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Drug addiction is a widespread social problem, which not only brings adverse consequences to the human body, but also causes great burden to the society. However, it's still unclear how the long-term and sustained cocaine exposure will affect clock genes’ expression in the reward related brain areas. We hypothesize that chronic cocaine exposure causes changes in the circadian rhythmic expression of clock genes in brain regions associated with reward, since previous studies have shown that cocaine use causes circadian disorders. Sprague-Dawley male rats were administrated with cocaine 20 mg/kg at ZT4 through intraperitoneal injection for 21 consecutive days. Twenty-four hours after the last cocaine administration brain samples were collected at 4-h intervals for 24 h (every 4h: ZT 0; ZT 4; ZT 8; ZT 12; ZT 16; ZT 20) to examine expression of rPer1, rPer2, rPer3, rCry, rBmal1 and rClock by quantitative real-time reverse-transcription polymerase chain reaction (RT-PCR). We found that chronic cocaine exposure to rats resulted in significantly disturbances in expression of clock genes in reward related brain areas compared to saline - treated rats. In cocaine-treated rats, rPer1 expression in the suprachiasmatic nucleus (SCN), prefrontal cortex (PFC) and ventral tegmental area (VTA); rPer2 expression in the nucleus accumbens (NAc) shell and hippocampus; rPer3 expression in the NAc core; rCry expression in the SCN and PFC; rBmal1 expression in the SCN and NAc core showed robust circadian rhythms that were essentially identical to those in control rats. However, robust circadian rhythm in rPer1 expression in the SCN and rCry expression in the PFC was nearly completely phase - reversed in cocaine-treated rats. A blunting of circadian oscillations of rPer1 expression occurred in the NAc core and shell and hippocampus; of rPer2 expression occurred in the SCN, PFC, NAc core and hippocampus; of rPer3 expression occurred in the SCN, PFC, NAc shell, hippocampus and VTA; of rCry expression occurred in the NAc core and shell, hippocampus and VTA; of rBmal1 expression occurred in the PFC, NAc shell, hippocampus and VTA in cocaine - treated rats. These rhythm changes accompanied by significant increase in rPer1, rPer2, rPer3 and rBmal1 in the PFC, rPer1, rPer2 and rBmal1 in the hippocampus; significant decrease in rPer2, rPer3 and rCry in the SCN, rPer3, rCry, rBmal1 and rClock in the NAc core compared to control rats. rClock expression in cocaine - treated rats showed no rhythmic change, identical to control rats.These results suggest that chronic cocaine exposure results in disturbances in clock genes’ expression in reward related areas.