Team:Calgary

From 2009.igem.org

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SPONSOR OF THE MONTH
 
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<p align="justify"><a href="http://www.vrwcanlab.com/">VWR</a><br>
 
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VWR International is a global laboratory supply and distribution company that has enabled research advancement for iGEM Calgary through the distribution of high quality lab supplies, reagents and equipments. VWR services the industrial, life science, clinical education and pharmaceutical markets as the world’s leading distributor of scientific equipment. Its tremendous support and contribution to the iGEM project has recognized VWR among this year’s Bronze sponsors. Thank you VWR and Congratulations.
 
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OUR SPONSORS
 
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iGEM - INTERNATIONAL GENETICALLY ENGINEERED MACHINES
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THE SECOND LIFE PROJECT
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The iGEM competition is a synthetic biology competition held annually at Massachusetts Institute of Technology (MIT) in November.  Started in 2004, the iGEM Jamboree brings together  teams from multiple universities to compete on an international stage.  The competition allows undergraduate teams from all over the world to be part of the emerging field of Synthetic Biology, an intertwining of  principles from Biology and Engineering. For more information about iGEM, please visit their <a href="http://www.igem.org" target="_blank">official website</a>.
 
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The U of C iGEM team is made up of 15 undergraduate students from Health Sciences, Engineering, Computer Science and Kinesiology as well as 4 facilitators.  For more information regarding the U of C iGEM Enterprise, please visit our <a href="http://igem.ucalgary.ca/ " target="_blank">website</a>.
 
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NAVIGATION
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An Introduction to Second Life
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Need help navigating our site? Click <a href="https://2009.igem.org/Team:Calgary/Sitemap">HERE</a> for a navigational guide and sitemap. Or, follow our tour:
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<a href="http://www.secondlife.com">Second Life</a> is an online, virtual world, where every object, costume, creature and patch of land is crafted by inhabitants. It is a 3D chat engine, videogame platform, and virtual classroom all rolled into one.
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A TOUR OF iGEM CALGARY
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Welcome to the iGEM Calgary wiki! This tour will give you a broad overview of our project, through our different subgroups and what we've been up to lately. This is the <b>first step</b> of our tour! Here you can click and see a few pictures of our adventures in synthetic biology, as well as leave some comments and read a brief overview of iGEM (which is above) and of our project (which is below). Once you've finished exploring our front page, please click <a href="https://2009.igem.org/Team:Calgary/Team#Tour">HERE</a> for an intro to our team!
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iGEM Calgary is venturing aggressively into Second Life, harnessing the power of its modeling and scripting tools to create interactive models of classical operons and synthetic biology systems. We will imagine the future of synthetic biology, and walk students through the laboratories of today. In the past, our team has run seminars and lectures to introduce new students to the terminology and technology behind iGEM. In the future, students will interact with model systems directly and experiment with them to see how they work.  
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THE PROJECT - COMMUNICATION
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Communication is essential in our everyday lives; it drives collaboration, understanding, and progress. The University of Calgary iGEM Team recognizes the importance of communication in developing the field of synthetic biology. This year, our team is exploring the development of a communication system in <i>E. coli</i>: the AI-2 signalling system. This system allows for the coordination of bacterial behaviour, essentially allowing a large group to act as a single organism.<br>
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Using mathematical modeling, we are developing models that allow us to predict and evaluate the signalling system's behaviour, thus characterizing the circuit. We have chosen to approach modelling of our system through membrane computing and Matlab.
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Beyond the development of a communication system between bacteria, we have also explored and demonstrated methods of communication with the public. For synthetic biology to flourish, there needs to be meaningful discourse between individuals, whether within the synthetic biology community, with other disciplines, or with the public. This is especially important when discussing the ethical issues that arise from synthetic biology. Our team is examining multiple aspects of concerns regarding synthetic biology, and looking at novel, interesting ways to communicate the results of our exploration to the public.
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Access to Second Life is free, simply create a free account <a href="http://www.secondlife.com">HERE</a>, download the client, and you're good to go!
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For meaningful discourse to occur, all participants require a working knowledge of the concepts they are discussing. Education is a fundamental aspect of providing and spreading such information. This year, our team is using multiple approaches in spreading information to the public regarding iGEM and synthetic biology, as well as providing educational opportunity to students. Such outreach programs include our High-School workshop. We are also developing an educational tool for teaching synthetic biology within the virtual program Second Life. In Second Life, we are creating the means to teach the potentials of synthetic biology, the assembly of genetic circuits, and molecular biology lab procedures. We hope that our virtual learning environment will allow for the training of future iGEMers in molecular biology.
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In addition to utilizing education and outreach to raise the profile of synthetic biology, our fundraising endeavors have also allowed us to create more interest in this field. Our communication with businesses in many industrial sectors allows for the discussion of the opportunities and future developments provided by synthetic biology and the potential applications of our signalling circuit.
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Another important aspect of communication in this competition is the availability of collaborative work, within our own team and as a community itself. Our team is made up of students from health sciences, kinesiology, and engineering;  who are actively participating in interdisciplinary work. This requires the ability to communicate information to people from different backgrounds and perspectives. As well, iGEM allows us to communicate with other teams at an international scale. We hope to establish means of communication and thus cooperation with other teams in our respective projects, enhancing the iGEM experience.
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The wetlab, modelling, second life, human practices, and fundraising components of our project have allowed us to establish communication at the cell, individual, and synthetic bio community levels.
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QUORUM SENSING and OUR PROJECT
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Second Life's Role in iGEM
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Bacteria are able to communicate by producing and releasing chemical signal molecules termed autoinducers in a process called Quorum Sensing (QS) (1).  An increase in local population density of bacteria results in the accumulation of autoinducers until a minimal threshold concentration is reached, whereby bacteria are able to organize their behaviour by coordinating their gene expression. Such coordinated behaviour includes virulence induction, swarming, biofilm formation and genetic competence (2).
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So what does iGEM have to do with Second Life? Well, the problem with doing an iGEM project at university is this: sooner or later all of the students graduate. Even those who decide to participate in an iGEM team several years in a row have to get on with their lives sooner or later. The result is that a huge amount of time is spent educating the new year of students, and this problem can be especially acute for teams of entirely undergraduates like ours. Many of our students are in their first or second year, many have never been in a molecular biology lab before, and they've got to learn all the ropes if they want to have a hope of competing at iGEM level.
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Ultimately, all this time spent training the next generation will pay off with a generation of new scientists, the synthetic biologists. But for right now, we really just need to get all the cloning and biobrick assembly and system tests and a dozen other kinds of work done by the end of summer.
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QS was first observed in the bioluminescent bacteria<i> Vibrio fischeri</i> (3), where light was emitted only at high population densities, but could be induced in low population densities with the presence of an extracellular substance, later identified as the autoinducer N-acylhomoserine  (AHL) (4).
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Enter Second Life. SL has gained a lot of attention for its potential as an educational platform. The most often touted feature is that SL can offer a classroom-like environment for people at any distance from one another. While the iGEM Calgary island will make an excellent hangout for idle iGEMers the world over, our focus is less on creating a classroom, and more on presenting concepts directly. We want to make it easier for new students to grasp the basics of synthetic biology by making it accessible and interactive. This is where SL's object creation and scripting facilities come into play: we can create anything we want, from molecules to cells to lab equipment, and then make it behave like the real thing.
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Further research in QS led to the discovery of the universal signaling molecule (5)  autoinducer-2 (AI-2), which has been characterized in the gram-negative, bioluminescent marine bacterium <i> Vibrio harveyi</i>  (1). AI-2 binds to the periplasmic protein LuxP forming an AI-2-LuxP complex that interacts with LuxQ, a membrane bound histidine kinase (6). At low population density corresponding to low AI-2 levels, this AI-2 signalling acts as a phosphorylation cascade, resulting in the phosphorylated form of luxO. Phospho-LuxO complexes with transcription factor σ54 to activate the transcription of the genes encoding five regulatory small RNAs (sRNAs) termed Qrr1-5 (7). These sRNAs bind and destabilize the mRNA of luxR (8) , a transcriptional activator of the luciferase operon luxCDABE (9). As the mRNA of luxR is degraded in the presence of low levels of AI-2 and low cell density, <i> V. harveyi </i>will not express bioluminescence.
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In high population densities and thus high AI-2 levels, LuxQ changes from a kinase to a phosphotase, and the result is unphosphorylated LuxO (1). There is no complexing with σ54, and no production of sRNAs. This leads to unblocked luxR mRNA allowing its translation that drives the expression of bioluminescence via luciferase.
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We, the University of Calgary's 2009 iGEM team, have engineered this <i> Vibrio harveyi</i> AI-2 signaling system in <i> Escherichia coli</i>  using the molecular cloning techniques used in the International Genetically Engineered Machines (iGEM) competition. This system is coupled with the expression of aiiA, a gene that encodes an AHL-degrading enzyme partaking in quorum quenching, allowing us to target biofilm maintenance.  
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<b>References</b>
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(1)Waters, C.M. & Bassler, B.L.. Quorum sensing: cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21, 319-346 (2005).
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(2)Hardman, A.M., Stewart, G.S. & Williams P. Quorum sensing and the cell-cell communication dependent regulation of gene expression in pathogenic and non-pathogenic bacteria. Antonie van Leeuwenhoek. 74, 199-210 (1998).
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(3)Nealson, K. H., Platt, T. & Hastings, W. Cellular Control of the synthesis and activity of the bacterial bioluminescent system. J. Bacteriol. 104, 313-322 (1970).
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(4)Eberhard, A., Burlingame, A.L., Kenyon, G.L., Nealson, K.H. & Oppenheimer, N.J. Structural identification of autoinducer of Photobacterium fischeri luciferase. Biochemistry. 20, 2444-2449 (1981).
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(5)Sun, J., Daniel, R., Wagner-Dobler I. & Zeng, A.P. Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways, BMC Evol. Biol. 4, 36 (2004).
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(6)Bassler, B.L., Wright, M., Silverman, M.R. Multiple signaling systems controlling expression of luminescence in Vibrio harveyi: sequence and function of genes encoding a second sensory pathway. Mol. Microbiol. 13, 273-286 (1994).
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(7)Lilley, B.N. & Bassler, B.L. Regulation of quorum sensing in Vibrio harveyi by LuxO and sigma-54. Mol. Microbiol. 36, 940–54 (2000).
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(8)Lenz, D.H., Mok, K.C., Lilley, B.N., Kulkarni, R.V., Wingreen, N.S. & Bassler, B.L.The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118, 69–82 (2004)
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(9)Swartzman, E., Silverman, M. & Meighen, E.A. The luxR gene product of Vibrio harveyi is a transcriptional activator of the lux promoter. J. Bacteriol. 174, 7490–7493 (1992)
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LATEST NEWS
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Our Projects
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<div class="heading">iGEM Calgary in UToday, September 18th</div>
 
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Our work in Second Life has been featured today in our University's online magazine, UToday!
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Our work in Second Life breaks down into three projects, each focusing on synthetic biology from a different perspective:
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<p>For more details, click <a href="https://2009.igem.org/Team:Calgary/News">HERE</a>.
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The Synthetic Domain is a vision of the future of synthetic biology. It is a collection of futuristic organisms, each with useful properties and abilities included in their design. We have cells to produce your vitamins for you, cells to fight off pathogens for you, and more. The Synthetic Domain is an introduction to the potential of synthetic biology for everyone, and serves as a source of inspiration for young scientists.  
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The Biobrick Simulator takes DNA, proteins, other molecules from the core of the registry of biological parts, and simulates their behaviours. Instead of trying to work out how all the regulation in common systems work on paper, students can quickly and easily build the systems online to get the hang of it. The simulator also includes a level based introduction to the most common kinds of biobrick parts, designed to make the introduction to iGEM easier.  
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The Virtual Lab provides an interactive introduction to the various techniques involved in the application of synthetic biology and allows for basic instruction through a lab through use of lab missions. The lab activities or mission incorporate procedures such as DNA extraction, bacterial transformation, and restriction digest, which are common practices during the process of constructing biological circuits that may be put to use within bacteria. These activities are separated by difficulty, time and there are also opportunities to apply what is learned from these activities to non-structured sections of the lab. It is meant to be understandable to high school students, who may apply their newly obtained knowledge after they have had a chance to grasp basic concepts of molecular and synthetic biology in the other domains of the island. It may also serve as a successful introduction to lab procedures for future iGEM team members.
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Revision as of 22:29, 2 October 2009

University of Calgary

UNIVERSITY OF CALGARY


THE SECOND LIFE PROJECT
An Introduction to Second Life
Second Life is an online, virtual world, where every object, costume, creature and patch of land is crafted by inhabitants. It is a 3D chat engine, videogame platform, and virtual classroom all rolled into one.

iGEM Calgary is venturing aggressively into Second Life, harnessing the power of its modeling and scripting tools to create interactive models of classical operons and synthetic biology systems. We will imagine the future of synthetic biology, and walk students through the laboratories of today. In the past, our team has run seminars and lectures to introduce new students to the terminology and technology behind iGEM. In the future, students will interact with model systems directly and experiment with them to see how they work.

Access to Second Life is free, simply create a free account HERE, download the client, and you're good to go!

Second Life's Role in iGEM
So what does iGEM have to do with Second Life? Well, the problem with doing an iGEM project at university is this: sooner or later all of the students graduate. Even those who decide to participate in an iGEM team several years in a row have to get on with their lives sooner or later. The result is that a huge amount of time is spent educating the new year of students, and this problem can be especially acute for teams of entirely undergraduates like ours. Many of our students are in their first or second year, many have never been in a molecular biology lab before, and they've got to learn all the ropes if they want to have a hope of competing at iGEM level.

Ultimately, all this time spent training the next generation will pay off with a generation of new scientists, the synthetic biologists. But for right now, we really just need to get all the cloning and biobrick assembly and system tests and a dozen other kinds of work done by the end of summer.

Enter Second Life. SL has gained a lot of attention for its potential as an educational platform. The most often touted feature is that SL can offer a classroom-like environment for people at any distance from one another. While the iGEM Calgary island will make an excellent hangout for idle iGEMers the world over, our focus is less on creating a classroom, and more on presenting concepts directly. We want to make it easier for new students to grasp the basics of synthetic biology by making it accessible and interactive. This is where SL's object creation and scripting facilities come into play: we can create anything we want, from molecules to cells to lab equipment, and then make it behave like the real thing.
Our Projects
Our work in Second Life breaks down into three projects, each focusing on synthetic biology from a different perspective:

The Synthetic Domain is a vision of the future of synthetic biology. It is a collection of futuristic organisms, each with useful properties and abilities included in their design. We have cells to produce your vitamins for you, cells to fight off pathogens for you, and more. The Synthetic Domain is an introduction to the potential of synthetic biology for everyone, and serves as a source of inspiration for young scientists.

The Biobrick Simulator takes DNA, proteins, other molecules from the core of the registry of biological parts, and simulates their behaviours. Instead of trying to work out how all the regulation in common systems work on paper, students can quickly and easily build the systems online to get the hang of it. The simulator also includes a level based introduction to the most common kinds of biobrick parts, designed to make the introduction to iGEM easier.

The Virtual Lab provides an interactive introduction to the various techniques involved in the application of synthetic biology and allows for basic instruction through a lab through use of lab missions. The lab activities or mission incorporate procedures such as DNA extraction, bacterial transformation, and restriction digest, which are common practices during the process of constructing biological circuits that may be put to use within bacteria. These activities are separated by difficulty, time and there are also opportunities to apply what is learned from these activities to non-structured sections of the lab. It is meant to be understandable to high school students, who may apply their newly obtained knowledge after they have had a chance to grasp basic concepts of molecular and synthetic biology in the other domains of the island. It may also serve as a successful introduction to lab procedures for future iGEM team members.