Abstract
In recent years, molecular biology has increasingly focused on how cellular effectors are modulated by the environment and, in turn, modulate each other to control cellular functions. In the opioid field, we concern ourselves both with signaling mechanisms within cells and the functions of neural circuitry in mediating the behavioral effects of opioids. All of these mechanisms identified to date have proven to be extremely complex, suggesting that behavioral outcomes mediated by opioids are dependent on the interactions of multiple gene products. Opioid-mediated behavioral outcomes such as tolerance, dependence, and addiction may reflect problems in the regulation of complex biological and emotional functions. From this, it follows that slight alterations in the expression or function of individual genes that still fall within the “normal” range could lead to pathological effects or behaviors. Genetic polymorphisms cause changes in the coding and regulatory regions of genes. Thus, in addition to changes in levels of protein expression, encoded proteins may have slightly different functions or undergo differential regulation in cells.
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References
Ramsay, G. (1998) DNA chips: State-of-the-art. Nature Biotechnol. 16, 40–44.
Watson, S. J. and Akil, H. (1999) Gene chips and arrays revealed: a primer on their power and their uses. Biol. Psych. 45, 533–543.
Marshall, A. and Hodgson, J. (1998) DNA chips: An array of possibilities. Nature Biotechnol. 16, 27–31.
Graves, D. J. (1999) Powerful tools for genetic analysis come of age. Tibtech 17, 127–134.
Zirlinger, M., Kreiman, G., and Anderson, D. J. (2001) Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei. Proc. Natl. Acad. Sci. USA 98, 5270–5275.
Sandberg, R., Yasuda, R., Pankratz, D., Carter, T., Del Rio, J., Wodicka, L., et al. (2000) Regional and stran-specific gene expression mapping in the adult mouse brain. Proc. Natl. Acad. Sci. USA 97, 11,038–11,043.
Hess, K. R., Zhang, W., Baggerly, K. A., Stivers, D. N., and Coombes, K. R. (2001) Microarrays: handling the deluge of data and extracting reliable information. Trends Biotechnol. 19, 463–468.
Wu, T. (2001) Analysing gene expression data from DNA microarrays to identify candidate genes. J. Pathol. 195, 53–65.
Brazma, A. and Vilo, J. (2000) Gene expression data analysis. FEBS Lett. 480, 17–24.
Lee, M., Kuo, F., Whitmore, G., and Sklar, J. (200) Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97, 9834–9839.
Livesey, F. and Hunt, S. (1996) Identifying changes in gene expression in the nervous system: mRNA differential display. Trends Neurosci. 19, 84–88.
Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995) Serial analysis of gene expression. Science 270, 484–487.
Velculescu, V. E. (1999) Essay: Amersham Pharmacia Biotech & Science prize. Tantalizing transcriptomes—SAGE and its use in global gene expression analysis. Science 286, 1491–1492.
Sagerstrom, C. G., Sun, B. I., and Sive, H. L. (1997). Subtractive cloning: past, present, and future. Ann. Rev. Biochem. 66, 751–783.
Williams, K. L. and Hochstrasser, D. F. (1997) Introduction to the proteome. In Proteome Research: New Frontiers in Functional Genomics (Wilkins, M. R., Williams, K. L., Appel, R. D. and Hochstrasser, D. F., eds.), Springer, Berlin pp. 1–12.
Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19, 1720–1730.
Anderson, L. and Seilhamer, J. (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18, 533–537.
Chambers, G., Lawrie, L., Cash, P., and Murray, G. I. (2000) Proteomics: a new approach to the study of disease. J. Pathol. 192, 280–288.
Godovac-Zimmermann, J. and Brown, L. R. (2001) Perspectives for mass spectrometry and functional proteomics. Mass Spectrom. Rev. 20, 1–57.
Naaby-Hansen, S., Waterfield, M. D., and Cramer, R. (2001) Proteomics—post-genomic cartography to understand gene function. Trends Pharmacol. Sci. 22, 376–384.
Herbert, B. (1999) Advances in protein solubilisation for two-dimensional electrophoresis. Electrophoresis 20, 660–663.
Gorg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., et al. (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21, 1037–1053.
Molloy, M. P., Herbert, B. R., Williams, K. L., and Gooley, A. A. (1999) Extraction of Escherichia coli proteins with organic solvents prior to two-dimensional electrophoresis. Electrophoresis 20, 701–704.
Hastie, N. D. and Bishop, J. O. (1976) The expression of three abundance classes of messenger RNA in mouse tissues. Cell 9, 761–774.
Herbert, B. R., Harry, J. L., Packer, N. H., Gooley, A. A., Pedersen, S. K., and Williams, K. L. (2001) What place for polyacrylamide in proteomics? Trends Biotechnol. 19, S3–9.
Corthals, G. L., Wasinger, V. C., Hochstrasser, D. F., and Sanchez, J. C. (2000) The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 21, 1104–1115.
Pasquali, C., Fialka, I. and Huber, L. A. (1999) Subcellular fractionation, electromigration analysis and mapping of organelles. J. Chromatogr. B. Biomed. Sci. Appl. 722, 89–102.
Molloy, M. P., Herbert, B. R., Walsh, B. J., Tyler, M. I., Traini, M., Sanchez, J. C., et al. (1998) Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 19, 837–844.
Klose, J. and Kobalz, U. (1995) Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16, 1034–1059.
Herbert, B. and Righetti, P. G. (2000) A turning point in proteome analysis: sample prefractionation via multicompartment electrolyzers with isoelectric membranes. Electrophoresis 21, 3639–3648.
Husi, H., Ward, M. A., Choudhary, J. S., Blackstock, W. P., and Grant, S. G. (2000) Proteomic analysis of NMDA receptor-adhesion protein signaling complexes. Natl. Neurosci. 3, 661–669.
Issaq, H. J. (2001) The role of separation science in proteomics research. Electrophoresis 22, 3629–3638.
Washburn, M. P., Wolters, D., and Yates, J. R., 3rd. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242–247.
Moseley, M. A. (2001) Current trends in differential expression proteomics: isotopically coded tags. Trends Biotechnol. 19, S10–16.
Lauber, W. M., Carroll, J. A., Dufield, D. R., Radabaugh, M. R., and Malone, J. P. (2001) Mass spectrometry compatibility of two-dimensional gel protein stains. Electrophoresis 22, 906–918.
Yan, J. X., Harry, R. A., Spibey, C., and Dunn, M. J. (2000) Postelectrophoretic staining of proteins separated by two-dimensional gel electrophoresis using SYPRO dyes. Electrophoresis 21, 3657–3665.
Miller, M. D., Jr., Acey, R. A., Lee, L. Y., and Edwards, A. J. (2001) Digital imaging considerations for gel electrophoresis analysis systems. Electrophoresis 22, 791–800.
Chalmers, M. J. and Gaskell, S. J. (2000) Advances in mass spectrometry for proteome analysis. Curr. Opin. Biotechnol. 11, 384–390.
Yates, J. R., 3rd. (1998) Mass spectrometry and the age of the proteome. J. Mass. Spectrom. 33, 1–19.
Fenyo, D. (2000) Identifying the proteome: software tools. Curr. Opin. Biotechnol. 11, 391–395.
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Moulédous, L., Gutstein, H.B. (2003). Gene Arrays and Proteomics. In: Pan, Z.Z. (eds) Opioid Research. Methods in Molecular Biology™, vol 84. Humana Press. https://doi.org/10.1385/1-59259-379-8:141
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DOI: https://doi.org/10.1385/1-59259-379-8:141
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Print ISBN: 978-1-58829-059-5
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