Andrew Gracey

Summary Statement of Research Interests

The primary focus of Andrew Gracey’s research is to understand the effect of factors such as temperature, oxygen concentration, and salinity on the physiological processes of animals, and how these organism-environment interactions affect performance, survival and distribution.  His studies explore the nature of adaptive responses and the evolutionary development of stress tolerance in a range of species spanning multiple phyla, including freshwater and marine fish, nematode worms, bivalve mollusks and hibernating mammals.  Since phenotype results ultimately from the combined expression of genes and gene complexes, understanding patterns of gene expression evoked during environmental change yields insights regarding the mechanisms underlying adaptation from the cellular to the whole organism level.  A key tool deployed in his research is the measurement of mRNA transcript levels by microarray hybridization.  The microarray-based approach monitors the expression of many thousands of genes simultaneously, providing a broad view of the transcriptional changes that accompany alterations in physiological state.  The utility of this approach is that it allows hitherto unknown responses to be discovered and new hypotheses to be formed.  The identification of differentially expressed genes in response to environmental change is thus an important first step in understanding the role of the genome within the complex natural history of an organism. 

Encyclopedia Article

• Gracey, A. Y. (2011). Global gene expression profiling in fish. (Anthony Farrell, Ed.).2055-2060. Vol. 3 Amsterdam: Encyclopedia of Fish Physiology: From Genome to Environment (published by Elsevier).

Journal Article

• Mandic, M., Ramon, M., Gerstein, A., Gracey, A. Y., Richards, J. (2018). Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpins. BMC Evol. Biol..
• Connor, K. M., Gracey, A. Y. (2016). Transcriptional and metabolomic characterization of spontaneous metabolic cycles in Mytilus californianus under subtidal conditions. Mar. Genomics. Vol. 30, pp. 35-41.
• Connor, K. M., Sung, A., Garcia, N., Gracey, A. Y., German, D. (2016). Modulation of digestive physiology and biochemistry in Mytilus californianus in response to feeding level acclimation and microhabitat. Biol. Open. Vol. 5, pp. 1200-1210.
• Hedgecock, D., Shin, G., Gracey, A. Y., Den Berg, D. V., Samanta, M. P. (2015). Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds. G3 (Bethesda). Vol. 5 (102015/08/08), pp. 2007-19.
• Lockwood, B. L., Connor, K. M., Gracey, A. Y. (2015). The environmentally tuned transcriptomes of Mytilus mussels. J Exp Biol. Vol. 218 (Pt 122015/06/19), pp. 1822-33.
• Rodriguez, D., Sanders, E., Farell, K., Langenbacher, A., Taketa, D., Hopper, M., Kennedy, M., Gracey, A. Y., De Tomaso, A. (2014). Analysis of the basal chordate Botryllus schlosseri reveals a set of genes associated with fertility. BMC Genomics. Vol. 15, pp. 1183.
• Mandic, M., Ramon, M. L., Gracey, A. Y., Richards, J. G. (2014). Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins. Mol Ecol. Vol. 23 (242014/11/06), pp. 6091-103.
• Sakamaki, K., Shimizu, K., Iwata, H., Imai, K., Satou, Y., Funayama, N., Nozaki, M., Yajima, M., Nishimura, O., Higuchi, M., Chiba, K., Yoshimoto, M., Kimura, H., Gracey, A. Y., Shimizu, T., Tomii, K., Gotoh, O., Akasaka, K., Sawasaki, T., Miller, D. J. (2014). The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution. Mol Biol Evol. Vol. 31 (122014/09/11), pp. 3282-301.
• Nydam, M. L., Netuschil, N., Sanders, E., Langenbacher, A., Lewis, D. D., Taketa, D. A., Marimuthu, A., Gracey, A. Y., De Tomaso, A. W. (2013). The candidate histocompatibility locus of a Basal chordate encodes two highly polymorphic proteins. PLoS One. Vol. 8 (62013/07/05), pp. e65980.
• Connor, K. L., Gracey, A. Y. (2012). High resolution analysis of metabolic cycles in the intertidal mussel Mytilus californianus. American Journal of Physiology – Regulatory, Integrative, and Comparative Physiology. Vol. 302 (Oct 19th 2011 [Epub ahead of print]), pp. R103-R111.
• Gracey, A. Y., Lee, B., Higashi, R., Fan, T. (2011). Hypoxia-induced mobilization of triglycerides in the euryoxic goby, Gillichthys mirabilis. Journal of Experimental Biology. Vol. 214, pp. 3005-3012.
• Connor, K. M., Gracey, A. Y. (2011). Circadian cycles are the dominant transcriptional rhythm in the intertidal mussel Mytilus californianus. Proceedings of the National Academy of Sciences USA. Vol. 108, pp. 16110-16115.
• Chaney, M. L., Gracey, A. Y. (2011). Mass mortality in Pacific oysters is associated with a specific gene expression signature. Molecular Ecology. Vol. 20, pp. 2942-2954.
• Li, W., Gracey, A. Y., Vieira Mello, L., Brass, A., Cossins, A. R. (2009). ExprAlign – the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles. BMC Genomics. Vol. 10 (560)
• Fedorov, V., Goropashnaya, A. V., Tøien, O., Stewart, N. C., Gracey, A. Y., Chang, C., Qin, S., Pertea, G., Quackenbush, J., Showe, L. C., Showe, M. K., Boyer, B. B., Barnes, B. M. (2009). Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus). Physiological Genomics. Vol. 10 (37), pp. 108-118.
• Gracey, A. Y., Chaney, M. L., Boomhower, J. P., Tyburczy, W. R., Connor, K., Somero, G. N. (2008). Rhythms of Gene Expression in a Fluctuating Intertidal Environment. Current Biology. Vol. 18 (19), pp. 1501-1507.
• Evans, H., De Tomaso, A., Quail, M., Rogers, J., Gracey, A. Y., Cossins, A. R., Berenbrink, M. (2008). Ancient and modern duplication events and the evolution of stearoyl-CoA desaturases in teleost fishes. Physiological Genomics. Vol. 35, pp. 18-29.
• Gracey, A. Y. (2008). The Gillichthys mirabilis Cooper array: a platform to investigate the molecular basis of phenotypic plasticity. Journal of Fish Biology. Vol. 72, pp. 2118-2132.
• Williams, D. R., Li, W., Hughes, M. A., Gonzalez, S. F., Vernon, C., Vidal, M. C., Jeney, Z., Jeney, G., Dixon, P., McAndrew, B., Bartfai, R., Oban, L., Trudeau, V., Rogers, J., Matthews, L., Fraser, E. J., Gracey, A. Y., Cossins, A. R. (2008). Genomic resources and microarrays for the common carp Cyprinus carpio L. Journal of Fish Biology. Vol. 72, pp. 2095-2117.
• Olohan, L. A., Li, W., Wulff, T., Jarmer, H., Gracey, A. Y., Cossins, A. R. (2008). Detection of anoxia-responsive genes in cultured cells of the rainbow trout Oncorhynchus mykiss (Walbaum), using an optimized, genome-wide oligoarray. Journal of Fish Biology. Vol. 72, pp. 2170-2186.
• McLean, L., Young, I. S., Doherty, M. K., Robertson, D. H., Cossins, A. R., Gracey, A. Y., Beynon, R. B., Whitfield, P. D. (2007). Global Cooling: Cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics. Vol. 15, pp. 2667-81.
• Ahdesmaki, M., Lahdesmaki, H., Gracey, A., Schmulevich, L., Yli-Harja, O. (2007). Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics. Vol. 8, pp. 233.
• Gracey, A. Y. (2007). Interpreting physiological responses to environmental change through gene expression profiling. Journal of Experimental Biology. Vol. 210, pp. 1593-1601.
• Haywood, S. A., Murray, P. A., Govan, G. G., Gracey, A. Y., Cossins, A. R. (2007). An explicit test of the phospholipid saturation hypothesis of acquired cold tolerance in Caenorhabditis elegans. Proceedings of the National Academy of Sciences USA. Vol. 104, pp. 5489-5494.
• Buckley, B. A., Gracey, A. Y., Somero, G. N. (2006). The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis. Journal of Experimental Biology. Vol. 209, pp. 2660-2667.
• Cossins, A. R., Fraser, E. J., Hughes, M., Gracey, A. Y. (2006). Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity. Journal of Experimental Biology. Vol. 209, pp. 2328-2336.
• Fraser, E. J., Vieira de Mello, L., Ward, D., Rees, H. R., Williams, D., Gracey, A. Y., Cossins, A. R. (2006). Hypoxia-inducible myoglobin expression in nonmuscle tissues. Proceedings of the National Academy of Sciences USA. Vol. 103, pp. 2977-2981.
• Williams, D., Epperson, L., Li, W., Hughes, M., Taylor, R. R., Rogers, J., Martin, S., Cossins, A. R., Gracey, A. Y. (2005). Seasonally hibernating phenotype assessed through transcript screening. Physiological Genomics. Vol. 24, pp. 13-22..
• Gracey, A. Y., Fraser, E. J., Li, W., Fang, Y., Taylor, R. R., Rogers, J., Brass, A. (2004). Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proceedings of the National Academy of Sciences USA. Vol. 101, pp. 16970-16975.
• Gracey, A. Y., Cossins, A. R. (2003). Application of microarray technology in environmental and comparative physiology. Annual Review of Physiology. Vol. 65, pp. 231-59.
• Cossins, A. R., Murray, P. A., Gracey, A. Y., Logue, J., Polley, S., Caddick, M., Brooks, S., Postle, T., Maclean, N. (2002). The role of desaturases in cold-induced lipid restructuring. Biochemical Society Transactions. Vol. 30(6), pp. 1082-6.
• Gracey, A. Y., Troll, J., Somero, G. N. (2001). Hypoxia-induced expression profiling in the euryoxic fish Gillichthys mirabilis. Proceedings of the National Academy of Sciences USA. Vol. 94, pp. 1993-1998.
• Tiku, P. E., Gracey, A. Y., Macartney, A. I., Beynon, R. B., Cossins, A. R. (1996). Cold-inducible expression of desaturase by transcriptional and post-translational mechanisms. Science. Vol. 271, pp. 815-818.

Professional Memberships

• Sigma Xi, 09/13/2006 –