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2024-03-28T17:33:38Z
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http://2013.igem.org/Team:Alberta/Attributions
Team:Alberta/Attributions
2013-11-14T22:52:18Z
<p>MEsau: </p>
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<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions" class="active">Attributions</a></li><br />
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<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team" class="active"><p>Roster</p></a><br />
<a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta"><p>Official Profile</p></a><br />
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<p class="content-title">Attributions</p><br />
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<div class="block"><br />
<p>All of the experimental work described herein was performed by the team with technical support from Prof. Ellison’s technician, <b>Nien-tsu Tseng (Rick)</b>. The TSP concept was inspired by the <b>Missouri-Davidson 2007 iGEM team</b> who broke the ice with their work on the Hamiltonian variation of TSB problem. The experimental approaches used here evolved over discussions with our supervisors during group meetings. The correct weighting algorithm that relates city path lengths to linker concentrations was developed by <b>Dr. Doug Ridgway</b>, a supervisor of the 2012 iGEM team. The plasmids used to create TSB compatible parts by PCR were a gift from <b><a href="http://www.genomikon.ca/">Genomikon Inc</a></b>. <br />
The creation of the violacin bricks that we will use in the test of the 5-city TSB would not have been possible without the violacein operon biobrick (K274002) that was created, submitted and carefully characterized by the <b>Cambridge 2009 iGEM team</b>. Wiki coding and design implementation was done by <b>Timo Hohn</b>, (B.Sc. in Computer Engineering).<br />
</p><br />
<br><br />
<p>Thanks to these individuals for donating their time and talents!</p><br />
</div><br />
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<div class="clear"></div><br />
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<br />
<!--html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/SafetyForm
Team:Alberta/SafetyForm
2013-10-29T03:54:01Z
<p>MEsau: </p>
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<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Precautions"><p>Lab members’ Safety and Protective Precautions</p></a><br />
<a href="#Public-Safety"><p>Public Safety</p></a><br />
<a href="#Environmental-Safety"><p>Environmental Safety</p></a><br />
<a href="#Future-Risks"><p>Future risks from Commercialism</p></a><br />
<a href="#Training"><p>Training</p></a><br />
<a href="#Committee"><p>Biosafety Committee</p></a><br />
<a href="#References"><p>References</p></a><br />
<a href="#More-Detail"><p>For more information</p></a><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/SafetyForm" class="active"><p>Safety Form</p></a><br />
<a href="/Team:Alberta/FAQ"><p>FAQ</p></a><br />
<a href="/Team:Alberta/Resources"><p>Resources</p></a><br />
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<div class="block"><br />
<p class="content-title"><img src="/wiki/images/thumb/4/43/Safety_form.png/466px-Safety_form.png" height="125"> Summary of Safety Form</img></p><br />
</div><br />
<div class="block">Since safety is a concern with laboratory projects, the following safety form was submitted to iGEM Headquarters and approved by the Safety Committee.</div><br />
<a class="anchor" id="Precautions"></a><br />
<div class="block"><br />
<h2>Lab members’ Safety and Protective Precautions</h2><br />
<p>There are no significant risks to lab members, as the biological parts are not reasonably able to cause any health issues<br />
to team members.</p><br />
<p>All the components of our project are quite standard in molecular biology labs and are not associated with<br />
significant risks. Our microorganisms, biological parts, laboratory equipment and chemicals are mostly<br />
comparably benign. The strains which our team intends to use and has used thus far are harmless <br />
(nonpathogenic and non-toxigenic). The biological parts we are using consist of color, antibiotic-resistance <br />
(Chloramphenicol, Kanamycin, Ampicillin, Tetracycline) and various promoters. In terms of chemicals,<br />
the myriad of flammable solvents in the lab pose a notable risk, and in addition the ethidium bromide <br />
(EtBr) is a dangerous toxin and mutagen. EtBr is used to visualize DNA by soaking agarose gels in a <br />
solution of the compound. EtBr works by intercalating between bases in the DNA’s helical structure, <br />
where is it able to fluoresce much more brightly than it does while in solution. It is generally established <br />
that intercalating agents are mutagens, and that mutagens are carcinogens and for this reason EtBr is <br />
treated with a high level of caution in our lab. Experiments have shown that EtBr is able to cause DNA <br />
damage in human cell lines so this carcinogenic potential is not just theoretical. To mitigate risks, <br />
relevant <br />
microbiological <a name="public">techniques</a> are consistently used in the lab and gloves are worn. Other precautions for <br />
EtBr include the labelling of designated containers for EtBr gels and EtBr waste, and the reuse of EtBr <br />
solution to minimize waste.</p><br />
<p>The most dangerous laboratory equipments we use are a transilluminator, gel apparatus, and the Bunsen<br />
burner. The risks posed by exposure to UV radiation, electric shocks and open flames can be easily<br />
controlled with proper safety training and protective equipment. A thick glass cover has been added to <br />
one UV visualizer in the lab to protect eyes when visualizing gels. Usually, a different UV visualizer is <br />
used for lab purposes because it photographs the gel without any UV exposure to eyes at all. Students <br />
are taught how to properly use equipment, dispose of wastes, autoclave used glassware and <br />
biologicallycontaminated waste, disinfect counters and know when to wear safety protection. Proper pipetting <br />
protocol is always used.</p><br />
</div><br />
<a class="anchor" id="Public-Safety"></a><br />
<div class="block"><br />
<h2>Public Safety</h2> <br />
<p>The DH5-α strain with which our group is working (which is a derivative of K-12) is non-pathogenic and<br />
non-toxigenic, so it poses no risk to public health and safety.</p><br />
<p><a name="environment">A public concern</a> is that the plasmids containing antibiotic resistance genes could be released into the<br />
environment. Since our project uses antibiotic resistance genes as selection tools, we ensure that these <br />
genes are properly disposed of by autoclaving.</p><br />
<p>In evaluating the risks, there is a lower chance of gene uptake by wild bacteria compared to our labstrain <br />
bacteria that have perforated membranes. In the case that wild bacteria did uptake the antibiotic <br />
resistance gene, that gene would eventually be lost in the population without exposure to the antibiotic, <br />
because it is then a disadvantage for the bacteria to carry the unused plasmids and use up energy <br />
to express them. Evidence for this was observed in multiple cases of measured declines in particular <br />
antibiotic resistances after the human population limited the antibiotic usage (Klotins, 2005).</p><br />
</div><br />
<a class="anchor" id="Environmental-Safety"></a><br />
<div class="block"><br />
<h2>Environmental Safety</h2><br />
<p>The bacteria that we use in the laboratory are not well suited to survival in the environment and even <br />
assuming they were able to do so, they do not have any destructive potential. <br />
The standard and well-characterized biobytes we are using do not have the potential to combine in <br />
dangerous ways. As with many other synthesized DNA constructs, we have found that our plasmids are <br />
lost from the bacteria over time (if plated without antibiotic present), due to the expression of colors <br />
being <br />
an unproductive strain on the cell’s resources. Consequently, there is little risk of our microorganisms <br />
spreading. Even if our <i>E. coli</i> strains survived and replicated in the wild, they are highly unlikely <br />
to <br />
cause harm to any humans or animals as risk level one microorganisms. The microorganisms we are <br />
creating in the lab would have less potential for malicious misuse than any bacteria normally found in the <br />
environment.</p><br />
<p>Although there is no intentional release to the environment and people, contamination is minimized<br />
by protective equipment (gloves) and disinfection. However, the microbe strain cannot survive outside <br />
the lab environment because it is engineered to be weak and dependent on a lab nutrient mix (Luria<br />
Broth, LB agar). In the improbable case that the microbe evolved (ex. By uptaking genes) to be able to <br />
synthesize one of the essential amino acids, it still would be deficient in multiple other ways.</p><br />
</div><br />
<a class="anchor" id="Future-Risks"></a><br />
<div class="block"><br />
<h2>Future risks from Commercialism</h2><br />
<p>Answering this question accurately is something of a complex endeavor, as one of the key aspects of<br />
<a name="training">our project</a> is that it is essentially a foundational advance. As such there are probably many approaches <br />
a focused group of minds might be able to develop using some of the principle and methods we have <br />
developed. However, even given the very open-ended nature of our project’s potential future, it is difficult <br />
to envision scenarios in which significant dangers are encountered. It is possible that in the distant <br />
future <br />
our methods might be modified and used with organisms and/or genes that entail greater risks than the <br />
non-pathogenic <i>E. coli</i> we have chosen to use. Even in this instance, the risks to personal, <br />
environmental <br />
and public safety are equal to the risks posed by the organisms and/or genes used and not modulated <br />
upward by the methods of our project in any conceivable way.</p><br />
</div><br />
<a class="anchor" id="Training"></a><br />
<div class="block"><br />
<h2>Training</h2><br />
<p>Laboratory safety training is given to undergraduate students in many of their laboratory courses. Specific <br />
to bio-safety, three of our team members have completed a comprehensive biological laboratory safety <br />
course in their Methods of Modern Biochemistry course (BIOCH 401) This course includes general <br />
biological, chemical, and WHMIS safety training). All students including the high school students were <br />
given on-site training for the specific techniques they would be using in the laboratory.</p><br />
</div><br />
<a class="anchor" id="Committee"></a><br />
<div class="block"><br />
<h2>Biosafety Committee</h2><br />
<p>As is the case with most universities, there is a local Biosafety Committee on the university of Alberta<br />
Campus that ensures research labs are following the safety protocols put in place by the national<br />
government. The University of Alberta Biosafety Committee is a division of the Environmental Health<br />
and Safety Faculty. This Committee oversees the handling of biohazardous materials and/or techniques, <br />
defined as “materials of biological origin or synthetic material which mimic biological entities and may <br />
induce adverse conditions to humans, other animals, plants, or the environment”. With respect to <br />
relevant national and international guidelines, our non-virulent strains of <i>E. coli</i> are considered <br />
Biosafety <br />
level 1 and are of limited potential hazard. Within our lab, standard practices are used, including but <br />
not limited to wearing gloves and sterilizing with bleach and/or ethanol and/or autoclaving. University <br />
policy states that the Biosafety committee need only be contacted when risk group level 2 organisms are <br />
to be worked with, or for other special concerns, and as such there is currently no need to discuss the <br />
project details with them to obtain their approval. However, the EHS provides documents on laboratory <br />
guidelines and university-specific ethidium bromide disposal (EHS, 2011), which have been reviewed by <br />
the team.</p><br />
<p>According to the WHO bio-safety manuscript, the living organisms with which this year’s University of <br />
Alberta iGEM team has worked (and will work with) all fall within the category of Risk Level 1, which <br />
the manuscript goes on to define as “unlikely to cause human or animal disease”. Since the strains which<br />
our team intends to use and has used thus far are harmless (non-pathogenic and non-toxigenic), they all <br />
fall into this category and as such, no major safety issues are raised by the biological components of our <br />
project.</p><br />
</div><br />
<a class="anchor" id="References"></a><br />
<div class="block"><br />
<h2>References:</h2><br />
<p><ul><li>Ethidium bromide – fact sheet. November 2011. <i>Environmental Health & Safety.</i><br />
Retrieved August 9, 2013, from <a href="http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf">www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/<br />
Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf</a></li><br />
<li>Klotins, K. (n.d.). Antibiotic use for growth improvement. <i>Ontario Ministry of Rural Affairs / <br />
Ministry <br />
of <br />
Agriculture and Food.</i> Retrieved August 2, 2013, from <br />
<a href="http://www.omafra.gov.on.ca/english/livestock/animalcare/amr/facts/05-041.htm"><br />
http://www.omafra.gov.on.ca/english/livestock/animalcare/amr/facts/05-041.htm</a></li><br />
<li><a href="http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/Manuals%20and%20Documents/Biosafety_Manual_Aug__03__2_.ashx"><br />
http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/<br />
Documents/Manuals%20and%20Documents/Biosafety_Manual_Aug__03__2_.ashx</a><br/><br />
(Found also from: <br />
<a href="http://www.ehs.ualberta.ca/EHSDivisions/Biosafety.aspx"> <br />
http://www.ehs.ualberta.ca/EHSDivisions/Biosafety.aspx</a>)</li><br />
<li><a href="http://canadianbiosafetystandards.collaboration.gc.ca/cbsg-nldcb/index-eng.php?page=1"><br />
http://canadianbiosafetystandards.collaboration.gc.ca/cbsg-nldcb/index-eng.php?page=1</a> and </li><br />
<li><a href="http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/"><br />
http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/.</a></li></ul></p><br />
</div><br />
<a class="anchor" id="More-Detail"></a><br />
<div class="block"><br />
<b>For more detail, see the full basic form <a href="/wiki/images/1/1c/IGEM_2013_Basic_Safety_Form-_Final3.pdf">part 1</a> submitted to iGEM Safety Committee</b><br /><br />
<b>as well as <a href="/wiki/images/7/77/2013-Alberta_safety_2.pdf">part 2</a>.</b><br />
<p><i>Safety forms were approved on 9/23/13 by Julie McNamara and David Lloyd on the iGEM Safety Committee. </i></p><br />
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MEsau
http://2013.igem.org/Team:Alberta/Resources
Team:Alberta/Resources
2013-10-29T03:53:49Z
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border-right:1px solid #CCC;<br />
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float: left;<br />
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color: #444;<br />
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margin:20px 0 0 0;<br />
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position:absolute;<br />
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display:block;<br />
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-moz-border-radius: 3px 3px 0 0;<br />
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.thumbnail img:hover {<br />
transform:scale(4,4);<br />
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</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><a href="/Team:Alberta">Home</a></li><br />
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<h5>Other Sections</h5><br />
<a href="/Team:Alberta/SafetyForm"><p>Safety Form</p></a><br />
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<p class="content-title"><img src="/wiki/images/thumb/8/84/Resouces_icon.png/458px-Resouces_icon.png"<br />
height="125"> Resources</img></p><br />
</div><br />
<div class="block"><br />
<ul><br />
<li>To other University of Alberta students: the Environmental Health and Safety Division provides<br />
safety support on common safety questions and situations, as well as documents on proper<br />
disposal.<br />
<ul><br />
<li>See their homepage at: <a href="http://www.ehs.ualberta.ca/">http://www.ehs.ualberta.ca/</a></li><br />
<li>Ethidium bromide disposal suggestions at: <a href="http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf">http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/ Documents/Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf.</a></li><br />
</ul><br />
</li><br/><br />
<li>To general students on a study break:<br />
<ul><br />
<li>See this basic and humourous not-to-do video (which was shown in University of<br />
Alberta’s EHS Biosafety Course): “Lab Unsafety and Septic Technique” by Jayson Masaki <br />
below or at <a href="http://www.youtube.com/watch?v=5aDLV0UHyNE">http://www.youtube.com/watch?v=5aDLV0UHyNE</a> </ul><br />
<iframe width="640" height="480" src="//www.youtube.com/embed/5aDLV0UHyNE" frameborder="0" allowfullscreen></iframe><br />
</li><br/><br />
<li>For students not yet familiar with iGEM nor their recommended guidelines:<br />
<ul><br />
<li>The World Health Organization gives a comprehensive guidebook for safety in labs at:<br />
<a href="http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf">http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf</a><br/><br />
(Reference: Laboratory Biosafety Manual. 2001. World Health Organization. Retrieved <br />
August 9, 2013, from <a href="http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf">http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf</a>)</li><br />
</ul><br />
</li><br />
</ul><br />
</div><br />
</div><br />
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</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/FAQ
Team:Alberta/FAQ
2013-10-29T03:53:31Z
<p>MEsau: </p>
<hr />
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zoom:1;<br />
}<br />
.navbar:before, .navbar:after {<br />
content: "";<br />
display: table;<br />
}<br />
.navbar:after {<br />
clear:both;<br />
}<br />
.navbar li {<br />
float:left;<br />
border-right:1px solid #CCC;<br />
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box-shadow: 1px 0 0 #EEE;<br />
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}<br />
.navbar a {<br />
float: left;<br />
padding: 12px 30px;<br />
color: #444;<br />
font: bold 12px Arial, Helvetica;<br />
text-decoration:none;<br />
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}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
color:#BBB;<br />
}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
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opacity: 0;<br />
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z-index:1;<br />
background:#FFF;<br />
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}<br />
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}<br />
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top:0;<br />
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}<br />
.navbar ul li {<br />
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box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
}<br />
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}<br />
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text-transform:none;<br />
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}<br />
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}<br />
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}<br />
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.centered {<br />
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}<br />
.centered-well {<br />
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}<br />
.thumbnails {<br />
padding: 35px;<br />
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}<br />
.thumbnail {<br />
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.thumbnail img{<br />
/* ... */<br />
height:100px;<br />
position:relative;<br />
-webkit-transition: all .25s ease-out;<br />
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.thumbnail img:hover {<br />
transform:scale(4,4);<br />
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<br />
} <br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
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<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
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<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
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</ul><br />
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<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ" class="active">FAQ</a></li><br />
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<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/SafetyForm"><p>Safety Form</p></a><br />
<a href="/Team:Alberta/FAQ" class="active"><p>FAQ</p></a><br />
<a href="/Team:Alberta/Resources"><p>Resources</p></a><br />
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<div class="main"><br />
<div class="block"><br />
<p class="content-title"><img src="/wiki/images/thumb/b/b0/Public_members.png/463px-Public_members.png " height="120"></img> FAQ</p><br />
</div><br />
<div class="block"><br />
<h3>Doesn’t <i>E. coli</i> cause food poisoning? If <i>E. coli</i> is so dangerous, why are they being used in labs?</h3><br />
<ul><br />
<li>Normal <i>E. coli</i> colonize the lower intestine of humans, while <b>producing Vitamin K</b> and <br />
<b>protecting infection</b> from other harmful bacteria.</li><br />
<li>Only some strains of <i>E. coli</i> cause food poisoning, but our group is using a <b>harmless, <br />
nonpathogenic strain</b>. This train is engineered to contain mutations that would not allow the <i>E. <br />
coli</i> to survive outside the lab without particular nutrients.</li><br />
<li><i>E. coli</i> provides a well-studied and well-known <b>model system</b> to test and troubleshoot new <br />
trials on.</li><br />
</ul><br />
<p>Reference: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1728375/"><br />
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1728375/</a></p><br />
<h3>What if plasmids containing <b>antibiotic resistance genes</b> were released into the environment despite<br />
precautions?</h3><br />
<ul><br />
<li>These genes are used in synthetic biology as selection tools.</li><br />
<li>There are lower chances of gene uptake by wild bacteria compared to lab-strain bacteria which<br />
have perforated membranes.</li><br />
<li>In the case that wild bacteria did uptake the antibiotic resistance gene, that gene would<br />
eventually be lost in the population without exposure to the antibiotic, because it is then a <br />
disadvantage for the bacteria to carry the unused plasmids. (Evidence observed in past with the <br />
decline of specific antibiotic resistance after the human population limited that antibiotic).</li><br />
</ul><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Attributions
Team:Alberta/Attributions
2013-10-29T03:49:38Z
<p>MEsau: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
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width:100%;<br />
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@-moz-document url-prefix() {<br />
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background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
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width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
margin-left:-95px;<br />
}<br />
}<br />
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background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
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position:fixed;<br />
width:23px;<br />
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margin-top:-17px;<br />
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.block {<br />
background-color:white;<br />
border:1px grey solid;<br />
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margin:10px;<br />
border-radius:5px;<br />
box-shadow: 0px 0px 30px #444444;<br />
}<br />
.titlebar {<br />
position:fixed;<br />
top:0px;<br />
height:130px;<br />
margin-left:-5px;<br />
width:975px;<br />
z-index:2;<br />
background-color:#FFF;<br />
}<br />
.content-title {<br />
text-align:center;<br />
font-size:3em;<br />
}<br />
.titlebar h3, h4 {<br />
text-align:center;<br />
}<br />
.sidebar {<br />
position: fixed;<br />
top: 157px;<br />
float: left;<br />
z-index: 3;<br />
padding: 10px 10px 10px 10px;<br />
width: 230px;<br />
}<br />
.sidebar_block {<br />
background-color:white;<br />
margin:1px;<br />
border:1px grey solid;<br />
padding:5px 10px 5px 10px;<br />
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position:relative;<br />
float:right;<br />
width:720px;<br />
}<br />
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clear:both;<br />
}<br />
.ualberta-logo {<br />
position:fixed;<br />
margin-left:70px;<br />
margin-top:-70px;<br />
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position:fixed;<br />
margin-left:650px;<br />
margin-top:-95px;<br />
width: 150px;<br />
}<br />
.igem-logo img {<br />
width:210px;<br />
}<br />
.igem-bar {<br />
position:relative;<br />
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.igem-bar a {<br />
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visibility: hidden;<br />
min-width:200px;<br />
max-width:500px;<br />
-webkit-transform: translateX(10px);<br />
-moz-transform: translateX(10px);<br />
-ms-transform: translateX(10px);<br />
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transform: translateX(10px);<br />
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.navbar li:hover > a {<br />
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}<br />
.navbar li a:hover { /* IE6 only */<br />
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}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
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.navbar li:hover > ul {<br />
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.navbar ul ul {<br />
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margin:0 0 0 20px;<br />
_margin:0;/*IE6 only*/<br />
-moz-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
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.navbar ul li {<br />
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border:0;<br />
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-webkit-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
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<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team" class="active"><p>Roster</p></a><br />
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<div class="main"><br />
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<p class="content-title">Attributions</p><br />
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<div class="block"><br />
<p>All of the experimental work described herein was performed by the team with technical support from Prof. Ellison’s technician, <b>Nien-tsu Tseng (Rick)</b>. The TSP concept was inspired by the <b>Missouri-Davidson 2007 iGEM team</b> who broke the ice with their work on the Hamiltonian variation of TSB problem. The experimental approaches used here evolved over discussions with our supervisors during group meetings. The correct weighting algorithm that relates city path lengths to linker concentrations was developed by <b>Dr. Doug Ridgway</b>, a supervisor of the 2012 iGEM team. The plasmids used to create TSB compatible parts by PCR were a gift from <b>Genomikon Inc</b>. <br />
The creation of the violacin bricks that we will use in the test of the 5-city TSB would not have been possible without the violacein operon biobrick (K274002) that was created, submitted and carefully characterized by the <b>Cambridge 2009 iGEM team</b>. Wiki coding and design implementation was done by <b>Timo Hohn</b>, (B.Sc. in Computer Engineering).<br />
</p><br />
<br><br />
<p>Thanks to these individuals for donating their time and talents!</p><br />
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For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Sponsors
Team:Alberta/Sponsors
2013-10-29T03:47:57Z
<p>MEsau: </p>
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<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team"><p>Roster</p></a><br />
<a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta"><p>Official Profile</p></a><br />
<a href="/Team:Alberta/Sponsors" class="active"><p>Sponsors</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Sponsors</p><br />
</div><br />
<div class="block"><br />
<b> We would like to thank the following sponsors for their generosity and support over the course of this project.</b><br /><br /><br />
<p><a href="http://www.ualberta.ca"><img src="/wiki/images/b/b3/Ualberta-logo.png" alt="The University of Alberta"></img></a><br />
</p><br /><br />
<p><a href="http://albertatechfutures.ca/"><img src="/wiki/images/a/a3/Albertatechfutures-logo.png" style="height:100px;" alt="The University of Alberta"></img></a><br />
</p><br />
<p><a href="http://genomealberta.ca/"><img src="/wiki/images/c/cc/Genomealberta-logo.jpg" style="height:150px;" alt="The University of Alberta"></img></a><br />
</p><br />
<p><a href="http://www.genomikon.ca/"><img src="/wiki/images/3/3d/Genomikon-logo.gif" style="height:100px;" alt="The University of Alberta"></img></a><br />
</p><br /><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
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<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Team
Team:Alberta/Team
2013-10-29T03:47:40Z
<p>MEsau: </p>
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<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
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<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="team" href="#" class="active">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team" class="active">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
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<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Mike-Ellison"><p>Mike Ellison</p></a><br />
<a href="#Dominic-Sauvageau"><p>Dominic Sauvageau</p></a><br />
<a href="#Mark-Rozema"><p>Mark Rozema</p></a><br />
<a href="#Cadence-Moorhouse"><p>Cadence Moorhouse</p></a><br />
<a href="#Dawson-Zeng"><p>Dawson Zeng</p></a><br />
<a href="#Michael-Esau"><p>Michael Esau</p></a><br />
<a href="#Rachel-Kwan"><p>Rachel Kwan</p></a><br />
<a href="#Stephanie-Chiu"><p>Stephanie Chiu</p></a><br />
<a href="#Larry-Zhang"><p>Larry Zhang</p></a><br />
<a href="#Cameron-Murray"><p>Cameron Murray</p></a><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team" class="active"><p>Roster</p></a><br />
<a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta"><p>Official Profile</p></a><br />
<a href="/Team:Alberta/Sponsors"><p>Sponsors</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<h1>Who We Are</h1><br />
<h5>Advisors</h5><br />
<ul>Professors:<br />
<ul><ul><li><b>Mike Ellison</b></li><br />
<li><b>Dominic Sauvageau</b></li></ul></ul><br />
</ul><br />
<h5>Team Members</h5><br />
<ul>Recent Graduates:<br />
<ul><ul><li><b>Mark Rozema</b></li><br />
<li><b>Larry Zhang</b></li><br />
<li><b>Michael Esau</b></li></ul></ul><br />
Undergraduates:<br />
<ul><ul><li><b>Dawson Zeng</b>: <i>Student Liaison</i></li><br />
<li><b>Rachel Kwan</b></li><br />
<li><b>Cadence Moorhouse</b></li></ul></ul><br />
High School Graduates:<br />
<ul><ul><li><b>Stephanie Chiu</b></li><br />
<li><b>Cameron Murray</b></li></ul></ul><br />
</ul><br />
</div><br />
<a class="anchor" id="Mike-Ellison"></a><br />
<div class="block"><br />
<h2>Mike Ellison</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/2/26/2013-Mellison.png"<br />
alt="Mike Ellison"></img></div><br />
Mike Ellison is a professor with the Department of Biochemistry at the University of <br />
Alberta.<br /><br />
His current focus on Synthetic Biology is to produce modular biological circuits of <br />
increasing sophistication using well-understood molecular components that can be <br />
reliably assembled into novel and useful forms of artificial life. He has been involved<br />
in iGEM for six years and continues to actively engage his undergraduate students <br />
in this synthetic biology competition.<br />
</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Dominic-Sauvageau"></a><br />
<div class="block"><br />
<h2>Dominic Sauvageau</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><br />
<img src="/wiki/images/d/d8/2013-Dsauvageau.jpg"<br />
alt="Team Member 9"></img></div>Dominic Sauvageau joined the Department of Chemical and Materials <br />
Engineering at the University of Alberta <br />
as an Assistant Professor in January 2011. His research involves the development of novel bacteriophage-<br />
based technologies and bioprocessing strategies for production in microbial systems. He joined the iGEM <br />
adventure last year when he supervised an iGEM-Entrepreneurial team (they won!). He's thrilled to be <br />
involved in iGEM again this year. He loves travelling and hopes he'll be able to use the E. coli we're <br />
working on to plan his next trip.</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Mark-Rozema"></a><br />
<div class="block"><br />
<h2>Mark Rozema</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/6/62/2013-Mrozema.jpg"<br />
alt="Team Member 9"></img></div><br />
Mark Rozema graduated from the Biochemistry program at the University of Alberta in April 2013 and is <br />
currently enrolled in the law program, also at the U of A. He enjoys running, early mornings, late nights <br />
and old scotch. Mark was involved in all facets of the project over the summer months, such as conceptual <br />
planning, establishing general protocol, part creation and part isolation but withdrew to focus on law <br />
school since the start of September.</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Cadence-Moorhouse"></a><br />
<div class="block"><br />
<h2>Cadence Moorhouse</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/f/f1/2013-Cmoorhouse.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a 4th year genetics student at the University of Alberta. Every since high school I have had an <br />
interest in genetics and I heard all about the applications of synthetic biology largely through social <br />
media. It was at a talk by biotech guru Andrew Hessel that I first learned of iGEM. I was delighted to find <br />
out that the U of A had a team and a couple of emails later I was on the roster. This project has given me <br />
the opportunity to learn standard lab techniques and to see an experiment evolve. My experience teaching and <br />
coaching allows me to easily convey complex ideas into simpler ones. I hope to utilize these skills over the <br />
course of this project. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Dawson-Zeng"></a><br />
<div class="block"><br />
<h2>Dawson Zeng</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/9/90/2013-Dzeng.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a 4th year student at the University of Alberta majoring in Biological Sciences. I first heard about <br />
the field of Synthetic Biology from a guest speaker. It was then that I looked into joining iGEM Team <br />
Alberta. Personally, I think it is the coolest thing that Synthetic Biology combines philosophies from both <br />
Biology and Engineering; something I never thought about. Overall, my knowledge and understanding of <br />
genetics and interactions between DNA molecules vastly increased throughout the summer. A true testament to <br />
Richard Feynman’s famous quote, “What I cannot create, I do not understand.” </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Michael-Esau"></a><br />
<div class="block"><br />
<h2>Michael Esau</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/b/b7/2013-Mesau.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a graduate from the Biochemistry Specialization program at the University of <br />
Alberta. I learned about iGEM from Dr. Mike Ellison’s biochemistry class, and am <br />
happy to be a part of this year’s team. I'm planning to go into the synthetic bio <br />
research field and will be joining up with Dr. Dominic Sauvageau's lab for the next <br />
year. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Rachel-Kwan"></a><br />
<div class="block"><br />
<h2>Rachel Kwan</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/f/f0/2013-Rkwan.jpg"<br />
alt="Team Member 9"></img></div><br />
<p>After my first discoveries on the possibilities of iGEM from the local newspaper, I searched online and admired various iGEM projects. At this time during high school, I was personally unclear of my desired career path, aside from studying science, with a focus on Biology or Chemistry. Also with my vague knowledge of biotechnological methods, I was wary about the bioethical side of “manipulating nature,” especially from public warnings in literature.</p><br />
<p>However, within studying Biochemistry in my undergrad, I found that current methodologies of biotechnology seemed to have controlled lab settings, careful precautions, and/or a balance with purposeful benefits. Looking at the variety of iGEM projects, they used in-school material for real-world, practical applications. IGEM also attracted me because I liked the idea of working in a team setting to balance strengths and weaknesses with others. I believe that iGEM is rewarding and relevant in that it challenges teamwork, independence, creativity, writing, presenting, and lab technique. As part of my work, I hope to offer organizational skills, interest in safety, and Wiki ideas.</p><br />
<p>Outside of iGEM work, I play the piano and clarinet, read, meditate, play board games, search for good sales, and grow pet plants like basil.</p><br />
<br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Stephanie-Chiu"></a><br />
<div class="block"><br />
<h2>Stephanie Chiu</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/3/30/2013-Schiu.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a first year student at the University of Alberta. I first heard about iGEM from friends at my high <br />
school and was privileged enough to join U of A’s team as I was finishing up my Grade 12 year. I am excited <br />
to learn more about what synthetic biology is and what working in a lab is like. I hope that I can offer a <br />
unique perspective to our team. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Larry-Zhang"></a><br />
<div class="block"><br />
<h2>Larry Zhang</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/8/83/2013-Lzhang.jpg"<br />
alt="Team Member 9"></img></div><br />
Passionate scientist born in the historical city of Yueyang, China; educated in the English for 8 years and <br />
has been under strict scientific indoctrination in the University of Alberta department of Biochemistry. <br />
Graduated with a Biochemistry degree with interest in genetics and genetic engineering, Larry Zhang has <br />
brought with him a huge idea cannon and a pair of magic pipetter’s hands; he is one of the most valuable <br />
assets in this team. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Cameron-Murray"></a><br />
<div class="block"><br />
<h2>Cameron Murray</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/7/78/2013-Cmurray.jpg"<br />
alt="Team Member 9"></img></div> <br />
I am a first year university student studying molecular genetics at the U of A, however when I joined the <br />
team I was in my grade twelve year of high school. I heard about Synthetic biology through quirks and <br />
quarks, the CBC radio program, and was immediately taken with it and it’s vast possibilities. I was so <br />
enthralled that I talked about it quite a bit to my friends one of whom told me about iGEM. So here I am <br />
hoping to learn about and deepen my interest in synthetic biology through iGEM.</p><br />
<div class="clear"></div><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<!--<br />
<br />
<html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{|align="justify"<br />
|Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium. Integer tincidunt. Cras dapibus. Vivamus elementum semper nisi. Aenean vulputate eleifend tellus. Aenean leo ligula, porttitor eu, consequat vitae, eleifend ac, enim. Aliquam lorem ante, dapibus in, viverra quis, feugiat a, tellus. Phasellus viverra nulla ut metus varius laoreet. Quisque rutrum. Aenean imperdiet. Etiam ultricies nisi vel augue. Curabitur ullamcorper ultricies nisi. Nam eget dui.<br />
|[[Image:Alberta_team.png|400px|right]]<br />
|-<br />
|}<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
'''Advisors:'''<br />
<br />
*'''Mike Ellison''': Professor<br />
*'''Advisor 2''': Professor<br />
<br />
<br />
'''Team Members:'''<br />
<br />
*'''Mark Rozema''': Graduate<br />
*'''Larry Zhang''': Graduate<br />
*'''Michael Esau''': Graduate<br />
*'''Saima Zamir''': Graduate<br />
*'''Dawson Zeng''': Student Liaison, Undergraduate<br />
*'''Rachel Kwon''': Undergraduate<br />
*'''Cadence Moorhouse''': Undergraduate<br />
*'''Stephanie Chiu''': High School Graduate<br />
*'''Cameron Murray''': High School Graduate<br />
<br />
<br />
|<br />
<gallery><br />
Image:alberta_Team_member_1.png|Team member 1<br />
Image:alberta_Team_member_2.png|Team member 2<br />
Image:alberta_Team_member_3.png|Team member 3<br />
Image:alberta_Team_member_4.png|Team member 4<br />
Image:alberta_Team_member_5.png|Team member 5<br />
Image:alberta_Team_member_6.png|Team member 6<br />
Image:alberta_Team_member_7.png|Team member 7<br />
Image:alberta_Team_member_8.png|Team member 8<br />
Image:alberta_Team_member_9.png|Team member 9<br />
</gallery><br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
<br />
== '''Where we're from''' ==<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Accomplishments
Team:Alberta/Accomplishments
2013-10-29T03:47:01Z
<p>MEsau: </p>
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width:100% !important;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments" class="active">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments" class="active"><p>Accomplishments</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Accomplishments</p><br />
</div><br />
<div class="block"><br />
<img src="/wiki/images/a/af/2013-Accomplishments.PNG" style="width:100%;"></img><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<h2> Awards<br />
</h2><br />
<br />
<img src="/wiki/images/thumb/9/95/Presentationpic.jpg/800px-Presentationpic.jpg " style="width:50%" align="right"></img><br />
<br />
<p>Team Alberta was thrilled to receive recognition at the North American Regional Jamboree competition:</p><br />
<br><br />
<p><b>Best Presentation</b> - in the undergraduate category </p><br />
<p><b>Gold Medal </b>– for fulfilling criteria</p><br />
<p><b>Advancement to World Finals</b></p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</div><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<br />
</body><br />
</html><br />
<br />
<br />
<!-- <html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Parts
Team:Alberta/Parts
2013-10-29T03:46:50Z
<p>MEsau: </p>
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</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts" class="active">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts" class="active"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Submitted Parts</p><br />
</div><br />
<div class="block"><br />
<p> Our 2013 parts submitted are a set of violacein genes derived from the violacein operon constructed and <br />
submitted by Cambridge in 2009 (BBa_K274002). We have made a number of modifications, including upgrading the <br />
plasmid backbone from pSB1K3 to pSB1C3 standard 10, and converting each of the five open reading frames into <br />
its own part with a common and improved ribosome binding site (BBa_B0030) such that they can be assembled in <br />
different combinations and permutations. All of the parts have been characterized and are functional, and we <br />
have found that a new combination, VioABCE, produces a new pigment which we call "Royal Blue". </p><br />
<img src="/wiki/images/f/f0/2013-Alberta-Submitted_parts.PNG" style="width:100%;"></img><br />
<br />
</html><br />
<groupparts>iGEM013 Alberta</groupparts><br />
<html><br />
<br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<br />
<!-- <html><br />
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<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
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<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Protocols
Team:Alberta/Protocols
2013-10-29T03:46:30Z
<p>MEsau: </p>
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<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols" class="active">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
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<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
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<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
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</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Parts"><p>The Parts</p></a><br />
<a href="#Build"><p>Building the Plasmids</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols" class="active"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
</div><br />
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<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Protocols</p><br />
</div><br />
<a class="anchor" id="Parts"></a><br />
<div class="block"><br />
<h2>The Parts</h2><br />
<p>The 6 genes that were required to assemble various routes were obtained by PCR from plasmids kindly provided by Genomikon Inc. Each gene (AmpR, KanR, ClrR, GFP, RFP and aCP) exist as self contained cassettes that are flanked by BsaI sites. Parts were then generated according to the schematic shown below:</p><br />
<img src="/wiki/images/c/c5/Making_parts_678x586.png" align="middle" style="width:100%;"><br />
</div><br />
<a class="anchor" id="Build"></a><br />
<div class="block"><br />
<h2>Building the Plasmids</h2><br />
<p>Our plasmid assembly system relies upon the achievements of previous Team Alberta iGEM entries, 2009’s BioBytes and 2010’s Genomikon assembly methods. This process begins with origins of replication anchored at one end to magnetic beads in a suspension within a reaction microfuge tube. The anchored strands have a single, free-floating sticky end, onto which successive genes are ligated. Once the new gene has been ligated on, we use a magnet to hold the beads (along with the anchored DNA) inside the reaction tube, while washing away the rest of the reaction, including the enzyme, buffers, and any non-ligated DNA that remains. The beads are then resuspended in a new reaction mixture, containing the next ligation step.</p><br />
<img src="/wiki/images/b/b4/2013Alberta-Poster2.jpg" align="middle" style="width:100%;"><br />
<p>Once all of the genes have been ligated, a tail-piece that complements the original bead-anchor DNA sequence is added, so that the finished product can be unbound from the beads and will close upon itself to form the circular plasmid. In this fashion, a four-gene, roughly 5000-base-pair plasmid is assembled in as little as an afternoon, cheaply and easily.</p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
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</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Results
Team:Alberta/Results
2013-10-29T03:45:21Z
<p>MEsau: </p>
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<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#First-Tests"><p>The First Tests</p></a><br />
<a href="#Linkers"><p>Perfecting the Linkers</p></a><br />
<a href="#Assembly"><p>The Full Assembly</p></a><br />
<a href="#Colour-Controls"><p>Colour Controls</p></a><br />
<a href="#Calibration"><p>Initial Calibration</p></a><br />
<a href="#TSP"><p>The Travelling Salesman Problem</p></a><br />
<a href="#Adapt-POP"><p>Increasing Complexity</p></a><br />
<a href="#Revised-Strategy"><p>A Revised Strategy</p></a><br />
<a href="#DNA-Library"><p>Cosmid DNA Library</p></a><br />
<a href="#PCR"><p>PCR Identification</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results" class="active"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
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<p class="content-title">Results</p><br />
</div><br />
<a class="anchor" id="First-Tests"></a><br />
<div class="block"><br />
<h2>The First Tests</h2><br />
<p>We performed some initial tests to confirm the efficacy of our assembly system. The Genomikon assembly method requires that we be able to successfully bind and elute DNA from magnetic beads, and that we be able to perform successive ligations on the bead-bound strands. These are necessary for building the plasmid "routes", as described in the project overview page. </p><br />
<br />
<p>In the gel below, the second lane displays the result of an origin of replication (Ori) sample that was bound to the bead, washed and then re-eluted – the presence of DNA at the desired mass in this lane confirms the successful binding and elution. The third lane demonstrates that we can successfully ligate genes (KanR in this case) directly to the Ori at high efficiency and still safely elute them. In the fourth lane, we have ligated a 13-base-pair linker onto the existing Ori-KanR, followed by a second gene, ChlorR. Although the high-mass band suggests that ligation was successful, the fact that there is still a stronger band at the Ori-KanR mass suggests that the ligation has not proceeded to completion.</p><br />
<p><img src="/wiki/images/7/7e/2013-Alberta-Results-Figure_1.png" style="width:100%;"></img><br /><br />
Figure 1: Agarose gel electrophoresis image from initial ligation trials. <br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Origin of replication, bound to the magnetic beads and then eluted. <br /><br />
Lane 3: KanR gene ligated to bead-bound Ori.<br /> <br />
Lane 4: Existing bead-bound Ori-KanR sample ligated with linker, then ligated with ChlorR <br /><br />
(beads are always washed between ligations).</p><br />
</div><br />
<a class="anchor" id="Linkers"></a><br />
<div class="block"><br />
<h2>Perfecting the Linkers</h2><br />
<p>The incomplete ligation of the previous step presents an obstacle for our system, but the issue appears to be isolated to the ligation step involving the short linker piece. To get a more effective ligation without extending the timeframe of our assembly, we made several adjustments. First, we raised ligation temperature from 4°C to 22°C in the hopes of increasing the enzyme activity. Second, we switched to a larger, 25-base-pair linker – we were able to successfully ligate large pieces in the case of the Ori and KanR ligation, so perhaps size plays a factor. Also, we used better-purified stocks of our genes, to eliminate the possibility that some interfering piece of the original plasmid was competing with our desired reaction. Finally, we attempted to increase the concentration of the linker in the hopes of driving the reaction to completion. Here, we can see that our changes have significantly improved the ligation efficiency, although changing the linker concentration has not created an appreciable benefit. </p><br />
<p><img src="/wiki/images/9/9e/2013-Alberta-Figure_2.png" style="width:100%;"></img><br /><br />
Figure 2: Agarose gel electrophoresis image from linker concentration comparison after<br />
ligation protocol adjustments.<br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Ori-KanR ligation to linker, then to ChlorR (as in Figure 1, Lane 4) using 10:1 ratio of <br />
linker to Ori. <br /><br />
Lane 3: As lane 2, with 50:1 ratio.<br /><br />
Lane 4: As lane 3, with 100:1 ratio. </p><br />
</div><br />
<a class="anchor" id="Assembly"></a><br />
<div class="block"><br />
<h2>The Full Assembly</h2><br />
<p>With our successful ligation protocol established, we moved on to attempting a full-scale <br />
assembly, with four genes (the quantity required for our proof-of-concept travelling salesman<br />
problem). In this gel, the four lanes show the successive addition of the four genes, which <br />
are, for the most part, successful. In each lane, there is some remainder of the previous <br />
products left behind, including (presumably) instances of strands that were incomplete in <br />
one reaction continuing to acquire genes in a successive one. Regardless, these incomplete <br />
genes represent only a small fraction of the total DNA. </p><br />
<p><img src="/wiki/images/3/37/2013-Alberta-Results-Figure_3.png" style="width:100%;"></img><br /><br />
Figure 3: Agarose gel electrophoresis image from full assembly test. <br /><br />
Lane 1: DNA Markers.<br /><br />
Lane 2: Ori to KanR ligation product.<br /><br />
Lane 3: Ori-KanR to linker to GFP ligation product.<br /><br />
Lane 4: Ori-KanR-Linker-GFP to linker to RFP ligation product.<br /><br />
Lane 5: Ori-KanR-Linker-GFP-Linker-RFP to linker to ChlorR ligation product. </p><br />
<p>The product plasmids from this assembly were transformed into a bacterial culture and <br />
grown on a Kan/Chlor plate to examine practical impact of the rate of incomplete ligations. <br />
The plate image is shown below – about 90% of the colonies display the desired RFP/GFP <br />
(orange colouration) phenotype indicating a perfect successful ligation of the plasmid. </p><br />
<img src="/wiki/images/4/4e/Ab_Assembly_efficiency.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Colour-Controls"></a><br />
<div class="block"><br />
<h2>Colour Controls</h2><br />
<p>In our planned, four-city proof-of-concept test (see the map below), there are exactly three <br />
possible solutions and three corresponding phenotypes: blue/green (dark green) bacteria <br />
with Amp/Chlor resistance, red/green (orange) bacteria with Chlor/Kan resistance, and <br />
red/blue (purple) bacteria with Amp/Kan resistance. </p><br />
<img src="/wiki/images/8/8d/2013Alberta-mapmaker-states.png" style="width:100%;"></img><br />
<p>To ensure we would be able to correctly identify plasmids based on phenotype we prepared <br />
a set of control plates, where bacteria grown from pure assemblies of the desired “route” <br />
plasmid were grown alongside bacteria possessing only one of the two colours from that <br />
route, for comparison purposes. The resulting plates can be seen above. </p><br />
</div><br />
<a class="anchor" id="Calibration"></a><br />
<div class="block"><br />
<h2>Initial Calibration</h2><br />
<p>In preparation for our initial travelling salesman problems, we attempted to discern the <br />
extent to which unexpected or unknown biases might affect the frequency of colonies <br />
growing with a particular gene.</p><br />
<p>In this test, we performed an assembly in which both GFP and aCP were included (in equal <br />
molar concentration) in the initial ligation onto the Ori, followed by a ligation of ChlorR, <br />
resulting in a mixture of Ori-GFP-ChlorR and Ori-aCP-ChlorR plasmids. We transformed these <br />
plasmids into a single bacterial culture, which we then spread on a Chlor-treated plate in <br />
order to count the resulting colonies. We repeated this test for each of the other four genes <br />
to be used in our proof-of-concept TSP, comparing each against GFP as a standard. This <br />
provided us with the following ratios of growth.</p><br />
<p>Table 1: 1GFP 6aCP<br /><img src="/wiki/images/5/5d/2013Alberta-Ratiotable.png" style="width:100%;"></img></p><br />
<p>We then attempted another assembly in which we calibrated for the bias. We used a 6:1 <br />
molar ratio of GFP to aCP in the new assembly, otherwise performing the experiment as <br />
before, and produced a new plate with a ratio of approximately 1:1 GFP colonies to aCP <br />
colonies. Although imperfect, this calibration was adequate for our proof-of-concept trial.</p><br />
</div><br />
<a class="anchor" id="TSP"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p> We have conducted a single successful travelling salesman problem following the procedure outlined in the project overview page. Relative to the previous assembly steps, the only key difference is that this time, several genes are included at each ligation step and at varying concentrations, so that the assembly produces a mix of plasmids, but favours some genes over others (creating a bias for shorter paths). See the overview page for more details on how this works. </p><br />
<p>This particular problem was based on a map of four cities in which four of the paths have an arbitrary unit distance of 1, and the remaining two paths have a distance of 4. Of the possible routes in this problem, one route has a total sum distance of 4, and the other two have distances of 10, making that route clearly preferable, and a suitable test of our biocomputer. The three possible routes, with correct gene-path assignment and distances listed for this problem, can be seen below. At each ligation step, we added a quantity of each gene based on the reciprocal of its distance, so that, for instance, the genes corresponding to paths of distance 4 had roughly one-quarter of the concentration (this value was then adjusted by our calibrations, as described above, to arrive at the actual concentration) of those with distance 1. </p><br />
<img src="/wiki/images/a/ab/2013Alberta-POP.png" style="width:100%;"></img><br />
<p>On the resulting plates, we counted 18 colonies corresponding to the ChlorR/GFP/aCP/AmpR route, and 21 colonies corresponding to the ChlorR/RFP/GFP/KanR route. For the optimal route, KanR/aCP/RFP/AmpR, we found 61 colonies, clearly identifying this as the solution to the problem. When the percentage of each of these three types of colonies on each plate is normalized to the best solution, the results of this trial are very close to the expected values calculated for this experiment. </p><br />
</div><br />
<a class="anchor" id="Adapt-POP"></a><br />
<div class="block"><br />
<h2>Can we adapt our POP to a much more complex problem?</h2><br />
<p>The ultimate limit of an approach such as this, depends upon the<br />
number of complete TSP solutions (plasmids) that can be clonally<br />
amplified through cell transformation. We estimate that solving a 15-city<br />
problem is within the realm of existing state-of-the-art, but not without<br />
major revisions to our POP work presented here. The 15-city problem is<br />
not trivial even by conventional computing standards. With 120 intercity<br />
links resulting in 87,178,291,200 possible solutions, 50 days would be<br />
required to identify the best solutions at a computational rate of 10,000<br />
solutions/second!</p><br />
<p>The challenges:</p><br />
<ol><br />
<li>In the POP, solutions are identified by visually<br />
determining the frequency of colonies exhibiting<br />
the appropriate path combinations represented by<br />
the three colour genes and the three drug<br />
resistance genes. Extending this approach to the<br />
15-city problem would require the acquisition of<br />
120 markers that are combined 87,178,291,200<br />
ways, well beyond the analytical resolution of<br />
standard plating methods.</li><br />
<li>A statistically significant sampling of complete<br />
solutions is well outside the plasmid transformation<br />
efficiencies of even the best competent cells<br />
available.</li><br />
<li>The precision and efficiency for assembling<br />
complete-solution plasmids (38 steps in all)<br />
remains to be tested.</li><br />
</ol><br />
<img src="/wiki/images/7/72/2013-Results_z1.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Revised-Strategy"></a><br />
<div class="block"><br />
<h2>A revised strategy</h2><br />
<p><b>Cities and Paths.</b> In the new approach we invert the role that DNA<br />
plays in defining cities and paths. Here, a city corresponds to a gene<br />
that complements an amino acid auxotrophy in E. coli (illustrated<br />
below). The city is therefore required for growth on defined media that<br />
lacks that amino acid. By extension, 15 different cities represented by<br />
15 a.a. auxotrophic markers would be required for survival of E. coli<br />
deficient for these genes when grown on media that lacks the<br />
corresponding amino acids. Complete plasmid solutions therefore are<br />
exclusively selected and amplified from their non-solution counterparts.<br />
Creating a 15-gene knockout in E. coli is not trivial but absolutely<br />
possible.</p><br />
<p>The ability to link any two city genes requires that each city has at<br />
its 5’ and 3’ ends, overhangs that are nonpalindromic,<br />
noncomplementary, and that are distinct in sequence from any of the 14<br />
other city genes.</p><br />
<p>The 120 path possibilities that are needed to link any two cities,<br />
are represented by a mixture of 120 synthetic duplex linkers where each<br />
linker has two different complementary ends that are capable of linking<br />
one of the 120 possible intercity pairs. Shorter intercity distances are<br />
favoured by adjusting the concentration of each linker in the mixture<br />
according to a new and improved weighting algorithm described below.<br />
We point out that in terms of economy, all 120 linkers can be produced<br />
from 30 oligos used in pair-wise combinations.</p><br />
<p>An unavoidable complication of this method is that any given city<br />
can occur more than once (at lower frequency) across the 15 available<br />
steps during sequential assembly (illustrated above for the three-city<br />
example). It should be noted however that any city duplication excludes<br />
the possibility of creating the complete set and will therefore be<br />
selected against post-transformation.</p><br />
<img src="/wiki/images/1/10/2013-Results_z2.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="DNA-Library"></a><br />
<div class="block"><br />
<h2>Creating a cosmid DNA library of that is highly biased for best<br />
solutions.</h2><br />
<p>To date, &lambda; phage-based recombinant libraries remain<br />
unprecedented in terms of the size and diversity of their DNA<br />
constituents. In its most advanced form, “cosmid” library kits are<br />
commercially available that produce 10<sup>10</sup> transformants. Cosmids retain<br />
the phage elements that are required for phage packaging and infection<br />
but lack the elements required for phage propagation and cell lysis. A<br />
plasmid origin allows them to replicate as plasmids.</p><br />
<p>Cosmids are constructed as linear molecules that begin and end<br />
with phage sequences the essential phage sequences(, &lambda;L and &lambda;R).<br />
Complementary 12-base overhangs that constitute the lambda cos and cos’<br />
sites are also required for efficient circularization once the cosmid has<br />
entered the cell.</p><br />
<p>In addition to its favourable tranformation properties, another<br />
attractive feature of using a cosmid-based system for TSP is that DNA<br />
molecules below a certain length threshold, package poorly, thereby<br />
contributing to the selection of full-length solutions.</p><br />
<p>An overview highlighting the key aspects of library creation is<br />
shown below. The assembly procedure uses magnetic beads where the<br />
cos’ sequence has been covalently linked. Asssembly begins with a cos- <br />
&lambda;L synthetic adapter that allows for the subsequent addition of &lambda;L. The<br />
addition of spacer sequences insure that total size of the construct is<br />
optimal for packaging (~50kB). Linker combinations are then added in<br />
alternation with city combinations until the city content is complete.<br />
Finally the construct is terminated with &lambda;R and a cos’ adapter. Following<br />
packaging cells are infected in selective liquid medium and the cosmid<br />
population is isolated for PCR analysis. The library is heavily biased 1)<br />
for complete solutions based on the assembly and packaging<br />
considerations already described and 2) for best solutions based on the<br />
path weights assigned to each linker addition step.</p><br />
<img src="/wiki/images/5/55/Results_z3.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="PCR"></a><br />
<div class="block"><br />
<h2>PCR-based identification of best solutions.</h2><br />
<p>The two types of data that is required for piecing best solutions together<br />
are 1) determining the cities that most frequently occupy each position<br />
from 1 to 15 and 2) determining the most frequently used intercity pairs<br />
as outlined below.</p><br />
<img src="/wiki/images/3/37/2013-Results_z4.PNG" style="width:100%;"></img><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Background
Team:Alberta/Background
2013-10-29T03:44:29Z
<p>MEsau: </p>
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<li><a href="/Team:Alberta/Results">Results</a></li><br />
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<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Real-World"><p>Real-World Issues</p></a><br />
<a href="#Computational"><p>The Computational Wall</p></a><br />
<a href="#Biocomputing"><p>Why Biocomputing?</p></a><br />
<a href="#Road"><p>A Long Road </p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background" class="active"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
</div><br />
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<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Background</p><br />
</div><br />
<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>MapMen is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:<br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Real-World"></a><br />
<div class="block"><br />
<h2>Real-World Issues</h2><br />
<p>The TSP is named after the concept of a hypothetical salesman who is planning a route to visit his <br />
customers in various neighbouring towns, but wants to maximize profits by using the shortest route — a <br />
helpful example to illustrate the usefulness of the problem: businesses around the world employ TSP-solving <br />
or related problem-solving software to help optimize their travelling needs, including in particular large <br />
courier companies that need to delivery millions of packages daily, and must reduce the expense of delivery <br />
vehicles and cut down travel time in any way possible, but also airliners, postal services, consumer GPS <br />
route-planning software, video-game pathfinding AI, and even electronics manufacture, in which a robot <br />
soldering arm must have an efficient path through the solder points to ensure maximum production over time. <br />
</p><br />
</div><br />
<a class="anchor" id="Computational"></a><br />
<div class="block"><br />
<h2>The Computational Wall</h2><br />
<p>The TSP is not only practically valuable, but also mathematically significant, because it belongs to a <br />
class of problems that are considered computationally difficult. The key difficulty with the TSP is due to <br />
the fact that it is an optimization problem: while for practical purposes any decent, short route is <br />
acceptable, a given TSP is nevertheless only considered "solved" when one verifies that one has obtained the <br />
shortest possible route. Mathematical verification of this sort requires what is called a "brute force" <br />
approach, in which one explores each and every possible route, tallying the total distance of each one, and <br />
then compares them all directly to guarantee the optimal route has been identified. As one increases the <br />
number of cities that must be included in the route, the time required for the brute-force approach becomes <br />
impossibly large.</p><br />
<img src="/wiki/images/9/9d/TSPcompWall.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Biocomputing"></a><br />
<div class="block"><br />
<h2>Why Biocomputing?</h2><br />
<p>Through synthetic biology, the creation of biological computers has opened a new avenue of possibility for <br />
solving TSPs more rapidly: using DNA molecules and bacterial cells as processors, one can compute billions <br />
of routes simultaneously, drastically reducing the time required through this massively parallel approach. <br />
By employing far more processors than there are routes through a given network, the processing time can be <br />
reduced to a standstill. A biological computer is also unique because it can solve problems stochastically: <br />
while every possible route is explored by the computer, preferable routes (short ones) will predominate <br />
among the generated products, allowing identification of the optimal route by population, rather than by a <br />
slower, deterministic approach. </p><br />
</div><br />
<a class="anchor" id="Road"></a><br />
<div class="block"><br />
<h2>A Long Road</h2><br />
<p>A number of previous attempts have been made to produce biocomputer solutions to the TSP, often involving pure DNA computing with no living organism present, including attempts by Leonard Adleman of RSA encryption fame, as well as previous efforts by the Davidson College/Missouri Western State University iGEM team, whose 2006 entry attempted to solve another challenging computational problem called the Burnt Pancake Problem, and in 2007 entered a DNA computing solution for the Hamiltonian Path Problem. Though related to the TSP, the Hamiltonian Path Problem attempts to discern if there is any possible route through a network, rather than picking the shortest possible one.</p><br />
<img src="/wiki/images/d/d4/Hgp_vs_tsp.png" style="width:100%;"></img><br />
<p>MapMen represents the latest in a line of attempts to refine the biological approach and create ever- increasingly powerful biological computers – and is the first of its kind to employ living cells to solve a travelling salesman problem. </p><br />
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!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
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MEsau
http://2013.igem.org/Team:Alberta/Overview
Team:Alberta/Overview
2013-10-29T03:43:36Z
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<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Biological-Terms"><p>In Biological Terms</p></a><br />
<a href="#Finding-the-Path"><p>Finding the Path</p></a><br />
<a href="#Mapmakers"><p>MapMakers at Work</p></a><br />
<a href="#Weight"><p>Calculating Gene Concentration</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
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<div class="block"><br />
<p class="content-title">Overview</p><br />
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<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>MapMen is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:</p><br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Biological-Terms"></a><br />
<div class="block"><br />
<h2>In Biological Terms</h2><br />
<p>To take advantage of the considerable information processing power of biology, we must create biochemical analogues for all of the components of the original problem. We begin by assigning a symbolic reporter gene or selectable marker gene to each of the six paths in our example map. The assignment is arbitrary; which gene is used for which path does not matter as long as it creates some kind of observable phenotype. For example, the path connecting the northeast city and the northwest city is symbolized by a gene coding for ampicillin resistance. The path from the northeast to city to the southeast meanwhile, is symbolized by a gene coding for kanamycin resistance.</p><br />
<img src="/wiki/images/4/4c/Bio_terms.png" style="width:100%;"></img><br />
<p>Now, just as the travelling salesman might describe taking a particular route to his customers – leaving from the northeast origin city and taking the road to the southwest, then turning up the north road from there, then back down the southeast, before returning northward home from, we can also represent that series of paths as a sequence of genes: ChlorR, RFP, GFP, and KanR.</p><br />
<img src="/wiki/images/b/bd/Path_to_gene.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Finding-the-Path"></a><br />
<div class="block"><br />
<h2>Finding the Path</h2><br />
<p>Just as a computer using a brute force approach to the travelling salesman problem would test every route and tally the sum distance of the paths travelled, our biocomputer assembles a multitude of plasmids, representing every possible combination of paths, through a set of ligations that represent the legs of the salesman’s journey. In the first leg, we depart from the origin city along any of the available roads: AmpR, ChlorR, or KanR. In the plasmid production, we begin with a combinatorial ligation – one where all three of the genes are being ligated with origins of replication, but only one of the three is able to ligate onto each Ori, resulting in a collection of incomplete plasmids that each includes just one of the three genes. </p><br />
<center><img src="/wiki/images/9/95/AB_Genemap.png" style="width:35%;"></img></center><br />
<p>Following the first gene ligation, a short linker piece is added, signifying the city that has been reached – all of the linkers are identical, there is no differentiation of routes based on this component. In the second leg of the journey, we perform a ligation with three more genes, representing all of the possible paths the salesman might take next – three colour genes. Again, each growing plasmid can only incorporate one of the new genes, so we obtain a random assortment of incomplete plasmids that each include one antibiotic resistance from the first ligation and one colour gene from the third ligation. </p><br />
<img src="/wiki/images/7/7e/AB_Assemblyfull.png" style="width:100%;"></img><br />
<p>The third leg of the journey is identical to the second, incorporating an additional colour gene, and the final leg uses the three antibiotic genes once again. At the end of this process, we will have obtained a randomized distribution of 76 different kinds of plasmids representing all of the different possible permutations of the genes, capable of producing 18 unique phenotypes, and representing the six bi-directional solutions to the four-city travelling salesman problem.<p/><br />
</div><br />
<a class="anchor" id="Mapmakers"></a><br />
<div class="block"><br />
<h2>MapMakers at Work</h2><br />
<p>Once the plasmids have been produced, how can we use them to identify the correct solution? The answer is in the frequency with which each plasmid occurs: We create bias in the ligations during assembly so that genes that represent shorter paths are more likely to be incorporated into the plasmids, meaning in turn that the final product plasmids are more likely to be composed of several short-path genes. As a result, although we still expect to see plasmids representing every possible route, those plasmids that represent the shortest routes through the map will be much more common than plasmids representing lengthy routes. By identifying the most abundant plasmid, we identify the shortest route and thus the optimal solution. </p><br />
<p>The bias is introduced through the concentration of the reactants in each ligation. If a gene is meant to represent a short path, its concentration in the ligation will be higher than the others, and conversely, genes that are meant to represent lengthy paths will be included in lower concentrations than the others. As a result, at any given ligation step, the gene symbolizing the shortest available path is more likely to be incorporated. Among the product plasmids, genes are incorporated at a rate inversely proportional to their length. The concentration used for each gene in the ligation is described by the expression: –ln[Gene]∝(path distance)</p><br />
<img src="/wiki/images/9/95/Proportions.png" style="width:100%;"></img><br />
<p>To identify which of the plasmids is most frequent, the products are transformed into a bacterial culture. Because each of the genes produces an easily interpreted phenotype, this allows us to infer the most frequently transformed plasmid from the frequency of the colonies produced on agar plates. The plasmid carried by any given colony on the plates below can be readily identified by the combination of the colony colour (purple colonies have RFP and aCP, orange colonies have RFP and GFP, and green colonies have GFP and aCP), and the antibiotic resistances it exhibits, which are inferred from the plate on which it is growing. As an example, a purple colony growing on the kan/amp plate must have the Amp-Red-Blue-Kan-plasmid shown in the first column below.<p/><br />
<img src="/wiki/images/6/6d/Ab_Solution_identification.png" style="width:100%;"></img><br />
<p>Many of the colonies do not correspond to any valid route. For instance, an orange colony on the kan/amp plate has the plasmid Amp-Red-Green-Kan, which does not describe a valid circuit visiting each city exactly once – but because we can tell that this is an invalid solution, we would not count this colony when assessing the frequency of the valid plasmids. Any four-city travelling salesman problem has just three unique solutions, and so there are only three phenotypes that must be counted: purple kan/amp, orange kan/chlor, and green amp/chlor. The colonies of these three phenotypes are counted and compared, and the most frequently occurring plasmid is the optimal solution! </p><br />
</div><br />
<a class="anchor" id="Weight"></a><br />
<div class="block"><br />
<h2>Calculating Gene Concentration</h2><br />
<img src="/wiki/images/5/57/2013Alberta_New_algorithm.png" style="width:100%;"></img><br />
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MEsau
http://2013.igem.org/Team:Alberta/Community
Team:Alberta/Community
2013-10-29T03:42:49Z
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MEsau
http://2013.igem.org/Team:Alberta/Outreach
Team:Alberta/Outreach
2013-10-29T03:42:37Z
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</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
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<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
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<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
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<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Outreach" class="active"><p>Outreach</p></a><br />
<a href="/Team:Alberta/Community"><p>Community</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Outreach: Consort, Alberta<p><br />
</div><br />
<div class="block"><br />
<p> As a part of our efforts to reach out to the local scientific community iGEM Alberta send one of <br />
our team members to the small town of Consort, Alberta to assist their emerging high school iGEM <br />
team. Consort is a town of about 700 people located east of Red Deer near the border with <br />
Saskatchewan and only has one secondary school. Remarkably students from this small town high<br />
school caught wind of the iGEM competition and decided to get involved. Their seclusion however was <br />
the source of several problems. The Consort team lacked the proper equipment, materials, and training <br />
to realize their goal of competing in iGEM. After hearing of their difficulties Mark Rozema travelled to <br />
the small town to lend his assistance. Mark, a recent graduate, was able to provide much needed <br />
materials such as ligase, buffer, and restriction enzymes. He also gave helpful suggestions to improve <br />
their presentation and delivery and helped develop their safety component and abstract. We were <br />
thrilled to be able to help a local high school iGEM team and look forward to future partnership with the <br />
Consort iGEM team. <br />
</p><br />
<div class="masonry"><br />
<div class="masonry-block"><br />
<img src="/wiki/images/2/2b/Consort-sign.png" style="width:100%;"></img><br />
<p>Consort, AB is a small town of about 700 people with one secondary school for its 70 high school <br />
students.</p><br />
</div><br />
<div class="masonry-block"><br />
<img src="/wiki/images/6/67/Consort-meeting.jpg" style="width:100%;"></img><br />
<p>The students practice their presentation in front of their parents<br />
and an Alberta iGEM team member, Mark Rozema.</p><br />
</div><br />
<div class="masonry-block"><br />
<img src="/wiki/images/5/50/Consort-map.png" style="width:100%;"></img><br />
<p>Consort, AB is located several hours from both Edmonton <br />
and Calgary. Having little access to any major biochemistry <br />
labs proved to be challenging for the team.</p><br />
</div><br />
</div><br />
<p>Images Courtesy of:<br/><br />
<a href="http://genomealberta.ca/blogs/university-of-alberta-igem-team-pitches-in-to-help-team-fromconsort.aspx">http://genomealberta.ca/blogs/university-of-alberta-igem-team-pitches-in-to-help-team-fromconsort.aspx</a><br/><br />
<a href="https://maps.google.ca">https://maps.google.ca</a><br/><br />
<a href="http://www.consort.ca/">http://www.consort.ca/</a><br/><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Attributions
Team:Alberta/Attributions
2013-10-29T03:42:14Z
<p>MEsau: </p>
<hr />
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<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
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<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions" class="active"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Attributions</p><br />
</div><br />
<div class="block"><br />
<p>All of the experimental work described herein was performed by the team with technical support from Prof. Ellison’s technician, <b>Nien-tsu Tseng (Rick)</b>. The TSP concept was inspired by the <b>Missouri-Davidson 2007 iGEM team</b> who broke the ice with their work on the Hamiltonian variation of TSB problem. The experimental approaches used here evolved over discussions with our supervisors during group meetings. The correct weighting algorithm that relates city path lengths to linker concentrations was developed by <b>Dr. Doug Ridgway</b>, a supervisor of the 2012 iGEM team. The plasmids used to create TSB compatible parts by PCR were a gift from <b>Genomikon Inc</b>. <br />
The creation of the violacin bricks that we will use in the test of the 5-city TSB would not have been possible without the violacein operon biobrick (K274002) that was created, submitted and carefully characterized by the <b>Cambridge 2009 iGEM team</b>. Wiki coding and design implementation was done by <b>Timo Hohn</b>, (B.Sc. in Computer Engineering).<br />
</p><br />
<br><br />
<p>Thanks to these individuals for donating their time and talents!</p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<!--html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Sponsors
Team:Alberta/Sponsors
2013-10-29T03:41:17Z
<p>MEsau: </p>
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.navbar ul li:first-child > a {<br />
-moz-border-radius: 3px 3px 0 0;<br />
-webkit-border-radius: 3px 3px 0 0;<br />
border-radius: 3px 3px 0 0;<br />
}<br />
.navbar ul li:first-child > a:after {<br />
content:'';<br />
position:absolute;<br />
left:40px;<br />
top:-6px;<br />
border-left:6px solid transparent;<br />
border-right:6px solid transparent;<br />
border-bottom:6px solid #FFF;<br />
}<br />
.navbar ul ul li:first-child a:after {<br />
left:-6px;<br />
top:50%;<br />
margin-top:-6px;<br />
border-left:0;<br />
border-bottom:6px solid transparent;<br />
border-top: 6px solid transparent;<br />
border-right:6px solid #3b3b3b;<br />
}<br />
.navbar ul li:first-child a:hover:after {<br />
border-bottom-color: #04acec;<br />
}<br />
.navbar ul ul li:first-child a:hover:after {<br />
border-right-color: #0299d3;<br />
border-bottom-color:transparent;<br />
}<br />
.navbar ul li:last-child > a {<br />
-moz-border-radius: 0 0 3px 3px;<br />
-webkit-border-radius: 0 0 3px 3px;<br />
border-radius: 0 0 3px 3px;<br />
}<br />
.centered {<br />
text-align:center;<br />
}<br />
.centered-well {<br />
text-align:center;<br />
width:80%;<br />
margin:0 auto;<br />
padding:5px;<br />
background-color:#CCC;<br />
border-radius:6px;<br />
-moz-border-radius:6px;<br />
-o-border-radius:6px;<br />
-webkit-border-radius:6px;<br />
}<br />
.thumbnails {<br />
padding: 35px;<br />
width:700px;<br />
margin:0 auto;<br />
}<br />
.thumbnail {<br />
position:relative;<br />
display:inline-block;<br />
left:180px;<br />
}<br />
.thumbnail img{<br />
/* ... */<br />
height:100px;<br />
position:relative;<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
-ms-transition: all .25s ease-out;<br />
-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
} <br />
.thumbnail img:hover {<br />
transform:scale(4,4);<br />
-webkit-transform:scale(4,4);<br />
-moz-transform:scale(4,4);<br />
-ms-transform:scale(4,4);<br />
-o-transform:scale(4,4);<br />
z-index:999;<br />
background-color:white;<br />
border:solid 2px #CCC;<br />
border-radius:1px;<br />
-moz-border-radius:1px;<br />
-o-border-radius:1px;<br />
-webkit-border-radius:1px;<br />
-moz-box-shadow: 0px 0px 30px #000;<br />
-o-box-shadow: 0px 0px 30px #000;<br />
-webkit-box-shadow: 0px 0px 30px #000;<br />
box-shadow: 0px 0px 30px #000;<br />
<br />
} <br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="team" href="#" class="active">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors" class="active">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team"><p>Roster</p></a><br />
<a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta"><p>Official Profile</p></a><br />
<a href="/Team:Alberta/Sponsors" class="active"><p>Sponsors</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Sponsors</p><br />
</div><br />
<div class="block"><br />
<b> We would like to thank the following sponsors for their generosity and support over the course of this project.</b><br /><br /><br />
<p><a href="http://www.ualberta.ca"><img src="/wiki/images/b/b3/Ualberta-logo.png" alt="The University of Alberta"></img></a><br />
</p><br /><br />
<p><a href="http://albertatechfutures.ca/"><img src="/wiki/images/a/a3/Albertatechfutures-logo.png" style="height:100px;" alt="The University of Alberta"></img></a><br />
</p><br />
<p><a href="http://genomealberta.ca/"><img src="/wiki/images/c/cc/Genomealberta-logo.jpg" style="height:150px;" alt="The University of Alberta"></img></a><br />
</p><br />
<p><a href="http://www.genomikon.ca/"><img src="/wiki/images/3/3d/Genomikon-logo.gif" style="height:100px;" alt="The University of Alberta"></img></a><br />
</p><br /><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<!--html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Team
Team:Alberta/Team
2013-10-29T03:41:04Z
<p>MEsau: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
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height:130px;<br />
width:100%;<br />
}<br />
.bin {<br />
background:url('/wiki/images/e/e4/2013AlbertaBackground.png');<br />
background-size:100% auto;<br />
padding-top:20px;<br />
}<br />
@-moz-document url-prefix() {<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
margin-left:-90px;<br />
}<br />
}<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
}<br />
.block {<br />
background-color:white;<br />
border:1px grey solid;<br />
padding:10px;<br />
margin:10px;<br />
border-radius:5px;<br />
box-shadow: 0px 0px 30px #444444;<br />
}<br />
.titlebar {<br />
position:fixed;<br />
top:0px;<br />
height:130px;<br />
margin-left:-5px;<br />
width:975px;<br />
z-index:2;<br />
background-color:#FFF;<br />
}<br />
.content-title {<br />
text-align:center;<br />
font-size:3em;<br />
}<br />
.titlebar h3, h4 {<br />
text-align:center;<br />
}<br />
.sidebar {<br />
position: fixed;<br />
top: 157px;<br />
float: left;<br />
z-index: 3;<br />
padding: 10px 10px 10px 10px;<br />
width: 230px;<br />
}<br />
.sidebar_block {<br />
background-color:white;<br />
margin:1px;<br />
border:1px grey solid;<br />
padding:5px 10px 5px 10px;<br />
border-radius:5px;<br />
box-shadow: 0px 0px 20px #444444;<br />
}<br />
.main {<br />
position:relative;<br />
float:right;<br />
width:720px;<br />
}<br />
.clear {<br />
clear:both;<br />
}<br />
.ualberta-logo {<br />
position:fixed;<br />
margin-left:70px;<br />
margin-top:-70px;<br />
width:180px;<br />
}<br />
.igem-logo {<br />
position:fixed;<br />
margin-left:650px;<br />
margin-top:-95px;<br />
width: 150px;<br />
}<br />
.igem-logo img {<br />
width:210px;<br />
}<br />
.igem-bar {<br />
position:relative;<br />
float:right;<br />
}<br />
.igem-bar a {<br />
padding:0 !important;<br />
}<br />
.igem-bar img {<br />
height:38px;<br />
}<br />
.tooltip {<br />
width:100%;<br />
}<br />
.tooltip .saying {<br />
background: #EEE;<br />
color: #444;<br />
left: 100px;<br />
margin-bottom: 15px;<br />
opacity: 0;<br />
padding: 20px;<br />
position: absolute;<br />
visibility: hidden;<br />
min-width:200px;<br />
max-width:500px;<br />
-webkit-transform: translateX(10px);<br />
-moz-transform: translateX(10px);<br />
-ms-transform: translateX(10px);<br />
-o-transform: translateX(10px);<br />
transform: translateX(10px);<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
-ms-transition: all .25s ease-out;<br />
-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
-webkit-border-radius:6px;<br />
-moz-border-radius:6px;<br />
-ms-border-radius:6px;<br />
-o-border-radius:6px;<br />
border-radius:6px;<br />
-webkit-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
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box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
}<br />
.tooltip .saying {<br />
content: " ";<br />
top:100px;<br />
display:block;<br />
left: 200px;<br />
max-height:1000px;<br />
position: absolute;<br />
} <br />
.tooltip .saying:after {<br />
border-bottom: solid transparent 10px;<br />
border-top: solid transparent 10px;<br />
border-right: solid #EEE 10px;<br />
left: 10px;<br />
top:10px;<br />
content: "";<br />
margin-left:-16px;<br />
position: absolute;<br />
width: 0;<br />
max-height:1000px;<br />
display:block;<br />
}<br />
.tooltip:hover .saying {<br />
opacity: 1;<br />
visibility: visible;<br />
-webkit-transform: translateX(0px);<br />
-moz-transform: translateX(0px);<br />
-ms-transform: translateX(0px);<br />
-o-transform: translateX(0px);<br />
transform: translateX(0px);<br />
}<br />
.active {<br />
color:#04acec !important;<br />
}<br />
.navbar, .navbar ul {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.navbar {<br />
width:963px;<br />
margin:60px auto;<br />
position:fixed;<br />
top:70px;<br />
z-index:4;<br />
border: 1px solid #DDD;<br />
background-color:#FFF;<br />
background-image: -moz-linear-gradient(#FFF, #DDD);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#DDD));<br />
background-image: -webkit-linear-gradient(#FFF, #DDD);<br />
background-image: -ms-linear-gradient(#FFF, #DDD);<br />
background-image: linear-gradient(#FFF, #DDD);<br />
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zoom:1;<br />
}<br />
.navbar:before, .navbar:after {<br />
content: "";<br />
display: table;<br />
}<br />
.navbar:after {<br />
clear:both;<br />
}<br />
.navbar li {<br />
float:left;<br />
border-right:1px solid #CCC;<br />
-moz-box-shadow:1px 0 0 #EEE;<br />
-webkit-box-shadow: 1px 0 0 #EEE;<br />
box-shadow: 1px 0 0 #EEE;<br />
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}<br />
.navbar a {<br />
float: left;<br />
padding: 12px 30px;<br />
color: #444;<br />
font: bold 12px Arial, Helvetica;<br />
text-decoration:none;<br />
/*text-shadow: 0 1px 0 #333;*/<br />
}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
color:#BBB;<br />
}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
opacity: 0;<br />
visibility: hidden;<br />
position:absolute;<br />
top:38px;<br />
left:0;<br />
z-index:1;<br />
background:#FFF;<br />
background: -moz-linear-gradient(#FFF, #CCC);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#CCC));<br />
background: -webkit-linear-gradient(#FFF, #CCC);<br />
background: -o-linear-gradient(#FFF, #CCC);<br />
background: -ms-linear-gradient(#FFF, #CCC);<br />
background: linear-gradient(#FFF, #CCC);<br />
-moz-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-webkit-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-box-shadow:0 -1px 0 rgba(255,255,255,.3);<br />
-moz-border-radius: 3px;<br />
-webkit-border-radius: 3px;<br />
border-radius: 3px;<br />
-webkit-transition: all .2s ease-in-out;<br />
-moz-transition: all .2s ease-in-out;<br />
-ms-transition: all .2s ease-in-out;<br />
-o-transition: all .2s ease-in-out;<br />
transition: all .2s ease-in-out;<br />
}<br />
.navbar li:hover > ul {<br />
opacity: 1;<br />
visibility: visible;<br />
margin:0;<br />
}<br />
.navbar ul ul {<br />
top:0;<br />
left:150px;<br />
margin:0 0 0 20px;<br />
_margin:0;/*IE6 only*/<br />
-moz-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
-webkit-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
}<br />
.navbar ul li {<br />
float:none;<br />
display:block;<br />
border:0;<br />
_line-height:0; /*IE6 only*/<br />
-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
-webkit-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
}<br />
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-moz-box-shadow:none;<br />
-webkit-box-shadow:none;<br />
box-shadow:none;<br />
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.navbar ul a {<br />
padding:10px;<br />
width:130px;<br />
_height:10px;/*IE6 only*/<br />
display:block;<br />
white-space:nowrap;<br />
float:none;<br />
text-transform:none;<br />
}<br />
.navbar ul a:hover {<br />
background-color:#0186ba;<br />
background-image: -moz-linear-gradient(#04acec, #0186ba);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#04acec), to(#0186ba));<br />
background-image: -webkit-linear-gradient(#04acec, #0186ba);<br />
background-image: -ms-linear-gradient(#04acec, #0186ba);<br />
background-image: linear-gradient(#04acec, #0186ba);<br />
}<br />
.navbar ul li:first-child > a {<br />
-moz-border-radius: 3px 3px 0 0;<br />
-webkit-border-radius: 3px 3px 0 0;<br />
border-radius: 3px 3px 0 0;<br />
}<br />
.navbar ul li:first-child > a:after {<br />
content:'';<br />
position:absolute;<br />
left:40px;<br />
top:-6px;<br />
border-left:6px solid transparent;<br />
border-right:6px solid transparent;<br />
border-bottom:6px solid #FFF;<br />
}<br />
.navbar ul ul li:first-child a:after {<br />
left:-6px;<br />
top:50%;<br />
margin-top:-6px;<br />
border-left:0;<br />
border-bottom:6px solid transparent;<br />
border-top: 6px solid transparent;<br />
border-right:6px solid #3b3b3b;<br />
}<br />
.navbar ul li:first-child a:hover:after {<br />
border-bottom-color: #04acec;<br />
}<br />
.navbar ul ul li:first-child a:hover:after {<br />
border-right-color: #0299d3;<br />
border-bottom-color:transparent;<br />
}<br />
.navbar ul li:last-child > a {<br />
-moz-border-radius: 0 0 3px 3px;<br />
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border-radius: 0 0 3px 3px;<br />
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.centered {<br />
text-align:center;<br />
}<br />
.centered-well {<br />
text-align:center;<br />
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margin:0 auto;<br />
padding:5px;<br />
background-color:#CCC;<br />
border-radius:6px;<br />
-moz-border-radius:6px;<br />
-o-border-radius:6px;<br />
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.thumbnails {<br />
padding: 35px;<br />
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margin:0 auto;<br />
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.thumbnail {<br />
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.thumbnail img{<br />
/* ... */<br />
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position:relative;<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
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transition: all .25s ease-out;<br />
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.thumbnail img:hover {<br />
transform:scale(2,2);<br />
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background-color:white;<br />
border:solid 2px #CCC;<br />
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<br />
}<br />
.expandable {<br />
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}<br />
.expandable img{<br />
position:relative;<br />
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/*left:0;*/<br />
transition: all 0.5s;<br />
-webkit-transition: all 0.5s;<br />
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}<br />
.expandable:hover img {<br />
position: relative;<br />
/*left: -px;*/<br />
width: 400px;<br />
z-index: 50;<br />
background-color: white;<br />
-webkit-border-radius:6px;<br />
-moz-border-radius:6px;<br />
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a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
.floatLeft {<br />
float:left;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
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<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Mike-Ellison"><p>Mike Ellison</p></a><br />
<a href="#Dominic-Sauvageau"><p>Dominic Sauvageau</p></a><br />
<a href="#Mark-Rozema"><p>Mark Rozema</p></a><br />
<a href="#Cadence-Moorhouse"><p>Cadence Moorhouse</p></a><br />
<a href="#Dawson-Zeng"><p>Dawson Zeng</p></a><br />
<a href="#Michael-Esau"><p>Michael Esau</p></a><br />
<a href="#Rachel-Kwan"><p>Rachel Kwan</p></a><br />
<a href="#Stephanie-Chiu"><p>Stephanie Chiu</p></a><br />
<a href="#Larry-Zhang"><p>Larry Zhang</p></a><br />
<a href="#Cameron-Murray"><p>Cameron Murray</p></a><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team" class="active"><p>Roster</p></a><br />
<a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta"><p>Official Profile</p></a><br />
<a href="/Team:Alberta/Sponsors"><p>Sponsors</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<h1>Who We Are</h1><br />
<h5>Advisors</h5><br />
<ul>Professors:<br />
<ul><ul><li><b>Mike Ellison</b></li><br />
<li><b>Dominic Sauvageau</b></li></ul></ul><br />
</ul><br />
<h5>Team Members</h5><br />
<ul>Recent Graduates:<br />
<ul><ul><li><b>Mark Rozema</b></li><br />
<li><b>Larry Zhang</b></li><br />
<li><b>Michael Esau</b></li></ul></ul><br />
Undergraduates:<br />
<ul><ul><li><b>Dawson Zeng</b>: <i>Student Liaison</i></li><br />
<li><b>Rachel Kwan</b></li><br />
<li><b>Cadence Moorhouse</b></li></ul></ul><br />
High School Graduates:<br />
<ul><ul><li><b>Stephanie Chiu</b></li><br />
<li><b>Cameron Murray</b></li></ul></ul><br />
</ul><br />
</div><br />
<a class="anchor" id="Mike-Ellison"></a><br />
<div class="block"><br />
<h2>Mike Ellison</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/2/26/2013-Mellison.png"<br />
alt="Mike Ellison"></img></div><br />
Mike Ellison is a professor with the Department of Biochemistry at the University of <br />
Alberta.<br /><br />
His current focus on Synthetic Biology is to produce modular biological circuits of <br />
increasing sophistication using well-understood molecular components that can be <br />
reliably assembled into novel and useful forms of artificial life. He has been involved<br />
in iGEM for six years and continues to actively engage his undergraduate students <br />
in this synthetic biology competition.<br />
</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Dominic-Sauvageau"></a><br />
<div class="block"><br />
<h2>Dominic Sauvageau</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><br />
<img src="/wiki/images/d/d8/2013-Dsauvageau.jpg"<br />
alt="Team Member 9"></img></div>Dominic Sauvageau joined the Department of Chemical and Materials <br />
Engineering at the University of Alberta <br />
as an Assistant Professor in January 2011. His research involves the development of novel bacteriophage-<br />
based technologies and bioprocessing strategies for production in microbial systems. He joined the iGEM <br />
adventure last year when he supervised an iGEM-Entrepreneurial team (they won!). He's thrilled to be <br />
involved in iGEM again this year. He loves travelling and hopes he'll be able to use the E. coli we're <br />
working on to plan his next trip.</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Mark-Rozema"></a><br />
<div class="block"><br />
<h2>Mark Rozema</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/6/62/2013-Mrozema.jpg"<br />
alt="Team Member 9"></img></div><br />
Mark Rozema graduated from the Biochemistry program at the University of Alberta in April 2013 and is <br />
currently enrolled in the law program, also at the U of A. He enjoys running, early mornings, late nights <br />
and old scotch. Mark was involved in all facets of the project over the summer months, such as conceptual <br />
planning, establishing general protocol, part creation and part isolation but withdrew to focus on law <br />
school since the start of September.</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Cadence-Moorhouse"></a><br />
<div class="block"><br />
<h2>Cadence Moorhouse</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/f/f1/2013-Cmoorhouse.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a 4th year genetics student at the University of Alberta. Every since high school I have had an <br />
interest in genetics and I heard all about the applications of synthetic biology largely through social <br />
media. It was at a talk by biotech guru Andrew Hessel that I first learned of iGEM. I was delighted to find <br />
out that the U of A had a team and a couple of emails later I was on the roster. This project has given me <br />
the opportunity to learn standard lab techniques and to see an experiment evolve. My experience teaching and <br />
coaching allows me to easily convey complex ideas into simpler ones. I hope to utilize these skills over the <br />
course of this project. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Dawson-Zeng"></a><br />
<div class="block"><br />
<h2>Dawson Zeng</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/9/90/2013-Dzeng.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a 4th year student at the University of Alberta majoring in Biological Sciences. I first heard about <br />
the field of Synthetic Biology from a guest speaker. It was then that I looked into joining iGEM Team <br />
Alberta. Personally, I think it is the coolest thing that Synthetic Biology combines philosophies from both <br />
Biology and Engineering; something I never thought about. Overall, my knowledge and understanding of <br />
genetics and interactions between DNA molecules vastly increased throughout the summer. A true testament to <br />
Richard Feynman’s famous quote, “What I cannot create, I do not understand.” </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Michael-Esau"></a><br />
<div class="block"><br />
<h2>Michael Esau</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/b/b7/2013-Mesau.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a graduate from the Biochemistry Specialization program at the University of <br />
Alberta. I learned about iGEM from Dr. Mike Ellison’s biochemistry class, and am <br />
happy to be a part of this year’s team. I'm planning to go into the synthetic bio <br />
research field and will be joining up with Dr. Dominic Sauvageau's lab for the next <br />
year. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Rachel-Kwan"></a><br />
<div class="block"><br />
<h2>Rachel Kwan</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/f/f0/2013-Rkwan.jpg"<br />
alt="Team Member 9"></img></div><br />
<p>After my first discoveries on the possibilities of iGEM from the local newspaper, I searched online and admired various iGEM projects. At this time during high school, I was personally unclear of my desired career path, aside from studying science, with a focus on Biology or Chemistry. Also with my vague knowledge of biotechnological methods, I was wary about the bioethical side of “manipulating nature,” especially from public warnings in literature.</p><br />
<p>However, within studying Biochemistry in my undergrad, I found that current methodologies of biotechnology seemed to have controlled lab settings, careful precautions, and/or a balance with purposeful benefits. Looking at the variety of iGEM projects, they used in-school material for real-world, practical applications. IGEM also attracted me because I liked the idea of working in a team setting to balance strengths and weaknesses with others. I believe that iGEM is rewarding and relevant in that it challenges teamwork, independence, creativity, writing, presenting, and lab technique. As part of my work, I hope to offer organizational skills, interest in safety, and Wiki ideas.</p><br />
<p>Outside of iGEM work, I play the piano and clarinet, read, meditate, play board games, search for good sales, and grow pet plants like basil.</p><br />
<br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Stephanie-Chiu"></a><br />
<div class="block"><br />
<h2>Stephanie Chiu</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/3/30/2013-Schiu.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a first year student at the University of Alberta. I first heard about iGEM from friends at my high <br />
school and was privileged enough to join U of A’s team as I was finishing up my Grade 12 year. I am excited <br />
to learn more about what synthetic biology is and what working in a lab is like. I hope that I can offer a <br />
unique perspective to our team. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Larry-Zhang"></a><br />
<div class="block"><br />
<h2>Larry Zhang</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/8/83/2013-Lzhang.jpg"<br />
alt="Team Member 9"></img></div><br />
Passionate scientist born in the historical city of Yueyang, China; educated in the English for 8 years and <br />
has been under strict scientific indoctrination in the University of Alberta department of Biochemistry. <br />
Graduated with a Biochemistry degree with interest in genetics and genetic engineering, Larry Zhang has <br />
brought with him a huge idea cannon and a pair of magic pipetter’s hands; he is one of the most valuable <br />
assets in this team. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Cameron-Murray"></a><br />
<div class="block"><br />
<h2>Cameron Murray</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/7/78/2013-Cmurray.jpg"<br />
alt="Team Member 9"></img></div> <br />
I am a first year university student studying molecular genetics at the U of A, however when I joined the <br />
team I was in my grade twelve year of high school. I heard about Synthetic biology through quirks and <br />
quarks, the CBC radio program, and was immediately taken with it and it’s vast possibilities. I was so <br />
enthralled that I talked about it quite a bit to my friends one of whom told me about iGEM. So here I am <br />
hoping to learn about and deepen my interest in synthetic biology through iGEM.</p><br />
<div class="clear"></div><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
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For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
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</html><br />
<br />
<br />
{|align="justify"<br />
|Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium. Integer tincidunt. Cras dapibus. Vivamus elementum semper nisi. Aenean vulputate eleifend tellus. Aenean leo ligula, porttitor eu, consequat vitae, eleifend ac, enim. Aliquam lorem ante, dapibus in, viverra quis, feugiat a, tellus. Phasellus viverra nulla ut metus varius laoreet. Quisque rutrum. Aenean imperdiet. Etiam ultricies nisi vel augue. Curabitur ullamcorper ultricies nisi. Nam eget dui.<br />
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<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
'''Advisors:'''<br />
<br />
*'''Mike Ellison''': Professor<br />
*'''Advisor 2''': Professor<br />
<br />
<br />
'''Team Members:'''<br />
<br />
*'''Mark Rozema''': Graduate<br />
*'''Larry Zhang''': Graduate<br />
*'''Michael Esau''': Graduate<br />
*'''Saima Zamir''': Graduate<br />
*'''Dawson Zeng''': Student Liaison, Undergraduate<br />
*'''Rachel Kwon''': Undergraduate<br />
*'''Cadence Moorhouse''': Undergraduate<br />
*'''Stephanie Chiu''': High School Graduate<br />
*'''Cameron Murray''': High School Graduate<br />
<br />
<br />
|<br />
<gallery><br />
Image:alberta_Team_member_1.png|Team member 1<br />
Image:alberta_Team_member_2.png|Team member 2<br />
Image:alberta_Team_member_3.png|Team member 3<br />
Image:alberta_Team_member_4.png|Team member 4<br />
Image:alberta_Team_member_5.png|Team member 5<br />
Image:alberta_Team_member_6.png|Team member 6<br />
Image:alberta_Team_member_7.png|Team member 7<br />
Image:alberta_Team_member_8.png|Team member 8<br />
Image:alberta_Team_member_9.png|Team member 9<br />
</gallery><br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
<br />
== '''Where we're from''' ==<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Accomplishments
Team:Alberta/Accomplishments
2013-10-29T03:40:50Z
<p>MEsau: </p>
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}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
color:#BBB;<br />
}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
opacity: 0;<br />
visibility: hidden;<br />
position:absolute;<br />
top:38px;<br />
left:0;<br />
z-index:1;<br />
background:#FFF;<br />
background: -moz-linear-gradient(#FFF, #CCC);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#CCC));<br />
background: -webkit-linear-gradient(#FFF, #CCC);<br />
background: -o-linear-gradient(#FFF, #CCC);<br />
background: -ms-linear-gradient(#FFF, #CCC);<br />
background: linear-gradient(#FFF, #CCC);<br />
-moz-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-webkit-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-box-shadow:0 -1px 0 rgba(255,255,255,.3);<br />
-moz-border-radius: 3px;<br />
-webkit-border-radius: 3px;<br />
border-radius: 3px;<br />
-webkit-transition: all .2s ease-in-out;<br />
-moz-transition: all .2s ease-in-out;<br />
-ms-transition: all .2s ease-in-out;<br />
-o-transition: all .2s ease-in-out;<br />
transition: all .2s ease-in-out;<br />
}<br />
.navbar li:hover > ul {<br />
opacity: 1;<br />
visibility: visible;<br />
margin:0;<br />
}<br />
.navbar ul ul {<br />
top:0;<br />
left:150px;<br />
margin:0 0 0 20px;<br />
_margin:0;/*IE6 only*/<br />
-moz-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
-webkit-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
}<br />
.navbar ul li {<br />
float:none;<br />
display:block;<br />
border:0;<br />
_line-height:0; /*IE6 only*/<br />
-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
-webkit-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
}<br />
.navbar ul li:last-child {<br />
-moz-box-shadow:none;<br />
-webkit-box-shadow:none;<br />
box-shadow:none;<br />
}<br />
.navbar ul a {<br />
padding:10px;<br />
width:130px;<br />
_height:10px;/*IE6 only*/<br />
display:block;<br />
white-space:nowrap;<br />
float:none;<br />
text-transform:none;<br />
}<br />
.navbar ul a:hover {<br />
background-color:#0186ba;<br />
background-image: -moz-linear-gradient(#04acec, #0186ba);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#04acec), to(#0186ba));<br />
background-image: -webkit-linear-gradient(#04acec, #0186ba);<br />
background-image: -ms-linear-gradient(#04acec, #0186ba);<br />
background-image: linear-gradient(#04acec, #0186ba);<br />
}<br />
.navbar ul li:first-child > a {<br />
-moz-border-radius: 3px 3px 0 0;<br />
-webkit-border-radius: 3px 3px 0 0;<br />
border-radius: 3px 3px 0 0;<br />
}<br />
.navbar ul li:first-child > a:after {<br />
content:'';<br />
position:absolute;<br />
left:40px;<br />
top:-6px;<br />
border-left:6px solid transparent;<br />
border-right:6px solid transparent;<br />
border-bottom:6px solid #FFF;<br />
}<br />
.navbar ul ul li:first-child a:after {<br />
left:-6px;<br />
top:50%;<br />
margin-top:-6px;<br />
border-left:0;<br />
border-bottom:6px solid transparent;<br />
border-top: 6px solid transparent;<br />
border-right:6px solid #3b3b3b;<br />
}<br />
.navbar ul li:first-child a:hover:after {<br />
border-bottom-color: #04acec;<br />
}<br />
.navbar ul ul li:first-child a:hover:after {<br />
border-right-color: #0299d3;<br />
border-bottom-color:transparent;<br />
}<br />
.navbar ul li:last-child > a {<br />
-moz-border-radius: 0 0 3px 3px;<br />
-webkit-border-radius: 0 0 3px 3px;<br />
border-radius: 0 0 3px 3px;<br />
}<br />
.centered {<br />
text-align:center;<br />
}<br />
.centered-well {<br />
text-align:center;<br />
width:80%;<br />
margin:0 auto;<br />
padding:5px;<br />
background-color:#CCC;<br />
border-radius:6px;<br />
-moz-border-radius:6px;<br />
-o-border-radius:6px;<br />
-webkit-border-radius:6px;<br />
}<br />
.thumbnails {<br />
padding: 35px;<br />
width:700px;<br />
margin:0 auto;<br />
}<br />
.thumbnail {<br />
position:relative;<br />
display:inline-block;<br />
left:180px;<br />
}<br />
.thumbnail img{<br />
/* ... */<br />
height:100px;<br />
position:relative;<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
-ms-transition: all .25s ease-out;<br />
-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
} <br />
.thumbnail img:hover {<br />
transform:scale(4,4);<br />
-webkit-transform:scale(4,4);<br />
-moz-transform:scale(4,4);<br />
-ms-transform:scale(4,4);<br />
-o-transform:scale(4,4);<br />
z-index:999;<br />
background-color:white;<br />
border:solid 2px #CCC;<br />
border-radius:1px;<br />
-moz-border-radius:1px;<br />
-o-border-radius:1px;<br />
-webkit-border-radius:1px;<br />
-moz-box-shadow: 0px 0px 30px #000;<br />
-o-box-shadow: 0px 0px 30px #000;<br />
-webkit-box-shadow: 0px 0px 30px #000;<br />
box-shadow: 0px 0px 30px #000;<br />
<br />
} <br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
#groupparts {<br />
/*margin-left:-11px;*/<br />
width:100% !important;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments" class="active">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments" class="active"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Accomplishments</p><br />
</div><br />
<div class="block"><br />
<img src="/wiki/images/a/af/2013-Accomplishments.PNG" style="width:100%;"></img><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<h2> Awards<br />
</h2><br />
<br />
<img src="/wiki/images/thumb/9/95/Presentationpic.jpg/800px-Presentationpic.jpg " style="width:50%" align="right"></img><br />
<br />
<p>Team Alberta was thrilled to receive recognition at the North American Regional Jamboree competition:</p><br />
<br><br />
<p><b>Best Presentation</b> - in the undergraduate category </p><br />
<p><b>Gold Medal </b>– for fulfilling criteria</p><br />
<p><b>Advancement to World Finals</b></p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</div><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<br />
</body><br />
</html><br />
<br />
<br />
<!-- <html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Parts
Team:Alberta/Parts
2013-10-29T03:40:36Z
<p>MEsau: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
.titlebar {<br />
height:130px;<br />
width:100%;<br />
}<br />
.bin {<br />
background:url('/wiki/images/e/e4/2013AlbertaBackground.png');<br />
background-size:100% auto;<br />
padding-top:20px;<br />
}<br />
@-moz-document url-prefix() {<br />
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background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
margin-left:-95px;<br />
}<br />
}<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
}<br />
.block {<br />
background-color:white;<br />
border:1px grey solid;<br />
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margin:10px;<br />
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box-shadow: 0px 0px 30px #444444;<br />
}<br />
.titlebar {<br />
position:fixed;<br />
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margin-left:-5px;<br />
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z-index:2;<br />
background-color:#FFF;<br />
}<br />
.content-title {<br />
text-align:center;<br />
font-size:3em;<br />
}<br />
.titlebar h3, h4 {<br />
text-align:center;<br />
}<br />
.sidebar {<br />
position: fixed;<br />
top: 157px;<br />
float: left;<br />
z-index: 3;<br />
padding: 10px 10px 10px 10px;<br />
width: 230px;<br />
}<br />
.sidebar_block {<br />
background-color:white;<br />
margin:1px;<br />
border:1px grey solid;<br />
padding:5px 10px 5px 10px;<br />
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box-shadow: 0px 0px 20px #444444;<br />
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}<br />
.clear {<br />
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margin-top:-70px;<br />
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}<br />
.igem-logo {<br />
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margin-left:650px;<br />
margin-top:-95px;<br />
width: 150px;<br />
}<br />
.igem-logo img {<br />
width:210px;<br />
}<br />
.igem-bar {<br />
position:relative;<br />
float:right;<br />
}<br />
.igem-bar a {<br />
padding:0 !important;<br />
}<br />
.igem-bar img {<br />
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}<br />
.tooltip {<br />
width:100%;<br />
}<br />
.tooltip .saying {<br />
background: #EEE;<br />
color: #444;<br />
left: 100px;<br />
margin-bottom: 15px;<br />
opacity: 0;<br />
padding: 20px;<br />
position: absolute;<br />
visibility: hidden;<br />
min-width:200px;<br />
max-width:500px;<br />
-webkit-transform: translateX(10px);<br />
-moz-transform: translateX(10px);<br />
-ms-transform: translateX(10px);<br />
-o-transform: translateX(10px);<br />
transform: translateX(10px);<br />
-webkit-transition: all .25s ease-out;<br />
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-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
-webkit-border-radius:6px;<br />
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margin-left:-16px;<br />
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}<br />
.tooltip:hover .saying {<br />
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.active {<br />
color:#04acec !important;<br />
}<br />
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}<br />
.navbar {<br />
width:963px;<br />
margin:60px auto;<br />
position:fixed;<br />
top:70px;<br />
z-index:4;<br />
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background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#DDD));<br />
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-moz-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
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zoom:1;<br />
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.navbar:before, .navbar:after {<br />
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display: table;<br />
}<br />
.navbar:after {<br />
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}<br />
.navbar li {<br />
float:left;<br />
border-right:1px solid #CCC;<br />
-moz-box-shadow:1px 0 0 #EEE;<br />
-webkit-box-shadow: 1px 0 0 #EEE;<br />
box-shadow: 1px 0 0 #EEE;<br />
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}<br />
.navbar a {<br />
float: left;<br />
padding: 12px 30px;<br />
color: #444;<br />
font: bold 12px Arial, Helvetica;<br />
text-decoration:none;<br />
/*text-shadow: 0 1px 0 #333;*/<br />
}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
color:#BBB;<br />
}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
opacity: 0;<br />
visibility: hidden;<br />
position:absolute;<br />
top:38px;<br />
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z-index:1;<br />
background:#FFF;<br />
background: -moz-linear-gradient(#FFF, #CCC);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#CCC));<br />
background: -webkit-linear-gradient(#FFF, #CCC);<br />
background: -o-linear-gradient(#FFF, #CCC);<br />
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border-radius: 3px;<br />
-webkit-transition: all .2s ease-in-out;<br />
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transition: all .2s ease-in-out;<br />
}<br />
.navbar li:hover > ul {<br />
opacity: 1;<br />
visibility: visible;<br />
margin:0;<br />
}<br />
.navbar ul ul {<br />
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margin:0 0 0 20px;<br />
_margin:0;/*IE6 only*/<br />
-moz-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
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.navbar ul li {<br />
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display:block;<br />
border:0;<br />
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-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
-webkit-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
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-webkit-box-shadow:none;<br />
box-shadow:none;<br />
}<br />
.navbar ul a {<br />
padding:10px;<br />
width:130px;<br />
_height:10px;/*IE6 only*/<br />
display:block;<br />
white-space:nowrap;<br />
float:none;<br />
text-transform:none;<br />
}<br />
.navbar ul a:hover {<br />
background-color:#0186ba;<br />
background-image: -moz-linear-gradient(#04acec, #0186ba);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#04acec), to(#0186ba));<br />
background-image: -webkit-linear-gradient(#04acec, #0186ba);<br />
background-image: -ms-linear-gradient(#04acec, #0186ba);<br />
background-image: linear-gradient(#04acec, #0186ba);<br />
}<br />
.navbar ul li:first-child > a {<br />
-moz-border-radius: 3px 3px 0 0;<br />
-webkit-border-radius: 3px 3px 0 0;<br />
border-radius: 3px 3px 0 0;<br />
}<br />
.navbar ul li:first-child > a:after {<br />
content:'';<br />
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}<br />
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/* ... */<br />
height:100px;<br />
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transform:scale(4,4);<br />
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border:solid 2px #CCC;<br />
border-radius:1px;<br />
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-o-border-radius:1px;<br />
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<br />
}<br />
a.anchor{<br />
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}<br />
#groupparts {<br />
/*margin-left:-11px;*/<br />
width:100% !important;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts" class="active">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts" class="active"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Submitted Parts</p><br />
</div><br />
<div class="block"><br />
<p> Our 2013 parts submitted are a set of violacein genes derived from the violacein operon constructed and <br />
submitted by Cambridge in 2009 (BBa_K274002). We have made a number of modifications, including upgrading the <br />
plasmid backbone from pSB1K3 to pSB1C3 standard 10, and converting each of the five open reading frames into <br />
its own part with a common and improved ribosome binding site (BBa_B0030) such that they can be assembled in <br />
different combinations and permutations. All of the parts have been characterized and are functional, and we <br />
have found that a new combination, VioABCE, produces a new pigment which we call "Royal Blue". </p><br />
<img src="/wiki/images/f/f0/2013-Alberta-Submitted_parts.PNG" style="width:100%;"></img><br />
<br />
</html><br />
<groupparts>iGEM013 Alberta</groupparts><br />
<html><br />
<br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<br />
<!-- <html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Protocols
Team:Alberta/Protocols
2013-10-29T03:40:21Z
<p>MEsau: </p>
<hr />
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}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols" class="active">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
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<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Parts"><p>The Parts</p></a><br />
<a href="#Build"><p>Building the Plasmids</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols" class="active"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
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<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Protocols</p><br />
</div><br />
<a class="anchor" id="Parts"></a><br />
<div class="block"><br />
<h2>The Parts</h2><br />
<p>The 6 genes that were required to assemble various routes were obtained by PCR from plasmids kindly provided by Genomikon Inc. Each gene (AmpR, KanR, ClrR, GFP, RFP and aCP) exist as self contained cassettes that are flanked by BsaI sites. Parts were then generated according to the schematic shown below:</p><br />
<img src="/wiki/images/c/c5/Making_parts_678x586.png" align="middle" style="width:100%;"><br />
</div><br />
<a class="anchor" id="Build"></a><br />
<div class="block"><br />
<h2>Building the Plasmids</h2><br />
<p>Our plasmid assembly system relies upon the achievements of previous Team Alberta iGEM entries, 2009’s BioBytes and 2010’s Genomikon assembly methods. This process begins with origins of replication anchored at one end to magnetic beads in a suspension within a reaction microfuge tube. The anchored strands have a single, free-floating sticky end, onto which successive genes are ligated. Once the new gene has been ligated on, we use a magnet to hold the beads (along with the anchored DNA) inside the reaction tube, while washing away the rest of the reaction, including the enzyme, buffers, and any non-ligated DNA that remains. The beads are then resuspended in a new reaction mixture, containing the next ligation step.</p><br />
<img src="/wiki/images/b/b4/2013Alberta-Poster2.jpg" align="middle" style="width:100%;"><br />
<p>Once all of the genes have been ligated, a tail-piece that complements the original bead-anchor DNA sequence is added, so that the finished product can be unbound from the beads and will close upon itself to form the circular plasmid. In this fashion, a four-gene, roughly 5000-base-pair plasmid is assembled in as little as an afternoon, cheaply and easily.</p><br />
</div><br />
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</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Results
Team:Alberta/Results
2013-10-29T03:39:53Z
<p>MEsau: </p>
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<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#First-Tests"><p>The First Tests</p></a><br />
<a href="#Linkers"><p>Perfecting the Linkers</p></a><br />
<a href="#Assembly"><p>The Full Assembly</p></a><br />
<a href="#Colour-Controls"><p>Colour Controls</p></a><br />
<a href="#Calibration"><p>Initial Calibration</p></a><br />
<a href="#TSP"><p>The Travelling Salesman Problem</p></a><br />
<a href="#Adapt-POP"><p>Increasing Complexity</p></a><br />
<a href="#Revised-Strategy"><p>A Revised Strategy</p></a><br />
<a href="#DNA-Library"><p>Cosmid DNA Library</p></a><br />
<a href="#PCR"><p>PCR Identification</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results" class="active"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
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<p class="content-title">Results</p><br />
</div><br />
<a class="anchor" id="First-Tests"></a><br />
<div class="block"><br />
<h2>The First Tests</h2><br />
<p>We performed some initial tests to confirm the efficacy of our assembly system. The Genomikon assembly method requires that we be able to successfully bind and elute DNA from magnetic beads, and that we be able to perform successive ligations on the bead-bound strands. These are necessary for building the plasmid "routes", as described in the project overview page. </p><br />
<br />
<p>In the gel below, the second lane displays the result of an origin of replication (Ori) sample that was bound to the bead, washed and then re-eluted – the presence of DNA at the desired mass in this lane confirms the successful binding and elution. The third lane demonstrates that we can successfully ligate genes (KanR in this case) directly to the Ori at high efficiency and still safely elute them. In the fourth lane, we have ligated a 13-base-pair linker onto the existing Ori-KanR, followed by a second gene, ChlorR. Although the high-mass band suggests that ligation was successful, the fact that there is still a stronger band at the Ori-KanR mass suggests that the ligation has not proceeded to completion.</p><br />
<p><img src="/wiki/images/7/7e/2013-Alberta-Results-Figure_1.png" style="width:100%;"></img><br /><br />
Figure 1: Agarose gel electrophoresis image from initial ligation trials. <br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Origin of replication, bound to the magnetic beads and then eluted. <br /><br />
Lane 3: KanR gene ligated to bead-bound Ori.<br /> <br />
Lane 4: Existing bead-bound Ori-KanR sample ligated with linker, then ligated with ChlorR <br /><br />
(beads are always washed between ligations).</p><br />
</div><br />
<a class="anchor" id="Linkers"></a><br />
<div class="block"><br />
<h2>Perfecting the Linkers</h2><br />
<p>The incomplete ligation of the previous step presents an obstacle for our system, but the issue appears to be isolated to the ligation step involving the short linker piece. To get a more effective ligation without extending the timeframe of our assembly, we made several adjustments. First, we raised ligation temperature from 4°C to 22°C in the hopes of increasing the enzyme activity. Second, we switched to a larger, 25-base-pair linker – we were able to successfully ligate large pieces in the case of the Ori and KanR ligation, so perhaps size plays a factor. Also, we used better-purified stocks of our genes, to eliminate the possibility that some interfering piece of the original plasmid was competing with our desired reaction. Finally, we attempted to increase the concentration of the linker in the hopes of driving the reaction to completion. Here, we can see that our changes have significantly improved the ligation efficiency, although changing the linker concentration has not created an appreciable benefit. </p><br />
<p><img src="/wiki/images/9/9e/2013-Alberta-Figure_2.png" style="width:100%;"></img><br /><br />
Figure 2: Agarose gel electrophoresis image from linker concentration comparison after<br />
ligation protocol adjustments.<br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Ori-KanR ligation to linker, then to ChlorR (as in Figure 1, Lane 4) using 10:1 ratio of <br />
linker to Ori. <br /><br />
Lane 3: As lane 2, with 50:1 ratio.<br /><br />
Lane 4: As lane 3, with 100:1 ratio. </p><br />
</div><br />
<a class="anchor" id="Assembly"></a><br />
<div class="block"><br />
<h2>The Full Assembly</h2><br />
<p>With our successful ligation protocol established, we moved on to attempting a full-scale <br />
assembly, with four genes (the quantity required for our proof-of-concept travelling salesman<br />
problem). In this gel, the four lanes show the successive addition of the four genes, which <br />
are, for the most part, successful. In each lane, there is some remainder of the previous <br />
products left behind, including (presumably) instances of strands that were incomplete in <br />
one reaction continuing to acquire genes in a successive one. Regardless, these incomplete <br />
genes represent only a small fraction of the total DNA. </p><br />
<p><img src="/wiki/images/3/37/2013-Alberta-Results-Figure_3.png" style="width:100%;"></img><br /><br />
Figure 3: Agarose gel electrophoresis image from full assembly test. <br /><br />
Lane 1: DNA Markers.<br /><br />
Lane 2: Ori to KanR ligation product.<br /><br />
Lane 3: Ori-KanR to linker to GFP ligation product.<br /><br />
Lane 4: Ori-KanR-Linker-GFP to linker to RFP ligation product.<br /><br />
Lane 5: Ori-KanR-Linker-GFP-Linker-RFP to linker to ChlorR ligation product. </p><br />
<p>The product plasmids from this assembly were transformed into a bacterial culture and <br />
grown on a Kan/Chlor plate to examine practical impact of the rate of incomplete ligations. <br />
The plate image is shown below – about 90% of the colonies display the desired RFP/GFP <br />
(orange colouration) phenotype indicating a perfect successful ligation of the plasmid. </p><br />
<img src="/wiki/images/4/4e/Ab_Assembly_efficiency.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Colour-Controls"></a><br />
<div class="block"><br />
<h2>Colour Controls</h2><br />
<p>In our planned, four-city proof-of-concept test (see the map below), there are exactly three <br />
possible solutions and three corresponding phenotypes: blue/green (dark green) bacteria <br />
with Amp/Chlor resistance, red/green (orange) bacteria with Chlor/Kan resistance, and <br />
red/blue (purple) bacteria with Amp/Kan resistance. </p><br />
<img src="/wiki/images/8/8d/2013Alberta-mapmaker-states.png" style="width:100%;"></img><br />
<p>To ensure we would be able to correctly identify plasmids based on phenotype we prepared <br />
a set of control plates, where bacteria grown from pure assemblies of the desired “route” <br />
plasmid were grown alongside bacteria possessing only one of the two colours from that <br />
route, for comparison purposes. The resulting plates can be seen above. </p><br />
</div><br />
<a class="anchor" id="Calibration"></a><br />
<div class="block"><br />
<h2>Initial Calibration</h2><br />
<p>In preparation for our initial travelling salesman problems, we attempted to discern the <br />
extent to which unexpected or unknown biases might affect the frequency of colonies <br />
growing with a particular gene.</p><br />
<p>In this test, we performed an assembly in which both GFP and aCP were included (in equal <br />
molar concentration) in the initial ligation onto the Ori, followed by a ligation of ChlorR, <br />
resulting in a mixture of Ori-GFP-ChlorR and Ori-aCP-ChlorR plasmids. We transformed these <br />
plasmids into a single bacterial culture, which we then spread on a Chlor-treated plate in <br />
order to count the resulting colonies. We repeated this test for each of the other four genes <br />
to be used in our proof-of-concept TSP, comparing each against GFP as a standard. This <br />
provided us with the following ratios of growth.</p><br />
<p>Table 1: 1GFP 6aCP<br /><img src="/wiki/images/5/5d/2013Alberta-Ratiotable.png" style="width:100%;"></img></p><br />
<p>We then attempted another assembly in which we calibrated for the bias. We used a 6:1 <br />
molar ratio of GFP to aCP in the new assembly, otherwise performing the experiment as <br />
before, and produced a new plate with a ratio of approximately 1:1 GFP colonies to aCP <br />
colonies. Although imperfect, this calibration was adequate for our proof-of-concept trial.</p><br />
</div><br />
<a class="anchor" id="TSP"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p> We have conducted a single successful travelling salesman problem following the procedure outlined in the project overview page. Relative to the previous assembly steps, the only key difference is that this time, several genes are included at each ligation step and at varying concentrations, so that the assembly produces a mix of plasmids, but favours some genes over others (creating a bias for shorter paths). See the overview page for more details on how this works. </p><br />
<p>This particular problem was based on a map of four cities in which four of the paths have an arbitrary unit distance of 1, and the remaining two paths have a distance of 4. Of the possible routes in this problem, one route has a total sum distance of 4, and the other two have distances of 10, making that route clearly preferable, and a suitable test of our biocomputer. The three possible routes, with correct gene-path assignment and distances listed for this problem, can be seen below. At each ligation step, we added a quantity of each gene based on the reciprocal of its distance, so that, for instance, the genes corresponding to paths of distance 4 had roughly one-quarter of the concentration (this value was then adjusted by our calibrations, as described above, to arrive at the actual concentration) of those with distance 1. </p><br />
<img src="/wiki/images/a/ab/2013Alberta-POP.png" style="width:100%;"></img><br />
<p>On the resulting plates, we counted 18 colonies corresponding to the ChlorR/GFP/aCP/AmpR route, and 21 colonies corresponding to the ChlorR/RFP/GFP/KanR route. For the optimal route, KanR/aCP/RFP/AmpR, we found 61 colonies, clearly identifying this as the solution to the problem. When the percentage of each of these three types of colonies on each plate is normalized to the best solution, the results of this trial are very close to the expected values calculated for this experiment. </p><br />
</div><br />
<a class="anchor" id="Adapt-POP"></a><br />
<div class="block"><br />
<h2>Can we adapt our POP to a much more complex problem?</h2><br />
<p>The ultimate limit of an approach such as this, depends upon the<br />
number of complete TSP solutions (plasmids) that can be clonally<br />
amplified through cell transformation. We estimate that solving a 15-city<br />
problem is within the realm of existing state-of-the-art, but not without<br />
major revisions to our POP work presented here. The 15-city problem is<br />
not trivial even by conventional computing standards. With 120 intercity<br />
links resulting in 87,178,291,200 possible solutions, 50 days would be<br />
required to identify the best solutions at a computational rate of 10,000<br />
solutions/second!</p><br />
<p>The challenges:</p><br />
<ol><br />
<li>In the POP, solutions are identified by visually<br />
determining the frequency of colonies exhibiting<br />
the appropriate path combinations represented by<br />
the three colour genes and the three drug<br />
resistance genes. Extending this approach to the<br />
15-city problem would require the acquisition of<br />
120 markers that are combined 87,178,291,200<br />
ways, well beyond the analytical resolution of<br />
standard plating methods.</li><br />
<li>A statistically significant sampling of complete<br />
solutions is well outside the plasmid transformation<br />
efficiencies of even the best competent cells<br />
available.</li><br />
<li>The precision and efficiency for assembling<br />
complete-solution plasmids (38 steps in all)<br />
remains to be tested.</li><br />
</ol><br />
<img src="/wiki/images/7/72/2013-Results_z1.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Revised-Strategy"></a><br />
<div class="block"><br />
<h2>A revised strategy</h2><br />
<p><b>Cities and Paths.</b> In the new approach we invert the role that DNA<br />
plays in defining cities and paths. Here, a city corresponds to a gene<br />
that complements an amino acid auxotrophy in E. coli (illustrated<br />
below). The city is therefore required for growth on defined media that<br />
lacks that amino acid. By extension, 15 different cities represented by<br />
15 a.a. auxotrophic markers would be required for survival of E. coli<br />
deficient for these genes when grown on media that lacks the<br />
corresponding amino acids. Complete plasmid solutions therefore are<br />
exclusively selected and amplified from their non-solution counterparts.<br />
Creating a 15-gene knockout in E. coli is not trivial but absolutely<br />
possible.</p><br />
<p>The ability to link any two city genes requires that each city has at<br />
its 5’ and 3’ ends, overhangs that are nonpalindromic,<br />
noncomplementary, and that are distinct in sequence from any of the 14<br />
other city genes.</p><br />
<p>The 120 path possibilities that are needed to link any two cities,<br />
are represented by a mixture of 120 synthetic duplex linkers where each<br />
linker has two different complementary ends that are capable of linking<br />
one of the 120 possible intercity pairs. Shorter intercity distances are<br />
favoured by adjusting the concentration of each linker in the mixture<br />
according to a new and improved weighting algorithm described below.<br />
We point out that in terms of economy, all 120 linkers can be produced<br />
from 30 oligos used in pair-wise combinations.</p><br />
<p>An unavoidable complication of this method is that any given city<br />
can occur more than once (at lower frequency) across the 15 available<br />
steps during sequential assembly (illustrated above for the three-city<br />
example). It should be noted however that any city duplication excludes<br />
the possibility of creating the complete set and will therefore be<br />
selected against post-transformation.</p><br />
<img src="/wiki/images/1/10/2013-Results_z2.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="DNA-Library"></a><br />
<div class="block"><br />
<h2>Creating a cosmid DNA library of that is highly biased for best<br />
solutions.</h2><br />
<p>To date, &lambda; phage-based recombinant libraries remain<br />
unprecedented in terms of the size and diversity of their DNA<br />
constituents. In its most advanced form, “cosmid” library kits are<br />
commercially available that produce 10<sup>10</sup> transformants. Cosmids retain<br />
the phage elements that are required for phage packaging and infection<br />
but lack the elements required for phage propagation and cell lysis. A<br />
plasmid origin allows them to replicate as plasmids.</p><br />
<p>Cosmids are constructed as linear molecules that begin and end<br />
with phage sequences the essential phage sequences(, &lambda;L and &lambda;R).<br />
Complementary 12-base overhangs that constitute the lambda cos and cos’<br />
sites are also required for efficient circularization once the cosmid has<br />
entered the cell.</p><br />
<p>In addition to its favourable tranformation properties, another<br />
attractive feature of using a cosmid-based system for TSP is that DNA<br />
molecules below a certain length threshold, package poorly, thereby<br />
contributing to the selection of full-length solutions.</p><br />
<p>An overview highlighting the key aspects of library creation is<br />
shown below. The assembly procedure uses magnetic beads where the<br />
cos’ sequence has been covalently linked. Asssembly begins with a cos- <br />
&lambda;L synthetic adapter that allows for the subsequent addition of &lambda;L. The<br />
addition of spacer sequences insure that total size of the construct is<br />
optimal for packaging (~50kB). Linker combinations are then added in<br />
alternation with city combinations until the city content is complete.<br />
Finally the construct is terminated with &lambda;R and a cos’ adapter. Following<br />
packaging cells are infected in selective liquid medium and the cosmid<br />
population is isolated for PCR analysis. The library is heavily biased 1)<br />
for complete solutions based on the assembly and packaging<br />
considerations already described and 2) for best solutions based on the<br />
path weights assigned to each linker addition step.</p><br />
<img src="/wiki/images/5/55/Results_z3.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="PCR"></a><br />
<div class="block"><br />
<h2>PCR-based identification of best solutions.</h2><br />
<p>The two types of data that is required for piecing best solutions together<br />
are 1) determining the cities that most frequently occupy each position<br />
from 1 to 15 and 2) determining the most frequently used intercity pairs<br />
as outlined below.</p><br />
<img src="/wiki/images/3/37/2013-Results_z4.PNG" style="width:100%;"></img><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Overview
Team:Alberta/Overview
2013-10-29T03:39:38Z
<p>MEsau: </p>
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<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview" class="active">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
</ul><br />
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<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
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<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
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<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
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<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Biological-Terms"><p>In Biological Terms</p></a><br />
<a href="#Finding-the-Path"><p>Finding the Path</p></a><br />
<a href="#Mapmakers"><p>MapMakers at Work</p></a><br />
<a href="#Weight"><p>Calculating Gene Concentration</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview" class="active"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Overview</p><br />
</div><br />
<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>MapMen is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:</p><br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Biological-Terms"></a><br />
<div class="block"><br />
<h2>In Biological Terms</h2><br />
<p>To take advantage of the considerable information processing power of biology, we must create biochemical analogues for all of the components of the original problem. We begin by assigning a symbolic reporter gene or selectable marker gene to each of the six paths in our example map. The assignment is arbitrary; which gene is used for which path does not matter as long as it creates some kind of observable phenotype. For example, the path connecting the northeast city and the northwest city is symbolized by a gene coding for ampicillin resistance. The path from the northeast to city to the southeast meanwhile, is symbolized by a gene coding for kanamycin resistance.</p><br />
<img src="/wiki/images/4/4c/Bio_terms.png" style="width:100%;"></img><br />
<p>Now, just as the travelling salesman might describe taking a particular route to his customers – leaving from the northeast origin city and taking the road to the southwest, then turning up the north road from there, then back down the southeast, before returning northward home from, we can also represent that series of paths as a sequence of genes: ChlorR, RFP, GFP, and KanR.</p><br />
<img src="/wiki/images/b/bd/Path_to_gene.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Finding-the-Path"></a><br />
<div class="block"><br />
<h2>Finding the Path</h2><br />
<p>Just as a computer using a brute force approach to the travelling salesman problem would test every route and tally the sum distance of the paths travelled, our biocomputer assembles a multitude of plasmids, representing every possible combination of paths, through a set of ligations that represent the legs of the salesman’s journey. In the first leg, we depart from the origin city along any of the available roads: AmpR, ChlorR, or KanR. In the plasmid production, we begin with a combinatorial ligation – one where all three of the genes are being ligated with origins of replication, but only one of the three is able to ligate onto each Ori, resulting in a collection of incomplete plasmids that each includes just one of the three genes. </p><br />
<center><img src="/wiki/images/9/95/AB_Genemap.png" style="width:35%;"></img></center><br />
<p>Following the first gene ligation, a short linker piece is added, signifying the city that has been reached – all of the linkers are identical, there is no differentiation of routes based on this component. In the second leg of the journey, we perform a ligation with three more genes, representing all of the possible paths the salesman might take next – three colour genes. Again, each growing plasmid can only incorporate one of the new genes, so we obtain a random assortment of incomplete plasmids that each include one antibiotic resistance from the first ligation and one colour gene from the third ligation. </p><br />
<img src="/wiki/images/7/7e/AB_Assemblyfull.png" style="width:100%;"></img><br />
<p>The third leg of the journey is identical to the second, incorporating an additional colour gene, and the final leg uses the three antibiotic genes once again. At the end of this process, we will have obtained a randomized distribution of 76 different kinds of plasmids representing all of the different possible permutations of the genes, capable of producing 18 unique phenotypes, and representing the six bi-directional solutions to the four-city travelling salesman problem.<p/><br />
</div><br />
<a class="anchor" id="Mapmakers"></a><br />
<div class="block"><br />
<h2>MapMakers at Work</h2><br />
<p>Once the plasmids have been produced, how can we use them to identify the correct solution? The answer is in the frequency with which each plasmid occurs: We create bias in the ligations during assembly so that genes that represent shorter paths are more likely to be incorporated into the plasmids, meaning in turn that the final product plasmids are more likely to be composed of several short-path genes. As a result, although we still expect to see plasmids representing every possible route, those plasmids that represent the shortest routes through the map will be much more common than plasmids representing lengthy routes. By identifying the most abundant plasmid, we identify the shortest route and thus the optimal solution. </p><br />
<p>The bias is introduced through the concentration of the reactants in each ligation. If a gene is meant to represent a short path, its concentration in the ligation will be higher than the others, and conversely, genes that are meant to represent lengthy paths will be included in lower concentrations than the others. As a result, at any given ligation step, the gene symbolizing the shortest available path is more likely to be incorporated. Among the product plasmids, genes are incorporated at a rate inversely proportional to their length. The concentration used for each gene in the ligation is described by the expression: –ln[Gene]∝(path distance)</p><br />
<img src="/wiki/images/9/95/Proportions.png" style="width:100%;"></img><br />
<p>To identify which of the plasmids is most frequent, the products are transformed into a bacterial culture. Because each of the genes produces an easily interpreted phenotype, this allows us to infer the most frequently transformed plasmid from the frequency of the colonies produced on agar plates. The plasmid carried by any given colony on the plates below can be readily identified by the combination of the colony colour (purple colonies have RFP and aCP, orange colonies have RFP and GFP, and green colonies have GFP and aCP), and the antibiotic resistances it exhibits, which are inferred from the plate on which it is growing. As an example, a purple colony growing on the kan/amp plate must have the Amp-Red-Blue-Kan-plasmid shown in the first column below.<p/><br />
<img src="/wiki/images/6/6d/Ab_Solution_identification.png" style="width:100%;"></img><br />
<p>Many of the colonies do not correspond to any valid route. For instance, an orange colony on the kan/amp plate has the plasmid Amp-Red-Green-Kan, which does not describe a valid circuit visiting each city exactly once – but because we can tell that this is an invalid solution, we would not count this colony when assessing the frequency of the valid plasmids. Any four-city travelling salesman problem has just three unique solutions, and so there are only three phenotypes that must be counted: purple kan/amp, orange kan/chlor, and green amp/chlor. The colonies of these three phenotypes are counted and compared, and the most frequently occurring plasmid is the optimal solution! </p><br />
</div><br />
<a class="anchor" id="Weight"></a><br />
<div class="block"><br />
<h2>Calculating Gene Concentration</h2><br />
<img src="/wiki/images/5/57/2013Alberta_New_algorithm.png" style="width:100%;"></img><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Background
Team:Alberta/Background
2013-10-29T03:38:55Z
<p>MEsau: </p>
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<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><a href="/Team:Alberta/Background" class="active">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
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<li><a href="/Team:Alberta/Team">Roster</a></li><br />
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<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Real-World"><p>Real-World Issues</p></a><br />
<a href="#Computational"><p>The Computational Wall</p></a><br />
<a href="#Biocomputing"><p>Why Biocomputing?</p></a><br />
<a href="#Road"><p>A Long Road </p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background" class="active"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Background</p><br />
</div><br />
<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>MapMen is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:<br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Real-World"></a><br />
<div class="block"><br />
<h2>Real-World Issues</h2><br />
<p>The TSP is named after the concept of a hypothetical salesman who is planning a route to visit his <br />
customers in various neighbouring towns, but wants to maximize profits by using the shortest route — a <br />
helpful example to illustrate the usefulness of the problem: businesses around the world employ TSP-solving <br />
or related problem-solving software to help optimize their travelling needs, including in particular large <br />
courier companies that need to delivery millions of packages daily, and must reduce the expense of delivery <br />
vehicles and cut down travel time in any way possible, but also airliners, postal services, consumer GPS <br />
route-planning software, video-game pathfinding AI, and even electronics manufacture, in which a robot <br />
soldering arm must have an efficient path through the solder points to ensure maximum production over time. <br />
</p><br />
</div><br />
<a class="anchor" id="Computational"></a><br />
<div class="block"><br />
<h2>The Computational Wall</h2><br />
<p>The TSP is not only practically valuable, but also mathematically significant, because it belongs to a <br />
class of problems that are considered computationally difficult. The key difficulty with the TSP is due to <br />
the fact that it is an optimization problem: while for practical purposes any decent, short route is <br />
acceptable, a given TSP is nevertheless only considered "solved" when one verifies that one has obtained the <br />
shortest possible route. Mathematical verification of this sort requires what is called a "brute force" <br />
approach, in which one explores each and every possible route, tallying the total distance of each one, and <br />
then compares them all directly to guarantee the optimal route has been identified. As one increases the <br />
number of cities that must be included in the route, the time required for the brute-force approach becomes <br />
impossibly large.</p><br />
<img src="/wiki/images/9/9d/TSPcompWall.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Biocomputing"></a><br />
<div class="block"><br />
<h2>Why Biocomputing?</h2><br />
<p>Through synthetic biology, the creation of biological computers has opened a new avenue of possibility for <br />
solving TSPs more rapidly: using DNA molecules and bacterial cells as processors, one can compute billions <br />
of routes simultaneously, drastically reducing the time required through this massively parallel approach. <br />
By employing far more processors than there are routes through a given network, the processing time can be <br />
reduced to a standstill. A biological computer is also unique because it can solve problems stochastically: <br />
while every possible route is explored by the computer, preferable routes (short ones) will predominate <br />
among the generated products, allowing identification of the optimal route by population, rather than by a <br />
slower, deterministic approach. </p><br />
</div><br />
<a class="anchor" id="Road"></a><br />
<div class="block"><br />
<h2>A Long Road</h2><br />
<p>A number of previous attempts have been made to produce biocomputer solutions to the TSP, often involving pure DNA computing with no living organism present, including attempts by Leonard Adleman of RSA encryption fame, as well as previous efforts by the Davidson College/Missouri Western State University iGEM team, whose 2006 entry attempted to solve another challenging computational problem called the Burnt Pancake Problem, and in 2007 entered a DNA computing solution for the Hamiltonian Path Problem. Though related to the TSP, the Hamiltonian Path Problem attempts to discern if there is any possible route through a network, rather than picking the shortest possible one.</p><br />
<img src="/wiki/images/d/d4/Hgp_vs_tsp.png" style="width:100%;"></img><br />
<p>MapMen represents the latest in a line of attempts to refine the biological approach and create ever- increasingly powerful biological computers – and is the first of its kind to employ living cells to solve a travelling salesman problem. </p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
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</body><br />
</html><br />
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For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
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<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
== '''Overall project''' ==<br />
<br />
Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
=== Part 2 ===<br />
<br />
<br />
<br />
<br />
<br />
=== The Experiments ===<br />
<br />
<br />
<br />
<br />
=== Part 3 ===<br />
<br />
<br />
<br />
<br />
== Results ==<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta
Team:Alberta
2013-10-29T03:38:12Z
<p>MEsau: </p>
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<li><a href="/Team:Alberta/Results">Results</a></li><br />
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<img src=" /wiki/images/2/2d/Background_icon.png " align="left" width="50" height="50"></img>Curious about the possibilities of biocomputing? Need of a crash course on travelling salesman problems? Visit our <a href="https://2013.igem.org/Team:Alberta/Background">background page</a> for more information on the real-world applications of our project.<br />
<br><br />
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<img src="/wiki/images/thumb/b/bf/Workings_icon.png/610px-Workings_icon.png " align="left" width="50" height="50"></img><br />
Want to get straight to the details of what Team Alberta has been working on this summer? Read up in the <a href="https://2013.igem.org/Team:Alberta/Overview">overview</a> and <a href="https://2013.igem.org/Team:Alberta/Results">results</a> pages to see what we've achieved.<br />
<br><br />
<br><br />
<img src=" /wiki/images/thumb/f/f6/Peoples_icon.png/618px-Peoples_icon.png" align="left" width="50" height="50"></img>Or maybe you'd like to get to know the team itself, those who have helped us along and those we've helped in turn? See the <a href="https://2013.igem.org/Team:Alberta/Team">team roster</a>, <a href="https://2013.igem.org/Team:Alberta/Attributions">sponsors</a> and <a href="https://2013.igem.org/Team:Alberta/Outreach">outreach</a> pages to meet everyone who's participated.<br />
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<!--div class="block"><br />
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<h3 class="centered"><br />
Welcome to the Team Alberta website! Our project pushes the limits of Synthetic Biology to create massively parallel, highly selective biological computers. <br />
</h3><br /><br />
<img src="/wiki/images/e/e8/Mapmaker-banner.jpg"<br />
style="width:85%;"></img><br />
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For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
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[[Image:Alberta_logo.png|500px|center]]<br />
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Team Alberta represents the University of Alberta, from Edmonton. Our project, "The Littlest Mapmakers", is an attempt to create a biological computer capable of solving the Traveling Salesman Problem</p></center></font></strong></html><br />
<br />
----<br />
<br />
<br />
<html><br />
<font size=3>The traveling salesman problem is a mathematical optimization problem that was first formally described in 1930, and has been intensively studied in the computer sciences as a benchmark for optimization algorithms. The problem asks: <br />
<html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; background-color: #ffffff;"><br />
<div id="template" style="text-align: center; color: #000000; padding: 5px;"><br />
Given a set of cities (or other destinations), and a list of the distances (or the travel time, fuel consumption, et cetera) between each pair of those cities, what is the shortest possible route that travels to every city exactly once, and then returns to the origin city?</div><br />
</div><br />
</html><br />
In our project, we use DNA to compute solutions by converting all of the elements of the problem into representative sequences of DNA: cities become selectable marker genes (specifically, antibiotic resistance genes), paths between the cities become short, sticky-ended linkers (each of which is only able to ligate to two specific “city” strands), and the distance of a given path is represented by the concentration of the corresponding linker in solution. These pieces of DNA are successively ligated together to produce plasmids that signify “routes”, where the order in which the genes appear in the plasmid indicates the order in which the cities are visited. <br />
{|align="center"<br />
|[[Image:sample_product.png|300px]][[Image:sample_route.png|650px]]<br />
|}<br />
<html><font size=3>The resulting plasmids are transformed into a bacterial culture, so that we can select for only those plasmids that include every city in the list. Then, plasmid DNA is extracted from the surviving bacterial colonies and analyzed to determine which plasmid (and thus which route) occurred the most frequently. This route, the one most favoured by the ligation reactions, is the optimal route!</font></html><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
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<html><a class="twitter-timeline" href="https://twitter.com/iGEMAlberta" data-widget-id="368908364702437377">Tweets by @iGEMAlberta</a><br />
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MEsau
http://2013.igem.org/Team:Alberta/Community
Team:Alberta/Community
2013-10-29T03:35:51Z
<p>MEsau: </p>
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<li><a href="/Team:Alberta/Results">Results</a></li><br />
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</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Outreach"><p>Outreach</p></a><br />
<a href="/Team:Alberta/Community" class="active"><p>Community</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Community</p><br />
</div><br />
<div class="block"><br />
<p><b>Get an inside look at the project by following us on social media.<b></p><br />
<p style="float:left;margin-left:85px;"><a href="https://twitter.com/iGEMAlberta"><img src="/wiki/images/thumb/e/e8/Twit.png/120px-Twit.png" style="height:150px;" alt="Twitter"></img></a><br />
<a href="https://www.facebook.com/pages/University-of-Alberta-iGEM-Team/117860431757664"><img src="/wiki/images/2/2b/Facebook-icon-256x256.png" style="height:150px;" alt="Facebook"></img></a></a><br />
<a href="http://statigr.am/tag/igemalberta2013"><img src="/wiki/images/9/93/Instagram-icon-256x256.png" style="height:150px;" alt="Instagram"></img></a></p><br />
<div class="clear"></div><br />
<div class="centered"><br />
<a class="twitter-timeline" href="https://twitter.com/iGEMAlberta" data-widget-id="368908364702437377">Tweets by @iGEMAlberta</a><br />
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Community
Team:Alberta/Community
2013-10-29T03:35:21Z
<p>MEsau: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
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.navbar {<br />
width:963px;<br />
margin:60px auto;<br />
position:fixed;<br />
top:70px;<br />
z-index:4;<br />
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left:-6px;<br />
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.centered {<br />
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.thumbnails {<br />
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.thumbnail {<br />
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.thumbnail img{<br />
/* ... */<br />
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.thumbnail img:hover {<br />
transform:scale(4,4);<br />
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<br />
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a.anchor{<br />
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</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="humanpractices" href="#" class="active">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community" class="active">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Outreach"><p>Outreach</p></a><br />
<a href="/Team:Alberta/Community" class="active"><p>Community</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Community</p><br />
</div><br />
<div class="block"><br />
<p><b>Get an inside look at the project by following us on social media.<b></p><br />
<p style="float:left;margin-left:85px;"><a href="https://twitter.com/iGEMAlberta"><img src="/wiki/images/thumb/e/e8/Twit.png/120px-Twit.png" style="height:150px;" alt="Twitter"></img></a><br />
<a href="https://www.facebook.com/pages/University-of-Alberta-iGEM-Team/117860431757664"><img src="/wiki/images/2/2b/Facebook-icon-256x256.png" style="height:150px;" alt="Facebook"></img></a></a><br />
<a href="http://statigr.am/tag/igemalberta2013"><img src="/wiki/images/9/93/Instagram-icon-256x256.png" style="height:150px;" alt="Instagram"></img></a></p></div><br />
<div class="clear"></div><br />
<div class="block"><br />
<div class="centered"><br />
<a class="twitter-timeline" href="https://twitter.com/iGEMAlberta" data-widget-id="368908364702437377">Tweets by @iGEMAlberta</a><br />
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script><br />
</div><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Community
Team:Alberta/Community
2013-10-29T03:34:42Z
<p>MEsau: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
.titlebar {<br />
height:130px;<br />
width:100%;<br />
}<br />
.bin {<br />
background:url('/wiki/images/e/e4/2013AlbertaBackground.png');<br />
background-size:100% auto;<br />
padding-top:20px;<br />
}<br />
@-moz-document url-prefix() {<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
margin-left:-155px;<br />
}<br />
}<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
}<br />
.block {<br />
background-color:white;<br />
border:1px grey solid;<br />
padding:10px;<br />
margin:10px;<br />
border-radius:5px;<br />
box-shadow: 0px 0px 30px #444444;<br />
}<br />
.titlebar {<br />
position:fixed;<br />
top:0px;<br />
height:130px;<br />
margin-left:-5px;<br />
width:975px;<br />
z-index:2;<br />
background-color:#FFF;<br />
}<br />
.content-title {<br />
text-align:center;<br />
font-size:3em;<br />
}<br />
.titlebar h3, h4 {<br />
text-align:center;<br />
}<br />
.sidebar {<br />
position: fixed;<br />
top: 157px;<br />
float: left;<br />
z-index: 3;<br />
padding: 10px 10px 10px 10px;<br />
width: 230px;<br />
}<br />
.sidebar_block {<br />
background-color:white;<br />
margin:1px;<br />
border:1px grey solid;<br />
padding:5px 10px 5px 10px;<br />
border-radius:5px;<br />
box-shadow: 0px 0px 20px #444444;<br />
}<br />
.main {<br />
position:relative;<br />
float:right;<br />
width:720px;<br />
}<br />
.clear {<br />
clear:both;<br />
}<br />
.ualberta-logo {<br />
position:fixed;<br />
margin-left:70px;<br />
margin-top:-70px;<br />
width:180px;<br />
}<br />
.igem-logo {<br />
position:fixed;<br />
margin-left:650px;<br />
margin-top:-95px;<br />
width: 150px;<br />
}<br />
.igem-logo img {<br />
width:210px;<br />
}<br />
.igem-bar {<br />
position:relative;<br />
float:right;<br />
}<br />
.igem-bar a {<br />
padding:0 !important;<br />
}<br />
.igem-bar img {<br />
height:38px;<br />
}<br />
.tooltip {<br />
width:100%;<br />
}<br />
.tooltip .saying {<br />
background: #EEE;<br />
color: #444;<br />
left: 100px;<br />
margin-bottom: 15px;<br />
opacity: 0;<br />
padding: 20px;<br />
position: absolute;<br />
visibility: hidden;<br />
min-width:200px;<br />
max-width:500px;<br />
-webkit-transform: translateX(10px);<br />
-moz-transform: translateX(10px);<br />
-ms-transform: translateX(10px);<br />
-o-transform: translateX(10px);<br />
transform: translateX(10px);<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
-ms-transition: all .25s ease-out;<br />
-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
-webkit-border-radius:6px;<br />
-moz-border-radius:6px;<br />
-ms-border-radius:6px;<br />
-o-border-radius:6px;<br />
border-radius:6px;<br />
-webkit-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
-moz-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
-ms-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
-o-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
}<br />
.tooltip .saying {<br />
content: " ";<br />
top:100px;<br />
display:block;<br />
left: 200px;<br />
max-height:1000px;<br />
position: absolute;<br />
} <br />
.tooltip .saying:after {<br />
border-bottom: solid transparent 10px;<br />
border-top: solid transparent 10px;<br />
border-right: solid #EEE 10px;<br />
left: 10px;<br />
top:10px;<br />
content: "";<br />
margin-left:-16px;<br />
position: absolute;<br />
width: 0;<br />
max-height:1000px;<br />
display:block;<br />
}<br />
.tooltip:hover .saying {<br />
opacity: 1;<br />
visibility: visible;<br />
-webkit-transform: translateX(0px);<br />
-moz-transform: translateX(0px);<br />
-ms-transform: translateX(0px);<br />
-o-transform: translateX(0px);<br />
transform: translateX(0px);<br />
}<br />
.active {<br />
color:#04acec !important;<br />
}<br />
.navbar, .navbar ul {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.navbar {<br />
width:963px;<br />
margin:60px auto;<br />
position:fixed;<br />
top:70px;<br />
z-index:4;<br />
border: 1px solid #DDD;<br />
background-color:#FFF;<br />
background-image: -moz-linear-gradient(#FFF, #DDD);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#DDD));<br />
background-image: -webkit-linear-gradient(#FFF, #DDD);<br />
background-image: -ms-linear-gradient(#FFF, #DDD);<br />
background-image: linear-gradient(#FFF, #DDD);<br />
-moz-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
-webkit-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
zoom:1;<br />
}<br />
.navbar:before, .navbar:after {<br />
content: "";<br />
display: table;<br />
}<br />
.navbar:after {<br />
clear:both;<br />
}<br />
.navbar li {<br />
float:left;<br />
border-right:1px solid #CCC;<br />
-moz-box-shadow:1px 0 0 #EEE;<br />
-webkit-box-shadow: 1px 0 0 #EEE;<br />
box-shadow: 1px 0 0 #EEE;<br />
position: relative;<br />
}<br />
.navbar a {<br />
float: left;<br />
padding: 12px 30px;<br />
color: #444;<br />
font: bold 12px Arial, Helvetica;<br />
text-decoration:none;<br />
/*text-shadow: 0 1px 0 #333;*/<br />
}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
color:#BBB;<br />
}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
opacity: 0;<br />
visibility: hidden;<br />
position:absolute;<br />
top:38px;<br />
left:0;<br />
z-index:1;<br />
background:#FFF;<br />
background: -moz-linear-gradient(#FFF, #CCC);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#CCC));<br />
background: -webkit-linear-gradient(#FFF, #CCC);<br />
background: -o-linear-gradient(#FFF, #CCC);<br />
background: -ms-linear-gradient(#FFF, #CCC);<br />
background: linear-gradient(#FFF, #CCC);<br />
-moz-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-webkit-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-box-shadow:0 -1px 0 rgba(255,255,255,.3);<br />
-moz-border-radius: 3px;<br />
-webkit-border-radius: 3px;<br />
border-radius: 3px;<br />
-webkit-transition: all .2s ease-in-out;<br />
-moz-transition: all .2s ease-in-out;<br />
-ms-transition: all .2s ease-in-out;<br />
-o-transition: all .2s ease-in-out;<br />
transition: all .2s ease-in-out;<br />
}<br />
.navbar li:hover > ul {<br />
opacity: 1;<br />
visibility: visible;<br />
margin:0;<br />
}<br />
.navbar ul ul {<br />
top:0;<br />
left:150px;<br />
margin:0 0 0 20px;<br />
_margin:0;/*IE6 only*/<br />
-moz-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
-webkit-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
}<br />
.navbar ul li {<br />
float:none;<br />
display:block;<br />
border:0;<br />
_line-height:0; /*IE6 only*/<br />
-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
-webkit-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
}<br />
.navbar ul li:last-child {<br />
-moz-box-shadow:none;<br />
-webkit-box-shadow:none;<br />
box-shadow:none;<br />
}<br />
.navbar ul a {<br />
padding:10px;<br />
width:130px;<br />
_height:10px;/*IE6 only*/<br />
display:block;<br />
white-space:nowrap;<br />
float:none;<br />
text-transform:none;<br />
}<br />
.navbar ul a:hover {<br />
background-color:#0186ba;<br />
background-image: -moz-linear-gradient(#04acec, #0186ba);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#04acec), to(#0186ba));<br />
background-image: -webkit-linear-gradient(#04acec, #0186ba);<br />
background-image: -ms-linear-gradient(#04acec, #0186ba);<br />
background-image: linear-gradient(#04acec, #0186ba);<br />
}<br />
.navbar ul li:first-child > a {<br />
-moz-border-radius: 3px 3px 0 0;<br />
-webkit-border-radius: 3px 3px 0 0;<br />
border-radius: 3px 3px 0 0;<br />
}<br />
.navbar ul li:first-child > a:after {<br />
content:'';<br />
position:absolute;<br />
left:40px;<br />
top:-6px;<br />
border-left:6px solid transparent;<br />
border-right:6px solid transparent;<br />
border-bottom:6px solid #FFF;<br />
}<br />
.navbar ul ul li:first-child a:after {<br />
left:-6px;<br />
top:50%;<br />
margin-top:-6px;<br />
border-left:0;<br />
border-bottom:6px solid transparent;<br />
border-top: 6px solid transparent;<br />
border-right:6px solid #3b3b3b;<br />
}<br />
.navbar ul li:first-child a:hover:after {<br />
border-bottom-color: #04acec;<br />
}<br />
.navbar ul ul li:first-child a:hover:after {<br />
border-right-color: #0299d3;<br />
border-bottom-color:transparent;<br />
}<br />
.navbar ul li:last-child > a {<br />
-moz-border-radius: 0 0 3px 3px;<br />
-webkit-border-radius: 0 0 3px 3px;<br />
border-radius: 0 0 3px 3px;<br />
}<br />
.centered {<br />
text-align:center;<br />
}<br />
.centered-well {<br />
text-align:center;<br />
width:80%;<br />
margin:0 auto;<br />
padding:5px;<br />
background-color:#CCC;<br />
border-radius:6px;<br />
-moz-border-radius:6px;<br />
-o-border-radius:6px;<br />
-webkit-border-radius:6px;<br />
}<br />
.thumbnails {<br />
padding: 35px;<br />
width:700px;<br />
margin:0 auto;<br />
}<br />
.thumbnail {<br />
position:relative;<br />
display:inline-block;<br />
left:180px;<br />
}<br />
.thumbnail img{<br />
/* ... */<br />
height:100px;<br />
position:relative;<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
-ms-transition: all .25s ease-out;<br />
-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
} <br />
.thumbnail img:hover {<br />
transform:scale(4,4);<br />
-webkit-transform:scale(4,4);<br />
-moz-transform:scale(4,4);<br />
-ms-transform:scale(4,4);<br />
-o-transform:scale(4,4);<br />
z-index:999;<br />
background-color:white;<br />
border:solid 2px #CCC;<br />
border-radius:1px;<br />
-moz-border-radius:1px;<br />
-o-border-radius:1px;<br />
-webkit-border-radius:1px;<br />
-moz-box-shadow: 0px 0px 30px #000;<br />
-o-box-shadow: 0px 0px 30px #000;<br />
-webkit-box-shadow: 0px 0px 30px #000;<br />
box-shadow: 0px 0px 30px #000;<br />
<br />
} <br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="humanpractices" href="#" class="active">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community" class="active">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Outreach"><p>Outreach</p></a><br />
<a href="/Team:Alberta/Community" class="active"><p>Community</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Community</p><br />
</div><br />
<div class="block"><br />
<p><b>Get an inside look at the project by following us on social media.<b></p><br />
<br />
<p style="float:left;margin-left:85px;"><a href="https://twitter.com/iGEMAlberta"><img src="/wiki/images/thumb/e/e8/Twit.png/120px-Twit.png" style="height:150px;" alt="Twitter"></img></a><br />
<a href="https://www.facebook.com/pages/University-of-Alberta-iGEM-Team/117860431757664"><img src="/wiki/images/2/2b/Facebook-icon-256x256.png" style="height:150px;" alt="Facebook"></img></a></a><br />
<a href="http://statigr.am/tag/igemalberta2013"><img src="/wiki/images/9/93/Instagram-icon-256x256.png" style="height:150px;" alt="Instagram"></img></a></p><br />
</div><br />
<div class="block"><br />
<div class="centered"><br />
<a class="twitter-timeline" href="https://twitter.com/iGEMAlberta" data-widget-id="368908364702437377">Tweets by @iGEMAlberta</a><br />
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script><br />
</div><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Community
Team:Alberta/Community
2013-10-29T03:34:22Z
<p>MEsau: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
.titlebar {<br />
height:130px;<br />
width:100%;<br />
}<br />
.bin {<br />
background:url('/wiki/images/e/e4/2013AlbertaBackground.png');<br />
background-size:100% auto;<br />
padding-top:20px;<br />
}<br />
@-moz-document url-prefix() {<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
margin-left:-155px;<br />
}<br />
}<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
}<br />
.block {<br />
background-color:white;<br />
border:1px grey solid;<br />
padding:10px;<br />
margin:10px;<br />
border-radius:5px;<br />
box-shadow: 0px 0px 30px #444444;<br />
}<br />
.titlebar {<br />
position:fixed;<br />
top:0px;<br />
height:130px;<br />
margin-left:-5px;<br />
width:975px;<br />
z-index:2;<br />
background-color:#FFF;<br />
}<br />
.content-title {<br />
text-align:center;<br />
font-size:3em;<br />
}<br />
.titlebar h3, h4 {<br />
text-align:center;<br />
}<br />
.sidebar {<br />
position: fixed;<br />
top: 157px;<br />
float: left;<br />
z-index: 3;<br />
padding: 10px 10px 10px 10px;<br />
width: 230px;<br />
}<br />
.sidebar_block {<br />
background-color:white;<br />
margin:1px;<br />
border:1px grey solid;<br />
padding:5px 10px 5px 10px;<br />
border-radius:5px;<br />
box-shadow: 0px 0px 20px #444444;<br />
}<br />
.main {<br />
position:relative;<br />
float:right;<br />
width:720px;<br />
}<br />
.clear {<br />
clear:both;<br />
}<br />
.ualberta-logo {<br />
position:fixed;<br />
margin-left:70px;<br />
margin-top:-70px;<br />
width:180px;<br />
}<br />
.igem-logo {<br />
position:fixed;<br />
margin-left:650px;<br />
margin-top:-95px;<br />
width: 150px;<br />
}<br />
.igem-logo img {<br />
width:210px;<br />
}<br />
.igem-bar {<br />
position:relative;<br />
float:right;<br />
}<br />
.igem-bar a {<br />
padding:0 !important;<br />
}<br />
.igem-bar img {<br />
height:38px;<br />
}<br />
.tooltip {<br />
width:100%;<br />
}<br />
.tooltip .saying {<br />
background: #EEE;<br />
color: #444;<br />
left: 100px;<br />
margin-bottom: 15px;<br />
opacity: 0;<br />
padding: 20px;<br />
position: absolute;<br />
visibility: hidden;<br />
min-width:200px;<br />
max-width:500px;<br />
-webkit-transform: translateX(10px);<br />
-moz-transform: translateX(10px);<br />
-ms-transform: translateX(10px);<br />
-o-transform: translateX(10px);<br />
transform: translateX(10px);<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
-ms-transition: all .25s ease-out;<br />
-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
-webkit-border-radius:6px;<br />
-moz-border-radius:6px;<br />
-ms-border-radius:6px;<br />
-o-border-radius:6px;<br />
border-radius:6px;<br />
-webkit-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
-moz-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
-ms-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
-o-box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
box-shadow: 2px 2px 6px rgba(0, 0, 0, 0.28);<br />
}<br />
.tooltip .saying {<br />
content: " ";<br />
top:100px;<br />
display:block;<br />
left: 200px;<br />
max-height:1000px;<br />
position: absolute;<br />
} <br />
.tooltip .saying:after {<br />
border-bottom: solid transparent 10px;<br />
border-top: solid transparent 10px;<br />
border-right: solid #EEE 10px;<br />
left: 10px;<br />
top:10px;<br />
content: "";<br />
margin-left:-16px;<br />
position: absolute;<br />
width: 0;<br />
max-height:1000px;<br />
display:block;<br />
}<br />
.tooltip:hover .saying {<br />
opacity: 1;<br />
visibility: visible;<br />
-webkit-transform: translateX(0px);<br />
-moz-transform: translateX(0px);<br />
-ms-transform: translateX(0px);<br />
-o-transform: translateX(0px);<br />
transform: translateX(0px);<br />
}<br />
.active {<br />
color:#04acec !important;<br />
}<br />
.navbar, .navbar ul {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.navbar {<br />
width:963px;<br />
margin:60px auto;<br />
position:fixed;<br />
top:70px;<br />
z-index:4;<br />
border: 1px solid #DDD;<br />
background-color:#FFF;<br />
background-image: -moz-linear-gradient(#FFF, #DDD);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#DDD));<br />
background-image: -webkit-linear-gradient(#FFF, #DDD);<br />
background-image: -ms-linear-gradient(#FFF, #DDD);<br />
background-image: linear-gradient(#FFF, #DDD);<br />
-moz-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
-webkit-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
zoom:1;<br />
}<br />
.navbar:before, .navbar:after {<br />
content: "";<br />
display: table;<br />
}<br />
.navbar:after {<br />
clear:both;<br />
}<br />
.navbar li {<br />
float:left;<br />
border-right:1px solid #CCC;<br />
-moz-box-shadow:1px 0 0 #EEE;<br />
-webkit-box-shadow: 1px 0 0 #EEE;<br />
box-shadow: 1px 0 0 #EEE;<br />
position: relative;<br />
}<br />
.navbar a {<br />
float: left;<br />
padding: 12px 30px;<br />
color: #444;<br />
font: bold 12px Arial, Helvetica;<br />
text-decoration:none;<br />
/*text-shadow: 0 1px 0 #333;*/<br />
}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
color:#BBB;<br />
}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
opacity: 0;<br />
visibility: hidden;<br />
position:absolute;<br />
top:38px;<br />
left:0;<br />
z-index:1;<br />
background:#FFF;<br />
background: -moz-linear-gradient(#FFF, #CCC);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#CCC));<br />
background: -webkit-linear-gradient(#FFF, #CCC);<br />
background: -o-linear-gradient(#FFF, #CCC);<br />
background: -ms-linear-gradient(#FFF, #CCC);<br />
background: linear-gradient(#FFF, #CCC);<br />
-moz-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-webkit-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-box-shadow:0 -1px 0 rgba(255,255,255,.3);<br />
-moz-border-radius: 3px;<br />
-webkit-border-radius: 3px;<br />
border-radius: 3px;<br />
-webkit-transition: all .2s ease-in-out;<br />
-moz-transition: all .2s ease-in-out;<br />
-ms-transition: all .2s ease-in-out;<br />
-o-transition: all .2s ease-in-out;<br />
transition: all .2s ease-in-out;<br />
}<br />
.navbar li:hover > ul {<br />
opacity: 1;<br />
visibility: visible;<br />
margin:0;<br />
}<br />
.navbar ul ul {<br />
top:0;<br />
left:150px;<br />
margin:0 0 0 20px;<br />
_margin:0;/*IE6 only*/<br />
-moz-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
-webkit-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
}<br />
.navbar ul li {<br />
float:none;<br />
display:block;<br />
border:0;<br />
_line-height:0; /*IE6 only*/<br />
-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
-webkit-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
}<br />
.navbar ul li:last-child {<br />
-moz-box-shadow:none;<br />
-webkit-box-shadow:none;<br />
box-shadow:none;<br />
}<br />
.navbar ul a {<br />
padding:10px;<br />
width:130px;<br />
_height:10px;/*IE6 only*/<br />
display:block;<br />
white-space:nowrap;<br />
float:none;<br />
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}<br />
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}<br />
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.thumbnail img:hover {<br />
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-o-transform:scale(4,4);<br />
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background-color:white;<br />
border:solid 2px #CCC;<br />
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-o-border-radius:1px;<br />
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-moz-box-shadow: 0px 0px 30px #000;<br />
-o-box-shadow: 0px 0px 30px #000;<br />
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box-shadow: 0px 0px 30px #000;<br />
<br />
} <br />
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display: block; <br />
position: relative; <br />
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visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><a href="/Team:Alberta">Home</a></li><br />
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<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
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<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
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<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="humanpractices" href="#" class="active">Human Practices</a><br />
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<li><a href="/Team:Alberta/Community" class="active">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
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</ul><br />
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</ul><br />
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<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
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<a href="/Team:Alberta/Community" class="active"><p>Community</p></a><br />
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<p class="content-title">Community</p><br />
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<p><b>Get an inside look at the project by following us on social media.<b></p><br />
<br />
<p style="float:left;margin-left:85px;"><a href="https://twitter.com/iGEMAlberta"><img src="/wiki/images/thumb/e/e8/Twit.png/120px-Twit.png" style="height:150px;" alt="Twitter"></img></a><br />
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<a href="http://statigr.am/tag/igemalberta2013"><img src="/wiki/images/9/93/Instagram-icon-256x256.png" style="height:150px;" alt="Instagram"></img></a></p><br />
<div class="clear"></div><br />
<div class="block"><br />
<div class="centered"><br />
<a class="twitter-timeline" href="https://twitter.com/iGEMAlberta" data-widget-id="368908364702437377">Tweets by @iGEMAlberta</a><br />
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<div class="clear"></div><br />
</div><br />
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</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Attributions
Team:Alberta/Attributions
2013-10-29T03:32:39Z
<p>MEsau: </p>
<hr />
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.navbar ul ul li:first-child a:after {<br />
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/* ... */<br />
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-moz-box-shadow: 0px 0px 30px #000;<br />
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<br />
}<br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions" class="active">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions" class="active"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Attributions</p><br />
</div><br />
<div class="block"><br />
<p>All of the experimental work described herein was performed by the team with technical support from Prof. Ellison’s technician, <b>Nien-tsu Tseng (Rick)</b>. The TSP concept was inspired by the <b>Missouri-Davidson 2007 iGEM team</b> who broke the ice with their work on the Hamiltonian variation of TSB problem. The experimental approaches used here evolved over discussions with our supervisors during group meetings. The correct weighting algorithm that relates city path lengths to linker concentrations was developed by <b>Dr. Doug Ridgway</b>, a supervisor of the 2012 iGEM team. The plasmids used to create TSB compatible parts by PCR were a gift from <b>Genomikon Inc</b>. <br />
The creation of the violacin bricks that we will use in the test of the 5-city TSB would not have been possible without the violacein operon biobrick (K274002) that was created, submitted and carefully characterized by the <b>Cambridge 2009 iGEM team</b>. Wiki coding and design implementation was done by <b>Timo Hohn</b>, (B.Sc. in Computer Engineering).<br />
</p><br />
<br><br />
<p>Thanks to these individuals for donating their time and talents!</p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Accomplishments
Team:Alberta/Accomplishments
2013-10-29T03:32:09Z
<p>MEsau: </p>
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<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments" class="active">Accomplishments</a></li><br />
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<li><a id="team" href="#">Team</a><br />
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<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
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<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments" class="active"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
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<p class="content-title">Accomplishments</p><br />
</div><br />
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<img src="/wiki/images/a/af/2013-Accomplishments.PNG" style="width:100%;"></img><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<h2> Awards<br />
</h2><br />
<br />
<img src="/wiki/images/thumb/9/95/Presentationpic.jpg/800px-Presentationpic.jpg " style="width:50%" align="right"></img><br />
<br />
<p>Team Alberta was thrilled to receive recognition at the North American Regional Jamboree competition:</p><br />
<br><br />
<p><b>Best Presentation</b> - in the undergraduate category </p><br />
<p><b>Gold Medal </b>– for fulfilling criteria</p><br />
<p><b>Advancement to World Finals</b></p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</div><br />
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<!-- <html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Parts
Team:Alberta/Parts
2013-10-29T03:31:51Z
<p>MEsau: </p>
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</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts" class="active">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts" class="active"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Submitted Parts</p><br />
</div><br />
<div class="block"><br />
<p> Our 2013 parts submitted are a set of violacein genes derived from the violacein operon constructed and <br />
submitted by Cambridge in 2009 (BBa_K274002). We have made a number of modifications, including upgrading the <br />
plasmid backbone from pSB1K3 to pSB1C3 standard 10, and converting each of the five open reading frames into <br />
its own part with a common and improved ribosome binding site (BBa_B0030) such that they can be assembled in <br />
different combinations and permutations. All of the parts have been characterized and are functional, and we <br />
have found that a new combination, VioABCE, produces a new pigment which we call "Royal Blue". </p><br />
<img src="/wiki/images/f/f0/2013-Alberta-Submitted_parts.PNG" style="width:100%;"></img><br />
<br />
</html><br />
<groupparts>iGEM013 Alberta</groupparts><br />
<html><br />
<br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<br />
<!-- <html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Protocols
Team:Alberta/Protocols
2013-10-29T03:31:21Z
<p>MEsau: </p>
<hr />
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<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols" class="active">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
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</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Parts"><p>The Parts</p></a><br />
<a href="#Build"><p>Building the Plasmids</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols" class="active"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Protocols</p><br />
</div><br />
<a class="anchor" id="Parts"></a><br />
<div class="block"><br />
<h2>The Parts</h2><br />
<p>The 6 genes that were required to assemble various routes were obtained by PCR from plasmids kindly provided by Genomikon Inc. Each gene (AmpR, KanR, ClrR, GFP, RFP and aCP) exist as self contained cassettes that are flanked by BsaI sites. Parts were then generated according to the schematic shown below:</p><br />
<img src="/wiki/images/c/c5/Making_parts_678x586.png" align="middle" style="width:100%;"><br />
</div><br />
<a class="anchor" id="Build"></a><br />
<div class="block"><br />
<h2>Building the Plasmids</h2><br />
<p>Our plasmid assembly system relies upon the achievements of previous Team Alberta iGEM entries, 2009’s BioBytes and 2010’s Genomikon assembly methods. This process begins with origins of replication anchored at one end to magnetic beads in a suspension within a reaction microfuge tube. The anchored strands have a single, free-floating sticky end, onto which successive genes are ligated. Once the new gene has been ligated on, we use a magnet to hold the beads (along with the anchored DNA) inside the reaction tube, while washing away the rest of the reaction, including the enzyme, buffers, and any non-ligated DNA that remains. The beads are then resuspended in a new reaction mixture, containing the next ligation step.</p><br />
<img src="/wiki/images/b/b4/2013Alberta-Poster2.jpg" align="middle" style="width:100%;"><br />
<p>Once all of the genes have been ligated, a tail-piece that complements the original bead-anchor DNA sequence is added, so that the finished product can be unbound from the beads and will close upon itself to form the circular plasmid. In this fashion, a four-gene, roughly 5000-base-pair plasmid is assembled in as little as an afternoon, cheaply and easily.</p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Results
Team:Alberta/Results
2013-10-29T03:27:09Z
<p>MEsau: </p>
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<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#First-Tests"><p>The First Tests</p></a><br />
<a href="#Linkers"><p>Perfecting the Linkers</p></a><br />
<a href="#Assembly"><p>The Full Assembly</p></a><br />
<a href="#Colour-Controls"><p>Colour Controls</p></a><br />
<a href="#Calibration"><p>Initial Calibration</p></a><br />
<a href="#TSP"><p>The Travelling Salesman Problem</p></a><br />
<a href="#Adapt-POP"><p>Increasing Complexity</p></a><br />
<a href="#Revised-Strategy"><p>A Revised Strategy</p></a><br />
<a href="#DNA-Library"><p>Cosmid DNA Library</p></a><br />
<a href="#PCR"><p>PCR Identification</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results" class="active"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
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<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Results</p><br />
</div><br />
<a class="anchor" id="First-Tests"></a><br />
<div class="block"><br />
<h2>The First Tests</h2><br />
<p>We performed some initial tests to confirm the efficacy of our assembly system. The Genomikon assembly method requires that we be able to successfully bind and elute DNA from magnetic beads, and that we be able to perform successive ligations on the bead-bound strands. These are necessary for building the plasmid "routes", as described in the project overview page. </p><br />
<br />
<p>In the gel below, the second lane displays the result of an origin of replication (Ori) sample that was bound to the bead, washed and then re-eluted – the presence of DNA at the desired mass in this lane confirms the successful binding and elution. The third lane demonstrates that we can successfully ligate genes (KanR in this case) directly to the Ori at high efficiency and still safely elute them. In the fourth lane, we have ligated a 13-base-pair linker onto the existing Ori-KanR, followed by a second gene, ChlorR. Although the high-mass band suggests that ligation was successful, the fact that there is still a stronger band at the Ori-KanR mass suggests that the ligation has not proceeded to completion.</p><br />
<p><img src="/wiki/images/7/7e/2013-Alberta-Results-Figure_1.png" style="width:100%;"></img><br /><br />
Figure 1: Agarose gel electrophoresis image from initial ligation trials. <br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Origin of replication, bound to the magnetic beads and then eluted. <br /><br />
Lane 3: KanR gene ligated to bead-bound Ori.<br /> <br />
Lane 4: Existing bead-bound Ori-KanR sample ligated with linker, then ligated with ChlorR <br /><br />
(beads are always washed between ligations).</p><br />
</div><br />
<a class="anchor" id="Linkers"></a><br />
<div class="block"><br />
<h2>Perfecting the Linkers</h2><br />
<p>The incomplete ligation of the previous step presents an obstacle for our system, but the issue appears to be isolated to the ligation step involving the short linker piece. To get a more effective ligation without extending the timeframe of our assembly, we made several adjustments. First, we raised ligation temperature from 4°C to 22°C in the hopes of increasing the enzyme activity. Second, we switched to a larger, 25-base-pair linker – we were able to successfully ligate large pieces in the case of the Ori and KanR ligation, so perhaps size plays a factor. Also, we used better-purified stocks of our genes, to eliminate the possibility that some interfering piece of the original plasmid was competing with our desired reaction. Finally, we attempted to increase the concentration of the linker in the hopes of driving the reaction to completion. Here, we can see that our changes have significantly improved the ligation efficiency, although changing the linker concentration has not created an appreciable benefit. </p><br />
<p><img src="/wiki/images/9/9e/2013-Alberta-Figure_2.png" style="width:100%;"></img><br /><br />
Figure 2: Agarose gel electrophoresis image from linker concentration comparison after<br />
ligation protocol adjustments.<br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Ori-KanR ligation to linker, then to ChlorR (as in Figure 1, Lane 4) using 10:1 ratio of <br />
linker to Ori. <br /><br />
Lane 3: As lane 2, with 50:1 ratio.<br /><br />
Lane 4: As lane 3, with 100:1 ratio. </p><br />
</div><br />
<a class="anchor" id="Assembly"></a><br />
<div class="block"><br />
<h2>The Full Assembly</h2><br />
<p>With our successful ligation protocol established, we moved on to attempting a full-scale <br />
assembly, with four genes (the quantity required for our proof-of-concept travelling salesman<br />
problem). In this gel, the four lanes show the successive addition of the four genes, which <br />
are, for the most part, successful. In each lane, there is some remainder of the previous <br />
products left behind, including (presumably) instances of strands that were incomplete in <br />
one reaction continuing to acquire genes in a successive one. Regardless, these incomplete <br />
genes represent only a small fraction of the total DNA. </p><br />
<p><img src="/wiki/images/3/37/2013-Alberta-Results-Figure_3.png" style="width:100%;"></img><br /><br />
Figure 3: Agarose gel electrophoresis image from full assembly test. <br /><br />
Lane 1: DNA Markers.<br /><br />
Lane 2: Ori to KanR ligation product.<br /><br />
Lane 3: Ori-KanR to linker to GFP ligation product.<br /><br />
Lane 4: Ori-KanR-Linker-GFP to linker to RFP ligation product.<br /><br />
Lane 5: Ori-KanR-Linker-GFP-Linker-RFP to linker to ChlorR ligation product. </p><br />
<p>The product plasmids from this assembly were transformed into a bacterial culture and <br />
grown on a Kan/Chlor plate to examine practical impact of the rate of incomplete ligations. <br />
The plate image is shown below – about 90% of the colonies display the desired RFP/GFP <br />
(orange colouration) phenotype indicating a perfect successful ligation of the plasmid. </p><br />
<img src="/wiki/images/4/4e/Ab_Assembly_efficiency.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Colour-Controls"></a><br />
<div class="block"><br />
<h2>Colour Controls</h2><br />
<p>In our planned, four-city proof-of-concept test (see the map below), there are exactly three <br />
possible solutions and three corresponding phenotypes: blue/green (dark green) bacteria <br />
with Amp/Chlor resistance, red/green (orange) bacteria with Chlor/Kan resistance, and <br />
red/blue (purple) bacteria with Amp/Kan resistance. </p><br />
<img src="/wiki/images/8/8d/2013Alberta-mapmaker-states.png" style="width:100%;"></img><br />
<p>To ensure we would be able to correctly identify plasmids based on phenotype we prepared <br />
a set of control plates, where bacteria grown from pure assemblies of the desired “route” <br />
plasmid were grown alongside bacteria possessing only one of the two colours from that <br />
route, for comparison purposes. The resulting plates can be seen above. </p><br />
</div><br />
<a class="anchor" id="Calibration"></a><br />
<div class="block"><br />
<h2>Initial Calibration</h2><br />
<p>In preparation for our initial travelling salesman problems, we attempted to discern the <br />
extent to which unexpected or unknown biases might affect the frequency of colonies <br />
growing with a particular gene.</p><br />
<p>In this test, we performed an assembly in which both GFP and aCP were included (in equal <br />
molar concentration) in the initial ligation onto the Ori, followed by a ligation of ChlorR, <br />
resulting in a mixture of Ori-GFP-ChlorR and Ori-aCP-ChlorR plasmids. We transformed these <br />
plasmids into a single bacterial culture, which we then spread on a Chlor-treated plate in <br />
order to count the resulting colonies. We repeated this test for each of the other four genes <br />
to be used in our proof-of-concept TSP, comparing each against GFP as a standard. This <br />
provided us with the following ratios of growth.</p><br />
<p>Table 1: 1GFP 6aCP<br /><img src="/wiki/images/5/5d/2013Alberta-Ratiotable.png" style="width:100%;"></img></p><br />
<p>We then attempted another assembly in which we calibrated for the bias. We used a 6:1 <br />
molar ratio of GFP to aCP in the new assembly, otherwise performing the experiment as <br />
before, and produced a new plate with a ratio of approximately 1:1 GFP colonies to aCP <br />
colonies. Although imperfect, this calibration was adequate for our proof-of-concept trial.</p><br />
</div><br />
<a class="anchor" id="TSP"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p> We have conducted a single successful travelling salesman problem following the procedure outlined in the project overview page. Relative to the previous assembly steps, the only key difference is that this time, several genes are included at each ligation step and at varying concentrations, so that the assembly produces a mix of plasmids, but favours some genes over others (creating a bias for shorter paths). See the overview page for more details on how this works. </p><br />
<p>This particular problem was based on a map of four cities in which four of the paths have an arbitrary unit distance of 1, and the remaining two paths have a distance of 4. Of the possible routes in this problem, one route has a total sum distance of 4, and the other two have distances of 10, making that route clearly preferable, and a suitable test of our biocomputer. The three possible routes, with correct gene-path assignment and distances listed for this problem, can be seen below. At each ligation step, we added a quantity of each gene based on the reciprocal of its distance, so that, for instance, the genes corresponding to paths of distance 4 had roughly one-quarter of the concentration (this value was then adjusted by our calibrations, as described above, to arrive at the actual concentration) of those with distance 1. </p><br />
<img src="/wiki/images/a/ab/2013Alberta-POP.png" style="width:100%;"></img><br />
<p>On the resulting plates, we counted 18 colonies corresponding to the ChlorR/GFP/aCP/AmpR route, and 21 colonies corresponding to the ChlorR/RFP/GFP/KanR route. For the optimal route, KanR/aCP/RFP/AmpR, we found 61 colonies, clearly identifying this as the solution to the problem. When the percentage of each of these three types of colonies on each plate is normalized to the best solution, the results of this trial are very close to the expected values calculated for this experiment. </p><br />
</div><br />
<a class="anchor" id="Adapt-POP"></a><br />
<div class="block"><br />
<h2>Can we adapt our POP to a much more complex problem?</h2><br />
<p>The ultimate limit of an approach such as this, depends upon the<br />
number of complete TSP solutions (plasmids) that can be clonally<br />
amplified through cell transformation. We estimate that solving a 15-city<br />
problem is within the realm of existing state-of-the-art, but not without<br />
major revisions to our POP work presented here. The 15-city problem is<br />
not trivial even by conventional computing standards. With 120 intercity<br />
links resulting in 87,178,291,200 possible solutions, 50 days would be<br />
required to identify the best solutions at a computational rate of 10,000<br />
solutions/second!</p><br />
<p>The challenges:</p><br />
<ol><br />
<li>In the POP, solutions are identified by visually<br />
determining the frequency of colonies exhibiting<br />
the appropriate path combinations represented by<br />
the three colour genes and the three drug<br />
resistance genes. Extending this approach to the<br />
15-city problem would require the acquisition of<br />
120 markers that are combined 87,178,291,200<br />
ways, well beyond the analytical resolution of<br />
standard plating methods.</li><br />
<li>A statistically significant sampling of complete<br />
solutions is well outside the plasmid transformation<br />
efficiencies of even the best competent cells<br />
available.</li><br />
<li>The precision and efficiency for assembling<br />
complete-solution plasmids (38 steps in all)<br />
remains to be tested.</li><br />
</ol><br />
<img src="/wiki/images/7/72/2013-Results_z1.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Revised-Strategy"></a><br />
<div class="block"><br />
<h2>A revised strategy</h2><br />
<p><b>Cities and Paths.</b> In the new approach we invert the role that DNA<br />
plays in defining cities and paths. Here, a city corresponds to a gene<br />
that complements an amino acid auxotrophy in E. coli (illustrated<br />
below). The city is therefore required for growth on defined media that<br />
lacks that amino acid. By extension, 15 different cities represented by<br />
15 a.a. auxotrophic markers would be required for survival of E. coli<br />
deficient for these genes when grown on media that lacks the<br />
corresponding amino acids. Complete plasmid solutions therefore are<br />
exclusively selected and amplified from their non-solution counterparts.<br />
Creating a 15-gene knockout in E. coli is not trivial but absolutely<br />
possible.</p><br />
<p>The ability to link any two city genes requires that each city has at<br />
its 5’ and 3’ ends, overhangs that are nonpalindromic,<br />
noncomplementary, and that are distinct in sequence from any of the 14<br />
other city genes.</p><br />
<p>The 120 path possibilities that are needed to link any two cities,<br />
are represented by a mixture of 120 synthetic duplex linkers where each<br />
linker has two different complementary ends that are capable of linking<br />
one of the 120 possible intercity pairs. Shorter intercity distances are<br />
favoured by adjusting the concentration of each linker in the mixture<br />
according to a new and improved weighting algorithm described below.<br />
We point out that in terms of economy, all 120 linkers can be produced<br />
from 30 oligos used in pair-wise combinations.</p><br />
<p>An unavoidable complication of this method is that any given city<br />
can occur more than once (at lower frequency) across the 15 available<br />
steps during sequential assembly (illustrated above for the three-city<br />
example). It should be noted however that any city duplication excludes<br />
the possibility of creating the complete set and will therefore be<br />
selected against post-transformation.</p><br />
<img src="/wiki/images/1/10/2013-Results_z2.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="DNA-Library"></a><br />
<div class="block"><br />
<h2>Creating a cosmid DNA library of that is highly biased for best<br />
solutions.</h2><br />
<p>To date, &lambda; phage-based recombinant libraries remain<br />
unprecedented in terms of the size and diversity of their DNA<br />
constituents. In its most advanced form, “cosmid” library kits are<br />
commercially available that produce 10<sup>10</sup> transformants. Cosmids retain<br />
the phage elements that are required for phage packaging and infection<br />
but lack the elements required for phage propagation and cell lysis. A<br />
plasmid origin allows them to replicate as plasmids.</p><br />
<p>Cosmids are constructed as linear molecules that begin and end<br />
with phage sequences the essential phage sequences(, &lambda;L and &lambda;R).<br />
Complementary 12-base overhangs that constitute the lambda cos and cos’<br />
sites are also required for efficient circularization once the cosmid has<br />
entered the cell.</p><br />
<p>In addition to its favourable tranformation properties, another<br />
attractive feature of using a cosmid-based system for TSP is that DNA<br />
molecules below a certain length threshold, package poorly, thereby<br />
contributing to the selection of full-length solutions.</p><br />
<p>An overview highlighting the key aspects of library creation is<br />
shown below. The assembly procedure uses magnetic beads where the<br />
cos’ sequence has been covalently linked. Asssembly begins with a cos- <br />
&lambda;L synthetic adapter that allows for the subsequent addition of &lambda;L. The<br />
addition of spacer sequences insure that total size of the construct is<br />
optimal for packaging (~50kB). Linker combinations are then added in<br />
alternation with city combinations until the city content is complete.<br />
Finally the construct is terminated with &lambda;R and a cos’ adapter. Following<br />
packaging cells are infected in selective liquid medium and the cosmid<br />
population is isolated for PCR analysis. The library is heavily biased 1)<br />
for complete solutions based on the assembly and packaging<br />
considerations already described and 2) for best solutions based on the<br />
path weights assigned to each linker addition step.</p><br />
<img src="/wiki/images/5/55/Results_z3.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="PCR"></a><br />
<div class="block"><br />
<h2>PCR-based identification of best solutions.</h2><br />
<p>The two types of data that is required for piecing best solutions together<br />
are 1) determining the cities that most frequently occupy each position<br />
from 1 to 15 and 2) determining the most frequently used intercity pairs<br />
as outlined below.</p><br />
<img src="/wiki/images/3/37/2013-Results_z4.PNG" style="width:100%;"></img><br />
</div><br />
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MEsau
http://2013.igem.org/Team:Alberta/Overview
Team:Alberta/Overview
2013-10-29T03:25:49Z
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<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview" class="active">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
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<li><a href="/Team:Alberta/Team">Roster</a></li><br />
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<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Biological-Terms"><p>In Biological Terms</p></a><br />
<a href="#Finding-the-Path"><p>Finding the Path</p></a><br />
<a href="#Mapmakers"><p>MapMakers at Work</p></a><br />
<a href="#Weight"><p>Calculating Gene Concentration</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview" class="active"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
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<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Overview</p><br />
</div><br />
<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>MapMen is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:</p><br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Biological-Terms"></a><br />
<div class="block"><br />
<h2>In Biological Terms</h2><br />
<p>To take advantage of the considerable information processing power of biology, we must create biochemical analogues for all of the components of the original problem. We begin by assigning a symbolic reporter gene or selectable marker gene to each of the six paths in our example map. The assignment is arbitrary; which gene is used for which path does not matter as long as it creates some kind of observable phenotype. For example, the path connecting the northeast city and the northwest city is symbolized by a gene coding for ampicillin resistance. The path from the northeast to city to the southeast meanwhile, is symbolized by a gene coding for kanamycin resistance.</p><br />
<img src="/wiki/images/4/4c/Bio_terms.png" style="width:100%;"></img><br />
<p>Now, just as the travelling salesman might describe taking a particular route to his customers – leaving from the northeast origin city and taking the road to the southwest, then turning up the north road from there, then back down the southeast, before returning northward home from, we can also represent that series of paths as a sequence of genes: ChlorR, RFP, GFP, and KanR.</p><br />
<img src="/wiki/images/b/bd/Path_to_gene.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Finding-the-Path"></a><br />
<div class="block"><br />
<h2>Finding the Path</h2><br />
<p>Just as a computer using a brute force approach to the travelling salesman problem would test every route and tally the sum distance of the paths travelled, our biocomputer assembles a multitude of plasmids, representing every possible combination of paths, through a set of ligations that represent the legs of the salesman’s journey. In the first leg, we depart from the origin city along any of the available roads: AmpR, ChlorR, or KanR. In the plasmid production, we begin with a combinatorial ligation – one where all three of the genes are being ligated with origins of replication, but only one of the three is able to ligate onto each Ori, resulting in a collection of incomplete plasmids that each includes just one of the three genes. </p><br />
<center><img src="/wiki/images/9/95/AB_Genemap.png" style="width:35%;"></img></center><br />
<p>Following the first gene ligation, a short linker piece is added, signifying the city that has been reached – all of the linkers are identical, there is no differentiation of routes based on this component. In the second leg of the journey, we perform a ligation with three more genes, representing all of the possible paths the salesman might take next – three colour genes. Again, each growing plasmid can only incorporate one of the new genes, so we obtain a random assortment of incomplete plasmids that each include one antibiotic resistance from the first ligation and one colour gene from the third ligation. </p><br />
<img src="/wiki/images/7/7e/AB_Assemblyfull.png" style="width:100%;"></img><br />
<p>The third leg of the journey is identical to the second, incorporating an additional colour gene, and the final leg uses the three antibiotic genes once again. At the end of this process, we will have obtained a randomized distribution of 76 different kinds of plasmids representing all of the different possible permutations of the genes, capable of producing 18 unique phenotypes, and representing the six bi-directional solutions to the four-city travelling salesman problem.<p/><br />
</div><br />
<a class="anchor" id="Mapmakers"></a><br />
<div class="block"><br />
<h2>MapMakers at Work</h2><br />
<p>Once the plasmids have been produced, how can we use them to identify the correct solution? The answer is in the frequency with which each plasmid occurs: We create bias in the ligations during assembly so that genes that represent shorter paths are more likely to be incorporated into the plasmids, meaning in turn that the final product plasmids are more likely to be composed of several short-path genes. As a result, although we still expect to see plasmids representing every possible route, those plasmids that represent the shortest routes through the map will be much more common than plasmids representing lengthy routes. By identifying the most abundant plasmid, we identify the shortest route and thus the optimal solution. </p><br />
<p>The bias is introduced through the concentration of the reactants in each ligation. If a gene is meant to represent a short path, its concentration in the ligation will be higher than the others, and conversely, genes that are meant to represent lengthy paths will be included in lower concentrations than the others. As a result, at any given ligation step, the gene symbolizing the shortest available path is more likely to be incorporated. Among the product plasmids, genes are incorporated at a rate inversely proportional to their length. The concentration used for each gene in the ligation is described by the expression: –ln[Gene]∝(path distance)</p><br />
<img src="/wiki/images/9/95/Proportions.png" style="width:100%;"></img><br />
<p>To identify which of the plasmids is most frequent, the products are transformed into a bacterial culture. Because each of the genes produces an easily interpreted phenotype, this allows us to infer the most frequently transformed plasmid from the frequency of the colonies produced on agar plates. The plasmid carried by any given colony on the plates below can be readily identified by the combination of the colony colour (purple colonies have RFP and aCP, orange colonies have RFP and GFP, and green colonies have GFP and aCP), and the antibiotic resistances it exhibits, which are inferred from the plate on which it is growing. As an example, a purple colony growing on the kan/amp plate must have the Amp-Red-Blue-Kan-plasmid shown in the first column below.<p/><br />
<img src="/wiki/images/6/6d/Ab_Solution_identification.png" style="width:100%;"></img><br />
<p>Many of the colonies do not correspond to any valid route. For instance, an orange colony on the kan/amp plate has the plasmid Amp-Red-Green-Kan, which does not describe a valid circuit visiting each city exactly once – but because we can tell that this is an invalid solution, we would not count this colony when assessing the frequency of the valid plasmids. Any four-city travelling salesman problem has just three unique solutions, and so there are only three phenotypes that must be counted: purple kan/amp, orange kan/chlor, and green amp/chlor. The colonies of these three phenotypes are counted and compared, and the most frequently occurring plasmid is the optimal solution! </p><br />
</div><br />
<a class="anchor" id="Weight"></a><br />
<div class="block"><br />
<h2>Calculating Gene Concentration</h2><br />
<img src="/wiki/images/5/57/2013Alberta_New_algorithm.png" style="width:100%;"></img><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Background
Team:Alberta/Background
2013-10-29T03:24:35Z
<p>MEsau: </p>
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<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background" class="active">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
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<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Real-World"><p>Real-World Issues</p></a><br />
<a href="#Computational"><p>The Computational Wall</p></a><br />
<a href="#Biocomputing"><p>Why Biocomputing?</p></a><br />
<a href="#Road"><p>A Long Road </p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background" class="active"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Background</p><br />
</div><br />
<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>MapMen is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:<br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Real-World"></a><br />
<div class="block"><br />
<h2>Real-World Issues</h2><br />
<p>The TSP is named after the concept of a hypothetical salesman who is planning a route to visit his <br />
customers in various neighbouring towns, but wants to maximize profits by using the shortest route — a <br />
helpful example to illustrate the usefulness of the problem: businesses around the world employ TSP-solving <br />
or related problem-solving software to help optimize their travelling needs, including in particular large <br />
courier companies that need to delivery millions of packages daily, and must reduce the expense of delivery <br />
vehicles and cut down travel time in any way possible, but also airliners, postal services, consumer GPS <br />
route-planning software, video-game pathfinding AI, and even electronics manufacture, in which a robot <br />
soldering arm must have an efficient path through the solder points to ensure maximum production over time. <br />
</p><br />
</div><br />
<a class="anchor" id="Computational"></a><br />
<div class="block"><br />
<h2>The Computational Wall</h2><br />
<p>The TSP is not only practically valuable, but also mathematically significant, because it belongs to a <br />
class of problems that are considered computationally difficult. The key difficulty with the TSP is due to <br />
the fact that it is an optimization problem: while for practical purposes any decent, short route is <br />
acceptable, a given TSP is nevertheless only considered "solved" when one verifies that one has obtained the <br />
shortest possible route. Mathematical verification of this sort requires what is called a "brute force" <br />
approach, in which one explores each and every possible route, tallying the total distance of each one, and <br />
then compares them all directly to guarantee the optimal route has been identified. As one increases the <br />
number of cities that must be included in the route, the time required for the brute-force approach becomes <br />
impossibly large.</p><br />
<img src="/wiki/images/9/9d/TSPcompWall.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Biocomputing"></a><br />
<div class="block"><br />
<h2>Why Biocomputing?</h2><br />
<p>Through synthetic biology, the creation of biological computers has opened a new avenue of possibility for <br />
solving TSPs more rapidly: using DNA molecules and bacterial cells as processors, one can compute billions <br />
of routes simultaneously, drastically reducing the time required through this massively parallel approach. <br />
By employing far more processors than there are routes through a given network, the processing time can be <br />
reduced to a standstill. A biological computer is also unique because it can solve problems stochastically: <br />
while every possible route is explored by the computer, preferable routes (short ones) will predominate <br />
among the generated products, allowing identification of the optimal route by population, rather than by a <br />
slower, deterministic approach. </p><br />
</div><br />
<a class="anchor" id="Road"></a><br />
<div class="block"><br />
<h2>A Long Road</h2><br />
<p>A number of previous attempts have been made to produce biocomputer solutions to the TSP, often involving pure DNA computing with no living organism present, including attempts by Leonard Adleman of RSA encryption fame, as well as previous efforts by the Davidson College/Missouri Western State University iGEM team, whose 2006 entry attempted to solve another challenging computational problem called the Burnt Pancake Problem, and in 2007 entered a DNA computing solution for the Hamiltonian Path Problem. Though related to the TSP, the Hamiltonian Path Problem attempts to discern if there is any possible route through a network, rather than picking the shortest possible one.</p><br />
<img src="/wiki/images/d/d4/Hgp_vs_tsp.png" style="width:100%;"></img><br />
<p>MapMen represents the latest in a line of attempts to refine the biological approach and create ever- increasingly powerful biological computers – and is the first of its kind to employ living cells to solve a travelling salesman problem. </p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<br />
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For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
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<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
== '''Overall project''' ==<br />
<br />
Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
=== Part 2 ===<br />
<br />
<br />
<br />
<br />
<br />
=== The Experiments ===<br />
<br />
<br />
<br />
<br />
=== Part 3 ===<br />
<br />
<br />
<br />
<br />
== Results ==<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Background
Team:Alberta/Background
2013-10-29T03:24:06Z
<p>MEsau: </p>
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<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
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<li><a href="/Team:Alberta/Background" class="active">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
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<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Real-World"><p>Real-World Issues</p></a><br />
<a href="#Computational"><p>The Computational Wall</p></a><br />
<a href="#Biocomputing"><p>Why Biocomputing?</p></a><br />
<a href="#Road"><p>A Long Road </p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background" class="active"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
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<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Background</p><br />
</div><br />
<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>MapMen is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:<br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Real-World"></a><br />
<div class="block"><br />
<h2>Real-World Issues</h2><br />
<p>The TSP is named after the concept of a hypothetical salesman who is planning a route to visit his <br />
customers in various neighbouring towns, but wants to maximize profits by using the shortest route — a <br />
helpful example to illustrate the usefulness of the problem: businesses around the world employ TSP-solving <br />
or related problem-solving software to help optimize their travelling needs, including in particular large <br />
courier companies that need to delivery millions of packages daily, and must reduce the expense of delivery <br />
vehicles and cut down travel time in any way possible, but also airliners, postal services, consumer GPS <br />
route-planning software, video-game pathfinding AI, and even electronics manufacture, in which a robot <br />
soldering arm must have an efficient path through the solder points to ensure maximum production over time. <br />
</p><br />
</div><br />
<a class="anchor" id="Computational"></a><br />
<div class="block"><br />
<h2>The Computational Wall</h2><br />
<p>The TSP is not only practically valuable, but also mathematically significant, because it belongs to a <br />
class of problems that are considered computationally difficult. The key difficulty with the TSP is due to <br />
the fact that it is an optimization problem: while for practical purposes any decent, short route is <br />
acceptable, a given TSP is nevertheless only considered "solved" when one verifies that one has obtained the <br />
shortest possible route. Mathematical verification of this sort requires what is called a "brute force" <br />
approach, in which one explores each and every possible route, tallying the total distance of each one, and <br />
then compares them all directly to guarantee the optimal route has been identified. As one increases the <br />
number of cities that must be included in the route, the time required for the brute-force approach becomes <br />
impossibly large.</p><br />
<img src="/wiki/images/9/9d/TSPcompWall.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Biocomputing"></a><br />
<div class="block"><br />
<h2>Why Biocomputing?</h2><br />
<p>Through synthetic biology, the creation of biological computers has opened a new avenue of possibility for <br />
solving TSPs more rapidly: using DNA molecules and bacterial cells as processors, one can compute billions <br />
of routes simultaneously, drastically reducing the time required through this massively parallel approach. <br />
By employing far more processors than there are routes through a given network, the processing time can be <br />
reduced to a standstill. A biological computer is also unique because it can solve problems stochastically: <br />
while every possible route is explored by the computer, preferable routes (short ones) will predominate <br />
among the generated products, allowing identification of the optimal route by population, rather than by a <br />
slower, deterministic approach. </p><br />
</div><br />
<a class="anchor" id="Road"></a><br />
<div class="block"><br />
<h2>A Long Road</h2><br />
<p>A number of previous attempts have been made to produce biocomputer solutions to the TSP, often involving pure DNA computing with no living organism present, including attempts by Leonard Adleman of RSA encryption fame, as well as previous efforts by the Davidson College/Missouri Western State University iGEM team, whose 2006 entry attempted to solve another challenging computational problem called the Burnt Pancake Problem, and in 2007 entered a DNA computing solution for the Hamiltonian Path Problem. Though related to the TSP, the Hamiltonian Path Problem attempts to discern if there is any possible route through a network, rather than picking the shortest possible one.</p><br />
<img src="/wiki/images/d/d4/Hgp_vs_tsp.png" style="width:100%;"></img><br />
<p>The Littlest MapMaker represents the latest in a line of attempts to refine the biological approach and create ever- increasingly powerful biological computers – and is the first of its kind to employ living cells to solve a travelling salesman problem. </p><br />
</div><br />
</div><br />
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</body><br />
</html><br />
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For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
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<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
== '''Overall project''' ==<br />
<br />
Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
=== Part 2 ===<br />
<br />
<br />
<br />
<br />
<br />
=== The Experiments ===<br />
<br />
<br />
<br />
<br />
=== Part 3 ===<br />
<br />
<br />
<br />
<br />
== Results ==<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Resources
Team:Alberta/Resources
2013-10-29T03:22:44Z
<p>MEsau: </p>
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.navbar:before, .navbar:after {<br />
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display: table;<br />
}<br />
.navbar:after {<br />
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.navbar li {<br />
float:left;<br />
border-right:1px solid #CCC;<br />
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.navbar a {<br />
float: left;<br />
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color: #444;<br />
font: bold 12px Arial, Helvetica;<br />
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}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
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}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
opacity: 0;<br />
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position:absolute;<br />
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z-index:1;<br />
background:#FFF;<br />
background: -moz-linear-gradient(#FFF, #CCC);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#CCC));<br />
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}<br />
.navbar ul ul {<br />
top:0;<br />
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margin:0 0 0 20px;<br />
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.navbar ul li {<br />
float:none;<br />
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-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
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}<br />
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.navbar ul a {<br />
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}<br />
.centered-well {<br />
text-align:center;<br />
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background-color:#CCC;<br />
border-radius:6px;<br />
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padding: 35px;<br />
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/* ... */<br />
height:100px;<br />
position:relative;<br />
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transition: all .25s ease-out;<br />
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.thumbnail img:hover {<br />
transform:scale(4,4);<br />
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z-index:999;<br />
background-color:white;<br />
border:solid 2px #CCC;<br />
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<br />
} <br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
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}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
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<li><a href="/Team:Alberta">Home</a></li><br />
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<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
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<h5>Other Sections</h5><br />
<a href="/Team:Alberta/SafetyForm"><p>Safety Form</p></a><br />
<a href="/Team:Alberta/FAQ"><p>FAQ</p></a><br />
<a href="/Team:Alberta/Resources" class="active"><p>Resources</p></a><br />
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</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Resources</p><br />
</div><br />
<div class="block"><br />
<ul><br />
<li>To other University of Alberta students: the Environmental Health and Safety Division provides<br />
safety support on common safety questions and situations, as well as documents on proper<br />
disposal.<br />
<ul><br />
<li>See their homepage at: <a href="http://www.ehs.ualberta.ca/">http://www.ehs.ualberta.ca/</a></li><br />
<li>Ethidium bromide disposal suggestions at: <a href="http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf">http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/ Documents/Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf.</a></li><br />
</ul><br />
</li><br/><br />
<li>To general students on a study break:<br />
<ul><br />
<li>See this basic and humourous not-to-do video (which was shown in University of<br />
Alberta’s EHS Biosafety Course): “Lab Unsafety and Septic Technique” by Jayson Masaki <br />
below or at <a href="http://www.youtube.com/watch?v=5aDLV0UHyNE">http://www.youtube.com/watch?v=5aDLV0UHyNE</a> </ul><br />
<iframe width="640" height="480" src="//www.youtube.com/embed/5aDLV0UHyNE" frameborder="0" allowfullscreen></iframe><br />
</li><br/><br />
<li>For students not yet familiar with iGEM nor their recommended guidelines:<br />
<ul><br />
<li>The World Health Organization gives a comprehensive guidebook for safety in labs at:<br />
<a href="http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf">http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf</a><br/><br />
(Reference: Laboratory Biosafety Manual. 2001. World Health Organization. Retrieved <br />
August 9, 2013, from <a href="http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf">http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf</a>)</li><br />
</ul><br />
</li><br />
</ul><br />
</div><br />
</div><br />
<div class="clear"></div><br />
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</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/FAQ
Team:Alberta/FAQ
2013-10-29T03:22:30Z
<p>MEsau: </p>
<hr />
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padding: 10px 10px 10px 10px;<br />
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.sidebar_block {<br />
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/*text-shadow: 0 1px 0 #333;*/<br />
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.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
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margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
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}<br />
.navbar ul ul {<br />
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margin:0 0 0 20px;<br />
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-webkit-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
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.navbar ul li {<br />
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-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
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box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
}<br />
.navbar ul li:last-child {<br />
-moz-box-shadow:none;<br />
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box-shadow:none;<br />
}<br />
.navbar ul a {<br />
padding:10px;<br />
width:130px;<br />
_height:10px;/*IE6 only*/<br />
display:block;<br />
white-space:nowrap;<br />
float:none;<br />
text-transform:none;<br />
}<br />
.navbar ul a:hover {<br />
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transition: all .25s ease-out;<br />
} <br />
.thumbnail img:hover {<br />
transform:scale(4,4);<br />
-webkit-transform:scale(4,4);<br />
-moz-transform:scale(4,4);<br />
-ms-transform:scale(4,4);<br />
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background-color:white;<br />
border:solid 2px #CCC;<br />
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-o-border-radius:1px;<br />
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box-shadow: 0px 0px 30px #000;<br />
<br />
} <br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
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<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
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</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="safety" href="/Team:Alberta/MainSafety" class="active">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ" class="active">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/SafetyForm"><p>Safety Form</p></a><br />
<a href="/Team:Alberta/FAQ" class="active"><p>FAQ</p></a><br />
<a href="/Team:Alberta/Resources"><p>Resources</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">FAQ</p><br />
</div><br />
<div class="block"><br />
<h3>Doesn’t <i>E. coli</i> cause food poisoning? If <i>E. coli</i> is so dangerous, why are they being used in labs?</h3><br />
<ul><br />
<li>Normal <i>E. coli</i> colonize the lower intestine of humans, while <b>producing Vitamin K</b> and <br />
<b>protecting infection</b> from other harmful bacteria.</li><br />
<li>Only some strains of <i>E. coli</i> cause food poisoning, but our group is using a <b>harmless, <br />
nonpathogenic strain</b>. This train is engineered to contain mutations that would not allow the <i>E. <br />
coli</i> to survive outside the lab without particular nutrients.</li><br />
<li><i>E. coli</i> provides a well-studied and well-known <b>model system</b> to test and troubleshoot new <br />
trials on.</li><br />
</ul><br />
<p>Reference: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1728375/"><br />
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1728375/</a></p><br />
<h3>What if plasmids containing <b>antibiotic resistance genes</b> were released into the environment despite<br />
precautions?</h3><br />
<ul><br />
<li>These genes are used in synthetic biology as selection tools.</li><br />
<li>There are lower chances of gene uptake by wild bacteria compared to lab-strain bacteria which<br />
have perforated membranes.</li><br />
<li>In the case that wild bacteria did uptake the antibiotic resistance gene, that gene would<br />
eventually be lost in the population without exposure to the antibiotic, because it is then a <br />
disadvantage for the bacteria to carry the unused plasmids. (Evidence observed in past with the <br />
decline of specific antibiotic resistance after the human population limited that antibiotic).</li><br />
</ul><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/SafetyForm
Team:Alberta/SafetyForm
2013-10-29T03:22:17Z
<p>MEsau: </p>
<hr />
<div><html><br />
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.titlebar {<br />
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z-index:2;<br />
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text-align:center;<br />
font-size:3em;<br />
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.titlebar h3, h4 {<br />
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.sidebar {<br />
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float: left;<br />
z-index: 3;<br />
padding: 10px 10px 10px 10px;<br />
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.sidebar_block {<br />
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margin:60px auto;<br />
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.navbar ul li {<br />
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-moz-transition: all .25s ease-out;<br />
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background-color:white;<br />
border:solid 2px #CCC;<br />
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-moz-box-shadow: 0px 0px 30px #000;<br />
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<br />
} <br />
a.anchor{<br />
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position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="safety" href="/Team:Alberta/MainSafety" class="active">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm" class="active">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Precautions"><p>Lab members’ Safety and Protective Precautions</p></a><br />
<a href="#Public-Safety"><p>Public Safety</p></a><br />
<a href="#Environmental-Safety"><p>Environmental Safety</p></a><br />
<a href="#Future-Risks"><p>Future risks from Commercialism</p></a><br />
<a href="#Training"><p>Training</p></a><br />
<a href="#Committee"><p>Biosafety Committee</p></a><br />
<a href="#References"><p>References</p></a><br />
<a href="#More-Detail"><p>For more information</p></a><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/SafetyForm" class="active"><p>Safety Form</p></a><br />
<a href="/Team:Alberta/FAQ"><p>FAQ</p></a><br />
<a href="/Team:Alberta/Resources"><p>Resources</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Summary of Safety Form</p><br />
</div><br />
<a class="anchor" id="Precautions"></a><br />
<div class="block"><br />
<h2>Lab members’ Safety and Protective Precautions</h2><br />
<p>There are no significant risks to lab members, as the biological parts are not reasonably able to cause any health issues<br />
to team members.</p><br />
<p>All the components of our project are quite standard in molecular biology labs and are not associated with<br />
significant risks. Our microorganisms, biological parts, laboratory equipment and chemicals are mostly<br />
comparably benign. The strains which our team intends to use and has used thus far are harmless <br />
(nonpathogenic and non-toxigenic). The biological parts we are using consist of color, antibiotic-resistance <br />
(Chloramphenicol, Kanamycin, Ampicillin, Tetracycline) and various promoters. In terms of chemicals,<br />
the myriad of flammable solvents in the lab pose a notable risk, and in addition the ethidium bromide <br />
(EtBr) is a dangerous toxin and mutagen. EtBr is used to visualize DNA by soaking agarose gels in a <br />
solution of the compound. EtBr works by intercalating between bases in the DNA’s helical structure, <br />
where is it able to fluoresce much more brightly than it does while in solution. It is generally established <br />
that intercalating agents are mutagens, and that mutagens are carcinogens and for this reason EtBr is <br />
treated with a high level of caution in our lab. Experiments have shown that EtBr is able to cause DNA <br />
damage in human cell lines so this carcinogenic potential is not just theoretical. To mitigate risks, <br />
relevant <br />
microbiological <a name="public">techniques</a> are consistently used in the lab and gloves are worn. Other precautions for <br />
EtBr include the labelling of designated containers for EtBr gels and EtBr waste, and the reuse of EtBr <br />
solution to minimize waste.</p><br />
<p>The most dangerous laboratory equipments we use are a transilluminator, gel apparatus, and the Bunsen<br />
burner. The risks posed by exposure to UV radiation, electric shocks and open flames can be easily<br />
controlled with proper safety training and protective equipment. A thick glass cover has been added to <br />
one UV visualizer in the lab to protect eyes when visualizing gels. Usually, a different UV visualizer is <br />
used for lab purposes because it photographs the gel without any UV exposure to eyes at all. Students <br />
are taught how to properly use equipment, dispose of wastes, autoclave used glassware and <br />
biologicallycontaminated waste, disinfect counters and know when to wear safety protection. Proper pipetting <br />
protocol is always used.</p><br />
</div><br />
<a class="anchor" id="Public-Safety"></a><br />
<div class="block"><br />
<h2>Public Safety</h2> <br />
<p>The DH5-α strain with which our group is working (which is a derivative of K-12) is non-pathogenic and<br />
non-toxigenic, so it poses no risk to public health and safety.</p><br />
<p><a name="environment">A public concern</a> is that the plasmids containing antibiotic resistance genes could be released into the<br />
environment. Since our project uses antibiotic resistance genes as selection tools, we ensure that these <br />
genes are properly disposed of by autoclaving.</p><br />
<p>In evaluating the risks, there is a lower chance of gene uptake by wild bacteria compared to our labstrain <br />
bacteria that have perforated membranes. In the case that wild bacteria did uptake the antibiotic <br />
resistance gene, that gene would eventually be lost in the population without exposure to the antibiotic, <br />
because it is then a disadvantage for the bacteria to carry the unused plasmids and use up energy <br />
to express them. Evidence for this was observed in multiple cases of measured declines in particular <br />
antibiotic resistances after the human population limited the antibiotic usage (Klotins, 2005).</p><br />
</div><br />
<a class="anchor" id="Environmental-Safety"></a><br />
<div class="block"><br />
<h2>Environmental Safety</h2><br />
<p>The bacteria that we use in the laboratory are not well suited to survival in the environment and even <br />
assuming they were able to do so, they do not have any destructive potential. <br />
The standard and well-characterized biobytes we are using do not have the potential to combine in <br />
dangerous ways. As with many other synthesized DNA constructs, we have found that our plasmids are <br />
lost from the bacteria over time (if plated without antibiotic present), due to the expression of colors <br />
being <br />
an unproductive strain on the cell’s resources. Consequently, there is little risk of our microorganisms <br />
spreading. Even if our <i>E. coli</i> strains survived and replicated in the wild, they are highly unlikely <br />
to <br />
cause harm to any humans or animals as risk level one microorganisms. The microorganisms we are <br />
creating in the lab would have less potential for malicious misuse than any bacteria normally found in the <br />
environment.</p><br />
<p>Although there is no intentional release to the environment and people, contamination is minimized<br />
by protective equipment (gloves) and disinfection. However, the microbe strain cannot survive outside <br />
the lab environment because it is engineered to be weak and dependent on a lab nutrient mix (Luria<br />
Broth, LB agar). In the improbable case that the microbe evolved (ex. By uptaking genes) to be able to <br />
synthesize one of the essential amino acids, it still would be deficient in multiple other ways.</p><br />
</div><br />
<a class="anchor" id="Future-Risks"></a><br />
<div class="block"><br />
<h2>Future risks from Commercialism</h2><br />
<p>Answering this question accurately is something of a complex endeavor, as one of the key aspects of<br />
<a name="training">our project</a> is that it is essentially a foundational advance. As such there are probably many approaches <br />
a focused group of minds might be able to develop using some of the principle and methods we have <br />
developed. However, even given the very open-ended nature of our project’s potential future, it is difficult <br />
to envision scenarios in which significant dangers are encountered. It is possible that in the distant <br />
future <br />
our methods might be modified and used with organisms and/or genes that entail greater risks than the <br />
non-pathogenic <i>E. coli</i> we have chosen to use. Even in this instance, the risks to personal, <br />
environmental <br />
and public safety are equal to the risks posed by the organisms and/or genes used and not modulated <br />
upward by the methods of our project in any conceivable way.</p><br />
</div><br />
<a class="anchor" id="Training"></a><br />
<div class="block"><br />
<h2>Training</h2><br />
<p>Laboratory safety training is given to undergraduate students in many of their laboratory courses. Specific <br />
to bio-safety, three of our team members have completed a comprehensive biological laboratory safety <br />
course in their Methods of Modern Biochemistry course (BIOCH 401) This course includes general <br />
biological, chemical, and WHMIS safety training). All students including the high school students were <br />
given on-site training for the specific techniques they would be using in the laboratory.</p><br />
</div><br />
<a class="anchor" id="Committee"></a><br />
<div class="block"><br />
<h2>Biosafety Committee</h2><br />
<p>As is the case with most universities, there is a local Biosafety Committee on the university of Alberta<br />
Campus that ensures research labs are following the safety protocols put in place by the national<br />
government. The University of Alberta Biosafety Committee is a division of the Environmental Health<br />
and Safety Faculty. This Committee oversees the handling of biohazardous materials and/or techniques, <br />
defined as “materials of biological origin or synthetic material which mimic biological entities and may <br />
induce adverse conditions to humans, other animals, plants, or the environment”. With respect to <br />
relevant national and international guidelines, our non-virulent strains of <i>E. coli</i> are considered <br />
Biosafety <br />
level 1 and are of limited potential hazard. Within our lab, standard practices are used, including but <br />
not limited to wearing gloves and sterilizing with bleach and/or ethanol and/or autoclaving. University <br />
policy states that the Biosafety committee need only be contacted when risk group level 2 organisms are <br />
to be worked with, or for other special concerns, and as such there is currently no need to discuss the <br />
project details with them to obtain their approval. However, the EHS provides documents on laboratory <br />
guidelines and university-specific ethidium bromide disposal (EHS, 2011), which have been reviewed by <br />
the team.</p><br />
<p>According to the WHO bio-safety manuscript, the living organisms with which this year’s University of <br />
Alberta iGEM team has worked (and will work with) all fall within the category of Risk Level 1, which <br />
the manuscript goes on to define as “unlikely to cause human or animal disease”. Since the strains which<br />
our team intends to use and has used thus far are harmless (non-pathogenic and non-toxigenic), they all <br />
fall into this category and as such, no major safety issues are raised by the biological components of our <br />
project.</p><br />
</div><br />
<a class="anchor" id="References"></a><br />
<div class="block"><br />
<h2>References:</h2><br />
<p><ul><li>Ethidium bromide – fact sheet. November 2011. <i>Environmental Health & Safety.</i><br />
Retrieved August 9, 2013, from <a href="http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf">www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/<br />
Chemical%20Safety/FactSheet_Ethidium_Bromide_-_2011.pdf</a></li><br />
<li>Klotins, K. (n.d.). Antibiotic use for growth improvement. <i>Ontario Ministry of Rural Affairs / <br />
Ministry <br />
of <br />
Agriculture and Food.</i> Retrieved August 2, 2013, from <br />
<a href="http://www.omafra.gov.on.ca/english/livestock/animalcare/amr/facts/05-041.htm"><br />
http://www.omafra.gov.on.ca/english/livestock/animalcare/amr/facts/05-041.htm</a></li><br />
<li><a href="http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/Documents/Manuals%20and%20Documents/Biosafety_Manual_Aug__03__2_.ashx"><br />
http://www.ehs.ualberta.ca/EHSDivisions/~/media/Environmental%20Health%20and%20Safety/<br />
Documents/Manuals%20and%20Documents/Biosafety_Manual_Aug__03__2_.ashx</a><br/><br />
(Found also from: <br />
<a href="http://www.ehs.ualberta.ca/EHSDivisions/Biosafety.aspx"> <br />
http://www.ehs.ualberta.ca/EHSDivisions/Biosafety.aspx</a>)</li><br />
<li><a href="http://canadianbiosafetystandards.collaboration.gc.ca/cbsg-nldcb/index-eng.php?page=1"><br />
http://canadianbiosafetystandards.collaboration.gc.ca/cbsg-nldcb/index-eng.php?page=1</a> and </li><br />
<li><a href="http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/"><br />
http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/.</a></li></ul></p><br />
</div><br />
<a class="anchor" id="More-Detail"></a><br />
<div class="block"><br />
<b>For more detail, see the full basic form <a href="/wiki/images/1/1c/IGEM_2013_Basic_Safety_Form-_Final3.pdf">part 1</a> submitted to iGEM Safety Committee</b><br /><br />
<b>as well as <a href="/wiki/images/7/77/2013-Alberta_safety_2.pdf">part 2</a>.</b><br />
<p><i>Safety forms were approved on 9/23/13 by Julie McNamara and David Lloyd on the iGEM Safety Committee. </i></p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
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</body><br />
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MEsau
http://2013.igem.org/Team:Alberta/Community
Team:Alberta/Community
2013-10-29T03:22:05Z
<p>MEsau: </p>
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transition: all .25s ease-out;<br />
} <br />
.thumbnail img:hover {<br />
transform:scale(4,4);<br />
-webkit-transform:scale(4,4);<br />
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z-index:999;<br />
background-color:white;<br />
border:solid 2px #CCC;<br />
border-radius:1px;<br />
-moz-border-radius:1px;<br />
-o-border-radius:1px;<br />
-webkit-border-radius:1px;<br />
-moz-box-shadow: 0px 0px 30px #000;<br />
-o-box-shadow: 0px 0px 30px #000;<br />
-webkit-box-shadow: 0px 0px 30px #000;<br />
box-shadow: 0px 0px 30px #000;<br />
<br />
} <br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
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<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="humanpractices" href="#" class="active">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community" class="active">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Outreach"><p>Outreach</p></a><br />
<a href="/Team:Alberta/Community" class="active"><p>Community</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Community</p><br />
</div><br />
<div class="block"><br />
<p><b>Get an inside look at the project by following us on social media.<b></p><br />
<br />
<p style="float:left;margin-left:85px;"><a href="https://twitter.com/iGEMAlberta"><img src="/wiki/images/thumb/e/e8/Twit.png/120px-Twit.png" style="height:150px;" alt="Twitter"></img></a><br />
<a href="https://www.facebook.com/pages/University-of-Alberta-iGEM-Team/117860431757664"><img src="/wiki/images/2/2b/Facebook-icon-256x256.png" style="height:150px;" alt="Facebook"></img></a></a><br />
<a href="http://statigr.am/tag/igemalberta2013"><img src="/wiki/images/9/93/Instagram-icon-256x256.png" style="height:150px;" alt="Instagram"></img></a></p><br />
<div class="clear"></div><br />
<a class="twitter-timeline" href="https://twitter.com/iGEMAlberta" data-widget-id="395021877959069696">Tweets by @iGEMAlberta</a><br />
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script><br />
</div><br />
<br />
<br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Outreach
Team:Alberta/Outreach
2013-10-29T03:21:53Z
<p>MEsau: </p>
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-moz-box-shadow: 0px 0px 30px #000;<br />
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.masonry {<br />
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.masonry-block {<br />
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margin-bottom: 20px;<br />
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} <br />
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display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="humanpractices" href="#" class="active">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach" class="active">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Outreach" class="active"><p>Outreach</p></a><br />
<a href="/Team:Alberta/Community"><p>Community</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Outreach: Consort, Alberta<p><br />
</div><br />
<div class="block"><br />
<p> As a part of our efforts to reach out to the local scientific community iGEM Alberta send one of <br />
our team members to the small town of Consort, Alberta to assist their emerging high school iGEM <br />
team. Consort is a town of about 700 people located east of Red Deer near the border with <br />
Saskatchewan and only has one secondary school. Remarkably students from this small town high<br />
school caught wind of the iGEM competition and decided to get involved. Their seclusion however was <br />
the source of several problems. The Consort team lacked the proper equipment, materials, and training <br />
to realize their goal of competing in iGEM. After hearing of their difficulties Mark Rozema travelled to <br />
the small town to lend his assistance. Mark, a recent graduate, was able to provide much needed <br />
materials such as ligase, buffer, and restriction enzymes. He also gave helpful suggestions to improve <br />
their presentation and delivery and helped develop their safety component and abstract. We were <br />
thrilled to be able to help a local high school iGEM team and look forward to future partnership with the <br />
Consort iGEM team. <br />
</p><br />
<div class="masonry"><br />
<div class="masonry-block"><br />
<img src="/wiki/images/2/2b/Consort-sign.png" style="width:100%;"></img><br />
<p>Consort, AB is a small town of about 700 people with one secondary school for its 70 high school <br />
students.</p><br />
</div><br />
<div class="masonry-block"><br />
<img src="/wiki/images/6/67/Consort-meeting.jpg" style="width:100%;"></img><br />
<p>The students practice their presentation in front of their parents<br />
and an Alberta iGEM team member, Mark Rozema.</p><br />
</div><br />
<div class="masonry-block"><br />
<img src="/wiki/images/5/50/Consort-map.png" style="width:100%;"></img><br />
<p>Consort, AB is located several hours from both Edmonton <br />
and Calgary. Having little access to any major biochemistry <br />
labs proved to be challenging for the team.</p><br />
</div><br />
</div><br />
<p>Images Courtesy of:<br/><br />
<a href="http://genomealberta.ca/blogs/university-of-alberta-igem-team-pitches-in-to-help-team-fromconsort.aspx">http://genomealberta.ca/blogs/university-of-alberta-igem-team-pitches-in-to-help-team-fromconsort.aspx</a><br/><br />
<a href="https://maps.google.ca">https://maps.google.ca</a><br/><br />
<a href="http://www.consort.ca/">http://www.consort.ca/</a><br/><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Sponsors
Team:Alberta/Sponsors
2013-10-29T03:21:09Z
<p>MEsau: </p>
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<div class="titlebar"><br />
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<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="team" href="#" class="active">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors" class="active">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team"><p>Roster</p></a><br />
<a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta"><p>Official Profile</p></a><br />
<a href="/Team:Alberta/Sponsors" class="active"><p>Sponsors</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Sponsors</p><br />
</div><br />
<div class="block"><br />
<b> We would like to thank the following sponsors for their generosity and support over the course of this project.</b><br /><br /><br />
<p><a href="http://www.ualberta.ca"><img src="/wiki/images/b/b3/Ualberta-logo.png" alt="The University of Alberta"></img></a><br />
</p><br /><br />
<p><a href="http://albertatechfutures.ca/"><img src="/wiki/images/a/a3/Albertatechfutures-logo.png" style="height:100px;" alt="The University of Alberta"></img></a><br />
</p><br />
<p><a href="http://genomealberta.ca/"><img src="/wiki/images/c/cc/Genomealberta-logo.jpg" style="height:150px;" alt="The University of Alberta"></img></a><br />
</p><br />
<p><a href="http://www.genomikon.ca/"><img src="/wiki/images/3/3d/Genomikon-logo.gif" style="height:100px;" alt="The University of Alberta"></img></a><br />
</p><br /><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<!--html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Team
Team:Alberta/Team
2013-10-29T03:20:36Z
<p>MEsau: </p>
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</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><a id="project" href="#">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><i class="nav-icon"></i><a id="team" href="#" class="active">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team" class="active">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
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<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
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<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Mike-Ellison"><p>Mike Ellison</p></a><br />
<a href="#Dominic-Sauvageau"><p>Dominic Sauvageau</p></a><br />
<a href="#Mark-Rozema"><p>Mark Rozema</p></a><br />
<a href="#Cadence-Moorhouse"><p>Cadence Moorhouse</p></a><br />
<a href="#Dawson-Zeng"><p>Dawson Zeng</p></a><br />
<a href="#Michael-Esau"><p>Michael Esau</p></a><br />
<a href="#Rachel-Kwan"><p>Rachel Kwan</p></a><br />
<a href="#Stephanie-Chiu"><p>Stephanie Chiu</p></a><br />
<a href="#Larry-Zhang"><p>Larry Zhang</p></a><br />
<a href="#Cameron-Murray"><p>Cameron Murray</p></a><br />
<h5>Other Sections</h5><br />
<a href="/Team:Alberta/Team" class="active"><p>Roster</p></a><br />
<a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta"><p>Official Profile</p></a><br />
<a href="/Team:Alberta/Sponsors"><p>Sponsors</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<h1>Who We Are</h1><br />
<h5>Advisors</h5><br />
<ul>Professors:<br />
<ul><ul><li><b>Mike Ellison</b></li><br />
<li><b>Dominic Sauvageau</b></li></ul></ul><br />
</ul><br />
<h5>Team Members</h5><br />
<ul>Recent Graduates:<br />
<ul><ul><li><b>Mark Rozema</b></li><br />
<li><b>Larry Zhang</b></li><br />
<li><b>Michael Esau</b></li></ul></ul><br />
Undergraduates:<br />
<ul><ul><li><b>Dawson Zeng</b>: <i>Student Liaison</i></li><br />
<li><b>Rachel Kwan</b></li><br />
<li><b>Cadence Moorhouse</b></li></ul></ul><br />
High School Graduates:<br />
<ul><ul><li><b>Stephanie Chiu</b></li><br />
<li><b>Cameron Murray</b></li></ul></ul><br />
</ul><br />
</div><br />
<a class="anchor" id="Mike-Ellison"></a><br />
<div class="block"><br />
<h2>Mike Ellison</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/2/26/2013-Mellison.png"<br />
alt="Mike Ellison"></img></div><br />
Mike Ellison is a professor with the Department of Biochemistry at the University of <br />
Alberta.<br /><br />
His current focus on Synthetic Biology is to produce modular biological circuits of <br />
increasing sophistication using well-understood molecular components that can be <br />
reliably assembled into novel and useful forms of artificial life. He has been involved<br />
in iGEM for six years and continues to actively engage his undergraduate students <br />
in this synthetic biology competition.<br />
</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Dominic-Sauvageau"></a><br />
<div class="block"><br />
<h2>Dominic Sauvageau</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><br />
<img src="/wiki/images/d/d8/2013-Dsauvageau.jpg"<br />
alt="Team Member 9"></img></div>Dominic Sauvageau joined the Department of Chemical and Materials <br />
Engineering at the University of Alberta <br />
as an Assistant Professor in January 2011. His research involves the development of novel bacteriophage-<br />
based technologies and bioprocessing strategies for production in microbial systems. He joined the iGEM <br />
adventure last year when he supervised an iGEM-Entrepreneurial team (they won!). He's thrilled to be <br />
involved in iGEM again this year. He loves travelling and hopes he'll be able to use the E. coli we're <br />
working on to plan his next trip.</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Mark-Rozema"></a><br />
<div class="block"><br />
<h2>Mark Rozema</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/6/62/2013-Mrozema.jpg"<br />
alt="Team Member 9"></img></div><br />
Mark Rozema graduated from the Biochemistry program at the University of Alberta in April 2013 and is <br />
currently enrolled in the law program, also at the U of A. He enjoys running, early mornings, late nights <br />
and old scotch. Mark was involved in all facets of the project over the summer months, such as conceptual <br />
planning, establishing general protocol, part creation and part isolation but withdrew to focus on law <br />
school since the start of September.</p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Cadence-Moorhouse"></a><br />
<div class="block"><br />
<h2>Cadence Moorhouse</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/f/f1/2013-Cmoorhouse.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a 4th year genetics student at the University of Alberta. Every since high school I have had an <br />
interest in genetics and I heard all about the applications of synthetic biology largely through social <br />
media. It was at a talk by biotech guru Andrew Hessel that I first learned of iGEM. I was delighted to find <br />
out that the U of A had a team and a couple of emails later I was on the roster. This project has given me <br />
the opportunity to learn standard lab techniques and to see an experiment evolve. My experience teaching and <br />
coaching allows me to easily convey complex ideas into simpler ones. I hope to utilize these skills over the <br />
course of this project. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Dawson-Zeng"></a><br />
<div class="block"><br />
<h2>Dawson Zeng</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/9/90/2013-Dzeng.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a 4th year student at the University of Alberta majoring in Biological Sciences. I first heard about <br />
the field of Synthetic Biology from a guest speaker. It was then that I looked into joining iGEM Team <br />
Alberta. Personally, I think it is the coolest thing that Synthetic Biology combines philosophies from both <br />
Biology and Engineering; something I never thought about. Overall, my knowledge and understanding of <br />
genetics and interactions between DNA molecules vastly increased throughout the summer. A true testament to <br />
Richard Feynman’s famous quote, “What I cannot create, I do not understand.” </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Michael-Esau"></a><br />
<div class="block"><br />
<h2>Michael Esau</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/b/b7/2013-Mesau.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a graduate from the Biochemistry Specialization program at the University of <br />
Alberta. I learned about iGEM from Dr. Mike Ellison’s biochemistry class, and am <br />
happy to be a part of this year’s team. I'm planning to go into the synthetic bio <br />
research field and will be joining up with Dr. Dominic Sauvageau's lab for the next <br />
year. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Rachel-Kwan"></a><br />
<div class="block"><br />
<h2>Rachel Kwan</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/f/f0/2013-Rkwan.jpg"<br />
alt="Team Member 9"></img></div><br />
<p>After my first discoveries on the possibilities of iGEM from the local newspaper, I searched online and admired various iGEM projects. At this time during high school, I was personally unclear of my desired career path, aside from studying science, with a focus on Biology or Chemistry. Also with my vague knowledge of biotechnological methods, I was wary about the bioethical side of “manipulating nature,” especially from public warnings in literature.</p><br />
<p>However, within studying Biochemistry in my undergrad, I found that current methodologies of biotechnology seemed to have controlled lab settings, careful precautions, and/or a balance with purposeful benefits. Looking at the variety of iGEM projects, they used in-school material for real-world, practical applications. IGEM also attracted me because I liked the idea of working in a team setting to balance strengths and weaknesses with others. I believe that iGEM is rewarding and relevant in that it challenges teamwork, independence, creativity, writing, presenting, and lab technique. As part of my work, I hope to offer organizational skills, interest in safety, and Wiki ideas.</p><br />
<p>Outside of iGEM work, I play the piano and clarinet, read, meditate, play board games, search for good sales, and grow pet plants like basil.</p><br />
<br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Stephanie-Chiu"></a><br />
<div class="block"><br />
<h2>Stephanie Chiu</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/3/30/2013-Schiu.jpg"<br />
alt="Team Member 9"></img></div><br />
I am a first year student at the University of Alberta. I first heard about iGEM from friends at my high <br />
school and was privileged enough to join U of A’s team as I was finishing up my Grade 12 year. I am excited <br />
to learn more about what synthetic biology is and what working in a lab is like. I hope that I can offer a <br />
unique perspective to our team. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Larry-Zhang"></a><br />
<div class="block"><br />
<h2>Larry Zhang</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/8/83/2013-Lzhang.jpg"<br />
alt="Team Member 9"></img></div><br />
Passionate scientist born in the historical city of Yueyang, China; educated in the English for 8 years and <br />
has been under strict scientific indoctrination in the University of Alberta department of Biochemistry. <br />
Graduated with a Biochemistry degree with interest in genetics and genetic engineering, Larry Zhang has <br />
brought with him a huge idea cannon and a pair of magic pipetter’s hands; he is one of the most valuable <br />
assets in this team. </p><br />
<div class="clear"></div><br />
</div><br />
<a class="anchor" id="Cameron-Murray"></a><br />
<div class="block"><br />
<h2>Cameron Murray</h2><br />
<p class="floatLeft"><br />
<div class="expandable"><img src="/wiki/images/7/78/2013-Cmurray.jpg"<br />
alt="Team Member 9"></img></div> <br />
I am a first year university student studying molecular genetics at the U of A, however when I joined the <br />
team I was in my grade twelve year of high school. I heard about Synthetic biology through quirks and <br />
quarks, the CBC radio program, and was immediately taken with it and it’s vast possibilities. I was so <br />
enthralled that I talked about it quite a bit to my friends one of whom told me about iGEM. So here I am <br />
hoping to learn about and deepen my interest in synthetic biology through iGEM.</p><br />
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{|align="justify"<br />
|Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Aenean commodo ligula eget dolor. Aenean massa. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Donec quam felis, ultricies nec, pellentesque eu, pretium quis, sem. Nulla consequat massa quis enim. Donec pede justo, fringilla vel, aliquet nec, vulputate eget, arcu. In enim justo, rhoncus ut, imperdiet a, venenatis vitae, justo. Nullam dictum felis eu pede mollis pretium. Integer tincidunt. Cras dapibus. Vivamus elementum semper nisi. Aenean vulputate eleifend tellus. Aenean leo ligula, porttitor eu, consequat vitae, eleifend ac, enim. Aliquam lorem ante, dapibus in, viverra quis, feugiat a, tellus. Phasellus viverra nulla ut metus varius laoreet. Quisque rutrum. Aenean imperdiet. Etiam ultricies nisi vel augue. Curabitur ullamcorper ultricies nisi. Nam eget dui.<br />
|[[Image:Alberta_team.png|400px|right]]<br />
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<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
'''Advisors:'''<br />
<br />
*'''Mike Ellison''': Professor<br />
*'''Advisor 2''': Professor<br />
<br />
<br />
'''Team Members:'''<br />
<br />
*'''Mark Rozema''': Graduate<br />
*'''Larry Zhang''': Graduate<br />
*'''Michael Esau''': Graduate<br />
*'''Saima Zamir''': Graduate<br />
*'''Dawson Zeng''': Student Liaison, Undergraduate<br />
*'''Rachel Kwon''': Undergraduate<br />
*'''Cadence Moorhouse''': Undergraduate<br />
*'''Stephanie Chiu''': High School Graduate<br />
*'''Cameron Murray''': High School Graduate<br />
<br />
<br />
|<br />
<gallery><br />
Image:alberta_Team_member_1.png|Team member 1<br />
Image:alberta_Team_member_2.png|Team member 2<br />
Image:alberta_Team_member_3.png|Team member 3<br />
Image:alberta_Team_member_4.png|Team member 4<br />
Image:alberta_Team_member_5.png|Team member 5<br />
Image:alberta_Team_member_6.png|Team member 6<br />
Image:alberta_Team_member_7.png|Team member 7<br />
Image:alberta_Team_member_8.png|Team member 8<br />
Image:alberta_Team_member_9.png|Team member 9<br />
</gallery><br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
<br />
== '''Where we're from''' ==<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Attributions
Team:Alberta/Attributions
2013-10-29T03:20:18Z
<p>MEsau: </p>
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<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
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<div class="main"><br />
<div class="block"><br />
<p class="content-title">Attributions</p><br />
</div><br />
<div class="block"><br />
<p>All of the experimental work described herein was performed by the team with technical support from Prof. Ellison’s technician, <b>Nien-tsu Tseng (Rick)</b>. The TSP concept was inspired by the <b>Missouri-Davidson 2007 iGEM team</b> who broke the ice with their work on the Hamiltonian variation of TSB problem. The experimental approaches used here evolved over discussions with our supervisors during group meetings. The correct weighting algorithm that relates city path lengths to linker concentrations was developed by <b>Dr. Doug Ridgway</b>, a supervisor of the 2012 iGEM team. The plasmids used to create TSB compatible parts by PCR were a gift from <b>Genomikon Inc</b>. <br />
The creation of the violacin bricks that we will use in the test of the 5-city TSB would not have been possible without the violacein operon biobrick (K274002) that was created, submitted and carefully characterized by the <b>Cambridge 2009 iGEM team</b>. Wiki coding and design implementation was done by <b>Timo Hohn</b>, (B.Sc. in Computer Engineering).<br />
</p><br />
<br><br />
<p>Thanks to these individuals for donating their time and talents!</p><br />
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<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Accomplishments
Team:Alberta/Accomplishments
2013-10-29T03:19:59Z
<p>MEsau: </p>
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.centered-well {<br />
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.thumbnails {<br />
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.thumbnail img{<br />
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.thumbnail img:hover {<br />
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</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments" class="active">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments" class="active"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Accomplishments</p><br />
</div><br />
<div class="block"><br />
<img src="/wiki/images/a/af/2013-Accomplishments.PNG" style="width:100%;"></img><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<h2> Awards<br />
</h2><br />
<br />
<img src="/wiki/images/thumb/9/95/Presentationpic.jpg/800px-Presentationpic.jpg " style="width:50%" align="right"></img><br />
<br />
<p>Team Alberta was thrilled to receive recognition at the North American Regional Jamboree competition:</p><br />
<br><br />
<p><b>Best Presentation</b> - in the undergraduate category </p><br />
<p><b>Gold Medal </b>– for fulfilling criteria</p><br />
<p><b>Advancement to World Finals</b></p><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
</div><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<br />
</body><br />
</html><br />
<br />
<br />
<!-- <html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Parts
Team:Alberta/Parts
2013-10-29T03:19:32Z
<p>MEsau: </p>
<hr />
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}<br />
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}<br />
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}<br />
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}<br />
.tooltip .saying {<br />
content: " ";<br />
top:100px;<br />
display:block;<br />
left: 200px;<br />
max-height:1000px;<br />
position: absolute;<br />
} <br />
.tooltip .saying:after {<br />
border-bottom: solid transparent 10px;<br />
border-top: solid transparent 10px;<br />
border-right: solid #EEE 10px;<br />
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content: "";<br />
margin-left:-16px;<br />
position: absolute;<br />
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max-height:1000px;<br />
display:block;<br />
}<br />
.tooltip:hover .saying {<br />
opacity: 1;<br />
visibility: visible;<br />
-webkit-transform: translateX(0px);<br />
-moz-transform: translateX(0px);<br />
-ms-transform: translateX(0px);<br />
-o-transform: translateX(0px);<br />
transform: translateX(0px);<br />
}<br />
.active {<br />
color:#04acec !important;<br />
}<br />
.navbar, .navbar ul {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.navbar {<br />
width:963px;<br />
margin:60px auto;<br />
position:fixed;<br />
top:70px;<br />
z-index:4;<br />
border: 1px solid #DDD;<br />
background-color:#FFF;<br />
background-image: -moz-linear-gradient(#FFF, #DDD);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#DDD));<br />
background-image: -webkit-linear-gradient(#FFF, #DDD);<br />
background-image: -ms-linear-gradient(#FFF, #DDD);<br />
background-image: linear-gradient(#FFF, #DDD);<br />
-moz-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
-webkit-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
zoom:1;<br />
}<br />
.navbar:before, .navbar:after {<br />
content: "";<br />
display: table;<br />
}<br />
.navbar:after {<br />
clear:both;<br />
}<br />
.navbar li {<br />
float:left;<br />
border-right:1px solid #CCC;<br />
-moz-box-shadow:1px 0 0 #EEE;<br />
-webkit-box-shadow: 1px 0 0 #EEE;<br />
box-shadow: 1px 0 0 #EEE;<br />
position: relative;<br />
}<br />
.navbar a {<br />
float: left;<br />
padding: 12px 30px;<br />
color: #444;<br />
font: bold 12px Arial, Helvetica;<br />
text-decoration:none;<br />
/*text-shadow: 0 1px 0 #333;*/<br />
}<br />
.navbar li:hover > a {<br />
color:#BBB;<br />
}<br />
.navbar li a:hover { /* IE6 only */<br />
color:#BBB;<br />
}<br />
.navbar ul {<br />
margin:20px 0 0 0;<br />
_margin: 0; /* IE6 only */<br />
opacity: 0;<br />
visibility: hidden;<br />
position:absolute;<br />
top:38px;<br />
left:0;<br />
z-index:1;<br />
background:#FFF;<br />
background: -moz-linear-gradient(#FFF, #CCC);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#CCC));<br />
background: -webkit-linear-gradient(#FFF, #CCC);<br />
background: -o-linear-gradient(#FFF, #CCC);<br />
background: -ms-linear-gradient(#FFF, #CCC);<br />
background: linear-gradient(#FFF, #CCC);<br />
-moz-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-webkit-box-shadow: 0 -1px rgba(255,255,255,.3);<br />
-box-shadow:0 -1px 0 rgba(255,255,255,.3);<br />
-moz-border-radius: 3px;<br />
-webkit-border-radius: 3px;<br />
border-radius: 3px;<br />
-webkit-transition: all .2s ease-in-out;<br />
-moz-transition: all .2s ease-in-out;<br />
-ms-transition: all .2s ease-in-out;<br />
-o-transition: all .2s ease-in-out;<br />
transition: all .2s ease-in-out;<br />
}<br />
.navbar li:hover > ul {<br />
opacity: 1;<br />
visibility: visible;<br />
margin:0;<br />
}<br />
.navbar ul ul {<br />
top:0;<br />
left:150px;<br />
margin:0 0 0 20px;<br />
_margin:0;/*IE6 only*/<br />
-moz-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
-webkit-box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
box-shadow:-1px 0 0 rgba(255,255,255,.3);<br />
}<br />
.navbar ul li {<br />
float:none;<br />
display:block;<br />
border:0;<br />
_line-height:0; /*IE6 only*/<br />
-moz-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
-webkit-box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
box-shadow: 0 1px 0 #AAA, 0 2px 0 #FFF;<br />
}<br />
.navbar ul li:last-child {<br />
-moz-box-shadow:none;<br />
-webkit-box-shadow:none;<br />
box-shadow:none;<br />
}<br />
.navbar ul a {<br />
padding:10px;<br />
width:130px;<br />
_height:10px;/*IE6 only*/<br />
display:block;<br />
white-space:nowrap;<br />
float:none;<br />
text-transform:none;<br />
}<br />
.navbar ul a:hover {<br />
background-color:#0186ba;<br />
background-image: -moz-linear-gradient(#04acec, #0186ba);<br />
background-image: -webkit-gradient(linear, left top, left bottom, from(#04acec), to(#0186ba));<br />
background-image: -webkit-linear-gradient(#04acec, #0186ba);<br />
background-image: -ms-linear-gradient(#04acec, #0186ba);<br />
background-image: linear-gradient(#04acec, #0186ba);<br />
}<br />
.navbar ul li:first-child > a {<br />
-moz-border-radius: 3px 3px 0 0;<br />
-webkit-border-radius: 3px 3px 0 0;<br />
border-radius: 3px 3px 0 0;<br />
}<br />
.navbar ul li:first-child > a:after {<br />
content:'';<br />
position:absolute;<br />
left:40px;<br />
top:-6px;<br />
border-left:6px solid transparent;<br />
border-right:6px solid transparent;<br />
border-bottom:6px solid #FFF;<br />
}<br />
.navbar ul ul li:first-child a:after {<br />
left:-6px;<br />
top:50%;<br />
margin-top:-6px;<br />
border-left:0;<br />
border-bottom:6px solid transparent;<br />
border-top: 6px solid transparent;<br />
border-right:6px solid #3b3b3b;<br />
}<br />
.navbar ul li:first-child a:hover:after {<br />
border-bottom-color: #04acec;<br />
}<br />
.navbar ul ul li:first-child a:hover:after {<br />
border-right-color: #0299d3;<br />
border-bottom-color:transparent;<br />
}<br />
.navbar ul li:last-child > a {<br />
-moz-border-radius: 0 0 3px 3px;<br />
-webkit-border-radius: 0 0 3px 3px;<br />
border-radius: 0 0 3px 3px;<br />
}<br />
.centered {<br />
text-align:center;<br />
}<br />
.centered-well {<br />
text-align:center;<br />
width:80%;<br />
margin:0 auto;<br />
padding:5px;<br />
background-color:#CCC;<br />
border-radius:6px;<br />
-moz-border-radius:6px;<br />
-o-border-radius:6px;<br />
-webkit-border-radius:6px;<br />
}<br />
.thumbnails {<br />
padding: 35px;<br />
width:700px;<br />
margin:0 auto;<br />
}<br />
.thumbnail {<br />
position:relative;<br />
display:inline-block;<br />
left:180px;<br />
}<br />
.thumbnail img{<br />
/* ... */<br />
height:100px;<br />
position:relative;<br />
-webkit-transition: all .25s ease-out;<br />
-moz-transition: all .25s ease-out;<br />
-ms-transition: all .25s ease-out;<br />
-o-transition: all .25s ease-out;<br />
transition: all .25s ease-out;<br />
} <br />
.thumbnail img:hover {<br />
transform:scale(4,4);<br />
-webkit-transform:scale(4,4);<br />
-moz-transform:scale(4,4);<br />
-ms-transform:scale(4,4);<br />
-o-transform:scale(4,4);<br />
z-index:999;<br />
background-color:white;<br />
border:solid 2px #CCC;<br />
border-radius:1px;<br />
-moz-border-radius:1px;<br />
-o-border-radius:1px;<br />
-webkit-border-radius:1px;<br />
-moz-box-shadow: 0px 0px 30px #000;<br />
-o-box-shadow: 0px 0px 30px #000;<br />
-webkit-box-shadow: 0px 0px 30px #000;<br />
box-shadow: 0px 0px 30px #000;<br />
<br />
}<br />
a.anchor{<br />
display: block; <br />
position: relative; <br />
top: -180px; <br />
visibility: hidden;<br />
}<br />
#groupparts {<br />
/*margin-left:-11px;*/<br />
width:100% !important;<br />
}<br />
</style><br />
</head><br />
<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts" class="active">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
<li><a href="/Team:Alberta/Outreach">Outreach</a></li><br />
<li><a href="/Team:Alberta/Community">Community</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
<li><a href="/Team:Alberta/FAQ">FAQ</a></li><br />
<li><a href="/Team:Alberta/Resources">Resources</a></li><br />
</ul><br />
</li><br />
<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts" class="active"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<div class="block"><br />
<p class="content-title">Submitted Parts</p><br />
</div><br />
<div class="block"><br />
<p> Our 2013 parts submitted are a set of violacein genes derived from the violacein operon constructed and <br />
submitted by Cambridge in 2009 (BBa_K274002). We have made a number of modifications, including upgrading the <br />
plasmid backbone from pSB1K3 to pSB1C3 standard 10, and converting each of the five open reading frames into <br />
its own part with a common and improved ribosome binding site (BBa_B0030) such that they can be assembled in <br />
different combinations and permutations. All of the parts have been characterized and are functional, and we <br />
have found that a new combination, VioABCE, produces a new pigment which we call "Royal Blue". </p><br />
<img src="/wiki/images/f/f0/2013-Alberta-Submitted_parts.PNG" style="width:100%;"></img><br />
<br />
</html><br />
<groupparts>iGEM013 Alberta</groupparts><br />
<html><br />
<br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html><br />
<br />
<br />
<!-- <html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.<br />
<br />
<br />
<groupparts>iGEM013 Alberta</groupparts><br />
<br />
--></div>
MEsau
http://2013.igem.org/Team:Alberta/Protocols
Team:Alberta/Protocols
2013-10-29T03:19:08Z
<p>MEsau: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
.titlebar {<br />
height:130px;<br />
width:100%;<br />
}<br />
.bin {<br />
background:url('/wiki/images/e/e4/2013AlbertaBackground.png');<br />
background-size:100% auto;<br />
padding-top:20px;<br />
}<br />
@-moz-document url-prefix() {<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
margin-left:-110px;<br />
}<br />
}<br />
.nav-icon {<br />
background-image:url('/wiki/images/6/69/Nav-icon.png');<br />
display:inline-block;<br />
position:fixed;<br />
width:23px;<br />
height:37px;<br />
margin-top:-17px;<br />
}<br />
.block {<br />
background-color:white;<br />
border:1px grey solid;<br />
padding:10px;<br />
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border-radius:5px;<br />
box-shadow: 0px 0px 30px #444444;<br />
}<br />
.titlebar {<br />
position:fixed;<br />
top:0px;<br />
height:130px;<br />
margin-left:-5px;<br />
width:975px;<br />
z-index:2;<br />
background-color:#FFF;<br />
}<br />
.content-title {<br />
text-align:center;<br />
font-size:3em;<br />
}<br />
.titlebar h3, h4 {<br />
text-align:center;<br />
}<br />
.sidebar {<br />
position: fixed;<br />
top: 157px;<br />
float: left;<br />
z-index: 3;<br />
padding: 10px 10px 10px 10px;<br />
width: 230px;<br />
}<br />
.sidebar_block {<br />
background-color:white;<br />
margin:1px;<br />
border:1px grey solid;<br />
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border-radius:5px;<br />
box-shadow: 0px 0px 20px #444444;<br />
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.main {<br />
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}<br />
.clear {<br />
clear:both;<br />
}<br />
.ualberta-logo {<br />
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margin-left:70px;<br />
margin-top:-70px;<br />
width:180px;<br />
}<br />
.igem-logo {<br />
position:fixed;<br />
margin-left:650px;<br />
margin-top:-95px;<br />
width: 150px;<br />
}<br />
.igem-logo img {<br />
width:210px;<br />
}<br />
.igem-bar {<br />
position:relative;<br />
float:right;<br />
}<br />
.igem-bar a {<br />
padding:0 !important;<br />
}<br />
.igem-bar img {<br />
height:38px;<br />
}<br />
.tooltip {<br />
width:100%;<br />
}<br />
.tooltip .saying {<br />
background: #EEE;<br />
color: #444;<br />
left: 100px;<br />
margin-bottom: 15px;<br />
opacity: 0;<br />
padding: 20px;<br />
position: absolute;<br />
visibility: hidden;<br />
min-width:200px;<br />
max-width:500px;<br />
-webkit-transform: translateX(10px);<br />
-moz-transform: translateX(10px);<br />
-ms-transform: translateX(10px);<br />
-o-transform: translateX(10px);<br />
transform: translateX(10px);<br />
-webkit-transition: all .25s ease-out;<br />
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.tooltip .saying {<br />
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.tooltip .saying:after {<br />
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border-top: solid transparent 10px;<br />
border-right: solid #EEE 10px;<br />
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content: "";<br />
margin-left:-16px;<br />
position: absolute;<br />
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.tooltip:hover .saying {<br />
opacity: 1;<br />
visibility: visible;<br />
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-o-transform: translateX(0px);<br />
transform: translateX(0px);<br />
}<br />
.active {<br />
color:#04acec !important;<br />
}<br />
.navbar, .navbar ul {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.navbar {<br />
width:963px;<br />
margin:60px auto;<br />
position:fixed;<br />
top:70px;<br />
z-index:4;<br />
border: 1px solid #DDD;<br />
background-color:#FFF;<br />
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background-image: -webkit-gradient(linear, left top, left bottom, from(#FFF), to(#DDD));<br />
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background-image: -ms-linear-gradient(#FFF, #DDD);<br />
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-moz-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
-webkit-box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
box-shadow: 0 1px 1px #444, 0 1px 0 #444;<br />
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}<br />
.navbar:before, .navbar:after {<br />
content: "";<br />
display: table;<br />
}<br />
.navbar:after {<br />
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}<br />
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<body><br />
<div class="titlebar"><br />
<br><br />
<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
</div><br />
<div class="bin"><br />
<ul class="navbar"><br />
<li><a href="/Team:Alberta">Home</a></li><br />
<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
<ul><br />
<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols" class="active">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
<li><a href="/Team:Alberta/Attributions">Attributions</a></li><br />
</ul><br />
</li><br />
<li><a id="team" href="#">Team</a><br />
<ul><br />
<li><a href="/Team:Alberta/Team">Roster</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Alberta">Official Profile</a></li><br />
<li><a href="/Team:Alberta/Sponsors">Sponsors</a></li><br />
</ul><br />
</li><br />
<li><a id="humanpractices" href="#">Human Practices</a><br />
<ul><br />
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</ul><br />
</li><br />
<li><a href="/Team:Alberta/MainSafety">Safety</a><br />
<ul><br />
<li><a href="/Team:Alberta/SafetyForm">Safety Form</a></li><br />
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<div class="igem-bar"><a href="https://2013.igem.org"><img src="/wiki/images/a/ad/IGem-logo.png"></img></a></div><br />
</ul><br />
<div class="sidebar"><br />
<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Parts"><p>The Parts</p></a><br />
<a href="#Build"><p>Building the Plasmids</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols" class="active"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
</div><br />
</div><br />
<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Protocols</p><br />
</div><br />
<a class="anchor" id="Parts"></a><br />
<div class="block"><br />
<h2>The Parts</h2><br />
<p>The 6 genes that were required to assemble various routes were obtained by PCR from plasmids kindly provided by Genomikon Inc. Each gene (AmpR, KanR, ClrR, GFP, RFP and aCP) exist as self contained cassettes that are flanked by BsaI sites. Parts were then generated according to the schematic shown below:</p><br />
<img src="/wiki/images/c/c5/Making_parts_678x586.png" align="middle" style="width:100%;"><br />
</div><br />
<a class="anchor" id="Build"></a><br />
<div class="block"><br />
<h2>Building the Plasmids</h2><br />
<p>Our plasmid assembly system relies upon the achievements of previous Team Alberta iGEM entries, 2009’s BioBytes and 2010’s Genomikon assembly methods. This process begins with origins of replication anchored at one end to magnetic beads in a suspension within a reaction microfuge tube. The anchored strands have a single, free-floating sticky end, onto which successive genes are ligated. Once the new gene has been ligated on, we use a magnet to hold the beads (along with the anchored DNA) inside the reaction tube, while washing away the rest of the reaction, including the enzyme, buffers, and any non-ligated DNA that remains. The beads are then resuspended in a new reaction mixture, containing the next ligation step.</p><br />
<img src="/wiki/images/b/b4/2013Alberta-Poster2.jpg" align="middle" style="width:100%;"><br />
<p>Once all of the genes have been ligated, a tail-piece that complements the original bead-anchor DNA sequence is added, so that the finished product can be unbound from the beads and will close upon itself to form the circular plasmid. In this fashion, a four-gene, roughly 5000-base-pair plasmid is assembled in as little as an afternoon, cheaply and easily.</p><br />
</div><br />
</div><br />
<div class="clear"></div><br />
</div><br />
</body><br />
</html></div>
MEsau
http://2013.igem.org/Team:Alberta/Results
Team:Alberta/Results
2013-10-29T03:18:37Z
<p>MEsau: </p>
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<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#First-Tests"><p>The First Tests</p></a><br />
<a href="#Linkers"><p>Perfecting the Linkers</p></a><br />
<a href="#Assembly"><p>The Full Assembly</p></a><br />
<a href="#Colour-Controls"><p>Colour Controls</p></a><br />
<a href="#Calibration"><p>Initial Calibration</p></a><br />
<a href="#TSP"><p>The Travelling Salesman Problem</p></a><br />
<a href="#Adapt-POP"><p>Increasing Complexity</p></a><br />
<a href="#Revised-Strategy"><p>A Revised Strategy</p></a><br />
<a href="#DNA-Library"><p>Cosmid DNA Library</p></a><br />
<a href="#PCR"><p>PCR Identification</p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results" class="active"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
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<div class="main"><br />
<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Results</p><br />
</div><br />
<a class="anchor" id="First-Tests"></a><br />
<div class="block"><br />
<h2>The First Tests</h2><br />
<p>We performed some initial tests to confirm the efficacy of our assembly system. The Genomikon assembly method requires that we be able to successfully bind and elute DNA from magnetic beads, and that we be able to perform successive ligations on the bead-bound strands. These are necessary for building the plasmid "routes", as described in the project overview page. </p><br />
<br />
<p>In the gel below, the second lane displays the result of an origin of replication (Ori) sample that was bound to the bead, washed and then re-eluted – the presence of DNA at the desired mass in this lane confirms the successful binding and elution. The third lane demonstrates that we can successfully ligate genes (KanR in this case) directly to the Ori at high efficiency and still safely elute them. In the fourth lane, we have ligated a 13-base-pair linker onto the existing Ori-KanR, followed by a second gene, ChlorR. Although the high-mass band suggests that ligation was successful, the fact that there is still a stronger band at the Ori-KanR mass suggests that the ligation has not proceeded to completion.</p><br />
<p><img src="/wiki/images/7/7e/2013-Alberta-Results-Figure_1.png" style="width:100%;"></img><br /><br />
Figure 1: Agarose gel electrophoresis image from initial ligation trials. <br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Origin of replication, bound to the magnetic beads and then eluted. <br /><br />
Lane 3: KanR gene ligated to bead-bound Ori.<br /> <br />
Lane 4: Existing bead-bound Ori-KanR sample ligated with linker, then ligated with ChlorR <br /><br />
(beads are always washed between ligations).</p><br />
</div><br />
<a class="anchor" id="Linkers"></a><br />
<div class="block"><br />
<h2>Perfecting the Linkers</h2><br />
<p>The incomplete ligation of the previous step presents an obstacle for our system, but the issue appears to be isolated to the ligation step involving the short linker piece. To get a more effective ligation without extending the timeframe of our assembly, we made several adjustments. First, we raised ligation temperature from 4°C to 22°C in the hopes of increasing the enzyme activity. Second, we switched to a larger, 25-base-pair linker – we were able to successfully ligate large pieces in the case of the Ori and KanR ligation, so perhaps size plays a factor. Also, we used better-purified stocks of our genes, to eliminate the possibility that some interfering piece of the original plasmid was competing with our desired reaction. Finally, we attempted to increase the concentration of the linker in the hopes of driving the reaction to completion. Here, we can see that our changes have significantly improved the ligation efficiency, although changing the linker concentration has not created an appreciable benefit. </p><br />
<p><img src="/wiki/images/9/9e/2013-Alberta-Figure_2.png" style="width:100%;"></img><br /><br />
Figure 2: Agarose gel electrophoresis image from linker concentration comparison after<br />
ligation protocol adjustments.<br /><br />
Lane 1: DNA Markers<br /><br />
Lane 2: Ori-KanR ligation to linker, then to ChlorR (as in Figure 1, Lane 4) using 10:1 ratio of <br />
linker to Ori. <br /><br />
Lane 3: As lane 2, with 50:1 ratio.<br /><br />
Lane 4: As lane 3, with 100:1 ratio. </p><br />
</div><br />
<a class="anchor" id="Assembly"></a><br />
<div class="block"><br />
<h2>The Full Assembly</h2><br />
<p>With our successful ligation protocol established, we moved on to attempting a full-scale <br />
assembly, with four genes (the quantity required for our proof-of-concept travelling salesman<br />
problem). In this gel, the four lanes show the successive addition of the four genes, which <br />
are, for the most part, successful. In each lane, there is some remainder of the previous <br />
products left behind, including (presumably) instances of strands that were incomplete in <br />
one reaction continuing to acquire genes in a successive one. Regardless, these incomplete <br />
genes represent only a small fraction of the total DNA. </p><br />
<p><img src="/wiki/images/3/37/2013-Alberta-Results-Figure_3.png" style="width:100%;"></img><br /><br />
Figure 3: Agarose gel electrophoresis image from full assembly test. <br /><br />
Lane 1: DNA Markers.<br /><br />
Lane 2: Ori to KanR ligation product.<br /><br />
Lane 3: Ori-KanR to linker to GFP ligation product.<br /><br />
Lane 4: Ori-KanR-Linker-GFP to linker to RFP ligation product.<br /><br />
Lane 5: Ori-KanR-Linker-GFP-Linker-RFP to linker to ChlorR ligation product. </p><br />
<p>The product plasmids from this assembly were transformed into a bacterial culture and <br />
grown on a Kan/Chlor plate to examine practical impact of the rate of incomplete ligations. <br />
The plate image is shown below – about 90% of the colonies display the desired RFP/GFP <br />
(orange colouration) phenotype indicating a perfect successful ligation of the plasmid. </p><br />
<img src="/wiki/images/4/4e/Ab_Assembly_efficiency.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Colour-Controls"></a><br />
<div class="block"><br />
<h2>Colour Controls</h2><br />
<p>In our planned, four-city proof-of-concept test (see the map below), there are exactly three <br />
possible solutions and three corresponding phenotypes: blue/green (dark green) bacteria <br />
with Amp/Chlor resistance, red/green (orange) bacteria with Chlor/Kan resistance, and <br />
red/blue (purple) bacteria with Amp/Kan resistance. </p><br />
<img src="/wiki/images/8/8d/2013Alberta-mapmaker-states.png" style="width:100%;"></img><br />
<p>To ensure we would be able to correctly identify plasmids based on phenotype we prepared <br />
a set of control plates, where bacteria grown from pure assemblies of the desired “route” <br />
plasmid were grown alongside bacteria possessing only one of the two colours from that <br />
route, for comparison purposes. The resulting plates can be seen above. </p><br />
</div><br />
<a class="anchor" id="Calibration"></a><br />
<div class="block"><br />
<h2>Initial Calibration</h2><br />
<p>In preparation for our initial travelling salesman problems, we attempted to discern the <br />
extent to which unexpected or unknown biases might affect the frequency of colonies <br />
growing with a particular gene.</p><br />
<p>In this test, we performed an assembly in which both GFP and aCP were included (in equal <br />
molar concentration) in the initial ligation onto the Ori, followed by a ligation of ChlorR, <br />
resulting in a mixture of Ori-GFP-ChlorR and Ori-aCP-ChlorR plasmids. We transformed these <br />
plasmids into a single bacterial culture, which we then spread on a Chlor-treated plate in <br />
order to count the resulting colonies. We repeated this test for each of the other four genes <br />
to be used in our proof-of-concept TSP, comparing each against GFP as a standard. This <br />
provided us with the following ratios of growth.</p><br />
<p>Table 1: 1GFP 6aCP<br /><img src="/wiki/images/5/5d/2013Alberta-Ratiotable.png" style="width:100%;"></img></p><br />
<p>We then attempted another assembly in which we calibrated for the bias. We used a 6:1 <br />
molar ratio of GFP to aCP in the new assembly, otherwise performing the experiment as <br />
before, and produced a new plate with a ratio of approximately 1:1 GFP colonies to aCP <br />
colonies. Although imperfect, this calibration was adequate for our proof-of-concept trial.</p><br />
</div><br />
<a class="anchor" id="TSP"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p> We have conducted a single successful travelling salesman problem following the procedure outlined in the project overview page. Relative to the previous assembly steps, the only key difference is that this time, several genes are included at each ligation step and at varying concentrations, so that the assembly produces a mix of plasmids, but favours some genes over others (creating a bias for shorter paths). See the overview page for more details on how this works. </p><br />
<p>This particular problem was based on a map of four cities in which four of the paths have an arbitrary unit distance of 1, and the remaining two paths have a distance of 4. Of the possible routes in this problem, one route has a total sum distance of 4, and the other two have distances of 10, making that route clearly preferable, and a suitable test of our biocomputer. The three possible routes, with correct gene-path assignment and distances listed for this problem, can be seen below. At each ligation step, we added a quantity of each gene based on the reciprocal of its distance, so that, for instance, the genes corresponding to paths of distance 4 had roughly one-quarter of the concentration (this value was then adjusted by our calibrations, as described above, to arrive at the actual concentration) of those with distance 1. </p><br />
<img src="/wiki/images/a/ab/2013Alberta-POP.png" style="width:100%;"></img><br />
<p>On the resulting plates, we counted 18 colonies corresponding to the ChlorR/GFP/aCP/AmpR route, and 21 colonies corresponding to the ChlorR/RFP/GFP/KanR route. For the optimal route, KanR/aCP/RFP/AmpR, we found 61 colonies, clearly identifying this as the solution to the problem. When the percentage of each of these three types of colonies on each plate is normalized to the best solution, the results of this trial are very close to the expected values calculated for this experiment. </p><br />
</div><br />
<a class="anchor" id="Adapt-POP"></a><br />
<div class="block"><br />
<h2>Can we adapt our POP to a much more complex problem?</h2><br />
<p>The ultimate limit of an approach such as this, depends upon the<br />
number of complete TSP solutions (plasmids) that can be clonally<br />
amplified through cell transformation. We estimate that solving a 15-city<br />
problem is within the realm of existing state-of-the-art, but not without<br />
major revisions to our POP work presented here. The 15-city problem is<br />
not trivial even by conventional computing standards. With 120 intercity<br />
links resulting in 87,178,291,200 possible solutions, 50 days would be<br />
required to identify the best solutions at a computational rate of 10,000<br />
solutions/second!</p><br />
<p>The challenges:</p><br />
<ol><br />
<li>In the POP, solutions are identified by visually<br />
determining the frequency of colonies exhibiting<br />
the appropriate path combinations represented by<br />
the three colour genes and the three drug<br />
resistance genes. Extending this approach to the<br />
15-city problem would require the acquisition of<br />
120 markers that are combined 87,178,291,200<br />
ways, well beyond the analytical resolution of<br />
standard plating methods.</li><br />
<li>A statistically significant sampling of complete<br />
solutions is well outside the plasmid transformation<br />
efficiencies of even the best competent cells<br />
available.</li><br />
<li>The precision and efficiency for assembling<br />
complete-solution plasmids (38 steps in all)<br />
remains to be tested.</li><br />
</ol><br />
<img src="/wiki/images/7/72/2013-Results_z1.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Revised-Strategy"></a><br />
<div class="block"><br />
<h2>A revised strategy</h2><br />
<p><b>Cities and Paths.</b> In the new approach we invert the role that DNA<br />
plays in defining cities and paths. Here, a city corresponds to a gene<br />
that complements an amino acid auxotrophy in E. coli (illustrated<br />
below). The city is therefore required for growth on defined media that<br />
lacks that amino acid. By extension, 15 different cities represented by<br />
15 a.a. auxotrophic markers would be required for survival of E. coli<br />
deficient for these genes when grown on media that lacks the<br />
corresponding amino acids. Complete plasmid solutions therefore are<br />
exclusively selected and amplified from their non-solution counterparts.<br />
Creating a 15-gene knockout in E. coli is not trivial but absolutely<br />
possible.</p><br />
<p>The ability to link any two city genes requires that each city has at<br />
its 5’ and 3’ ends, overhangs that are nonpalindromic,<br />
noncomplementary, and that are distinct in sequence from any of the 14<br />
other city genes.</p><br />
<p>The 120 path possibilities that are needed to link any two cities,<br />
are represented by a mixture of 120 synthetic duplex linkers where each<br />
linker has two different complementary ends that are capable of linking<br />
one of the 120 possible intercity pairs. Shorter intercity distances are<br />
favoured by adjusting the concentration of each linker in the mixture<br />
according to a new and improved weighting algorithm described below.<br />
We point out that in terms of economy, all 120 linkers can be produced<br />
from 30 oligos used in pair-wise combinations.</p><br />
<p>An unavoidable complication of this method is that any given city<br />
can occur more than once (at lower frequency) across the 15 available<br />
steps during sequential assembly (illustrated above for the three-city<br />
example). It should be noted however that any city duplication excludes<br />
the possibility of creating the complete set and will therefore be<br />
selected against post-transformation.</p><br />
<img src="/wiki/images/1/10/2013-Results_z2.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="DNA-Library"></a><br />
<div class="block"><br />
<h2>Creating a cosmid DNA library of that is highly biased for best<br />
solutions.</h2><br />
<p>To date, &lambda; phage-based recombinant libraries remain<br />
unprecedented in terms of the size and diversity of their DNA<br />
constituents. In its most advanced form, “cosmid” library kits are<br />
commercially available that produce 10<sup>10</sup> transformants. Cosmids retain<br />
the phage elements that are required for phage packaging and infection<br />
but lack the elements required for phage propagation and cell lysis. A<br />
plasmid origin allows them to replicate as plasmids.</p><br />
<p>Cosmids are constructed as linear molecules that begin and end<br />
with phage sequences the essential phage sequences(, &lambda;L and &lambda;R).<br />
Complementary 12-base overhangs that constitute the lambda cos and cos’<br />
sites are also required for efficient circularization once the cosmid has<br />
entered the cell.</p><br />
<p>In addition to its favourable tranformation properties, another<br />
attractive feature of using a cosmid-based system for TSP is that DNA<br />
molecules below a certain length threshold, package poorly, thereby<br />
contributing to the selection of full-length solutions.</p><br />
<p>An overview highlighting the key aspects of library creation is<br />
shown below. The assembly procedure uses magnetic beads where the<br />
cos’ sequence has been covalently linked. Asssembly begins with a cos- <br />
&lambda;L synthetic adapter that allows for the subsequent addition of &lambda;L. The<br />
addition of spacer sequences insure that total size of the construct is<br />
optimal for packaging (~50kB). Linker combinations are then added in<br />
alternation with city combinations until the city content is complete.<br />
Finally the construct is terminated with &lambda;R and a cos’ adapter. Following<br />
packaging cells are infected in selective liquid medium and the cosmid<br />
population is isolated for PCR analysis. The library is heavily biased 1)<br />
for complete solutions based on the assembly and packaging<br />
considerations already described and 2) for best solutions based on the<br />
path weights assigned to each linker addition step.</p><br />
<img src="/wiki/images/5/55/Results_z3.PNG" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="PCR"></a><br />
<div class="block"><br />
<h2>PCR-based identification of best solutions.</h2><br />
<p>The two types of data that is required for piecing best solutions together<br />
are 1) determining the cities that most frequently occupy each position<br />
from 1 to 15 and 2) determining the most frequently used intercity pairs<br />
as outlined below.</p><br />
<img src="/wiki/images/3/37/2013-Results_z4.PNG" style="width:100%;"></img><br />
</div><br />
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http://2013.igem.org/Team:Alberta
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<li><i class="nav-icon"></i><a href="/Team:Alberta" class="active">Home</a></li><br />
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<li><a href="/Team:Alberta/Background">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
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<img src=" /wiki/images/2/2d/Background_icon.png " align="left" width="50" height="50"></img>Curious about the possibilities of biocomputing? Need of a crash course on travelling salesman problems? Visit our <a href="https://2013.igem.org/Team:Alberta/Background">background page</a> for more information on the real-world applications of our project.<br />
<br><br />
<br><br />
<img src="/wiki/images/thumb/b/bf/Workings_icon.png/610px-Workings_icon.png " align="left" width="50" height="50"></img><br />
Want to get straight to the details of what Team Alberta has been working on this summer? Read up in the <a href="https://2013.igem.org/Team:Alberta/Overview">overview</a> and <a href="https://2013.igem.org/Team:Alberta/Results">results</a> pages to see what we've achieved.<br />
<br><br />
<br><br />
<img src=" /wiki/images/thumb/f/f6/Peoples_icon.png/618px-Peoples_icon.png" align="left" width="50" height="50"></img>Or maybe you'd like to get to know the team itself, those who have helped us along and those we've helped in turn? See the <a href="https://2013.igem.org/Team:Alberta/Team">team roster</a>, <a href="https://2013.igem.org/Team:Alberta/Attributions">sponsors</a> and <a href="https://2013.igem.org/Team:Alberta/Outreach">outreach</a> pages to meet everyone who's participated.<br />
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<!--div class="block"><br />
<img src="/wiki/images/e/e8/Mapmaker-banner.jpg"></img><br />
</div--><br />
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<h3 class="centered"><br />
Welcome to the Team Alberta website! Our project pushes the limits of Synthetic Biology to create massively parallel, highly selective biological computers. <br />
</h3><br /><br />
<img src="/wiki/images/e/e8/Mapmaker-banner.jpg"<br />
style="width:85%;"></img><br />
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<!--<br />
--------<br />
<br />
<html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #000000;"><br />
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"><br />
For visitors: this site is currently under construction. Please contact our Student Liason, Dawson at daocun@ualberta.ca, for more information on our current project and how to support us!<br />
</div><br />
</div><br />
</html><br />
<br />
<br />
[[Image:Alberta_logo.png|500px|center]]<br />
<br />
<br />
<html><p><font size=4><strong><center><br />
Team Alberta represents the University of Alberta, from Edmonton. Our project, "The Littlest Mapmakers", is an attempt to create a biological computer capable of solving the Traveling Salesman Problem</p></center></font></strong></html><br />
<br />
----<br />
<br />
<br />
<html><br />
<font size=3>The traveling salesman problem is a mathematical optimization problem that was first formally described in 1930, and has been intensively studied in the computer sciences as a benchmark for optimization algorithms. The problem asks: <br />
<html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; background-color: #ffffff;"><br />
<div id="template" style="text-align: center; color: #000000; padding: 5px;"><br />
Given a set of cities (or other destinations), and a list of the distances (or the travel time, fuel consumption, et cetera) between each pair of those cities, what is the shortest possible route that travels to every city exactly once, and then returns to the origin city?</div><br />
</div><br />
</html><br />
In our project, we use DNA to compute solutions by converting all of the elements of the problem into representative sequences of DNA: cities become selectable marker genes (specifically, antibiotic resistance genes), paths between the cities become short, sticky-ended linkers (each of which is only able to ligate to two specific “city” strands), and the distance of a given path is represented by the concentration of the corresponding linker in solution. These pieces of DNA are successively ligated together to produce plasmids that signify “routes”, where the order in which the genes appear in the plasmid indicates the order in which the cities are visited. <br />
{|align="center"<br />
|[[Image:sample_product.png|300px]][[Image:sample_route.png|650px]]<br />
|}<br />
<html><font size=3>The resulting plasmids are transformed into a bacterial culture, so that we can select for only those plasmids that include every city in the list. Then, plasmid DNA is extracted from the surviving bacterial colonies and analyzed to determine which plasmid (and thus which route) occurred the most frequently. This route, the one most favoured by the ligation reactions, is the optimal route!</font></html><br />
<br />
<br />
<br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
<html><a class="twitter-timeline" href="https://twitter.com/iGEMAlberta" data-widget-id="368908364702437377">Tweets by @iGEMAlberta</a><br />
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--></div>
MEsau
http://2013.igem.org/Team:Alberta/Background
Team:Alberta/Background
2013-10-29T03:17:46Z
<p>MEsau: </p>
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<img src="/wiki/images/4/41/Ab_mapmen_title.png" width="600" height="95"></img><img src="/wiki/images/a/a5/2013-igem-logo.png" width="198" height="95"></img><br />
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<li><i class="nav-icon"></i><a id="project" href="#" class="active">Project</a><br />
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<li><a href="/Team:Alberta/Background" class="active">Background</a></li><br />
<li><a href="/Team:Alberta/Overview">Overview</a></li><br />
<li><a href="/Team:Alberta/Results">Results</a></li><br />
<li><a href="/Team:Alberta/Protocols">Protocols</a></li><br />
<li><a href="/Team:Alberta/Parts">Submitted Parts</a></li><br />
<li><a href="/Team:Alberta/Accomplishments">Accomplishments</a></li><br />
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<li><a id="team" href="#">Team</a><br />
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<li><a href="/Team:Alberta/Team">Roster</a></li><br />
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<div class="sidebar_block"><br />
<h5>Places</h5><br />
<a href="#Top"><p>Top</p></a><br />
<a href="#Travelling"><p>Travelling Salesman Problem</p></a><br />
<a href="#Real-World"><p>Real-World Issues</p></a><br />
<a href="#Computational"><p>The Computational Wall</p></a><br />
<a href="#Biocomputing"><p>Why Biocomputing?</p></a><br />
<a href="#Road"><p>A Long Road </p></a><br />
<h5>Project Sections</h5><br />
<a href="/Team:Alberta/Background" class="active"><p>Background</p></a><br />
<a href="/Team:Alberta/Overview"><p>Overview</p></a><br />
<a href="/Team:Alberta/Results"><p>Results</p></a><br />
<a href="/Team:Alberta/Protocols"><p>Protocols</p></a><br />
<a href="/Team:Alberta/Parts"><p>Submitted Parts</p></a><br />
<a href="/Team:Alberta/Accomplishments"><p>Accomplishments</p></a><br />
<a href="/Team:Alberta/Attributions"><p>Attributions</p></a><br />
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<a class="anchor" id="Top"></a><br />
<div class="block"><br />
<p class="content-title">Background</p><br />
</div><br />
<a class="anchor" id="Travelling"></a><br />
<div class="block"><br />
<h2>The Travelling Salesman Problem</h2><br />
<p>The Littlest Mapmaker is Team Alberta's endeavour to create a biological computer capable of solving <br />
Travelling Salesman Problems (TSP), a general form of problem that asks:<br />
<p class="centered-well">Given a set of cities, and a list of the distances between each pair of those cities, <br />
what is the shortest possible route that travels to every city exactly once and then returns to the origin <br />
city?</p><br />
<p><center><img src="/wiki/images/6/6c/TSPexample.png" align="middle" style="width:33%;"></center></p><br />
</div><br />
<a class="anchor" id="Real-World"></a><br />
<div class="block"><br />
<h2>Real-World Issues</h2><br />
<p>The TSP is named after the concept of a hypothetical salesman who is planning a route to visit his <br />
customers in various neighbouring towns, but wants to maximize profits by using the shortest route — a <br />
helpful example to illustrate the usefulness of the problem: businesses around the world employ TSP-solving <br />
or related problem-solving software to help optimize their travelling needs, including in particular large <br />
courier companies that need to delivery millions of packages daily, and must reduce the expense of delivery <br />
vehicles and cut down travel time in any way possible, but also airliners, postal services, consumer GPS <br />
route-planning software, video-game pathfinding AI, and even electronics manufacture, in which a robot <br />
soldering arm must have an efficient path through the solder points to ensure maximum production over time. <br />
</p><br />
</div><br />
<a class="anchor" id="Computational"></a><br />
<div class="block"><br />
<h2>The Computational Wall</h2><br />
<p>The TSP is not only practically valuable, but also mathematically significant, because it belongs to a <br />
class of problems that are considered computationally difficult. The key difficulty with the TSP is due to <br />
the fact that it is an optimization problem: while for practical purposes any decent, short route is <br />
acceptable, a given TSP is nevertheless only considered "solved" when one verifies that one has obtained the <br />
shortest possible route. Mathematical verification of this sort requires what is called a "brute force" <br />
approach, in which one explores each and every possible route, tallying the total distance of each one, and <br />
then compares them all directly to guarantee the optimal route has been identified. As one increases the <br />
number of cities that must be included in the route, the time required for the brute-force approach becomes <br />
impossibly large.</p><br />
<img src="/wiki/images/9/9d/TSPcompWall.png" style="width:100%;"></img><br />
</div><br />
<a class="anchor" id="Biocomputing"></a><br />
<div class="block"><br />
<h2>Why Biocomputing?</h2><br />
<p>Through synthetic biology, the creation of biological computers has opened a new avenue of possibility for <br />
solving TSPs more rapidly: using DNA molecules and bacterial cells as processors, one can compute billions <br />
of routes simultaneously, drastically reducing the time required through this massively parallel approach. <br />
By employing far more processors than there are routes through a given network, the processing time can be <br />
reduced to a standstill. A biological computer is also unique because it can solve problems stochastically: <br />
while every possible route is explored by the computer, preferable routes (short ones) will predominate <br />
among the generated products, allowing identification of the optimal route by population, rather than by a <br />
slower, deterministic approach. </p><br />
</div><br />
<a class="anchor" id="Road"></a><br />
<div class="block"><br />
<h2>A Long Road</h2><br />
<p>A number of previous attempts have been made to produce biocomputer solutions to the TSP, often involving pure DNA computing with no living organism present, including attempts by Leonard Adleman of RSA encryption fame, as well as previous efforts by the Davidson College/Missouri Western State University iGEM team, whose 2006 entry attempted to solve another challenging computational problem called the Burnt Pancake Problem, and in 2007 entered a DNA computing solution for the Hamiltonian Path Problem. Though related to the TSP, the Hamiltonian Path Problem attempts to discern if there is any possible route through a network, rather than picking the shortest possible one.</p><br />
<img src="/wiki/images/d/d4/Hgp_vs_tsp.png" style="width:100%;"></img><br />
<p>The Littlest MapMaker represents the latest in a line of attempts to refine the biological approach and create ever- increasingly powerful biological computers – and is the first of its kind to employ living cells to solve a travelling salesman problem. </p><br />
</div><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Alberta|Home]]<br />
!align="center"|[[Team:Alberta/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Alberta Official Team Profile]<br />
!align="center"|[[Team:Alberta/Project|Project]]<br />
!align="center"|[[Team:Alberta/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Alberta/Modeling|Modeling]]<br />
!align="center"|[[Team:Alberta/Notebook|Notebook]]<br />
!align="center"|[[Team:Alberta/Safety|Safety]]<br />
!align="center"|[[Team:Alberta/Attributions|Attributions]]<br />
|}<br />
<br />
== '''Overall project''' ==<br />
<br />
Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)<br />
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== Project Details==<br />
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=== Part 2 ===<br />
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=== The Experiments ===<br />
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=== Part 3 ===<br />
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== Results ==<br />
--></div>
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