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Since the first cloned sheep was produced in 1996, cloning has attracted considerable attention because of its great potential in animal breeding. Somatic cell nuclear transfer (SCNT) is widely used for creating clones. However, SCNT is very complicated to manipulate and inevitably causes intracellular damage during manipulation. Typically, only less than 1% of reconstructed embryos develop into live cloned animals. This low success rate is considered to be the major limitation in the extensive application of cloning techniques. In this study, we proposed an intracellular strain evaluation-based oocyte enucleation method to reduce potential intracellular damage in SCNT. We first calculated the intracellular strain based on the intracellular velocity field and then used the intracellular strain as a criterion to improve the enucleation operation. We then developed a robotic batch SCNT system to apply this micromanipulation method to animal cloning. Experimental results showed that we increased the blastocyst rate from 10.0% to 20.8%, and we successfully produced 17 cloned piglets by robotic SCNT for the first time. The success rate of cloning was significantly increased compared to that of traditional methods (2.50% vs 0.73% on average). In addition to the cloning technique, the intracellular strain evaluation-based enucleation method is expected to be applicable to other biological operations and for establishing a universal cell manipulation protocol to reduce intracellular damage.