Graduation date: 2007The extent to which responses to stress are maladaptive or adaptive to the long-term survival of fish remains to be better understood. The aim of this study was to identify differentially expressed genes in the livers of rainbow trout, Oncorhynchus mykiss, responding to an experimental stressor. Gene expression responses were measured using an oligonucleotide microarray specific for Oncorhynchus mykiss, to highlight genes responding to a stressor and to serve as a basis for hypothesis development. We conducted replicate experiments at two different times. In both experiments, fish exposed to a three-hour stressor were compared to control (unstressed) fish. In the second experiment, there were additional treatments of fish that were exposed to only a half-hour of stress and of fish sampled 21 hours after experiencing a three-hour stressor. This 21 hour post-stress treatment was a means to study gene expression during recovery from stress. Plasma cortisol was measured to document the physiological stress response of the fish. Real-time PCR (qPCR) of candidate genes was used to validate the microarray findings. In both experiments the microarray revealed many genes with differential expression after three hours of stress. The genes we report as differentially expressed met a criteria of at least a 1.4 fold change and a statistical difference (p≤0.05) from control levels of expression. Among these, five genes responded similarly in both experiments, suggesting that they are robust indicators of stress. These genes are a major histocompatibility complex class I molecule (MHCI), JunB, glucose 6-phosphatase (G6Pase), nuclear protein 1 (Nupr1) and tumor necrosis factor decoy receptor (TNFDR). Interestingly, transcripts of Nupr1 did not return to control levels in the 21 hours after stress. In fact, the transcripts continued to increase during recovery.