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To explore the difference of gene expression in rat mesenchymal stem cell (MSC) and in the hippocampus of the Alzheimerpsilas disease (AD) model rats on Natural Brain-Kinetine by Gene chips. Methods: Rat MSC is primary cultured according to method-routie. The MSCs have two groups, the control group and treatment group without or with Natural Brain-Kinetine (NBK) respectively. MSCs gene expression is detected and analyze through the Affymetrix microarray. In addition, we analyze the gene expression in hippocampus of rats. The rats were randomly divided into 3 groups : sham group, AD model group (injected 25 mug Amyloid peptide beta1-40 in bilateral hippocampus), AD model treatment group. They were fed for 30 days with nature salt solution and Natural Brain-Kinetine respectively. Results: In MSCs, the expression of 18 genes are significantly increased (FC > 2) and lower of 28 genes (FC <-2) compared with the control group. The animal experiments show that in treatment group, there is 58 genes up regulated and 25 genes down regulated compared with the sham group, there is 15 genes up regulated and 28 genes down regulated compared with the AD model group. Those genes are possible involved the ones including cellular proliferation, cell differentiation and development, cell adhesion, nerve growth, cellular function regulation, cell signal transduction, cellular material and energy metabolism, immune response, and so on. Conclusion: We speculate that Natural Brain-Kinetine can regulate some target genes in the growth and differentiation of MSCs, and regulate hippocampus function in rats with a multi pathway to regulate the function of brains.