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The charge of the microorganism is usually negative. The cell membrane is a phospholipid bilayer which is polar, the outside is usually negative. Depending on the staining protocol, a dye will be repelled by or attracted to the cell. Sometimes you use two different dyes- one to color the cell and then one to color the background or surrounding area. Sometimes you want to color the inside of the cell, so you need to melt the cell membrane or cell wall away with heat or chemicals. This allows the dye back in. Sometimes there are steps to resolidify this barrier to trap the dye inside prior to rinsing the slide with water or whatever. These steps are tricky and easy to screw up completely, resulting in a clear or invisible specimen because the dye didn't "take".

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Q: Microbiology How does the charge on a Microorganism affect staining Which staining protocols rely on which charges What are the outcomes?
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