Team:TUDelft

From 2009.igem.org

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=Welcome to the award winning 2009 Bacterial Relay Race=
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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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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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='''Home'''=
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==The Project - Bacterial Relay Race==
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This is the first template of the TU Delft 2009 iGEM team wiki! On this page information about the project and its progress can be found.
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== The Team ==
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This is the second year the TU Delft participates in the iGEM competition.
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The group consists of : (list of members to come here)
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a number of instructors and a lot of advisors, willing to help out and think with us when this 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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== The Meetings (as the meetings section, I can not understand my difference with the notebook section...)==
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'''Minutes, action points'''
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=== April 7th, 2009 ===  
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'''Orr'''
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'''Project description'''
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*''Bologna 2008 - Ecoli.PROM: an Erasable and Programmable Genetic Memory with E. coli''
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The Bologna team created here a genetic memory for E.coli that would switch between two states as a response to a certain signal (a UVc signal would inhibit Lex A (an inhibitor of LacI), thus allowing the production of LacI, whereas an IPTG signal would inhibit LacI and allow the production of TetR).
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*''Cambridge 2008 - iBrain: Foundations for an Artificial Nervous System using Self-Organizing Electrical Patterning''
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In this project, the Cambridge team decided to do three simultaneous sub-projects: one involved the creation of an artificial neurological system for E.coli (using potassium channels to transfer the ion and thus allow for a gradient of the ions), the second involved generating Turing patterns in order to integrate two signalling systems into Bacillus subtilis, and the third part involved generating standardized tools and techniques for B. subtilis. We learned from this project an important lesson: quality is definitely more important than quantity, and there is no point of doing many simultaneous experiments if we cannot finish any one of them properly.
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*''KULeuven 2008 - Dr. Coli, the bacterial drug delivery system''
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In this project, the KU Leuven team presented the idea of using E.coli as a transporter of medication in such a way that it would be targeted at a specific location. Furthermore, the E.coli would react to the presence of foreign organisms and would express certain proteins to destroy them, followed by it's self destruction after the area would be completely cured. It is important to emphasise that the project was not intended to produce a specific medication to a specific disease, but merely as a way to show that the general concept of curing a disease in a direct manner is possible.
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'''Sriram'''
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*''Illinois - Biomolecular fluorescence biosensor system: cell bases biosensor system''
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*''Ljubljana, Slovenia - Virotrap - A synthetic biology approach against HIV''
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*''Ljubljana, Slovenia - Engineered Human cells - say no to sepsis''
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'''Tim Weenink'''
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*''ESBS Strasbourg - Binary generation counting in Yeast''
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*''University of Ottowa - Puslegenerator in Yeast''
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*''Calgary Wetware - Quorum coupled bacteriocin release (engineering a champion)''
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===17th April 2009===
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'''Tim Vos'''
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*''MIT - Biogurt: A Sustainable and Savory Drug Delivery System''
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*''Groningen - Conway’s Game of Life in real life''
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*''UFreiburg - Modular Synthetic Receptor System''
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'''Daniel'''
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*''Harvard - bactricity''
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*''ETH Zurich - Random walks towards the minimal genome''
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*''Slovenia - Immunobricks''
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'''Saeed'''
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*''Caltech - Engenering multi-functional probiotic bacteria''
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The human gut houses a diverse collection of microorganisms, with important implications for the health and welfare of the host. They aimed to engineer a member of this microbial community to provide innovative medical treatments. Our work focuses on four main areas: (1) pathogen defense either by expression of pathogen-specific bacteriophage or by targeted bursts of reactive oxygen species; (2) prevention of birth defects by folate over-expression and delivery; (3) treatment of lactose intolerance by cleaving lactose to allow absorption in the large intestine; and (4) regulation of these three treatment functions to produce renewable subpopulations specialized for each function. E-Coli a non-pathogenic microbe in the guts.
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Nissle 1917 is a commercially available[2] non-pathogenic, probiotic strain of E. coli.
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Oxidative Burst.
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In order to help guard against infections of the gut, we wish to engineer a strain of E. coli capable of killing bacterial pathogens. White bloodcells are able to do this, but they do migrate to large intestinal lumen where pathogens can reside. Since E-coli is adapted to this environment, it is a good candidate .
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Acylhomoserine lactones(AHL) are small communication molecules between bacteria. AHL is able to diffuse across membrane. This communication system contains two main components LuxI, an AHL producer and LuxR  an AHL dependent transcriptional activator. Engenired E.Coli strain is able to detect AHL from pathogens. This pathogen detection activates pyruvate oxidase which uses pyruvate to produce hydrogen perioxide, to kill the pathogens. An E.Coli catalase was used to protect the cell from cells killing, so they first were able to accumulate hydrogen perioxide before oxidative burst otherwise perioxide production would lead killing of the cell only.
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LuxR activates several gene including LuxI. Here they used LuxR in a sensing mechanism.
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When LuxR binds AHL its will overexpress hydrogen perioxide coding genes.
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Entire system was onto a high copy plasmide in E.Coli.
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They showed the system is able to detect and kill pathogens by a coculture assay. They have successfully demonstrated the overproduction of hydrogen peroxide in E. coli (JI377) using the pyruvate oxidase from S. pneumoniae. This “oxidative burst” is sufficient to kill a competing strain of JI377 cells in co-culture assays
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Difficulties:
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The most surprising finding was that the cells began expressing hydrogen peroxide a full hour before they were induced with AHL. The current hypothesis is that some component of the rich SOC media mimicked AHL and activated LuxR. However, no such autoinduction occurred in the defined minimal media M9. It would be interesting to see if LuxR spontaneously activates expression in a rich defined media
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Production of hydrogen peroxide is not a normal occurrence in the large intestine, and its effects would need to be investigated before the engineered strain could be used to fight fection.
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*''Heidelberg - Ecolicense to kill''
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*''Valencia - Hot Yeast''
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Idea:
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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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Heat is vital for life. Some organisms are able to maintain their internal temperature constant, while other not. UCP1, thermogenin is a mammalian uncoupling protein in the mitochondrial inner membrane. When protons pass through the  UPC complex instead of the ATP synthase complex they produce heat instead of ATP. They tried to express the UPC1 in a S.cerevisiae strain, so this strain would be able to maintain its temperature constant in a given range.
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Applications:
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'''Our project is made up of three modules:'''
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- A cell which is able to maintain its own temperature so no external heating would be necessary, this could reduce the electrical costs in a lab.
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- The system could be implement in some plant species. If a plan6 would be able to maintain its own temperature it could grow in a colder temperature or survival frost.
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1) [https://2009.igem.org/Team:TUDelft/Conjugation_Overview Conjugation]
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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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In order to detect and measure temperature production they build a Liquid Cultured Calorimeter(LCC). Therefore they used commercial thermo flasks, isolation material(Armaflex), hardware and software. The isolation material Armaflex caused some problems because it reacts with water.  
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2) [https://2009.igem.org/Team:TUDelft/SDP_Overview Self Destructive Plasmid] (SDP)
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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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They build a UPC + strain, a UPC - strain and two mutants. Gly 76 and Gly 175 mutant(deletion in 76 or 175 Gly triplet). LCC experiments showed that the two mutants where able to heat up there own medium compared to the UPC + and UPC- strain. Growth kinetic experiments were done ass well. These showed that the UPC + and the two mutants growth much slower than the UPC – strain, due to uncoupling and thus no ATP production.
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They made a  PROPOSAL FOR A CODE OF ETHICAL PRACTICES
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3) [https://2009.igem.org/Team:TUDelft/Module_3_Overview Delay device]
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FOR SYNTHETIC BIOLOGY BASED ON THE HOT YEAST PROJECT.
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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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{|align="justify"
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'''Some potential applications for this project are'''
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|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.
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Welcome to the Wiki of the TU Delft team for iGEM 2009. The site is still under construction, but as soon as it is finished, we hope to keep with the standards of the TU Delft team last year.
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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.
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|[[Image:Example_logo.png|200px|right|frame]]
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#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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<!--- ''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''--->
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#To control the amplitude of the pulse created by the plasmid
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With our 7 participants and 4 instructors, we are enthusiastic to start working on our project (whatever it may be).
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==The Team==
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This is the second year, TUDelft participates in the iGEM competition.
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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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|[[Image:Teamtudelft.png|right|frame|Your team picture]]
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{{Template:TUDelftiGEM2009_end}}
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|align="center"|[[Team:TUDelft | Team Example]]
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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.

Retrieved from "http://2009.igem.org/Team:TUDelft"