View source for BYU iGEM/Archive

{{Template:BYU iGEM}}

==Parts Database==

[[https://spreadsheets.google.com/spreadsheet/ccc?hl=en&key=tAVBWBda3ggmyLcxX5FH6dw&hl=en#gid=0|BYU iGEM Biological Parts Database]]

==Articles==

===OxyR_Peroxide===

Regulation of the OxyR transcription factor by hydrogen peroxide and the cellular thiol—disulfide status. [http://www.pnas.org/content/96/11/6161.full]

Sequence Data

OxyR Binding domain on the mnth gene

[[Image:MNTH Gene binding site.jpeg]]

Site 1: TTTTCGTAGT'''CATAATCCTGGTCTATC'''AGAGAAATCA   Source: [http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU0-7321]

Site 2: CTATCAGAGA'''AATCACCACAATCCAT'''TTAAATGAATT   Source: [http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU0-7321]

SoxR Binding domain on the SoxS gene

[[Image:SoxR Gene biniding domain.jpeg]]

Site 1: AATCGCTTTA'''CCTCAAGTTAACTTGAGGA'''ATTATACTCC   [http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00211]

<b><i>E. coli</i> Colon cancer detector</b>

<b>Thermosensors</b>

[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-4C5HD56-4-1&_cdi=7051&_user=456938&_pii=S0092867402009054&_origin=search&_coverDate=09/06/2002&_sk=998899994&view=c&wchp=dGLbVtz-zSkzk&md5=70e234399b3f96ac4373f26c9551a459&ie=/sdarticle.pdf That paper that Dr. Griffitts suggested]

[[:Image:TSprimers.pdf|PDF with primer sequences]]

[[:Image:ThermoswitchSequencesBYUiGEM.pdf|PDF with ΔTRS mutation sequences]]

[http://www.reference-global.com/doi/pdf/10.1515/BC.2008.150 Thermoswitch Sequence]

<b>Multiple Cloning Site Map</b>

[[Image:IMAG0070.jpg|thumb|center|Click image to enlarge.]]

<b>Useful ROS Transcription factor articles</b>

[http://ecocyc.org/ Ecocyc.org (anything you want to know about E. coli]

[http://www.ncbi.nlm.nih.gov/gene/1039198 SoxR Sequence Info at NCBI]

[http://www.ncbi.nlm.nih.gov/nucleotide/?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=948462 OxyR Sequence Info at NCBI]

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-42BSR1X-11&_user=456938&_coverDate=03%2F01%2F2001&_alid=1618440669&_rdoc=1&_fmt=high&_orig=search&_origin=search&_zone=rslt_list_item&_cdi=5181&_sort=r&_st=13&_docanchor=&view=c&_ct=42&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=243c76c742f72641b4bcf88997d33f07&searchtype=a Redox-operated genetic switches: the SoxR and OxyR transcription factors (Review)]

[http://www.ncbi.nlm.nih.gov/pubmed/19892202 Techniques to isolate O2-sensitive proteins: [4Fe-4S]-FNR as an example.]

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-50H1WM2-8&_user=456938&_coverDate=02/01/2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1625952567&_rerunOrigin=google&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=9cee4c02a4a02ca16abc322336de97cc&searchtype=a A genetically encoded sensor for H2O2 with expanded dynamic range (OxyR with YFP)]

[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2009.04514.x/full Rapid in vivo screening system for anti-oxidant activity using bacterial redox sensor strains.]

[http://www.annualreviews.org/doi/pdf/10.1146/annurev.biochem.77.061606.161055 Cellular Defenses against Superoxide and Hydrogen Peroxide]

<b>AND Gate Articles</b>

[http://partsregistry.org/Part:BBa_F2620 Logical "And" switch part from iGEM registry]

<b>Other Colon Cancer Articles</b>

[http://cebp.aacrjournals.org/content/12/10/1095.full.pdf+html Detection of Gastric Cancer and Premalignant Lesions by Novel Marker Glycoprotein 87 Using Monoclonal Antibody Adnab-9]

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475556/ Colon Cancer biomarker (Lgr5 protein)]

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-3W269GC-28&_user=456938&_coverDate=12/31/1996&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=46cc917f0f9e034d94b8c32b3ed3a73b&searchtype=a Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon - A review]

[http://clincancerres.aacrjournals.org/content/13/20/5991.full The Universal Character of the Tumor-Associated Antigen Survivin]

[http://clincancerres.aacrjournals.org/content/7/5/1118.full Biomarkers for Early Detection of Colon Cancer]

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-42BSR1X-11&_user=456938&_coverDate=03%2F01%2F2001&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1618397411&_rerunOrigin=scholar.google&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=a53c60889b46317652c5182edccccc70&searchtype=a OxyR and Soxr Transcription Factors]

<b>Biomarkers</b>

[http://partsregistry.org/wiki/index.php?title=Part:BBa_K115002 Parts that activate translation at 37°C -- for more parts, change the final 2 in URL to 3 or 9]

[http://video.google.com/videoplay?docid=-2704243649439977137# Bio Thermometer 1 (youTube video)]

[http://igem-victoria.pbworks.com/w/page/7992064/Bio-Thermometer Bio Thermometer 2]

[http://en.wikipedia.org/wiki/Carcinoembryonic_antigen Carcinoembryonic antigen]

[http://en.wikipedia.org/wiki/Prostate_Specific_Antigen Prostate-specific antigen]

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN2-4NRMDCT-3&_user=456938&_coverDate=12%2F31%2F2007&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1613028817&_rerunOrigin=google&_acct=C000021830&_version=1&_urlVersion=0&_userid=456938&md5=6434a6e2cbf35e44e5540c2b1799759c&searchtype=a ROS is decreased in cancerous cells]

<b>Toolbox</b>

[http://www.hindawi.com/journals/jbb/2010/130781.html Synthetic Biology Tools]

[http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html Synthetic Biology and Engineering Rules]

[http://www.annualreviews.org/doi/full/10.1146/annurev.biophys.36.040306.132600?amp;searchHistoryKey=${searchHistoryKey} Synthetic Gene Circuit]

[http://www.pnas.org/content/99/26/16587.full Directed Evolution of a Genetic Circuit]

[http://www.hindawi.com/journals/jbb/2010/459760.html Microbial Metabolism]

[http://www.hindawi.com/journals/jbb/2010/541609.html Mathematical Modeling]

[http://www.hindawi.com/journals/jbb/2010/232016.html Biology by Design]

<b>Inversion Recombinase Mechanisms</b>

[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002815 Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory]

<b>Schools for Synthetic Biology</b>
[http://syntheticbiology.org/Graduate.html]

<b>Potential Mechanisms</b>
<p>[[Image:IGEM Mechanism.jpg|650px|center]]</p>
<p>[[Image:Flip Recombinase.JPG|650px|center]]</p>
<p>[[Image:Cre-Lox Mech.JPG|700px|center]]</p>