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We have shown earlier that irradiation with UV induces duplication of foot in regenerating middle pieces of hydra. The present study was undertaken to elucidate the underlying mechanism(s) leading to this curious phenomenon. UV irradiation induced duplicated foot in about 30% of regenerating middle pieces. Metalloproteinases are important in foot formation, while Wnt pathway genes are important in head formation in hydra. The effect of UV irradiation on expression of these genes was studied by in situ hybridization and q-PCR. In whole polyps and middle pieces, UV irradiation led to up-regulation of HMP2 and HMMP, the two metalloproteinases involved in foot formation in hydra. HMP2 expression was significantly increased starting from 30 min post exposure to UV at 254 nm (500 J/m(2)), while HMMP showed significant up-regulation 6 h post UV exposure onwards. In middle pieces, increased expression of both metalloproteinases was observed only at 48 h. In whole polyps as well as in middle pieces, expression of Wnt3 and β-catenin was detected within 30 min of UV exposure and was accompanied by up-regulation of GSK3β, DKK3 and DKK1/2/4, inhibitors of the Wnt pathway. These conditions likely lead to inactivation of Wnt signaling. We therefore conclude that duplication of foot due to UV irradiation in regenerating middle pieces of hydra is a combined effect of up-regulation of metalloproteinases and inactivation of the Wnt pathway. Our results suggest that UV irradiation can be employed as a tool to understand patterning mechanisms during foot formation in hydra.