Team:TU Delft/Project/references

From 2010.igem.org

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__NOTOC__
==References==
==References==
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====Alkane Degradation====
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#'''Fujii, T., Narikawa, T., Takeda, K., Kato, J.''', Biotransformation of various alkanes using the Escherichia coli expressing an alkane hydroxylase system from ''Gordonia sp. TF6''. ''Bioscience, biotechnology, and biochemistry'', 68(10) 2171-2177 ('''2004''')
 +
#'''Liu Li, Xueqian Liu, Wen Yang, Feng Xu, Wei Wang, Lu Feng, Mark Bartlam, Lei Wang and Zihe Rao.''' Crystal Structure of Long-Chain Alkane Monooxygenase (LadA) in Complex with Coenzyme FMN: Unveiling the Long-Chain Alkane Hydroxylase. ''Journal of molecular biology'', 376: 453-465 ('''2008''')
 +
#'''Tomohisa Kato, Asuka Miyanaga, Mitsuru Haruki, Tadayuki Imanaka, Masaaki Morikawa & Shigenori Kanaya.''' Gene Cloning of an Alcohol Dehydrogenase from Thermophilic Alkane-Degrading ''Bacillus thermoleovorans B23''. ''Journal of Bioscience and Bioengineering'' 91(1):100-102 ('''2001''')
 +
#'''Tomohisa Kato, Asuka Miyanaga, Shigenori Kanaya, Masaaki Morikawa.''' Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading ''Geobacillus thermoleovorans B23''. ''Extremophiles'' 14:33-39 ('''2010''')
 +
#'''Sulzenbacher, G., et al.''', Crystal structure of E-coli alcohol dehydrogenase YqhD: Evidence of a covalently modified NADP coenzyme. ''Journal of Molecular Biology'' 342(2):489-502 ('''2004''')
 +
#http://mbel.kaist.ac.kr/lab/research/protein_en1.html
 +
#'''Hoffmann F. and Rinas U'''. Stress Induced by Recombinant Protein Production in ''Escherichia coli'' ''Advances in Biochemical Engineering/Biotechnology'', Vol. 89, pp. 73-92.('''2004''')
 +
 +
====Sensing====
 +
#'''Canosa, I., J. M. Sanchez-Romero, et al.''' A positive feedback mechanism controls expression of AlkS, the transcriptional regulator of the Pseudomonas oleovorans alkane degradation pathway. ''Molecular Microbiology'' 35(4): 791-799 ('''2000''')
 +
#'''Moreno, R., A. Ruiz-Manzano, et al.''' The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator. ''Molecular Microbiology'' 64(3): 665-675 ('''2007''')
 +
#'''van Beilen, J. B., S. Panke, et al.''' Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. ''Microbiology-Sgm'' 147: 1621-1630 ('''2001''')
 +
#'''Rojo, F.''' , Degradation of alkanes by bacteria. ''Environmental Microbiology''  11: 2477-2490 ('''2009''')
 +
#'''Kotte, O, Zaugg, J., Heinemann, M. ''', ‘Bacterial adaptation through distributed sensing of metabolic fluxes’, ''Molecular Systems Biology'', 6:355,  doi:10.1038/msb.2010.10 ('''2010''')
 +
#'''Kremling, A., Bettenbrock, K., Gilles, E.D.''', ‘Analysis of global control of Escherichia coli carbohydrate uptake’, ''BMC Systems Biology'', 1:42, doi:10.1186/1752-0509-1-42 ('''2007''')
 +
#'''Lin, H. Y., Mathiszik, B., Xu, B.,  Enfors, S.-O., Neubauer, P.''', ‘Determination of the Maximum Specific Uptake Capacities for  Glucose and Oxygen in Glucose-Limited Fed-Batch Cultivations of ''Escherichia coli''’, ''Biotechnology and Bioengineering'', 73, 347-357 ('''2001''')
 +
#'''Alon, U. (ed.)''', An Introduction to Systems Biology: Design Principles of Biological Circuits, ''CRC Press'' ('''2007''')
 +
#EcoCyc: [http://BioCyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CPLX0-226 click here]
 +
 +
====Survival====
 +
#'''S. Tanaka,K. Ikeda, H. Miyasaka''', Enhanced Tolerance Against Salt-Stress and Freezing-Stress of Escherichia coli Cells Expressing Algal bbc1 Gene. ''Current Microbiology'', 42:173-177 ('''2001''')
 +
#'''Y. Suda,T. Yoshikawa,Y. Okuda,M. Tsunemoto,S. Tanaka,K. Ikeda,H. Miyasaka,M. Watanabe,K. Sasaki,K. Harada,T. Bamba,K. Hirata''', Isolation and characterization of a novel antistress gene from ''Chlamydomonas sp. W80''. ''Journal of Bioscience and Bioengineering'', 107(4) 352-354 ('''2009''')
 +
#'''Y. Hase, S. Yokoyama, A. Muto, et al.''' , Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells. ''RNA Society'', 15:1766-1774 ('''2009''')
 +
#'''Mihaela Marilena Lăzăroaie''',Investigation of saturated and aromatichydrocarbon resistance mechanismsin ''Pseudomonas aeruginosa'' IBB ''Cent. Eur. J. Biol.'' 4(4) 469-481 ('''2009''')
 +
#'''M. Okochi, K. Kanie,  M. Kurimoto ,M. Yohda & Hiroyuki Honda''' Overexpression of prefoldin from the hyperthermophilic archaeum ''Pyrococcus horikoshii'' OT3 endowed ''Escherichia coli'' with organic solvent tolerance ''Appl Microbiol Biotechnol'' 79:443-449 ('''2008''')
 +
====Solubility====
 +
#'''Walzer, G., Rosenberg, E. and Ron, E.Z.''' The Acinetobacter outer membrane protein A (OmpA) is a secreted emulsifier. ''Environmental Microbiology.'' 8:1026-1032.('''2006''')
 +
#'''Toren, A., Segal, G., Ron, E.Z. and Rosenberg, E.'''  Structure--function studies of the recombinant protein bioemulsifier AlnA. ''Environmental Microbiology.'' 4:257-261.('''2002''')
 +
#'''Navon-Venezia, S., et al.'''  Alasan, a new bioemulsifier from Acinetobacter radioresistens. ''Applied and Environmental Microbiology.'' 61:3240-3244.('''1995''')
 +
#'''Toren, A., Orr, E., Paitan, Y., Ron, E.Z. and Rosenberg, E.'''  The active component of the bioemulsifier alasan from Acinetobacter radioresistens KA53 is an OmpA-like protein. ''The Journal of Bacteriology.'' 184:165-170.('''2002''')
 +
#'''Toren, A., Navon-Venezia, S., Ron, E.Z. and Rosenberg, E.'''  Emulsifying activities of purified Alasan proteins from Acinetobacter radioresistens KA53. ''Applied and Environmental Microbiology.'' 67:1102-1106.
 +
#'''Ron, E.Z. and Rosenberg, E.''' (2002) Biosurfactants and oil bioremediation. ''Current Opinion in Biotechnology.'' 13:249-252.('''2001''')
 +
#'''Suresh Kumar, A., Mody, K. and Jha, B.''' Evaluation of biosurfactant/bioemulsifier production by a marine bacterium. ''Bulletin of Environmental Contamination and Toxicology.'' 79:617-621.('''2007''')

Latest revision as of 22:59, 27 October 2010

References

Alkane Degradation

  1. Fujii, T., Narikawa, T., Takeda, K., Kato, J., Biotransformation of various alkanes using the Escherichia coli expressing an alkane hydroxylase system from Gordonia sp. TF6. Bioscience, biotechnology, and biochemistry, 68(10) 2171-2177 (2004)
  2. Liu Li, Xueqian Liu, Wen Yang, Feng Xu, Wei Wang, Lu Feng, Mark Bartlam, Lei Wang and Zihe Rao. Crystal Structure of Long-Chain Alkane Monooxygenase (LadA) in Complex with Coenzyme FMN: Unveiling the Long-Chain Alkane Hydroxylase. Journal of molecular biology, 376: 453-465 (2008)
  3. Tomohisa Kato, Asuka Miyanaga, Mitsuru Haruki, Tadayuki Imanaka, Masaaki Morikawa & Shigenori Kanaya. Gene Cloning of an Alcohol Dehydrogenase from Thermophilic Alkane-Degrading Bacillus thermoleovorans B23. Journal of Bioscience and Bioengineering 91(1):100-102 (2001)
  4. Tomohisa Kato, Asuka Miyanaga, Shigenori Kanaya, Masaaki Morikawa. Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading Geobacillus thermoleovorans B23. Extremophiles 14:33-39 (2010)
  5. Sulzenbacher, G., et al., Crystal structure of E-coli alcohol dehydrogenase YqhD: Evidence of a covalently modified NADP coenzyme. Journal of Molecular Biology 342(2):489-502 (2004)
  6. http://mbel.kaist.ac.kr/lab/research/protein_en1.html
  7. Hoffmann F. and Rinas U. Stress Induced by Recombinant Protein Production in Escherichia coli Advances in Biochemical Engineering/Biotechnology, Vol. 89, pp. 73-92.(2004)

Sensing

  1. Canosa, I., J. M. Sanchez-Romero, et al. A positive feedback mechanism controls expression of AlkS, the transcriptional regulator of the Pseudomonas oleovorans alkane degradation pathway. Molecular Microbiology 35(4): 791-799 (2000)
  2. Moreno, R., A. Ruiz-Manzano, et al. The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator. Molecular Microbiology 64(3): 665-675 (2007)
  3. van Beilen, J. B., S. Panke, et al. Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology-Sgm 147: 1621-1630 (2001)
  4. Rojo, F. , Degradation of alkanes by bacteria. Environmental Microbiology 11: 2477-2490 (2009)
  5. Kotte, O, Zaugg, J., Heinemann, M. , ‘Bacterial adaptation through distributed sensing of metabolic fluxes’, Molecular Systems Biology, 6:355, doi:10.1038/msb.2010.10 (2010)
  6. Kremling, A., Bettenbrock, K., Gilles, E.D., ‘Analysis of global control of Escherichia coli carbohydrate uptake’, BMC Systems Biology, 1:42, doi:10.1186/1752-0509-1-42 (2007)
  7. Lin, H. Y., Mathiszik, B., Xu, B., Enfors, S.-O., Neubauer, P., ‘Determination of the Maximum Specific Uptake Capacities for Glucose and Oxygen in Glucose-Limited Fed-Batch Cultivations of Escherichia coli’, Biotechnology and Bioengineering, 73, 347-357 (2001)
  8. Alon, U. (ed.), An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC Press (2007)
  9. EcoCyc: [http://BioCyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CPLX0-226 click here]

Survival

  1. S. Tanaka,K. Ikeda, H. Miyasaka, Enhanced Tolerance Against Salt-Stress and Freezing-Stress of Escherichia coli Cells Expressing Algal bbc1 Gene. Current Microbiology, 42:173-177 (2001)
  2. Y. Suda,T. Yoshikawa,Y. Okuda,M. Tsunemoto,S. Tanaka,K. Ikeda,H. Miyasaka,M. Watanabe,K. Sasaki,K. Harada,T. Bamba,K. Hirata, Isolation and characterization of a novel antistress gene from Chlamydomonas sp. W80. Journal of Bioscience and Bioengineering, 107(4) 352-354 (2009)
  3. Y. Hase, S. Yokoyama, A. Muto, et al. , Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells. RNA Society, 15:1766-1774 (2009)
  4. Mihaela Marilena Lăzăroaie,Investigation of saturated and aromatichydrocarbon resistance mechanismsin Pseudomonas aeruginosa IBB Cent. Eur. J. Biol. 4(4) 469-481 (2009)
  5. M. Okochi, K. Kanie, M. Kurimoto ,M. Yohda & Hiroyuki Honda Overexpression of prefoldin from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 endowed Escherichia coli with organic solvent tolerance Appl Microbiol Biotechnol 79:443-449 (2008)

Solubility

  1. Walzer, G., Rosenberg, E. and Ron, E.Z. The Acinetobacter outer membrane protein A (OmpA) is a secreted emulsifier. Environmental Microbiology. 8:1026-1032.(2006)
  2. Toren, A., Segal, G., Ron, E.Z. and Rosenberg, E. Structure--function studies of the recombinant protein bioemulsifier AlnA. Environmental Microbiology. 4:257-261.(2002)
  3. Navon-Venezia, S., et al. Alasan, a new bioemulsifier from Acinetobacter radioresistens. Applied and Environmental Microbiology. 61:3240-3244.(1995)
  4. Toren, A., Orr, E., Paitan, Y., Ron, E.Z. and Rosenberg, E. The active component of the bioemulsifier alasan from Acinetobacter radioresistens KA53 is an OmpA-like protein. The Journal of Bacteriology. 184:165-170.(2002)
  5. Toren, A., Navon-Venezia, S., Ron, E.Z. and Rosenberg, E. Emulsifying activities of purified Alasan proteins from Acinetobacter radioresistens KA53. Applied and Environmental Microbiology. 67:1102-1106.
  6. Ron, E.Z. and Rosenberg, E. (2002) Biosurfactants and oil bioremediation. Current Opinion in Biotechnology. 13:249-252.(2001)
  7. Suresh Kumar, A., Mody, K. and Jha, B. Evaluation of biosurfactant/bioemulsifier production by a marine bacterium. Bulletin of Environmental Contamination and Toxicology. 79:617-621.(2007)
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