BYU iGEM/Archive: Difference between revisions
| (22 intermediate revisions by 5 users not shown) | |||
| Line 1: | Line 1: | ||
{{Template:BYU iGEM}} | {{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== | ==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] | |||
Redox sensing by prokaryotic transcription factors. [http://www.sciencedirect.com/science/article/pii/S0006295299002890#toc1] | |||
===OxyR_Binding=== | |||
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli. [http://jb.asm.org/cgi/content/full/183/15/4571] | |||
===OxyR_End=== | |||
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><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> | <b>Useful ROS Transcription factor articles</b> | ||
| Line 17: | Line 63: | ||
[http://www.ncbi.nlm.nih.gov/pubmed/19892202 Techniques to isolate O2-sensitive proteins: [4Fe-4S]-FNR as an example.] | [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= | [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://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.] | ||
| Line 40: | Line 86: | ||
[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] | [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> | <b>Biomarkers</b> | ||
| Line 79: | Line 124: | ||
[http://syntheticbiology.org/Graduate.html] | [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:Flip Recombinase.JPG|650px|center]]</p> | ||
<p>[[Image:Cre-Lox Mech.JPG|700px|center]]</p> | <p>[[Image:Cre-Lox Mech.JPG|700px|center]]</p> | ||
Latest revision as of 12:54, 20 July 2011
|
Parts Database
[iGEM Biological Parts Database]
Articles
OxyR_Peroxide
Regulation of the OxyR transcription factor by hydrogen peroxide and the cellular thiol—disulfide status. [1]
Redox sensing by prokaryotic transcription factors. [2]
OxyR_Binding
Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli. [3]
OxyR_End
Sequence Data
OxyR Binding domain on the mnth gene
Site 1: TTTTCGTAGTCATAATCCTGGTCTATCAGAGAAATCA Source: [4]
Site 2: CTATCAGAGAAATCACCACAATCCATTTAAATGAATT Source: [5]
SoxR Binding domain on the SoxS gene
Site 1: AATCGCTTTACCTCAAGTTAACTTGAGGAATTATACTCC [6]
E. coli Colon cancer detector
Thermosensors
That paper that Dr. Griffitts suggested
PDF with ΔTRS mutation sequences
Multiple Cloning Site Map
Useful ROS Transcription factor articles
Ecocyc.org (anything you want to know about E. coli
Redox-operated genetic switches: the SoxR and OxyR transcription factors (Review)
Techniques to isolate O2-sensitive proteins: [4Fe-4S-FNR as an example.]
A genetically encoded sensor for H2O2 with expanded dynamic range (OxyR with YFP)
Rapid in vivo screening system for anti-oxidant activity using bacterial redox sensor strains.
Cellular Defenses against Superoxide and Hydrogen Peroxide
AND Gate Articles
Logical "And" switch part from iGEM registry
Other Colon Cancer Articles
Colon Cancer biomarker (Lgr5 protein)
Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon - A review
The Universal Character of the Tumor-Associated Antigen Survivin
Biomarkers for Early Detection of Colon Cancer
OxyR and Soxr Transcription Factors
Biomarkers
Parts that activate translation at 37°C -- for more parts, change the final 2 in URL to 3 or 9
Bio Thermometer 1 (youTube video)
ROS is decreased in cancerous cells
Toolbox
Synthetic Biology and Engineering Rules
Directed Evolution of a Genetic Circuit
Inversion Recombinase Mechanisms
Schools for Synthetic Biology [7]
Potential Mechanisms
