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Metabolite changes in Nile tilapia in response to carbonate alkalinity stress were investigated by transferring the fish directly from freshwater into different carbonate alkaline water. Levels of plasma pH/HCO
3
−
concentration, the mRNA and protein expression of two carbonic anhydrases (CAhz and CAIV), and two HCO
3
−
transporters (Na
+
/HCO
3
−
cotransporter and Cl
−
/HCO
3
–
exchanger) in the gill, kidney, and intestine were determined using a pH meter, UV spectrophotometer, quantitative real-time PCR, and western blotting within 192 h of exposure. Plasma pH showed an “up-peak-down” variation, whereas HCO
3
−
concentration decreased at first and then increased in all alkaline water groups. The overall mRNA expression was regulated in an alkalinity- and time-dependent manner. Western blot results showed that the Cl
−
/HCO
3
−
exchanger protein was detected in all tissues examined, whereas the two carbonic anhydrases and Na
+
/HCO
3
−
cotransporter proteins were only expressed in the gill and kidney. Therefore, the studied carbonic anhydrases and HCO
3
−
transporters are involved in the HCO
3
−
metabolism and transport to maintain acid–base balance in Nile tilapia under carbonate alkalinity stress.