http://2011.igem.org/wiki/index.php?title=Special:Contributions/Swanson&feed=atom&limit=50&target=Swanson&year=&month=2011.igem.org - User contributions [en]2024-03-28T11:19:22ZFrom 2011.igem.orgMediaWiki 1.16.0http://2011.igem.org/File:Washington_Bottle.jpgFile:Washington Bottle.jpg2011-09-28T23:56:27Z<p>Swanson: uploaded a new version of &quot;File:Washington Bottle.jpg&quot;</p>
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<div></div>Swansonhttp://2011.igem.org/File:Washington_Bottle.jpgFile:Washington Bottle.jpg2011-09-28T23:55:09Z<p>Swanson: uploaded a new version of &quot;File:Washington Bottle.jpg&quot;</p>
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<div></div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/ResultsTeam:Washington/Alkanes/Results2011-09-28T19:58:53Z<p>Swanson: /* GCMS confirms The PetroBrick enables diesel production from sugar using E. coli */</p>
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<div>{{Template:Team:Washington/Templates/Top}}<br />
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<center><big><big><big><big>'''Diesel Production: Results Summary'''</big></big></big></big></center><br><br><br />
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='''GCMS confirms The PetroBrick enables diesel production from sugar using ''E. coli'''''=<br />
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We preformed GC-MS analysis on extracts from cell cultures expressing both [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032 Acyl-ACP Reductase] (AAR) and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031 Aldehyde Decarbonylase] (ADC) (this composite part is designated [http://partsregistry.org/Part:BBa_K590025 The PetroBrick]). To act as controls and in order to show that the alkane production system is working as expected, we also analyzed cell cultures expressing either only AAR, or only ADC.<br />
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[[Image:Washington_2011_PetroBrick.png|300px|frameless|border|left|link=http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025]]<br />
[[Image:Washinton_AARADCGC-MS.png|center|600px|thumb|GCMS confirms PetroBrick diesel production from sugar using E. coli]]<br />
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'''No significant hydrocarbons peaks in samples extracted from cells expressing only ADC.''' The blue GCMS chromatagram trace on the bottom show no significant peaks are found on the ADC only control within the time range that we expect alkane signal based upon GC-MS runs on chemical standards (8-10.5 minutes). This is expected, as ''E. coli'' does not normally produce any long chain length aldehyde substrates.<br />
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'''C16 alcohols are observed when AAR is expressed on its own.''' The red GCMS chromatagram trace in the middle has a significant peak at 10.2 minutes corresponding to the C16 alcohol (as confirmed by comparison of the peak's MS spectra to a reference library) is observed when AAR is expressed in MG1655 E. coli. The production of C16 alcohols in cells expressing AAR (but not in cells expressing only ADC) is consistent with AAR reducing even chain length Acyl-ACPs into even chain length fatty aldehydes, which are further reduced by aldehyde dehydrogenases to the alcohol.<br />
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'''The PetroBrick Works! C13, C15, and C17 alkanes are produced when both AAR and ADC are expressed.''' <br />
[[File:Washington2011 Spectra.png|right|550px|thumb|Comparasion of the NIST reference C15 alkane spectrum( in blue) to the C15 peak spectrum taken from a PetroBrick culture (in red). Note the strong m/z peak at 212, corresponding to the parent ion of the C15 alkane. For spectra of the C13 alkane and C17 alkene, refer to our [https://2011.igem.org/Team:Washington/Alkanes/spectra Spectra Page.]]]<br />
The green GCMS chromatagram trace in the middle has a significant new peaks corresponding to the C13 (8.2min) and C15 (9.2min) alkanes, as well as a peak at 10.2 minutes that contains both the C14 alcohol and the C17 alkene. The fact that the C17 alkene peak overlaps with the C14 alcohol peak makes exact quantification of C17 akene yields impossible, but we have sufficient evidence to determine that both molecules are present in the 10.2 minute peak( the earlier section of the peak has an MS spectra consistent with the C16 alcohol, and the later section is consistent with the C17 alkene). The C13 and C15 alkane peaks showed MS spectra highly consistent with C13 and C15 alkane reference spectra(for these spectra, as well as the C17 alkene spectrum, refer to our [https://2011.igem.org/Team:Washington/Alkanes/spectra Spectra Page.]). In addition, both alkane molecules eluted off of the GC at the same time as C13 and C15 alkane standards, further increasing confidence that the 8.2 min and 9.2 min peaks do correspond to the C13 and C15 alkanes. Odd chain length alkane production is what is expected from our system, as ADC removes a carbonyl group from even chain length aldehydes produced by AAR, yielding an odd chain length alkane. Using the PetroBrick, we can turn simple sugars into diesel, a fuel fully compatible with modern infrastructure.<br />
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='''Initial Quantization of Alkane Production'''=<br />
In order to be able to know how much alkane was being produced by our ''E. coli'', we spiked known amounts of alkane into cell cultures known to not produce alkanes. We then extracted using ethyl acetate, and analyzed extracts using GC-MS. Since peak area corresponds to the amount of each substance present, we used these GC plots to make a standard curve that allows us to convert peak area into an absolute yield. To determine how much alkane was being produced by the Petrobrick, we grew up 3 MG1655 cell cultures transformed with the PetroBrick in M9 production media ([https://2011.igem.org/Team:Washington/alkanebiosynthesis link]), and analyzed using GC-MS.<br />
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[[File:Washington_alkanestandardcurve.png|right|450px|thumb|Standard curve for converting peak area to an absolute amount. Note that this curve is almost perfectly linear.]]<br />
[[File:Washinton 2011 Pre-Optimization Quant.png|left|450px|thumb|Diagram showing yields of the C13 and C15 alkanes. Note: This C17 alkane is not included due to inability to quantify.]]<br />
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='''Optimized Production'''=<br />
By optimizing the method of growth, media, vectors, and cell line we were able to successfully increase alkane yield over 80-fold. Note that this improvement doesn't include C17 alkene production, as we were unable to quantify the C17 alkene peak due to co-elution with the C14 alcohol. The parameters we adjusted for optimization are discussed in detail at [https://2011.igem.org/Team:Washington/Alkanes/Future/Vector our systems optimization] page under future directions, as this is an on going process.<br />
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[[File:Washinton 2011 Optimization Quant.png|center|550px|thumb|Diagram showing yields of the C13 and C15 alkanes, and C17 alkenes.]]</div>Swansonhttp://2011.igem.org/Team:WashingtonTeam:Washington2011-09-28T06:17:38Z<p>Swanson: /* Make It or Break It: Diesel Production and Gluten Destruction, the Synthetic Biology Way */</p>
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=<center>'''Make It or Break It: <br/> Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<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 />
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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 convert fatty acid synthesis intermediates into alkanes. <br />
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[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 />
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[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 bring to the Parts Registry 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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[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/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://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/]]</div>Swansonhttp://2011.igem.org/File:Washington_Fire.jpgFile:Washington Fire.jpg2011-09-28T06:06:11Z<p>Swanson: uploaded a new version of &quot;File:Washington Fire.jpg&quot;</p>
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<div></div>Swansonhttp://2011.igem.org/File:Washington_Bottle.jpgFile:Washington Bottle.jpg2011-09-28T06:04:48Z<p>Swanson: uploaded a new version of &quot;File:Washington Bottle.jpg&quot;</p>
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<div></div>Swansonhttp://2011.igem.org/File:Washington_Fire.jpgFile:Washington Fire.jpg2011-09-28T06:01:20Z<p>Swanson: uploaded a new version of &quot;File:Washington Fire.jpg&quot;</p>
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<div></div>Swansonhttp://2011.igem.org/File:Washington_Bottle.jpgFile:Washington Bottle.jpg2011-09-28T06:00:44Z<p>Swanson: uploaded a new version of &quot;File:Washington Bottle.jpg&quot;</p>
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<div></div>Swansonhttp://2011.igem.org/File:Washington_Bottle.jpgFile:Washington Bottle.jpg2011-09-28T05:56:38Z<p>Swanson: </p>
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<div></div>Swansonhttp://2011.igem.org/File:Washington_Fire.jpgFile:Washington Fire.jpg2011-09-28T05:55:35Z<p>Swanson: </p>
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<div></div>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-28T05:05:12Z<p>Swanson: /* Improved Parts */</p>
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__NOTOC__<br />
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<center><big><big><big><big>'''Data Page'''</big></big></big></big></center><br><br><br />
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<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 />
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</gallery></center><br />
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='''Data Summary'''=<br />
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==''Data for Favorite New Parts''==<br />
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==='''Diesel Production'''===<br />
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:: '''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 />
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==='''Gluten Destruction'''===<br />
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:: '''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 />
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==='''Gibson Assembly Toolkit'''===<br />
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::'''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 />
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==='''Magnetosome Toolkit'''===<br />
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:: '''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 />
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:: '''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 />
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==''Data for Existing Parts''==<br />
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::'''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 />
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==''Improved Parts''==<br />
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::'''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 />
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='''All Submitted Parts'''=<br />
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<center><groupparts>iGEM011 Washington</groupparts></center></div>Swansonhttp://2011.igem.org/Team:Washington/Team/MembersTeam:Washington/Team/Members2011-09-28T01:43:05Z<p>Swanson: /* iGEM Toolkits */</p>
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<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
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<!---------------------------------------PAGE CONTENT GOES BELOW THIS----------------------------------------><br />
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== '''Who we are''' ==<br />
<br />
<gallery caption="Undergraduate Team Members" widths="180px" heights="120px" perrow="4"><br />
Image:Washington Casey Ager Profile1.jpg|<center>Casey Ager <br/> Biochemistry</center><br />
Image:Washington Photo-0088A.png|<center>Juhye An <br/> Biochemistry </center><br />
Image: Profile_Michael_Brasino.jpg|<center>Michael Brasino <br/> Materials Science and Engineering</center><br />
Image:Washington_.jpg|<center>Marika Cheng <br/> Microbiology</center><br />
Image:Washington_choe_chris.png|<center>Chris Choe <br/> Undecided</center><br />
Image:Washington DeLeon 2011.jpg|<center>Justin De Leon <br/> Microbiology</center><br />
File:Princess Peachy.JPG|<center>Sydney Gordon <br/> Biochemistry, Music</center><br />
Image:CIMG0021.jpg|<center>Daniel Hadidi <br/> Neurobiology</center><br />
Image:Washington_Matthew_Harger.JPG|<center>Matthew Harger <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Elaine.jpg|<center>Elaine Lai <br/> Microbiology, Chemistry</center><br />
Image:Washington_2011_Lab_Ben.png|<center>Benjamin Mo <br/> Bioengineering</center><br />
Image:Washington 2011 CIMG0015-A.jpg|<center>Austin Moon <br/> Cellular and Molecular Biology, Microbiology</center><br />
Image:Washington_iGEM2011_Rashmi.jpg|<center>Rashmi Ravichandran <br/> Microbiology</center><br />
Image:rsz_cats.png|<center>Seth Sagulo <br/> Biochemistry</center><br />
File:Washington_Liz.png|<center>Liz Stanley <br/> Microbiology, Chemistry</center><br />
Image:Washington_Angus_Pic.jpg|<center>Angus Toland <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Sarah Wolf <br/> Biochemistry</center><br />
Image:Washington_igem11whowearepicture.jpg|<center>SauShun (Alicia) Wong <br/> Materials Science and Engineering</center><br />
Image:Washington_Cindy.jpg|<center>Cindy Wu <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Sean_Wu.jpg|<center>Sean Wu <br/> Computer Science and Engineering</center><br />
Image:Washington_.jpg|<center>Lei Zheng <br/> Biochemistry</center><br />
Image:Washington_david_zong.jpg|<center>David Zong <br/> Bioengineering</center><br />
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</gallery><br />
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<br />
<gallery caption="Advisors" widths="180px" heights="120px" perrow="4"><br />
File:Aaron_bike_UW.png|<center>Aaron Chevalier <br/> Bioengineering </center><br />
Image:Regbert.jpg|<center>Rob Egbert <br/> Electrical Engineering </center><br />
Image:CEiben.jpg|<center>Chris Eiben <br/> Biochemistry </center><br />
Image:IMG_0129.jpg|<center>Jeremy Mills <br/> Biochemistry </center><br />
Image:Siegel_UW_2011.jpg|<center>Justin Siegel <br/> Biomolecular Structure and Design</center><br />
Image:Washington2011_Matthew-d-smith.jpg|<center>Matt Smith <br/> Molecular and Cellular Biology</center><br />
File:Washington_Ingrid_Pic_1.jpg|<center>Ingrid Swanson Pultz<br/> Microbiology </center><br />
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<gallery caption="Faculty" widths="180px" heights="120px" perrow="5"><br />
image:Washington_David_Baker.jpg|<center>David Baker <br/> Biochemistry</center><br />
Image:Washington_Klavins.jpg|<center>Eric Klavins <br/> Electrical Engineering</center><br />
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<gallery caption="Collaborators and Support" widths="140px" heights="100px" perrow="5"><br />
<br />
Image:Washington_OSLI.png|<center><b>Oil Sand Leadership Initiative</b> <br/> Funding to support Travel and Registration Costs</center><br />
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Image:Washington_UniversitySeal.gif|<center><b>UW Biochemistry</b> <br/> Lab space</center><br />
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Image:Washington_Anaspec.gif|<center><b>Anaspec</b> <br/> Peptide Discounts</center><br />
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Image:Washington_ARPA-E_Logo.png|<center><b>Advanced Research Projects Agency - Energy </b><br/> Registration Support</center><br />
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Image:Washington2011_Hhmi_362_72.jpg|<center><b>Howard Hughes Medical Institute</b> <br/> Lab materials and supplies</center><br />
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<br />
== '''Who did what''' ==<br />
The teams were assembled during our winter quarter. During this term we went around to classes and had weekly meetings to introduce students to synthetic biology through a series of guest lectures. During the spring, students participated in brainstorming projects related to the sponsoring Faculty advisors labs (Baker and Klavins) and came up with the project they wanted to carry out. Students also planned and partcipated in community outreach events where we taught our community about synthetic biology. Over the summer, students completed all of the experimental work, but worked closely with both graduate students and faculty advisors to plan the most pertinent experiments and make the most of our limited time. '''The work documented here in this wiki and on our presentation is entirely the work of iGEM students - it does not represent the project of any host lab, advisor, or instructor participating in iGEM.'''<br />
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=== Diesel Production ===<br />
After producing promising results, in future directions:<br />
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Casey Ager, Austin Moon, and Seth Sagulo worked on Enzyme Localization via Direct Fusion and Zinc Finger Fusion methods.<br />
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Juhye An, Elaine Lai, and Benjamin Mo worked on Decarbonylase Redesign<br />
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Marika Cheng and Justin De Leon worked on Alternative Chassis<br />
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Chris Choe and David Zong worked on Alternate Aldehyde Production<br />
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Matthew Harger worked on Branched Alkanes Production<br />
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Matthew Harger and Lei Zheng worked on System Optimization<br />
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=== Gluten Destruction ===<br />
Sydney Gordon, Daniel Hadidi, Liz Stanley, Angus Toland, Sarah Wolf, and Sean Wu designed, built, and tested Kumamolisin-As and over 100 mutants to combat gluten intolerance by increasing the activity on the PQLP antigenic peptide.<br />
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=== iGEM Toolkits ===<br />
Michael Brasino, Rashmi Ravichandran, and Alicia Wong worked on extracting the essential genes for magnetosomes, made the fusion proteins, and did the experimental measurements. They also did work regarding constructing and testing the GibsonBrick constructs, building on work that started in 2010 with 2010 UW iGEM students.<br />
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=== Community Outreach ===<br />
Cindy Wu headed and organized all iGEM 2011 Community Outreach events.</div>Swansonhttp://2011.igem.org/Team:Washington/Team/MembersTeam:Washington/Team/Members2011-09-28T01:41:14Z<p>Swanson: /* iGEM Toolkits */</p>
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<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
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== '''Who we are''' ==<br />
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<gallery caption="Undergraduate Team Members" widths="180px" heights="120px" perrow="4"><br />
Image:Washington Casey Ager Profile1.jpg|<center>Casey Ager <br/> Biochemistry</center><br />
Image:Washington Photo-0088A.png|<center>Juhye An <br/> Biochemistry </center><br />
Image: Profile_Michael_Brasino.jpg|<center>Michael Brasino <br/> Materials Science and Engineering</center><br />
Image:Washington_.jpg|<center>Marika Cheng <br/> Microbiology</center><br />
Image:Washington_choe_chris.png|<center>Chris Choe <br/> Undecided</center><br />
Image:Washington DeLeon 2011.jpg|<center>Justin De Leon <br/> Microbiology</center><br />
File:Princess Peachy.JPG|<center>Sydney Gordon <br/> Biochemistry, Music</center><br />
Image:CIMG0021.jpg|<center>Daniel Hadidi <br/> Neurobiology</center><br />
Image:Washington_Matthew_Harger.JPG|<center>Matthew Harger <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Elaine.jpg|<center>Elaine Lai <br/> Microbiology, Chemistry</center><br />
Image:Washington_2011_Lab_Ben.png|<center>Benjamin Mo <br/> Bioengineering</center><br />
Image:Washington 2011 CIMG0015-A.jpg|<center>Austin Moon <br/> Cellular and Molecular Biology, Microbiology</center><br />
Image:Washington_iGEM2011_Rashmi.jpg|<center>Rashmi Ravichandran <br/> Microbiology</center><br />
Image:rsz_cats.png|<center>Seth Sagulo <br/> Biochemistry</center><br />
File:Washington_Liz.png|<center>Liz Stanley <br/> Microbiology, Chemistry</center><br />
Image:Washington_Angus_Pic.jpg|<center>Angus Toland <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Sarah Wolf <br/> Biochemistry</center><br />
Image:Washington_igem11whowearepicture.jpg|<center>SauShun (Alicia) Wong <br/> Materials Science and Engineering</center><br />
Image:Washington_Cindy.jpg|<center>Cindy Wu <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Sean_Wu.jpg|<center>Sean Wu <br/> Computer Science and Engineering</center><br />
Image:Washington_.jpg|<center>Lei Zheng <br/> Biochemistry</center><br />
Image:Washington_david_zong.jpg|<center>David Zong <br/> Bioengineering</center><br />
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</gallery><br />
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<gallery caption="Advisors" widths="180px" heights="120px" perrow="4"><br />
File:Aaron_bike_UW.png|<center>Aaron Chevalier <br/> Bioengineering </center><br />
Image:Regbert.jpg|<center>Rob Egbert <br/> Electrical Engineering </center><br />
Image:CEiben.jpg|<center>Chris Eiben <br/> Biochemistry </center><br />
Image:IMG_0129.jpg|<center>Jeremy Mills <br/> Biochemistry </center><br />
Image:Siegel_UW_2011.jpg|<center>Justin Siegel <br/> Biomolecular Structure and Design</center><br />
Image:Washington2011_Matthew-d-smith.jpg|<center>Matt Smith <br/> Molecular and Cellular Biology</center><br />
File:Washington_Ingrid_Pic_1.jpg|<center>Ingrid Swanson Pultz<br/> Microbiology </center><br />
</gallery><br />
<br />
<br />
<gallery caption="Faculty" widths="180px" heights="120px" perrow="5"><br />
image:Washington_David_Baker.jpg|<center>David Baker <br/> Biochemistry</center><br />
Image:Washington_Klavins.jpg|<center>Eric Klavins <br/> Electrical Engineering</center><br />
</gallery><br />
<br />
<br />
<gallery caption="Collaborators and Support" widths="140px" heights="100px" perrow="5"><br />
<br />
Image:Washington_OSLI.png|<center><b>Oil Sand Leadership Initiative</b> <br/> Funding to support Travel and Registration Costs</center><br />
<br />
Image:Washington_UniversitySeal.gif|<center><b>UW Biochemistry</b> <br/> Lab space</center><br />
<br />
Image:Washington_Anaspec.gif|<center><b>Anaspec</b> <br/> Peptide Discounts</center><br />
<br />
Image:Washington_ARPA-E_Logo.png|<center><b>Advanced Research Projects Agency - Energy </b><br/> Registration Support</center><br />
<br />
Image:Washington2011_Hhmi_362_72.jpg|<center><b>Howard Hughes Medical Institute</b> <br/> Lab materials and supplies</center><br />
<br />
<br />
</gallery><br />
<br />
== '''Who did what''' ==<br />
The teams were assembled during our winter quarter. During this term we went around to classes and had weekly meetings to introduce students to synthetic biology through a series of guest lectures. During the spring, students participated in brainstorming projects related to the sponsoring Faculty advisors labs (Baker and Klavins) and came up with the project they wanted to carry out. Students also planned and partcipated in community outreach events where we taught our community about synthetic biology. Over the summer, students completed all of the experimental work, but worked closely with both graduate students and faculty advisors to plan the most pertinent experiments and make the most of our limited time. '''The work documented here in this wiki and on our presentation is entirely the work of iGEM students - it does not represent the project of any host lab, advisor, or instructor participating in iGEM.'''<br />
<br />
=== Diesel Production ===<br />
After producing promising results, in future directions:<br />
<br />
Casey Ager, Austin Moon, and Seth Sagulo worked on Enzyme Localization via Direct Fusion and Zinc Finger Fusion methods.<br />
<br />
Juhye An, Elaine Lai, and Benjamin Mo worked on Decarbonylase Redesign<br />
<br />
Marika Cheng and Justin De Leon worked on Alternative Chassis<br />
<br />
Chris Choe and David Zong worked on Alternate Aldehyde Production<br />
<br />
Matthew Harger worked on Branched Alkanes Production<br />
<br />
Matthew Harger and Lei Zheng worked on System Optimization<br />
<br />
=== Gluten Destruction ===<br />
Sydney Gordon, Daniel Hadidi, Liz Stanley, Angus Toland, Sarah Wolf, and Sean Wu designed, built, and tested Kumamolisin-As and over 100 mutants to combat gluten intolerance by increasing the activity on the PQLP antigenic peptide.<br />
<br />
=== iGEM Toolkits ===<br />
Michael Brasino, Rashmi Ravichandran, and Alicia Wong worked on extracting the essential genes for magnetosomes, made the fusion proteins, and did the experimental measurements. They also did the work regarding constructing and testing the GibsonBrick constructs.<br />
<br />
=== Community Outreach ===<br />
Cindy Wu headed and organized all iGEM 2011 Community Outreach events.</div>Swansonhttp://2011.igem.org/Team:Washington/Team/MembersTeam:Washington/Team/Members2011-09-28T01:40:44Z<p>Swanson: /* iGEM Toolkits */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<!---------------------------------------PAGE CONTENT GOES BELOW THIS----------------------------------------><br />
<br />
== '''Who we are''' ==<br />
<br />
<gallery caption="Undergraduate Team Members" widths="180px" heights="120px" perrow="4"><br />
Image:Washington Casey Ager Profile1.jpg|<center>Casey Ager <br/> Biochemistry</center><br />
Image:Washington Photo-0088A.png|<center>Juhye An <br/> Biochemistry </center><br />
Image: Profile_Michael_Brasino.jpg|<center>Michael Brasino <br/> Materials Science and Engineering</center><br />
Image:Washington_.jpg|<center>Marika Cheng <br/> Microbiology</center><br />
Image:Washington_choe_chris.png|<center>Chris Choe <br/> Undecided</center><br />
Image:Washington DeLeon 2011.jpg|<center>Justin De Leon <br/> Microbiology</center><br />
File:Princess Peachy.JPG|<center>Sydney Gordon <br/> Biochemistry, Music</center><br />
Image:CIMG0021.jpg|<center>Daniel Hadidi <br/> Neurobiology</center><br />
Image:Washington_Matthew_Harger.JPG|<center>Matthew Harger <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Elaine.jpg|<center>Elaine Lai <br/> Microbiology, Chemistry</center><br />
Image:Washington_2011_Lab_Ben.png|<center>Benjamin Mo <br/> Bioengineering</center><br />
Image:Washington 2011 CIMG0015-A.jpg|<center>Austin Moon <br/> Cellular and Molecular Biology, Microbiology</center><br />
Image:Washington_iGEM2011_Rashmi.jpg|<center>Rashmi Ravichandran <br/> Microbiology</center><br />
Image:rsz_cats.png|<center>Seth Sagulo <br/> Biochemistry</center><br />
File:Washington_Liz.png|<center>Liz Stanley <br/> Microbiology, Chemistry</center><br />
Image:Washington_Angus_Pic.jpg|<center>Angus Toland <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Sarah Wolf <br/> Biochemistry</center><br />
Image:Washington_igem11whowearepicture.jpg|<center>SauShun (Alicia) Wong <br/> Materials Science and Engineering</center><br />
Image:Washington_Cindy.jpg|<center>Cindy Wu <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Sean_Wu.jpg|<center>Sean Wu <br/> Computer Science and Engineering</center><br />
Image:Washington_.jpg|<center>Lei Zheng <br/> Biochemistry</center><br />
Image:Washington_david_zong.jpg|<center>David Zong <br/> Bioengineering</center><br />
<br />
</gallery><br />
<br />
<br />
<gallery caption="Advisors" widths="180px" heights="120px" perrow="4"><br />
File:Aaron_bike_UW.png|<center>Aaron Chevalier <br/> Bioengineering </center><br />
Image:Regbert.jpg|<center>Rob Egbert <br/> Electrical Engineering </center><br />
Image:CEiben.jpg|<center>Chris Eiben <br/> Biochemistry </center><br />
Image:IMG_0129.jpg|<center>Jeremy Mills <br/> Biochemistry </center><br />
Image:Siegel_UW_2011.jpg|<center>Justin Siegel <br/> Biomolecular Structure and Design</center><br />
Image:Washington2011_Matthew-d-smith.jpg|<center>Matt Smith <br/> Molecular and Cellular Biology</center><br />
File:Washington_Ingrid_Pic_1.jpg|<center>Ingrid Swanson Pultz<br/> Microbiology </center><br />
</gallery><br />
<br />
<br />
<gallery caption="Faculty" widths="180px" heights="120px" perrow="5"><br />
image:Washington_David_Baker.jpg|<center>David Baker <br/> Biochemistry</center><br />
Image:Washington_Klavins.jpg|<center>Eric Klavins <br/> Electrical Engineering</center><br />
</gallery><br />
<br />
<br />
<gallery caption="Collaborators and Support" widths="140px" heights="100px" perrow="5"><br />
<br />
Image:Washington_OSLI.png|<center><b>Oil Sand Leadership Initiative</b> <br/> Funding to support Travel and Registration Costs</center><br />
<br />
Image:Washington_UniversitySeal.gif|<center><b>UW Biochemistry</b> <br/> Lab space</center><br />
<br />
Image:Washington_Anaspec.gif|<center><b>Anaspec</b> <br/> Peptide Discounts</center><br />
<br />
Image:Washington_ARPA-E_Logo.png|<center><b>Advanced Research Projects Agency - Energy </b><br/> Registration Support</center><br />
<br />
Image:Washington2011_Hhmi_362_72.jpg|<center><b>Howard Hughes Medical Institute</b> <br/> Lab materials and supplies</center><br />
<br />
<br />
</gallery><br />
<br />
== '''Who did what''' ==<br />
The teams were assembled during our winter quarter. During this term we went around to classes and had weekly meetings to introduce students to synthetic biology through a series of guest lectures. During the spring, students participated in brainstorming projects related to the sponsoring Faculty advisors labs (Baker and Klavins) and came up with the project they wanted to carry out. Students also planned and partcipated in community outreach events where we taught our community about synthetic biology. Over the summer, students completed all of the experimental work, but worked closely with both graduate students and faculty advisors to plan the most pertinent experiments and make the most of our limited time. '''The work documented here in this wiki and on our presentation is entirely the work of iGEM students - it does not represent the project of any host lab, advisor, or instructor participating in iGEM.'''<br />
<br />
=== Diesel Production ===<br />
After producing promising results, in future directions:<br />
<br />
Casey Ager, Austin Moon, and Seth Sagulo worked on Enzyme Localization via Direct Fusion and Zinc Finger Fusion methods.<br />
<br />
Juhye An, Elaine Lai, and Benjamin Mo worked on Decarbonylase Redesign<br />
<br />
Marika Cheng and Justin De Leon worked on Alternative Chassis<br />
<br />
Chris Choe and David Zong worked on Alternate Aldehyde Production<br />
<br />
Matthew Harger worked on Branched Alkanes Production<br />
<br />
Matthew Harger and Lei Zheng worked on System Optimization<br />
<br />
=== Gluten Destruction ===<br />
Sydney Gordon, Daniel Hadidi, Liz Stanley, Angus Toland, Sarah Wolf, and Sean Wu designed, built, and tested Kumamolisin-As and over 100 mutants to combat gluten intolerance by increasing the activity on the PQLP antigenic peptide.<br />
<br />
=== iGEM Toolkits ===<br />
Michael Brasino, Rashmi Ravichandran, and Alicia Wong worked on extracting the essential genes for magnetosomes, made the fusion proteins, and did the experimental measurements.<br />
<br />
=== Community Outreach ===<br />
Cindy Wu headed and organized all iGEM 2011 Community Outreach events.</div>Swansonhttp://2011.igem.org/Team:Washington/Team/MembersTeam:Washington/Team/Members2011-09-28T01:40:27Z<p>Swanson: /* iGEM Toolkits */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<!---------------------------------------PAGE CONTENT GOES BELOW THIS----------------------------------------><br />
<br />
== '''Who we are''' ==<br />
<br />
<gallery caption="Undergraduate Team Members" widths="180px" heights="120px" perrow="4"><br />
Image:Washington Casey Ager Profile1.jpg|<center>Casey Ager <br/> Biochemistry</center><br />
Image:Washington Photo-0088A.png|<center>Juhye An <br/> Biochemistry </center><br />
Image: Profile_Michael_Brasino.jpg|<center>Michael Brasino <br/> Materials Science and Engineering</center><br />
Image:Washington_.jpg|<center>Marika Cheng <br/> Microbiology</center><br />
Image:Washington_choe_chris.png|<center>Chris Choe <br/> Undecided</center><br />
Image:Washington DeLeon 2011.jpg|<center>Justin De Leon <br/> Microbiology</center><br />
File:Princess Peachy.JPG|<center>Sydney Gordon <br/> Biochemistry, Music</center><br />
Image:CIMG0021.jpg|<center>Daniel Hadidi <br/> Neurobiology</center><br />
Image:Washington_Matthew_Harger.JPG|<center>Matthew Harger <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Elaine.jpg|<center>Elaine Lai <br/> Microbiology, Chemistry</center><br />
Image:Washington_2011_Lab_Ben.png|<center>Benjamin Mo <br/> Bioengineering</center><br />
Image:Washington 2011 CIMG0015-A.jpg|<center>Austin Moon <br/> Cellular and Molecular Biology, Microbiology</center><br />
Image:Washington_iGEM2011_Rashmi.jpg|<center>Rashmi Ravichandran <br/> Microbiology</center><br />
Image:rsz_cats.png|<center>Seth Sagulo <br/> Biochemistry</center><br />
File:Washington_Liz.png|<center>Liz Stanley <br/> Microbiology, Chemistry</center><br />
Image:Washington_Angus_Pic.jpg|<center>Angus Toland <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Sarah Wolf <br/> Biochemistry</center><br />
Image:Washington_igem11whowearepicture.jpg|<center>SauShun (Alicia) Wong <br/> Materials Science and Engineering</center><br />
Image:Washington_Cindy.jpg|<center>Cindy Wu <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Sean_Wu.jpg|<center>Sean Wu <br/> Computer Science and Engineering</center><br />
Image:Washington_.jpg|<center>Lei Zheng <br/> Biochemistry</center><br />
Image:Washington_david_zong.jpg|<center>David Zong <br/> Bioengineering</center><br />
<br />
</gallery><br />
<br />
<br />
<gallery caption="Advisors" widths="180px" heights="120px" perrow="4"><br />
File:Aaron_bike_UW.png|<center>Aaron Chevalier <br/> Bioengineering </center><br />
Image:Regbert.jpg|<center>Rob Egbert <br/> Electrical Engineering </center><br />
Image:CEiben.jpg|<center>Chris Eiben <br/> Biochemistry </center><br />
Image:IMG_0129.jpg|<center>Jeremy Mills <br/> Biochemistry </center><br />
Image:Siegel_UW_2011.jpg|<center>Justin Siegel <br/> Biomolecular Structure and Design</center><br />
Image:Washington2011_Matthew-d-smith.jpg|<center>Matt Smith <br/> Molecular and Cellular Biology</center><br />
File:Washington_Ingrid_Pic_1.jpg|<center>Ingrid Swanson Pultz<br/> Microbiology </center><br />
</gallery><br />
<br />
<br />
<gallery caption="Faculty" widths="180px" heights="120px" perrow="5"><br />
image:Washington_David_Baker.jpg|<center>David Baker <br/> Biochemistry</center><br />
Image:Washington_Klavins.jpg|<center>Eric Klavins <br/> Electrical Engineering</center><br />
</gallery><br />
<br />
<br />
<gallery caption="Collaborators and Support" widths="140px" heights="100px" perrow="5"><br />
<br />
Image:Washington_OSLI.png|<center><b>Oil Sand Leadership Initiative</b> <br/> Funding to support Travel and Registration Costs</center><br />
<br />
Image:Washington_UniversitySeal.gif|<center><b>UW Biochemistry</b> <br/> Lab space</center><br />
<br />
Image:Washington_Anaspec.gif|<center><b>Anaspec</b> <br/> Peptide Discounts</center><br />
<br />
Image:Washington_ARPA-E_Logo.png|<center><b>Advanced Research Projects Agency - Energy </b><br/> Registration Support</center><br />
<br />
Image:Washington2011_Hhmi_362_72.jpg|<center><b>Howard Hughes Medical Institute</b> <br/> Lab materials and supplies</center><br />
<br />
<br />
</gallery><br />
<br />
== '''Who did what''' ==<br />
The teams were assembled during our winter quarter. During this term we went around to classes and had weekly meetings to introduce students to synthetic biology through a series of guest lectures. During the spring, students participated in brainstorming projects related to the sponsoring Faculty advisors labs (Baker and Klavins) and came up with the project they wanted to carry out. Students also planned and partcipated in community outreach events where we taught our community about synthetic biology. Over the summer, students completed all of the experimental work, but worked closely with both graduate students and faculty advisors to plan the most pertinent experiments and make the most of our limited time. '''The work documented here in this wiki and on our presentation is entirely the work of iGEM students - it does not represent the project of any host lab, advisor, or instructor participating in iGEM.'''<br />
<br />
=== Diesel Production ===<br />
After producing promising results, in future directions:<br />
<br />
Casey Ager, Austin Moon, and Seth Sagulo worked on Enzyme Localization via Direct Fusion and Zinc Finger Fusion methods.<br />
<br />
Juhye An, Elaine Lai, and Benjamin Mo worked on Decarbonylase Redesign<br />
<br />
Marika Cheng and Justin De Leon worked on Alternative Chassis<br />
<br />
Chris Choe and David Zong worked on Alternate Aldehyde Production<br />
<br />
Matthew Harger worked on Branched Alkanes Production<br />
<br />
Matthew Harger and Lei Zheng worked on System Optimization<br />
<br />
=== Gluten Destruction ===<br />
Sydney Gordon, Daniel Hadidi, Liz Stanley, Angus Toland, Sarah Wolf, and Sean Wu designed, built, and tested Kumamolisin-As and over 100 mutants to combat gluten intolerance by increasing the activity on the PQLP antigenic peptide.<br />
<br />
=== iGEM Toolkits ===<br />
Michael Brasino, Rashmi Ravichandran, and Alicia Wong worked on extracting the essential genes for magnetosomes.<br />
<br />
=== Community Outreach ===<br />
Cindy Wu headed and organized all iGEM 2011 Community Outreach events.</div>Swansonhttp://2011.igem.org/Team:Washington/Team/MembersTeam:Washington/Team/Members2011-09-28T01:40:03Z<p>Swanson: /* Diesel Production */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<!---------------------------------------PAGE CONTENT GOES BELOW THIS----------------------------------------><br />
<br />
== '''Who we are''' ==<br />
<br />
<gallery caption="Undergraduate Team Members" widths="180px" heights="120px" perrow="4"><br />
Image:Washington Casey Ager Profile1.jpg|<center>Casey Ager <br/> Biochemistry</center><br />
Image:Washington Photo-0088A.png|<center>Juhye An <br/> Biochemistry </center><br />
Image: Profile_Michael_Brasino.jpg|<center>Michael Brasino <br/> Materials Science and Engineering</center><br />
Image:Washington_.jpg|<center>Marika Cheng <br/> Microbiology</center><br />
Image:Washington_choe_chris.png|<center>Chris Choe <br/> Undecided</center><br />
Image:Washington DeLeon 2011.jpg|<center>Justin De Leon <br/> Microbiology</center><br />
File:Princess Peachy.JPG|<center>Sydney Gordon <br/> Biochemistry, Music</center><br />
Image:CIMG0021.jpg|<center>Daniel Hadidi <br/> Neurobiology</center><br />
Image:Washington_Matthew_Harger.JPG|<center>Matthew Harger <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Elaine.jpg|<center>Elaine Lai <br/> Microbiology, Chemistry</center><br />
Image:Washington_2011_Lab_Ben.png|<center>Benjamin Mo <br/> Bioengineering</center><br />
Image:Washington 2011 CIMG0015-A.jpg|<center>Austin Moon <br/> Cellular and Molecular Biology, Microbiology</center><br />
Image:Washington_iGEM2011_Rashmi.jpg|<center>Rashmi Ravichandran <br/> Microbiology</center><br />
Image:rsz_cats.png|<center>Seth Sagulo <br/> Biochemistry</center><br />
File:Washington_Liz.png|<center>Liz Stanley <br/> Microbiology, Chemistry</center><br />
Image:Washington_Angus_Pic.jpg|<center>Angus Toland <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Sarah Wolf <br/> Biochemistry</center><br />
Image:Washington_igem11whowearepicture.jpg|<center>SauShun (Alicia) Wong <br/> Materials Science and Engineering</center><br />
Image:Washington_Cindy.jpg|<center>Cindy Wu <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Sean_Wu.jpg|<center>Sean Wu <br/> Computer Science and Engineering</center><br />
Image:Washington_.jpg|<center>Lei Zheng <br/> Biochemistry</center><br />
Image:Washington_david_zong.jpg|<center>David Zong <br/> Bioengineering</center><br />
<br />
</gallery><br />
<br />
<br />
<gallery caption="Advisors" widths="180px" heights="120px" perrow="4"><br />
File:Aaron_bike_UW.png|<center>Aaron Chevalier <br/> Bioengineering </center><br />
Image:Regbert.jpg|<center>Rob Egbert <br/> Electrical Engineering </center><br />
Image:CEiben.jpg|<center>Chris Eiben <br/> Biochemistry </center><br />
Image:IMG_0129.jpg|<center>Jeremy Mills <br/> Biochemistry </center><br />
Image:Siegel_UW_2011.jpg|<center>Justin Siegel <br/> Biomolecular Structure and Design</center><br />
Image:Washington2011_Matthew-d-smith.jpg|<center>Matt Smith <br/> Molecular and Cellular Biology</center><br />
File:Washington_Ingrid_Pic_1.jpg|<center>Ingrid Swanson Pultz<br/> Microbiology </center><br />
</gallery><br />
<br />
<br />
<gallery caption="Faculty" widths="180px" heights="120px" perrow="5"><br />
image:Washington_David_Baker.jpg|<center>David Baker <br/> Biochemistry</center><br />
Image:Washington_Klavins.jpg|<center>Eric Klavins <br/> Electrical Engineering</center><br />
</gallery><br />
<br />
<br />
<gallery caption="Collaborators and Support" widths="140px" heights="100px" perrow="5"><br />
<br />
Image:Washington_OSLI.png|<center><b>Oil Sand Leadership Initiative</b> <br/> Funding to support Travel and Registration Costs</center><br />
<br />
Image:Washington_UniversitySeal.gif|<center><b>UW Biochemistry</b> <br/> Lab space</center><br />
<br />
Image:Washington_Anaspec.gif|<center><b>Anaspec</b> <br/> Peptide Discounts</center><br />
<br />
Image:Washington_ARPA-E_Logo.png|<center><b>Advanced Research Projects Agency - Energy </b><br/> Registration Support</center><br />
<br />
Image:Washington2011_Hhmi_362_72.jpg|<center><b>Howard Hughes Medical Institute</b> <br/> Lab materials and supplies</center><br />
<br />
<br />
</gallery><br />
<br />
== '''Who did what''' ==<br />
The teams were assembled during our winter quarter. During this term we went around to classes and had weekly meetings to introduce students to synthetic biology through a series of guest lectures. During the spring, students participated in brainstorming projects related to the sponsoring Faculty advisors labs (Baker and Klavins) and came up with the project they wanted to carry out. Students also planned and partcipated in community outreach events where we taught our community about synthetic biology. Over the summer, students completed all of the experimental work, but worked closely with both graduate students and faculty advisors to plan the most pertinent experiments and make the most of our limited time. '''The work documented here in this wiki and on our presentation is entirely the work of iGEM students - it does not represent the project of any host lab, advisor, or instructor participating in iGEM.'''<br />
<br />
=== Diesel Production ===<br />
After producing promising results, in future directions:<br />
<br />
Casey Ager, Austin Moon, and Seth Sagulo worked on Enzyme Localization via Direct Fusion and Zinc Finger Fusion methods.<br />
<br />
Juhye An, Elaine Lai, and Benjamin Mo worked on Decarbonylase Redesign<br />
<br />
Marika Cheng and Justin De Leon worked on Alternative Chassis<br />
<br />
Chris Choe and David Zong worked on Alternate Aldehyde Production<br />
<br />
Matthew Harger worked on Branched Alkanes Production<br />
<br />
Matthew Harger and Lei Zheng worked on System Optimization<br />
<br />
=== Gluten Destruction ===<br />
Sydney Gordon, Daniel Hadidi, Liz Stanley, Angus Toland, Sarah Wolf, and Sean Wu designed, built, and tested Kumamolisin-As and over 100 mutants to combat gluten intolerance by increasing the activity on the PQLP antigenic peptide.<br />
<br />
=== iGEM Toolkits ===<br />
Michael Brasino, Rashmi Ravichandran, and Alicia Wong worked on extracting the essential genes for magnetosome...<br />
<br />
=== Community Outreach ===<br />
Cindy Wu headed and organized all iGEM 2011 Community Outreach events.</div>Swansonhttp://2011.igem.org/Team:Washington/Team/MembersTeam:Washington/Team/Members2011-09-28T01:39:37Z<p>Swanson: /* Who did what */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<!---------------------------------------PAGE CONTENT GOES BELOW THIS----------------------------------------><br />
<br />
== '''Who we are''' ==<br />
<br />
<gallery caption="Undergraduate Team Members" widths="180px" heights="120px" perrow="4"><br />
Image:Washington Casey Ager Profile1.jpg|<center>Casey Ager <br/> Biochemistry</center><br />
Image:Washington Photo-0088A.png|<center>Juhye An <br/> Biochemistry </center><br />
Image: Profile_Michael_Brasino.jpg|<center>Michael Brasino <br/> Materials Science and Engineering</center><br />
Image:Washington_.jpg|<center>Marika Cheng <br/> Microbiology</center><br />
Image:Washington_choe_chris.png|<center>Chris Choe <br/> Undecided</center><br />
Image:Washington DeLeon 2011.jpg|<center>Justin De Leon <br/> Microbiology</center><br />
File:Princess Peachy.JPG|<center>Sydney Gordon <br/> Biochemistry, Music</center><br />
Image:CIMG0021.jpg|<center>Daniel Hadidi <br/> Neurobiology</center><br />
Image:Washington_Matthew_Harger.JPG|<center>Matthew Harger <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Elaine.jpg|<center>Elaine Lai <br/> Microbiology, Chemistry</center><br />
Image:Washington_2011_Lab_Ben.png|<center>Benjamin Mo <br/> Bioengineering</center><br />
Image:Washington 2011 CIMG0015-A.jpg|<center>Austin Moon <br/> Cellular and Molecular Biology, Microbiology</center><br />
Image:Washington_iGEM2011_Rashmi.jpg|<center>Rashmi Ravichandran <br/> Microbiology</center><br />
Image:rsz_cats.png|<center>Seth Sagulo <br/> Biochemistry</center><br />
File:Washington_Liz.png|<center>Liz Stanley <br/> Microbiology, Chemistry</center><br />
Image:Washington_Angus_Pic.jpg|<center>Angus Toland <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Sarah Wolf <br/> Biochemistry</center><br />
Image:Washington_igem11whowearepicture.jpg|<center>SauShun (Alicia) Wong <br/> Materials Science and Engineering</center><br />
Image:Washington_Cindy.jpg|<center>Cindy Wu <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Sean_Wu.jpg|<center>Sean Wu <br/> Computer Science and Engineering</center><br />
Image:Washington_.jpg|<center>Lei Zheng <br/> Biochemistry</center><br />
Image:Washington_david_zong.jpg|<center>David Zong <br/> Bioengineering</center><br />
<br />
</gallery><br />
<br />
<br />
<gallery caption="Advisors" widths="180px" heights="120px" perrow="4"><br />
File:Aaron_bike_UW.png|<center>Aaron Chevalier <br/> Bioengineering </center><br />
Image:Regbert.jpg|<center>Rob Egbert <br/> Electrical Engineering </center><br />
Image:CEiben.jpg|<center>Chris Eiben <br/> Biochemistry </center><br />
Image:IMG_0129.jpg|<center>Jeremy Mills <br/> Biochemistry </center><br />
Image:Siegel_UW_2011.jpg|<center>Justin Siegel <br/> Biomolecular Structure and Design</center><br />
Image:Washington2011_Matthew-d-smith.jpg|<center>Matt Smith <br/> Molecular and Cellular Biology</center><br />
File:Washington_Ingrid_Pic_1.jpg|<center>Ingrid Swanson Pultz<br/> Microbiology </center><br />
</gallery><br />
<br />
<br />
<gallery caption="Faculty" widths="180px" heights="120px" perrow="5"><br />
image:Washington_David_Baker.jpg|<center>David Baker <br/> Biochemistry</center><br />
Image:Washington_Klavins.jpg|<center>Eric Klavins <br/> Electrical Engineering</center><br />
</gallery><br />
<br />
<br />
<gallery caption="Collaborators and Support" widths="140px" heights="100px" perrow="5"><br />
<br />
Image:Washington_OSLI.png|<center><b>Oil Sand Leadership Initiative</b> <br/> Funding to support Travel and Registration Costs</center><br />
<br />
Image:Washington_UniversitySeal.gif|<center><b>UW Biochemistry</b> <br/> Lab space</center><br />
<br />
Image:Washington_Anaspec.gif|<center><b>Anaspec</b> <br/> Peptide Discounts</center><br />
<br />
Image:Washington_ARPA-E_Logo.png|<center><b>Advanced Research Projects Agency - Energy </b><br/> Registration Support</center><br />
<br />
Image:Washington2011_Hhmi_362_72.jpg|<center><b>Howard Hughes Medical Institute</b> <br/> Lab materials and supplies</center><br />
<br />
<br />
</gallery><br />
<br />
== '''Who did what''' ==<br />
The teams were assembled during our winter quarter. During this term we went around to classes and had weekly meetings to introduce students to synthetic biology through a series of guest lectures. During the spring, students participated in brainstorming projects related to the sponsoring Faculty advisors labs (Baker and Klavins) and came up with the project they wanted to carry out. Students also planned and partcipated in community outreach events where we taught our community about synthetic biology. Over the summer, students completed all of the experimental work, but worked closely with both graduate students and faculty advisors to plan the most pertinent experiments and make the most of our limited time. '''The work documented here in this wiki and on our presentation is entirely the work of iGEM students - it does not represent the project of any host lab, advisor, or instructor participating in iGEM.'''<br />
<br />
=== Diesel Production ===<br />
After producing promising results, in future directions <br />
<br />
Casey Ager, Austin Moon, and Seth Sagulo worked on Enzyme Localization via Direct Fusion and Zinc Finger Fusion methods.<br />
<br />
Juhye An, Elaine Lai, and Benjamin Mo worked on Decarbonylase Redesign<br />
<br />
Marika Cheng and Justin De Leon worked on Alternative Chassis<br />
<br />
Chris Choe and David Zong worked on Alternate Aldehyde Production<br />
<br />
Matthew Harger worked on Branched Alkanes Production<br />
<br />
Matthew Harger and Lei Zheng worked on System Optimization<br />
<br />
=== Gluten Destruction ===<br />
Sydney Gordon, Daniel Hadidi, Liz Stanley, Angus Toland, Sarah Wolf, and Sean Wu designed, built, and tested Kumamolisin-As and over 100 mutants to combat gluten intolerance by increasing the activity on the PQLP antigenic peptide.<br />
<br />
=== iGEM Toolkits ===<br />
Michael Brasino, Rashmi Ravichandran, and Alicia Wong worked on extracting the essential genes for magnetosome...<br />
<br />
=== Community Outreach ===<br />
Cindy Wu headed and organized all iGEM 2011 Community Outreach events.</div>Swansonhttp://2011.igem.org/Team:WashingtonTeam:Washington2011-09-28T01:36:10Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
=<center>'''Make It or Break It: <br/> Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<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 />
[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 bring to the Parts Registry 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|15px]]<br />
[[Image:UW Diesel Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Alkanes/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
[[Image:UW Gluten Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Celiacs/Background]]<br />
[[File:Washington_Spacer.jpg|5px]]<br />
[[Image:UW Toolkits Front Page.png|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Background]]<br />
[[File:Washington_Spacer.jpg|10px]]<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://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>Swansonhttp://2011.igem.org/Team:WashingtonTeam:Washington2011-09-25T17:48:04Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
=<center>'''Make It or Break It: Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<br />
<br/><br />
<br />
<center><gallery widths="250px" heights="300px" perrow="3"><br />
Image:Diesel Production for Wiki.png|'''Make It: Diesel Production'''<br />
Image:Gluten Destruction for Wiki.png|'''Break It: Gluten Destruction'''<br />
Image:Gibson Assembly and Magnetosomes for Wiki.png|'''The GibsonBricks and Magnetosome ToolKit'''<br><br />
<br />
</gallery></center><br />
<br />
<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 />
[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 bring to the Parts Registry the Magnetosome Toolkit: a set of genes for biofabrication of magnetic particles.<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://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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-25T17:46:32Z<p>Swanson: </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><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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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 />
<br />
==''Improved Parts''==<br />
<br />
::'''8.''' [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. This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-25T17:45:59Z<p>Swanson: </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><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 Magnetosom ToolKit'''<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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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 />
<br />
==''Improved Parts''==<br />
<br />
::'''8.''' [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. This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Swansonhttp://2011.igem.org/Team:WashingtonTeam:Washington2011-09-25T17:44:51Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<br />
<center><gallery widths="250px" heights="300px" perrow="3"><br />
Image:Diesel Production for Wiki.png|'''Make It: Diesel Production'''<br />
Image:Gluten Destruction for Wiki.png|'''Break It: Gluten Destruction'''<br />
Image:Gibson Assembly and Magnetosomes for Wiki.png|'''The GibsonBricks and Magnetosome ToolKit'''<br><br />
<br />
</gallery></center><br />
<br />
<br/><br />
=<center>'''Make It or Break It: Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<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 />
[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 bring to the Parts Registry the Magnetosome Toolkit: a set of genes for biofabrication of magnetic particles.<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://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>Swansonhttp://2011.igem.org/Team:WashingtonTeam:Washington2011-09-25T17:41:37Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<br />
<center><gallery widths="250px" heights="300px" perrow="3"><br />
Image:Diesel Production for Wiki.png|'''Make It: Diesel Production'''<br />
Image:Gluten Destruction for Wiki.png|'''Break It: Gluten Destruction'''<br />
Image:Gibson Assembly and Magnetosomes for Wiki.png|'''The GibsonBricks and Magnetosome ToolKit'''<br><br />
<br />
</gallery></center><br />
<br />
=<center>'''Make It or Break It: Diesel Production and Gluten Destruction, the Synthetic Biology Way'''</center>=<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 />
[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 bring to the Parts Registry the Magnetosome Toolkit: a set of genes for biofabrication of magnetic particles.<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://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>Swansonhttp://2011.igem.org/Team:Washington/Magnetosomes/BackgroundTeam:Washington/Magnetosomes/Background2011-09-25T17:34:45Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Background'''</big></big></big></big></center><br><br><br />
<br />
As with the expansion of the iGEM competition, many iGEM teams have started to investigate the possibility of working with large-scale genomes. Large-scale gene manipulation often requires the use of tools which allow multiple gene inserts as to bring the cloning project from single gene level to a multiple gene level. However, the current BioBrick standard vectors available through iGEM are not designed for multiple-insert cloning. Therefore, the UW iGEM team decided to research methods to improve cloning efficiency and as a result, two "toolkits" were submitted to the registry. <br />
<br />
-----<br />
<br><br />
= '''Gibson Assembly Toolkit''' =<br />
To expand on work started by the [https://2010.igem.org/Team:Washington/Tools_Used/Next-Gen_Cloning 2010 UW IGEM team], this year we developed and submitted a set of plasmid backbones for BioBricks that are optimized for Gibson assembly. Based on the bglBrick standard [http://dspace.mit.edu/bitstream/handle/1721.1/46747/BBFRFC21.pdf?sequence=1 RFC 21], these "pGA" vectors comprise the [https://2011.igem.org/Team:Washington/Magnetosomes/GibsonVectors Gibson Assembly Toolkit]. These vectors have much higher cloning efficiencies than the equivalent pSB vector and are fully compliant with BioBrick [http://www.synbio.org.uk/gibson/downloads/files/RFC57.pdf RFC 57] developed by the 2010 [https://2010.igem.org/Team:Cambridge Cambridge] iGEM team.<br />
<br />
[[File:Igem2011 GibsonToolkit.png|left|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/GibsonVectors]] <br />
;'''What's in the Gibson Assembly Toolkit?'''<br />
* Five plasmid backbones<br />
* 2 high copy vectors for gene extraction and cloning: '''pGA1A3, pGA1C3'''<br />
* 1 medium copy expression vector: '''pGA3K3'''<br />
* 2 low copy expression vectors: '''pGA4A5, pGA4C5'''<br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br/><br/><br />
-----<br />
<br/><br />
<br />
='''Magnetosome Toolkit'''=<br />
To demonstrate the utility of pGA vectorsIn addition, we were also ambitious about assembling a large gene-construct of over 16 kb. Therefore, utilizing the pGA vectors and Gibson cloning methods, we assembled the [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit Magnetosome Toolkit] with the goal to generate magnetic ''E. coli''; a novel characteristic observed in magnetotactic bacteria such as ''Magnetospirillum magneticum''.<br />
<br />
<br />
<br />
[[File:Igem2011 MagnetToolkit.png|left|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit]]<br />
'''What’s in the Magnetosome Toolkit?'''<br />
<br />
*A set of the 18 essential genes for the various steps of magnetosome formation. <br />
*Our favorite genes in pGA vectors<br />
*A table compiling individual gene functions from our literature search</div>Swansonhttp://2011.igem.org/Team:Washington/Magnetosomes/BackgroundTeam:Washington/Magnetosomes/Background2011-09-25T17:34:13Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Background'''</big></big></big></big></center><br><br><br />
<br />
As with the expansion of the iGEM competition, many iGEM teams have started to investigate the possibility of working with large-scale genomes. Large-scale gene manipulation often requires the use of tools which allow multiple gene inserts as to bring the cloning project from single gene level to a multiple gene level. However, the current BioBrick standard vectors available through iGEM are not designed for multiple-insert cloning. Therefore, the UW iGEM team decided to research methods to improve cloning efficiency and as a result, two "toolkits" were submitted to the registry. <br />
<br />
-----<br />
<br><br />
= '''Gibson Assembly Toolkit''' =<br />
To expand on work started by the [https://2010.igem.org/Team:Washington/Tools_Used/Next-Gen_Cloning 2010 UW IGEM team], this year we developed and submitted a set of plasmid backbones for BioBricks that are optimized for Gibson assembly. Based on the bglBrick standard [http://dspace.mit.edu/bitstream/handle/1721.1/46747/BBFRFC21.pdf?sequence=1 RFC 21], these "pGA" vectors comprise the [https://2011.igem.org/Team:Washington/Magnetosomes/GibsonVectors Gibson Assembly Toolkit]. These vectors have much higher cloning efficiencies than the equivalent pSB vector and are fully compliant with BioBrick [http://www.synbio.org.uk/gibson/downloads/files/RFC57.pdf RFC 57] developed by the 2010 [https://2010.igem.org/Team:Cambridge Cambridge] iGEM team.<br />
<br />
[[File:Igem2011 GibsonToolkit.png|left|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/GibsonVectors]] <br />
;'''What's in the Gibson Assembly Toolkit?'''<br />
* Five plasmid backbones<br />
* 2 high copy vectors for gene extraction and cloning: '''pGA1A3, pGA1C3'''<br />
* 1 medium copy expression vector: '''pGA3K3'''<br />
* 2 low copy expression vectors: '''pGA4A5, pGA4C5'''<br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br/><br/><br />
-----<br />
<br />
='''Magnetosome Toolkit'''=<br />
To demonstrate the utility of pGA vectorsIn addition, we were also ambitious about assembling a large gene-construct of over 16 kb. Therefore, utilizing the pGA vectors and Gibson cloning methods, we assembled the [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit Magnetosome Toolkit] with the goal to generate magnetic ''E. coli''; a novel characteristic observed in magnetotactic bacteria such as ''Magnetospirillum magneticum''.<br />
<br />
<br />
<br />
[[File:Igem2011 MagnetToolkit.png|left|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit]]<br />
'''What’s in the Magnetosome Toolkit?'''<br />
<br />
*A set of the 18 essential genes for the various steps of magnetosome formation. <br />
*Our favorite genes in pGA vectors<br />
*A table compiling individual gene functions from our literature search</div>Swansonhttp://2011.igem.org/Team:Washington/Magnetosomes/BackgroundTeam:Washington/Magnetosomes/Background2011-09-25T17:32:38Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''iGEM Toolkits: Background'''</big></big></big></big></center><br><br><br />
<br />
As with the expansion of the iGEM competition, many iGEM teams have started to investigate the possibility of working with large-scale genomes. Large-scale gene manipulation often requires the use of tools which allow multiple gene inserts as to bring the cloning project from single gene level to a multiple gene level. However, the current BioBrick standard vectors available through iGEM are not designed for multiple-insert cloning. Therefore, the UW iGEM team decided to research methods to improve cloning efficiency and as a result, two "toolkits" were submitted to the registry. <br />
<br />
-----<br />
<br><br />
= '''Gibson Assembly Toolkit''' =<br />
To expand on work started by the [https://2010.igem.org/Team:Washington/Tools_Used/Next-Gen_Cloning 2010 UW IGEM team], this year we developed and submitted a set of plasmid backbones for BioBricks that are optimized for Gibson assembly. Based on the bglBrick standard [http://dspace.mit.edu/bitstream/handle/1721.1/46747/BBFRFC21.pdf?sequence=1 RFC 21], these "pGA" vectors comprise the [https://2011.igem.org/Team:Washington/Magnetosomes/GibsonVectors Gibson Assembly Toolkit]. These vectors have much higher cloning efficiencies than the equivalent pSB vector and are fully compliant with BioBrick [http://www.synbio.org.uk/gibson/downloads/files/RFC57.pdf RFC 57] developed by the 2010 [https://2010.igem.org/Team:Cambridge Cambridge] iGEM team.<br />
<br />
[[File:Igem2011 GibsonToolkit.png|left|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/GibsonVectors]] <br />
;'''What's in the Gibson Assembly Toolkit?'''<br />
* Five plasmid backbones<br />
* 2 high copy vectors for gene extraction and cloning: '''pGA1A3, pGA1C3'''<br />
* 1 medium copy expression vector: '''pGA3K3'''<br />
* 2 low copy expression vectors: '''pGA4A5, pGA4C5'''<br />
<br />
-----<br />
<br/><br/><br/><br/><br/><br/><br/><br/><br />
<br />
='''Magnetosome Toolkit'''=<br />
To demonstrate the utility of pGA vectorsIn addition, we were also ambitious about assembling a large gene-construct of over 16 kb. Therefore, utilizing the pGA vectors and Gibson cloning methods, we assembled the [https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit Magnetosome Toolkit] with the goal to generate magnetic ''E. coli''; a novel characteristic observed in magnetotactic bacteria such as ''Magnetospirillum magneticum''.<br />
<br />
<br />
<br />
[[File:Igem2011 MagnetToolkit.png|left|300px|link=https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit]]<br />
'''What’s in the Magnetosome Toolkit?'''<br />
<br />
*A set of the 18 essential genes for the various steps of magnetosome formation. <br />
*Our favorite genes in pGA vectors<br />
*A table compiling individual gene functions from our literature search</div>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-25T17:24:20Z<p>Swanson: /* Gluten Destruction */</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><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|'''The GibsonBricks ToolKit'''<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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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 />
<br />
==''Improved Parts''==<br />
<br />
::'''8.''' [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. This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-25T17:23:36Z<p>Swanson: /* Data for Existing Parts */</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><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|'''The GibsonBricks ToolKit'''<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: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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 />
<br />
==''Improved Parts''==<br />
<br />
::'''8.''' [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. This was accomplished by the Alternate Aldehyde branch of the Alkane Production team.<br />
<br />
<br />
='''All Submitted Parts'''=<br />
<br />
<center><groupparts>iGEM011 Washington</groupparts></center></div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/FutureTeam:Washington/Alkanes/Future2011-09-25T17:20:07Z<p>Swanson: </p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<center><big><big><big><big>'''Diesel Production: Future Directions'''</big></big></big></big></center><br><br><br />
<br />
Our current ''in vivo'' alkane production system efficiently makes C15 alkanes. However, to be efficient enough for factory production, there are two broad goals to be done: <br />
# Increase production efficiency <br />
# Increase the diversity of the range of alkanes that can be produced. <br />
# Increase the scale of the system for industrial processes. <br />
We have already begun efforts to expand the efficiency and scope of alkane production, '''check them out below!'''<br />
<br />
[[Image:UW_2011_Alkane_Future_Work_Image.png|7px||right]]<br />
<br />
[[Image:Washington system optimization.png|140px||left|link=https://2011.igem.org/Team:Washington/Alkanes/Future/Vector]]<br />
<br><br><br />
[https://2011.igem.org/Team:Washington/Alkanes/Future/Vector '''System Optimization''']<br />
:<nowiki> The efficiency of this system was reported to be much higher than our initial system, but the growth conditions of the assay and the DNA was not available to us. We increased production efficiency by altering the initial environmental conditions in the assay.</nowiki><br />
<br><br><br />
<br />
[[Image:Washington_2011_ADC_Redesign.png|140px||left|link=https://2011.igem.org/Team:Washington/Alkanes/Future/DecarbDesign]]<br />
<br><br><br />
[https://2011.igem.org/Team:Washington/Alkanes/Future/DecarbDesign '''Decarbonylase Redesign''']<br />
:<nowiki>One way to diversify the kind of alkanes produced is to alter the substrate specificity of the proteins involved. Since an alternative alkane-producing enzyme has not been found, we decided to mutate the aldehyde decarbonylase to produce shorter-chain alkanes.</nowiki><br />
<br><br><br />
<br />
[[Image:Washington_2011_LuxCDE.png|140px||left|link=https://2011.igem.org/Team:Washington/Alkanes/Future/LuxCDE]]<br />
<br><br />
[https://2011.igem.org/Team:Washington/Alkanes/Future/LuxCDE '''Alternative Aldehyde''']<br />
:<nowiki>Another way to diversify our system is to use alternative proteins. Our current system uses acyl-ACP reductase, and we've identified an hypothetical alternative system that produces aldehydes: LuxCDE, made from parts from the 2010 competition.</nowiki><br />
<br><br><br><br />
<br />
[[Image:Washington_2011_fabh2_branch.png|140px||left|link=https://2011.igem.org/Team:Washington/Alkanes/Future/FabH2]]<br />
<br><br />
[https://2011.igem.org/Team:Washington/Alkanes/Future/FabH2 '''Branched Alkane Biosynthesis''']<br />
:<nowiki> Our system is only capable of producing unbranched alkanes, as the cell mainly utilizes straight chained fatty acids. However, fuel we use are also composed largely of branched alkanes that affect very important properties of the fuel such as flash point and freezing point. If our fuels are truly intended to be synthesized in bacteria, we need to work on methods of making those crucial branched chained alkanes. We explored FabH2, a protein that when involved in fatty acid synthesis makes branched fatty acids. </nowiki><br />
<br><br />
<br />
[[Image:Washington 2011 Protein Localization.png|140px||left|link=https://2011.igem.org/Team:Washington/Alkanes/Future/Localization]]<br />
<br><br />
[https://2011.igem.org/Team:Washington/Alkanes/Future/Localization '''Enzyme Localization''']<br />
:<nowiki> The easiest way to increase yield is to increase the concentration; if the number of molecules remained the same but the volume decreased, the reaction speed increases with occurrences of molecular collisions. However, this is only easily done with purified protein assays. However, there are ways to "increase the concentration" of reactions in cells. We cannot make the cells literally denser, but we can localize the enzymes involved in the reaction, which either decreases the volume of the cell in which the enzymes reside and/or limit the number of reaction steps.</nowiki><br />
[[Image:Washington_2011_Alternate_Chassis.png|140px||left|link=https://2011.igem.org/Team:Washington/Alkanes/Future/Yeast]]<br />
<br><br />
[https://2011.igem.org/Team:Washington/Alkanes/Future/Yeast '''Alternative Chassis''']<br />
:<nowiki> By synthesizing alkanes in organisms, alkanes can become a useful renewable energy source; CO2 emitted from burning the alkanes are converted to glucose through photosynthesis, and then the glucose can be fed to alkane-synthesizing organisms to restart the cycle. This cycle can be drastically improved if there were fewer steps in the cycle. We explored the possibility of optimizing the alkane biosynthesis system in different micro-organisms, with the idea that perhaps with autotrophic organisms, we do not need to obtain glucose for the reaction.</nowiki></div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-25T17:13:38Z<p>Swanson: /* Effects of Changing Initial Cell Density */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that produced alkanes may have been evaporating, reducing apparent yield. Therefore, we performed tests where the tubes were either capped the standard way, or capped with foil coverting the opening, thereby reducing evaporation. Tests were conducted in glass tubes with M9 production media, with MG1655 innoculated to an initial OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkanes, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkanes. Initial experiments were done in MG1655, and we decided to test XL-1 blue (a commercial supercopentent variant of DH5a) for the ability to produce alkanes. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkanes than MG1655. Therefore, future tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass (note that the test was conducted in open culture tubes for aerobic cultures, and sealed glass vials for microaerobic cultures, with M9 production media in XL21-blue cells.)<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield (before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes (aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Triton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, inducing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-25T17:12:22Z<p>Swanson: /* Media composition */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that produced alkanes may have been evaporating, reducing apparent yield. Therefore, we performed tests where the tubes were either capped the standard way, or capped with foil coverting the opening, thereby reducing evaporation. Tests were conducted in glass tubes with M9 production media, with MG1655 innoculated to an initial OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkanes, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkanes. Initial experiments were done in MG1655, and we decided to test XL-1 blue (a commercial supercopentent variant of DH5a) for the ability to produce alkanes. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkanes than MG1655. Therefore, future tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass (note that the test was conducted in open culture tubes for aerobic cultures, and sealed glass vials for microaerobic cultures, with M9 production media in XL21-blue cells.)<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield (before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes (aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Triton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-25T17:11:30Z<p>Swanson: /* pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that produced alkanes may have been evaporating, reducing apparent yield. Therefore, we performed tests where the tubes were either capped the standard way, or capped with foil coverting the opening, thereby reducing evaporation. Tests were conducted in glass tubes with M9 production media, with MG1655 innoculated to an initial OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkanes, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkanes. Initial experiments were done in MG1655, and we decided to test XL-1 blue (a commercial supercopentent variant of DH5a) for the ability to produce alkanes. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkanes than MG1655. Therefore, future tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass (note that the test was conducted in open culture tubes for aerobic cultures, and sealed glass vials for microaerobic cultures, with M9 production media in XL21-blue cells.)<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield (before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes (aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-25T17:10:53Z<p>Swanson: /* Aerobic vs Microaerobic Growth */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that produced alkanes may have been evaporating, reducing apparent yield. Therefore, we performed tests where the tubes were either capped the standard way, or capped with foil coverting the opening, thereby reducing evaporation. Tests were conducted in glass tubes with M9 production media, with MG1655 innoculated to an initial OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkanes, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkanes. Initial experiments were done in MG1655, and we decided to test XL-1 blue (a commercial supercopentent variant of DH5a) for the ability to produce alkanes. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkanes than MG1655. Therefore, future tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass (note that the test was conducted in open culture tubes for aerobic cultures, and sealed glass vials for microaerobic cultures, with M9 production media in XL21-blue cells.)<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield (before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes(aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-25T17:08:50Z<p>Swanson: /* Sealed vs. Open Tubes */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that produced alkanes may have been evaporating, reducing apparent yield. Therefore, we performed tests where the tubes were either capped the standard way, or capped with foil coverting the opening, thereby reducing evaporation. Tests were conducted in glass tubes with M9 production media, with MG1655 innoculated to an initial OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkanes, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkanes. Initial experiments were done in MG1655, and we decided to test XL-1 blue (a commercial supercopentent variant of DH5a) for the ability to produce alkanes. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkanes than MG1655. Therefore, future tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass( note that the test was conducted in open culture tubes for aerobic, but sealed glass vials with M9 production media in XL21-blue cells.<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield( before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes(aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-25T17:08:22Z<p>Swanson: /* Sealed vs. Open Tubes */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that produced alkanes may have been evaporating, reducing apparent yield. Therefore, we performed tests where the tubes were either capped the standard way, or capped with foil coverting the opening, thereby reducing evaporation. Tests were conducted in glass tubes with M9 production media, with MG1655 innoculated to an initial OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkane, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkanes. Initial experiments were done in MG1655, and we decided to test XL-1 blue (a commercial supercopentent variant of DH5a) for the ability to produce alkanes. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkanes than MG1655. Therefore, future tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass( note that the test was conducted in open culture tubes for aerobic, but sealed glass vials with M9 production media in XL21-blue cells.<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield( before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes(aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-25T17:06:57Z<p>Swanson: /* Use of Different Strains */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that alkane evaporation may have been evaporating, reducing apparent yield. Therefore, we performed tests were the tubes were either capped like normal, or capped with foil coverting the opening, reducing evaporation. Tests were conducted in M9 production media, in glass, with MG1655 innoculated to an OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkane, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkanes. Initial experiments were done in MG1655, and we decided to test XL-1 blue (a commercial supercopentent variant of DH5a) for the ability to produce alkanes. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkanes than MG1655. Therefore, future tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass( note that the test was conducted in open culture tubes for aerobic, but sealed glass vials with M9 production media in XL21-blue cells.<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield( before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes(aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-23T05:29:25Z<p>Swanson: /* Effects of Changing Initial Cell Density */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that alkane evaporation may have been evaporating, reducing apparent yield. Therefore, we performed tests were the tubes were either capped like normal, or capped with foil coverting the opening, reducing evaporation. Tests were conducted in M9 production media, in glass, with MG1655 innoculated to an OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkane, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkane. Initial experiments were done in MG1655, and we decided to test XL-1 blue( a commercial supercopentent variant of DH5a) for the ability to produce alkane. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkane than MG1655. Therefore, futures tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass( note that the test was conducted in open culture tubes for aerobic, but sealed glass vials with M9 production media in XL21-blue cells.<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield( before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes(aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue (to a final OD600 in a range of 0.01 to 10) in M9 production media (in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-23T05:27:57Z<p>Swanson: /* Media composition */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that alkane evaporation may have been evaporating, reducing apparent yield. Therefore, we performed tests were the tubes were either capped like normal, or capped with foil coverting the opening, reducing evaporation. Tests were conducted in M9 production media, in glass, with MG1655 innoculated to an OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkane, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkane. Initial experiments were done in MG1655, and we decided to test XL-1 blue( a commercial supercopentent variant of DH5a) for the ability to produce alkane. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkane than MG1655. Therefore, futures tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass( note that the test was conducted in open culture tubes for aerobic, but sealed glass vials with M9 production media in XL21-blue cells.<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield( before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes(aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in [[#References |[1]]]. We did not know if all of the additional components not found in a normal media (buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue( to a final OD600 in a range of 0.01 to 10) in M9 production media( in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Alkanes/Future/VectorTeam:Washington/Alkanes/Future/Vector2011-09-23T05:27:37Z<p>Swanson: /* Media composition */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
='''System Optimization'''=<br />
<br />
Using our initial, non-optimized growth conditions, we were able to obtain alkane/ene yields of approximately 2 mg/L. In order to make analysis easier, and to make it easier to determine the effects of the addition of additional modules, we wanted to increase yield. Our efforts focused on how by varying system conditions, we could increase yield.<br />
<br />
=='''Sealed vs. Open Tubes'''==<br />
We were concerned that alkane evaporation may have been evaporating, reducing apparent yield. Therefore, we performed tests were the tubes were either capped like normal, or capped with foil coverting the opening, reducing evaporation. Tests were conducted in M9 production media, in glass, with MG1655 innoculated to an OD600 of 1.<br />
[[File:Washinton_open_sealed.png|center|500px|thumb|Sealing Culture Tubes Increases Yield.]]<br />
Covered tubes showed significantly more alkane, so all further tests would be conducted in sealed tubes.<br />
<br />
=='''Use of Different Strains'''==<br />
We had suspected that different strains of ''E. coli'' would produce varying amounts of alkane. Initial experiments were done in MG1655, and we decided to test XL-1 blue( a commercial supercopentent variant of DH5a) for the ability to produce alkane. Tests were conducted in sealed glass culture tubes in M9 production media . Cells were innoculated to an OD600 of 1 when conducting this test.<br />
[[File:Washinton_XL21vsMG1655.png|center|500px|thumb|XL-1 Blue Produces more Alkane than MG1655]]<br />
XL-1 blue was able to produce more alkane than MG1655. Therefore, futures tests were conducted in XL-1 Blue.<br />
<br />
=='''Aerobic vs Microaerobic Growth'''==<br />
In many industrial production applications, growth in conditions with little or no oxygen can improve yield. Therefore, we tested alkane yield in cultures grown in airtight vials with only a small amount of air on the top in order to severely limit oxygen availability. Tests were conducted in glass( note that the test was conducted in open culture tubes for aerobic, but sealed glass vials with M9 production media in XL21-blue cells.<br />
[[File:Washington_aerobicVsMicroaerobic.png|center|500px|thumb|Oxygen has a Positive Effect on Alkane Production]]<br />
Based upon this data, aerobic growth appears to be better for alkane yield. Note that this difference is not likely due to differences in growth rate, as both cultures were inoculated to a high OD600 of 1. The fact that this tube was not covered means that the actual alkane yield( before evaporation) was likely higher. Therefore, microaerobic conditions are unlikely to improve yield.<br />
<br />
=='''pSB1C3-ADC-AAR vs pSB3k3-ADC/pSB4C5-AAR'''==<br />
The original study expressed ADC and AAR on seperate low copy number vectors. If we could get high alkane yields using low copy number vectors, the lesser protien and vector production would make the use of a lower copy number vector preferable. Tests were conducted in covered glass culture tubes(aerobic conditions) with M9 production media. Cells were XL1-Blue, and were innoculated to an OD600 of 1.<br />
[[File:Washington_copynumber.png|center|500px|thumb|Greater ADC/AAR Expression Results in More Alkane Production.]]<br />
The fact that high copynumber vector use results in an increase in yield means that high expression levels of ADC and/or AAR are required for high alkane yields.<br />
<br />
=='''Media composition'''==<br />
Our initial media was based upon the media used in ([[#References |[1]]]). We did not know if all of the additional components not found in a normal media ( buffer, thiamine, Tritton, iron) actually improved yield. In order to determine if each of these components imporved yield, we analyzed cultures inoculated into M9 medias without each of these 4 compounds. In addition, we tested media with additional trace metals. These tests were conducted in covered glass culture tubes with XL-1 blue cells.<br />
[[File:Washington_mediaconditions.png|center|500px|thumb|Effects of Media Composition on Alkane Yield.]]<br />
None of the modifications we made resulted in a significant increase in yield. Therefore, no further modifications to the media used was made.<br />
<br />
=='''Effects of Changing Initial Cell Density'''==<br />
Earlier tests were done with an initial OD600 of 1. However, we had never established what the optimal initial OD would be. If significant alkane production occurs during stationary phase, inoculation to a high initial OD may increase alkane production. For this test, we inoculated XL-1 blue( to a final OD600 in a range of 0.01 to 10) in M9 production media( in covered glass culture tubes). We extracted from these cultures after 16 hours of growth. <br />
[[File:Washington_alkaneODcurve.png|center|500px|thumb|Greater Initial Cell Density Results in Higher Alkane Yield.]]<br />
Higher cell density cultures showed significantly higher alkane yields than lower cell density cultures. The increase of alkane yields at cell densities as high as 10 implies that high amounts of alkane production occurs during stationary phase. Therefore, alkane production scales with cell density. In addition, performing alkane production during stationary phase decreases the amount of glucose going towards cellular growth instead of alkane production.<br />
=='''References'''==<br />
Microbial Biosynthesis of Alkanes Andreas Schirmer, Mathew A. Rude, Xuezhi Li, Emanuela Popova and Stephen B. del Cardayre Science 30 July 2010: Vol. 329 no. 5991 pp. 559-562 http://www.sciencemag.org/content/329/5991/559</div>Swansonhttp://2011.igem.org/Team:Washington/Magnetosomes/Magnet_ResultsTeam:Washington/Magnetosomes/Magnet Results2011-09-23T05:26:39Z<p>Swanson: </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></div>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:25:20Z<p>Swanson: /* Improved Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Team's Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''8.''' [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 parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:24:41Z<p>Swanson: </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><gallery caption="An Overview of the 2011 UW iGEM Team's Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''8.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/Team/MembersTeam:Washington/Team/Members2011-09-23T05:23:55Z<p>Swanson: /* Who we are */</p>
<hr />
<div>{{Template:Team:Washington/Templates/Top}}<br />
__NOTOC__<br />
<br />
<!---------------------------------------PAGE CONTENT GOES BELOW THIS----------------------------------------><br />
<br />
== '''Who we are''' ==<br />
<br />
<gallery caption="Undergraduate Team Members" widths="180px" heights="120px" perrow="4"><br />
Image:Washington Casey Ager Profile1.jpg|<center>Casey Ager <br/> Biochemistry</center><br />
Image:Washington Photo-0088A.png|<center>Juhye An <br/> Biochemistry </center><br />
Image: Profile_Michael_Brasino.jpg|<center>Michael Brasino <br/> Materials Science and Engineering</center><br />
Image:Washington_.jpg|<center>Marika Cheng <br/> Microbiology</center><br />
Image:Washington_choe_chris.png|<center>Chris Choe <br/> Major</center><br />
Image:Washington_.jpg|<center>Justin De Leon <br/> Microbiology</center><br />
File:Princess Peachy.JPG|<center>Sydney Gordon <br/> Biochemistry, Music</center><br />
Image:CIMG0021.jpg|<center>Daniel Hadidi <br/> Neurobiology</center><br />
Image:Washington_Matthew_Harger.JPG|<center>Matthew Harger <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Elaine.jpg|<center>Elaine Lai <br/> Microbiology, Chemistry</center><br />
Image:Washington_2011_BATMAN.jpg|<center>Benjamin Mo <br/> Bioengineering</center><br />
Image:Washington 2011 CIMG0015-2.jpg|<center>Austin Moon <br/> Cellular and Molecular Biology, Microbiology</center><br />
Image:Washington_.jpg|<center>Rashmi Ravichandran <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Seth Sagulo <br/> Biochemistry</center><br />
File:Washington_Liz.png|<center>Liz Stanley <br/> Microbiology, Chemistry</center><br />
Image:Washington_.jpg|<center>Angus Toland <br/> Microbiology</center><br />
Image:Washington_.jpg|<center>Sarah Wolf <br/> Biochemistry</center><br />
Image:Washington_.jpg|<center>SauShun (Alicia) Wong <br/> Materials Science and Engineering</center><br />
Image:Washington_Cindy.jpg|<center>Cindy Wu <br/> Cellular and Molecular Biology</center><br />
Image:Washington_Sean_Wu.jpg|<center>Sean Wu <br/> Computer Science and Engineering</center><br />
Image:Washington_2011_BATMAN.jpg|<center>Lei Zheng <br/> Biochemistry</center><br />
Image:Washington_david_zong.jpg|<center>David Zong <br/> Bioengineering</center><br />
<br />
</gallery><br />
<br />
<br />
<gallery caption="Advisors" widths="180px" heights="120px" perrow="4"><br />
Image:Washington_.jpg|<center>Aaron Chevalier <br/> Bioengineering </center><br />
Image:Regbert.jpg|<center>Rob Egbert <br/> Electrical Engineering </center><br />
Image:Washington_.jpg|<center>Chris Eiben <br/> Biochemistry </center><br />
Image:Washington_.jpg|<center>Jeremy Mills <br/> Biochemistry </center><br />
Image:Siegel_UW_2011.jpg|<center>Justin Siegel <br/> Biomolecular Structure and Design</center><br />
Image:Washington2011_Matthew-d-smith.jpg|<center>Matt Smith <br/> Molecular and Cellular Biology</center><br />
File:Washington_Ingrid_Pic_1.jpg|<center>Ingrid Swanson Pultz<br/> Microbiology </center><br />
</gallery><br />
<br />
<br />
<gallery caption="Faculty" widths="180px" heights="120px" perrow="5"><br />
image:Washington_David_Baker.jpg|<center>David Baker <br/> Biochemistry</center><br />
Image:Washington_Klavins.jpg|<center>Eric Klavins <br/> Electrical Engineering</center><br />
</gallery><br />
<br />
<br />
<gallery caption="Collaborators and Support" widths="140px" heights="100px" perrow="5"><br />
<br />
Image:Washington_OSLI.png|<center><b>Oil Sand Leadership Initiative</b> <br/> Funding to support Travel and Registration Costs</center><br />
<br />
Image:Washington_UniversitySeal.gif|<center><b>Biochemistry</b> <br/> Lab space</center><br />
<br />
Image:Washington_Anaspec.gif|<center>Anaspec <br/> <b>Peptide Discounts</b></center><br />
<br />
Image:Washington_ARPA-E_Logo.png|<center><b>Advanced Research Projects Agency - Energy </b><br/> Registration Support</center><br />
<br />
Image:Washington2011_Hhmi_362_72.jpg|<center><b>Howard Hughes Medical Institute</b> <br/> Lab materials and supplies</center><br />
<br />
<br />
</gallery><br />
<br />
== '''Who did what''' ==<br />
The teams were assembled during our winter quarter. During this term we went around to classes and had weekly meetings to introduce students to synthetic biology through a series of guest lectures. During the spring, students participated in brainstorming projects related to the sponsoring Faculty advisors labs (Baker and Klavins) and came up with the project they wanted to carry out. Students also planned and partcipated in community outreach events where we taught our community about synthetic biology. Over the summer, students completed all of the experimental work, but worked closely with both graduate students and faculty advisors to plan the most pertinent experiments and make the most of our limited time.<br />
<br />
=== Diesel Production ===<br />
After producing promising results, in future directions <br />
<br />
Casey Ager, Austin Moon, and Seth Sagulo worked on Enzyme Localization via Direct Fusion and Zinc Finger Fusion methods.<br />
<br />
Juhye An, Elaine Lai, and Benjamin Mo worked on Decarbonylase Redesign<br />
<br />
Marika Cheng and Justin De Leon worked on Alternative Chassis<br />
<br />
Chris Choe and David Zong worked on Alternate Aldehyde Production<br />
<br />
Matthew Harger worked on Branched Alkanes Production<br />
<br />
Matthew Harger and Lei Zheng worked on System Optimization<br />
<br />
=== Gluten Destruction ===<br />
Sydney Gordon, Daniel Hadidi, Liz Stanley, Angus Toland, Sarah Wolf, and Sean Wu designed, built, and tested Kumamolisin-As and over 100 mutants to combat gluten intolerance by increasing the activity on the PQLP antigenic peptide.<br />
<br />
=== iGEM Toolkits ===<br />
Michael Brasino, Rashmi Ravichandran, and Alicia Wong<br />
<br />
=== Community Outreach ===<br />
Cindy Wu headed and organized all iGEM 2011 Community Outreach events.</div>Swansonhttp://2011.igem.org/File:Washington_Ingrid_Pic_1.jpgFile:Washington Ingrid Pic 1.jpg2011-09-23T05:21:51Z<p>Swanson: </p>
<hr />
<div></div>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:19:06Z<p>Swanson: /* Improved Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Teams Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''8.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:18:56Z<p>Swanson: /* Data for Existing Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Teams Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<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.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''1.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:18:23Z<p>Swanson: /* Improved Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Teams Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''1.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick.<br />
<br />
==''Improved Parts''==<br />
<br />
::'''1.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:17:54Z<p>Swanson: /* Data for Existing Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Teams Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''1.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick.<br />
<br />
=='''Improved Parts'''==<br />
<br />
::'''1.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:16:54Z<p>Swanson: /* Data for Existing Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Teams Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<br />
<br />
==''Data for Existing Parts''==<br />
<br />
::'''1.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, and determined that 0.5 uM IPTG is sufficient to express our system.<br />
<br />
=='''Improved Parts'''==<br />
<br />
::'''1.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:16:42Z<p>Swanson: /* Data for Favorite New Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Teams Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<br />
<br />
=='''Data for Existing Parts'''==<br />
<br />
::'''1.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, and determined that 0.5 uM IPTG is sufficient to express our system.<br />
<br />
=='''Improved Parts'''==<br />
<br />
::'''1.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swansonhttp://2011.igem.org/Team:Washington/PartsTeam:Washington/Parts2011-09-23T05:15:30Z<p>Swanson: /* Improved Parts */</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><gallery caption="An Overview of the 2011 UW iGEM Teams Summer Projects" widths="250px" heights="400px" 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|'''The GibsonBricks ToolKit'''<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_K590023 BBa_K590023: '''KumamaMax''']- 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_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590011 BBa_K590011: '''pGA1C3_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590012 BBa_K590012: '''pGA4C5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590013 BBa_K590013: '''pGA4A5_pLacGFP'''], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K590014 BBa_K590014: '''pGA3K3_pLacGFP'''] - These are plasmid backbones optimized for use in Gibson cloning, with a variety of copy numbers and antibiotic resistances.<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, fused to sfGFP, in the backbone of pGA1C3. MamK was previously reported to be required for proper alignment of magnetosomes in a chain in magnetic bacteria.<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, sfGFP in the backbone of pGA1C3. MamI is a membrane-localized protein that localizes magnetic vesicles to the surface of cells, thus forming characteristic magnetosome chains.<br />
<br />
=='''Data for Existing Parts'''==<br />
<br />
::'''1.''' [http://partsregistry.org/Part:BBa_K314100:Experience K314100: '''High Constitutive Expression Cassette'''] (Washington, iGEM 2010) - We used this part to express our Petrobrick, and determined that 0.5 uM IPTG is sufficient to express our system.<br />
<br />
=='''Improved Parts'''==<br />
<br />
::'''1.''' [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'''] - Formerly parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325902 BBa_K325902] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K325903 BBa_K325903]. ''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. 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>Swanson