Microbiological Analysis Support—Troubleshooting

The green dye in the kit will label all the cells as it is a cell-permeant nucleic acid stain. The red dye is not cell permeant, and will only stain the cells with compromised membranes (dead cells). Therefore, any cells with red signal will be considered dead. It is possible that you will have some cells that are only red, some that are red and green, and some that are only green. Sometimes the red dye will displace the green dye. In any case, any red cells are dead.

Also, the green dye emission may bleed through into the red channel. Do a single-color staining and examine under both green and red filter sets to determine the level of bleedthrough. To avoid this bleedthrough, use a lower concentration of dye, and, if possible, use narrow bandpass filters.

Very often, mycoplasma contamination cannot be removed from the culture so it should be discarded. You may have a unique culture that you prefer not to discard and would like to try to clean it. Ciprofloxacin and Plasmocin™ have reportedly been used for this application. If interested in a protocol or directions for use, check with the antibiotic supplier or published literature. Note that mycoplasma are very difficult to remove from culture and spread easily so the treated cultures should be quarantined until clear of mycoplasma and the laboratory should be thoroughly cleaned.

Bacteria grown in rich medium (high glucose) are difficult to lyse. Try reducing the glucose concentration. Bacteria and organisms lysed with B-PER Reagent include E. coli, Acetinobacter, Archaebacteria, S. aureus, H. pylori, Baculovirus, nematodes, and insect cells. B-PER Reagent can lyse some gram-positive bacteria, but tends to be more efficient with gram-negative bacteria. If lysis is inefficient for a particular bacterial strain, freeze cells before extraction. Add lysozyme for the most efficient extraction, however, for some over-expressed proteins, the addition of lysozyme is not required.