Team:SMTexas/Design

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Formaldehyde induces the frmR gene, functioning as a regulatory gene of Green Fluorescent protein. When transcribed, it expresses a regulatory protein that binds to an downstream operator that prevents the movement of RNA polymerase. Under typical conditions, the promoter downstream of the regulatory gene increases the affinity of RNA polymerase to the DNA strand, but the transcription enzyme cannot bypass the operator and transcribe GFP, the gene that is ultimately under regulation. In such a scenario, the regulatory protein that frmR expresses functions as a repressor and effectively inhibits transcription of the coding sequence. Formaldehyde, on the other hand, induces the transcription of GFP and ultimately causes bacterial fluorescence. Acting as a corepressor, the VOC binds to the regulatory protein and conforms it into an inactive shape, allowing for the passage of RNA polymerase through the operator and transcribe the GFP protein.
Formaldehyde induces the frmR gene, functioning as a regulatory gene of Green Fluorescent protein. When transcribed, it expresses a regulatory protein that binds to an downstream operator that prevents the movement of RNA polymerase. Under typical conditions, the promoter downstream of the regulatory gene increases the affinity of RNA polymerase to the DNA strand, but the transcription enzyme cannot bypass the operator and transcribe GFP, the gene that is ultimately under regulation. In such a scenario, the regulatory protein that frmR expresses functions as a repressor and effectively inhibits transcription of the coding sequence. Formaldehyde, on the other hand, induces the transcription of GFP and ultimately causes bacterial fluorescence. Acting as a corepressor, the VOC binds to the regulatory protein and conforms it into an inactive shape, allowing for the passage of RNA polymerase through the operator and transcribe the GFP protein.
<table><tr><td width="1200" align="left" style="vertical-align:middle"><img src="https://static.igem.org/mediawiki/2014hs/1/11/FrmR.png"></td><td width="1200" align="right" style="vertical-align:middle"><img src="https://static.igem.org/mediawiki/2014hs/3/3e/FrmR2.png"></td></tr></table>
<table><tr><td width="1200" align="left" style="vertical-align:middle"><img src="https://static.igem.org/mediawiki/2014hs/1/11/FrmR.png"></td><td width="1200" align="right" style="vertical-align:middle"><img src="https://static.igem.org/mediawiki/2014hs/3/3e/FrmR2.png"></td></tr></table>
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<header><h2>References</h2></header></section></div>
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<p><br>General:<br><br>
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Society of Thoracic Surgeons. (2014, January 28). Exhaled breath may help identify early lung cancer. ScienceDaily. Retrieved June 15, 2014 from www.sciencedaily.com/releases/2014/01/140128094145.htm<br><br>
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American Lung Association. (2012, April). Providing Guidance on Lung Cancer Screening To Patients and Physicians. Retrieved from http://www.lung.org/lung-disease/lung-cancer/lung-cancer-screening-guidelines/lung-cancer-screening.pdf<br><br>
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Pfizer Oncology. Lung Cancer and Biomarkers. Retrieved from http://www.lungcancerprofiles.com/lung_cancer_and_biomarkers.<br><br>
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Hakim, M., Broza, Y. Y., Barash, O., Peled, N., Phillips, M., Amann, A., & Haick, H. (2012). Volatile Organic Compounds of Lung Cancer and Possible Biochemical Pathways. Chemical Reviews, 112(11), 5949-5966. doi: 10.1021/cr300174a<br><br>
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Fu, X., Li, M., Knipp, R. J., Nantz, M. H., & Bousamra, M. (2013). Noninvasive detection of lung cancer using exhaled breath. Cancer Medicine, 3, 174-181. doi:10.1002/cam4.162<br><br>
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Mazzone, MD, MPH, FRCPC, FCCP, (July 2008). Analysis of Volatile Organic Compounds in the Exhaled Breath for the Diagnosis of Lung Cancer. Journal of Thoracic Oncology . 3 (7), pp.774-781<br><br>
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Phillips, M., Gleeson, K., B Hughes, J. M., Greenberg, J., Cataneo, R. N., & Baker, L. Volatile organic compounds in breath as markers of lung cancer: a cross-sectional study . Early Report, 353, 1930-1936.<br><br>
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Fuchs, P., Loeseken, C., Schubert, J. K., & Miekisch, W. Breath gas aldehydes as biomarkers of lung cancer. International Journal of Cancer, 126, 2663-2670.<br><br>
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Bajtarevic, A., Ager, C., Pienz, M., Klieber, M., Schwarz, K., Ligor, M., et al. Noninvasive detection of lung cancer by analysis of exhaled breath. BMC Cancer, 9.<br><br>
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Wang, Y., Hu, Y., Wang, Di., Yu, K., Wang, L., Zou, Y., Zhao, C., Zhang, X., Wang, P., & Ying, K. The analysis of volatile organic compounds biomarkers for lung cancer in exhaled breath, tissues and cell lines. Cancer Biomarkers, 11, 128-137. doi:10.3233/CBM-2012-00270.<br><br>
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Clinical Trials. (2012). Exhaled Breath Biomarkers in Lung Cancer. Retrieved from http://clinicaltrials.gov/show/NCT01386203<br><br>
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xylR gene: <br><br>
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EcoCyc (n.d. )Escherichia coli K-12 substr. MG1655 Polypeptide: XylR transcriptional activator. Retrieved from http://ecocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=EG20253-MONOMER<br><br>
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Nucleic Acids Research 39:D583-90 2011 <br><br>
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WikiGenes (n.d.) xyIR-xyIR Pseudomonas Putida. Retrieved from http://www.wikigenes.org/e/gene/e/1218757.html
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SmoColi. (n.d.) How we calculated the concentration of m-xylene in the medium…. Retrieved from https://2011.igem.org/Team:ETH_Zurich/xylene<br><br>
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aldB gene: <br><br>
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Xu, J., Diderichsen, B., Ho, K. K. Wiki Genes. aldB  - aldehyde dehydrogenase BEscherichia coli str. K-12 substr. MG1655. Retrieved From http://www.wikigenes.org/e/gene/e/948104.html <br><br>
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Xu, J., & Johnson, R. C. National Center for Biotechnology Information. aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp. Retrieved From http://www.ncbi.nlm.nih.gov/pmc/articles/PMC177007/<br><br>
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EcoCyc. (n.d.). Escherichia coli K-12 substr. MG1655 Enzyme: acetaldehyde dehydrogenase. Retrieved From http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG12292<br><br>
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PortEco. (2013). aldB:gene. Retrieved from http://ecoliwiki.net/colipedia/index.php/aldB:Gene<br><br>
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frmR gene: <br><br>
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Tokyo Metropolitan University. (n.d.) Parts. Retrieved from https://2012.igem.org/Team:TMU-Tokyo/Parts <br><br>
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PortEco. (n.d.) Retrieved from http://heptamer.tamu.edu/fgb2/gbrowse/MG1655/?plugin=FastaDumper&q=NC_000913:378830..379105&plugin_action=Go <br><br>
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PortEco. (2013). frmR gene. Retrieved from http://ecoliwiki.net/colipedia/index.php/frmR:Gene
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Wang, S., Deng, K., Zaremba, S., Deng, X., Lin, C., Wang, Q., et al. (2009, August 7). Transcriptomic Response of Escherichia coli O157:H7 to Oxidative Stress. Retrieved  from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753066/
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EcoCyc. (n.d.) Escherichia coli K-12 substr. MG1655 Polypeptide: regulator protein. Retrieved from http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=G6209<br><br>
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Latest revision as of 14:28, 20 June 2014