Global gene response in Saccharomyces cerevisiae exposed to silver nanoparticles

Applied Biochemistry and Biotechnology

Volumn 164, Issue 8, 2011, Pages 1278-1291

  Niazi, Javed H ^a,b,c   Sang, Byoung In ^b,d   Kim, Yeon Seok ^a   Gu, Man Bock ^a  

^a Korea University   (South Korea)

^b Korea Institute of Science and Technology   (South Korea)

^c SABANCI UNIVERSITY   (Turkey)

^d Hanyang University   (South Korea)

Author keywords

Microarray; Nanotoxicity; Silver nanoparticles; Transcriptome analysis; Yeast genome analysis

Indexed keywords

CHEMICAL STIMULI; DIFFERENTIAL EXPRESSIONS; ECOTOXICITY; GENE RESPONSE; HIGH RESISTANCE; ION TRANSPORTS; METALLOPROTEIN; NANOTOXICITY; PRINCIPAL COMPONENTS; SILVER NANOPARTICLES; SIZE RANGES; TRANSCRIPTOME ANALYSIS; TRANSCRIPTOME PROFILES; TRANSPORT PROCESS; YEAST GENOME ANALYSIS; YEAST SACCHAROMYCES CEREVISIAE;

CLUSTER ANALYSIS; GENE EXPRESSION; IONS; NANOPARTICLES; PRINCIPAL COMPONENT ANALYSIS; YEAST;

SILVER;

COPPER; METALLOPROTEIN; PROTEIN CUP1 1; PROTEIN CUP1 2; SACCHAROMYCES CEREVISIAE PROTEIN; SILVER NANOPARTICLE; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL STRESS; CONTROLLED STUDY; CYTOTOXICITY; DOWN REGULATION; EXPOSURE; FUNGAL GENE; GENE EXPRESSION; GENE FUNCTION; GENOME; HOMEOSTASIS; ION TRANSPORT; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOMICS; TRANSMISSION ELECTRON MICROSCOPY; TRANSPORT AT THE CELLULAR LEVEL; UPREGULATION;

CATIONS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; METAL NANOPARTICLES; METALLOTHIONEIN; MUTAGENICITY TESTS; PRINCIPAL COMPONENT ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SILVER;

SACCHAROMYCES CEREVISIAE;

EID: 80052022299     PISSN: 02732289     EISSN: 15590291     Source Type: Journal    
DOI: 10.1007/s12010-011-9212-4     Document Type: Article

References (53)

1. Somorjai, G. A. (2004). Nature, 430(7001), 730.
2. Doraiswamy, N., & Marks, L. D. (1996). Surface Science, 348(1-2), L67-L69.
3. De Wild, M., Berner, S., Suzuki, H., Ramoino, L., Baratoff, A., & Jung, T. A. (2003). Annals of the New York Academy of Sciences, 1006, 291-305.
4. Brooking, J., Davis, S. S., & Illum, L. (2001). Journal of Drug Targeting, 9(4), 267-279.
5. Morones, J. R., Elechiguerra, J. L., Camacho, A., Holt, K., Kouri, J. B., Ramirez, J. T., et al. (2005). Nanotechnology, 16, 2346-2353.
6. Braydich-Stolle, L., Hussain, S., Schlager, J. J., & Hofmann, M. C. (2005). Toxicological Sciences, 88 (2), 412-419.
7. Ding, L., Stilwell, J., Zhang, T., Elboudwarej, O., Jiang, H., Selegue, J. P., et al. (2005). Nano Letters, 5 (12), 2448-2464.
8. Borm, P. J., Robbins, D., Haubold, S., Kuhlbusch, T., Fissan, H., Donaldson, K., et al. (2006). Part Fibre Toxicol, 3, 11.
9. Van Hoecke, K., Quik, J. T., Mankiewicz-Boczek, J., De Schamphelaere, K. A., Elsaesser, A., Van der Meeren, P., et al. (2009). Environmental Science & Technology, 43(12), 4537-4546.
10. Moore, M. N. (2006). Environment International, 32, 967-976.
11. Oberdorster, E., Zhu, S., Blickley, T.M., McClellan-Green, P., & Haasch, M. L. (2006). Carbon, 44, 1112-1120.
12. Oberdorster, G., Stone, V., & Donaklson, K. (2007). Nanotoxicology, 1, 2-25.
13. Hwang, E. T., Lee, J. H., Chae, Y. J., Kim, Y. S., Kim, B. C., Sang, B. I., et al. (2008). Small, 4(6), 746-750.
14. Heinlaan, M., Ivask, A., Blinova, I., Dubourguier, H. C., & Kahru, A. (2008). Chemosphere, 71, 1308-1316.
15. Fang, J., Lyon, D. Y., Wiesner, M. R., Dong, J., & Alvarez, P. J. (2007). Environmental Science & Technology, 41(7), 2636-2642.
16. Oberdorster, G., Oberdorster, E., & Oberdorster, J. (2005). Environmental Health Perspectives, 113(7), 823-839.
17. SCENIHR. (2006). Available at: http://ec.europa.eu/health/opinions2/en/ nanotechnologies/l-3/9-conclusion.htm.
18. Guggenbichler, J. P., Boswald, M., Lugauer, S., & Krall, T. (1999). Infection, 27(Suppl 1), S16-S23.
19. Kearney, J. N., Arain, T., & Holland, K. T. (1988). The Journal of Hospital Infection, 11(1), 68-76.
20. Solioz, M., & Odermatt, A. (1995). The Journal of Biological Chemistry, 270(16), 9217-9221.
21. Solioz, M., & Vulpe, C. (1996). Trends in Biochemical Sciences, 21(7), 237-241.
22. Jin, Y. H., Dunlap, P. E., McBride, S. J., Al-Refai, H., Bushel, P. R., & Freedman, J. H. (2008). PLoS Genetics, 4(4), e1000053.
23. Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., et al. (2004). Genome Biology, 5(10), R80.1-R80.16.
24. Team, R. D. C. R. (2007). A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
25. Smyth, G. K. (2005). Limma: Linear models for microarray data. In R. Gentleman VC, S. Dudoit, R. Irizarry, & W. Huber (Eds.), Bioinformatics and computational biology solutions using R and bioconductor (pp. 397-420). New York: Springer.
26. Smyth, G. K., & Speed, T. (2003). Methods, 31(4), 265-273.
27. Tusher, V. G., Tibshirani, R., & Chu, G. (2001). Proceedings of the National Academy of Sciences of the United States of America, 98(9), 5116-5121.
28. Zupan, B., & Demsar, J. (2008). Clinics in Laboratory Medicine, 28(1), 37-54. vi.
29. Saldanha, A. J. (2004). Bioinformatics, 20(17), 3246-3248.
30. De Hoon, M. J., Imoto, S., Nolan, J., & Miyano, S. (2004). Bioinformatics, 20(9), 1453-1454.
31. Raychaudhuri S., Stuart J., Altman R. (2000). Principal components analysis to summarize microarray experiments: Application to sporulation time series. In 2000: NIH Public Access (p. 455).
32. Li, L., & Kaplan, J. (2004). The Journal of Biological Chemistry, 279(32), 33653-33661.
33. Winge, D. R. (1998). Progress in Nucleic Acid Research and Molecular Biology, 58, 165-195.
34. Parveen, M., Hasan, M. K., Takahashi, J., Murata, Y., Kitagawa, E., Kodama, O., et al. (2004). The Journal of Antimicrobial Chemotherapy, 54(1), 46-55.
35. Mandala, S. M., Thornton, R., Tu, Z., Kurtz, M. B., Nickels, J., Broach, J., et al. (1998). Proceedings of the National Academy of Sciences of the United States of America, 95(1), 150-155.
36. Skrzypek, M. S., Nagiec, M. M., Lester, R. L., & Dickson, R. C. (1999). Journal of Bacteriology, 181 (4), 1134-1140.
37. Hurlimann, H. C., Stadler-Waibel, M., Werner, T. P., & Freimoser, F. M. (2007). Molecular Biology of the Cell, 18(11), 4438-4445.
38. Varela, J. C., van Beekvelt, C., Planta, R. J., & Mager, W. H. (1992). Molecular Microbiology, 6(15), 2183-2190.
39. Kapteyn, J. C., ter Riet, B., Vink, E., Blad, S., De Nobel, H., Van Den Ende, H., et al. (2001). Molecular Microbiology, 39(2), 469-479.
40. Graybill, E. R., Rouhier, M. F., Kirby, C. E., & Hawes, J. W. (2007). Archives of Biochemistry and Biophysics, 465(1), 26-37.
41. Luikenhuis, S., Perrone, G., Dawes, I. W., & Grant, C. M. (1998). Molecular Biology of the Cell, 9(5), 1081-1091.
42. Riggle, P. J., & Kumamoto, C. A. (2000). Journal of Bacteriology, 182(17), 4899-4905.
43. Odermatt, A., Krapf, R., & Solioz, M. (1994). Biochemical and Biophysical Research Communications, 202(1), 44-48.
44. Butt, T. R., Sternberg, E., Herd, J., & Crooke, S. T. (1984). Gene, 27(1), 23-33.
45. Yuan, D. S., Stearman, R., Dancis, A., Dunn, T., Beeler, T., & Klausner, R. D. (1995). Proceedings of the National Academy of Sciences of the United States of America, 92(7), 2632-2636.
46. Lenburg, M. E., & O'Shea, E. K. (1996). Trends in Biochemical Sciences, 21(10), 383-387.
47. Yoshihisa, T., & Anraku, Y. (1989). Biochemical and Biophysical Research Communications, 163(2),48.
48. Amoroso, G., Morell-Avrahov, L., Muller, D., Klug, K., & Sultemeyer, D. (2005). Molecular Microbiology, 56(2), 549-558.
49. Gotz, R., Gnann, A., & Zimmermann, F. K. (1999). Yeast, 15(10A), 855-864.
50. Protchenko, O., Ferea, T., Rashford, J., Tiedeman, J., Brown, P. O., Botstein, D., et al. (2001). The Journal of Biological Chemistry, 276(52), 49244-49250.
51. Haurie, V., Boucherie, H., & Sagliocco, F. (2003). The Journal of Biological Chemistry, 278(46), 45391-45396.
52. De Freitas, J., Wintz, H., Kim, J. H., Poynton, H., Fox, T., & Vulpe, C. (2003). Biometals, 16(1), 185-197.
53. Lubick, N. (2008). Environmental Science & Technology, 42(23), 8617.