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Thank you all for your suggestions! 

As many of you suggested, it looks like it is indeed quenching. The protein of interest is a known dimer so it's also possible that she got "lucky" and her GFP happens to be located in such a way it quenches when dimerized or it could be expression level. She is moving forward with plans to tease out those options. 

For those of you interested in our troubleshooting strategy: Before posting to the listserv we attempted to determine if there was quenching by modulating the FRAP intensity and looking for increase of the FRAP area intensity immediately after the "bleach" event but we didn't see that--just bleaching or no bleaching. In retrospect we were probably too course with our setting choices and missed the sweat spot that would cause de-quenching. After confirmation from listserv suggestions that quenching was a likely cause, we tried a different strategy--i ncreasing the imaging illumination intensity a bit but not doing the bleaching event (ie, bleaching the whole cell). We finally saw intensity of the whole cell increase then decrease with similar rates. This is, of course, consistent with initial bleaching of the "quenching" population, thereby allowing emission, followed by bleaching of the remaining emitting population. 

I am reminded again to always question your assumptions: In this case, lower intensity was not necessarily lower expression level! 

Many thanks again! 
Wendy 

~~~~~~~~~~~~~~~~~~~~~~~ 
Wendy Salmon 
Light Microscopy Specialist 
Whitehead Institute for Biomedical Research 
W.M. Keck Imaging Facility 
9 Cambridge Center, Rm 447 
Cambridge, MA 02142 
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w: http://staffa.wi.mit.edu/microscopy/