http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Chev1n&year=&month=2012.igem.org - User contributions [en]2024-03-28T22:07:23ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:Queens_CanadaTeam:Queens Canada2013-01-15T03:05:29Z<p>Chev1n: </p>
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<h3>ChimeriQ</h3><br />
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<span class="ca-quote">&ldquo;</span><br />
<span>Engineering chimeric flagella for a better world</span><br />
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<h6>Using flagella as scaffolds</h6><br />
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This year, our team is investigating new methods of increasing the efficiency of biosynthesis and bioremediation using modified bacteria. Most bacteria possess tail-like appendages called flagella, which can be genetically altered for novel functions. Each flagellum is made up of a number of polymerizing proteins, often called flagellin.<br />
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By making chimeric insertions in the variable domain of the flagellin, we can incorporate fluorescent proteins, enzymes, and scaffolding proteins to extend the possible applications. By having a protein inserted into each monomer, it is possible to cluster thousands of proteins in close proximity to each other, thereby increasing the efficiency of production and break-down of various products.<br />
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<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/ChimeriQ">Description</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/ChimeriQ/Results">Results</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/ChimeriQ/Parts">Parts</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Notebook/Week1">Notebook</a></li><br />
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<h3>Chimeric Proteins</h3><br />
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<span>A handy guide for introducing you to chimeric protein design.</span><br />
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<h6>How to make chimeric proteins</h6><br />
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<p>There are a lot of considerations that need to be made in the design of chimeric proteins. To help introduce future teams to chimeric proteins and their standard design, we have summarized our work into a resourceful guide that covers all (or almost all) of the considerations that need to be made in designing a chimeric protein from start to finish.</p><br />
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<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Guide/DNA">Part 1: DNA </a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Guide/mRNA">Part 2: mRNA</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Guide/Protein_Structure">Part 3: Protein Structure</a></li><br />
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<h3>SynthetiQ</h3><br />
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<span>The first dance group to perform at a research conference</span><br />
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<h6>SynthetiQ</h6><br />
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<p>SynthetiQ Experimental Dance is a group devoted to creating, testing and analyzing movement, in the form of dance, as a means of explaining scientific concepts. Inspired by Dr. John Bohannon's “Dance Your PhD Contest” and his TEDxBrussels talk in 2011, our first project was partnered with the Queen's Genetically Engineered Machine (QGEM) Team. Because our research and learning goals align perfectly with those of the QGEM team, we will be researching and presenting together at the International Genetically Engineered Machine Competition in the fall.</p><br />
<p>As a part of our 2012 iGEM project, we started this group, devoted to using dance to explain concepts associated with synthetic biology, as well as our own research.<br />
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<p>We made dance into our own unique tool for teaching others scientific concepts, as an alternative to use powerpoint presentations. </p><br />
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<li><a href="https://2012.igem.org/Team:Queens_Canada/SynthetiQ">Read more</a></li><br />
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<h3>Team</h3><br />
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<span>Who we arespan><br />
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<h6>Team</h6><br />
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<p>QGEM is an undergraduate team composed of both full-time members and volunteers. All faculties of the university are eligible to participate in the iGEM team and previous members have from the departments of Chemical and Mechanical Engineering, Engineering Chemistry, Biology, Biochemistry, Life Science and Computing.</p><br />
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<li><a href="https://2012.igem.org/Team:Queens_Canada/Team">Read more</a></li><br />
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<h3>Partners</h3><br />
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<span>We would once again like to thank our generous sponsors.</span><br />
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<h6>Partners</h6><br />
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<p>We would like to thank our sponsors who have supported us financially, allowing us to pursue this project. In particular, we would like to thank Queen's University and the Oil Sands Leadership Initiative. </p><br />
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<li><a href="https://2012.igem.org/Team:Queens_Canada/Partners">Read more</a></li><br />
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<h3>Safety</h3><br />
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<span> Safety doesn't happen by accident.</span><br />
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<h6>Safety</h6><br />
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<p> Would any of your project ideas raise safety issues in terms of...researcher safety, public safety, environmental safety?</p><br />
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<li><a href="https://2012.igem.org/Team:Queens_Canada/Safety">Read more</a></li><br />
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</html></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/SynthetiQ/howTeam:Queens Canada/SynthetiQ/how2013-01-15T02:21:00Z<p>Chev1n: </p>
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<h1>How?</h1><br />
<p><b>This is our methods section.</b> This page will highlight some of the key points that brought our project together.<br />
<h3>Inspiration:</h3><br />
The initial inspiration for this project came from two main things:<br />
<ol><br />
<li>John Bohnanon's talk TEDxBrussels:<br />
<ul><br />
<li>This was a brilliant demonstration and proposal of the idea of using dance to explain and teach scientific concepts.<br />
</ul><br />
<li>Emma Ware winning the social sciences category of the 2011 Dance Your PhD Contest:<br />
<ul><br />
<li>Emma was a PhD student with Department of Psychology, and fellow dancer. After finding out about this news shortly after watching John Bohannon's talk. DYPhD and the idea of using dance to demonstrate science felt a lot closer to home.<br />
</ul><br />
</ol><br />
<h3>Recruitment:</h3><br />
Here are a few key reasons why this idea might sound appealing to a dancer, or anyone:<br />
<ul><br />
<li>It's a unique opportunity and experience<br />
<li>International exposure<br />
<li>This is the perfect research setting (Would any professional level conference really find this appropriate and/or worth the effort?)<br />
<li>Synbio research is awesome.<br />
<li>Why not?<br />
</ul><br />
<br><b>The Summer</b><br />
<p>The summer work started by contacting a number of different dancers, or others involved with dance about this idea. Initially, there was very little response. This could have been for a number of reasons:</p><br />
<ul><br />
<li>No one actually thought this was a good idea<br />
<li>Everyone was out of town for the summer or busy<br />
<li>We weren't promoting this properly<br />
</ul><br />
<p>Had we started contacting people before the summer started, we might have had better results.</p><br />
<ol><br />
<li>John Bohannon:<br><br />
There were few things that Dr. Bohannon suggested.<br />
<ul><br />
<li>Find a dancer that knows people in the dance community and will be able to lead the project. Maybe even hire this person as an artist in residence.<br />
<li>Make it fun, hilarious and incorporate other dance styles.<br />
<li>University campuses are crawling with dancers.<br />
</ul><br />
<li>Melissa Wilton:<br><br />
Melissa gave us lots of advice on the logistics of putting together a routine for our presentation as well as recruitment. Her involvement and interest was very inspirational and her connections helped us with the recruitment of our dance team. Her support lead us to our article in the <a href="http://www.emckingston.com/20120809/lifestyle/Dance+like+everybody%27s+watching">Kingston EMC</a>. </li><br />
</ol><br />
<h3>PCR</h3><br />
<p>Over the rest of the summer, we worked on just doing some general bodystorm, which lead to our DNA model. And, we gathered everyone together to make our video about PCR. Even though we filmed this around the end of July, and intended to release it shortly after. We ended up spending pretty much all of our time trying to get our lab work to actually work. But, we were hoping to get more content in the video and talk specifically about amplifying DNA out of a genome. In the end, the video was finished and uploaded during the week of the wiki-freeze.</p><br />
<h3>September</h3><br />
<p><br />
September rolled around way faster than we had hoped, and our lab stuff wasn't going very well at all either. However, with the publicity from our article in the Kingston EMC and the return of Queen's students for the school semester, we made another recruitment push.<br><br />
<p><br />
We got in touch with the Queen's Dance Club, who passed our information to their group of teachers. In the first week of September, our first meetings were with Devon Ryan, who became our choreographer and Sam Demetrious, who became a dancer on our team. So we quickly put together a draft of our script, which only really talked about some of the foundation of our project (because we didn't have any results yet), and we worked together on how we could actually make this into a dance. Now that all the students have returned to Queen's, Devon and Sam were able help us with recruitment.</p><br />
<p>Next, we started practicing as a group.</p><br />
<h3>Logistics and the Regional Jamboree</h3><br />
<p>Naturally, research conferences in general are not designed to accommodate dance routines, and some lecture halls, particularly in the sciences, have large, fixed tables at the front of the rooms for running demos. There is also travel and accommodations to look after.</p><br />
<ol><br />
<li>Travel<br />
<ul><li>Because we were bringing so many people to the iGEM Jamboree, transportation was a bit challenging and this was probably the largest additional cost. We had considered paying to rent a bus, that would travel with all of the iGEM teams from Ontario, and split the cost. This started out as a really great idea, and an awesome way to meet our neighboring teams, but this didn't end up working out. Possibly because it was a little too close to the competition when we started planning this. In the end, we decided to opt for rental cars but, we were short on drivers. So we asked a few friends, rented 3 vans and made it to the jamboree. And, we only got a little bit lost.<br />
</ul><br />
<li>Accommodations<br />
<ul><br />
<li>Accommodations was the second additional cost. We ended up renting one extra room to accommodate our entire team and dancers, which was only one more than what we would have done normally. We probably could have saved money by renting at a cheaper hotel nearby but we stuck with the iGEM rate at the Pittsburgh Marriott and kept our entire group together.<br />
</ul><br />
<li>Presentation Space<br />
<ul><br />
<li>And this was probably the biggest challenge. Leading up to the competition, it was really important that we get as much information as we could about what sort of presentation space we would be using for the actual presentation. Initially we had a lot of help from the Americas East Regional Jamboree organizer, Sarah Clements from IBE. However, simply because of the way that the schedule is made, and the timing of things leading up to it, we ended up being scheduled in a room that had large, unmovable, demo table in the front of it. After finding out our placement, we went there first thing in the morning to look at it. After some last minute switches, we ended up being shifted to a space which had a movable table, and we were able to perform. So special thanks goes out to Sarah and Meagan Lizarazo for helping us arrange this.<br />
</ul><br />
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<h3>After the Jamboree</h3><br />
<p>We won the Best Model award! This was an amazing achievement for our team, and the first time that we have won an individual award. Originally, this project was more aimed at human practices. However, the explanation for why this was an excellent modelling project made perfect sense. This project, and its website, initially had very little documentation attached to it, with virtually no feedback, or detailed content. Ideally, we would have liked to really get this going, and possibly even do some testing to see whether or not people retained information better from the dance compared to a pure powerpoint presentation. There is so much potential to do some really creative outreach and get more people involved. But, we'll have to leave this for the future. For now, we are working on perfecting our routine and making a few additions based on some feedback after the regionals and a little bit of content we wanted to add here and there.</p><br />
<h3>At the finals!</h3><br />
In this second presentation, many of the logistics and aspects of the presentation went much more smoothly now that we'd had a bit more experience. The weekend was wonderful for both our dancers and iGEMers and we got a lot of excellent feedback on our presentation. Next, we'll be waiting for our video footage from iGEM so that we can share our presentation with everyone!<br />
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</br></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/SynthetiQ/whowhyTeam:Queens Canada/SynthetiQ/whowhy2013-01-15T01:41:25Z<p>Chev1n: </p>
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<h1>Why?</h1><br />
<p><b>This is the big question.</b> Why would anyone do this? What are the advantages? Is it worth the effort? And there are so many different answers to these questions. Some of these answers can be found in Dr. Bohannon's TEDxBrussels talk can be found from feedback of the Dance Your PhD Contest. In his series of articles in Science, called the <a href="http://www.sciencemag.org/site/feature/misc/webfeat/gonzoscientist/">Gonzo Scientist</a>, he talks about each year of the competition as well as number of his other projects. In Episode 13, he asked the participants of the DYPhD Contest why they did it.</p><br />
<p>In general, dancing their science helped them:</p><br />
<ul><br />
<li>Get jobs and scholarships.<br />
<li>Summarize extensive research, into a few minutes of video.<br />
<li>Explain their work to friends and family.<br />
<li>Have lots of fun<br />
</ul><br />
<p><b>The kinesthetic learning style in scientific theory is virtually non-existent.</b> Lectures and textbooks are the predominant form of teaching. But, there's so much potential in teaching with movement. Everyone remembers the "Right-hand rule", be it from physics, or the helical direction of DNA. Teaching and learning through dance or movement can extrapolate from that basic idea. We can make science more like riding a bike, even if your mind doesn't quite remember how to do it, your body does, and after just a couple tries, it's just like you've been doing it for years.</p><br />
<p><b>One of the big goals of the DYPhD contest, is to make your research easier to understand, using a few words as possible.</b> Overall, we want there to be a better understanding by the public. On a larger scale, it's important for the general public to have an understanding of the impact of scientific research. By gaining more support and awareness from the public, research and development can become more of a priority for the government and future elections.</p><br />
<p><b>We all have friends and families that ask about our research.</b> By using this form of communication, we are able to simplify things. So that they can understand what we're doing and why it's exciting, and then they can get excited and tell or show others our research.</p><br />
<p><b>Body language is something that everyone can speak.</b> So whether you're trying to explain something to somebody who doesn't have a scientific background, or doesn't even speak the same language as you, this method will be the most effective way of communicating the ideas. This doesn't just appeal to interpretation by the mind, but to also basic human instincts and how we interpret the expression or movement of another human being.</p><br />
<h3>What about us?</h3><br />
<p><b>In our presentation at the iGEM Americas East Regional Competition, we wanted to test what it would be like to do something like this in an actual research setting.</b> We imagined a situation in which dance is the commonly used method to present research. And that's how we designed our presentation, incorporating the dancers to explain our research naturally, without pointing out that these are our dancers.</p><br />
<p>This presentation has already turned up results:</p><br />
<ul><br />
<li>A packed auditorium for our presentation.<br />
<li>The Best Model Award<br />
<li>Advancement to the World Finals<br />
<li>Gold Medal<br />
<li>Lots of attention at our school and worldwide<br />
<li>Everyone learned something new about synthetic biology<br />
</ul><br />
<p>And these are just our initial results. Because our team is composed solely of undergraduate students from many different backgrounds, we're are still waiting to see how this unique experience will benefit them in their futures. And there is so much potential. In addition to learning a new, unique dance routine, we have learned from the experiences and challenges that we have overcome and are incredibly excited to see what comes next.</p><br />
<hr><br />
<h1>Who are we?</h1><br />
<table id="syntable" align="center"><br />
<tr><br />
<td id="syntdl"><br />
<h3>Devon Ryan</h3><br />
<img src="https://static.igem.org/mediawiki/2012/e/e1/Devon2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>Choreographer, 3rd Year, Civil Engineering</b><br><br />
The moment I got the email invitation to be a part of QGEM I knew that I wanted to be a part of it. My whole life I’ve looked for ways to combine my artistic and scientific worlds. This was an amazing outlet to work with some of my favorite dancers, develop my choreography skills with challenging concepts and be on the front lines of a brand new relationship between science and dance. I am a better choreographer and academic for joining QGEM. </p><br />
</td><br />
<td id="syntdr"><br />
<h3>Sam Demetrious</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/Samd.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th Year, Sociology Major</b><br><br />
I think the Queen’s IGEM team is so unique this year in such a fantastic way! By using dance to represent the scientific concepts, the research provided by the Queen's team can reach a wider audience and even impact individuals outside the synthetic biology community. The collaboration of arts and science is a wonderful learning tool, especially for those just beginning to learn about biology, such as a sociology student like myself. </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Michelle Rea</h3><br />
<img src="https://static.igem.org/mediawiki/2012/9/9f/Michelle.png" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd, Chemical Engineering</b><br><br />
I was approached at the beginning of the school year about this project and thought it was an amazing opportunity to combine my art with research that I am interested in. Using dance as teaching and presenting tool in science is a totally new concept and the experience was definitely one of a kind as I learned about the research through dancing it out!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Leandra Guillet</h3><br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Leandra2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Arts and Science</b><br><br />
Being able to be part of something like qGEM in my first year is kind of ridiculous. It’s not something I ever thought I would be doing, but I’m so glad I got the opportunity to combine dance and science. I have really enjoyed learning more about science while using my dance background to interpret the research. It’s probably the highlight of my first year so far.</p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Melissa Guertin</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/Melissa2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd year, Civil Engineering</b><br><br />
When I was first asked to dance in a piece portraying research, I really had no idea what to expect. I went in with an open mind, and found myself very rewarded. It was so neat to not only visually represent the research, but also get my own visual aid to understand things I have not learned. I felt very rewarded when people understood our representations and interpretations at the iGem competition in Pittsburgh, as well as here at Queen's. This is such an innovative concept and I am ecstatic that I get to be a part of this new beginning!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Christina Robitaille</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/56/Chrissy.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>2nd Year, Life Science</b><br><br />
This whole experience has been amazing for me. At first I was unsure of how successful melding science and the arts would be, but kudos to Devon and Kevin because our hard work has really paid off. The SynthetiQ project has proven to be both effective and very rewarding for all of us lucky enough to be involved. I'm so glad that I got the opportunity to be a part of the team, and I really admire QGEM for taking this risk with their project. It's been an incredible journey, and I can't wait to see where they go from here!</p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Alisha Giglio</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/79/Alisha2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>2nd year, Chemistry Major</b><br><br />
Being apart of Queen’s iGEM this year has been a truly amazing experience. By combining synthetic biology and dance, I believe we have helped broaden many people’s views and hopefully made many think about new and innovative ways to portray their research, which could potentially change the world of boring science presentations as we know it. This whole experience has been rewarding as I have been able to combine two things I am interested in, as well, I am really excited to see how this concept will develop and what it will mean for dance and science in the future!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Jaclyn Kemp</h3><br />
<img src="https://static.igem.org/mediawiki/2012/1/14/Jaclyn.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Physical and Health Education</b><br><br />
I found out about the opportunity to dance for QGEM through our choreographer Devon Ryan. I was thrilled to be able to use the art of dance to model and help explain scientific concepts. I think that this approach reaches out to a broader audience who are not as familiar with synthetic biology. The movement and visual images that are created in our presentation have helped me to understand the various concepts. My hope is that this new approach to presenting information can be used and expanded on in the future!<br><br> </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Brittany Groom</h3><br />
<img src="https://static.igem.org/mediawiki/2012/f/fd/Brittany.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd Year, Nursing</b><br><br />
I am honoured to be a part of the Queen’s iGEM team and have the opportunity to portray their innovative research through a mode of communication that is not seen very often in the science field. This experience has given me so much respect for the immense amount of time and work that every team puts forth to make this event possible. I can tell that the passion the Queen’s research team has for their work is the same passion that I have for dancing and, that is ultimately why we work together so seamlessly.</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Kevin Chen</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/53/Kevin2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th year, Biochemistry</b><br>I was the overall lead of the project, covering the logistical sides of things, website, videos, driving and speaking in the actual presentation. It is really hard to describe what I have learned and gained from this project. It's just been unreal, definitely the highlight of my undergraduate degree and probably my life so far. My only dance knowledge comes from BBoying, since first year. So, I've learned a lot working with these dancers. <br />
<br />
</p><br />
</td><br />
</tr><br />
</table></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/SynthetiQ/whowhyTeam:Queens Canada/SynthetiQ/whowhy2013-01-15T01:41:05Z<p>Chev1n: </p>
<hr />
<div>{{Template:Queens_Canada/Header}}<br />
<html><br />
<br />
<br />
<body><br />
<br><br />
<br><br />
<div id="pagecontent"><br />
<h1>Why?</h1><br />
<p><b>This is the big question.</b> Why would anyone do this? What are the advantages? Is it worth the effort? And there are so many different answers to these questions. Some of these answers can be found in Dr. Bohannon's TEDxBrussels talk can be found from feedback of the Dance Your PhD Contest. In his series of articles in Science, called the <a href="http://www.sciencemag.org/site/feature/misc/webfeat/gonzoscientist/">Gonzo Scientist</a>, he talks about each year of the competition as well as number of his other projects. In Episode 13, he asked the participants of the DYPhD Contest why they did it.</p><br />
<p>In general, dancing their science helped them:</p><br />
<ul><br />
<li>Get jobs and scholarships.<br />
<li>Summarize extensive research, into a few minutes of video.<br />
<li>Explain their work to friends and family.<br />
<li>Have lots of fun<br />
</ul><br />
<p><b>The kinesthetic learning style in scientific theory is virtually non-existent.</b> Lectures and textbooks are the predominant form of teaching. But, there's so much potential in teaching with movement. Everyone remembers the "Right-hand rule", be it from physics, or the helical direction of DNA. Teaching and learning through dance or movement can extrapolate from that basic idea. We can make science more like riding a bike, even if your mind doesn't quite remember how to do it, your body does, and after just a couple tries, it's just like you've been doing it for years.</p><br />
<p><b>One of the big goals of the DYPhD contest, is to make your research easier to understand, using a few words as possible.</b> Overall, we want there to be a better understanding by the public. On a larger scale, it's important for the general public to have an understanding of the impact of scientific research. By gaining more support and awareness from the public, research and development can become more of a priority for the government and future elections.</p><br />
<p><b>We all have friends and families that ask about our research.</b> By using this form of communication, we are able to simplify things. So that they can understand what we're doing and why it's exciting, and then they can get excited and tell or show others our research.</p><br />
<p><b>Body language is something that everyone can speak.</b> So whether you're trying to explain something to somebody who doesn't have a scientific background, or doesn't even speak the same language as you, this method will be the most effective way of communicating the ideas. This doesn't just appeal to interpretation by the mind, but to also basic human instincts and how we interpret the expression or movement of another human being.</p><br />
<h3>What about us?</h3><br />
<p><b>In our presentation at the iGEM Americas East Regional Competition, we wanted to test what it would be like to do something like this in an actual research setting.</b> We imagined a situation in which dance is the commonly used method to present research. And that's how we designed our presentation, incorporating the dancers to explain our research naturally, without pointing out that these are our dancers.</p><br />
<p>This presentation has already turned up results:</p><br />
<ul><br />
<li>A packed auditorium for our presentation.<br />
<li>The Best Model Award<br />
<li>Advancement to the World Finals<br />
<li>Gold Medal<br />
<li>Lots of attention at our school and worldwide<br />
<li>Everyone learned something new about synthetic biology<br />
</ul><br />
<p>And these are just our initial results. Because our team is composed solely of undergraduate students from many different backgrounds, we're are still waiting to see how this unique experience will benefit them in their futures. And there is so much potential. In addition to learning a new, unique dance routine, we have learned from the experiences and challenges that we have overcome and are incredibly excited to see what comes next.</p><br />
<hr><br />
<h1>Who are we?</h1><br />
<table id="syntable" align="center"><br />
<tr><br />
<td id="syntdl"><br />
<h3>Devon Ryan</h3><br />
<img src="https://static.igem.org/mediawiki/2012/e/e1/Devon2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>Choreographer, 3rd Year, Civil Engineering</b><br><br />
The moment I got the email invitation to be a part of QGEM I knew that I wanted to be a part of it. My whole life I’ve looked for ways to combine my artistic and scientific worlds. This was an amazing outlet to work with some of my favorite dancers, develop my choreography skills with challenging concepts and be on the front lines of a brand new relationship between science and dance. I am a better choreographer and academic for joining QGEM. </p><br />
</td><br />
<td id="syntdr"><br />
<h3>Sam Demetrious</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/Samd.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th Year, Sociology Major</b><br><br />
I think the Queen’s IGEM team is so unique this year in such a fantastic way! By using dance to represent the scientific concepts, the research provided by the Queen's team can reach a wider audience and even impact individuals outside the synthetic biology community. The collaboration of arts and science is a wonderful learning tool, especially for those just beginning to learn about biology, such as a sociology student like myself. </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Michelle Rea</h3><br />
<img src="https://static.igem.org/mediawiki/2012/9/9f/Michelle.png" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd, Chemical Engineering</b><br><br />
I was approached at the beginning of the school year about this project and thought it was an amazing opportunity to combine my art with research that I am interested in. Using dance as teaching and presenting tool in science is a totally new concept and the experience was definitely one of a kind as I learned about the research through dancing it out!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Leandra Guillet</h3><br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Leandra2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Arts and Science</b><br><br />
Being able to be part of something like qGEM in my first year is kind of ridiculous. It’s not something I ever thought I would be doing, but I’m so glad I got the opportunity to combine dance and science. I have really enjoyed learning more about science while using my dance background to interpret the research. It’s probably the highlight of my first year so far.</p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Melissa Guertin</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/Melissa2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd year, Civil Engineering</b><br><br />
When I was first asked to dance in a piece portraying research, I really had no idea what to expect. I went in with an open mind, and found myself very rewarded. It was so neat to not only visually represent the research, but also get my own visual aid to understand things I have not learned. I felt very rewarded when people understood our representations and interpretations at the iGem competition in Pittsburgh, as well as here at Queen's. This is such an innovative concept and I am ecstatic that I get to be a part of this new beginning!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Christina Robitaille</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/56/Chrissy.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>2nd Year, Life Science</b><br><br />
This whole experience has been amazing for me. At first I was unsure of how successful melding science and the arts would be, but kudos to Devon and Kevin because our hard work has really paid off. The SynthetiQ project has proven to be both effective and very rewarding for all of us lucky enough to be involved. I'm so glad that I got the opportunity to be a part of the team, and I really admire QGEM for taking this risk with their project. It's been an incredible journey, and I can't wait to see where they go from here!</p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Alisha Giglio</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/79/Alisha2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>2nd year, Chemistry Major</b><br><br />
Being apart of Queen’s iGEM this year has been a truly amazing experience. By combining synthetic biology and dance, I believe we have helped broaden many people’s views and hopefully made many think about new and innovative ways to portray their research, which could potentially change the world of boring science presentations as we know it. This whole experience has been rewarding as I have been able to combine two things I am interested in, as well, I am really excited to see how this concept will develop and what it will mean for dance and science in the future!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Jaclyn Kemp</h3><br />
<img src="https://static.igem.org/mediawiki/2012/1/14/Jaclyn.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Physical and Health Education</b><br><br />
I found out about the opportunity to dance for QGEM through our choreographer Devon Ryan. I was thrilled to be able to use the art of dance to model and help explain scientific concepts. I think that this approach reaches out to a broader audience who are not as familiar with synthetic biology. The movement and visual images that are created in our presentation have helped me to understand the various concepts. My hope is that this new approach to presenting information can be used and expanded on in the future!<br><br> </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Brittany Groom</h3><br />
<img src="https://static.igem.org/mediawiki/2012/f/fd/Brittany.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd Year, Nursing</b><br><br />
I am honoured to be a part of the Queen’s iGEM team and have the opportunity to portray their innovative research through a mode of communication that is not seen very often in the science field. This experience has given me so much respect for the immense amount of time and work that every team puts forth to make this event possible. I can tell that the passion the Queen’s research team has for their work is the same passion that I have for dancing and, that is ultimately why we work together so seamlessly.</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Kevin Chen</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/53/Kevin2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th year, Biochemistry</b><br>I was the overall lead of the project, covering the logisitical sides of things, website, videos, driving and speaking in the actual presentation. It is really hard to describe what I have learned and gained from this project. It's just been unreal, definitely the highlight of my undergraduate degree and probably my life so far. My only dance knowledge comes from BBoying, since first year. So, I've learned a lot working with these dancers. <br />
<br />
</p><br />
</td><br />
</tr><br />
</table></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/SynthetiQ/whowhyTeam:Queens Canada/SynthetiQ/whowhy2012-10-27T03:49:31Z<p>Chev1n: </p>
<hr />
<div>{{Template:Queens_Canada/Header}}<br />
<html><br />
<br />
<br />
<body><br />
<br><br />
<br><br />
<div id="pagecontent"><br />
<h1>Why?</h1><br />
<p><b>This is the big question.</b> Why would anyone do this? What are the advantages? Is it worth the effort? And there are so many different answers to these questions. Some of these answers can be found in Dr. Bohannon's TEDxBrussels talk can be found from feedback of the Dance Your PhD Contest. In his series of articles in Science, called the <a href="http://www.sciencemag.org/site/feature/misc/webfeat/gonzoscientist/">Gonzo Scientist</a>, he talks about each year of the competition as well as number of his other projects. In Episode 13, he asked the participants of the DYPhD Contest why they did it.</p><br />
<p>In general, dancing their science helped them:</p><br />
<ul><br />
<li>Get jobs and scholarships.<br />
<li>Summarize extensive research, into a few minutes of video.<br />
<li>Explain their work to friends and family.<br />
<li>Have lots of fun<br />
</ul><br />
<p><b>The kinesthetic learning style in scientific theory is virtually non-existent.</b> Lectures and textbooks are the predominant form of teaching. But, there's so much potential in teaching with movement. Everyone remembers the "Right-hand rule", be it from physics, or the helical direction of DNA. Teaching and learning through dance or movement can extrapolate from that basic idea. We can make science more like riding a bike, even if your mind doesn't quite remember how to do it, your body does, and after just a couple tries, it's just like you've been doing it for years.</p><br />
<p><b>One of the big goals of the DYPhD contest, is to make your research easier to understand, using a few words as possible.</b> Overall, we want there to be a better understanding by the public. On a larger scale, it's important for the general public to have an understanding of the impact of scientific research. By gaining more support and awareness from the public, research and development can become more of a priority for the government and future elections.</p><br />
<p><b>We all have friends and families that ask about our research.</b> By using this form of communication, we are able to simplify things. So that they can understand what we're doing and why it's exciting, and then they can get excited and tell or show others our research.</p><br />
<p><b>Body language is something that everyone can speak.</b> So whether you're trying to explain something to somebody who doesn't have a scientific background, or doesn't even speak the same language as you, this method will be the most effective way of communicating the ideas. This doesn't just appeal to interpretation by the mind, but to also basic human instincts and how we interpret the expression or movement of another human being.</p><br />
<h3>What about us?</h3><br />
<p><b>In our presentation at the iGEM Americas East Regional Competition, we wanted to test what it would be like to do something like this in an actual research setting.</b> We imagined a situation in which dance is the commonly used method to present research. And that's how we designed our presentation, incorporating the dancers to explain our research naturally, without pointing out that these are our dancers.</p><br />
<p>This presentation has already turned up results:</p><br />
<ul><br />
<li>A packed auditorium for our presentation.<br />
<li>The Best Model Award<br />
<li>Advancement to the World Finals<br />
<li>Gold Medal<br />
<li>Lots of attention at our school and worldwide<br />
<li>Everyone learned something new about synthetic biology<br />
</ul><br />
<p>And these are just our initial results. Because our team is composed solely of undergraduate students from many different backgrounds, we're are still waiting to see how this unique experience will benefit them in their futures. And there is so much potential. In addition to learning a new, unique dance routine, we have learned from the experiences and challenges that we have overcome and are incredibly excited to see what comes next.</p><br />
<hr><br />
<h1>Who are we?</h1><br />
<table id="syntable" align="center"><br />
<tr><br />
<td id="syntdl"><br />
<h3>Devon Ryan</h3><br />
<img src="https://static.igem.org/mediawiki/2012/e/e1/Devon2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>Choreographer, 3rd Year, Civil Engineering</b><br><br />
The moment I got the email invitation to be a part of QGEM I knew that I wanted to be a part of it. My whole life I’ve looked for ways to combine my artistic and scientific worlds. This was an amazing outlet to work with some of my favorite dancers, develop my choreography skills with challenging concepts and be on the front lines of a brand new relationship between science and dance. I am a better choreographer and academic for joining QGEM. </p><br />
</td><br />
<td id="syntdr"><br />
<h3>Sam Demetrious</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/Samd.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th Year, Sociology Major</b><br><br />
I think the Queen’s IGEM team is so unique this year in such a fantastic way! By using dance to represent the scientific concepts, the research provided by the Queen's team can reach a wider audience and even impact individuals outside the synthetic biology community. The collaboration of arts and science is a wonderful learning tool, especially for those just beginning to learn about biology, such as a sociology student like myself. </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Michelle Rea</h3><br />
<img src="https://static.igem.org/mediawiki/2012/9/9f/Michelle.png" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd, Chemical Engineering</b><br><br />
I was approached at the beginning of the school year about this project and thought it was an amazing opportunity to combine my art with research that I am interested in. Using dance as teaching and presenting tool in science is a totally new concept and the experience was definitely one of a kind as I learned about the research through dancing it out!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Leandra Guillet</h3><br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Leandra2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Arts and Science</b><br><br />
Being able to be part of something like qGEM in my first year is kind of ridiculous. It’s not something I ever thought I would be doing, but I’m so glad I got the opportunity to combine dance and science. I have really enjoyed learning more about science while using my dance background to interpret the research. It’s probably the highlight of my first year so far.</p><br />
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<h3>Melissa Guertin</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/Melissa2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd year, Civil Engineering</b><br><br />
When I was first asked to dance in a piece portraying research, I really had no idea what to expect. I went in with an open mind, and found myself very rewarded. It was so neat to not only visually represent the research, but also get my own visual aid to understand things I have not learned. I felt very rewarded when people understood our representations and interpretations at the iGem competition in Pittsburgh, as well as here at Queen's. This is such an innovative concept and I am ecstatic that I get to be a part of this new beginning!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Christina Robitaille</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/56/Chrissy.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>2nd Year, Life Science</b><br><br />
This whole experience has been amazing for me. At first I was unsure of how successful melding science and the arts would be, but kudos to Devon and Kevin because our hard work has really paid off. The SynthetiQ project has proven to be both effective and very rewarding for all of us lucky enough to be involved. I'm so glad that I got the opportunity to be a part of the team, and I really admire QGEM for taking this risk with their project. It's been an incredible journey, and I can't wait to see where they go from here!</p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Alisha Giglio</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/79/Alisha2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>2nd year, Chemistry Major</b><br><br />
Being apart of Queen’s iGEM this year has been a truly amazing experience. By combining synthetic biology and dance, I believe we have helped broaden many people’s views and hopefully made many think about new and innovative ways to portray their research, which could potentially change the world of boring science presentations as we know it. This whole experience has been rewarding as I have been able to combine two things I am interested in, as well, I am really excited to see how this concept will develop and what it will mean for dance and science in the future!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Jaclyn Kemp</h3><br />
<img src="https://static.igem.org/mediawiki/2012/1/14/Jaclyn.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Physical and Health Education</b><br><br />
I found out about the opportunity to dance for QGEM through our choreographer Devon Ryan. I was thrilled to be able to use the art of dance to model and help explain scientific concepts. I think that this approach reaches out to a broader audience who are not as familiar with synthetic biology. The movement and visual images that are created in our presentation have helped me to understand the various concepts. My hope is that this new approach to presenting information can be used and expanded on in the future!<br><br> </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Brittany Groom</h3><br />
<img src="https://static.igem.org/mediawiki/2012/f/fd/Brittany.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd Year, Nursing</b><br><br />
I am honoured to be a part of the Queen’s iGEM team and have the opportunity to portray their innovative research through a mode of communication that is not seen very often in the science field. This experience has given me so much respect for the immense amount of time and work that every team puts forth to make this event possible. I can tell that the passion the Queen’s research team has for their work is the same passion that I have for dancing and, that is ultimately why we work together so seamlessly.</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Kevin Chen</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/53/Kevin2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th year, Biochemistry</b><br>I was the overall lead of the project, covering the logisitical sides of things, website, videos, driving and speaking in the actual presentation. It is really hard to describe what I have learned and gained from this project. It's just been unreal, definitely the highlight of my undergraduate degree and probably my life so far. My only dance knowledge comes from BBoying, since first year. So, I've learned a lot working with these dancers. <br />
<br />
<br><br>And now these bios are symmetrical. Yay!</p><br />
</td><br />
</tr><br />
</table></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/AttributionsTeam:Queens Canada/Attributions2012-10-27T03:43:31Z<p>Chev1n: </p>
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Thanks to Dr. Ian Chin-Sang's lab for graciously allowing us to use their reagents for our project. <br />
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E. coli fliC Deletion Strains" and write "strains JW1908-1 and YK4516 from the Yale Coli Genetic Stock Center (CGSC)<br />
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Equipment<br />
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<li><br />
Special to Dr. William Bendena for allowing us to use his lab for working on our project, and students in Dr. Ian Chin-Sang's lab, Tony, Jeff, and Jun for all their help. <br />
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Plasmids<br />
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Dr. Craig Gehren - University of Alberta - Provided plasmids containing Rv2579<br />
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Jennifer Gehret McCarthy - University of Michigan - Provided plasmids containing the dmmA gene<br />
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Dr. Yuji Nagata - Tohoku University - Provided plasmids containing the LinB gene<br />
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Dr. Tom Peat - Commonwealth Scientific and Industrial Research Organisation - Provided plasmids containing the linB gene<br />
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Dr. Steven Smith - Queen's University - Provided plasmids containing Cohesin and Dockerin domains<br />
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<li>Wiki Design and coding: Phillip Tsang</li><br />
<li>Videography: Kevin Chen</li><br />
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Reagents<br />
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<li><br />
Thanks to Dr. Ian Chin-Sang's lab for graciously allowing us to use their reagents for our project. <br />
</li><br />
<li><br />
E. coli fliC Deletion Strains" and write "strains JW1908-1 and YK4516 from the Yale Coli Genetic Stock Center (CGSC)<br />
</li><br />
<br><br />
</br><br />
</div><br />
<div id="Equip" class="contenttitle"><br />
Equipment<br />
</div><br />
<br />
<div class="contentbox"><br />
<li><br />
Special to Dr. William Bendena for allowing us to use his lab for working on our project, and students in Dr. Ian Chin-Sang's lab, Tony, Jeff, and Jun for all their help. <br />
</li><br />
<br><br />
</br><br />
</div><br />
<div id="Plasmids" class="contenttitle"><br />
Plasmids<br />
</div><br />
<div class="contentbox"><br />
<li><br />
Dr. Craig Gehren - University of Alberta - Provided plasmids containing Rv2579<br />
</li><br />
<li><br />
Jennifer Gehret McCarthy - University of Michigan - Provided plasmids containing the dmmA gene<br />
</li><br />
<li><br />
Dr. Yuji Nagata - Tohoku University - Provided plasmids containing the LinB gene<br />
</li><br />
<li><br />
Dr. Tom Peat - Commonwealth Scientific and Industrial Research Organisation - Provided plasmids containing the linB gene<br />
</li><br />
<li><br />
Dr. Steven Smith - Queen's University - Provided plasmids containing Cohesin and Dockerin domains<br />
</li><br />
<br><br />
</br><br />
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<div id="Plasmids" class="contenttitle"><br />
Plasmids<br />
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<li>Wiki Design and coding: Phillip Tsang</li><br />
<li>Videography: Kevin Chen</li><br />
</div><br />
</div><br />
</body><br />
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<div></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/ChimeriQ/ResultsTeam:Queens Canada/ChimeriQ/Results2012-10-27T03:37:27Z<p>Chev1n: </p>
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<p>ChimeriQ - Results</p><br />
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<li> <a href="#Fluoresence"> Fluorescence</a> </li><br />
<li> <a href="#Catalysis"> Catalysis </a> </li><br />
<li> <a href="#CohDoc">Cohesin and Dockerin</a> </li><br />
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Overview<br />
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As the goal of our project was to create chimeric flagella, the majority of our results were based around the creation of flagella with various inserts. In order to do so, we needed to make a mechanism by which we could easily create this chimeric primers. In doing so, we were able to create the part <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781000"> K781000 </a>. This is the complete flagellin coding sequence with biobrick standard cut sites removed, under the promoter R0010 and RBS B0034. This part can be used to over express the flagellin monomer. PCR overlap extension will make an insertion at the annotated site, given that the insert is in the appropriate format. The resulting chimera will express protein immediately after the PCR reaction is transformed. <br />
<br><br />
<br><br />
<b>We are still in the process of obtaining results. What you see below is some initial testing of our parts. Sequencing data as well as additional motility assays and catalysis testing will soon follow.</b><br />
</br><br />
</div><br />
<div id="Fluoresence" class="contenttitle"><br />
Fluorescence<br />
</div><br />
<div id="contentbox" style="border-bottom:none"><br />
<p>The majority of our results fell under this section of our work as we were able to create both the RFP-FliC Insertion and deletion chimeras. These parts were successfully characterized and determined to show expression of the red fluorescent protein from J04500. As can be seen below, there appears to be less detectable fluorescence in cell cultures expressing the different types of chimeras. This result can be expected for a number of possible reasons. </p><br />
<br />
<li> The chimeric protein may not be as stable as the free RFP.</li><br />
<li> The RFP may be polymerizing in flagella, resulting in a quenching effect as the fluorescent light may be absorbed by other RFP molecules arranged in close proximity. </li><br />
<li> The flagellin domains may hinder proper folding of the RFP. This may be why the more constrained deletion variant is showing less expression compared to the insertion variant, which has more flexibility. </li><br />
<br />
<div class="thumb tleft"><div class="thumbinner" style="width: 400px;" ><a href="/File:D3_RFP.JPG" class="image"><img alt="" src="/wiki/images/thumb/e/e7/D3_RFP.JPG/500px-D3_RFP.JPG" width="400" height="300" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:D3_RFP.JPG" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 1</b> The motility assay for the K781001 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct.</div></div></div><br />
<div class="thumb tright" width: 400px; float: right; margin-left: 0px; padding-right: 35px;><div class="thumbinner" style="width:422px;"><a href="/File:Rfp_flic_results_1.JPG" class="image"><img alt="" src="/wiki/images/thumb/9/9c/Rfp_flic_results_1.JPG/420px-Rfp_flic_results_1.JPG" width="420" height="272" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Rfp_flic_results_1.JPG" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 2:</b> TOP10 <i>E. coli</i> expressing J04450, the RFP insertion chimeric flagellin (K781001) and the RFP deletion chimeric flagellin (K781006).</div></div></div><br />
<div class="thumb tleft"><div class="thumbinner" style="width:902px;"><a href="/File:Rfp_spectra.png" class="image"><img alt="" src="/wiki/images/thumb/b/b3/Rfp_spectra.png/900px-Rfp_spectra.png" width="900" height="283" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Rfp_spectra.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 3:</b> The fluorescence spectra of TOP10 <i>E. coli</i> cells expressing the RFP flagellin insertion <a href="http://partsregistry.org/Part:BBa_K781001" class="external text" rel="nofollow">K781001</a> and deletion <a href="http://partsregistry.org/Part:BBa_K781006" class="external text" rel="nofollow">K781006</a> constructs compared against <a href="http://partsregistry.org/Part:BBa_J04450" class="external text" rel="nofollow">J04450</a>, the corresponding RFP control.</div></div></div><br />
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Catalysis<br />
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Our work with catalysis mainly involved working with three enzymes: LinB, Rv2579, and XylE. Using K781000, we were able to create three parts: <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781005"> BBa_K781005 </a>, <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781004"> BBa_K781004 </a>, and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781007"> BBa_K781007 </a>. Based on the images below, it appears as if we were able to incorporate these enzymes into the bacteria, but more research much be done in order to characterize the enzyme activity. <br><br />
<div class="thumb tleft"><div class="thumbinner" style="width:402px;"><a href="/File:Rv2579_edit.png" class="image"><img alt="" src="/wiki/images/thumb/8/81/Rv2579_edit.png/500px-Rv2579_edit.png" width="400" height="300" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Rv2579_edit.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 4</b> The motility assay for the K781004 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar.</div></div></div><br />
<div class="thumb tleft"><div class="thumbinner" style="width:402px;"><a href="/File:Linb_mot.png" class="image"><img alt="" src="/wiki/images/thumb/f/fd/Linb_mot.png/500px-Linb_mot.png" width="400" height="300" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Linb_mot.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 5</b> The motility assay for the K781005 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar.</div></div></div><br />
<br><br />
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The Cohesin-Dockerin System<br />
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Our work the Cohesin-Dockerin system had the ultimate goal of being able to create a chimeric flagella with a Dockerin insert, which would be able to bind with a specific Cohesin domain secreted by the bacteria. Unfortunately we were not able to reach this point, but were were able to create a part with type II cohesin from Clostridium Thermocellum as a chimeric insertion into flagellin (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781003"> K781003 </a>). <br />
<div class="thumb tleft"><div class="thumbinner" style="width:502px; margin-left: 219px;"><a href="/Image:Cohesin_mot.png" class="image" title="Fig. 1 The motility assay for the K781003 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar."><img alt="Fig. 1 The motility assay for the K781003 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar." src="https://static.igem.org/mediawiki/2012/7/7a/Cohesin_mot.png" width="500" height="375" border="0" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/Image:Cohesin_mot.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 6</b> The motility assay for the K781003 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar.</div></div></div><br />
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<p>ChimeriQ - Results</p><br />
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<li> <a href="#Fluoresence"> Fluorescence</a> </li><br />
<li> <a href="#Catalysis"> Catalysis </a> </li><br />
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Overview<br />
</div><br />
<div id="contentbox"><br />
As the goal of our project was to create chimeric flagella, the majority of our results were based around the creation of flagella with various inserts. In order to do so, we needed to make a mechanism by which we could easily create this chimeric primers. In doing so, we were able to create the part <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781000"> K781000 </a>. This is the complete flagellin coding sequence with biobrick standard cut sites removed, under the promoter R0010 and RBS B0034. This part can be used to over express the flagellin monomer. PCR overlap extension will make an insertion at the annotated site, given that the insert is in the appropriate format. The resulting chimera will express protein immediately after the PCR reaction is transformed. <br />
<br><br />
<b>We are still in the process of obtaining results. What you see below is some initial testing of our parts. Sequencing data as well as additional motility assays and catalysis testing will soon follow.</b><br />
</br><br />
</div><br />
<div id="Fluoresence" class="contenttitle"><br />
Fluorescence<br />
</div><br />
<div id="contentbox" style="border-bottom:none"><br />
<p>The majority of our results fell under this section of our work as we were able to create both the RFP-FliC Insertion and deletion chimeras. These parts were successfully characterized and determined to show expression of the red fluorescent protein from J04500. As can be seen below, there appears to be less detectable fluorescence in cell cultures expressing the different types of chimeras. This result can be expected for a number of possible reasons. </p><br />
<br />
<li> The chimeric protein may not be as stable as the free RFP.</li><br />
<li> The RFP may be polymerizing in flagella, resulting in a quenching effect as the fluorescent light may be absorbed by other RFP molecules arranged in close proximity. </li><br />
<li> The flagellin domains may hinder proper folding of the RFP. This may be why the more constrained deletion variant is showing less expression compared to the insertion variant, which has more flexibility. </li><br />
<br />
<div class="thumb tleft"><div class="thumbinner" style="width: 400px;" ><a href="/File:D3_RFP.JPG" class="image"><img alt="" src="/wiki/images/thumb/e/e7/D3_RFP.JPG/500px-D3_RFP.JPG" width="400" height="300" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:D3_RFP.JPG" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 1</b> The motility assay for the K781001 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct.</div></div></div><br />
<div class="thumb tright" width: 400px; float: right; margin-left: 0px; padding-right: 35px;><div class="thumbinner" style="width:422px;"><a href="/File:Rfp_flic_results_1.JPG" class="image"><img alt="" src="/wiki/images/thumb/9/9c/Rfp_flic_results_1.JPG/420px-Rfp_flic_results_1.JPG" width="420" height="272" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Rfp_flic_results_1.JPG" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 2:</b> TOP10 <i>E. coli</i> expressing J04450, the RFP insertion chimeric flagellin (K781001) and the RFP deletion chimeric flagellin (K781006).</div></div></div><br />
<div class="thumb tleft"><div class="thumbinner" style="width:902px;"><a href="/File:Rfp_spectra.png" class="image"><img alt="" src="/wiki/images/thumb/b/b3/Rfp_spectra.png/900px-Rfp_spectra.png" width="900" height="283" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Rfp_spectra.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 3:</b> The fluorescence spectra of TOP10 <i>E. coli</i> cells expressing the RFP flagellin insertion <a href="http://partsregistry.org/Part:BBa_K781001" class="external text" rel="nofollow">K781001</a> and deletion <a href="http://partsregistry.org/Part:BBa_K781006" class="external text" rel="nofollow">K781006</a> constructs compared against <a href="http://partsregistry.org/Part:BBa_J04450" class="external text" rel="nofollow">J04450</a>, the corresponding RFP control.</div></div></div><br />
<br><br />
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Catalysis<br />
</div><br />
<div id="contentbox" style="border-bottom: none;"><br />
Our work with catalysis mainly involved working with three enzymes: LinB, Rv2579, and XylE. Using K781000, we were able to create three parts: <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781005"> BBa_K781005 </a>, <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781004"> BBa_K781004 </a>, and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781007"> BBa_K781007 </a>. Based on the images below, it appears as if we were able to incorporate these enzymes into the bacteria, but more research much be done in order to characterize the enzyme activity. <br><br />
<div class="thumb tleft"><div class="thumbinner" style="width:402px;"><a href="/File:Rv2579_edit.png" class="image"><img alt="" src="/wiki/images/thumb/8/81/Rv2579_edit.png/500px-Rv2579_edit.png" width="400" height="300" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Rv2579_edit.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 4</b> The motility assay for the K781004 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar.</div></div></div><br />
<div class="thumb tleft"><div class="thumbinner" style="width:402px;"><a href="/File:Linb_mot.png" class="image"><img alt="" src="/wiki/images/thumb/f/fd/Linb_mot.png/500px-Linb_mot.png" width="400" height="300" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/File:Linb_mot.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 5</b> The motility assay for the K781005 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar.</div></div></div><br />
<br><br />
</br><br />
</div><br />
<div id="CohDoc" class="contenttitle" style="clear:both; border-top: 1px dashed black;"><br />
The Cohesin-Dockerin System<br />
</div><br />
<div id="contentbox" style="border-bottom:none;"><br />
Our work the Cohesin-Dockerin system had the ultimate goal of being able to create a chimeric flagella with a Dockerin insert, which would be able to bind with a specific Cohesin domain secreted by the bacteria. Unfortunately we were not able to reach this point, but were were able to create a part with type II cohesin from Clostridium Thermocellum as a chimeric insertion into flagellin (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K781003"> K781003 </a>). <br />
<div class="thumb tleft"><div class="thumbinner" style="width:502px; margin-left: 219px;"><a href="/Image:Cohesin_mot.png" class="image" title="Fig. 1 The motility assay for the K781003 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar."><img alt="Fig. 1 The motility assay for the K781003 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar." src="https://static.igem.org/mediawiki/2012/7/7a/Cohesin_mot.png" width="500" height="375" border="0" class="thumbimage" /></a> <div class="thumbcaption"><div class="magnify"><a href="/Image:Cohesin_mot.png" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div><b>Fig. 6</b> The motility assay for the K781003 construct compared against controls expressing no flagellin construct and a non-chimeric flagellin construct. Inoculations made on 0.25% swimming agar.</div></div></div><br />
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fas<br />
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<h3> Sponsor List </h3><br />
<p class="sponsorcontent"><br />
We would like to thank the following sponsors for their contribution to our 2012 iGEM project:<br />
</p><br />
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<p class="sponsortitle"><br />
Platinum Sponsor(s)<br />
</p><br />
<br><br />
<p class="sponsorname"><br />
Oil Sands Leadership Initiatives (OSLI)<br />
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<p><br />
<img align="left" style="margin-bottom:8px; width: 200px; padding:0; clear:both;" src="https://static.igem.org/mediawiki/2011/c/cc/Queens_Canada_SponsorsOSLI.png"> <br />
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<p class="sponsorcontent"><br />
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<p class="sponsorname"><br />
Queen’s University<br />
</p><br />
<p><br />
<img align="left" style="margin-bottom:8px; width:200px; padding:0;" src="https://static.igem.org/mediawiki/2011/3/37/Queens_Canada_SponsorQueens.png" ><br />
</p><br />
<p class="sponsortitle"><br />
<b> Gold Sponsor(s) </b><br />
</p><br />
<p class="sponsorname"><br />
New England Biolabs Canada<br />
</p><br />
<p><br />
<img align="left" style="margin-bottom:8px; width: 200px; padding:0; clear:both;" src="https://static.igem.org/mediawiki/2011/5/5d/Queens_Canada_SponsorsNEB.png"> <br />
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<p class="sponsorcontent"><br />
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<p class="sponsortitle"><br />
<b> Silver Sponsor(s) </b><br />
</p><br />
<p class="sponsorname"><br />
Calibrate<br />
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<p><br />
<img align="left" style="margin-bottom:8px; width: 200px; padding:0; clear:both;" src="https://static.igem.org/mediawiki/2011/1/15/Queens_Canada_SponsorsCalibrate.png"> <br />
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<p class="sponsorcontent"><br />
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<p class="sponsorname"><br />
Novus Biologicals<br />
</p><br />
<p><br />
<img align="left" style="margin-bottom:8px; width: 200px; padding:0; clear:both;" src="https://static.igem.org/mediawiki/2012/1/15/Novus_logo.png"> <br />
</p><br />
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<p class="sponsorname"><br />
Geneious<br />
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<p><br />
<img align="left" style="margin-bottom:8px; width: 200px; padding:0; clear:both;" src="https://static.igem.org/mediawiki/2012/6/64/Geneious_Logo.png"> <br />
</p><br />
<p class="sponsorcontent"><br />
</p><br />
<p class="sponsortitle"><br />
<b> Bronze Sponsor(s) </b><br />
<br><br />
<p class="sponsorname"><br />
Integrated DNA Technologies<br />
<p><br />
<img align="left" style="margin-bottom:8px; width: 200px; padding:0; clear:both;" src="https://static.igem.org/mediawiki/2011/b/be/Queens_Canada_SponsorsIDT.png"> <br />
</p><br />
<br />
<p class="sponsorcontent"><br />
</p><br />
<br />
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<p class="sponsorcontent"><br />
</p><br />
<br />
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<p>Attributions</p><br />
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<li> <a href="#Reagents"> Reagents</a> </li><br />
<li> <a href="#Equip"> Lab Equipment</a> </li><br />
<li> <a href="#Plasmids"> Plasmids </a> </li><br />
<li> <a href="#Media"> Media </a> </li><br />
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Reagents<br />
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<div class="contentbox"><br />
<li><br />
Thanks to Dr. Ian Chin-Sang's lab for graciously allowing us to use their reagents for our project. <br />
</li><br />
<br><br />
</br><br />
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<div id="Equip" class="contenttitle"><br />
Equipment<br />
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<br />
<div class="contentbox"><br />
<li><br />
Special to Dr. William Bendena for allowing us to use his lab for working on our project, and students in Dr. Ian Chin-Sang's lab, Tony, Jeff, and Jun for all their help. <br />
</li><br />
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<div id="Plasmids" class="contenttitle"><br />
Plasmids<br />
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<div class="contentbox"><br />
<li><br />
Dr. Craig Gehren - University of Alberta - Provided plasmids containing Rv2579<br />
</li><br />
<li><br />
Jennifer Gehret McCarthy - University of Michigan - Provided plasmids containing the dmmA gene<br />
</li><br />
<li><br />
Dr. Yuji Nagata - Tohoku University - Provided plasmids containing the LinB gene<br />
</li><br />
<li><br />
Dr. Tom Peat - Commonwealth Scientific and Industrial Research Organisation - Provided plasmids containing the linB gene<br />
</li><br />
<li><br />
Dr. Steven Smith - Queen's University - Provided plasmids containing Cohesin and Dockerin domains<br />
</li><br />
<br><br />
</br><br />
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<div id="Plasmids" class="contenttitle"><br />
Plasmids<br />
</div><br />
<div class="contentbox"><br />
<li>Wiki Design and coding: Phillip Tsang</li><br />
<li>Videography: Kevin Chen</li><br />
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<p>Guide to making Chimeric Proteins- Protein Expression</p><br />
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<li> <a href="#Linkers"> Linkers </a> </li><br />
<li> <a href="#Structures"> Structures on PDB</a> </li><br />
<li> <a href="#Pymol">PYmol Building</a> </li><br />
<li> <a href="#Gromacs">GROMACS Simulations</a> </li><br />
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Linkers<br />
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<div class="contentbox"><br />
<p>In our chimeras we have linker sequences on either side of the chimeric insert sequence. The linkers we chose to use were inert, and flexible linker sequences, with different sequences on either side so that overlap extension will be successful.<br />
</p><br />
<h2>FliC -GGGGS- insert -GGSGG- FliC</h2><br />
<p> It is important to also consider the flexible regions of the protein in which you are making your insertion. Flexible regions may be able to accommodate a protein insertion, and would not require very long linkers. However, longer linkers may be required to introduce enough flexibility for the inserted protein to fold properly.<br />
</p><br />
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<div id="Structures" class="contenttitle"><br />
Structures<br />
</div><br />
<div class="contentbox"><br />
<p>The protein database is possibly the most important tool in chimeric protein design. Without having any previous knowledge of your structure, it is impossible to really say where or how you would design your chimeric protein.<br />
In our case, the crystal structure for E. coli flagellin is not available on the protein database. However, the structure for the flagellin of S. typhymurium was available and is very similar to the structure of E. coli flagellin. The PDB ID is 1UCU.</p><br />
<p>Additionally, some general assumptions can be made when searching for a good place to make an insertion. For example, the site that we chose to make our variable domain insertions is:</p><br />
<h2>...AVTVANDGTVTMATG...</h2><br />
<p>The insertion was made in between AVT and TVT, replacing the amino acid sequence VANDG. We needed to have some spacing in between the overlap regions for PCR overlap extension, which is why VANDG was replaced.</p><br />
<p>The presence of several threonine, alanine, valine and glycine residues is indicative of a loop region, which would make a good spot for an insertion. Additionally, when we used PCR to make the overlapping regions for the insertion, we amplified off of the already existing linker used for ovarlapping as a deletion. Hence our total linker was:<br />
<h2>...AVTTTGGGGS-insert-GGSGGTSTVT...</h2><br />
</div><br />
<div id="Pymol" class="contenttitle"><br />
PYmol<br />
</div><br />
<div class="contentbox"><br />
<p><b>The following two sections are incomplete. They are on their way!</b></p><br />
<p>First, you'll have to install it (don't worry, it's free): <a href="pymol.org">pymol.org</a></p><br />
<p>Pymol is a really useful program for viewing and modifying protein structures. Here we'll quickly go step by step into specifically building proteins in PYmol and what you need to know</p><br />
<ul><br />
<li>Load your protein in PYmol: under 'plugins' choose 'PDB loader service' and enter the 4-digit PDB ID for your desired protein.<br />
<li>Right now you'll be in viewing mode, which lets you rotate and move the camera. To switch to "Editing mode" click on the box in the bottom right that reads "3-button viewing mode". This will switch you to editing mode.<br />
<li>Here you'll have all the options for actually moving your protein around and rotating it.<br />
<li>On the PYmol menu and script window, you can switch to "Builder". This will give you specific options for adding amino acids and other molecules to your structure.<br />
<li>To make an insertion, you'll have to delete a bond. This is one of the options in the Builder window. Or you can delete a residue or residues, by selecting a residue in viewer mode, right clicking and choosing remove.<br />
<li>Now you have free bonds where you can build residues. Simply click on the atom where you want to add a residue (usually a terminal N or C=O), then click on the residue you want to add in the Builder window. The default secondary structure is in a parallel beta sheet, which is essentially just a straight line.<br />
<li>Rotating bonds can be done by clicking on an atom and then double-click and hold the part that you want to rotate. Remember, don't rotate between N and C=O bonds!<br />
<li>The last and most important thing you'll need to know, which isn't obvious at first is how Pymol actually make bonds. It does it purely by proximity. So if you have atoms that are within 1.5 angstroms, Pymol will automatically make a bond between those two atoms after you save and reload the .pdb file.<br />
<li>The code "distance (pk1),(pk2)" will measure the distance between two selected atoms. You may also use the measurement wizard to find distances and well as phi and psi angles.<br />
<li>Move and twist your bonds and proteins to build your chimeric protein and then save them as one .pdb file!<br />
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GROMACS<br />
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This is something that we are just getting into. Basically, what GROMACS does is simulates your protein structure or other molecule floating in a solvent (usually water). This can be really useful in estimating how your protein will actually behave with regards to its stability and flexibility. After running this you'll be able to see whether or not your enzyme's catalytic site might be facing the wrong way!<br />
Below is a link to a script, which contains a breakdown of each variable and how to actually do the run. <br />
<a href="https://static.igem.org/mediawiki/2012/e/e6/Run_md_gromos_cutoff.txt">Click here!</a> and then rename the script to a .sh instead of .txt.<br />
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<p>DNA</p><br />
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<li> <a href="#Cut-sites"> Cut-sites </a> </li><br />
<li> <a href="#Bio_Fus"> Biobrick Fusion Standards</a> </li><br />
<li> <a href="#Cloning_methods"> Cloning methods</a> </li><br />
<li> <a href="#expression"> Parts for protein expression</a> </li><br />
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Cut Sites<br />
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Restriction Enzyme Cut sites are an essential element for creating protein chimers of any kind, not only for the creation of BioBrick Protein Chimers. As part of the protocol for creating these protein chimers, digestion and ligation will be involved. More often than not, digestion sites for restriction enzymes will be incorporated to the ends of the insert and the adjacent parts in order to ligate them together and into a plasmid. Therefore, it is critical to ensure that there are no cut sites present for the restriction enzymes that you will be using for digestion and ligation, otherwise it will be very difficult to get the full part ligated together with themselves and into the plasmid. For instance, if there is an EcoRI cut site present in the insert, then while you are digesting with the insert with EcoRI, the insert will be cut prematurely, and its function will likely be reduced. <br />
Removing restriction enzyme cut sites can be a very simple, or a very difficult process, depending on the location of the cut site in the desired part. If the part is close to the beginning or the end of the desired part, it may be simple to do a site directed mutagenesis. In order to do so, you would need to create a primer that overlaps the desired cut site, and change one nucleotide (preferably one that causes a silent mutation in the protein), such that the primer will still anneal to the template DNA, but will induce a single base pair nucleotide change that will remove the cut site from the PCR product. While the former is a very simple process, if the cut site is far enough away from the ends of the template DNA, this process is unlikely to work, as the primers will be too long. In this case, the simplest way to remove the cut site will be to have the DNA directly synthesized, although this can end up being a very costly process.<br />
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Below are the Restriction Enzyme cut sites for various BioBrick standards<br />
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<table style="vertical-align: text-top;"><br />
<td width="25%" text-align="center"><br />
BB RFC [10]<br />
<ul><br />
<li>EcoRI site: GAATTC </li><br />
<li>XbaI site: TCTAGA </li><br />
<li>SpeI site: ACTAGT </li><br />
<li>PstI site: CTGCAG </li><br />
<li>NotI site: GCGGCCGC </li><br />
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BioBrick BB-2 RFC[12]<br />
<ul><br />
<li>EcoRI site: GAATTC </li><br />
<li>SpeI site: ACTAGT </li><br />
<li>NheI site, GCTAGC </li><br />
<li>PstI site: CTGCAG </li><br />
<li>NotI site: GCGGCCGC </li><br />
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Berkeley RFC[21]<br />
<ul><br />
<li>EcoRI site: GAATTC </li><br />
<li>BglII site: AGATCT </li><br />
<li>BamHI site: GGATCC </li><br />
<li>XhoI site: CTCGAG </li><br />
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Silver RFC[23]<br />
<ul><br />
<li>EcoRI site: GAATTC </li><br />
<li>XbaI site: TCTAGA </li><br />
<li>SpeI site: ACTAGT </li><br />
<li>PstI site: CTGCAG </li><br />
<li>NotI site: GCGGCCGC </li><br />
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<div id="Cloning_methods" class="contenttitle"><br />
Cloning Methods<br />
</div><br />
<div class="contentbox"><br />
<h3>PCR Overlap Extension</h3><br />
<p>When cloning parts into our construct, we chose to use PCR overlap extension and digestion/ligation<br />
techniques. In order to perform PCR Overlap extension (our preferred method of cloning) we were<br />
required to fabricate a set of primers that were ligated onto the insert. These primer extensions served<br />
to add overlap sites that match those of the parts we were adding. This allowed for PCR to extend<br />
the part onto another part with a matching overlap site; with the primers on either end of the inserts<br />
acting as the site of initiation for Taq polymerase. Our primary resource was this <a href=http://www.biotechniques.com/BiotechniquesJournal/2010/June/Overlap-extension-PCR-cloning-a-simple-and-reliable-way-to-create-recombinant-plasmids/biotechniques-280116.html>paper</a>. A picture<br />
representation of PCR-Overlap Extension can be seen below:</p><br />
<img src="https://static.igem.org/mediawiki/2012/thumb/b/ba/Pcroe.png/800px-Pcroe.png"></img><br />
<br />
<h3>High Throughput Cloning</h3><br />
<p>The protocol for this method is standard.</p><br />
98C for 30s<br><br />
60C for 30s<br><br />
72C for 1.5/kb<br><br />
- 18 cycles optimum<br><br />
72C for 10min (final extension)<br><br />
37C for 30min - Add Dpn1 (digest methylated DNA)<br><br />
Tranform<br><br />
<p><br />
The choice of polyemerase is important! The article suggests using Phusion DNA Polymerase for the best results. We used Kapa Hi-Fi Hotsart Mix and confirm that it worked. The reference includes data for other polymerases as well.</p><br />
Obtained from the following reference, under the Supplementary Material:<br><br />
<a href="http://www.biotechniques.com/BiotechniquesJournal/2010/June/Overlap-extension-PCR-cloning-a-simple-and-reliable-way-to-create-recombinant-plasmids/biotechniques-280116.html">LINK</a> Anton V. Bryksin and Ichiro Matsumura. (2010) Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids. BioTechniques, Vol. 48, No. 6, pp. 463–465<br><br />
<br />
<p>Because this method is standard over all of our parts, we can use it for high throughput cloning. For example, if we had 96 parts in our standard, we can fill a 96 well PCR plate and run this program, digest with Dpn1, then transform all of these parts. This would about 3-4 hours, with the main amount of time being the PCR reaction. So in the case of chimeric protein design, if we wanted to screen a number of cloned structures configurations to find one that folded the way we wanted it to, we could use this method to rapidly clone and test a series of trials.</p><br />
<p>We can liken this to crystallography, which can be done at high throughput by robots.</p><br />
<p><b>An RFC is in the process of being submitted for this standard.</b></p><br />
<br />
<h3>Standard Cloning</h3><br />
<p>The other method of cloning made use of the cut sites found in our insert and a few restriction enzymes.<br />
Early on we noted the BioBrick standard caused a very problematic frame-shifts within the scar when<br />
ligating 2 or more parts. We tried to circumvent the problem by adding 1 or 2 nucleotides onto our DNA<br />
sequence to fix the frame but found this to be tedious due to the fact that this varied based on the part<br />
we wanted to ligate.</p><br />
<br />
<p>Therefore we started doing research into other assembly standards to see if any of them alleviated<br />
the problem. We judged the merits and flaws of each one (a list of the assembly standards considered<br />
can be found <a href=http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats>here</a>). What we searched for was a standard that would avoid frame-shifts and nonsense<br />
mutations when doing protein fusion, avoid N-terminal destabilization signals and dam methylation sites<br />
and preserve most of the restriction enzymes from the original BBa standard.</p><br />
<br />
<p>Considering these reasons, we chose to switch our prefixes and suffixes to Tom Knight’s BBa 2 standard<br />
that allowed seamless in-frame ligations between multiple sequences of successive DNA. This change<br />
resulted in only 1 restriction enzyme (Xba1 to Nhe1) that differed from original BBa standard therefore<br />
providing the flexibility we needed to simultaneously work with both standards. For ligation, we used T4<br />
ligase. A pictorial representation of the BBa 2 standard can be seen below:</p><br />
<div id="seqbox"><br />
<pre><br />
Prefix Suffix<br />
EcoRI SpeI NheI PstI<br />
5' GAATTC...ACTAGT ...part... GCTAGC...CTGCAG 3'<br />
<br />
Fusing two parts would then leave the following scar:<br />
5' ...part A... GCTAGT ...part B... 3'<br />
A S<br />
</pre><br />
</div><br />
<p>We also considered making our own artificial restriction enzymes in order to cut DNA off-site. To do<br />
so, we would have made zinc fingers to bind DNA and combined them with enzymes capable of cutting<br />
away from the binding site. This would allow us to cut as close to the gene as possible.</p><br />
<br><br />
</br><br />
</div><br />
<div id="Bio_Fus" class="contenttitle"><br />
Biobrick Fusion Standards<br />
</div><br />
<div class="contentbox"><br />
<p>When designing our flagella construct we examined a number of different ways of creating fusion proteins. Using the original BioBrick assembly standard does not work for fusion proteins, as it results in a frame shift and stop codon in the scar. At first we worked on creating a new method of fusion protein production, however we ran into many of the same problems as the standards that were already present. We went through the various fusion standards present on the openwetware web page, analyzing their different merits, eventually settling on Tom Knight’s BB-2 standard. You can follow this <a href=http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats>link</a> for some information on the various standards we examined.</p> <br />
<h3>Biofusion (Silver Lab)</h3><br />
<div id="seqbox"><br />
<pre><br />
Prefix Suffix<br />
5’ GAATTC GCGGCCGC T TCTAGA ...part... ACTAGT A GCGGCCG CTGCAG 3’<br />
EcoRI NotI XbaI SpeI NotI PstI<br />
<br />
This results in the following scar:<br />
<br />
5’ ...part A...ACTAGA...part B...3’<br />
ThrArg<br />
</pre><br />
<p>The Biofusion standard slightly adjusted the original BioBrick standard such that the scar would now code for arginine instead of a stop codon, and the fusion would be in frame. Also, this standard uses the same enzymes as the original, so no new enzymes must be purchased. However, some issues do arise.These include the fact that the arginine present in the scar may be problematic in some cases due to its large size and the fact that it is coded by a rare codon. Also, Dam methylation may block cloning if the fused protein begins with Serine.</p><br />
</div><br />
<h3>Fusion Parts (Freiburg iGEM 2007)</h3><br />
<div id="seqbox"><br />
<pre><br />
Prefix Suffix<br />
5' GAATTC GCGGCCGC T TCTAGA TG GCCGGC...part...ACCGGT TAAT ACTAGT A GCGGCCG CTGCAG 3'<br />
EcoRI NotI XbaI Met NgoMI AgeI SpeI NotI PstI<br />
<br />
This results in the following scar:<br />
<br />
5’ ...part A...ACCGGC...part B... 3’<br />
ThrGly<br />
</pre><br />
<p>The Fusion Parts standard proposed by Freiburg serves to allow fusion proteins but remove some of the disadvantages of the Biofusion standard. It does this by adding two new restriction enzymes: NgoMI and AgeI. This standard allows a less disruptive scar of threonine and glycine, while maintaining in frame fusions. However, this does require the purchase of two new restriction enzymes.</p><br />
</div><br />
<h3>BglBricks (Berkeley)</h3><br />
<div id="seqbox"><br />
<pre><br />
Prefix Suffix<br />
5’ GAATTC ATG AGATCT...part...GGATCC TAA CTCGAG 3’<br />
EcoRI BglII BamHI XhoI<br />
<br />
This results in the following scar:<br />
<br />
5’ ...part A...GGATCT...part B...3’<br />
GlySer<br />
</pre><br />
<p>The BglBricks standard allows in frame production of fusion proteins with a benign scar of of glycine and serine. The prefix and suffix are also quite simple, containing only the 2 restriction sites connected by 3 bases. However, this method uses 3 new enzymes: BglII, BamHI and XhoI, of which BglII and BamHI cannot be heat-inactivated.</p><br />
</div><br />
<h3>BB-2 (Tom Knight)</h3><br />
<div id="seqbox"><br />
<pre><br />
Prefix Suffix<br />
5’ GAATTC...ACTAGT...part...GCTAGC...CTGCAG 3’<br />
EcoRI SpeI NheI PstI<br />
<br />
This results in the following scar:<br />
<br />
5’...part A...GCTAGT...part B... 3’<br />
AlaSer<br />
</pre><br />
<p>The BB-2 standard proposed by Tom Knight was the method we ended up following to produce our chimeric flagella. This standard requires the addition of only one new restriction enzyme (NheI), and produces in frame fusions with a benign scar of alanine and serine. Also, the NheI cut site is fairly rare in E. coli, decreasing the likelihood of having cut sites within proteins, and this enzyme can be heat-inactivated. The main concern with this method is that it has not yet been tested extensively to prove its value as a standard method of Biobrick assembly.</p><br />
<br><br />
</br><br />
</div><br />
</div><br />
<br />
<div id="expression" class="contenttitle"><br />
Parts for protein expression<br />
</div><br />
<div class="contentbox"><br />
<br />
<h3>Protein Expression</h3><br />
<div><br />
<p>As with any other gene sequences and parts, it was important to consider how to control the rate<br />
of expression for the protein, i.e. induce transcription of the insert and subsequent translation.<br />
Different promoter sequences are often incorporated upstream of the gene of interest to allow RNA<br />
polymerase a site to bind to in which to start transcription. Likewise ribosomal binding sites (RBS) are<br />
added downstream of the promoter to allow ribosomes to attach to the transcribe mRNA sequence.<br />
Depending on the promoter and RBS used, the level of expression for the protein can change anywhere<br />
from being produced in abundance or having little produced at all.</p><br />
<br />
<p>In our project we decided to use the <b>IPTG (Isopropyl β-D-1-thiogalactopyranoside) inducible promoter<br />
with RBS (Part:BBa J04500)</b>. The complex is made up of the LacI regulated promoter found naturally in<br />
E.coli and an rbs based off of a repressilator.</p><br />
</div><br />
<br />
<h3>Promoter</h3><br />
<div><br />
<p>The promoter used is the natural promoter from the LacZYA operon. It contains two protein binding<br />
sites; the first is for the CAP protein which is found in E.coli and associated with cell health and glucose<br />
supply. The second site binds LacI protein which is expressed to inhibit expression of the Lac operon<br />
when no lactose is present. In the absence of the CAP protein and LacI, the promoter will increase<br />
transcription. However, the promoter is naturally constitutive (meaning that by default it is in an ON<br />
state) in E.coli strains that have low expression of LacI proteins (such as Top 10). Because of this fact<br />
and prior experience with the part, we decided to keep using this promoter. In theory (and most likely<br />
practice) any other constitutive promoter part would have sufficed for our project.</p><br />
<br />
<p>A crucial fact to note is that this part is incompatible in species containing active LacI coding regions<br />
and environments containing lactose and lactose analogs. The former reason is because active LacI<br />
expression will limit the efficiency of the promoter, the later because the presence of lactose would<br />
continuously activate the promoter. Therefore these factors were considered before adoption of this<br />
promoter.</p><br />
<br><br />
</br><br />
</div><br />
</div><br />
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</html></div>Chev1nhttp://2012.igem.org/Team:Queens_CanadaTeam:Queens Canada2012-10-27T02:23:30Z<p>Chev1n: </p>
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<h3>ChimeriQ</h3><br />
<h4><br />
<span class="ca-quote">&ldquo;</span><br />
<span>Engineering chimeric flagella for a better world</span><br />
</h4><br />
<a href="#" class="ca-more">more...</a><br />
</div><br />
<div class="ca-content-wrapper"><br />
<div class="ca-content"><br />
<h6>Using flagella as scaffolds</h6><br />
<a href="#" class="ca-close">close</a><br />
<div class="ca-content-text"><br />
<p><br />
This year, our team is investigating new methods of increasing the efficiency of biosynthesis and bioremediation using modified bacteria. Most bacteria possess tail-like appendages called flagella, which can be genetically altered for novel functions. Each flagellum is made up of a number of polymerizing proteins, often called flagellin.<br />
</p><br />
</p><br />
By making chimeric insertions in the variable domain of the flagellin, we can incorporate fluorescent proteins, enzymes, and scaffolding proteins to extend the possible applications. By having a protein inserted into each monomer, it is possible to cluster thousands of proteins in close proximity to each other, thereby increasing the efficiency of production and break-down of various products.<br />
</p><br />
<br />
</div><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/ChimeriQ">Description</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/ChimeriQ/Results">Results</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/ChimeriQ/Parts">Parts</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Notebook/Week1">Notebook</a></li><br />
</ul><br />
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<div class="ca-icon"></div><br />
<h3>Chimeric Proteins</h3><br />
<h4><br />
<span class="ca-quote">&ldquo;</span><br />
<span>A handy guide for introducing you to chimeric protein design.</span><br />
</h4><br />
<a href="#" class="ca-more">more...</a><br />
</div><br />
<div class="ca-content-wrapper"><br />
<div class="ca-content"><br />
<h6>How to make chimeric proteins</h6><br />
<a href="#" class="ca-close">close</a><br />
<div class="ca-content-text"><br />
<p>There are a lot of considerations that need to be made in the design of chimeric proteins. To help introduce future teams to chimeric proteins and their standard design, we have summarized our work into a resourceful guide that covers all (or almost all) of the considerations that need to be made in designing a chimeric protein from start to finish.</p><br />
</div><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Guide/DNA">Part 1: DNA </a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Guide/mRNA">Part 2: mRNA</a></li><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Guide/Protein_Structure">Part 3: Protein Structure</a></li><br />
</ul><br />
</div><br />
</div><br />
</div><br />
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<h3>SynthetiQ</h3><br />
<h4><br />
<span class="ca-quote">&ldquo;</span><br />
<span>The first dance group to perform at a research conference</span><br />
</h4><br />
<a href="#" class="ca-more">more...</a><br />
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<h6>SynthetiQ</h6><br />
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<div class="ca-content-text" style="padding-bottom: 0px;"><br />
<p>SynthetiQ Experimental Dance is a group devoted to creating, testing and analyzing movement, in the form of dance, as a means of explaining scientific concepts. Inspired by Dr. John Bohannon's “Dance Your PhD Contest” and his TEDxBrussels talk in 2011, our first project was partnered with the Queen's Genetically Engineered Machine (QGEM) Team. Because our research and learning goals align perfectly with those of the QGEM team, we will be researching and presenting together at the International Genetically Engineered Machine Competition in the fall.</p><br />
<p>As a part of our 2012 iGEM project, we started this group, devoted to using dance to explain concepts associated with synthetic biology, as well as our own research.<br />
</p><br />
<br><br />
<p>We made dance into our own unique tool for teaching others scientific concepts, as an alternative to use powerpoint presentations. </p><br />
</div><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/SynthetiQ">Read more</a></li><br />
<br />
</ul><br />
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<h3>Team</h3><br />
<h4><br />
<span class="ca-quote">&ldquo;</span><br />
<span>There's no I in team</span><br />
</h4><br />
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<h6>Team</h6><br />
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<div class="ca-content-text" style="padding-bottom: 0px;"><br />
<img src="http://dl.dropbox.com/u/46807995/teamphoto.jpg" width="600px"><br />
<p>QGEM is an undergraduate team composed of both full-time members and volunteers. All faculties of the university are eligible to participate in the iGEM team and previous members have from the departments of Chemical and Mechanical Engineering, Engineering Chemistry, Biology, Biochemistry, Life Science and Computing.</p><br />
</div><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Team">Read more</a></li><br />
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<h3>Partners</h3><br />
<h4><br />
<span class="ca-quote">&ldquo;</span><br />
<span>We would once again like to thank our generous sponsors.</span><br />
</h4><br />
<a href="#" class="ca-more">more...</a><br />
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<h6>Partners</h6><br />
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<div class="ca-content-text"><br />
<p>We would like to thank our sponsors who have supported us financially, allowing us to pursue this project. In particular, we would like to thank Queen's University and the Oil Sands Leadership Initiative. </p><br />
</div><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Partners">Read more</a></li><br />
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<h3>Safety</h3><br />
<h4><br />
<span class="ca-quote">&ldquo;</span><br />
<span>It's important! More coming soon....</span><br />
</h4><br />
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<h6>Safety</h6><br />
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<p>More coming soon.....</p><br />
</div><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Queens_Canada/Safety">Read more</a></li><br />
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<img src="https://static.igem.org/mediawiki/2012/c/cf/Trollface.jpg" align="right" height="200"></img><br />
<h1>Flight of the Flagellin</h1><br />
<b>Flight of the Flagellin takes protein structures and give them a hilarious, fun, new perspective.</b><br />
<br><br />
<p>What is this page really? Well, we recently discovered how easy it is to import 3D protein structures into an open-source flight simulator called FlightGear. It seems pretty ridiculous, but this could be a great way of teaching protein or molecular structure to people both young and old. It's also really surreal to be bringing some of the smallest units of life, and exploring them, in the setting of some of the largest man-made vehicles.</p><br />
<p>Flying is just fun. Lots of people play flight simulators just to fly around some generated landscape. Now in this case, you're flying our somebody's hard earned scientific data instead. With the amount of work that went into getting this data, it's hard to say whether we're taking full advantage of it and using it to its full potential, or just completely bastardizing it.</p><br />
<p>Something like this could also lead into new games, like EteRNA or Fold-it, in which the player is assigned the puzzle of solving a protein or RNA structure. The higher your score, the better you did, and your solution can actually contribute to scientific data. More specifically, we can swap out that plane model for, say, a ligand. Then, using this same idea, we can power docking experiments, in which players have to try and land a ligand in the active site of an enzyme, for example. This kind of computer modelling is common practice in drug design.</p><br />
<hr><br />
<h1>The Game</h1><br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Fgfs-screen-006.png" height="200" align="right"></img><br />
<p>Download and Installation: </p><br />
<p>First download and install the game from <a href="http://www.flightgear.org/">http://www.flightgear.org/</a><br />
<p>Next, download and install the Flight of the Flagellin Maps! We wish we could make this a little bit easier but, we're inexperienced! Follow these step by step instructions:</p><br />
<ul><br />
<li>Download and extract the map files: <a href="http://ubuntuone.com/0tDBQNcyBm43iPw3SW7St8">proteinflight.zip</a><br />
<li>Install the map files:<br />
<ol><br />
<li>Edit Objects/w080n40/w072n42/1777947.stg with any simple text editor.<br />
<li>Scroll to the bottom of the file.<br />
<li>Replace YOURPATHHERE with the file path to your downloads folder, or wherever you choose to store the protein models.<br />
<li>Copy the Objects and Terrain folder to your Flightgear Scenery folder, ex: c:\Program Files\FlightGear\data\Scenery.<br />
</ol><br />
<li>Run flightgear and pick to take off from the Boston Airport! (ID:KBOS)<br />
</ul><br />
<img src="https://static.igem.org/mediawiki/2012/f/fd/Helicopter.png" height="200" align="right"></img><br />
<br />
<p>Below are a series of challenges that we have made in our level:</p><br />
<br />
<br />
<br />
<h3>Challenge #1: Flight of the Flagellin</h3><br />
<br />
<p><br />
In your glider, fly down through the helical constant domain of the flagellin monomer, landing safely in the Boston airport. (Right in time for the world finals :) ). Bonus: The larger the aircraft you can fly through, the better.</p><br />
<p>Starting Coordinates:<br><br />
Latitude: 42.472766<br><br />
Longitude: -71.028729<br><br />
Altitude ASL: 27059.96<br><br />
Heading: 166.5<br><br />
</p><br />
<br />
<h3>Challenge #2: Red Fluorescent Protein</h3><br />
<p><br />
Land a helicopter on the chromophore of RFP. To make it easier, we've put a nice flat landing pad there for you.</p><br />
<img src="https://static.igem.org/mediawiki/2012/3/3f/Beta.png" height="200" align="right"></img><br />
<br />
<h3>Challenge #3: Land on beta sheet</h3><br />
<p><br />
Land any plane on the beta sheet. The larger the plane, the better. Need more of a challenge? Make the betasheet smaller.</p><br />
<h3>Import your own proteins!</h3><br />
<p>Here we'll talk a bit about how we actually did it. Basically,</p><br />
<ol><br />
<li><a href="http://epmv.scripps.edu/">Get the ePMY version of Blender</a> or another 3D design software.<br />
<li>Import PDB files, increase the size, rotate and manipulate as needed. Save as .AC format <a href="http://wiki.flightgear.org/Blender">See this link for the plugin.</a><br />
<li>Insert your objects into your favourite city using <a href="http://wiki.flightgear.org/Howto:Place_3D_objects_with_the_UFO">this guide.</a><br />
<li>Fly, fly away!<br />
</ol></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/flightTeam:Queens Canada/flight2012-10-27T01:28:22Z<p>Chev1n: </p>
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<body><br />
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<br><br />
<div id="pagecontent"><br />
<img src="https://static.igem.org/mediawiki/2012/c/cf/Trollface.jpg" align="right" height="200"></img><br />
<h1>Flight of the Flagellin</h1><br />
<b>Flight of the Flagellin takes protein structures and give them a hilarious, fun, new perspective.</b><br />
<br><br />
<p>What is this page really? Well, we recently discovered how easy it is to import 3D protein structures into an open-source flight simulator called FlightGear. It seems pretty ridiculous, but this could be a great way of teaching protein or molecular structure to people both young and old. It's also really surreal to be bringing some of the smallest units of life, and exploring them, in the setting of some of the largest man-made vehicles.</p><br />
<p>Flying is just fun. Lots of people play flight simulators just to fly around some generated landscape. Now in this case, you're flying our somebody's hard earned scientific data instead. With the amount of work that went into getting this data, it's hard to say whether we're taking full advantage of it and using it to its full potential, or just completely bastardizing it.</p><br />
<p>Something like this could also lead into new games, like EteRNA or Fold-it, in which the player is assigned the puzzle of solving a protein or RNA structure. The higher your score, the better you did, and your solution can actually contribute to scientific data. More specifically, we can swap out that plane model for, say, a ligand. Then, using this same idea, we can power docking experiments, in which players have to try and land a ligand in the active site of an enzyme, for example. This kind of computer modelling is common practice in drug design.</p><br />
<hr><br />
<h1>The Game</h1><br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Fgfs-screen-006.png" height="200" align="right"></img><br />
<p>Download and Installation: </p><br />
<p>First download and install the game from <a href="http://www.flightgear.org/">http://www.flightgear.org/</a><br />
<p>Next, download and install the Flight of the Flagellin Maps! We wish we could make this a little bit easier but, we're inexperienced! Follow these step by step instructions:</p><br />
<ul><br />
<li>Download and extract the map files: <a href="http://ubuntuone.com/0tDBQNcyBm43iPw3SW7St8">proteinflight.zip</a><br />
<li>Install the map files:<br />
<ol><br />
<li>Edit Objects/w080n40/w072n42/1777947.stg with any simple text editor.<br />
<li>Scroll to the bottom of the file.<br />
<li>Replace YOURPATHHERE with the file path to your downloads folder, or wherever you choose to store the protein models.<br />
<li>Copy the Objects folder to your Flightgear Scenery folder, ex: c:\Program Files\FlightGear\data\Scenery.<br />
</ol><br />
<li>Run flightgear and pick to take off from the Boston Airport! (ID:KBOS)<br />
</ul><br />
<img src="https://static.igem.org/mediawiki/2012/f/fd/Helicopter.png" height="200" align="right"></img><br />
<br />
<p>Below are a series of challenges that we have made in our level:</p><br />
<br />
<br />
<br />
<h3>Challenge #1: Flight of the Flagellin</h3><br />
<br />
<p><br />
In your glider, fly down through the helical constant domain of the flagellin monomer, landing safely in the Boston airport. (Right in time for the world finals :) ). Bonus: The larger the aircraft you can fly through, the better.</p><br />
<p>Starting Coordinates:<br><br />
Latitude: 42.472766<br><br />
Longitude: -71.028729<br><br />
Altitude ASL: 27059.96<br><br />
Heading: 166.5<br><br />
</p><br />
<br />
<h3>Challenge #2: Red Fluorescent Protein</h3><br />
<p><br />
Land a helicopter on the chromophore of RFP. To make it easier, we've put a nice flat landing pad there for you.</p><br />
<img src="https://static.igem.org/mediawiki/2012/3/3f/Beta.png" height="200" align="right"></img><br />
<br />
<h3>Challenge #3: Land on beta sheet</h3><br />
<p><br />
Land any plane on the beta sheet. The larger the plane, the better. Need more of a challenge? Make the betasheet smaller.</p><br />
<h3>Import your own proteins!</h3><br />
<p>Here we'll talk a bit about how we actually did it. Basically,</p><br />
<ol><br />
<li><a href="http://epmv.scripps.edu/">Get the ePMY version of Blender</a> or another 3D design software.<br />
<li>Import PDB files, increase the size, rotate and manipulate as needed. Save as .AC format <a href="http://wiki.flightgear.org/Blender">See this link for the plugin.</a><br />
<li>Insert your objects into your favourite city using <a href="http://wiki.flightgear.org/Howto:Place_3D_objects_with_the_UFO">this guide.</a><br />
<li>Fly, fly away!<br />
</ol></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/SynthetiQ/whowhyTeam:Queens Canada/SynthetiQ/whowhy2012-10-27T01:24:37Z<p>Chev1n: </p>
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<h1>Why?</h1><br />
<p><b>This is the big question.</b> Why would anyone do this? What are the advantages? Is it worth the effort? And there are so many different answers to these questions. Some of these answers can be found in Dr. Bohannon's TEDxBrussels talk can be found from feedback of the Dance Your PhD Contest. In his series of articles in Science, called the <a href="http://www.sciencemag.org/site/feature/misc/webfeat/gonzoscientist/">Gonzo Scientist</a>, he talks about each year of the competition as well as number of his other projects. In Episode 13, he asked the participants of the DYPhD Contest why they did it.</p><br />
<p>In general, dancing their science helped them:</p><br />
<ul><br />
<li>Get jobs and scholarships.<br />
<li>Summarize extensive research, into a few minutes of video.<br />
<li>Explain their work to friends and family.<br />
<li>Have lots of fun<br />
</ul><br />
<p><b>The kinesthetic learning style in scientific theory is virtually non-existent.</b> Lectures and textbooks are the predominant form of teaching. But, there's so much potential in teaching with movement. Everyone remembers the "Right-hand rule", be it from physics, or the helical direction of DNA. Teaching and learning through dance or movement can extrapolate from that basic idea. We can make science more like riding a bike, even if your mind doesn't quite remember how to do it, your body does, and after just a couple tries, it's just like you've been doing it for years.</p><br />
<p><b>One of the big goals of the DYPhD contest, is to make your research easier to understand, using a few words as possible.</b> Overall, we want there to be a better understanding by the public. On a larger scale, it's important for the general public to have an understanding of the impact of scientific research. By gaining more support and awareness from the public, research and development can become more of a priority for the government and future elections.</p><br />
<p><b>We all have friends and families that ask about our research.</b> By using this form of communication, we are able to simplify things. So that they can understand what we're doing and why it's exciting, and then they can get excited and tell or show others our research.</p><br />
<p><b>Body language is something that everyone can speak.</b> So whether you're trying to explain something to somebody who doesn't have a scientific background, or doesn't even speak the same language as you, this method will be the most effective way of communicating the ideas. This doesn't just appeal to interpretation by the mind, but to also basic human instincts and how we interpret the expression or movement of another human being.</p><br />
<h3>What about us?</h3><br />
<p><b>In our presentation at the iGEM Americas East Regional Competition, we wanted to test what it would be like to do something like this in an actual research setting.</b> We imagined a situation in which dance is the commonly used method to present research. And that's how we designed our presentation, incorporating the dancers to explain our research naturally, without pointing out that these are our dancers.</p><br />
<p>This presentation has already turned up results:</p><br />
<ul><br />
<li>A packed auditorium for our presentation.<br />
<li>The Best Model Award<br />
<li>Advancement to the World Finals<br />
<li>Gold Medal<br />
<li>Lots of attention at our school and worldwide<br />
<li>Everyone learned something new about synthetic biology<br />
</ul><br />
<p>And these are just our initial results. Because our team is composed solely of undergraduate students from many different backgrounds, we're are still waiting to see how this unique experience will benefit them in their futures. And there is so much potential. In addition to learning a new, unique dance routine, we have learned from the experiences and challenges that we have overcome and are incredibly excited to see what comes next.</p><br />
<hr><br />
<h1>Who are we?</h1><br />
<table id="syntable" align="center"><br />
<tr><br />
<td id="syntdl"><br />
<h3>Devon Ryan</h3><br />
<img src="https://static.igem.org/mediawiki/2012/e/e1/Devon2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>Choreographer, 3rd Year, Civil Engineering</b><br><br />
The moment I got the email invitation to be a part of QGEM I knew that I wanted to be a part of it. My whole life I’ve looked for ways to combine my artistic and scientific worlds. This was an amazing outlet to work with some of my favorite dancers, develop my choreography skills with challenging concepts and be on the front lines of a brand new relationship between science and dance. I am a better choreographer and academic for joining QGEM. </p><br />
</td><br />
<td id="syntdr"><br />
<h3>Sam Demetrious</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/7a/Samd.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th Year, Sociology Major</b><br><br />
I think the Queen’s IGEM team is so unique this year in such a fantastic way! By using dance to represent the scientific concepts, the research provided by the Queen's team can reach a wider audience and even impact individuals outside the synthetic biology community. The collaboration of arts and science is a wonderful learning tool, especially for those just beginning to learn about biology, such as a sociology student like myself. </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Michelle Rea</h3><br />
<img src="https://static.igem.org/mediawiki/2012/9/9f/Michelle.png" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd, Chemical Engineering</b><br><br />
I was approached at the beginning of the school year about this project and thought it was an amazing opportunity to combine my art with research that I am interested in. Using dance as teaching and presenting tool in science is a totally new concept and the experience was definitely one of a kind as I learned about the research through dancing it out!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Leandra Guillet</h3><br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Leandra2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Arts and Science</b><br><br />
Being able to be part of something like qGEM in my first year is kind of ridiculous. It’s not something I ever thought I would be doing, but I’m so glad I got the opportunity to combine dance and science. I have really enjoyed learning more about science while using my dance background to interpret the research. It’s probably the highlight of my first year so far.</p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Melissa Guertin</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/Melissa2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd year, Civil Engineering</b><br><br />
When I was first asked to dance in a piece portraying research, I really had no idea what to expect. I went in with an open mind, and found myself very rewarded. It was so neat to not only visually represent the research, but also get my own visual aid to understand things I have not learned. I felt very rewarded when people understood our representations and interpretations at the iGem competition in Pittsburgh, as well as here at Queen's. This is such an innovative concept and I am ecstatic that I get to be a part of this new beginning!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Christina Robitaille</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/56/Chrissy.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>2nd Year, Life Science</b><br><br />
This whole experience has been amazing for me. At first I was unsure of how successful melding science and the arts would be, but kudos to Devon and Kevin because our hard work has really paid off. The SynthetiQ project has proven to be both effective and very rewarding for all of us lucky enough to be involved. I'm so glad that I got the opportunity to be a part of the team, and I really admire QGEM for taking this risk with their project. It's been an incredible journey, and I can't wait to see where they go from here!</p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Alisha Giglio</h3><br />
<img src="https://static.igem.org/mediawiki/2012/7/79/Alisha2.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>2nd year, Chemistry Major</b><br><br />
Being apart of Queen’s iGEM this year has been a truly amazing experience. By combining synthetic biology and dance, I believe we have helped broaden many people’s views and hopefully made many think about new and innovative ways to portray their research, which could potentially change the world of boring science presentations as we know it. This whole experience has been rewarding as I have been able to combine two things I am interested in, as well, I am really excited to see how this concept will develop and what it will mean for dance and science in the future!</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Jaclyn Kemp</h3><br />
<img src="https://static.igem.org/mediawiki/2012/1/14/Jaclyn.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>1st Year, Physical and Health Education</b><br><br />
I found out about the opportunity to dance for QGEM through our choreographer Devon Ryan. I was thrilled to be able to use the art of dance to model and help explain scientific concepts. I think that this approach reaches out to a broader audience who are not as familiar with synthetic biology. The movement and visual images that are created in our presentation have helped me to understand the various concepts. My hope is that this new approach to presenting information can be used and expanded on in the future!<br><br> </p><br />
</td><br />
</tr><br />
<tr><br />
<td id="syntdl"><br />
<h3>Brittany Groom</h3><br />
<img src="https://static.igem.org/mediawiki/2012/f/fd/Brittany.jpg" align="right" style="padding-left:5px;padding-top:5px;"></img><br />
<p><b>3rd Year, Nursing</b><br><br />
I am honoured to be a part of the Queen’s iGEM team and have the opportunity to portray their innovative research through a mode of communication that is not seen very often in the science field. This experience has given me so much respect for the immense amount of time and work that every team puts forth to make this event possible. I can tell that the passion the Queen’s research team has for their work is the same passion that I have for dancing and, that is ultimately why we work together so seamlessly.</p><br />
</td><br />
<td id="syntdr"><br />
<h3>Kevin Chen</h3><br />
<img src="https://static.igem.org/mediawiki/2012/5/53/Kevin2.jpg" align="left" style="padding-right:5px;padding-top:5px;"></img><br />
<p><b>4th year, Biochemistry</b><br>I was the overall lead of the project, covering the logisitical sides of things, website, videos, driving and speaking in the actual presentation. It is really hard to describe what I have learned and gained from this project. It's just been unreal, definitely the highlight of my undergraduate degree and probably my life so far. My dance knowledge comes from BBoying, since first year. So, I've learned a lot working with these dancers. <br />
<br />
<br><br>And now these bios are symmetrical. Yay!</p><br />
</td><br />
</tr><br />
</table></div>Chev1nhttp://2012.igem.org/File:Brittany.jpgFile:Brittany.jpg2012-10-27T01:23:56Z<p>Chev1n: </p>
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}<br />
<br />
#menu { position: relative; top: 0; left: 0; overflow: hidden; height: 1000px;}<br />
#menu .colourful { display: block; position: absolute; background: #f0ad22; height: 35px; width: 85px; top: 4px; left: -100px; }<br />
#menu ul { margin: 0; padding: 0; list-style: none; float: left; position: absolute; top: 0; left: 0; z-index: 1; }<br />
#menu li { float: left; }<br />
#menu a:link, #menu a:visited, #menu a:hover, #menu a:active { color: #000; text-align: center; display: block; border: solid; border-width: 4px 0 0; line-height: 40px; width: 85px; height: 35px; }<br />
#menu li a:hover { text-decoration: none; color: #fff; text-shadow: 0 0 1px #999; }<br />
<br />
#globalWrapper<br />
{<br />
width: 99.3%;<br />
<br />
<br />
}<br />
#top-section { height: 20px; margin-bottom: 5; !important;<br />
border: none; font-size: 12px; background-color:#C5E2ED; <br />
-webkit-border-radius: 10px;<br />
-khtml-border-radius: 10px; <br />
-moz-border-radius: 10px;<br />
border-radius: 0px 10px 10px 0px;<br />
-moz-box-shadow: 3px 3px 4px #000; <br />
-webkit-box-shadow: 3px 3px 4px #000; <br />
box-shadow: 3px 3px 4px #000;<br />
margin-bottom: 2px;<br />
padding-top: 5px;<br />
padding-bottom: 5px;<br />
position:fixed;<br />
top: 33%;<br />
left: 0px;<br />
z-index:99;<br />
opacity: 0.8;}<br />
#p-logo { height:0px; overflow:hidden; display: none;}<br />
<br />
#search-controls { overflow:hidden; display:block; background: none; position: absolute; top: 100px; right: 40px;}<br />
<br />
#content<br />
{<br />
border-left: none;<br />
border-right: none;<br />
background-color: transparent;<br />
width:100%<br />
}<br />
<br />
#bodyContent { border: none; padding:0; margin:0; width: 100%; height:100%; <br />
}<br />
.firstHeading { display: none;}<br />
<br />
#content2<br />
{<br />
-khtml-border-radius: 10px; <br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
-moz-box-shadow: 3px 3px 4px #000; <br />
-webkit-box-shadow: 3px 3px 4px #000; <br />
box-shadow: 3px 3px 4px #000;<br />
margin-bottom: 10px;<br />
background-color: white; <br />
}<br />
<br />
<br />
<br />
#searchform { overflow:hidden; display:block; background: none; position: absolute; top: 100px; right: 40px;}<br />
body {background-color: white; width: 100%;}<br />
h3#siteSub { display: none;}<br />
#contentSub {display: none;}<br />
<br />
#top-section<br />
{<br />
width:auto;<br />
height: auto;<br />
}<br />
#menubar<br />
{<br />
width: 75px;<br />
position:relative;<br />
}<br />
<br />
.left-menu, .left-menu a {<br />
left: 0px;<br />
text-align: left;<br />
color: black;<br />
text-transform: lowercase;<br />
clear: both;<br />
display: block;<br />
}<br />
<br />
.left-menu:hover {<br />
color: black;<br />
background-color: transparent;<br />
}<br />
<br />
.right-menu<br />
{<br />
position:relative;<br />
display:block;<br />
}<br />
<br />
#menubar ul<br />
{<br />
background-color: #9999ff<br />
opacity: 0;<br />
<br />
}<br />
<br />
.left-menu.noprint<br />
{<br />
display: inline;<br />
background-color: #9999ff<br />
opacity: 0;<br />
padding-top: 5px;<br />
<br />
}<br />
.selected<br />
{<br />
<br />
display: inline;<br />
<br />
}<br />
<br />
a {<br />
text-decoration: none;<br />
}<br />
.right-menu.noprint<br />
{<br />
width: 75px;<br />
}<br />
.right-menu li a<br />
{<br />
padding: 0 0 0 0;<br />
}<br />
<br />
.right-menu li a.new {<br />
color: black;<br />
padding-top: 0px;<br />
}<br />
<br />
#menubar li {<br />
display: inline;<br />
position: relative;<br />
cursor: pointer;<br />
padding-left: 0px;<br />
padding-right: 0px;<br />
color: black;<br />
font-family: "Trebuchet MS", Helvetica, sans-serif;<br />
font-size: 14px;<br />
padding-top: 5px;<br />
<br />
}<br />
.left-menu li<br />
{<br />
color: black;<br />
}<br />
.left-menu li a {<br />
padding: 0px 10px 0px 0px;<br />
}<br />
.left-menu .selected {<br />
color: black;<br />
padding-top: 5px;<br />
}<br />
#.left-menu .selected:hover {<br />
color: black;<br />
#}<br />
<br />
.left-menu:hover a {<br />
color: black;<br />
}<br />
.left-menu ul<br />
{<br />
margin-left: 10px;<br />
padding-right: 10px;<br />
}<br />
.right-menu ul<br />
{<br />
margin-left: 10px;<br />
padding-right: 10px;<br />
}<br />
.right-menu li {<br />
# background-color: #9999ff;<br />
padding: 0px 0px 0px 0px;<br />
display: block;<br />
text-align: left;<br />
}<br />
.right-menu li a {<br />
padding: 0px 0px 0px 0px;<br />
color: black;<br />
background-color: transparent;<br />
clear:both;<br />
display:block;<br />
text-align: left;<br />
}<br />
.right-menu li a:hover {<br />
color: black;<br />
text-decoration: underline;<br />
padding: 0px 0px 0px 0px;<br />
}<br />
.right-menu li a.new {<br />
color: black;<br />
padding-top: 0px;<br />
}<br />
.right-menu li a.new:hover {<br />
color: black;<br />
text-decoration: underline;<br />
padding-top: 0px;<br />
}<br />
<br />
#header<br />
{<br />
height: 150px;<br />
width: 1000px;<br />
-webkit-border-radius: 10px;<br />
-khtml-border-radius: 10px; <br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
-moz-box-shadow: 3px 3px 4px #000; <br />
-webkit-box-shadow: 3px 3px 4px #000; <br />
box-shadow: 3px 3px 4px #000;<br />
margin-bottom: 10px;<br />
line-spacing: 100%;<br />
text-align: center;<br />
background-image:url('https://static.igem.org/mediawiki/2012/9/96/Headerv2.png');<br />
background-repeat:no-repeat;<br />
background-color:#ffffff;<br />
z-index: 2;<br />
position: relative;<br />
margin-left:auto;<br />
margin-right:auto;<br />
}<br />
#headerfont1<br />
{<br />
font-size: 4em;<br />
}<br />
#headerfont1 a {<br />
color:black;<br />
text-decoration: none;<br />
}<br />
<br />
#headerfont1 a:hover<br />
{<br />
color: black;<br />
text-decoration: none;<br />
<br />
<br />
}<br />
<br />
#qboxlink {<br />
position: absolute;<br />
top:18px;<br />
left:669px;<br />
width:90px;<br />
height:65px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
#iboxlink {<br />
position: absolute;<br />
top:0px;<br />
right:0px;<br />
width:75px;<br />
height:61px;<br />
background-color: transparent;<br />
border: none;<br />
z-index: 99;<br />
}<br />
<br />
<br />
h2{color:#96d446; }<br />
h2,h4, h5, h2.noline, h2.topheader{font-family:"Segoe WP", serif; font-size:200%; line-height:35px; border-bottom:0; margin-bottom:5px; border-top:0px; margin-top:10px; padding-top:30px; font-weight:light;}<br />
h2.noline{ border-top:0; margin-top:0; padding-top:0; margin-bottom:0; line-height:20px; padding-top:2px; font-size:20px;}<br />
h2.topheader{border-top:0; padding-top:0; margin-top:5px; font-weight:normal}<br />
<br />
h1<br />
{<br />
font-family: "Trebuchet MS", Helvetica ,sans-serif;<br />
border:none<br />
}<br />
<br />
h3<br />
{<br />
font-family: "Trebuchet MS", Helvetica ,sans-serif;<br />
}<br />
<br />
#catlinks<br />
{<br />
display:none;<br />
}<br />
f1<br />
{<br />
font-size: 70px;<br />
font-family: "Trebuchet MS";<br />
}<br />
<br />
f1 a:link<br />
{<br />
color: black<br />
}<br />
<br />
f1 a:hover<br />
{<br />
color: black;<br />
text-decoration: none;<br />
}<br />
f1 a:active<br />
{<br />
color: black; <br />
}<br />
<br />
f1 a:visited<br />
{<br />
color: black;<br />
}<br />
<br />
#footer-box <br />
{<br />
-webkit-border-radius: 10px;<br />
-khtml-border-radius: 10px; <br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
margin-bottom: 5 px;<br />
padding-top: 5px;<br />
padding-bottom: 5px;<br />
background-color: white;<br />
border-color: transparent;<br />
width:1000px;<br />
opacity: 0.8;<br />
background-color: transparent;<br />
<br />
<br />
}<br />
#teamtable<br />
{<br />
font-family:"Trebuchet MS", Helvetica, sans-serif;<br />
font-size:12px;<br />
text-align: center;<br />
background:none;<br />
border-spacing:20pt;<br />
border:0pt;<br />
}<br />
#teamtd, #teamth<br />
{<br />
border:30px;<br />
width:170px;<br />
vertical-align:top;<br />
}<br />
#teamth<br />
{<br />
text-align:left;<br />
font-size:20px;<br />
color:gray;<br />
}<br />
#caption {<br />
background: #333;<br />
border-right: 1px solid #666;<br />
border-bottom: 1px solid #666;<br />
border-left: 1px solid #666;<br />
border-top: 1px solid #666;<br />
font-family: Verdana;<br />
font-size: 11px;<br />
padding: 4px;<br />
-moz-border-radius-bottomright: 6px;<br />
-moz-border-radius-bottomleft: 6px;<br />
-webkit-border-bottom-right-radius: 6px;<br />
-webkit-border-bottom-left-radius: 6px;<br />
color: #eee;<br />
}<br />
#upbutton<br />
{<br />
background-color:DarkGreen;<br />
-khtml-border-radius: 10px; <br />
-moz-border-radius: 10px;<br />
border-radius: 10px;<br />
-moz-box-shadow: 3px 3px 4px #000; <br />
-webkit-box-shadow: 3px 3px 4px #000; <br />
box-shadow: 3px 3px 4px #000; <br />
right: 5px;<br />
bottom: 5px;<br />
position: fixed;<br />
color: white;<br />
font-weight: bold;<br />
font-size: 3em;<br />
z-index: 999; <br />
opacity: .8;<br />
height: 40px;<br />
width: 40px;<br />
background-image: url('https://static.igem.org/mediawiki/2012/b/b6/Upbutton1.png');<br />
display:none;<br />
}<br />
#contentmain<br />
{<br />
margin-bottom: 10px;<br />
width:745px;<br />
background-color: transparent;<br />
padding: 10px 10px 10px 10px<br />
display:inline;<br />
float:left;<br />
margin-top: 50px;<br />
}<br />
#twitter_wrapper<br />
{<br />
width: 200px;<br />
background-color: white;<br />
right: 0px;<br />
display:inline;<br />
float:right;<br />
margin-top: 25px;<br />
<br />
}<br />
ul#submenu {<br />
margin: 0px;<br />
padding: 0px;<br />
top: 0px;<br />
right: 200px;<br />
list-style: none;<br />
z-index:999999;<br />
z-index: 0;<br />
}<br />
ul#submenu li {<br />
display:inline;<br />
float:left;<br />
width:100px;<br />
margin-left:1px;<br />
z-index: 0;<br />
<br />
}<br />
#submenu_container<br />
{<br />
position: absolute;<br />
height: 75px;<br />
display:block;<br />
left: 200px;<br />
display:none;<br />
}<br />
ul#submenu li a {<br />
display: block;<br />
font-weight:bold;<br />
text-shadow:1px 1px 1px #fff;<br />
float:left;<br />
height: 35px;<br />
width: 100%;<br />
color:#603d05;<br />
background-color: grey;<br />
text-decoration:none;<br />
text-align:center;<br />
cursor:pointer;<br />
postion: relative;<br />
left: 65px;<br />
<br />
z-index: 0;<br />
<br />
}<br />
ul#submenu li a:hover{<br />
<br />
}<br />
<br />
ul#submenu<br />
{<br />
}<br />
#controlbar<br />
{<br />
left:0px;<br />
width:50px;<br />
height: 20px;<br />
font-size: 1em;<br />
position:fixed;<br />
bottom:0px;<br />
background-color: dodgerblue;<br />
color:white;<br />
text-align: center;<br />
cursor:default;<br />
display:none;<br />
<br />
}<br />
#headercontainer<br />
{<br />
width:100%<br />
}<br />
#pagecontent<br />
{<br />
width: 1000px;<br />
margin-left:auto;<br />
margin-right:auto;<br />
margin-top: 150px;<br />
background-image: url('http://dl.dropbox.com/u/46807995/retina_wood.png');<br />
border-radius: 15px;<br />
}<br />
#topbarcontainer<br />
{<br />
background-color: #C5E2ED;<br />
background-repeat: repeat-x;<br />
width: 100%;<br />
min-width: 1000px;<br />
height: 60px;<br />
position: absolute;<br />
top: 0px;<br />
left: 0px;<br />
margin-bottom: 25px;<br />
box-shadow: 0 0px 3px rgba(0, 0, 0, 0.5);<br />
}<br />
#topbar<br />
{<br />
margin-left: auto;<br />
margin-right: auto;<br />
height: 60px;<br />
position:relative;<br />
width: 1000px;<br />
background-color: transparent;<br />
bottom: 0px;<br />
<br />
}<br />
<br />
#igemlogocontainer<br />
{<br />
position:absolute; width:75px; right:0px; top:0px;<br />
}<br />
.ca-container{<br />
position:relative;<br />
margin:25px auto 20px auto;<br />
width:990px;<br />
height:450px;<br />
background-color: transparent;<br />
}<br />
.ca-wrapper{<br />
width:100%;<br />
height:100%;<br />
position:relative;<br />
}<br />
.ca-item{<br />
position:relative;<br />
float:left;<br />
width:330px;<br />
height:100%;<br />
text-align:center;<br />
}<br />
.ca-more{<br />
position: absolute;<br />
bottom: 10px;<br />
right:0px;<br />
padding:4px 15px;<br />
font-weight:bold;<br />
background: #ccbda2;<br />
text-align:center;<br />
color: white;<br />
font-family: "Georgia","Times New Roman",serif;<br />
font-style:italic;<br />
text-shadow:1px 1px 1px #897c63;<br />
}<br />
.ca-close{<br />
position:absolute;<br />
top:10px;<br />
right:10px;<br />
background:#fff url('https://photos-2.dropbox.com/btj/fb944905/MtnDr20-rnUT6e81x8dYhcU0Gmu0f1ylMwkTjp1s2UQ/cross.png') no-repeat center center;<br />
width:27px;<br />
height:27px;<br />
text-indent:-9000px;<br />
outline:none;<br />
-moz-box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
-webkit-box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
opacity:0.7;<br />
}<br />
.ca-close:hover{<br />
opacity:1.0;<br />
}<br />
.ca-item-main{<br />
padding:20px;<br />
position:absolute;<br />
top:5px;<br />
left:5px;<br />
right:5px;<br />
bottom:5px;<br />
background:#fff;<br />
overflow:hidden;<br />
-moz-box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
-webkit-box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
}<br />
.ca-icon{<br />
width:189px;<br />
height:189px;<br />
position:relative;<br />
margin:0 auto;<br />
background:transparent url('http://dl.dropbox.com/u/46807995/QGEM%202012%20Logo3.png') no-repeat center center;<br />
}<br />
.ca-item-2 .ca-icon{<br />
background-image:url('http://dl.dropbox.com/u/46807995/QGEM%202012%20Logo3.png');<br />
}<br />
.ca-item-3 .ca-icon{<br />
background-image:url(../images/animal3.png);<br />
}<br />
.ca-item-4 .ca-icon{<br />
background-image:url(../images/animal4.png);<br />
}<br />
.ca-item-5 .ca-icon{<br />
background-image:url(../images/animal5.png);<br />
}<br />
.ca-item-6 .ca-icon{<br />
background-image:url(../images/animal6.png);<br />
}<br />
.ca-item-7 .ca-icon{<br />
background-image:url(../images/animal7.png);<br />
}<br />
.ca-item-8 .ca-icon{<br />
background-image:url(../images/animal8.png);<br />
}<br />
.ca-item h3{<br />
font-family: 'Coustard', sans-serif;<br />
text-transform:uppercase;<br />
font-size:30px;<br />
color:#000;<br />
margin-bottom:20px;<br />
height:85px;<br />
text-align:center;<br />
text-shadow: 0px 1px 1px #e4ebe9;<br />
}<br />
.ca-item h4{<br />
font-family: 'Philosopher', sans-serif;;<br />
font-style:italic;<br />
font-size:12px;<br />
text-align:left;<br />
border-left:10px solid #b0ccc6;<br />
padding-left:10px;<br />
line-height:24px;<br />
margin:10px;<br />
position:relative;<br />
}<br />
.ca-item h4 span{<br />
text-indent:40px;<br />
display:block;<br />
}<br />
.ca-item h4 span.ca-quote{<br />
color:#f4eee3;<br />
font-size:100px;<br />
position:absolute;<br />
top:20px;<br />
left:0px;<br />
text-indent:0px;<br />
}<br />
.ca-content-wrapper{<br />
background:#b0ccc6;<br />
position:absolute;<br />
width:0px; /* expands to width of the wrapper minus 1 element */<br />
height:440px;<br />
top:5px;<br />
text-align:left;<br />
z-index:10000;<br />
overflow:hidden;<br />
}<br />
.ca-content{<br />
width:660px;<br />
overflow:hidden;<br />
}<br />
.ca-content-text{<br />
font-size: 14px;<br />
font-style: italic;<br />
font-family: "Georgia","Times New Roman",serif;<br />
margin:10px 20px;<br />
padding:10px 20px;<br />
line-height:24px;<br />
list-style-type: none;<br />
}<br />
.ca-content-text p{<br />
padding-bottom:5px;<br />
}<br />
.ca-content h6{<br />
margin:25px 20px 0px 35px;<br />
font-size:32px;<br />
padding-bottom:5px;<br />
color:#000;<br />
font-family: 'Coustard', sans-serif;<br />
color:#60817a;<br />
border-bottom:2px solid #99bcb4;<br />
text-shadow: 1px 1px 1px #99BCB4;<br />
}<br />
.ca-content ul{<br />
margin:20px 35px;<br />
height:30px;<br />
list-style:none;<br />
}<br />
.ca-content ul li{<br />
float:left;<br />
margin:0px 2px;<br />
}<br />
.ca-content ul li a{<br />
color:#fff;<br />
background:#000;<br />
padding:3px 6px;<br />
font-size:14px;<br />
font-family: "Georgia","Times New Roman",serif;<br />
font-style:italic;<br />
}<br />
.ca-content ul li a:hover{<br />
background:#fff;<br />
color:#000;<br />
text-shadow:none;<br />
}<br />
.ca-nav span{<br />
width:25px;<br />
height:38px;<br />
background:transparent url('https://photos-1.dropbox.com/btj/4159138c/aALpyYLbAaADO2-Ebio68A3s-L7ioYLKSv_9ocokcRY/arrows.png?size=1024x768') no-repeat top left;<br />
position:absolute;<br />
top:50%;<br />
margin-top:-19px;<br />
left:-40px;<br />
text-indent:-9000px;<br />
opacity:0.7;<br />
cursor:pointer;<br />
z-index:100;<br />
}<br />
.ca-nav span.ca-nav-next{<br />
background-position:top right;<br />
left:auto;<br />
right:-40px;<br />
}<br />
.ca-nav span:hover{<br />
opacity:1.0;<br />
}<br />
.ca-container{<br />
position:relative;<br />
margin:25px auto 20px auto;<br />
width:990px;<br />
height:450px;<br />
}<br />
.ca-wrapper{<br />
width:100%;<br />
height:100%;<br />
position:relative;<br />
}<br />
.ca-item{<br />
position:relative;<br />
float:left;<br />
width:330px;<br />
height:100%;<br />
text-align:center;<br />
}<br />
.ca-more{<br />
position: absolute;<br />
bottom: 10px;<br />
right:0px;<br />
padding:4px 15px;<br />
font-weight:bold;<br />
background: #ccbda2;<br />
text-align:center;<br />
color: white;<br />
font-family: "Georgia","Times New Roman",serif;<br />
font-style:italic;<br />
text-shadow:1px 1px 1px #897c63;<br />
}<br />
.ca-close{<br />
position:absolute;<br />
top:10px;<br />
right:10px;<br />
background:#fff url(../images/cross.png) no-repeat center center;<br />
width:27px;<br />
height:27px;<br />
text-indent:-9000px;<br />
outline:none;<br />
-moz-box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
-webkit-box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
box-shadow:1px 1px 2px rgba(0,0,0,0.2);<br />
opacity:0.7;<br />
}<br />
.ca-close:hover{<br />
opacity:1.0;<br />
}<br />
.ca-item-main{<br />
padding:20px;<br />
position:absolute;<br />
top:5px;<br />
left:5px;<br />
right:5px;<br />
bottom:5px;<br />
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</html></div>Chev1nhttp://2012.igem.org/Team:Queens_Canada/flightTeam:Queens Canada/flight2012-10-27T01:15:29Z<p>Chev1n: </p>
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<h1>Flight of the Flagellin</h1><br />
<b>Flight of the Flagellin takes protein structures and give them a hilarious, fun, new perspective.</b><br />
<br><br />
<p>What is this page really? Well, we recently discovered how easy it is to import 3D protein structures into an open-source flight simulator called FlightGear. It seems pretty ridiculous, but this could be a great way of teaching protein or molecular structure to people both young and old. It's also really surreal to be bringing some of the smallest units of life, and exploring them, in the setting of some of the largest man-made vehicles.</p><br />
<p>Flying is just fun. Lots of people play flight simulators just to fly around some generated landscape. Now in this case, you're flying our somebody's hard earned scientific data instead. With the amount of work that went into getting this data, it's hard to say whether we're taking full advantage of it and using it to its full potential, or just completely bastardizing it.</p><br />
<p>Something like this could also lead into new games, like EteRNA or Fold-it, in which the player is assigned the puzzle of solving a protein or RNA structure. The higher your score, the better you did, and your solution can actually contribute to scientific data. More specifically, we can swap out that plane model for, say, a ligand. Then, using this same idea, we can power docking experiments, in which players have to try and land a ligand in the active site of an enzyme, for example. This kind of computer modelling is common practice in drug design.</p><br />
<hr><br />
<h1>The Game</h1><br />
<img src="https://static.igem.org/mediawiki/2012/f/f6/Fgfs-screen-006.png" height="200" align="right"></img><br />
<p>Download and Installation: </p><br />
<p>First download and install the game from <a href="http://www.flightgear.org/">http://www.flightgear.org/</a><br />
<p>Next, download and install the Flight of the Flagellin Maps! We wish we could make this a little bit easier but, we're inexperienced! Follow these step by step instructions:</p><br />
<ul><br />
<li>Download the map files: <a href="http://ubuntuone.com/0tDBQNcyBm43iPw3SW7St8">proteinflight.zip</a><br />
<li>Install the map files:<br />
<ol><br />
<li>Edit Objects/w080n40/w072n42/1777947.stg with any simple text editor.<br />
<li>Scroll to the bottom of the file.<br />
<li>Replace YOURPATHHERE with the file path to your downloads folder, or wherever you choose to store the protein models.<br />
<li>Copy the Objects folder to your Flightgear Scenery folder, ex: c:\Program Files\FlightGear\data\Scenery.<br />
</ol><br />
<li>Run flightgear and pick to take off from the Boston Airport! (ID:KBOS)<br />
</ul><br />
<img src="https://static.igem.org/mediawiki/2012/f/fd/Helicopter.png" height="200" align="right"></img><br />
<br />
<p>Below are a series of challenges that we have made in our level:</p><br />
<br />
<br />
<br />
<h3>Challenge #1: Flight of the Flagellin</h3><br />
<br />
<p><br />
In your glider, fly down through the helical constant domain of the flagellin monomer, landing safely in the Boston airport. (Right in time for the world finals :) ). Bonus: The larger the aircraft you can fly through, the better.</p><br />
<p>Starting Coordinates:<br><br />
Latitude: 42.472766<br><br />
Longitude: -71.028729<br><br />
Altitude ASL: 27059.96<br><br />
Heading: 166.5<br><br />
</p><br />
<br />
<h3>Challenge #2: Red Fluorescent Protein</h3><br />
<p><br />
Land a helicopter on the chromophore of RFP. To make it easier, we've put a nice flat landing pad there for you.</p><br />
<img src="https://static.igem.org/mediawiki/2012/3/3f/Beta.png" height="200" align="right"></img><br />
<br />
<h3>Challenge #3: Land on beta sheet</h3><br />
<p><br />
Land any plane on the beta sheet. The larger the plane, the better. Need more of a challenge? Make the betasheet smaller.</p><br />
<h3>Import your own proteins!</h3><br />
<p>Here we'll talk a bit about how we actually did it. Basically,</p><br />
<ol><br />
<li><a href="http://epmv.scripps.edu/">Get the ePMY version of Blender</a> or another 3D design software.<br />
<li>Import PDB files, increase the size, rotate and manipulate as needed. Save as .AC format <a href="http://wiki.flightgear.org/Blender">See this link for the plugin.</a><br />
<li>Insert your objects into your favourite city using <a href="http://wiki.flightgear.org/Howto:Place_3D_objects_with_the_UFO">this guide.</a><br />
<li>Fly, fly away!<br />
</ol></div>Chev1n