http://2011.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=50&target=Robere2011.igem.org - User contributions [en]2024-03-29T06:34:24ZFrom 2011.igem.orgMediaWiki 1.16.0http://2011.igem.org/Team:Washington/Team/SponsorsTeam:Washington/Team/Sponsors2011-12-02T17:09:21Z<p>Robere: </p>
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[[File:Washington2011_NSFlogo.jpg|frameless|border|link=http://www.nsf.gov/|National Science Foundation]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/Team:Washington/Team/SponsorsTeam:Washington/Team/Sponsors2011-12-02T17:08:35Z<p>Robere: </p>
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[[File:Washington_HHMI.jpg|frameless|border|link=http://www.hhmi.org|Howard Hughes Medical Institute]]<br />
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[[File:Washington_OSLI.png|frameless|border|link=http://www.osli.ca|Oil Sands Leadership Intiative]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/Team:Washington/Team/SponsorsTeam:Washington/Team/Sponsors2011-12-02T17:08:20Z<p>Robere: </p>
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[[File:Washington_HHMI.jpg|frameless|border|link=http://www.hhmi.org|Howard Hughes Medical Institute]]<br />
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[[File:Washington2011_NSFlogo.jpg|frameless|border|link=http://www.nsf.gov/|National Science Foundation]]<br />
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[[File:Washington_UniversitySeal.gif|frameless|border|link=http://www.washington.edu|University of Washington]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/Team:Washington/Team/SponsorsTeam:Washington/Team/Sponsors2011-12-02T17:08:02Z<p>Robere: </p>
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[[File:Washington_HHMI.jpg|frameless|border|link=http://www.hhmi.org|Howard Hughes Medical Institute]]<br />
[[File:Washington_Spacer.jpg|45px]]<br />
[[File:Washington_OSLI.png|frameless|border|link=http://www.osli.ca|Oil Sands Leadership Intiative]]<br />
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[[File:Washington2011_NSFlogo.jpg|frameless|border|link=http://www.nsf.gov/|National Science Foundation]]<br />
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[[File:Washington_UniversitySeal.gif|frameless|border|link=http://www.washington.edu|University of Washington]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/File:Washington2011_NSFlogo.jpgFile:Washington2011 NSFlogo.jpg2011-12-02T17:04:18Z<p>Robere: uploaded a new version of &quot;File:Washington2011 NSFlogo.jpg&quot;</p>
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<div></div>Roberehttp://2011.igem.org/Team:WashingtonTeam:Washington2011-12-02T17:01:48Z<p>Robere: </p>
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<html><meta name="google-site-verification" content="fg3_xZB6BF10NZTT7oSIbF6AmRx0o-b-VZdgok0O3Ok" /></html><br />
=<center>'''Make It or Break It: <br/> Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<br />
<br />
<center>Synthetic biology holds great promise regarding the production of important compounds, and the degradation of harmful ones. This summer, we harnessed the power of synthetic biology to meet the world’s needs for fuel and medicine.</center><br />
<br/><br />
[[Image:Washington_Fire.jpg|left|320px|borderless|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[Image:Washington_Bottle.jpg|right|200px|borderless|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
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[https://2011.igem.org/Team:Washington/Alkanes/Background '''Make It: Diesel Production'''] We constructed a strain of ''Escherichia coli'' that produces a variety of alkanes, the main constituents of diesel fuel, by introducing a pair of genes recently shown to convert fatty acid synthesis intermediates into alkanes. <br />
<br />
[https://2011.igem.org/Team:Washington/Celiacs/Background '''Break It: Gluten Destruction'''] We identified a protease with gluten-degradation potential, and then reengineered it to have greatly increased gluten-degrading activity, allowing for the breakdown of gluten in the digestive track when taken in pill form. <br />
<br />
[https://2011.igem.org/Team:Washington/Magnetosomes/Background '''iGEM Toolkits'''] To enable next-generation cloning of standard biological parts, we built BioBrick vectors optimized for Gibson assembly and used them to create the Magnetosome Toolkit: a set of 18 genes from an essential operon in magnetotactic bacteria which we are characterizing to create magnetic ''E. coli''.<br />
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[[File:Washington_UniversitySeal.gif|frameless|border|100px|link=http://www.washington.edu|University of Washington]]<br />
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[[File:Washington_ARPA-E_Logo.png|frameless|border|150px|link=http://arpa-e.energy.gov/ProgramsProjects/Electrofuels.aspx|Advanced Research Projects Agency - Energy]]<br />
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[[File:Washington2011_Hhmi_362_72.jpg|link=http://www.hhmi.org/|Howard Hughes Medical Institute]]<br />
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[[File:Washington2011_NSFlogo.jpg|frameless|border|link=http://www.nsf.gov/|National Science Foundation]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|100px|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/Team:WashingtonTeam:Washington2011-12-02T16:55:57Z<p>Robere: </p>
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<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
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<html><meta name="google-site-verification" content="fg3_xZB6BF10NZTT7oSIbF6AmRx0o-b-VZdgok0O3Ok" /></html><br />
=<center>'''Make It or Break It: <br/> Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<br />
<br />
<center>Synthetic biology holds great promise regarding the production of important compounds, and the degradation of harmful ones. This summer, we harnessed the power of synthetic biology to meet the world’s needs for fuel and medicine.</center><br />
<br/><br />
[[Image:Washington_Fire.jpg|left|320px|borderless|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[Image:Washington_Bottle.jpg|right|200px|borderless|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
<br />
[https://2011.igem.org/Team:Washington/Alkanes/Background '''Make It: Diesel Production'''] We constructed a strain of ''Escherichia coli'' that produces a variety of alkanes, the main constituents of diesel fuel, by introducing a pair of genes recently shown to convert fatty acid synthesis intermediates into alkanes. <br />
<br />
[https://2011.igem.org/Team:Washington/Celiacs/Background '''Break It: Gluten Destruction'''] We identified a protease with gluten-degradation potential, and then reengineered it to have greatly increased gluten-degrading activity, allowing for the breakdown of gluten in the digestive track when taken in pill form. <br />
<br />
[https://2011.igem.org/Team:Washington/Magnetosomes/Background '''iGEM Toolkits'''] To enable next-generation cloning of standard biological parts, we built BioBrick vectors optimized for Gibson assembly and used them to create the Magnetosome Toolkit: a set of 18 genes from an essential operon in magnetotactic bacteria which we are characterizing to create magnetic ''E. coli''.<br />
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[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
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[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
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[[File:Washington_UniversitySeal.gif|frameless|border|100px|link=http://www.washington.edu|University of Washington]]<br />
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[[File:Washington_ARPA-E_Logo.png|frameless|border|link=http://arpa-e.energy.gov/ProgramsProjects/Electrofuels.aspx|Advanced Research Projects Agency - Energy]]<br />
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[[File:Washington2011_Hhmi_362_72.jpg|link=http://www.hhmi.org/|Howard Hughes Medical Institute]]<br />
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[[File:Washington2011_NSFlogo.jpg|frameless|border|link=http://www.nsf.gov/|National Science Foundation]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|100px|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/Team:WashingtonTeam:Washington2011-12-02T16:55:23Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<html><meta name="google-site-verification" content="fg3_xZB6BF10NZTT7oSIbF6AmRx0o-b-VZdgok0O3Ok" /></html><br />
=<center>'''Make It or Break It: <br/> Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<br />
<br />
<center>Synthetic biology holds great promise regarding the production of important compounds, and the degradation of harmful ones. This summer, we harnessed the power of synthetic biology to meet the world’s needs for fuel and medicine.</center><br />
<br/><br />
[[Image:Washington_Fire.jpg|left|320px|borderless|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[Image:Washington_Bottle.jpg|right|200px|borderless|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
<br />
[https://2011.igem.org/Team:Washington/Alkanes/Background '''Make It: Diesel Production'''] We constructed a strain of ''Escherichia coli'' that produces a variety of alkanes, the main constituents of diesel fuel, by introducing a pair of genes recently shown to convert fatty acid synthesis intermediates into alkanes. <br />
<br />
[https://2011.igem.org/Team:Washington/Celiacs/Background '''Break It: Gluten Destruction'''] We identified a protease with gluten-degradation potential, and then reengineered it to have greatly increased gluten-degrading activity, allowing for the breakdown of gluten in the digestive track when taken in pill form. <br />
<br />
[https://2011.igem.org/Team:Washington/Magnetosomes/Background '''iGEM Toolkits'''] To enable next-generation cloning of standard biological parts, we built BioBrick vectors optimized for Gibson assembly and used them to create the Magnetosome Toolkit: a set of 18 genes from an essential operon in magnetotactic bacteria which we are characterizing to create magnetic ''E. coli''.<br />
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[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
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[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
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[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
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[[File:Washington_OSLI.png|frameless|border|link=http://www.osli.ca|Oil Sands Leadership Intiative]]<br />
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[[File:Washington_UniversitySeal.gif|frameless|border|100px|link=http://www.washington.edu|University of Washington]]<br />
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[[File:Washington_ARPA-E_Logo.png|frameless|border|link=http://arpa-e.energy.gov/ProgramsProjects/Electrofuels.aspx|Advanced Research Projects Agency - Energy]]<br />
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[[File:Washington2011_Hhmi_362_72.jpg|link=http://www.hhmi.org/|Howard Hughes Medical Institute]]<br />
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[[File:Washington2011_NSFlogo.jpg|frameless|border|100px|link=http://www.nsf.gov/|National Science Foundation]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|100px|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/File:Washington2011_NSFlogo.jpgFile:Washington2011 NSFlogo.jpg2011-12-02T16:52:51Z<p>Robere: </p>
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<div></div>Roberehttp://2011.igem.org/Team:WashingtonTeam:Washington2011-12-02T16:51:38Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<html><meta name="google-site-verification" content="fg3_xZB6BF10NZTT7oSIbF6AmRx0o-b-VZdgok0O3Ok" /></html><br />
=<center>'''Make It or Break It: <br/> Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<br />
<br />
<center>Synthetic biology holds great promise regarding the production of important compounds, and the degradation of harmful ones. This summer, we harnessed the power of synthetic biology to meet the world’s needs for fuel and medicine.</center><br />
<br/><br />
[[Image:Washington_Fire.jpg|left|320px|borderless|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[Image:Washington_Bottle.jpg|right|200px|borderless|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
<br />
[https://2011.igem.org/Team:Washington/Alkanes/Background '''Make It: Diesel Production'''] We constructed a strain of ''Escherichia coli'' that produces a variety of alkanes, the main constituents of diesel fuel, by introducing a pair of genes recently shown to convert fatty acid synthesis intermediates into alkanes. <br />
<br />
[https://2011.igem.org/Team:Washington/Celiacs/Background '''Break It: Gluten Destruction'''] We identified a protease with gluten-degradation potential, and then reengineered it to have greatly increased gluten-degrading activity, allowing for the breakdown of gluten in the digestive track when taken in pill form. <br />
<br />
[https://2011.igem.org/Team:Washington/Magnetosomes/Background '''iGEM Toolkits'''] To enable next-generation cloning of standard biological parts, we built BioBrick vectors optimized for Gibson assembly and used them to create the Magnetosome Toolkit: a set of 18 genes from an essential operon in magnetotactic bacteria which we are characterizing to create magnetic ''E. coli''.<br />
<br />
<br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
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[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
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[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
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[[File:Washington_OSLI.png|frameless|border|link=http://www.osli.ca|Oil Sands Leadership Intiative]]<br />
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[[File:Washington_UniversitySeal.gif|frameless|border|110px|link=http://www.washington.edu|University of Washington]]<br />
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[[File:Washington_ARPA-E_Logo.png|frameless|border|link=http://arpa-e.energy.gov/ProgramsProjects/Electrofuels.aspx|Advanced Research Projects Agency - Energy]]<br />
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[[File:Washington2011_Hhmi_362_72.jpg|link=http://www.hhmi.org/|Howard Hughes Medical Institute]]<br />
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[[File:Washington2011_NSFlogo.jpg|link=http://nsf.gov/|National Science Foundation]]<br />
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[[File:Washington_Anaspec.gif|frameless|border|120px|link=http://www.anaspec.com|Anaspec]]</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ToolkitTeam:Washington/Magnetosomes/Magnet Toolkit2011-10-27T18:45:43Z<p>Robere: /* What are magnetosomes? Where do they come from? */</p>
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<center><big><big><big><big>'''iGEM Toolkits: Magnetosomes'''</big></big></big></big></center><br><br><br />
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===What are magnetosomes? Where do they come from?===<br />
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[[File:Washington iGEM2011 magnetotatic bacteria picture.jpg|thumb|right|350px|Magnetotactic Bacteria (left) and Magnetosome chains (right)]]<br />
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<br> Magnetotactic bacteria are prokaryotic organisms that possess the unique ability to align themselves along a magnetic field. This form of taxis is made possible by the formation of a magnetosome. Magnetosomes are small invaginations of the bacterial inner membrane that contain magnetite particles.<br />
<br />
These particles range in size between 20 and several hundred nanometers and are aligned in one or several chains along the long axis of the bacteria. These particles act together to form a magnetic dipole across the bacteria, allowing it to sense the earth’s magnetic field. Magnetotactic bacteria are microaerophilic; therefore, magnetosomes are thought to help aid the organism in its search for the optimal oxygen level from a search in three dimensional space (in all directions) to a one dimensional space along a single path.<br />
<br><br><br><br />
<center>Video demonstration of magnetic property of AMB-1 ([http://youtu.be/evrZEe_q4V4 direct link]):</center><br />
<html><center><iframe width="420" height="315" src="http://www.youtube.com/embed/evrZEe_q4V4" frameborder="0" allowfullscreen></iframe></center></html><br />
<br> <br><br />
<i>Narration text from video:</i> Magnetotactic bacteria are named for their ability to respond to and move along magnetic fields. They were first discovered in 1975 by Richard Blakemore when he noticed bacteria collecting on the north most edge of a water droplet he had placed on a microscope slide. Magnetotactic bacteria use a chain of vesicle-bound magnetite particles (known as magnetosomes) as a biological compass to orient themselves along the earth's magnetic field lines. They then swim along these field lines with flagella. It is thought that this process evolved to allow magnetotactic bacteria to search for certain micro-environments more efficiently. Magnetotactic bacteria in the northern hemisphere usually swim northward while those found in the southern hemisphere swim southward. In both cases this would direct the bacterium downward and is thought to allow it to find bottom sediments in an aqueous environment. As shown here, when a strong magnetic field is applied to the bacteria they can be moved as the magnetite particles within them become polarized and attracted to the magnetic field source.<br />
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===A Closer look at Magnetosome Formation ===<br />
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[[File:F6.medium.png|300px|thumb|right|Diagram of stepwise magnetosome construction within AMB-1]]<br />
<br> <br />
The formation of the magnetosome organelle is a highly regulated, step-wise process requiring a cascade of essential genes. The process is generally hypothesized as four stages: <br />
# Membrane invagination<br />
# Acquiring minerals for magnetite formation <br />
# Iron-oxidation and reduction<br />
# Magnetite nucleation and morphology regulation.<br />
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<br> Earlier gene products must be present for later gene products to be formed as shown in the diagram on the right[http://www.pnas.org/content/107/12/5593.full.pdf+html]:<br />
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<br><br><br> <br />
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===What did the UW iGEM team do with Magnetotactic Bacteria?=== <br />
<br> <br />
It is thought that many of the essential genes associated with magnetosome formation are located within a well-conserved region known as the magnetosome island (MAI). The MAI consists of 14 gene clusters labeled R1-R14 (see diagram below).Our team focused on the genes of the mamAB gene cluster (R5), as they were previously shown to be the only cluster essential for magnetosome membrane biogenesis in AMB-1 (diagram show below).[http://www.pnas.org/content/107/12/5593/F1.expansion.html].<br />
<br />
The goal of our project was to extract all the essential genes from (R5) required for magnetosome formation and express them in ''E. coli''. We are doing this to learn more about magnetosome formation and the magnet synthesis mechanism, because many of the genes' functions are still unknown in the host species. Using the information we have gained, we have organized a '''Magnetosome Toolkit''' containing most of the essential genes for proper magnetosome formation. Ultimately, we would like to continue expanding the magnetosome toolkit to have enough parts to show complete magnetosome formation in ''E.coli''.<br />
[[File:MamAB.png|center|500px|thumb|Fig. 3: The mamAB operon (R5) located in the magnetosome island (MAI).]]<br />
<br><br />
==='''About the Magnetosome Toolkit'''===<br />
<br><br />
Using standard synthetic biology protocols and the vectors we created in our Gibson Assembly Toolkit, our team created the '''"Magnetosome Toolkit"''' which contains many of the genes required for magnetosome formation. Providing this toolkit to the Parts Registry will help allow future iGEM teams to manipulate and further understand magnetosome formation to eventually synthesize magnets in multiple organisms. <br />
<br> <br/><br />
As previously noted, magnetosome formation within the host-organism, ''Magnetospirillium magneticum'', strain AMB-1, is a highly regulated step-wise process. As shown in diagram of stepwise magnetosome construction above, some genes encode proteins that form an invagination of the inner membrane, other genes which help align the magnetosomes into their characteristics chains, and others which regulate the biomineralization of magnetic particles. Our team chose to focus on genes specifically related to magnetosome scaffolding/alignment since they are the essential foundation for magnetosome development. In addition, the creation of a scaffold to which other genes localize is highly applicable to systems in synthetic biology. (for more information, please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Future Future Directions] page)<br />
<br><br />
<br />
The genes we focused on are <i>mamK</i> and <i>mamI</i> since they have known functions related to localization of the magnetosome. Specifically, MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamK is also shown to localize the MamI, which when lost inhibits vesicle formation. <br />
(for other gene functions, please see the iGEM Toolkits parts submitted page)<br />
<br> <br><br />
<br />
==='''Toolkit Contruction'''===<br />
[[File:Washington Methode image.jpg|700px|center]]<br />
<br />
<br/>Please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Results Result Summary] page for to see how far we were able to get this summer!<br />
<br />
<br/><br />
<br />
=References:=<br />
<br />
<br />
# Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A.T., Murase, Y., Takeyama, H. (2005). Complete genome sequence of the facultative anaerobic Magnetotactic bacterium Magnetospirillum sp. strain AMB-1. ''DNA research''; 12: 157-166. Doi:10.1093/dnares/dsi002. <br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Supporting Information. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Quinlan, A., Murat, D., Vali, H., Komeili, A. (2011).The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization. ''Molecular Microbiology''; 80 (4): 855-1131. Doi:10.1111/j.1365-2958.2011.07631.x.<br />
# Richter, M., Kube, M., Bazylinski, D.A., Lombardot, T.,Glockner, F.O., Reinhardt, R., Shuler, D. (2007). Comparative genome analysis of four Magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. ''Journal of Bacteriology''; 189(13): 4899-4910. Doi:10.1128/JB.00119-07.<br />
# Rioux, J.B., Philippe, N., Pereia, S., Pignol, D., Wu, L.F., Ginet, N. (2010). A second actin-like mamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. ''PLoS ONE''; 5(2): e9151. Doi:10.1371/journal.pone.0009151.</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ToolkitTeam:Washington/Magnetosomes/Magnet Toolkit2011-10-27T18:27:10Z<p>Robere: /* What are magnetosomes? Where do they come from? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Magnetosomes'''</big></big></big></big></center><br><br><br />
<br />
===What are magnetosomes? Where do they come from?===<br />
<br />
[[File:Washington iGEM2011 magnetotatic bacteria picture.jpg|thumb|right|350px|Magnetotactic Bacteria (left) and Magnetosome chains (right)]]<br />
<br />
<br> Magnetotactic bacteria are prokaryotic organisms that possess the unique ability to align themselves along a magnetic field. This form of taxis is made possible by the formation of a magnetosome. Magnetosomes are small invaginations of the bacterial inner membrane that contain magnetite particles.<br />
<br />
These particles range in size between 20 and several hundred nanometers and are aligned in one or several chains along the long axis of the bacteria. These particles act together to form a magnetic dipole across the bacteria, allowing it to sense the earth’s magnetic field. Magnetotactic bacteria are microaerophilic; therefore, magnetosomes are thought to help aid the organism in its search for the optimal oxygen level from a search in three dimensional space (in all directions) to a one dimensional space along a single path.<br />
<br><br><br><br />
<center>Video demonstration of Magnetic property of AMB-1 ([http://youtu.be/evrZEe_q4V4 direct link]):</center><br />
<html><center><iframe width="420" height="315" src="http://www.youtube.com/embed/evrZEe_q4V4" frameborder="0" allowfullscreen></iframe></center></html><br />
<br> <br><br />
<i>Narration text from video:</i> Magnetotactic bacteria are named for their ability to respond to and move along magnetic fields. They were first discovered in 1975 by Richard Blakemore when he noticed bacteria collecting on the north most edge of a water droplet he had placed on a microscope slide. Magnetotactic bacteria use a chain of vesicle-bound magnetite particles (known as magnetosomes) as a biological compass to orient themselves along the earth's magnetic field lines. They then swim along these field lines with flagella. It is thought that this process evolved to allow magnetotactic bacteria to search for certain micro-environments more efficiently. Magnetotactic bacteria in the northern hemisphere usually swim northward while those found in the southern hemisphere swim southward. In both cases this would direct the bacterium downward and is thought to allow it to find bottom sediments in an aqueous environment. As shown here, when a strong magnetic field is applied to the bacteria they can be moved as the magnetite particles within them become polarized and attracted to the magnetic field source.<br />
<br />
===A Closer look at Magnetosome Formation ===<br />
<br />
[[File:F6.medium.png|300px|thumb|right|Diagram of stepwise magnetosome construction within AMB-1]]<br />
<br> <br />
The formation of the magnetosome organelle is a highly regulated, step-wise process requiring a cascade of essential genes. The process is generally hypothesized as four stages: <br />
# Membrane invagination<br />
# Acquiring minerals for magnetite formation <br />
# Iron-oxidation and reduction<br />
# Magnetite nucleation and morphology regulation.<br />
<br />
<br> Earlier gene products must be present for later gene products to be formed as shown in the diagram on the right[http://www.pnas.org/content/107/12/5593.full.pdf+html]:<br />
<br />
<br><br><br> <br />
<br />
===What did the UW iGEM team do with Magnetotactic Bacteria?=== <br />
<br> <br />
It is thought that many of the essential genes associated with magnetosome formation are located within a well-conserved region known as the magnetosome island (MAI). The MAI consists of 14 gene clusters labeled R1-R14 (see diagram below).Our team focused on the genes of the mamAB gene cluster (R5), as they were previously shown to be the only cluster essential for magnetosome membrane biogenesis in AMB-1 (diagram show below).[http://www.pnas.org/content/107/12/5593/F1.expansion.html].<br />
<br />
The goal of our project was to extract all the essential genes from (R5) required for magnetosome formation and express them in ''E. coli''. We are doing this to learn more about magnetosome formation and the magnet synthesis mechanism, because many of the genes' functions are still unknown in the host species. Using the information we have gained, we have organized a '''Magnetosome Toolkit''' containing most of the essential genes for proper magnetosome formation. Ultimately, we would like to continue expanding the magnetosome toolkit to have enough parts to show complete magnetosome formation in ''E.coli''.<br />
[[File:MamAB.png|center|500px|thumb|Fig. 3: The mamAB operon (R5) located in the magnetosome island (MAI).]]<br />
<br><br />
==='''About the Magnetosome Toolkit'''===<br />
<br><br />
Using standard synthetic biology protocols and the vectors we created in our Gibson Assembly Toolkit, our team created the '''"Magnetosome Toolkit"''' which contains many of the genes required for magnetosome formation. Providing this toolkit to the Parts Registry will help allow future iGEM teams to manipulate and further understand magnetosome formation to eventually synthesize magnets in multiple organisms. <br />
<br> <br/><br />
As previously noted, magnetosome formation within the host-organism, ''Magnetospirillium magneticum'', strain AMB-1, is a highly regulated step-wise process. As shown in diagram of stepwise magnetosome construction above, some genes encode proteins that form an invagination of the inner membrane, other genes which help align the magnetosomes into their characteristics chains, and others which regulate the biomineralization of magnetic particles. Our team chose to focus on genes specifically related to magnetosome scaffolding/alignment since they are the essential foundation for magnetosome development. In addition, the creation of a scaffold to which other genes localize is highly applicable to systems in synthetic biology. (for more information, please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Future Future Directions] page)<br />
<br><br />
<br />
The genes we focused on are <i>mamK</i> and <i>mamI</i> since they have known functions related to localization of the magnetosome. Specifically, MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamK is also shown to localize the MamI, which when lost inhibits vesicle formation. <br />
(for other gene functions, please see the iGEM Toolkits parts submitted page)<br />
<br> <br><br />
<br />
==='''Toolkit Contruction'''===<br />
[[File:Washington Methode image.jpg|700px|center]]<br />
<br />
<br/>Please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Results Result Summary] page for to see how far we were able to get this summer!<br />
<br />
<br/><br />
<br />
=References:=<br />
<br />
<br />
# Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A.T., Murase, Y., Takeyama, H. (2005). Complete genome sequence of the facultative anaerobic Magnetotactic bacterium Magnetospirillum sp. strain AMB-1. ''DNA research''; 12: 157-166. Doi:10.1093/dnares/dsi002. <br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Supporting Information. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Quinlan, A., Murat, D., Vali, H., Komeili, A. (2011).The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization. ''Molecular Microbiology''; 80 (4): 855-1131. Doi:10.1111/j.1365-2958.2011.07631.x.<br />
# Richter, M., Kube, M., Bazylinski, D.A., Lombardot, T.,Glockner, F.O., Reinhardt, R., Shuler, D. (2007). Comparative genome analysis of four Magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. ''Journal of Bacteriology''; 189(13): 4899-4910. Doi:10.1128/JB.00119-07.<br />
# Rioux, J.B., Philippe, N., Pereia, S., Pignol, D., Wu, L.F., Ginet, N. (2010). A second actin-like mamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. ''PLoS ONE''; 5(2): e9151. Doi:10.1371/journal.pone.0009151.</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ToolkitTeam:Washington/Magnetosomes/Magnet Toolkit2011-10-27T18:15:44Z<p>Robere: /* What are magnetosomes? Where do they come from? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Magnetosomes'''</big></big></big></big></center><br><br><br />
<br />
===What are magnetosomes? Where do they come from?===<br />
<br />
[[File:Washington iGEM2011 magnetotatic bacteria picture.jpg|thumb|right|350px|Magnetotactic Bacteria (left) and Magnetosome chains (right)]]<br />
<br />
<br> Magnetotactic bacteria are prokaryotic organisms that possess the unique ability to align themselves along a magnetic field. This form of taxis is made possible by the formation of a magnetosome. Magnetosomes are small invaginations of the bacterial inner membrane that contain magnetite particles.<br />
<br />
These particles range in size between 20 and several hundred nanometers and are aligned in one or several chains along the long axis of the bacteria. These particles act together to form a magnetic dipole across the bacteria, allowing it to sense the earth’s magnetic field. Magnetotactic bacteria are microaerophilic; therefore, magnetosomes are thought to help aid the organism in its search for the optimal oxygen level from a search in three dimensional space (in all directions) to a one dimensional space along a single path.<br />
<br><br><br><br />
<center>Video demonstration of Magnetic property of AMB-1 ([http://www.youtube.com/watch?v=1qWK_BZS-CU direct link]):</center><br />
<html><center><iframe width="420" height="315" src="http://www.youtube.com/embed/1qWK_BZS-CU" frameborder="0" allowfullscreen></iframe></center></html><br />
<br> <br><br />
<i>Narration text from video:</i> Magnetotactic bacteria are named for their ability to respond to and move along magnetic fields. They were first discovered in 1975 by Richard Blakemore when he noticed bacteria collecting on the north most edge of a water droplet he had placed on a microscope slide. Magnetotactic bacteria use a chain of vesicle-bound magnetite particles (known as magnetosomes) as a biological compass to orient themselves along the earth's magnetic field lines. They then swim along these field lines with flagella. It is thought that this process evolved to allow magnetotactic bacteria to search for certain micro-environments more efficiently. Magnetotactic bacteria in the northern hemisphere usually swim northward while those found in the southern hemisphere swim southward. In both cases this would direct the bacterium downward and is thought to allow it to find bottom sediments in an aqueous environment. As shown here, when a strong magnetic field is applied to the bacteria they can be moved as the magnetite particles within them become polarized and attracted to the magnetic field source.<br />
<br />
===A Closer look at Magnetosome Formation ===<br />
<br />
[[File:F6.medium.png|300px|thumb|right|Diagram of stepwise magnetosome construction within AMB-1]]<br />
<br> <br />
The formation of the magnetosome organelle is a highly regulated, step-wise process requiring a cascade of essential genes. The process is generally hypothesized as four stages: <br />
# Membrane invagination<br />
# Acquiring minerals for magnetite formation <br />
# Iron-oxidation and reduction<br />
# Magnetite nucleation and morphology regulation.<br />
<br />
<br> Earlier gene products must be present for later gene products to be formed as shown in the diagram on the right[http://www.pnas.org/content/107/12/5593.full.pdf+html]:<br />
<br />
<br><br><br> <br />
<br />
===What did the UW iGEM team do with Magnetotactic Bacteria?=== <br />
<br> <br />
It is thought that many of the essential genes associated with magnetosome formation are located within a well-conserved region known as the magnetosome island (MAI). The MAI consists of 14 gene clusters labeled R1-R14 (see diagram below).Our team focused on the genes of the mamAB gene cluster (R5), as they were previously shown to be the only cluster essential for magnetosome membrane biogenesis in AMB-1 (diagram show below).[http://www.pnas.org/content/107/12/5593/F1.expansion.html].<br />
<br />
The goal of our project was to extract all the essential genes from (R5) required for magnetosome formation and express them in ''E. coli''. We are doing this to learn more about magnetosome formation and the magnet synthesis mechanism, because many of the genes' functions are still unknown in the host species. Using the information we have gained, we have organized a '''Magnetosome Toolkit''' containing most of the essential genes for proper magnetosome formation. Ultimately, we would like to continue expanding the magnetosome toolkit to have enough parts to show complete magnetosome formation in ''E.coli''.<br />
[[File:MamAB.png|center|500px|thumb|Fig. 3: The mamAB operon (R5) located in the magnetosome island (MAI).]]<br />
<br><br />
==='''About the Magnetosome Toolkit'''===<br />
<br><br />
Using standard synthetic biology protocols and the vectors we created in our Gibson Assembly Toolkit, our team created the '''"Magnetosome Toolkit"''' which contains many of the genes required for magnetosome formation. Providing this toolkit to the Parts Registry will help allow future iGEM teams to manipulate and further understand magnetosome formation to eventually synthesize magnets in multiple organisms. <br />
<br> <br/><br />
As previously noted, magnetosome formation within the host-organism, ''Magnetospirillium magneticum'', strain AMB-1, is a highly regulated step-wise process. As shown in diagram of stepwise magnetosome construction above, some genes encode proteins that form an invagination of the inner membrane, other genes which help align the magnetosomes into their characteristics chains, and others which regulate the biomineralization of magnetic particles. Our team chose to focus on genes specifically related to magnetosome scaffolding/alignment since they are the essential foundation for magnetosome development. In addition, the creation of a scaffold to which other genes localize is highly applicable to systems in synthetic biology. (for more information, please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Future Future Directions] page)<br />
<br><br />
<br />
The genes we focused on are <i>mamK</i> and <i>mamI</i> since they have known functions related to localization of the magnetosome. Specifically, MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamK is also shown to localize the MamI, which when lost inhibits vesicle formation. <br />
(for other gene functions, please see the iGEM Toolkits parts submitted page)<br />
<br> <br><br />
<br />
==='''Toolkit Contruction'''===<br />
[[File:Washington Methode image.jpg|700px|center]]<br />
<br />
<br/>Please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Results Result Summary] page for to see how far we were able to get this summer!<br />
<br />
<br/><br />
<br />
=References:=<br />
<br />
<br />
# Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A.T., Murase, Y., Takeyama, H. (2005). Complete genome sequence of the facultative anaerobic Magnetotactic bacterium Magnetospirillum sp. strain AMB-1. ''DNA research''; 12: 157-166. Doi:10.1093/dnares/dsi002. <br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Supporting Information. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Quinlan, A., Murat, D., Vali, H., Komeili, A. (2011).The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization. ''Molecular Microbiology''; 80 (4): 855-1131. Doi:10.1111/j.1365-2958.2011.07631.x.<br />
# Richter, M., Kube, M., Bazylinski, D.A., Lombardot, T.,Glockner, F.O., Reinhardt, R., Shuler, D. (2007). Comparative genome analysis of four Magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. ''Journal of Bacteriology''; 189(13): 4899-4910. Doi:10.1128/JB.00119-07.<br />
# Rioux, J.B., Philippe, N., Pereia, S., Pignol, D., Wu, L.F., Ginet, N. (2010). A second actin-like mamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. ''PLoS ONE''; 5(2): e9151. Doi:10.1371/journal.pone.0009151.</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ToolkitTeam:Washington/Magnetosomes/Magnet Toolkit2011-10-27T18:15:14Z<p>Robere: /* What are magnetosomes? Where do they come from? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Magnetosomes'''</big></big></big></big></center><br><br><br />
<br />
===What are magnetosomes? Where do they come from?===<br />
<br />
[[File:Washington iGEM2011 magnetotatic bacteria picture.jpg|thumb|right|350px|Magnetotactic Bacteria (left) and Magnetosome chains (right)]]<br />
<br />
<br> Magnetotactic bacteria are prokaryotic organisms that possess the unique ability to align themselves along a magnetic field. This form of taxis is made possible by the formation of a magnetosome. Magnetosomes are small invaginations of the bacterial inner membrane that contain magnetite particles.<br />
<br />
These particles range in size between 20 and several hundred nanometers and are aligned in one or several chains along the long axis of the bacteria. These particles act together to form a magnetic dipole across the bacteria, allowing it to sense the earth’s magnetic field. Magnetotactic bacteria are microaerophilic; therefore, magnetosomes are thought to help aid the organism in its search for the optimal oxygen level from a search in three dimensional space (in all directions) to a one dimensional space along a single path.<br />
<br><br><br><br />
<center>Video demonstration of Magnetic property of AMB-1 ([http://www.youtube.com/watch?v=1qWK_BZS-CU direct link]):</center><br />
<html><center><iframe width="420" height="315" src="http://www.youtube.com/embed/1qWK_BZS-CU" frameborder="0" allowfullscreen></iframe></center></html><br />
<br> <br><br />
<html><iframe width="420" height="315" src="http://www.youtube.com/embed/1qWK_BZS-CU" frameborder="0" allowfullscreen></iframe></html><br />
<i>Narration text from video:</i> Magnetotactic bacteria are named for their ability to respond to and move along magnetic fields. They were first discovered in 1975 by Richard Blakemore when he noticed bacteria collecting on the north most edge of a water droplet he had placed on a microscope slide. Magnetotactic bacteria use a chain of vesicle-bound magnetite particles (known as magnetosomes) as a biological compass to orient themselves along the earth's magnetic field lines. They then swim along these field lines with flagella. It is thought that this process evolved to allow magnetotactic bacteria to search for certain micro-environments more efficiently. Magnetotactic bacteria in the northern hemisphere usually swim northward while those found in the southern hemisphere swim southward. In both cases this would direct the bacterium downward and is thought to allow it to find bottom sediments in an aqueous environment. As shown here, when a strong magnetic field is applied to the bacteria they can be moved as the magnetite particles within them become polarized and attracted to the magnetic field source.<br />
<br />
===A Closer look at Magnetosome Formation ===<br />
<br />
[[File:F6.medium.png|300px|thumb|right|Diagram of stepwise magnetosome construction within AMB-1]]<br />
<br> <br />
The formation of the magnetosome organelle is a highly regulated, step-wise process requiring a cascade of essential genes. The process is generally hypothesized as four stages: <br />
# Membrane invagination<br />
# Acquiring minerals for magnetite formation <br />
# Iron-oxidation and reduction<br />
# Magnetite nucleation and morphology regulation.<br />
<br />
<br> Earlier gene products must be present for later gene products to be formed as shown in the diagram on the right[http://www.pnas.org/content/107/12/5593.full.pdf+html]:<br />
<br />
<br><br><br> <br />
<br />
===What did the UW iGEM team do with Magnetotactic Bacteria?=== <br />
<br> <br />
It is thought that many of the essential genes associated with magnetosome formation are located within a well-conserved region known as the magnetosome island (MAI). The MAI consists of 14 gene clusters labeled R1-R14 (see diagram below).Our team focused on the genes of the mamAB gene cluster (R5), as they were previously shown to be the only cluster essential for magnetosome membrane biogenesis in AMB-1 (diagram show below).[http://www.pnas.org/content/107/12/5593/F1.expansion.html].<br />
<br />
The goal of our project was to extract all the essential genes from (R5) required for magnetosome formation and express them in ''E. coli''. We are doing this to learn more about magnetosome formation and the magnet synthesis mechanism, because many of the genes' functions are still unknown in the host species. Using the information we have gained, we have organized a '''Magnetosome Toolkit''' containing most of the essential genes for proper magnetosome formation. Ultimately, we would like to continue expanding the magnetosome toolkit to have enough parts to show complete magnetosome formation in ''E.coli''.<br />
[[File:MamAB.png|center|500px|thumb|Fig. 3: The mamAB operon (R5) located in the magnetosome island (MAI).]]<br />
<br><br />
==='''About the Magnetosome Toolkit'''===<br />
<br><br />
Using standard synthetic biology protocols and the vectors we created in our Gibson Assembly Toolkit, our team created the '''"Magnetosome Toolkit"''' which contains many of the genes required for magnetosome formation. Providing this toolkit to the Parts Registry will help allow future iGEM teams to manipulate and further understand magnetosome formation to eventually synthesize magnets in multiple organisms. <br />
<br> <br/><br />
As previously noted, magnetosome formation within the host-organism, ''Magnetospirillium magneticum'', strain AMB-1, is a highly regulated step-wise process. As shown in diagram of stepwise magnetosome construction above, some genes encode proteins that form an invagination of the inner membrane, other genes which help align the magnetosomes into their characteristics chains, and others which regulate the biomineralization of magnetic particles. Our team chose to focus on genes specifically related to magnetosome scaffolding/alignment since they are the essential foundation for magnetosome development. In addition, the creation of a scaffold to which other genes localize is highly applicable to systems in synthetic biology. (for more information, please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Future Future Directions] page)<br />
<br><br />
<br />
The genes we focused on are <i>mamK</i> and <i>mamI</i> since they have known functions related to localization of the magnetosome. Specifically, MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamK is also shown to localize the MamI, which when lost inhibits vesicle formation. <br />
(for other gene functions, please see the iGEM Toolkits parts submitted page)<br />
<br> <br><br />
<br />
==='''Toolkit Contruction'''===<br />
[[File:Washington Methode image.jpg|700px|center]]<br />
<br />
<br/>Please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Results Result Summary] page for to see how far we were able to get this summer!<br />
<br />
<br/><br />
<br />
=References:=<br />
<br />
<br />
# Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A.T., Murase, Y., Takeyama, H. (2005). Complete genome sequence of the facultative anaerobic Magnetotactic bacterium Magnetospirillum sp. strain AMB-1. ''DNA research''; 12: 157-166. Doi:10.1093/dnares/dsi002. <br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Supporting Information. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Quinlan, A., Murat, D., Vali, H., Komeili, A. (2011).The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization. ''Molecular Microbiology''; 80 (4): 855-1131. Doi:10.1111/j.1365-2958.2011.07631.x.<br />
# Richter, M., Kube, M., Bazylinski, D.A., Lombardot, T.,Glockner, F.O., Reinhardt, R., Shuler, D. (2007). Comparative genome analysis of four Magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. ''Journal of Bacteriology''; 189(13): 4899-4910. Doi:10.1128/JB.00119-07.<br />
# Rioux, J.B., Philippe, N., Pereia, S., Pignol, D., Wu, L.F., Ginet, N. (2010). A second actin-like mamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. ''PLoS ONE''; 5(2): e9151. Doi:10.1371/journal.pone.0009151.</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ToolkitTeam:Washington/Magnetosomes/Magnet Toolkit2011-10-27T18:14:27Z<p>Robere: /* What are magnetosomes? Where do they come from? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Magnetosomes'''</big></big></big></big></center><br><br><br />
<br />
===What are magnetosomes? Where do they come from?===<br />
<br />
[[File:Washington iGEM2011 magnetotatic bacteria picture.jpg|thumb|right|350px|Magnetotactic Bacteria (left) and Magnetosome chains (right)]]<br />
<br />
<br> Magnetotactic bacteria are prokaryotic organisms that possess the unique ability to align themselves along a magnetic field. This form of taxis is made possible by the formation of a magnetosome. Magnetosomes are small invaginations of the bacterial inner membrane that contain magnetite particles.<br />
<br />
These particles range in size between 20 and several hundred nanometers and are aligned in one or several chains along the long axis of the bacteria. These particles act together to form a magnetic dipole across the bacteria, allowing it to sense the earth’s magnetic field. Magnetotactic bacteria are microaerophilic; therefore, magnetosomes are thought to help aid the organism in its search for the optimal oxygen level from a search in three dimensional space (in all directions) to a one dimensional space along a single path.<br />
<br><br><br><br />
<center>Video demonstration of Magnetic property of AMB-1:</center><br />
<html><center><iframe width="420" height="315" src="http://www.youtube.com/embed/1qWK_BZS-CU" frameborder="0" allowfullscreen></iframe></center></html><br />
<br> <br><br />
<html><iframe width="420" height="315" src="http://www.youtube.com/embed/1qWK_BZS-CU" frameborder="0" allowfullscreen></iframe></html><br />
<i>Narration text from video:</i> Magnetotactic bacteria are named for their ability to respond to and move along magnetic fields. They were first discovered in 1975 by Richard Blakemore when he noticed bacteria collecting on the north most edge of a water droplet he had placed on a microscope slide. Magnetotactic bacteria use a chain of vesicle-bound magnetite particles (known as magnetosomes) as a biological compass to orient themselves along the earth's magnetic field lines. They then swim along these field lines with flagella. It is thought that this process evolved to allow magnetotactic bacteria to search for certain micro-environments more efficiently. Magnetotactic bacteria in the northern hemisphere usually swim northward while those found in the southern hemisphere swim southward. In both cases this would direct the bacterium downward and is thought to allow it to find bottom sediments in an aqueous environment. As shown here, when a strong magnetic field is applied to the bacteria they can be moved as the magnetite particles within them become polarized and attracted to the magnetic field source.<br />
<br />
===A Closer look at Magnetosome Formation ===<br />
<br />
[[File:F6.medium.png|300px|thumb|right|Diagram of stepwise magnetosome construction within AMB-1]]<br />
<br> <br />
The formation of the magnetosome organelle is a highly regulated, step-wise process requiring a cascade of essential genes. The process is generally hypothesized as four stages: <br />
# Membrane invagination<br />
# Acquiring minerals for magnetite formation <br />
# Iron-oxidation and reduction<br />
# Magnetite nucleation and morphology regulation.<br />
<br />
<br> Earlier gene products must be present for later gene products to be formed as shown in the diagram on the right[http://www.pnas.org/content/107/12/5593.full.pdf+html]:<br />
<br />
<br><br><br> <br />
<br />
===What did the UW iGEM team do with Magnetotactic Bacteria?=== <br />
<br> <br />
It is thought that many of the essential genes associated with magnetosome formation are located within a well-conserved region known as the magnetosome island (MAI). The MAI consists of 14 gene clusters labeled R1-R14 (see diagram below).Our team focused on the genes of the mamAB gene cluster (R5), as they were previously shown to be the only cluster essential for magnetosome membrane biogenesis in AMB-1 (diagram show below).[http://www.pnas.org/content/107/12/5593/F1.expansion.html].<br />
<br />
The goal of our project was to extract all the essential genes from (R5) required for magnetosome formation and express them in ''E. coli''. We are doing this to learn more about magnetosome formation and the magnet synthesis mechanism, because many of the genes' functions are still unknown in the host species. Using the information we have gained, we have organized a '''Magnetosome Toolkit''' containing most of the essential genes for proper magnetosome formation. Ultimately, we would like to continue expanding the magnetosome toolkit to have enough parts to show complete magnetosome formation in ''E.coli''.<br />
[[File:MamAB.png|center|500px|thumb|Fig. 3: The mamAB operon (R5) located in the magnetosome island (MAI).]]<br />
<br><br />
==='''About the Magnetosome Toolkit'''===<br />
<br><br />
Using standard synthetic biology protocols and the vectors we created in our Gibson Assembly Toolkit, our team created the '''"Magnetosome Toolkit"''' which contains many of the genes required for magnetosome formation. Providing this toolkit to the Parts Registry will help allow future iGEM teams to manipulate and further understand magnetosome formation to eventually synthesize magnets in multiple organisms. <br />
<br> <br/><br />
As previously noted, magnetosome formation within the host-organism, ''Magnetospirillium magneticum'', strain AMB-1, is a highly regulated step-wise process. As shown in diagram of stepwise magnetosome construction above, some genes encode proteins that form an invagination of the inner membrane, other genes which help align the magnetosomes into their characteristics chains, and others which regulate the biomineralization of magnetic particles. Our team chose to focus on genes specifically related to magnetosome scaffolding/alignment since they are the essential foundation for magnetosome development. In addition, the creation of a scaffold to which other genes localize is highly applicable to systems in synthetic biology. (for more information, please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Future Future Directions] page)<br />
<br><br />
<br />
The genes we focused on are <i>mamK</i> and <i>mamI</i> since they have known functions related to localization of the magnetosome. Specifically, MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamK is also shown to localize the MamI, which when lost inhibits vesicle formation. <br />
(for other gene functions, please see the iGEM Toolkits parts submitted page)<br />
<br> <br><br />
<br />
==='''Toolkit Contruction'''===<br />
[[File:Washington Methode image.jpg|700px|center]]<br />
<br />
<br/>Please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Results Result Summary] page for to see how far we were able to get this summer!<br />
<br />
<br/><br />
<br />
=References:=<br />
<br />
<br />
# Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A.T., Murase, Y., Takeyama, H. (2005). Complete genome sequence of the facultative anaerobic Magnetotactic bacterium Magnetospirillum sp. strain AMB-1. ''DNA research''; 12: 157-166. Doi:10.1093/dnares/dsi002. <br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Supporting Information. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Quinlan, A., Murat, D., Vali, H., Komeili, A. (2011).The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization. ''Molecular Microbiology''; 80 (4): 855-1131. Doi:10.1111/j.1365-2958.2011.07631.x.<br />
# Richter, M., Kube, M., Bazylinski, D.A., Lombardot, T.,Glockner, F.O., Reinhardt, R., Shuler, D. (2007). Comparative genome analysis of four Magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. ''Journal of Bacteriology''; 189(13): 4899-4910. Doi:10.1128/JB.00119-07.<br />
# Rioux, J.B., Philippe, N., Pereia, S., Pignol, D., Wu, L.F., Ginet, N. (2010). A second actin-like mamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. ''PLoS ONE''; 5(2): e9151. Doi:10.1371/journal.pone.0009151.</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ToolkitTeam:Washington/Magnetosomes/Magnet Toolkit2011-10-27T18:09:44Z<p>Robere: /* What are magnetosomes? Where do they come from? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Magnetosomes'''</big></big></big></big></center><br><br><br />
<br />
===What are magnetosomes? Where do they come from?===<br />
<br />
[[File:Washington iGEM2011 magnetotatic bacteria picture.jpg|thumb|right|350px|Magnetotactic Bacteria (left) and Magnetosome chains (right)]]<br />
<br />
<br> Magnetotactic bacteria are prokaryotic organisms that possess the unique ability to align themselves along a magnetic field. This form of taxis is made possible by the formation of a magnetosome. Magnetosomes are small invaginations of the bacterial inner membrane that contain magnetite particles.<br />
<br />
These particles range in size between 20 and several hundred nanometers and are aligned in one or several chains along the long axis of the bacteria. These particles act together to form a magnetic dipole across the bacteria, allowing it to sense the earth’s magnetic field. Magnetotactic bacteria are microaerophilic; therefore, magnetosomes are thought to help aid the organism in its search for the optimal oxygen level from a search in three dimensional space (in all directions) to a one dimensional space along a single path.<br />
<br><br><br><br />
<center>Video demonstration of Magnetic property of AMB-1:</center><br />
<html><center><iframe width="420" height="315" src="http://www.youtube.com/embed/1qWK_BZS-CU" frameborder="0" allowfullscreen></iframe></center></html><br />
<br> <br><br />
<i>Narration text from video:</i> Magnetotactic bacteria are named for their ability to respond to and move along magnetic fields. They were first discovered in 1975 by Richard Blakemore when he noticed bacteria collecting on the north most edge of a water droplet he had placed on a microscope slide. Magnetotactic bacteria use a chain of vesicle-bound magnetite particles (known as magnetosomes) as a biological compass to orient themselves along the earth's magnetic field lines. They then swim along these field lines with flagella. It is thought that this process evolved to allow magnetotactic bacteria to search for certain micro-environments more efficiently. Magnetotactic bacteria in the northern hemisphere usually swim northward while those found in the southern hemisphere swim southward. In both cases this would direct the bacterium downward and is thought to allow it to find bottom sediments in an aqueous environment. As shown here, when a strong magnetic field is applied to the bacteria they can be moved as the magnetite particles within them become polarized and attracted to the magnetic field source.<br />
<br />
===A Closer look at Magnetosome Formation ===<br />
<br />
[[File:F6.medium.png|300px|thumb|right|Diagram of stepwise magnetosome construction within AMB-1]]<br />
<br> <br />
The formation of the magnetosome organelle is a highly regulated, step-wise process requiring a cascade of essential genes. The process is generally hypothesized as four stages: <br />
# Membrane invagination<br />
# Acquiring minerals for magnetite formation <br />
# Iron-oxidation and reduction<br />
# Magnetite nucleation and morphology regulation.<br />
<br />
<br> Earlier gene products must be present for later gene products to be formed as shown in the diagram on the right[http://www.pnas.org/content/107/12/5593.full.pdf+html]:<br />
<br />
<br><br><br> <br />
<br />
===What did the UW iGEM team do with Magnetotactic Bacteria?=== <br />
<br> <br />
It is thought that many of the essential genes associated with magnetosome formation are located within a well-conserved region known as the magnetosome island (MAI). The MAI consists of 14 gene clusters labeled R1-R14 (see diagram below).Our team focused on the genes of the mamAB gene cluster (R5), as they were previously shown to be the only cluster essential for magnetosome membrane biogenesis in AMB-1 (diagram show below).[http://www.pnas.org/content/107/12/5593/F1.expansion.html].<br />
<br />
The goal of our project was to extract all the essential genes from (R5) required for magnetosome formation and express them in ''E. coli''. We are doing this to learn more about magnetosome formation and the magnet synthesis mechanism, because many of the genes' functions are still unknown in the host species. Using the information we have gained, we have organized a '''Magnetosome Toolkit''' containing most of the essential genes for proper magnetosome formation. Ultimately, we would like to continue expanding the magnetosome toolkit to have enough parts to show complete magnetosome formation in ''E.coli''.<br />
[[File:MamAB.png|center|500px|thumb|Fig. 3: The mamAB operon (R5) located in the magnetosome island (MAI).]]<br />
<br><br />
==='''About the Magnetosome Toolkit'''===<br />
<br><br />
Using standard synthetic biology protocols and the vectors we created in our Gibson Assembly Toolkit, our team created the '''"Magnetosome Toolkit"''' which contains many of the genes required for magnetosome formation. Providing this toolkit to the Parts Registry will help allow future iGEM teams to manipulate and further understand magnetosome formation to eventually synthesize magnets in multiple organisms. <br />
<br> <br/><br />
As previously noted, magnetosome formation within the host-organism, ''Magnetospirillium magneticum'', strain AMB-1, is a highly regulated step-wise process. As shown in diagram of stepwise magnetosome construction above, some genes encode proteins that form an invagination of the inner membrane, other genes which help align the magnetosomes into their characteristics chains, and others which regulate the biomineralization of magnetic particles. Our team chose to focus on genes specifically related to magnetosome scaffolding/alignment since they are the essential foundation for magnetosome development. In addition, the creation of a scaffold to which other genes localize is highly applicable to systems in synthetic biology. (for more information, please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Future Future Directions] page)<br />
<br><br />
<br />
The genes we focused on are <i>mamK</i> and <i>mamI</i> since they have known functions related to localization of the magnetosome. Specifically, MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamK is also shown to localize the MamI, which when lost inhibits vesicle formation. <br />
(for other gene functions, please see the iGEM Toolkits parts submitted page)<br />
<br> <br><br />
<br />
==='''Toolkit Contruction'''===<br />
[[File:Washington Methode image.jpg|700px|center]]<br />
<br />
<br/>Please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Results Result Summary] page for to see how far we were able to get this summer!<br />
<br />
<br/><br />
<br />
=References:=<br />
<br />
<br />
# Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A.T., Murase, Y., Takeyama, H. (2005). Complete genome sequence of the facultative anaerobic Magnetotactic bacterium Magnetospirillum sp. strain AMB-1. ''DNA research''; 12: 157-166. Doi:10.1093/dnares/dsi002. <br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Supporting Information. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Quinlan, A., Murat, D., Vali, H., Komeili, A. (2011).The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization. ''Molecular Microbiology''; 80 (4): 855-1131. Doi:10.1111/j.1365-2958.2011.07631.x.<br />
# Richter, M., Kube, M., Bazylinski, D.A., Lombardot, T.,Glockner, F.O., Reinhardt, R., Shuler, D. (2007). Comparative genome analysis of four Magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. ''Journal of Bacteriology''; 189(13): 4899-4910. Doi:10.1128/JB.00119-07.<br />
# Rioux, J.B., Philippe, N., Pereia, S., Pignol, D., Wu, L.F., Ginet, N. (2010). A second actin-like mamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. ''PLoS ONE''; 5(2): e9151. Doi:10.1371/journal.pone.0009151.</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ToolkitTeam:Washington/Magnetosomes/Magnet Toolkit2011-10-27T18:09:19Z<p>Robere: /* What are magnetosomes? Where do they come from? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Magnetosomes'''</big></big></big></big></center><br><br><br />
<br />
===What are magnetosomes? Where do they come from?===<br />
<br />
[[File:Washington iGEM2011 magnetotatic bacteria picture.jpg|thumb|right|350px|Magnetotactic Bacteria (left) and Magnetosome chains (right)]]<br />
<br />
<br> Magnetotactic bacteria are prokaryotic organisms that possess the unique ability to align themselves along a magnetic field. This form of taxis is made possible by the formation of a magnetosome. Magnetosomes are small invaginations of the bacterial inner membrane that contain magnetite particles.<br />
<br />
These particles range in size between 20 and several hundred nanometers and are aligned in one or several chains along the long axis of the bacteria. These particles act together to form a magnetic dipole across the bacteria, allowing it to sense the earth’s magnetic field. Magnetotactic bacteria are microaerophilic; therefore, magnetosomes are thought to help aid the organism in its search for the optimal oxygen level from a search in three dimensional space (in all directions) to a one dimensional space along a single path.<br />
<br><br><br><br />
<center>Video demonstration of Magnetic property of AMB-1:</center><br />
<html><center><iframe width="420" height="315" src="http://www.youtube.com/embed/1qWK_BZS-CU" frameborder="0" allowfullscreen></iframe></center></html><br />
<br />
<i>Narration text from video:</i> Magnetotactic bacteria are named for their ability to respond to and move along magnetic fields. They were first discovered in 1975 by Richard Blakemore when he noticed bacteria collecting on the north most edge of a water droplet he had placed on a microscope slide. Magnetotactic bacteria use a chain of vesicle-bound magnetite particles (known as magnetosomes) as a biological compass to orient themselves along the earth's magnetic field lines. They then swim along these field lines with flagella. It is thought that this process evolved to allow magnetotactic bacteria to search for certain micro-environments more efficiently. Magnetotactic bacteria in the northern hemisphere usually swim northward while those found in the southern hemisphere swim southward. In both cases this would direct the bacterium downward and is thought to allow it to find bottom sediments in an aqueous environment. As shown here, when a strong magnetic field is applied to the bacteria they can be moved as the magnetite particles within them become polarized and attracted to the magnetic field source.<br />
<br> <br><br />
<br />
===A Closer look at Magnetosome Formation ===<br />
<br />
[[File:F6.medium.png|300px|thumb|right|Diagram of stepwise magnetosome construction within AMB-1]]<br />
<br> <br />
The formation of the magnetosome organelle is a highly regulated, step-wise process requiring a cascade of essential genes. The process is generally hypothesized as four stages: <br />
# Membrane invagination<br />
# Acquiring minerals for magnetite formation <br />
# Iron-oxidation and reduction<br />
# Magnetite nucleation and morphology regulation.<br />
<br />
<br> Earlier gene products must be present for later gene products to be formed as shown in the diagram on the right[http://www.pnas.org/content/107/12/5593.full.pdf+html]:<br />
<br />
<br><br><br> <br />
<br />
===What did the UW iGEM team do with Magnetotactic Bacteria?=== <br />
<br> <br />
It is thought that many of the essential genes associated with magnetosome formation are located within a well-conserved region known as the magnetosome island (MAI). The MAI consists of 14 gene clusters labeled R1-R14 (see diagram below).Our team focused on the genes of the mamAB gene cluster (R5), as they were previously shown to be the only cluster essential for magnetosome membrane biogenesis in AMB-1 (diagram show below).[http://www.pnas.org/content/107/12/5593/F1.expansion.html].<br />
<br />
The goal of our project was to extract all the essential genes from (R5) required for magnetosome formation and express them in ''E. coli''. We are doing this to learn more about magnetosome formation and the magnet synthesis mechanism, because many of the genes' functions are still unknown in the host species. Using the information we have gained, we have organized a '''Magnetosome Toolkit''' containing most of the essential genes for proper magnetosome formation. Ultimately, we would like to continue expanding the magnetosome toolkit to have enough parts to show complete magnetosome formation in ''E.coli''.<br />
[[File:MamAB.png|center|500px|thumb|Fig. 3: The mamAB operon (R5) located in the magnetosome island (MAI).]]<br />
<br><br />
==='''About the Magnetosome Toolkit'''===<br />
<br><br />
Using standard synthetic biology protocols and the vectors we created in our Gibson Assembly Toolkit, our team created the '''"Magnetosome Toolkit"''' which contains many of the genes required for magnetosome formation. Providing this toolkit to the Parts Registry will help allow future iGEM teams to manipulate and further understand magnetosome formation to eventually synthesize magnets in multiple organisms. <br />
<br> <br/><br />
As previously noted, magnetosome formation within the host-organism, ''Magnetospirillium magneticum'', strain AMB-1, is a highly regulated step-wise process. As shown in diagram of stepwise magnetosome construction above, some genes encode proteins that form an invagination of the inner membrane, other genes which help align the magnetosomes into their characteristics chains, and others which regulate the biomineralization of magnetic particles. Our team chose to focus on genes specifically related to magnetosome scaffolding/alignment since they are the essential foundation for magnetosome development. In addition, the creation of a scaffold to which other genes localize is highly applicable to systems in synthetic biology. (for more information, please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Future Future Directions] page)<br />
<br><br />
<br />
The genes we focused on are <i>mamK</i> and <i>mamI</i> since they have known functions related to localization of the magnetosome. Specifically, MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamK is also shown to localize the MamI, which when lost inhibits vesicle formation. <br />
(for other gene functions, please see the iGEM Toolkits parts submitted page)<br />
<br> <br><br />
<br />
==='''Toolkit Contruction'''===<br />
[[File:Washington Methode image.jpg|700px|center]]<br />
<br />
<br/>Please see our [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Results Result Summary] page for to see how far we were able to get this summer!<br />
<br />
<br/><br />
<br />
=References:=<br />
<br />
<br />
# Matsunaga, T., Okamura, Y., Fukuda, Y., Wahyudi, A.T., Murase, Y., Takeyama, H. (2005). Complete genome sequence of the facultative anaerobic Magnetotactic bacterium Magnetospirillum sp. strain AMB-1. ''DNA research''; 12: 157-166. Doi:10.1093/dnares/dsi002. <br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Murat, D., Quinlan, A., Vali, H., Komeili, A. (2010). Supporting Information. ''PNAS''; 107 (12): 5593-5598. Doi:10.1073/pnas.0914439107.<br />
# Quinlan, A., Murat, D., Vali, H., Komeili, A. (2011).The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization. ''Molecular Microbiology''; 80 (4): 855-1131. Doi:10.1111/j.1365-2958.2011.07631.x.<br />
# Richter, M., Kube, M., Bazylinski, D.A., Lombardot, T.,Glockner, F.O., Reinhardt, R., Shuler, D. (2007). Comparative genome analysis of four Magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. ''Journal of Bacteriology''; 189(13): 4899-4910. Doi:10.1128/JB.00119-07.<br />
# Rioux, J.B., Philippe, N., Pereia, S., Pignol, D., Wu, L.F., Ginet, N. (2010). A second actin-like mamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. ''PLoS ONE''; 5(2): e9151. Doi:10.1371/journal.pone.0009151.</div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:54:55Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 970px;" align="center" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. The first is a set of five BioBrick vectors optimized for Gibson assembly. The second is a set of genes essential for magnetosome formation characterized in ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:53:54Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 965px;" align="center" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. The first is a set of five BioBrick vectors optimized for Gibson assembly. The second is a set of genes essential for magnetosome formation characterized in ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:53:42Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 900px;" align="center" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. The first is a set of five BioBrick vectors optimized for Gibson assembly. The second is a set of genes essential for magnetosome formation characterized in ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:52:31Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 975px;" align="center" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. The first is a set of five BioBrick vectors optimized for Gibson assembly. The second is a set of genes essential for magnetosome formation characterized in ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:51:53Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; align: center; text-align: center; width: 975px;" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. The first is a set of five BioBrick vectors optimized for Gibson assembly. The second is a set of genes essential for magnetosome formation characterized in ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:49:22Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 970px;" border="5"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="5"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. The first is a set of five BioBrick vectors optimized for Gibson assembly. The second is a set of genes essential for magnetosome formation characterized in ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:48:45Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 970px;" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. The first is a set of five BioBrick vectors optimized for Gibson assembly. The second is a set of genes essential for magnetosome formation characterized in ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:45:07Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 970px;" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''.<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:43:51Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 970px;" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: left; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:43:21Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 970px;" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly<br>and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: justify; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:39:44Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 965px;" border="0"<br />
| '''Make It: Diesel Production'''<br />
| '''Break It: Gluten Destruction'''<br />
| '''iGEM Toolkits: Gibson Assembly and Magnetosomes'''<br />
|}<br />
{| style="background: white; text-align: center; width: 965px;" border="0"<br />
|We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
|Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
|We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:38:22Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 965px;" border="0"<br />
| '''Make It: Diesel Production''' <br><br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br><br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''iGEM Toolkits: Gibson Assembly and Magnetosomes''' <br><br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:37:46Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 965px;" border="0"<br />
| '''Make It: Diesel Production''' <br><br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br><br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''iGEM Toolkits: Gibson Assembly and Magnetosomes''' <br><br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:36:31Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
{| style="background: white; text-align: center; width: 965px;" border="0"<br />
| '''Make It: Diesel Production''' <br><br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br><br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''iGEM Toolkits: Gibson Assembly and Magnetosomes''' <br><br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:33:52Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
{| class="wikitable" style="background: white; text-align: center; width: 965px;" border="0"<br />
|-<br />
| '''Make It: Diesel Production''' <br><br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br><br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''iGEM Toolkits: Gibson Assembly and Magnetosomes''' <br><br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:32:56Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
{| class="wikitable" style="background: white; text-align: center; width: 965px;"<br />
|-<br />
| '''Make It: Diesel Production''' <br><br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br><br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''iGEM Toolkits: Gibson Assembly and Magnetosomes''' <br><br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:31:13Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
{| class="wikitable" style="text-align: center; width: 965px;"<br />
|-<br />
| '''Make It: Diesel Production''' <br><br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br><br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''iGEM Toolkits: Gibson Assembly and Magnetosome''' <br><br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:30:26Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
{| class="wikitable" style="text-align: center; width: 965px;"<br />
|-<br />
| '''Make It: Diesel Production''' <br><br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br><br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''Gibson Assembly and Magnetosome Toolkits''' <br><br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:28:45Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
{| class="wikitable" style="text-align: center; width: 965px;"<br />
|-<br />
| '''Make It: Diesel Production''' <br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''Gibson Assembly and Magnetosome Toolkits''' <br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:25:43Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
{| class="wikitable" style="text-align: full; width: 1000px;"<br />
|-<br />
| '''Make It: Diesel Production''' <br> We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
| '''Break It: Gluten Destruction''' <br> Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP.<br />
| '''Gibson Assembly and Magnetosome Toolkits''' <br> We built two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
|}<br />
<br />
<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:15:06Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
<br />
<center><br />
'''Make It: Diesel Production'''<br>We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL|<br />
'''Break It: Gluten Destruction'''<br>Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP. |<br />
'''GibsonBricks and Magnetosome ToolKits'''<br>We completed two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
</center><br />
<br />
<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:14:42Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
<center><big>An overview of the 2011 UW iGEM team's summer projects</big></center><br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
<br />
<gallery><center><br />
'''Make It: Diesel Production'''<br>We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL|<br />
'''Break It: Gluten Destruction'''<br>Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP. |<br />
'''GibsonBricks and Magnetosome ToolKits'''<br>We completed two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
<br />
</gallery></center><br />
<br />
<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-29T01:12:22Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
<br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
<br />
<center><gallery caption="An Overview of the 2011 UW iGEM Team's Summer Projects" widths="250px" heights="300px" perrow="3"><br />
Image:Diesel Production for Wiki.png|'''Make It: Diesel Production'''<br>We designed and constructed a modular alkane production BioBrick, the PetroBrick, to generate alkanes, the main constituent of diesel. By expressing this BioBrick in ''E. coli'', we were able to produce alkanes of yields over 100 mg/mL.<br />
Image:Gluten Destruction for Wiki.png|'''Break It: Gluten Destruction'''<br>Gluten intolerance stems from an inappropriate immune response to PQLP, the most common motif in the immunogenic peptide. We reengineered a protease, active at low pH, for strongly enhanced activity against PQLP. <br />
Image:Gibson Assembly and Magnetosomes for Wiki.png|'''GibsonBricks and Magnetosome ToolKits'''<br>We completed two iGEM toolkits. In the first we created five Gibson Cloning versions of traditional biobrick vectors, and in the second we cloned the genes essential for magnetosome formation and transformed two into ''E. coli''<br />
<br />
</gallery></center><br />
<br />
<br />
<br />
<br />
='''Data Summary'''=<br />
<br />
==''Data for Favorite New Parts''==<br />
<br />
<br />
==='''Diesel Production'''===<br />
<br />
:: '''1, 2.''' [http://partsregistry.org/Part:BBa_K590025 BBa_K590025: '''The PetroBrick'''] - A modular and open platform for the biological production of diesel fuel. The PetroBrick consists of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 AAR] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 ADC], each behind a standard Elowitz RBS. All of this is under regulation by a high constitutive promoter in pSB1C3.<br />
<br />
==='''Gluten Destruction'''===<br />
<br />
:: '''3.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590087 BBa_K590087: '''KumaMax''']- A modified version of the enzyme Kumamolisin, a protease ofthe sedolisin family native to ''Alicyclobacillus sendaiensis'' known to be active at low pH and elevated temperatures. To Kumamolisin, the mutations N291D, G319S D358G, D368H increase activity to the PQLP peptide, an antigenic epitope in gliadin, 118-fold.<br />
<br />
==='''Gibson Assembly Toolkit'''===<br />
<br />
::'''4.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590010 BBa_K590010: '''pGA1A3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3'''] - These are plasmid backbones based on the bglBrick standard (BBF RFC 21) and optimized for use in Gibson assembly. These vectors are suitable replacements for the equivalent pSB vectors for iGEM teams using Gibson cloning to assemble their constructs.<br />
<br />
==='''Magnetosome Toolkit'''===<br />
<br />
:: '''5.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590015 BBa_K590015: '''sfGFP_mamK_pGA1C3'''] - This part consists of the ''mamK'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamK creates an actin-like filament that orients itself along the long-axis of the cell and acts as the scaffold for the alignment of magnetosome vesicles.<br />
<br />
:: '''6.''' [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590016 BBa_K590016 '''sfGFP_mamI_pGA1C3'''] - This part consists of ''mamI'' gene from ''Magnetospirillum magneticum'' strain AMB-1, as a superfolder GFP fusion, in the pGA1C3 backbone. MamI is a membrane-localized protein required for magnetosome vesicle formation that also binds the poly-MamK filament.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''7.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, found that it works well for expression, and entered this information in the part experience page.<br />
::'''8.''' [http://partsregistry.org/Part:pSB1A3:Experience pSB1A3] - As part of the Gibson Vector Toolkit we characterized the cloning efficiency of this plasmid backbone for Gibson assembly, using the prefix and suffix regions as primers. We found that pSB1A3 had a proper insert efficiency of 11%, compared to 99% for the equivalent Gibson-optimized pGA1A3 vector.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''9.''' [http://partsregistry.org/Part:BBa_K590059 BBa_K590059], [http://partsregistry.org/Part:BBa_K590060 BBa_K590060], [http://partsregistry.org/Part:BBa_K590061 BBa_K590061: '''LuxC, D, and E'''] (Cambridge, iGEM 2010) - Formerly part of the [http://partsregistry.org/Part:BBa_K325909 LuxBrick] the genes ''luxC, D,'' and ''E'' were not separated or codon-optimized. We codon-optimized these genes and put them under the control of standard Elowitz RBS's (B0034). This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Roberehttp://2011.igem.org/Team:WashingtonTeam:Washington2011-09-29T01:08:49Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Make It or Break It: <br/><br/> Diesel Production and Gluten Destruction, <br/><br/>the Synthetic Biology Way'''</big></big></big></big></center><br><br />
<br />
Synthetic biology holds great promise regarding the production of important compounds, and the degradation of harmful ones. This summer, we harnessed the power of synthetic biology to meet the world’s needs for fuel and medicine. <br />
<br/><br />
[[Image:Washington_Fire.jpg|left|320px|borderless|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[Image:Washington_Bottle.jpg|right|200px|borderless|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
<br />
[https://2011.igem.org/Team:Washington/Alkanes/Background '''Make It: Diesel Production'''] We constructed a strain of ''Escherichia coli'' that produces a variety of alkanes, the main constituents of diesel fuel, by introducing a pair of genes recently shown convert fatty acid synthesis intermediates into alkanes. <br />
<br />
[https://2011.igem.org/Team:Washington/Celiacs/Background '''Break It: Gluten Destruction'''] We identified a protease with gluten-degradation potential, and then reengineered it to have greatly increased gluten-degrading activity, allowing for the breakdown of gluten in the digestive track when taken in pill form. <br />
<br />
[https://2011.igem.org/Team:Washington/Magnetosomes/Background '''iGEM Toolkits'''] To enable next-generation cloning of standard biological parts, we built BioBrick vectors optimized for Gibson assembly and used them to create the Magnetosome Toolkit: a set of 18 genes from an essential operon in magnetotactic bacteria which we are characterizing to create magnetic ''E. coli''.<br />
<br />
<br />
[[File:Washington_Spacer.jpg|1px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|20px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
<br />
<br />
<br/><br />
[[File:Washington_Spacer.jpg|35px]]<br />
[[File:Washington_OSLI.png|frameless|border|link=http://www.osli.ca|Oil Sands Leadership Intiative]]<br />
[[File:Washington_Spacer.jpg|35px]]<br />
[[File:Washington_UniversitySeal.gif|frameless|border|110px|link=http://www.washington.edu|University of Washington]]<br />
[[File:Washington_Spacer.jpg|35px]]<br />
[[File:Washington_Anaspec.gif|frameless|border|120px|link=http://www.anaspec.com|Anaspec]]<br />
[[File:Washington_Spacer.jpg|35px]]<br />
[[File:Washington_ARPA-E_Logo.png|frameless|border|link=http://arpa-e.energy.gov/ProgramsProjects/Electrofuels.aspx|Advanced Research Projects Agency - Energy]]<br />
[[File:Washington_Spacer.jpg|35px]]<br />
[[File:Washington2011_Hhmi_362_72.jpg|link=http://www.hhmi.org/]]</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T01:06:11Z<p>Robere: /* sfGFP-MamI: Membrane localization */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as fusions with superfolder GFP are <i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===sfGFP-MamK: Scaffold formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E. coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, MamK is a filament which runs along the long axis of the bacteria. In the our images of sfGFP-MamK, scaffold-like structures can be clearly seen running through the length of most of the cells, in some cases looping back within a single cell for "figure-8" shaped filaments. In other cases, the filaments seem to prevent the cells from dividing properly, resulting in long chains of ''E. coli''. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br><br />
<br />
===sfGFP-MamI: Membrane localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For <i>mamI</i>, the gene product localizes to the cell membrane, consistent with its known role in inner membrane vesicle invagination. The membran localization is easily seen by the fluorescence profile analysis seen on the panel on the right. The graph shows that the fluorescence levels peak near the cell membrane and decrease to a minimum in the middle of the cytoplasm.<br />
<br />
<br> <br><br />
-----<br />
<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br/><br/><br />
<br />
== '''A set of the 18 genes from the mamAB operon essential for magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel extracts of magnetosome gene clusters]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}.<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T01:05:24Z<p>Robere: /* A set of the 18 genes from the mamAB operon essential for magnetosome formation */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as fusions with superfolder GFP are <i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===sfGFP-MamK: Scaffold formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E. coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, MamK is a filament which runs along the long axis of the bacteria. In the our images of sfGFP-MamK, scaffold-like structures can be clearly seen running through the length of most of the cells, in some cases looping back within a single cell for "figure-8" shaped filaments. In other cases, the filaments seem to prevent the cells from dividing properly, resulting in long chains of ''E. coli''. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br><br />
<br />
===sfGFP-MamI: Membrane localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For <i>mamI</i>, the gene product localizes to the cell membrane, consistent with its known role in inner membrane vesicle invagination. This fluorescence profile is easily seen by the fluorescence profile analysis seen on the panel on the right. The graph shows that the fluorescence levels peak near the cell membrane and decrease to a minimum in the middle of the cytoplasm.<br />
<br />
<br> <br><br />
-----<br />
<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br/><br/><br />
<br />
== '''A set of the 18 genes from the mamAB operon essential for magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel extracts of magnetosome gene clusters]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}.<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T01:04:58Z<p>Robere: /* A set of the 18 essential genes for the various steps of magnetosome formation */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as fusions with superfolder GFP are <i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===sfGFP-MamK: Scaffold formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E. coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, MamK is a filament which runs along the long axis of the bacteria. In the our images of sfGFP-MamK, scaffold-like structures can be clearly seen running through the length of most of the cells, in some cases looping back within a single cell for "figure-8" shaped filaments. In other cases, the filaments seem to prevent the cells from dividing properly, resulting in long chains of ''E. coli''. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br><br />
<br />
===sfGFP-MamI: Membrane localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For <i>mamI</i>, the gene product localizes to the cell membrane, consistent with its known role in inner membrane vesicle invagination. This fluorescence profile is easily seen by the fluorescence profile analysis seen on the panel on the right. The graph shows that the fluorescence levels peak near the cell membrane and decrease to a minimum in the middle of the cytoplasm.<br />
<br />
<br> <br><br />
-----<br />
<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br/><br/><br />
<br />
== '''A set of the 18 genes from the mamAB operon essential for magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}.<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T01:04:05Z<p>Robere: /* Construction of the R5 region of the Magnetosome Island in E.coli */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as fusions with superfolder GFP are <i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===sfGFP-MamK: Scaffold formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E. coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, MamK is a filament which runs along the long axis of the bacteria. In the our images of sfGFP-MamK, scaffold-like structures can be clearly seen running through the length of most of the cells, in some cases looping back within a single cell for "figure-8" shaped filaments. In other cases, the filaments seem to prevent the cells from dividing properly, resulting in long chains of ''E. coli''. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br><br />
<br />
===sfGFP-MamI: Membrane localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For <i>mamI</i>, the gene product localizes to the cell membrane, consistent with its known role in inner membrane vesicle invagination. This fluorescence profile is easily seen by the fluorescence profile analysis seen on the panel on the right. The graph shows that the fluorescence levels peak near the cell membrane and decrease to a minimum in the middle of the cytoplasm.<br />
<br />
<br> <br><br />
-----<br />
<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br/><br/><br />
<br />
== '''A set of the 18 essential genes for the various steps of magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}. <br />
<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T01:03:12Z<p>Robere: /* mamK: Filament formation */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as fusions with superfolder GFP are <i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===sfGFP-MamK: Scaffold formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E. coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, MamK is a filament which runs along the long axis of the bacteria. In the our images of sfGFP-MamK, scaffold-like structures can be clearly seen running through the length of most of the cells, in some cases looping back within a single cell for "figure-8" shaped filaments. In other cases, the filaments seem to prevent the cells from dividing properly, resulting in long chains of ''E. coli''. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br><br />
<br />
===sfGFP-MamI: Membrane localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For <i>mamI</i>, the gene product localizes to the cell membrane, consistent with its known role in inner membrane vesicle invagination. This fluorescence profile is easily seen by the fluorescence profile analysis seen on the panel on the right. The graph shows that the fluorescence levels peak near the cell membrane and decrease to a minimum in the middle of the cytoplasm.<br />
<br />
<br> <br><br />
-----<br />
<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br />
== '''A set of the 18 essential genes for the various steps of magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}. <br />
<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T01:02:53Z<p>Robere: /* mamI: Membrane Localization */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as fusions with superfolder GFP are <i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===mamK: Filament formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E. coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, MamK is a filament which runs along the long axis of the bacteria. In the our images of sfGFP-MamK, scaffold-like structures can be clearly seen running through the length of most of the cells, in some cases looping back within a single cell for "figure-8" shaped filaments. In other cases, the filaments seem to prevent the cells from dividing properly, resulting in long chains of ''E. coli''. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br> <br />
===sfGFP-MamI: Membrane localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For <i>mamI</i>, the gene product localizes to the cell membrane, consistent with its known role in inner membrane vesicle invagination. This fluorescence profile is easily seen by the fluorescence profile analysis seen on the panel on the right. The graph shows that the fluorescence levels peak near the cell membrane and decrease to a minimum in the middle of the cytoplasm.<br />
<br />
<br> <br><br />
-----<br />
<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br />
== '''A set of the 18 essential genes for the various steps of magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}. <br />
<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T01:02:29Z<p>Robere: /* Superfolder GFP-magnetosome gene protein fusions */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as fusions with superfolder GFP are <i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===mamK: Filament formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E. coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, MamK is a filament which runs along the long axis of the bacteria. In the our images of sfGFP-MamK, scaffold-like structures can be clearly seen running through the length of most of the cells, in some cases looping back within a single cell for "figure-8" shaped filaments. In other cases, the filaments seem to prevent the cells from dividing properly, resulting in long chains of ''E. coli''. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br> <br />
===mamI: Membrane Localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For <i>mamI</i>, the gene product localizes to the cell membrane, consistent with its known role in inner membrane vesicle invagination. This fluorescence profile is easily seen by the fluorescence profile analysis seen on the panel on the right. The graph shows that the fluorescence levels peak near the cell membrane and decrease to a minimum in the middle of the cytoplasm.<br />
<br />
<br> <br><br />
-----<br />
<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br />
== '''A set of the 18 essential genes for the various steps of magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}. <br />
<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T00:51:44Z<p>Robere: /* What’s in the Magnetosome Toolkit? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br><br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as superfolder GFP fusions are ,<i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===mamK: Filament formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E.coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, mamK is a filament which runs through the length of the bacteria. In the our images of mamK, filamentous structures can be clearly seen running through the length of ''many'' bacteria. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br> <br />
===mamI: Membrane Localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For mamI, the gene product is seen to fluorescent around the bacterial cell membrane of the bacteria but mostly concentrated at the ends. This can be seen in the fluorescence profile analysis that was taken while imaging the cells. The graph shows that as the arrow crosses the cell membrane, the fluorescent peaks are at a maximum, and through the center of the cell, the level of fluorescence decreases.<br />
<br />
<br> <br><br />
-----<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br />
== '''A set of the 18 essential genes for the various steps of magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}. <br />
<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T00:51:33Z<p>Robere: /* What’s in the Magnetosome Toolkit? */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
<br> <br />
-----<br />
<br />
== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
<br />
The two genes we characterized as superfolder GFP fusions are ,<i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
<br />
===mamK: Filament formation=== <br />
<br><br />
<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
<br />
The results we obtained with our sfGFP fusions inside ''E.coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, mamK is a filament which runs through the length of the bacteria. In the our images of mamK, filamentous structures can be clearly seen running through the length of ''many'' bacteria. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
<br />
<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
<br> <br />
===mamI: Membrane Localization===<br />
<br />
<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
<br />
For mamI, the gene product is seen to fluorescent around the bacterial cell membrane of the bacteria but mostly concentrated at the ends. This can be seen in the fluorescence profile analysis that was taken while imaging the cells. The graph shows that as the arrow crosses the cell membrane, the fluorescent peaks are at a maximum, and through the center of the cell, the level of fluorescence decreases.<br />
<br />
<br> <br><br />
-----<br />
=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
<br />
After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
<br />
== '''A set of the 18 essential genes for the various steps of magnetosome formation'''==<br />
<br />
Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
<br />
[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}. <br />
<br />
<br />
== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Roberehttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-29T00:51:13Z<p>Robere: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Magnetosome Toolkit: Results Summary'''</big></big></big></big></center><br><br><br />
<br />
=='''What’s in the Magnetosome Toolkit?'''==<br />
<br />
* A set of 10 gene clusters from the essential mamAB operon of strain AMB-1<br />
* Our favorite genes as translational fusions with superfolder <i>gfp</i> in pGA vectors<br />
* A table compiling individual gene functions from our literature search<br />
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== '''Superfolder GFP-magnetosome gene protein fusions'''==<br />
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The two genes we characterized as superfolder GFP fusions are ,<i>mamK</i> and <i>mamI</i>. They each perform core functions of magnetosome formation. MamK is a bacterial actin-like cytoskeleton protein required for proper alignment of the magnetosomes in a chain. MamI is a membrane-localized protein required for magnetosome vesicle formation that has also been shown to localize on the MamK filament. For more information, see the <i>mamAB</i> description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page]. Using our two genes of interest, we created C-terminal sfGFP fusions so we could track the localization of each gene separately within ''E.coli.'' <br />
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===mamK: Filament formation=== <br />
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<center> [[File:Washington igem11 MamK fusion full 01.jpg|400px|middle]][[File:Washington igem11 MamK fusion gfp 01.jpg||400px|middle]]</center><br />
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The results we obtained with our sfGFP fusions inside ''E.coli'' were comparable to those done through other studies in the host organism ''Magnetospirillum magneticum''. Within AMB-1, mamK is a filament which runs through the length of the bacteria. In the our images of mamK, filamentous structures can be clearly seen running through the length of ''many'' bacteria. In our experimental result, there was an over- expression of mamK which connected the ''E.coli'' cells together. <br />
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<gallery widths=180px heights=150px caption="More images of E.coli with sfGFP mamK fusion" ><br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) crop.jpg <br />
File:Washington igem11 SfGFP-K-1A3-100iptg-02(20ms exp) gfp.jpg<br />
File:Washington SfGFP K 4C5-col1 03 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 03 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 05 gfp.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 crop.jpg<br />
File:Washington igem11 SfGFP K 4C5-col1 04 gfp.jpg<br />
<br />
</gallery><br />
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===mamI: Membrane Localization===<br />
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<center>[[File:Washington igem11 MamIfusion full.jpg|200px]][[File:Washington_igem11_MamIfusion_GFP.jpg|200px]][[File:Washington_igem11_mamI_graph.png|350px]] </center><br />
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For mamI, the gene product is seen to fluorescent around the bacterial cell membrane of the bacteria but mostly concentrated at the ends. This can be seen in the fluorescence profile analysis that was taken while imaging the cells. The graph shows that as the arrow crosses the cell membrane, the fluorescent peaks are at a maximum, and through the center of the cell, the level of fluorescence decreases.<br />
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=='''Construction of the R5 region of the Magnetosome Island in ''E.coli'' '''==<br />
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After verifying that the construction of the sfGFP-MamK scaffold worked as expected, we proceeded to create a full assembly of the <i>mamAB</i> operon by building three super-assemblies: ''mamHIEJKL'', ''mamMNOPA'', and ''mamQRBSTUV''. The PCR products of these intermediate assemblies are shown below. The ''mamHIEJKL'' and ''mamQRBSTUV'' have been partially sequence-confirmed, and we are currently working on designing primers to fill in the gap sequences. Despite these gaps, when cells with the ''mamHIEJKL'' construct were imaged, they appeared to be forming chains.<br/><br />
<center>[[File:Washington_iGEM2011_magentosome_HIEJKL3k3.png|500px|middle]]:[[File:Washington_iGEM2011_magentosome_MNOPA.png|100px|middle]][[File:Washington_iGEM2011_magentosome_QRBSTUV.png|100px|middle]]<br />
</center><br />
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== '''A set of the 18 essential genes for the various steps of magnetosome formation'''==<br />
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Before piecing together the 16 kb genome of the mamAB gene cluster within the magnetosome island (MAI), we extracted out the genes in the following groups: <br />
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[[File:Washington_iGEM2011_magentosome_all_gel.png|right|thumb|700px|Gel Extracts of Individual Magnetosome Genes]]<br />
{| class="wikitable"<br />
|-<br />
! Gene groups<br />
! Length (bp)<br />
|-<br />
| mamHI<br />
| 1541<br />
|-<br />
| mamE<br />
| 2172<br />
|-<br />
| mamJ<br />
| 1538<br />
|-<br />
| mamKL<br />
| 1336<br />
|- <br />
| mamMN<br />
| 2323 <br />
|-<br />
| mamO<br />
| 1914<br />
|-<br />
| mamPA<br />
| 1493<br />
|-<br />
| mamQRB<br />
| 2029<br />
|- <br />
| mamSTU<br />
| 2030<br />
|-<br />
| mamV<br />
| 1002<br />
|-<br />
|}. <br />
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== '''A table of individual gene functions ''' ==<br />
Please see our <i>mamAB</i> genes description [https://2011.igem.org/Team:Washington/Magnetosomes/mamDescriptions page].</div>Robere