Jantare,

Applying separately shouldn't be a problem unless you coach her about what are you studying, which place, university etc etc. The bottomline is that don't let the visa officer doubt about your marriage because she doesn't have  your detailed information. They don't care about the marriage certificate (at least didn't care in my case) because they know that fake documents can be made easily in Nepal. One of my friends didn't do traditional marriage (in fact he had eloped) and when the time came for his wife to apply, there was a big problem. She got rejected many times just because she couldn't provide a photograph of "jagge". I'm not trying to discourage you, but just warning you what problems you might face. They may not give your wife a hard time, but you never know.

By the way I'm a microbiology major too :)

Good luck.