12-HSL induces the expression of genes under the control of pLasR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
[[File:ETH2014_piG0040_Map.png|link=https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt piG0041]<br />
<br />
LuxR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0041_Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt piG0042]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042_Map.png|link=https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt piG0042max]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by an RBS optimised for RhlR ([https://salis.psu.edu/software/forward RBS calculator]). RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042max_Map.png|link=https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt piG0046]<br />
<br />
LuxR is expressed under the weak constitutive promoter [http://parts.igem.org/Part:BBa_J23109 BBa_J23109] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0046_Map.png|link=https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt]] <br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt piG0047]<br />
<br />
LuxR is expressed under the medium strong constitutive promoter [http://parts.igem.org/Part:BBa_J23111 BBa_J23111 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0047_Map.png|link=https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt]]<br />
<br />
==Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt piG0049]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049_Map.png|link=https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt piG0049max]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LasI ([https://salis.psu.edu/software/forward RBS calculator]). LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049max_Map.png|link=https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt piG0050]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0050_Map.png|link=https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt piG0050max]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0050max_Map.png|link=https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt piG0051]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051_Map.png|link=https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt piG0051max]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for RhlI ([https://salis.psu.edu/software/forward RBS calculator]). RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051max_Map.png|link=https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt]]<br />
<br />
==Sensor Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt piG0058]<br />
<br />
Expression of sfGFP is induced when LasR bound to 3OC12-HSL bind to pLasR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0058 sensor plasRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt piG0059]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0059 sensor pluxRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt piG0060]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0060 sensor prhlRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt piG0062]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0062 sensor pluxRcr12yRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt piG0065]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0065 sensor pluxRRR12y-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt piG0066]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0066 sensor prhlRRR12-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt piG0109]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0109 is a derivate of piG0065 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0109 pluxRRR12y-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt piG0110]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0110 is a derivate of piG0066 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0110 prhlRRR12-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
==BUFFER Gate Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt piG0067]<br />
<br />
The directional terminator [http://parts.igem.org/Part:BBa_B0015 BBa_B0015] blocks transcription of sfGFP under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100]. Only if the integrase Bxb1 flips B0015 between the attP and the attB sites, transcription of sfGFP is possible. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup><br />
<br />
<br />
[[File:ETH2014 piG0067 logic bxb1 BUFFER-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt]]<br />
<br />
==Signal Propagation Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt piG0071]<br />
<br />
Expression of the integrase Bxb1 and the fluorophore mCherry is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of Bxb1 and mCherry, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0071 sensor pluxRRR12y bxb1 mCherry Map.png|link=https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt]]<br />
<br />
==Combined Sensor and Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt piG0096]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]).The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0096 pluxRRR12y-sfGFP-maxRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt piG0097]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt piG0099]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The expression level of sfGFP and LuxI is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.png|link=https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt]]<br />
<br />
<br />
<html></article></html><br />
{{:Team:ETH_Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/File:ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI_Map.pngFile:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png2014-10-17T21:03:22Z<p>Meistefa: uploaded a new version of &quot;File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png&quot;: Reverted to version as of 18:09, 17 October 2014</p>
<hr />
<div></div>Meistefahttp://2014.igem.org/File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.pngFile:ETH2014 piG0099 pluxstRBS-sfGFP-stRBS-luxI Map.png2014-10-17T21:03:02Z<p>Meistefa: uploaded a new version of &quot;File:ETH2014 piG0099 pluxstRBS-sfGFP-stRBS-luxI Map.png&quot;: Reverted to version as of 18:09, 17 October 2014</p>
<hr />
<div></div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/lab/sequencesTeam:ETH Zurich/lab/sequences2014-10-17T21:02:13Z<p>Meistefa: /* Combined Sensor and Producer Constructs */</p>
<hr />
<div>{{:Team:ETH_Zurich/tpl/head|Sequences}}<br />
<html><article></html><br />
<br />
The plasmid sequences can be accessed by clicking on the plasmid name (e.g. [https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]) or the plasmid picture.<br />
<br />
Construct types:<br />
<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Regulator_Constructs|Regulator Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Producer_Constructs|Producer Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Sensor Constructs|Sensor Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#BUFFER_Gate_Construct|BUFFER Gate Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Signal_Propagation_Construct|Signal Propagation Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Combined_Sensor_and_Producer_Constructs|Combined Sensor and Producer Constructs]]<br />
<br />
<br />
==Regulator Constructs==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]<br />
<br />
LasR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasR bound to 3OC12-HSL induces the expression of genes under the control of pLasR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
[[File:ETH2014_piG0040_Map.png|link=https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt piG0041]<br />
<br />
LuxR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0041_Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt piG0042]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042_Map.png|link=https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt piG0042max]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by an RBS optimised for RhlR ([https://salis.psu.edu/software/forward RBS calculator]). RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042max_Map.png|link=https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt piG0046]<br />
<br />
LuxR is expressed under the weak constitutive promoter [http://parts.igem.org/Part:BBa_J23109 BBa_J23109] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0046_Map.png|link=https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt]] <br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt piG0047]<br />
<br />
LuxR is expressed under the medium strong constitutive promoter [http://parts.igem.org/Part:BBa_J23111 BBa_J23111 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0047_Map.png|link=https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt]]<br />
<br />
==Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt piG0049]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049_Map.png|link=https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt piG0049max]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LasI ([https://salis.psu.edu/software/forward RBS calculator]). LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049max_Map.png|link=https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt piG0050]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0050_Map.png|link=https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt piG0050max]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0050max_Map.png|link=https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt piG0051]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051_Map.png|link=https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt piG0051max]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for RhlI ([https://salis.psu.edu/software/forward RBS calculator]). RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051max_Map.png|link=https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt]]<br />
<br />
==Sensor Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt piG0058]<br />
<br />
Expression of sfGFP is induced when LasR bound to 3OC12-HSL bind to pLasR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0058 sensor plasRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt piG0059]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0059 sensor pluxRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt piG0060]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0060 sensor prhlRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt piG0062]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0062 sensor pluxRcr12yRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt piG0065]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0065 sensor pluxRRR12y-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt piG0066]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0066 sensor prhlRRR12-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt piG0109]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0109 is a derivate of piG0065 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0109 pluxRRR12y-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt piG0110]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0110 is a derivate of piG0066 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0110 prhlRRR12-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
==BUFFER Gate Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt piG0067]<br />
<br />
The directional terminator [http://parts.igem.org/Part:BBa_B0015 BBa_B0015] blocks transcription of sfGFP under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100]. Only if the integrase Bxb1 flips B0015 between the attP and the attB sites, transcription of sfGFP is possible. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup><br />
<br />
<br />
[[File:ETH2014 piG0067 logic bxb1 BUFFER-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt]]<br />
<br />
==Signal Propagation Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt piG0071]<br />
<br />
Expression of the integrase Bxb1 and the fluorophore mCherry is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of Bxb1 and mCherry, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0071 sensor pluxRRR12y bxb1 mCherry Map.png|link=https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt]]<br />
<br />
==Combined Sensor and Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt piG0096]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]).The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0096 pluxRRR12y-sfGFP-maxRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt piG0097]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is influenced by the RBS B0034. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt piG0099]<br />
<br />
Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The expression level of sfGFP and LuxI is influenced by the RBS B0034. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.png|link=https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt]]<br />
<br />
<br />
<html></article></html><br />
{{:Team:ETH_Zurich/tpl/foot}}</div>Meistefahttp://2014.igem.org/Team:ETH_Zurich/lab/sequencesTeam:ETH Zurich/lab/sequences2014-10-17T20:58:14Z<p>Meistefa: </p>
<hr />
<div>{{:Team:ETH_Zurich/tpl/head|Sequences}}<br />
<html><article></html><br />
<br />
The plasmid sequences can be accessed by clicking on the plasmid name (e.g. [https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]) or the plasmid picture.<br />
<br />
Construct types:<br />
<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Regulator_Constructs|Regulator Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Producer_Constructs|Producer Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Sensor Constructs|Sensor Constructs]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#BUFFER_Gate_Construct|BUFFER Gate Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Signal_Propagation_Construct|Signal Propagation Construct]]<br />
<br />
[[Team:ETH_Zurich/lab/sequences#Combined_Sensor_and_Producer_Constructs|Combined Sensor and Producer Constructs]]<br />
<br />
<br />
==Regulator Constructs==<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt piG0040]<br />
<br />
LasR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasR bound to 3OC12-HSL induces the expression of genes under the control of pLasR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
[[File:ETH2014_piG0040_Map.png|link=https://static.igem.org/mediawiki/2014/f/f6/ETH2014_piG0040.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt piG0041]<br />
<br />
LuxR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0041_Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/ETH2014_piG0041.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt piG0042]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042_Map.png|link=https://static.igem.org/mediawiki/2014/d/db/ETH2014_piG0042.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt piG0042max]<br />
<br />
RhlR is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100] while the expression level is influenced by an RBS optimised for RhlR ([https://salis.psu.edu/software/forward RBS calculator]). RhlR bound to C4-HSL induces the expression of genes under the control of pRhlR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0042max_Map.png|link=https://static.igem.org/mediawiki/2014/c/ce/ETH2014_piG0042max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt piG0046]<br />
<br />
LuxR is expressed under the weak constitutive promoter [http://parts.igem.org/Part:BBa_J23109 BBa_J23109] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0046_Map.png|link=https://static.igem.org/mediawiki/2014/1/18/ETH2014_piG0046.txt]] <br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt piG0047]<br />
<br />
LuxR is expressed under the medium strong constitutive promoter [http://parts.igem.org/Part:BBa_J23111 BBa_J23111 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxR bound to 3OC6-HSL induces the expression of genes under the control of pLuxR. The plasmid pBR322 and its derivatives have a copy number of 15 to 20<sup>[[Team:ETH_Zurich/project/references#refBolivar|[15]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0047_Map.png|link=https://static.igem.org/mediawiki/2014/1/1b/ETH2014_piG0047.txt]]<br />
<br />
==Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt piG0049]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049_Map.png|link=https://static.igem.org/mediawiki/2014/4/43/ETH2014_piG0049.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt piG0049max]<br />
<br />
LasI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LasI ([https://salis.psu.edu/software/forward RBS calculator]). LasI produces the quorum sensing molecule 3OC12-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized <sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0049max_Map.png|link=https://static.igem.org/mediawiki/2014/b/bc/ETH2014_piG0049max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt piG0050]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0050_Map.png|link=https://static.igem.org/mediawiki/2014/4/49/ETH2014_piG0050.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt piG0050max]<br />
<br />
LuxI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]). LuxI produces the quorum sensing molecule 3OC6-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
<br />
[[File:ETH2014_piG0050max_Map.png|link=https://static.igem.org/mediawiki/2014/5/50/ETH2014_piG0050max.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt piG0051]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is influenced by the RBS [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]. RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051_Map.png|link=https://static.igem.org/mediawiki/2014/0/00/ETH2014_piG0051.txt]]<br />
<br />
<br />
[https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt piG0051max]<br />
<br />
RhlI is expressed under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100 ] while the expression level is increased by an RBS optimised for RhlI ([https://salis.psu.edu/software/forward RBS calculator]). RhlI produces the quorum sensing molecule C4-HSL. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup>.<br />
<br />
[[File:ETH2014_piG0051max_Map.png|link=https://static.igem.org/mediawiki/2014/9/94/ETH2014_piG0051max.txt]]<br />
<br />
==Sensor Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt piG0058]<br />
<br />
Expression of sfGFP is induced when LasR bound to 3OC12-HSL bind to pLasR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0058 sensor plasRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/a/a7/ETH2014_piG0058_sensor_plasRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt piG0059]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0059 sensor pluxRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/0/0f/ETH2014_piG0059_sensor_pluxRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt piG0060]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0060 sensor prhlRstRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/22/PiG0060_sensor_prhlRstRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt piG0062]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0062 sensor pluxRcr12yRBS-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/2c/PiG0062_sensor_pluxRcr12yRBS-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt piG0065]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0065 sensor pluxRRR12y-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/d/da/ETH2014_piG0065_sensor_pluxRRR12y-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt piG0066]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0066 sensor prhlRRR12-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/2/24/ETH2014_piG0066_sensor_prhlRRR12-sfGFP.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt piG0109]<br />
<br />
Expression of sfGFP is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0109 is a derivate of piG0065 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0109 pluxRRR12y-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/9/95/ETH2014_piG0109_pluxRRR12y-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt piG0110]<br />
<br />
Expression of sfGFP is induced when RhlR bound to 4C-HSL bind to pRhlR. The cis-repressive element (crR12) inhibits the translation of sfGFP, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>. PiG0110 is a derivate of piG0066 where the restriction sites EcoRI and XbaI have been removed. Thus, the two constructs slightly differ in the sequence of the 3'-end of the trans-activating element and in the sequence of the 5'-end of the cis-repressive element.<br />
<br />
[[File:ETH2014 piG0110 prhlRRR12-sfGFP EcoRI- XbaI- Map.png|link=https://static.igem.org/mediawiki/2014/f/f9/ETH2014_piG0110_prhlRRR12-sfGFP_EcoRI-_XbaI-.txt]]<br />
<br />
==BUFFER Gate Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt piG0067]<br />
<br />
The directional terminator [http://parts.igem.org/Part:BBa_B0015 BBa_B0015] blocks transcription of sfGFP under the strong constitutive promoter [http://parts.igem.org/Part:BBa_J23100 BBa_J23100]. Only if the integrase Bxb1 flips B0015 between the attP and the attB sites, transcription of sfGFP is possible. The pBBR1 origin is present at a copy number of approximately 5, however, the origin is poorly characterized<sup>[[Team:ETH_Zurich/project/references#refLennen|[16]]]</sup><br />
<br />
<br />
[[File:ETH2014 piG0067 logic bxb1 BUFFER-sfGFP Map.png|link=https://static.igem.org/mediawiki/2014/5/59/ETH2014_piG0067_logic_bxb1_BUFFER-sfGFP.txt]]<br />
<br />
==Signal Propagation Construct==<br />
<br />
[https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt piG0071]<br />
<br />
Expression of the integrase Bxb1 and the fluorophore mCherry is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of Bxb1 and mCherry, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
<br />
[[File:ETH2014 piG0071 sensor pluxRRR12y bxb1 mCherry Map.png|link=https://static.igem.org/mediawiki/2014/1/1d/ETH2014_piG0071_sensor_pluxRRR12y_bxb1_mCherry.txt]]<br />
<br />
==Combined Sensor and Producer Constructs==<br />
<br />
[https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt piG0096]<br />
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Expression of sfGFP and LuxI is induced when LuxR bound to 3OC6-HSL bind to pLuxR. The cis-repressive element (crR12y) inhibits the translation of the succeeding gene, since the RBS is blocked by secondary structures of the mRNA. The transcript of the trans-activating element (taR12y) binds to the transcript of the cis-repressive element, hence the RBS is not blocked anymore. The two elements build a [https://2014.igem.org/Team:ETH_Zurich/expresults#Riboregulators riboregulator] that decreases leakiness of pLuxR. The expression level of LuxI is increased by an RBS optimised for LuxI ([https://salis.psu.edu/software/forward RBS calculator]).The p15A is present at a copy number of approximately 15 to 25<sup>[[Team:ETH_Zurich/project/references#refChang|[35]]]</sup>.<br />
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[[File:ETH2014 piG0096 pluxRRR12y-sfGFP-maxRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/f5/ETH2014_piG0096_pluxRRR12y-sfGFP-maxRBS-luxI.txt]]<br />
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[https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt piG0097]<br />
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[[File:ETH2014 piG0097 pluxRRR12y-sfGFP-stRBS-luxI Map.png|link=https://static.igem.org/mediawiki/2014/f/fc/ETH2014_piG0097_pluxRRR12y-sfGFP-stRBS-luxI.txt]]<br />
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[https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt piG0099]<br />
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[[File:ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI_Map.png|link=https://static.igem.org/mediawiki/2014/6/69/ETH2014_piG0099_pluxstRBS-sfGFP-stRBS-luxI.txt]]<br />
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