Team:Calgary/Project/References
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- | </ | + | <li>2009 iGEM Calgary. <a href="https://2009.igem.org/Team:Calgary/Notebook"> https://2009.igem.org/Team:Calgary/Notebook</a> </li><br> |
- | < | + | |
- | <li> | + | <li>Asenjo JA. (1949). Bioreactor system design. New York (NY): Marcel Dekker Inc.</li><br> |
- | </ | + | |
- | < | + | <li>Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, and Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006 Feb;1-11.</li><br> |
- | <li>Canadian Centre for Occupational Health and Safety: Health Effects of Sulfur | + | |
+ | <li>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.</li></br> | ||
+ | |||
+ | <li>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.</li></br> | ||
+ | |||
+ | <li>Behar FH, Albrecht P. Correlations between carboxylic acids and hydrocarbons in several crude oils alteration by biodegradation. Org Geochem 1984;6:597-604. </li><br> | ||
+ | |||
+ | <li>Bergman L. Growth and maintenance of yeast. Methods in Molecular Biology. 2001May; 177: 9-39.</li><br> | ||
+ | |||
+ | <li>Biran I, Levcov K, Hengge-Aronis R, Ron EZ, Rishpon J. On-line monitoring of gene expression. Microbiology.1999 April;145:2129-2133.</li><br> | ||
+ | |||
+ | <li>Canadian Centre for Occupational Health and Safety: Health Effects of Sulfur Dioxid. <a href="http://www.ccohs.ca/oshanswers/chemicals/chem_profiles/sulfurdi/health_sul.html">http://www.ccohs.ca/oshanswers/chemicals/chem_profiles/sulfurdi/health_sul.html</a> (Retrieved: 09/18/2012)</li><br> | ||
+ | |||
+ | <li>Clemente JS, Fedorak PM. A review of the occurrences, analyses, toxicity, and biodegradation of naphthenic acids. Chemosphere 2005 Feb 6;60(5):585-600.</li><br> | ||
+ | |||
+ | <li>Clemente JS, Prasad NGN, MacKinnon MD, Fedorak PM. A statistical comparison of naphthenic acids characterized by gas chromatography-mass spectrometry. Chemosphere 2003. 50:1265-1274.</li><br> | ||
+ | |||
+ | <li>Cromie MJ, Groisman EA. Promoter and riboswitch control of the Mg2+ transporter MgtA from Salmonella enterica. J Bacteriol 2010 Jan;192(2):604-607.</li><br> | ||
<li>Dana G, Kuiken T, Rejeski D & Snow A (2012) Synthetic biology: Four steps to avoid a synthetic-biology disaster. Nature 483:29.</li><br> | <li>Dana G, Kuiken T, Rejeski D & Snow A (2012) Synthetic biology: Four steps to avoid a synthetic-biology disaster. Nature 483:29.</li><br> | ||
+ | |||
+ | <li>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. </li></br> | ||
<li>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. </li><br> | <li>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. </li><br> | ||
- | <li>Galán B, Díaz E, García JL. Enhancing | + | <li>Dingwall C, Lomonossoff GP, Laskey RA. High sequence specificity of micrococcal nuclease. Nucleic Acids Res 1981 Jun 25;9(12):2659-2673. </li><br> |
+ | |||
+ | <li>Diaz E, Garcia, JL. Genetics Engineering for Removal of Sulfur and Nitrogen from Fuel Heterocycles. Handbook of Hydrocarbon and Lipid Microbiology: 2144-2157. Springer, 2010. </li><br> | ||
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+ | <li>Egan SM, Schleif RF, others. A regulatory cascade in the inductionof rhaBAD. J Mol Biol 1993;234(1):87-98.</li><br> | ||
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+ | <li>Environmental Protection Agency, (1995), Nitrogen oxides (NOx) Why and how they are controlled. <a href="http://www.epa.gov/ttn/catc/dir1/fnoxdoc.pdf">http://www.epa.gov/ttn/catc/dir1/fnoxdoc.pdf</a> </li><br> | ||
+ | |||
+ | <li>Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. A genome-scale metabolic reconstruction for <i>Escherichia coli</i> K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3 2007 Jun; 121.</li></br> | ||
+ | |||
+ | <li>Frank RA, Fischer K, Kavanagh R, Burnison BK, Aresenault G, Headley J, Peru KM, VanDerKraak G, Solomon K. Effect of Carboxylic Acid Content on the Acute Toxicity of Oil Sands Naphthenic Acids. Environ Sci Technol 2009 Dec 11;43(2):266–271.</li><br> | ||
+ | |||
+ | <li>Galán B, Díaz E, García JL. Enhancing desulfurization by engineering a flavin reductase-encoding gene cassette in recombinant biocatalysts. Environ microbiol. 2000 Dec; 2(6): 687-94 </li><br> | ||
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+ | <li>German Collection of Microorganisms and Cell Cultures (DSMZ): Nocardia iowensis. <a href="https://www.dsmz.de/catalogues/details/culture/DSM-45197.html">http://www.dsmz.de/catalogues/details/culture/DSM-45197.html</a></li><br> | ||
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+ | <li>Groisman EA. The Pleiotropic Two-Component Regulatory System PhoP-PhoQ. J. Bacteriol. 2001 Mar; 183 (6): 1835-42</li><br> | ||
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+ | <li>Gopinath AV, Russell D. An Inexpensive Field-Portable Programmable Potentiostat. Chem. Educator.2006 July;11:23-28.</li><br> | ||
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+ | <li>Harayama S, Rekik M, Wasserfallen A and Bairoch A. Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids. MGG Mol Gen.Genet.1987; 210(2): 241–247.</li><br> | ||
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+ | <li>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.</li><br> | ||
+ | |||
+ | <li>Heckman KL, Pease LR. Gene splicing and mutagenesis by PCR-driven overlap extension. Nature Protocols 2007 2;4 924-932.</li><br> | ||
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+ | <li>Helmann J. Measuring metals with RNA. J Mol Cell 2007 Sept 21; 27(6) 859-860. </li></br> | ||
<li>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.</li><br> | <li>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.</li><br> | ||
+ | |||
+ | <li>Hirrlinger B, Stolz A, Knackmuss HJ. Purification and properties of an amidase from Rhodococcus erythropolis MP50 which enantioselectively hydrolyzes 2-arylpropionamides. J Bacteriology 1996; 178(12) 3501-3507.</li><br> | ||
<li>Holowenko FM, Mackinnon MD, Fedorak PM. Naphthenic acids and surrogate naphthenic acids in methanogenic microcosms. Water Res 2001 Aug;35(11):2595-2606. </li><br> | <li>Holowenko FM, Mackinnon MD, Fedorak PM. Naphthenic acids and surrogate naphthenic acids in methanogenic microcosms. Water Res 2001 Aug;35(11):2595-2606. </li><br> | ||
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+ | <li>Jeske M, Altenbuchner J. The Escherichia coli rhamnose promoterrhaP BAD is in Pseudomonas putida KT2440 independent of Crp--cAMPactivation. Appl Microbiol Biotechnol 2010;85(6):1923-1933.</li><br> | ||
<li>Kamali N, Tavallaie M, Bambai B, Karkhane AA, Miri M. Site-directed mutagenesis enhances the activity of NADH-FMN oxidoreductase (DszD) activity of <i>Rhodococcus erythropolis</i>. Biotechnol Lett. 2010; 32: 921-927</li><br> | <li>Kamali N, Tavallaie M, Bambai B, Karkhane AA, Miri M. Site-directed mutagenesis enhances the activity of NADH-FMN oxidoreductase (DszD) activity of <i>Rhodococcus erythropolis</i>. Biotechnol Lett. 2010; 32: 921-927</li><br> | ||
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+ | <li>Lewenza S, Falsafi RK, Winsor G, Gooderham WJ, McPhee JB, Brinkman FS, et al. Construction of a mini-Tn5-luxCDABE mutant library in <i>Pseudomonas aeruginosa</i> PAO1: a tool for identifying differentially regulated genes. Genome Res 2005 Apr;15(4):583-589. </li><br> | ||
<li>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 <i>Rhodococcus erythropolis</i>. Appl Environ Microbiol. 2008 Feb; 74(4): 971-6 </li><br> | <li>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 <i>Rhodococcus erythropolis</i>. Appl Environ Microbiol. 2008 Feb; 74(4): 971-6 </li><br> | ||
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<li>Ma T. The Desulfurization Pathway in <i>Rhodococcus</i>. Microbiology Monographs 2010; 16: 207-230.</li><br> | <li>Ma T. The Desulfurization Pathway in <i>Rhodococcus</i>. Microbiology Monographs 2010; 16: 207-230.</li><br> | ||
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+ | <li>Morales M, Le Borgne S. Microorganisms Utilizing Nitrogen-Containing Heterocyclic Hydrocarbons. Handbook of Hydrocarbon and Lipid Microbiology: 2144-2157. Springer, 2010.</li><br> | ||
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+ | <li>Nakai C, Kagamiyama H, Nozaki M. Complete nucleotide sequence of the metapyrocatechase gene on the TOL plasmid of <i>Pseudomonas putida </i> mt-2. J Biol Chem. 1983 Mar; 258(5):2923-2928.</li><br> | ||
<li>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 <i>Rhodococcus erythropolis</i> KA2-5-1 by site-directed mutagenesis. Biosci Biotechnol Biochem. 2007 Nov.; 71(11):2815-21</li><br> | <li>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 <i>Rhodococcus erythropolis</i> KA2-5-1 by site-directed mutagenesis. Biosci Biotechnol Biochem. 2007 Nov.; 71(11):2815-21</li><br> | ||
+ | <li>Parts Registry: The PetroBrick – Strong Constitutive Expression of ADC and AAR in pSB1C3 <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025 (Retrieved 8/28/2012">http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025 (Retrieved 8/28/2012</a> </li><br> | ||
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References
- 2009 iGEM Calgary. https://2009.igem.org/Team:Calgary/Notebook
- Asenjo JA. (1949). Bioreactor system design. New York (NY): Marcel Dekker Inc.
- Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, and Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006 Feb;1-11.
- 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.
- Behar FH, Albrecht P. Correlations between carboxylic acids and hydrocarbons in several crude oils alteration by biodegradation. Org Geochem 1984;6:597-604.
- Bergman L. Growth and maintenance of yeast. Methods in Molecular Biology. 2001May; 177: 9-39.
- Biran I, Levcov K, Hengge-Aronis R, Ron EZ, Rishpon J. On-line monitoring of gene expression. Microbiology.1999 April;145:2129-2133.
- Canadian Centre for Occupational Health and Safety: Health Effects of Sulfur Dioxid. http://www.ccohs.ca/oshanswers/chemicals/chem_profiles/sulfurdi/health_sul.html (Retrieved: 09/18/2012)
- Clemente JS, Fedorak PM. A review of the occurrences, analyses, toxicity, and biodegradation of naphthenic acids. Chemosphere 2005 Feb 6;60(5):585-600.
- Clemente JS, Prasad NGN, MacKinnon MD, Fedorak PM. A statistical comparison of naphthenic acids characterized by gas chromatography-mass spectrometry. Chemosphere 2003. 50:1265-1274.
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