Team:UCL London/Bibliography

From 2011.igem.org

Bibliography

Supercoiliology

  1. Menzel, R. and M. Gellert, Modulation of Transcription by DNA Supercoiling - a Deletion Analysis of the Escherichia-Coli Gyra and Gyrb Promoters. Proceedings of the National Academy of Sciences of the United States of America, 1987. 84(12): p. 4185-4189.
  2. Reese, R.J. and A. Maxwell, DNA gyrase: structure and function. Crit Rev Biochem Mol Biol, 1991. 26(3-4): p. 335-75.
  3. Sinden, R.R., J.O. Carlson, and D.E. Pettijohn, Torsional Tension in the DNA Double Helix Measured with Trimethylpsoralen in Living Escherichia-Coli-Cells - Analogous Measurements in Insect and Human-Cells. Cell, 1980. 21(3): p. 773-783.
  4. Zechiedrich, E.L., et al., Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. Journal of Biological Chemistry, 2000. 275(11): p. 8103-8113.
  5. P.R. Jensen et al., 1999. Extensive regulation compromises the extent to which DNA gyrase controls supercoiling and growth rate of Escherichia coli. Eur. I. Biochem., 266: 874.
  6. Barth, Dederich and Dedon (2009). An improved method for large-scale preparation of negatively and positively supercoiled plasmid DNA. BioTechniques 47:633-635
  7. DNA Conformations.pdf, [Online] Available at:[Accessed on September 1 2011)

Magneto - Sites

  1. Reese, R.J. and A. Maxwell, DNA gyrase: structure and function. Crit Rev Biochem Mol Biol, 1991. 26(3-4): p. 335-75.
  2. Pato, M.L., et al., Characterization of Mu prophage lacking the central strong gyrase binding site: localization of the block in replication. J Bacteriol, 1995. 177(20): p. 5937-42.
  3. Wahle, E. and A. Kornberg, The Partition Locus of Plasmid Psc101 Is a Specific Binding-Site for DNA Gyrase. Embo Journal, 1988. 7(6): p. 1889-1895.
  4. Miller, C. and S.N. Cohen, Separate roles of Escherichia coli replication proteins in synthesis and partitioning of pSC101 plasmid DNA. J Bacteriol, 1999. 181(24): p. 7552-7.
  5. Miller, C.A., H. Ingmer, and S.N. Cohen, Boundaries of the pSC101 minimal replicon are conditional. J Bacteriol, 1995. 177(17): p. 4865-71.
  6. Oram, M., et al., A biochemical analysis of the interaction of DNA gyrase with the bacteriophage Mu, pSC101 and pBR322 strong gyrase sites: the role of DNA sequence in modulating gyrase supercoiling and biological activity. Mol Microbiol, 2003. 50(1): p. 333-47.

Extractery

  1. Winstanley, C., et al., Differential Regulation of Lambda-Pl and Lambda-Pr Promoters by a Ci Repressor in a Broad-Host-Range Thermoregulated Plasmid Marker System. Applied and Environmental Microbiology, 1989. 55(4): p. 771-777.
  2. Delorenzo, V., et al., An Upstream Xylr-Induced and Ihf-Induced Nucleoprotein Complex Regulates the Sigma-54-Dependent Pu Promoter of Tol Plasmid. Embo Journal, 1991. 10(5): p. 1159-1167.
  3. Young, R.Y., Bacteriophage Lysis - Mechanism and Regulation. Microbiological Reviews, 1992. 56(3): p. 430-481.
  4. Sayers, J.R. and F. Eckstein, Properties of Overexpressed Phage-T5 D15 Exonuclease - Similarities with Escherichia-Coli DNA-Polymerase-I 5'-3' Exonuclease. Journal of Biological Chemistry, 1990. 265(30): p. 18311-18317.
  5. Sayers, J.R., D. Evans, and J.B. Thomson, Identification and eradication of a denatured DNA isolated during alkaline lysis-based plasmid purification procedures. Analytical Biochemistry, 1996. 241(2): p. 186-189.
  6. Carnes, A.E., et al., Plasmid DNA Production Combining Antibiotic-Free Selection, Inducible High Yield Fermentation, and Novel Autolytic Purification. Biotechnology and Bioengineering, 2009. 104(3): p. 505-515.

Stresslights 2.0

  1. Hagenmaier, S., Y.D. Stierhof, and U. Henning, A new periplasmic protein of Escherichia coli which is synthesized in spheroplasts but not in intact cells. J Bacteriol, 1997. 179(6): p. 2073-6.
  2. Bardwell, J.C.A., et al., Genetic selection designed to stabilize proteins uncovers a chaperone called Spy. Nature Structural & Molecular Biology, 2011. 18(3): p. 262-U41.
  3. Raffa, R.G. and T.L. Raivio, A third envelope stress signal transduction pathway in Escherichia coli. Mol Microbiol, 2002. 45(6): p. 1599-611.
  4. Raivio, T.L. and T.J. Silhavy, Transduction of envelope stress in Escherichia coli by the Cpx two-component system. Journal of Bacteriology, 1997. 179(24): p. 7724-7733.
  5. Raivio, T.L. and N.L. Price, Characterization of the Cpx Regulon in Escherichia coli Strain MC4100. Journal of Bacteriology, 2009. 191(6): p. 1798-1815.
  6. Yamaguchi, A., K. Nishino, and T. Honda, Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system. Journal of Bacteriology, 2005. 187(5): p. 1763-1772.
  7. Ishihama, A., K. Yamamoto, and H. Ogasawarab, Involvement of multiple transcription factors for metal-induced spy gene expression in Escherichia coli. Journal of Biotechnology, 2008. 133(2): p. 196-200.
  8. Bury-Mone, S., et al., Global Analysis of Extracytoplasmic Stress Signaling in Escherichia coli. Plos Genetics, 2009. 5(9).
  9. Tokuda, H., et al., Effects of lipoprotein overproduction on the induction of DegP (HtrA) involved in quality control in the Escherichia coli periplasm. Journal of Biological Chemistry, 2004. 279(38): p. 39807-39813.
  10. Ortega, J., et al., The inner cavity of Escherichia coli DegP protein is not essential for molecular chaperone and proteolytic activity. Journal of Bacteriology, 2007. 189(3): p. 706-716.
  11. Danese, P.N., et al., The Cpx two-component signal transduction pathway of Escherichia coli regulates transcription of the gene specifying the stress-inducible periplasmic protease, DegP. Genes Dev, 1995. 9(4): p. 387-98.
  12. Ruiz, N. and T.J. Silhavy, Sensing external stress: watchdogs of the Escherichia coli cell envelope. Curr Opin Microbiol, 2005. 8(2): p. 122-6.
  13. Kolesnikow, T., I. Schroder, and R.P. Gunsalus, Regulation of narK gene expression in Escherichia coli in response to anaerobiosis, nitrate, iron, and molybdenum. J Bacteriol, 1992. 174(22): p. 7104-11.
  14. Unden, G. and M. Trageser, Oxygen regulated gene expression in Escherichia coli: control of anaerobic respiration by the FNR protein. Antonie Van Leeuwenhoek, 1991. 59(2): p. 65-76.
  15. Spiro, S. and J.R. Guest, FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol Rev, 1990. 6(4): p. 399-428.
  16. Shimomura, O., F.H. Johnson, and Y. Saiga, Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from Luminous Hydromedusan, Aequorea. Journal of Cellular and Comparative Physiology, 1962. 59(3): p. 223-7.
  17. Andersen, J.B., et al., New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol, 1998. 64(6): p. 2240-6.
  18. van Oudenaarden, A., et al., Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature, 2007. 450(7173): p. 1249-1252.

Supercoilometer

  1. Brahms, J.G., et al., Activation and Inhibition of Transcription by Supercoiling. Journal of Molecular Biology, 1985. 181(4): p. 455-465.
  2. Straney, R., R. Krah, and R. Menzel, Mutations in the -10 TATAAT Sequence of the Gyra Promoter Affect Both Promoter Strength and Sensitivity to DNA Supercoiling. Journal of Bacteriology, 1994. 176(19): p. 5999-6006.
  3. Pemberton, I.K., et al., The G+C-rich discriminator region of the tyrT promoter antagonises the formation of stable preinitiation complexes. Journal of Molecular Biology, 2000. 299(4): p. 859-864.
  4. Lamond, A.I., Supercoiling response of a bacterial tRNA gene. Embo Journal, 1985. 4(2): p. 501-7.
  5. Bowater, R.P., D.R. Chen, and D.M.J. Lilley, Modulation of Tyrt Promoter Activity by Template Supercoiling in-Vivo. Embo Journal, 1994. 13(23): p. 5647-5655.
  6. El Hanafi, D. and L. Bossi, Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome. Molecular Microbiology, 2000. 37(3): p. 583-594.
  7. Bossi, L., et al., The supercoiling sensitivity of a bacterial tRNA promoter parallels its responsiveness to stringent control. Embo Journal, 1998. 17(8): p. 2359-2367.

Manufacturing

  1. Williams, J.A. and Carnes, A. E., 2007. Plasmid DNA manufacturing technology. Recent Patents on Biotechnology, Vol.1, No.2.
  2. Williams, J.A. and Carnes, A. E., 2007. Plasmid DNA manufacturing technology. Recent Patents on Biotechnology, Vol.1, No.2.
  3. Lin-Chao, S, Bremer, H., 1986. Effect of the bacterial growth rate on replication control of plasmid pBR322 in Escherichia coli. Molecular and General Genetics. 203(1):143-9
  4. O'Kennedy, R.D., et al., 2000. Effects of growth medium selection on plasmid DNA production and initial processing steps. Journal of Biotechnology. 76(2-3):175-83.
  5. Levy, M. S., et al., 1999. Effect of shear on plasmid DNA solution. Bioprocess Engineering, 20, 7-13.
  6. U.S. Food and Drug Administration, 2007. Guidance for industry: consideration for plasmid DNA vaccines for infectious disease indications.
  7. Catanese Jr, D.J. et al, 2011. Supercoiled minivector DNA resists shear forces associated with gene therapy delivery. Gene Therapy, 1-7
  8. Carnes, A.E., 2005. Fermentation Design for the manufacture of therapeutic plasmid DNA. Bioprocess Technical.
  9. Hoare, M., et al., 2005. Bioprocess engineering issues that would be faced in producing a DNA vaccine at up to 100m3 fermentation scale for an influenza pandemic. Biotechnology Progress, 2005, 21, 1577-1592.
  10. Oram, M., et al., 2003. A biochemical analysis of the interaction of DNA gyrase with the bacteriophage Mu, pSC101 and pBR322 strong gyrase sites: the role of DNA sequence in modulating gyrase supercoiling and biological activity. Molecular Microbiology, 50 (1): 333-347.
  11. Ferreira, G.N.M, et al., 2000. Downstream Processing of plasmid DNA for gene therapy and DNA vaccine applications. Trends in biotechnology, 18.
  12. Dorman CJ. et al., 1991. DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression. Infection and Immunity, 59(3): 745–749.
  13. Hsieh, L.S., et al., 1991. Bacterial dna supercoiling and [ATP]/[ADP] changes associated with a transition to anaerobic growth. Journal of Molecular Biology, 219(3):443-50.
  14. Hopkins D.J., et al., 1987. Effects of dissolved oxygen shock on the stability of recombinant ecoli containing plasmid pKN401. Biotechnology and Bioengineering, 29 (1): 85-91.
  15. Durland, R.H., and Easman, E.M., 1998. Manufacturing and quality control of plasmid based gene expression of pBR322-derived plasmids intended for human gene therapy by employing a temperature-controllable point mutation. Advanced Drug Delivery Review, 2;30(1-3):33-48.
  16. Cupillard, L., et al., 2005. Impact of plasmid supercoiling on the efficacy of a rabies DNA vaccine to protect cats. Vaccine, 23: 1910–1916.
  17. Carnes, A.E., et al., 2009. Plasmid DNA Production Combining Antibiotic-Free Selection, Inducible High Yield Fermentation, and Novel Autolytic Purification. Biotechnology and Engineering, 104 (3): 505-515.

Medicine

  1. http://www.tsim.org.tw/article/A95/abstract/10-afternoon/Rm102/H5N1-3.pdf
  2. WHO, Avian Influenza, [Online] Available at: [Accessed on 16 September 2011)
  3. TED, Seth Berkley: HIV and flu -- the vaccine strategy, [Online] Available at: [Accessed on 14 September 2011)
  4. http://www.medscape.com/viewarticle/487616
  5. Recombinant/ purified protein vaccines, [Online] Available at: [Accessed on 17 September 2011)
  6. Discover Magazine: Vaccine Production Is Horribly Outdated. Here Are 3 Ways to Fix It. [Online] Available at: [Accessed on 17 September 2011)
  7. www.pitt.edu/~super7/32011-33001/32731.ppt
  8. NAE Website - Cell-Culture-Based Vaccine Production: Technological Options, [Online] Available at: [Accessed on 16 September 2011)
  9. David B. Weiner and Ronald C. Kennedy, 1999. Genetic Vaccines. Scientific American, July Issue, pp. 50-57. Cui, Z., 2005. DNA vaccine. Advances in Genetics, Volume 54, pp. 257-289. DNA vaccination: Immune response raised by DNA vaccines [online] Available at: [Accessed on 7 September 2011] David B. Weiner and Ronald C. Kennedy, 1999. How DNA Vaccines Work. [diagram] Same journal.
  10. Wikipedia, Gene gun, [online] Available at: [Accessed on 8 September 2011)
  11. Inovio, Technology: Electroporation-Based DNA Delivery, [online] Available at: [Accessed on 8 September 2011)
  12. Pilling et al., 2002. The Assessment of Local Tolerance, Acute Toxicity, and DNA Biodistribution Following Particle-Mediated Delivery of a DNA Vaccine to Minipigs. Toxicologic Pathology, 30(3), pp 298-305.
  13. Sheets et al., 2006. Biodistribution of DNA Plasmid Vaccines against HIV-1, Ebola, Severe Acute Respiratory Syndrome, or West Nile Virus Is Similar, without Integration, despite Differing Plasmid Backbones or Gene Inserts. Toxicological Sciences, 91(2), pp 610-619.
  14. Sheets et al., 2006. Toxicological Safety Evaluation of DNA Plasmid Vaccines against HIV-1, Ebola, Severe Acute Respiratory Syndrome, or West Nile Virus Is Similar Despite Differing Plasmid Backbones or Gene-Inserts. Toxicological Sciences, 91(2), pp 620-630
  15. http://www.academicjournals.org/AJB/PDF/pdf2011/7Sep/Roy%20et%20al.pdf
  16. NAE Website - Cell-Culture-Based Vaccine Production: Technological Options, [Online] Available at: [Accessed on 7 September 2011)
  17. Strategies for production of viral vaccines, [Online] Available at: [Accessed on 14 September 2011)
  18. Strategies for production of viral vaccines, [Online] Available at: [Accessed on 14 September 2011)
  19. Strategies for production of viral vaccines, [Online] Available at: [Accessed on 14 September 2011)
  20. U.S. Department of Health and Human Services, CBER and FDA Guidance document. Guidance for Industry: Considerations for Plasmid DNA Vaccines for Infectious Disease Indications (11/07)
  21. Urthaler et al., 2005. Improvement of transfection efficiency by using supercoiled plasmid DNA purified with arginine affinity chromatography. J Gene Med, 11(1): 79-88.
  22. Cupillard et al., 2005. Impact of plasmid supercoiling on the efficacy of a rabies DNA vaccine to protect cats. Vaccine, 23: 1910-1916.
  23. Jensen et al., 1999. Extensive regulation compromises the extent to which DNA gyrase controls supercoiling and growth rate of Escherichia coli. Eur. I. Biochem., 266: 865-877.
  24. Trigueros S and Roca J, 2002. Failure to relax negative supercoiling of DNA is a primary cause of mitotic hyper-recombination in topoisomerase-deficient yeast cells. J Biol Chem., 277(40):37207-11.
  25. Yarwood et al., 2004, Cracking mothers’ attitudes to childhood immunisation 1991-2001, submitted for publication.

Safety

  1. Cupillard, L. et al., 2005. Impact of plasmid supercoiling on the efficacy of a rabies DNA vaccines to protect cats. Vaccine 23: 1910-1916.
  2. Reece, R.J. and Maxwell, A., 1991. DNA Gyrase: Structure and Function. Critical Reviews in Biochemistry and Molecular Biology. 26 (3/4):335-375.
  3. Safety Handbook, 2010/2011. Department of Biochemical Engineering,UCL.
  4. Institute of Child Health Flow Cytometry Core Facility, UCL Biosafety: Important health and safety documents, [online]
    Available from: http://www.ucl.ac.uk/ich/services/lab-services/FCCF/biosafety (Accessed on 25 August 2011)

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