We also investigated whether chronic morphine exposure would alter Htr3a mRNA levels within specific brainstem nuclei that were previously associated with physical dependence on opioids. The amygdala [38,39], dorsal raphe [38,40], and periaqueductal gray [41] are brainstem nuclei and are known to modulate signs of opioid dependence and withdrawal. Tissue from these three brainstem regions was harvested from dependence-developing C57BL/6J mice by LCM. Htr3a mRNA expression in all three of these brainstem nuclei was markedly reduced (two-fold to five-fold) after chronic morphine treatment (Fig. 6). Consistent with the computational prediction, therefore, there are strain-specific differences in the effect of chronic morphine exposure on CNS Htr3a mRNA expression, and chronic morphine exposure reduced Htr3a mRNA in three brainstem nuclei associated with opioid dependence.