Team:TUDelft

From 2009.igem.org

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(The Project - Bacterial Relay Race)
 
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=Welcome to the 2009 Bacterial Relay Race=
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=Welcome to the award winning 2009 Bacterial Relay Race=
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We are currently working on a cell to cell communication system with possible applications in reducing antibiotic resistance of bacteria. Furthermore, we are working on ethical issues in synthetic biology. The survey on reductionism in synthetic biology can be found here: [http://spreadsheets.google.com/viewform?formkey=dElEZjI4Vk0wWmxHTWoycG03b2RrQ3c6MA.. '''Survey''']. Your contribution would be very much appreciated.
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<br>
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Our team acquired a '''Gold medal''' and was awarded with [https://igem.org/Results?year=2009 '''Best information processing project'''], during the 2009 iGEM Jamoboree at MIT, Boston.<br>
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==The Team==
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<br>
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This is the second year the TUDelft participates in the iGEM competition.
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In our project we aim to create a cell-to-cell communication system that allows the propagation of a multi-task message with the capability of being reset. To achieve this, the system will include a reengineered conjugation system, a time-delay genetic circuit and a self-destructive plasmid. This system could be the basis for creating a long distance biosensor and/or be applied in reducing antibiotic resistance of bacteria. Furthermore, we have done a parallel research on the different perceptions of iGEM participants and supervisors on  [https://2009.igem.org/Team:TUDelft/Ethics ethical issues in synthetic biology]. We focused on the consequences of the ultimate conditions of the top-down and bottom-up approaches as applied in biology. We thank everyone who participated in our survey on these ethical issues in synthetic biology.
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The group consists of 7 students, 4 instructors and a lot of advisors from TUDelft willing to help out and think with us when it is necessary. An overview of the people involved and our competences can be found on the [[Team:TUDelft/Team|team]] page.
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With our 7 participants and 4 instructors, we are enthusiastic to start working on our project: Cell to cell communication with re-engineered plasmids.
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==The Project - Bacterial Relay Race==
==The Project - Bacterial Relay Race==
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<br>
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'''Project description'''
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[[Image:TUDelft_relayrace.gif|frame]]
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Our project is the Bacterial Relay Race. As our team logo and the animation below show, we want to build an improved cell to cell communication system. We choose this subject since most applications or tasks we set to our synthetic biological systems are generally completed by a population of cells, not a single cell. Gaining new insights into cell to cell communication and designing manageable cell to cell communication systems will provide us with a wide range of new possibilities. Manageable cell to cell communication systems could have applications in different fields like therapeutic applications or fermentation technology applications. We are attempting to construct an E.coli strain which is capable of passing a GFP signal through conjugation to other E.coli cells only once, with communication appearing population wide. Our work builds on projects of previous iGEM teams from Berkeley UC and Peking University.
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'''Project description'''
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<center>
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Our project is Bacterial Relay Race. As our team logo and the animation shows we want to build an improved cell to cell communication system. We choose cell to cell communication as subject because of the great importance of it. Cell to cell communication systems are important because most applications or task we set to our synthetic biological systems are generally completed by a population of cells, not a single cell<html><sup id="cite_ref-0" class="reference"><a href="#cite_note-0"><span>[</span>1<span>]</span></a></sup></html>.Gaining new insights at cell to cell communication and designing manageable cell to cell communication systems will provide us a scale of new possibilities. Manageable cell to cell communication systems could have applications in different fields like therapeutic application or fermentation technology applications.
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<embed
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We want to construct an E.coli strain which is capable of passing a GFP signal through conjugation to other E.coli cells only once. Communication appears population wide.
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  src="https://static.igem.org/mediawiki/2009/c/cd/TUDRelayRace.swf"
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Our work builds on projects of previous iGEM teams from Berkeley UC and Peking University.
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'''Our project is made up of three modules:'''
'''Our project is made up of three modules:'''
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1) Conjugation system
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1) [https://2009.igem.org/Team:TUDelft/Conjugation_Overview Conjugation]
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2) Self destructive plasmid
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Our cell to cell communication system is based on bacterial conjugation. We use this to pass a message, initially GFP, along to other bacteria in the culture.
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3) Delay device
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2) [https://2009.igem.org/Team:TUDelft/SDP_Overview Self Destructive Plasmid] (SDP)
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1) Conjugation system
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In order for our signal to be reset the signal plasmid must be able to self-destruct. The Self Destructive Plasmid (SDP) is degigned to test this functionality. It contains a GFP message, inducible endonuclease gene, and restriction site of this endonuclease. The plasmid is able to degrade itself after receiving the destructing signal.
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We want to build a cell to cell communication system in which communication is based on conjugation. Through conjugation a GFP message is passed to other bacteria in the culture.
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3) [https://2009.igem.org/Team:TUDelft/Module_3_Overview Delay device]
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2) Self destructive plasmid (SDP)
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It is important that there is a time delay between the time that the signal plasmid is received and its destruction. This gives the cell time to pass the signal plasmid to other cells. If the signal plasmid is degraded too fast after it is received, our relay race would end before reaching the finish line. We therefore constructed a device which is capable of delaying the expression of the endonuclease.
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The plasmid contains a GFP message, inducible endonuclease gene and restriction site of this endonuclease. The plasmid is able to degrade itself after receiving the destructing signal.
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3) Delay device
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It is important that there is a time delay between the moment of passing the SDP and the destructing of it. If the SDP is degraded to fast after conjugation, the degradation of the SDP will not be detected. Therefore we construct a device in this system which delays expression of the endonuclease.
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'''Some potential applications for this project are'''
'''Some potential applications for this project are'''
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#Grasping of bacterial communication - the communication between bacteria can advance through bacterial networks, and in this sense our project would allow to better understand those communication networks
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#Grasping of bacterial communication - the communication between bacteria using DNA can advance through bacterial networks, and in this sense our project would allow to send multiple messages in a single DNA, thereby to better understand those bacterial communication networks.
#Understanding of bacterial antibiotic resistance - these days, bacterial infections are often treated with antibiotics. Unfortunately, bacteria have the tendancy to pass antibiotic resistance to other bacteria through the process of [http://en.wikipedia.org/wiki/Bacterial_conjugation conjugation], thus making the antibiotics useless. Using our project, it might be possible for future researchers to better understand the mechanism by which antibiotic resistance passes among bacterial colonies, and perhaps even inhibit it
#Understanding of bacterial antibiotic resistance - these days, bacterial infections are often treated with antibiotics. Unfortunately, bacteria have the tendancy to pass antibiotic resistance to other bacteria through the process of [http://en.wikipedia.org/wiki/Bacterial_conjugation conjugation], thus making the antibiotics useless. Using our project, it might be possible for future researchers to better understand the mechanism by which antibiotic resistance passes among bacterial colonies, and perhaps even inhibit it
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#To test one condition and return to the original state without killing the cell or changing any of its previous genetic and physiological characteristics
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#To generate a pulse in the expression of a certain gene
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#To control the amplitude of the pulse created by the plasmid
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==References==
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==The Team==
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<ol><li id="cite_note-0"><cite id="CITEREFMolSysBio2006" class="article" style="font-style: normal;">
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This is the second year, TUDelft participates in the iGEM competition.  
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Andrianantoandro, E., Basu, S., Karig, D.K., Weiss, R., "Synthetic biology: new engineering rules for an emerging discipline", Molecular Systems Biology (2006), 1-14.</cite></ol>
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The group consists of 6 students, 3 instructors and a lot of advisors from TUDelft willing to help out and think with us when it is necessary. An overview of the people involved and our competences can be found on the [[Team:TUDelft/Team|team]] page.
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{{Template:TUDelftiGEM2009_end}}

Latest revision as of 15:19, 2 March 2010

Welcome to the award winning 2009 Bacterial Relay Race


Our team acquired a Gold medal and was awarded with Best information processing project, during the 2009 iGEM Jamoboree at MIT, Boston.

In our project we aim to create a cell-to-cell communication system that allows the propagation of a multi-task message with the capability of being reset. To achieve this, the system will include a reengineered conjugation system, a time-delay genetic circuit and a self-destructive plasmid. This system could be the basis for creating a long distance biosensor and/or be applied in reducing antibiotic resistance of bacteria. Furthermore, we have done a parallel research on the different perceptions of iGEM participants and supervisors on ethical issues in synthetic biology. We focused on the consequences of the ultimate conditions of the top-down and bottom-up approaches as applied in biology. We thank everyone who participated in our survey on these ethical issues in synthetic biology.

The Project - Bacterial Relay Race


Project description

Our project is the Bacterial Relay Race. As our team logo and the animation below show, we want to build an improved cell to cell communication system. We choose this subject since most applications or tasks we set to our synthetic biological systems are generally completed by a population of cells, not a single cell. Gaining new insights into cell to cell communication and designing manageable cell to cell communication systems will provide us with a wide range of new possibilities. Manageable cell to cell communication systems could have applications in different fields like therapeutic applications or fermentation technology applications. We are attempting to construct an E.coli strain which is capable of passing a GFP signal through conjugation to other E.coli cells only once, with communication appearing population wide. Our work builds on projects of previous iGEM teams from Berkeley UC and Peking University.

Our project is made up of three modules:

1) Conjugation

Our cell to cell communication system is based on bacterial conjugation. We use this to pass a message, initially GFP, along to other bacteria in the culture.

2) Self Destructive Plasmid (SDP)

In order for our signal to be reset the signal plasmid must be able to self-destruct. The Self Destructive Plasmid (SDP) is degigned to test this functionality. It contains a GFP message, inducible endonuclease gene, and restriction site of this endonuclease. The plasmid is able to degrade itself after receiving the destructing signal.

3) Delay device

It is important that there is a time delay between the time that the signal plasmid is received and its destruction. This gives the cell time to pass the signal plasmid to other cells. If the signal plasmid is degraded too fast after it is received, our relay race would end before reaching the finish line. We therefore constructed a device which is capable of delaying the expression of the endonuclease.

Some potential applications for this project are

  1. Grasping of bacterial communication - the communication between bacteria using DNA can advance through bacterial networks, and in this sense our project would allow to send multiple messages in a single DNA, thereby to better understand those bacterial communication networks.
  2. Understanding of bacterial antibiotic resistance - these days, bacterial infections are often treated with antibiotics. Unfortunately, bacteria have the tendancy to pass antibiotic resistance to other bacteria through the process of [http://en.wikipedia.org/wiki/Bacterial_conjugation conjugation], thus making the antibiotics useless. Using our project, it might be possible for future researchers to better understand the mechanism by which antibiotic resistance passes among bacterial colonies, and perhaps even inhibit it
  3. To test one condition and return to the original state without killing the cell or changing any of its previous genetic and physiological characteristics
  4. To generate a pulse in the expression of a certain gene
  5. To control the amplitude of the pulse created by the plasmid

The Team

This is the second year, TUDelft participates in the iGEM competition. The group consists of 6 students, 3 instructors and a lot of advisors from TUDelft willing to help out and think with us when it is necessary. An overview of the people involved and our competences can be found on the team page.