Team:Calgary/Notebook/References

From 2013.igem.org

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<li>Hernandez, J., Prado, V., Torres, D., Waldenström, J., Haemig, P. D., Olsen, B. (2007) Enteropathogenic <i>Escherichia coli</i> (EPEC) in Antarctic fur seals <i>Arctocephalus gazella</i>. <i>Polar Biology</i>. doi:10.1007/s00300-007-0282-2</li>
<li>Hernandez, J., Prado, V., Torres, D., Waldenström, J., Haemig, P. D., Olsen, B. (2007) Enteropathogenic <i>Escherichia coli</i> (EPEC) in Antarctic fur seals <i>Arctocephalus gazella</i>. <i>Polar Biology</i>. doi:10.1007/s00300-007-0282-2</li>
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<li>Junillon, T., Vimont, A., Mosticone, D., Mallen, B., Baril, F., Rozand, C., Flandrois, J. P. (December 2012). Simplified detection of food-borne pathogens: an in situ high affinity capture and staining concept. <i>Journal of Microbial Methods</i> 91(3), 501-505. doi: 10.1016/j.mimet.2012.09.015</li>
<li>Mermin, J. H., Griffin, P. M. (1999) Invited commentary: public health: outbreaks of <i>Escherichia coli</i> O157:H7 infections in Japan. <i>American Journal of Epidemiology.</i>  150(8), 797-803.</li>
<li>Mermin, J. H., Griffin, P. M. (1999) Invited commentary: public health: outbreaks of <i>Escherichia coli</i> O157:H7 infections in Japan. <i>American Journal of Epidemiology.</i>  150(8), 797-803.</li>

Revision as of 02:39, 29 October 2013

References

Our Project

  • Belson, K., Fahim, K. (2007, October 6) After extensive beef recall, Topps goes out of business. The New York Times. Retrieved from http://www.nytimes.com/2007/10/06/us/06topps.html?pagewanted=all&_r=0
  • CBC News. (2010, May 10) Inside Walkerton: Canada's worst ever E. coli contamination: the shock, the investigation and the aftermath. CBC News
  • Centers for Disease Control and Prevention. (2011) Enterohemorrhagic Escherichia coli. Retrieved from http://www.cdc.gov/ecoli/general/
  • Chase-Topping, M., Gally, D., Low, C., Matthews, L., Woolhouse, M. (2008). Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157. Nature Reviews Microbiology, 6(12):904-12. doi: 10.1038/nrmicro2029
  • Cross, A. (2012, October 2) Most extensive beef recall in Canadian history expanded again. National Post.
  • FOA/WHO (Food and Agriculture Organization of the United Nations/World Health Organization). (2011) Enterohaemorrhagic Escherichia coli in raw beef and beef product: approaches for the provision of scientific advice. Microbial Risk Assessment Series No 18. Geneva. 126pp.
  • Food Safety News. (2012, August 27) E. coli outbreak linked to Australian petting zoo sickens 12. Retrieved from http://www.foodsafetynews.com/2013/08/e-coli-outbreak-at-australian-petting-zoo-sickens-12/#.Um7YCpTTXTg
  • Hernandez, J., Prado, V., Torres, D., Waldenström, J., Haemig, P. D., Olsen, B. (2007) Enteropathogenic Escherichia coli (EPEC) in Antarctic fur seals Arctocephalus gazella. Polar Biology. doi:10.1007/s00300-007-0282-2
  • Junillon, T., Vimont, A., Mosticone, D., Mallen, B., Baril, F., Rozand, C., Flandrois, J. P. (December 2012). Simplified detection of food-borne pathogens: an in situ high affinity capture and staining concept. Journal of Microbial Methods 91(3), 501-505. doi: 10.1016/j.mimet.2012.09.015
  • Mermin, J. H., Griffin, P. M. (1999) Invited commentary: public health: outbreaks of Escherichia coli O157:H7 infections in Japan. American Journal of Epidemiology. 150(8), 797-803.
  • Okeke, I. (2009). Diarrheagenic Escherichia coli in sub-Saharan Africa: status, uncertainties and necessities. The Journal Of Infection In Developing Countries, 3(11), 817-842. doi:10.3855/jidc.586
  • World Health Organization. (2011) Outbreak of E. coli O104:h4 infection: update 30. Retrieved from http://www.euro.who.int/en/health-topics/disease-prevention/food-safety/news/news/2011/07/outbreaks-of-e.-coli-o104h4-infection-update-30

    • Detector

  • Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., … Bonas, U. (2009). Breaking the code of DNA binding specificity of TAL-type III effectors. Science (New York, N.Y.), 326(5959), 1509–12. doi:10.1126/science.1178811
  • Bogdanove, A. J., Schornack, S., & Lahaye, T. (2010). TAL effectors: finding plant genes for disease and defense. Current Opinion in Plant Biology, 13(4), 394–401. doi:10.1016/j.pbi.2010.04.010
  • Bogdanove, A. J., & Voytas, D. F. (2011). TAL effectors: customizable proteins for DNA targeting. Science (New York, N.Y.), 3336051), 1843–6. doi:10.1126/science.1204094
  • Cong, L., Zhou, R., Kuo, Y., Cunniff, M., & Zhang, F. (2013). Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nature Communications. doi:10.1038/ncomms1962.Comprehensive
  • Meckler, J.F., Bhakta, M.S., Kim, M.S., Ovadia, R., Habrian, C.H., Zykovich, A., ... Baldwin, E.P. (2013). Quantitative analysis of TALE-DNA interactions suggests polarity effects. Nucleic Acids Research, 41(7), 4118–28. doi:10.1093/nar/gkt085
  • Mussolino, C., & Cathomen, T. (2012). TALE nucleases: tailored genome engineering made easy. Current Opinion in Biotechnology, 23(5), 644–50. doi:10.1016/j.copbio.2012.01.013

    • Prussian Blue

  • Ford, A. G. C., Harrison, P. M., Rice, D. W., Smith, J. M. A., Treffry, A., White, J. L., & Yariv, J. (1984). Ferritin : design and formation of an iron-storage molecule source . Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 304(1121), 551-65. Retrieved from http://www.jstor.org/stable/2396121
  • Harrison, P.-M., & Arosio, P. (1996). The ferritins: molecular properties, iron storage function and cellular regulation. Biochimica et Biophysica Acta, 1275(3), 161-203. doi:10.1016/0005-2728(96)00022-9
  • Lawson, D. M., Artymiuk, P. J., Yewdall, S. J., Smith, J. M., Livingstone, J. C., Treffry, A., Luzzago, A., Levi, S., Arosio, P., Cesareni, G. (1991). Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature, 349(6309), 541–4. doi:10.1038/349541a0
  • Munro, H.N. (1990). Iron regulation of ferritin gene expression. Journal of Cellular Biochemistry 44(2), 107-115.
  • Zhang, W., Zhang, Y., Chen, Y., Li, S., Gu, N., Hu, S., Sun, Y., Chen, X., & Li, Q. (2013). Prussian blue modified ferritin as peroxidase mimetics and its applications in biological detection, Journal of Nanoscience and Nanotechnology, 12, 1–8. doi:10.1166/jnn.2012.6871
  • Zhang, X.-Q., Gong, S.-W., Zhang, Y., Yang, T., Wang, C.-Y., & Gu, N. (2010). Prussian blue modified iron oxide magnetic nanoparticles and their high peroxidase-like activity. Journal of Materials Chemistry, 20(24), 5110. doi:10.1039/c0jm00174k

    • Beta-Lactamase

  • Kong, Y., Yao, H., Ren, H., Subbian, S., Cirillo, S. L. G., Sacchettini, J. C., … Cirillo, J. D. (2010). Imaging tuberculosis with endogenous beta-lactamase reporter enzyme fluorescence in live mice. Proceedings of the National Academy of Sciences of the United States of America, 107(27), 12239–44. doi:10.1073/pnas.1000643107
  • Moore, J.T., Davis, S.T., & Dev, I.K. (1997). The development of beta-lactamase as a highly versatile genetic reporter for eukaryotic cells. Analytical Biochemistry, 247(2), 203–9. doi:10.1006/abio.1997.2092
  • Qureshi, S. (2007). β-Lactamase: an ideal reporter system for monitoring gene expression in live eukaryotic cells. BioTechniques, 42(1), 91–96. doi:10.2144/000112292
  • Remy, I., Ghaddar, G., & Michnick, S. W. (2007). Using the beta-lactamase protein-fragment complementation assay to probe dynamic protein-protein interactions. Nature Protocols, 2(9), 2302–6. doi:10.1038/nprot.2007.356
  • Wehrman, T., Kleaveland, B., Her, J.-H., Balint, R. F., & Blau, H. M. (2002). Protein-protein interactions monitored in mammalian cells via complementation of beta -lactamase enzyme fragments. Proceedings of the National Academy of Sciences of the United States of America, 99(6), 3469–74. doi:10.1073/pnas.062043699

    • Linker

  • Huh, Y. S., & Kim, I. H. (2003). Purification of fusion ferritin from recombinant E. coli using two-step sonications. Biotechnology Letters, 25(12), 993–6. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/12889837
  • Litowski, J. R., & Hodges, R. S. (2002). Designing heterodimeric two-stranded alpha-helical coiled-coils. Effects of hydrophobicity and alpha-helical propensity on protein folding, stability, and specificity. The Journal of Biological Chemistry, 277(40), 37272–9. doi:10.1074/jbc.M204257200
  • Zhang, X.-Q., Gong, S.-W., Zhang, Y., Yang, T., Wang, C.-Y., & Gu, N. (2010). Prussian blue modified iron oxide magnetic nanoparticles and their high peroxidase-like activity. Journal of Materials Chemistry, 20(24), 5110. doi:10.1039/c0jm00174k

    • Journals and Parts Pages on the Registry of Standard Biological Parts

  • Apostolovic, B., & Klok, H.-A. (2008). pH-sensitivity of the E3/K3 heterodimeric coiled coil. Biomacromolecules, 9(11), 3173–80. doi:10.1021/bm800746e
  • Arthur, T.M., Keen, J.E., Bosilevac, J.M, Brichta-Harhay, D.M., Kalchayanand, N., Shackelford, S.D., … Koohmaraie, M. (2009). Longitudinal study of Escherichia coli O157:H7 in a beef cattle feedlot and role of high-level shedders in hide contamination. Applied and Environmental Microbiology, 75(20), 6515-23. doi: 10.1128/AEM.00081-09
  • Beurdeley, M., Bietz, F., Li, J., Thomas, S., Stoddard, T., Juillerat, A., … Silva, G. H. (2013). Compact designer TALENs for efficient genome engineering. Nature Communications, 4, 1762. doi:10.1038/ncomms2782
  • Besant, J.D., Das, J., Sargent, E.H., Kelley, SO. (2013) Proximal bacterial lysis and detection in nanoliter wells using electrochemistry. American Chemical Society Nano, 7(9), 8183-9.
  • Blais, B.W., Gauthier, M., Descheênes, M., & Huszczynski G. (2012). Polyester cloth-based hybridization array system for identification of enterohemorrhagic Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157. Journal of Food Protection, 75(9), 1691-7. doi: 10.4315/0362-028X.JFP-12-116
  • Bushart, S., Bradbury, D., Elder, G., Duffield, J., Pascual, I., & Ratcliffe, N. (2006). The development of magnetic molecules for the selective removal of contaminants. In Waste Management Conference. Tuczon, AZ. Retrieved from http://www.wmsym.org/archives/2006/pdfs/6190.pdf
  • Carvalho, R. H., Lemos, F., Lemos, M. A., Vojinović, V., Fonseca, L. P., & Cabral, J. M. S. (2006). Kinetic modelling of phenol co-oxidation using horseradish peroxidase. Bioprocess and Biosystems Engineering, 29(2), 99–108. doi:10.1007/s00449-006-0057-0
  • Cermak, T., Doyle, E.L., Christian, M., Wang, L., Zhang, Y.,Schmidt, C., … Voytas, D.F. (2011). Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research, 39(12), e82.
  • Chase-Topping, M., Gally, D., Low, C., Matthews, L., Woolhouse, M. (2008). Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157. Nature Reviews Microbiology, 6(12):904-12. doi: 10.1038/nrmicro2029
  • Cornish-Bowden, A. (2012). Fundamentals of Enzyme Kinetics (4th ed.). Weinheim, Germany: Wiley-Blackwell.
  • De Lange, O., Schreiber, T., Schandry, N., Radeck, J., Braun, K. H., Koszinowski, J., … Lahaye, T. (2013). Breaking the DNA-binding code of Ralstonia solanacearum TAL effectors provides new possibilities to generate plant resistance genes against bacterial wilt disease. The New Phytologist, 199(3), 773–86. doi:10.1111/nph.12324
  • Dörner, M. H., Salfeld, J., Will, H., Leibold, E. A., Vass, J. K., & Munro, H. N. (1985). Structure of human ferritin light subunit messenger RNA: comparison with heavy subunit message and functional implications. Proceedings of the National Academy of Sciences of the United States of America, 82(10), 3139–43. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=397730&tool=pmcentrez&rendertype=abstract
  • Engler, C., Kandzia, R., & Marillonnet, S. (2008). A one pot, one step, precision cloning method with high throughput capability. PLoS ONE, 3(11), e3647. doi: 10.1371/journal.pone.0003647
  • Feng, P., & Lampel, K.A. (1994). Genetic analysis of uidA expression in enterohaemorrhagic Escherichia coli serotype O157:H7. Microbiology, 140, 2101-2107.
  • Fortin, N.Y., Mulchandani, A., & Chen, W. (2001). Use of real-time polymerase chain reaction and molecular beacons for the detection of Escherichia coli O157:H7. Analytical Biochemistry , 289(2), 281-8.
  • Gibson, D.G., Young, L., Chuang, R.Y., Venter, J.C., Hutchison, C.A. 3rd, Smith, H.O. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods, 6(5), 343-5. doi: 10.1038/nmeth.1318
  • Gill, A., Martinez-Perez, A., McIIwham, S., & Blais, B. (2012). Development of a method for the detection of verotoxin-producing Escherichia coli in food. Journal of Food Protection, 75(5), 827-837.
  • He, Y., Zhang, S., Zhang, X., Baloda, M., Gurung, A. S., Xu, H., … Liu, G. (2011). Ultrasensitive nucleic acid biosensor based on enzyme-gold nanoparticle dual label and lateral flow strip biosensor. Biosensors & Bioelectronics, 26(5), 2018–24. doi:10.1016/j.bios.2010.08.079
  • Huang, Z. (1991). Kinetic fluorescence measurement of fluorescein di-.beta.-D-galactoside hydrolysis by .beta.-galactosidase: intermediate channeling in stepwise catalysis by a free single enzyme. Biochemistry, 30(35), 8535–8540. doi:10.1021/bi00099a006
  • Huh, Y. S., & Kim, I. H. (2003). Purification of fusion ferritin from recombinant E. coli using two-step sonications. Biotechnology Letters, 25(12), 993–6. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/12889837
  • Ingrassia, R., Gerardi, G., Biasiotto, G., & Arosio, P. (2006). Mutations of ferritin H chain C-terminus produced by nucleotide insertions have altered stability and functional properties. Journal of Biochemistry, 139(5), 881–5. doi:10.1093/jb/mvj101
  • Jeon, S.J., Elzo, M., DiLorenzo, N., Lamb, G.C., & Jeong, K.C. (2013). Evaluation of animal genetic and physiological factors that affect the prevalence of Escherichia coli O157 in Cattle. PLoS ONE, 8(2), e55728. doi:10.1371/journal.pone.0055728
  • Jordan, V. C., Caplan, M. R., & Bennett, K. M. (2010). Simplified synthesis and relaxometry of magnetoferritin for magnetic resonance imaging. Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 64(5), 1260–6. doi:10.1002/mrm.22526
  • Kim, S.-E., Ahn, K.-Y., Park, J.-S., Kim, K. R., Lee, K. E., Han, S.-S., & Lee, J. (2011). Fluorescent ferritin nanoparticles and application to the aptamer sensor. Analytical Chemistry, 83(15), 5834–43. doi:10.1021/ac200657s
  • Lee, J., Kim, S. W., Kim, Y. H., & Ahn, J. Y. (2002). Active human ferritin H/L-hybrid and sequence effect on folding efficiency in Escherichia coli. Biochemical and Biophysical Research Communications, 298(2), 225–9. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/12387819
  • Levi, S., Corsi, B., Rovida, E., Cozzi, A., Santambrogio, P., Albertini, A., & Arosio, P. (1994). Construction of a ferroxidase center in human ferritin L-chain. The Journal of Biological Chemistry, 269(48), 30334–9. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7982945
  • Li, B., & Chen, J.Q. (2012). Real-time PCR methodology for selective detection of viable Escherichia coli O157:H7 cells by targeting Z3276 as a genetic marker. Applied and Environmental Microbiology, 78(15):5297-304. doi: 10.1128/AEM.00794-12
  • Li, D., Yang, M., Hu, J., Zhang, Y., Chang, H., & Jin, F. (2008). Determination of penicillin G and its degradation products in a penicillin production wastewater treatment plant and the receiving river. Water Research, 42(1-2), 307–17. doi:10.1016/j.watres.2007.07.016
  • Lohsse, A., Ullrich, S., Katzmann, E., Borg, S., Wanner, G., Richter, M., … Schüler, D. (2011). Functional analysis of the magnetosome island in Magnetospirillum gryphiswaldense: the mamAB operon is sufficient for magnetite biomineralization. PloS ONE, 6(10), e25561. doi:10.1371/journal.pone.0025561
  • Luzzago, A., & Cesareni, G. (1989). Isolation of point mutations that affect the folding of the H chain of human ferritin in E. coli. The EMBO Journal, 8(2), 569–76. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=400843&tool=pmcentrez&rendertype=abstract
  • Maloy, S., Stewart, V., and Taylor, R. (1996). Genetic Analysis of Pathogenic Bacteria. New York: Cold Spring Harbor Laboratory Press.
  • Meckler, J.F., Bhakta, M.S., Kim, M.S., Ovadia, R., Habrian, C.H., Zykovich, A., ... Baldwin, E.P. (2013). Quantitative analysis of TALE-DNA interactions suggests polarity effects. Nucleic Acids Research, 41(7), 4118–28. doi:10.1093/nar/gkt085
  • Mercer, A.C., Gaj, T. Fuller, R.P., & Barbas, C.F. 3rd (2012). Chimeric TALE recombinases with programmable DNA sequence specificity. Nucleic Acids Research, 40(21), 11163-72. doi: 10.1093/nar/gks875
  • Metelkin, E. A., Lebedeva, G. V., Goryanin, I. I., & Demin, O. V. (2009). A kinetic model of Escherichia coli β-galactosidase. Biophysics, 54(2), 156–162. doi:10.1134/S0006350909020067
  • Miller, J.C., Tan, S., Qiao, G., Barlow, K.A., Wang, J., Xia, D.F., Rebar, E.J. (2011). A TALE nuclease architecture for efficient genome editing. Nature Biotechnology, 29(2), 143-148.
  • Mussolino, C., & Cathomen, T. (2012). TALE nucleases: tailored genome engineering made easy. Current Opinion in Biotechnology, 23(5), 644–50. doi:10.1016/j.copbio.2012.01.013
  • Naito, M., Iwahori, K., Miura, A., Yamane, M., & Yamashita, I. (2010). Circularly polarized luminescent CdS quantum dots prepared in a protein nanocage. Angewandte Chemie International Edition, 49(39), 7006-7009.
  • Nakajima, Y., & Ohmiya, Y. (2010). Bioluminescence assays: multicolor luciferase assay, secreted luciferase assay and imaging luciferase assay. Expert Opinion on Drug Discovery, 5(9), 835–849. doi:10.1517/17460441.2010.506213
  • Parker, M. J., Allen, M. A., Ramsay, B., Klem, M. T., Young, M., Douglas, T. (2008) Expanding the temperature range of biomimetic synthesis using a ferritin from the hyperthermophile Pyrococcus furiosus. Chemistry of Materials, 20(4), 1541–1547. doi:10.1021/cm702732x
  • Perna, N. T., Plunkett, G., Burland, V., Mau, B., Glasner, J. D., Rose, D. J., ... Blattner, F. R. (2000) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Letters to Nature. 409, 529-533. doi:10.1038/35054089
  • Pfleger, K. D. G., & Eidne, K. A. (2006). Illuminating insights into protein-protein interactions using bioluminescence resonance energy transfer (BRET). Nature Methods, 3(3), 165–174. doi:10.1038/nmeth841
  • Piston, D. W., & Kremers, G.-J. (2007). Fluorescent protein FRET: the good, the bad and the ugly. Trends in Biochemical Sciences, 32(9), 407–414. doi:10.1016/j.tibs.2007.08.003
  • Santambrogio, P., Levi, S., Cozzi, A., Rovida, E., Albertini, A., & Arosio, P. (1993). Production and characterization of recombinant heteropolymers of human ferritin H and L chains. The Journal of Biological Chemistry, 268(17), 12744–8. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8509409
  • Streubel, J., Blücher, C., Landgraf, A., & Boch, J. (2012). TAL effector RVD specificities and efficiencies. Nature Biotechnology, 30(7), 593–5. doi:10.1038/nbt.2304
  • USDA Laboratory Guidebook. (2012) FSIS Procedure for the Use of Escherichia coli O157:H7 Screening Tests for Meat Products and Carcass and Environmental Sponges. Retrieved from http://www.fsis.usda.gov/wps/wcm/connect/6d1b7f96-1db7-4b0d-8081-e861206aedab/MLG-5A.pdf?MOD=AJPERES
  • Watt, G. D., Kim, J.-W., Zhang, B., Miller, T., Harb, J. N., Davis, R. C., & Choi, S. H. (2012). A protein-based ferritin bio-nanobattery. Journal of Nanotechnology, 2012, 1–9. doi:10.1155/2012/516309
  • Wong, K. K. W., Douglas, T., Gider, S., Awschalom, D. D., & Mann, S. (1998). Biomimetic synthesis and characterization of magnetic proteins (magnetoferritin). Chemistry of Materials, 10(1), 279–285. doi:10.1021/cm970421o
  • Yoshitomi, K.J., Jinneman, K.C., & Weagant, S.D. (2003). Optimization of a 3'-minor groove binder-DNA probe targeting the uidA gene for rapid identification of Escherichia coli O157:H7 using real-time PCR. Molecular and Cellular Probes, 17(6):275-80.
  • Yoshitomi, K.J, Zapata, R. Jinneman, K.C., Weagant, S.D., & Fedio, W. (2012). Recovery of E. coli O157 strains after exposure to acidification at pH 2. Letters in Applied Microbiology, 54(6), 499-503. doi: 10.1111/j.1472-765X.2012.03250.x

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