Yes, open the color gradient controls in the Emitter tab of the Inspector and add opacity tags to the opacity gradient (white stripe) over the color gradient. It represents the opacity of the cells over their lives - add black tags to reduce opacity at specific times, e.g. have them fade in and fade out.
Freelance Producer/Editor/Motion Graphics Artist
Apple-certified Master Trainer
Author, Motion 4 from Peachpit Press http://www.applemotion.net