Dear Adam:
Your explanation seems possible given the pattern of staining with your
two antibodies. One thought is that, it seems like your staining is
adequate for your purposes without worrying about the color of the
staining, so perhaps you could just accept it. But to check it out, I
would be tempted to try DAB staining without the nickel enhancement. Or
do the nickel-DAB staining with a dilution curve of the antibody. If you
dilute your antibody, do you revert to the regular blue-clack color? 

Another thought is that the brown color means less DAB product, which
might occur if the viral vector expression produces a slightly different
protein that does not bind as much antibody. Are you expressing the full
length receptor, or only part of the receptor?  

Sarah

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