Are you planning to use "used" toilet paper rolls? I would just be concerned of bacteria on them, from all the dirty hands using them in the washroom. You have to think how much the toilet paper tube is handled until it runs empty and most times hands don't get washed till after the toilet paper is used.
You can buy cardboard tubes that are pet safe from stores.
Apple branches, if you are getting them from outside, should be cleaned properly. I personally scrub mine in the sink and then boil in water.
Bake in the oven for an hour to two hours (check on it every so often to make sure it is baking, but not burning. The house will smell really nice when your baking apple wood! I love it!) afterwards at about 200 degrees.
It's just to properly prepare it to get rid of harmful micro organisms or insects that may be living in the wood. Good luck with everything!