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The aim of this study was to assess the independent and additive effects of soy protein isolate (SPI) and moderate-intensity exercise (EX) on bone turnover and bone mineral density (BMD).This study used a placebo-controlled, double-blind (soy), randomized 2 (SPI vs milk protein isolate [MPI]) × 2 (EX vs no EX) design. Sixty-one postmenopausal women were randomized, and 43 (62 ± 5 y) completed the 9-month intervention (SPI, n = 10; MPI, n = 12; SPI + EX, n = 11; MPI + EX, n = 10). Serum C-terminal cross-linked telopeptides of type I collagen and serum bone-specific alkaline phosphatase were measured as markers of bone resorption and formation, respectively. BMD was measured by dual-energy x-ray absorptiometry.At 9 months, SPI reduced serum C-terminal cross-linked telopeptides (−13.3% ± 15.3% vs −1.5% ± 21.0%; P = 0.02) and serum bone-specific alkaline phosphatase (−4.7% ± 14.7% vs 6.5% ± 17.7%; P = 0.02) compared to milk protein isolate. EX attenuated the reduction in serum C-terminal cross-linked telopeptides (−1.9% ± 21.6% vs −12.4% ± 15.3%; P = 0.04); however, no EX effects were apparent in serum bone-specific alkaline phosphatase at 9 months (2.8% ± 16.1% vs −1.0% ± 18.3%; P = 0.28). Neither SPI nor EX affected BMD at any site; however, change in BMD was related to change in fat mass (r = 0.40, P < 0.05).In postmenopausal women (1) SPI reduces bone turnover with no impact on BMD over 9 months; (2) moderate-intensity endurance exercise training did not favorably alter bone turnover and had no impact on BMD; and (3) there were no additive effects of soy and exercise on bone turnover or BMD.