References

• Asenjo J.A. (1949).Bioreactor system design. New York (NY): Marcel Dekker Inc.

• Reit K., & Tramper J. (1991). Basic bioreactor design. New York (NY):Marcel Dekker Inc.

• Canadian Centre for Occupational Health and Safety: Health Effects of Sulfur Dioxide, http://www.ccohs.ca/oshanswers/chemicals/chem_profiles/sulfurdi/health_sul.html (Retrieved: 09/18/2012)


• Dana G, Kuiken T, Rejeski D & Snow A (2012) Synthetic biology: Four steps to avoid a synthetic-biology disaster. Nature 483:29.


• Del Rio LF, Hadwin AK, Pinto LJ, MacKinnon MD, Moore MM. Degradation of naphthenic acids by sediment micro-organisms. J Appl Microbiol 2006 Nov;101(5):1049-1061.


• Diaz, E. & Garcia, J.L. Genetics Engineering for Removal of Sulfur and Nitrogen from Fuel Heterocycles. Handbook of Hydrocarbon and Lipid Microbiology: 2144-2157. Springer, 2010.


• Galán B, Díaz E, García JL. Enhancing desulphurization by engineering a flavin reductase-encoding gene cassette in recombinant biocatalysts. Environmental microbiology. 2000 Dec; 2(6): 687-94


• Herman DC, Fedorak PM, MacKinnon MD, Costerton JW. Biodegradation of naphthenic acids by microbial populations indigenous to oil sands tailings. Can J Microbiol 1994 Jun;40(6):467-477.


• Holowenko FM, Mackinnon MD, Fedorak PM. Naphthenic acids and surrogate naphthenic acids in methanogenic microcosms. Water Res 2001 Aug;35(11):2595-2606.


• Kamali N, Tavallaie M, Bambai B, Karkhane AA, Miri M. Site-directed mutagenesis enhances the activity of NADH-FMN oxidoreductase (DszD) activity of Rhodococcus erythropolis. Biotechnol Lett. 2010; 32: 921-927


• Katzer JR, Sivasubramanian R. Process and Catalyst Needs for Hydrodenitrogenation. Catalysis Reviews: Science and Engineering 1979; 20(2):155-208.


• Lewenza S, Falsafi RK, Winsor G, Gooderham WJ, McPhee JB, Brinkman FS, et al. Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes. Genome Res 2005 Apr;15(4):583-589.


• Li GQ, Li SS, Zhang ML, Wang J, Zhu L, Liang FL, Liu RL, Ma T. Genetic rearrangement strategy for optimizing the dibenzothiophene biodesulfurization pathway in Rhodococcus erythropolis. Appl Environ Microbiol. 2008 Feb; 74(4): 971-6


• Li MZ, Squires CH, Monticello DJ, Childs JD. Genetic analysis of the dsz promoter and associated regulatory regions of Rhodococcus erythropolis IGTS8. J Bacteriol. 1996 Nov; 178(22): 6409-18


• Lim HN, Lee Y, Hussein R. Fundamental relationship between operon organization and gene expression. Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10626-31.


• Ma T. The Desulfurization Pathway in Rhodococcus. Microbiology Monographs 2010; 16: 207-230.


• Nakai C, Kagamiyama H, Nozaki M. Complete nucleotide sequence of the metapyrocatechase gene on the TOL plasmid of Pseudomonas putida mt-2. J Biol Chem. 1983 Mar; 258(5):2923-2928.


• Oshiro T, Ohkita R, Takikawa T, Manabe M, Lee WC, Tanokura M, Izumi Y. Improvement of 2'-hydroxybiphenyl-2-sulfinate desulfinase, an enzyme involved in the dibenzothiophene desulfurization pathway, from Rhodococcus erythropolis KA2-5-1 by site-directed mutagenesis. Biosci Biotechnol Biochem. 2007 Nov.; 71(11):2815-21


• Phillips R, Kondev J, Theriot J. Physical Biology of the Cell. 1st ed. Garland Science. 2008.


• Ramos-Padron E, Bordenave S, Lin S, Bhaskar IM, Dong X, Sensen CW, et al. Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond. Environ Sci Technol 2011 Jan 15;45(2):439-446.


• Reznikoff WS. Transposon Tn5. Annu Rev Genet 2008;42:269-286.


• Schweigert N, Zehnder AJ, Eggen RI. Chemical properties of catechols and their molecular modes of toxic action in cells, from microorganisms to mammals. Environ Microbiol 2001 Feb; 3(2):81-91


• Sheridan DL, Hughes TE. A faster way to make GFP-based biosensors: two new transposons for creating multicolored libraries of fluorescent fusion proteins. BMC Biotechnol 2004 Aug 18;4:17.


• Shu L, Chiou Y, Orville AM, Miller MA, Lipscomb JD, Que L. X-ray absorption spectroscopic studies of the Fe(II) active site of catechol 2,3-dioxygenase. Implications for the extradiol cleavage mechanism. Biochem 1995; 34:6649-6659.


• So J. Mini-transposon Tn5gfp constructs for differential tagging of microorganisms. Biotechnology and Bioprocess Engineering 1999;4(2):154-156.


• Timms-Wilson TM, Bailey MJ. Reliable use of green fluorescent protein in fluorescent pseudomonads. J Microbiol Methods 2001 Jul 30;46(1):77-80.


• United Nations Environment Programme: Sulfur Air Pollution, http://www.unep.org/transport/pcfv/pdf/Ethiopia-AirPollutionsulphur.pdf (Retrieved: 09/18/2012)


• United States Environmental Protection Agency: Sulfur Dioxide, http://www.epa.gov/air/sulfurdioxide/ (Retrieved: 09/18/2012)


• Vaillancourt FH, Bolin JT, Eltis LD. The ins and outs of ring-cleaving dioxygenases. Crit Rev Biochem Mol. 2006; 41:241-267.


• Vogel U, Jensen KF. The RNA chain elongation rate in Escherichia coli depends on the growth rate. J Bacteriol. 1994 May;176(10):2807-13.


• Wright JK, Overath P. Purification of the lactose:H+ carrier of Escherichia coli and characterization of galactoside binding and transport. Eur J Biochem.1984 Feb 1;138(3):497-508.


• Xiong AS, Peng RH, Cheng ZM, Li Y, Liu JG, Zhuang J, Gao F, Xu F, Qiao YS, Zhang Z, Chen JM, Yao QH. Concurrent mutations in six amino acids in beta-glucuronidase improve its thermostability. Protein Eng Des Sel. 2007 Jul;20(7):319-25. Epub 2007 Jun 8.


• Yoshimura F, Nikaido H. Permeability of Pseudomonas aeruginosa outer membrane to hydrophilic solutes. J Bacteriol. 1982 Nov;152(2):636-42.


• Young R, Bremer H. Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate. Biochem J. 1976 Nov 15;160(2):185-94.


• Zhang X, Wiseman S, Yu H, Liu H, Giesy JP, Hecker M. Assessing the toxicity of naphthenic acids using a microbial genome wide live cell reporter array system. Environ Sci Technol 2011 Mar 1;45(5):1984-1991.


• 2009 iGEM Calgary, 2009.igem.org/Team:Calgary/Notebook


• He A, Li T, Daniels L, Fotheringham I, Rosazza J.P.N. Nocardia sp. Carboxylic Acid Reductase: Cloning, Expression, and Characterization of a New Aldehyde Oxidoreductase Family. Applied and Environmental Microbiology 2004 Mar;70(3):1874–1881.


• Venkitasubramanian P, Daniels L, Rosazza J.P.N. Reduction of Carboxylic Acids by Nocardia Aldehyde Oxidoreductase Requires a Phosphopantetheinylated Enzyme. Journal of Biological Chemistry 2007 Nov 13;282(1):478-485.


• Rude M.A, Baron T.S, Brubaker S, Alibhai M, Del Cardayre S.B, and Schirmer A. Terminal olefin (1-alkene) biosynthesis by a novel p450 fatty acid decarboxylase from Jeotgalicoccus species. Applied and Environmental Microbiology 2011 Mar;77(5):1718–1727.


• Clemente J.S, Fedorak P.M. A review of the occurrences, analyses, toxicity, and biodegradation of naphthenic acids. Chemosphere 2005 Feb 6;60(5):585-600.


• Frank R.A, Fischer K, Kavanagh R, Burnison B.K, Aresenault G, Headley J, Peru K.M, VanDerKraak G, Solomon K. Effect of Carboxylic Acid Content on the Acute Toxicity of Oil Sands Naphthenic Acids. EnvironSciTechnol 2009 Dec 11;43(2):266–271.


• Slavcheva E, Shone B, Turnbull A. Review of napthenic acid corrosion in oilrefining. British Corrosion Journal 1999 Feb;34(2):125-131.


• Behar F.H, Albrecht P. Correlations between carboxylic acids and hydrocarbons in several crude oils alteration by biodegradation. Organic Geochemistry 1984;6:597-604.


• German Collection of Microorganisms and Cell Cultures (DSMZ): Nocardia iowensis. https://www.dsmz.de/catalogues/details/culture/DSM-45197.html (retrieved 8/28/2012)


• UW iGEM: Diesel Production Background. https://2011.igem.org/Team:Washington/Alkanes/Background (retrieved 8/28/2012)


• Parts Registry: The PetroBrick – Strong Constitutive Expression of ADC and AAR in pSB1C3. http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025 (retrieved 8/28/2012)


• Asenjo J.A. (1949).Bioreactor system design. New York (NY): Marcel Dekker Inc.


• Reit K., & Tramper J. (1991). Basic bioreactor design. New York (NY):Marcel Dekker Inc.


• Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature Protocols 2 2007 Mar; 727-723.


• Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 6 2011 Aug; 1290-1307.


• Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 3 2007 Jun; 121.


• TOMLAB Optimization, MatLab Optimization, http://tomopt.com/tomlab/


• Gopinath AV, Russell D. An Inexpensive Field-Portable Programmable Potentiostat. Chem.Educator.2006 July;11:23-28.


• Biran I, Levcov K, Hengge-Aronis R, Ron EZ, Rishpon J. On-line monitoring of gene expression. Microbiology.1999 April;145:2129-2133.


• Waters LS, Sandoval M, and Storz G. The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. J Bacteriol 2011 Nov; 193(21) 5887-97.


• Ramesh A, Wakeman CA, and Winkler WC. Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. J Mol Biol 2011 Apr 8; 407(4) 556-70.


• Helmann J. Measuring metals with RNA. J Mol Cell 2007 Sept 21; 27(6) 859-860.


• Daus B, Mattusch J, Paschke A, Wennrich R, and Weiss H. Kinetics of the arsenite oxidation in seepage water from a tin mill tailings pond. Talanta 2000 May 5; 51(6) 1087-95.