design formula question
You can't (easily) use a single design, since clone is nested within diabetic status, so you were correct using two separate designs. Your designs are correct.

If you really wanted to use a single design for some reason, it'd be ~clone+structure and for the latter comparison you'd end up using a rather complicated contrast (something like c(rep(c(1,-1), 3), 0)). I really can't recommend that unless you have a very compelling reason, since it's vastly easier to think in terms of factors for your experiment and you're not hurting anything by fitting twice.