Acquired immune and mitochondrial dysfunction hypothesis
A stressor of some kind (virus, accident, surgery, chemical or other toxic exposure, other trauma) causes mitochondrial disorders and immune dysfunction in genetically susceptible people. The mitochondrial and immune dysfunction could have been occurring prior to the stressor due to infectious agents, acquired over the lifetime of the affected individual. The mitochondrial dysfunction could cause or contribute to the immune dysfunction.
After the stressor has come and gone, low-level infectious agents living throughout the body reactivate, and inflammation, including mast cell activation, occurs. Inflammation, from reactivated infections, low gut motility/SIBO, new exposures to toxins (with a more sensitized immune system), et al., affects the body and the brain. Microglial activation in the brain causes Hypothalamic-pituitary-adrenal axis (HPA) dysregulation. A downward spiral of infectious reactivation, inflammation, dysautonomia, and HPA axis dysregulation is set up, which perpetuates the illness.
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mitochondria - Important parts of the biological cell, with each mitochondrion encased within a mitochondrial membrane. Mitochondria are best known for their role in energy production, earning them the nickname "the powerhouse of the cell". Mitochondria also participate in the detection of threats and the response to these threats. One of the responses to threats orchestrated by mitochondria is apoptosis, a cell suicide program used by cells when the threat can not be eliminated.
microglia - A type of immune cell, called a macrophage, that lives in the brain. For historical reasons, macrophages have different names based on the part of the body that they normally live in. Macrophages that normally live in the blood are called monocytes. Macrophages that normally live in the skin are called Langerhans cells. Macrophages that normally live in the liver are called Kupffer cells. And macrophages that normally live in the central nervous system are called microglia. Microglia were originally classified as glial cells, under the assumption that the cells had a merely structural function, before it was realized that the cells were in fact immune cells. As the "sentinel cells" of the central nervous system, microglia survey their environment for abnormalities such as infection or tissue damage, and then initiate an immune response to fight the infection or repair the tissue damage.