IGEM:VGEM/2007

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==<font color="#FF6600"><center>2007 Virginia Genetically Engineered Machine Team</center></font>==
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==<font color="#FF6600"><center>2007 Virginia Genetically Engineered Machine (VGEM) Team</center></font>==
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Welcome to the 2007 VGEM Team's OpenWetWare wiki.  This wiki contains the internal workings of our team, including our online lab notebook, project designs and other useful information. The VGEM Team is an undergraduate research group interested in synthetic biology and biological engineering, and will compete in MIT's 2007 international Genetically Engineered Machines competition [http://www.igem2007.com (iGEM)] in November.  Check on [http://parts.mit.edu/igem07/index.php/Virginia our official iGEM wiki] for our final project description and [http://seas.virginia.edu/VGEM our external website] for more information about the team.<br />   
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Welcome to the Virginia Genetically Engineered Machine (VGEM) Team's wiki! The VGEM Team is an undergraduate research group interested in synthetic biology and biological engineering, and will compete in MIT's 2007 international Genetically Engineered Machines competition [http://www.igem2007.com (iGEM)] in November.  We'll be adding new information regularly, so be sure to check up on us soon. - George McArthur<br />   
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==<center>Acknowledgements</center>==
==<center>Acknowledgements</center>==
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<center>This team was made possible by the generous support from the following:</center>
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<center>The VGEM Team was made possible by the generous support from the following groups at the University of Virginia:</center>
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<center>[http://www.seas.virginia.edu '''The School of Engineering and Applied Science''']</center>
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<center>The Departments of [http://www.bme.virginia.edu '''Biomedical Engineering'''], [http://www.che.virginia.edu '''Chemical Engineering'''], [http://www.virginia.edu/biology '''Biology'''], and [http://www.healthsystem.virginia.edu/internet/microbiology/ '''Microbiology''']</center>
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<center>[http://www.seas.virginia.edu/vef/ '''The Virginia Engineering Foundation''']</center>
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<center>[http://www.seas.virginia.edu '''The School of Engineering and Applied Science'''] and the [http://www.seas.virginia.edu/vef/ '''The Virginia Engineering Foundation''']</center>
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<center>[http://www.virginia.edu/vprgs/ '''The Office of the Vice President for Research''']</center>
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<center>[http://www.virginia.edu/vprgs/ '''The Office of the Vice President for Research and Graduate Studies''']</center>
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<center>[http://www.che.virginia.edu '''The Department of Chemical Engineering''']</center>
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<center>[http://http://www.healthsystem.virginia.edu/internet/som/home.cfm '''The School of Medicine''']</center><br />
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<center>[http://www.bme.virginia.edu '''The Department of Biomedical Engineering''']</center>
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<center> We would like to acknowledge and thank our 2007 corporate sponsor:</center>
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<center>[http://www.virginia.edu/biology '''The Department of Biology''']</center><br/ >
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<center> [http://www.dna20.com/ http://tbn0.google.com/images?q=tbn:twELO5rfkLG1VM:http://www.teknova.com/dna20/us/images/dna_c.jpg]</center>
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<center> The VGEM team would like to especially thank the following for in-kind support:</center>
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<div id="mainpage"></div>
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<center> [http://www.newprgroup.com/ http://www.newprgroup.com/images/newprlogo.jpg]</center>
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<div id="about">
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We have three (top secret) medically-related projects.  More details will be available soon.  Our group is also interested in environmental biological engineering and we'll be pursuing additional projects throughout the summer. <br />
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Our 2007 project is focused on energy biotechnology and is titled '''"Harvesting Plant Biomass and Sunlight to Power Butanol Biosynthesis: A Synthetic Biology Approach to Metabolic Pathway Engineering."''' More information about our project can be found at our official iGEM wiki, which you can get to by clicking the iGEM logo below. Please check out our other project designs by clicking the "projects" link listed below the iGEM logo.
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*[[IGEM:VGEM/2007/Timeline| <font color="#000000">Timeline</font>]]
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<center>[http://parts.mit.edu/igem07/index.php/Virginia http://www.openwetware.org/images/f/ff/IGEM-logo.png]</center><br />
*[[IGEM:VGEM/2007/Projects| <font color="#000000">Projects</font>]]
*[[IGEM:VGEM/2007/Projects| <font color="#000000">Projects</font>]]
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===Planning===
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*[[IGEM:VGEM/2007/Timeline| <font color="#000000">Timeline</font>]]
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During our weekly meetings throughout the spring semester, we'll be discussing relevant literature and developing project ideas. Our actual experiments will occur during the summer session, and we hope to have our results in order by the beginning of the fall semester in September.
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*[http://www.google.com/calendar/embed?src=pi9gjqgh83id5hokqqd6ciei08%40group.calendar.google.com <font color="#000000">Calendar</font>]
*[[IGEM:VGEM/2007/Meetings| <font color="#000000">Meetings</font>]]
*[[IGEM:VGEM/2007/Meetings| <font color="#000000">Meetings</font>]]
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===Documentation===
 
*[[IGEM:VGEM/2007/Notebook| <font color="#000000">Lab Notebook</font>]]
*[[IGEM:VGEM/2007/Notebook| <font color="#000000">Lab Notebook</font>]]
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===iGEM Links===
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*[[IGEM:VGEM/2007/Journal Club| <font color="#000000">Summer Journal Club</font>]]
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*[http://www.igem2007.com/<font color="#000000">iGEM 2007 website</font>]
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*[http://www.geneart.com/index.php?id=252<font color="#000000">GENEART</font>]]
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*[http://parts.mit.edu/registry/index.php/Main_Page <font color="#000000">Registry for Standard Biological Parts</font>]
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*[[IGEM:Help| <font color="#000000">Protocols</font>]]
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===Resources===
===Resources===
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*[http://www.DNA20.com<font color="#000000">DNA2.0</font>]
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*[http://www.geneart.com/index.php?id=252<font color="#000000">GENEART</font>]
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*[http://parts.mit.edu/registry/index.php/Main_Page <font color="#000000">Registry for Standard Biological Parts</font>]
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*[[IGEM:Help| <font color="#000000">Guides</font>]]
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*[https://new.fishersci.com/wps/portal/HOME<font color="#000000">Fisher Scientific</font>]
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*[http://www.dnahack.com <font color="#000000">DNA Hack</font>]
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*[http://www.ncbi.nlm.nih.gov <font color="#000000">NCBI website</font>]
*[http://sbml.org <font color="#000000">Systems Biology Workbench</font>]
*[http://sbml.org <font color="#000000">Systems Biology Workbench</font>]
*[http://syntheticbiology.org <font color="#000000">Synthetic Biology Community</font>]
*[http://syntheticbiology.org <font color="#000000">Synthetic Biology Community</font>]
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*[http://www.dnahack.com <font color="#000000">DNA Hack</font>]
 
*[http://www.springer.com/west/home?SGWID=4-102-70-173669004-0&changeHeader=true&SHORTCUT=www.springer.com/11693 <font color="#000000">Systems and Synthetic Biology Journal</font>]
*[http://www.springer.com/west/home?SGWID=4-102-70-173669004-0&changeHeader=true&SHORTCUT=www.springer.com/11693 <font color="#000000">Systems and Synthetic Biology Journal</font>]
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*[http://www.theiet.org/publications/journals/synbio/index.cfm<font color="#000000">IET Synthetic Biology Journal</font>]
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*[http://www.ietdl.org/IET-STB<font color="#000000">IET Synthetic Biology Journal</font>]
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*[http://webcast.berkeley.edu/event_details.php?webcastid=15766<font color="#000000">Synthetic Biology 2.0 Conference</font>]
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*[http://video.google.com/videoplay?docid=-8615490726732890001&q=synthetic+biology+video&hl=en<font color="#000000">''Pimp my genome'' video</font>]
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*[http://www.dnai.org<font color="#000000">DNAi website</font>]
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*[http://synthesis.typepad.com/<font color="#000000">Rob Carlson's Blog</font>]
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*[http://www.paraschopra.com/blog/biohacking.php<font color="#000000">Biohacking Blog</font>]
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*[http://www.ebiweb.org/research.htm<font color="#000000">Energy Biosciences Institute</font>]
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*[http://i-r-squared.blogspot.com/2006/05/bio-butanol.html<font color="#000000">R-Squared Energy Blog</font>]
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Our group is an interdisciplinary conglomeration that includes researchers from The School of Engineering and Applied Science, The College of Arts and Sciences, and the School of Medicine. <br />
Our group is an interdisciplinary conglomeration that includes researchers from The School of Engineering and Applied Science, The College of Arts and Sciences, and the School of Medicine. <br />
<br />
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[[Image:VGEM_Team.jpg|center|275px]]
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[[Image:VGEM Team pic for Cav Daily.jpg|center|275px]]
<center>[mailto:mcarthur@virginia.edu?subject=VGEM_Query <font color="#FFFFFF"> '''email the VGEM team'''</font>]</center>
<center>[mailto:mcarthur@virginia.edu?subject=VGEM_Query <font color="#FFFFFF"> '''email the VGEM team'''</font>]</center>
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*[[User:rpkhan| <font color="#000000">'''Ranjan Khan'''</font>]], Biomedical Engineering
*[[User:rpkhan| <font color="#000000">'''Ranjan Khan'''</font>]], Biomedical Engineering
*[[User:eruhi| <font color="#000000">'''Emre Ruhi'''</font>]], Biology
*[[User:eruhi| <font color="#000000">'''Emre Ruhi'''</font>]], Biology
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*'''Snowflake''', Albino gorilla
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===<center>Graduate Mentor</center>===
===<center>Graduate Mentor</center>===
*<font color="#000000">'''Brianne Ray'''</font>, Microbiology
*<font color="#000000">'''Brianne Ray'''</font>, Microbiology
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''Engineering is a great profession. There is the satisfaction of watching a figment of the imagination emerge through the aid of science to a plan on paper. Then it moves to realisation in stone or metal or energy. Then it brings homes to men or women. Then it elevates the standard of living and adds to the comforts of life. This is the engineer's high privilege.''<br/ >
''Engineering is a great profession. There is the satisfaction of watching a figment of the imagination emerge through the aid of science to a plan on paper. Then it moves to realisation in stone or metal or energy. Then it brings homes to men or women. Then it elevates the standard of living and adds to the comforts of life. This is the engineer's high privilege.''<br/ >
<center> - Herbert Hoover (1874-1964)</center>
<center> - Herbert Hoover (1874-1964)</center>
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<center></html>Papers</h3>
<center></html>Papers</h3>
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===Introductory Papers===
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===Introductions===
*[http://www.nature.com/nature/comics/syntheticbiologycomic/index.html <font color="#000000">Adventures in Synthetic Biology</font>] a comic by [[User:Endy| <font color="#000000">Drew Endy</font>]]
*[http://www.nature.com/nature/comics/syntheticbiologycomic/index.html <font color="#000000">Adventures in Synthetic Biology</font>] a comic by [[User:Endy| <font color="#000000">Drew Endy</font>]]
*[http://www.etcgroup.org/en/materials/publications.html?id=602 <font color="#000000">Extreme genetic engineering: An introduction to synthetic biology</font>]
*[http://www.etcgroup.org/en/materials/publications.html?id=602 <font color="#000000">Extreme genetic engineering: An introduction to synthetic biology</font>]
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===Reviews and Perspective Papers===
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*[http://www.economist.com/business/displaystory.cfm?story_id=7854314<font color="#000000">''Life 2.0'' Economist article</font>]
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*[http://www.journals.royalsoc.ac.uk/media/6p8qdjvgwr3kq1l4fatn/contributions/e/7/5/2/e752118j23177633.pdf <font color="#000000">Biology by Design</font>] by You ''et al''
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*[http://www.msnbc.msn.com/id/18882828/site/newsweek/page/0/<font color="#000000">''Life 2.0'' Newsweek article</font>]
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===Reviews and Perspectives===
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*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17251159&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum <font color="#000000">Biology by Design</font>] by You ''et al''
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-3&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=55327bdfbda5081b078808963c8a92b6 <font color="#000000">Genetic parts to program bacteria</font>] by Chris Voigt
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-3&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=55327bdfbda5081b078808963c8a92b6 <font color="#000000">Genetic parts to program bacteria</font>] by Chris Voigt
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4 <font color="#000000">Systems biology as a foundation for genome-scale synthetic biology</font>] by B. Palsson ''et al''
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4 <font color="#000000">Systems biology as a foundation for genome-scale synthetic biology</font>] by B. Palsson ''et al''
*[http://www3.interscience.wiley.com/cgi-bin/abstract/112633378/ABSTRACT?CRETRY=1&SRETRY=0 <font color="#000000">A perspective of synthetic biology: Assembling building blocks for novel functions</font>] by Patrick Fu
*[http://www3.interscience.wiley.com/cgi-bin/abstract/112633378/ABSTRACT?CRETRY=1&SRETRY=0 <font color="#000000">A perspective of synthetic biology: Assembling building blocks for novel functions</font>] by Patrick Fu
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===Foundational Papers===
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===Foundations===
*[http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html <font color="#000000">A synthetic oscillatory network of transcriptional regulators</font>] by Michael B. Elowitz and Stanislas Leibler
*[http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html <font color="#000000">A synthetic oscillatory network of transcriptional regulators</font>] by Michael B. Elowitz and Stanislas Leibler
*[http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html <font color="#000000">Construction of a genetic toggle switch in ''Escherichia coli''</font>] by James J. Collins ''et al''
*[http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html <font color="#000000">Construction of a genetic toggle switch in ''Escherichia coli''</font>] by James J. Collins ''et al''
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*[http://dspace.mit.edu/bitstream/1721.1/21168/1/biobricks.pdf <font color="#000000">Biobricks<font>] by Tom Knight
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*[http://dspace.mit.edu/handle/1721.1/21168 <font color="#000000">Biobricks</font>] by Tom Knight
*[http://www.nature.com/nature/journal/v438/n7067/abs/nature04342.html;jsessionid=3E7E09FF4E647671DF79F2A37BC3632F <font color="#000000">Foundations for engineering biology</font>] by Drew Endy
*[http://www.nature.com/nature/journal/v438/n7067/abs/nature04342.html;jsessionid=3E7E09FF4E647671DF79F2A37BC3632F <font color="#000000">Foundations for engineering biology</font>] by Drew Endy
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===Current Research Papers===
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===Current Research===
*[http://www.nature.com/nchembio/journal/v2/n12/abs/nchembio836.html;jsessionid=EFAF8B58DDCC1CB3D2EB61B11223039B <font color="#000000">Production of isoprenoid pharmaceuticals by engineered microbes</font>] by Jay Keasling ''et al''
*[http://www.nature.com/nchembio/journal/v2/n12/abs/nchembio836.html;jsessionid=EFAF8B58DDCC1CB3D2EB61B11223039B <font color="#000000">Production of isoprenoid pharmaceuticals by engineered microbes</font>] by Jay Keasling ''et al''
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*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17239639&ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum<font color="#000000">Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli</font>] by Jay Keasling ''et al''
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4HJRXGD-4&_user=709071&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=cac1dbad4022f85af3724a9ba787d3dd <font color="#000000">Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria</font>] by Chris Voigt ''et al''
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4HJRXGD-4&_user=709071&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=cac1dbad4022f85af3724a9ba787d3dd <font color="#000000">Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria</font>] by Chris Voigt ''et al''
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===Implications===
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*[http://www.nature.com/nbt/journal/v25/n6/pdf/nbt0607-627.pdf<font color="#000000">DNA synthesis and biological security</font>]
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Current revision

uva_logo.gif RotundaKaiHui300x225.jpg

2007 Virginia Genetically Engineered Machine Team

Welcome to the 2007 VGEM Team's OpenWetWare wiki. This wiki contains the internal workings of our team, including our online lab notebook, project designs and other useful information. The VGEM Team is an undergraduate research group interested in synthetic biology and biological engineering, and will compete in MIT's 2007 international Genetically Engineered Machines competition (iGEM) in November. Check on our official iGEM wiki for our final project description and our external website for more information about the team.

Acknowledgements

The VGEM Team was made possible by the generous support from the following groups at the University of Virginia:
The Departments of Biomedical Engineering, Chemical Engineering, Biology, and Microbiology
The School of Engineering and Applied Science and the The Virginia Engineering Foundation
The Office of the Vice President for Research and Graduate Studies
The School of Medicine

We would like to acknowledge and thank our 2007 corporate sponsor:
dna_c.jpg

Resources Project


Our 2007 project is focused on energy biotechnology and is titled "Harvesting Plant Biomass and Sunlight to Power Butanol Biosynthesis: A Synthetic Biology Approach to Metabolic Pathway Engineering." More information about our project can be found at our official iGEM wiki, which you can get to by clicking the iGEM logo below. Please check out our other project designs by clicking the "projects" link listed below the iGEM logo.

IGEM-logo.png

Resources





















People Personnel


Our group is an interdisciplinary conglomeration that includes researchers from The School of Engineering and Applied Science, The College of Arts and Sciences, and the School of Medicine.

email the VGEM team


Undergraduate Team


Graduate Mentor

  • Brianne Ray, Microbiology


Lab Specialist

  • Kay Christopher, Biology


Faculty Advisors


Financial Administrator


Additional Contact Information

Photographs


Engineering is a great profession. There is the satisfaction of watching a figment of the imagination emerge through the aid of science to a plan on paper. Then it moves to realisation in stone or metal or energy. Then it brings homes to men or women. Then it elevates the standard of living and adds to the comforts of life. This is the engineer's high privilege.

- Herbert Hoover (1874-1964)



Papers


Introductions

Reviews and Perspectives

Foundations

Current Research

Implications





















Personal tools