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Abstract Metabolic syndrome (MetS) is a combination of disorders that increase one's risk for type 2 diabetes (DM2) and cardiovascular disease (CVD). Both lifestyle and genetic factors have been established to be involved in the aetiology of MetS. Improving our knowledge about the pathophysiology of MetS could provide more effective therapeutic approaches and reduce the risk of developing DM2 and CVD. Lower levels of adiponectin, an adipose-derived protein, has been shown to be associated with the components of MetS. Common variants in a number of candidate genes related to MetS have been shown to be associated with changes in the serum adiponectin level. This study was designed to evaluate the putative effects of military lifestyle, as well as common polymorphisms of the peroxisome proliferator activated receptor gamma 2 (PPARγ2), insulin receptor substrate-1 (IRS-1) and adiponectin (APM1) genes on serum adiponectin level in a cohort of Finnish servicemen. Results of this study have showed that serum adiponectin significantly decreased during the six-month follow up in military service compared to baseline levels. This decrease was even shown in subjects that experienced a 5-10 % weight loss after six-months. Subjects with the Ala12Ala genotype of PPARγ2 had significantly higher levels of serum adiponectin compared with subjects with the Pro12Ala and Pro12Pro genotypes. Subjects having the X12Ala genotype of PPARγ2 with > 10% weight reduction showed a significant increase in serum adiponectin compared to other groups during the follow up. Those having the Ala12Ala genotype of PPARγ2 + Gly972Gly genotype of IRS-1 combination had significantly higher adiponectin compared with subjects with the Pro12Pro + Gly972Gly and Pro12Ala + Gly972Gly genotype combinations. Adiponectin levels were significantly higher in men with the T276T genotype compared with subjects with the G276T or G276G genotypes of SNP+276 of the APM1 gene. In conclusion, this study shows a possible impact of a military lifestyle as well as, candidate gene variations, and their interactions upon the regulation of serum adiponectin levels as a marker of MetS. This study could serve as a pilot for the further extensive studies with longer follow up periods as well as more accurate information on specific lifestyle factors.

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