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is there some way to experimentally determine the density distribution of those two molecular motors in a Neuron? Fluorescence labeling would be impossible(?) as GFP markers would probably alter the motor dynamics. Any ideas? Or do any studies exist which looked into this topic?

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I have next to no knowledge of this area, but I do know that Peter Baas has done extensive studies of Kinesin-5 in neuronal growth cones during development. I mention that in the off chance that some of his imaging techniques might be helpful to you. –  jonsca Jul 2 at 12:31
Are you sure that GFP tagged motors don't function properly in these two cases? I'm almost certain I've seen motors tagged before. –  leonardo Jul 2 at 12:51

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