Polly: Dr. Cheney feels that increasing glutathione levels is key to the recovery of his chronic fatigue patients. At one time he was using glutathione supplements, but later he found that undenatured whey, which increases glutathione levels, was better tolerated by many of his patients. (For more detail, see the section on oxygen in the Acid And Alkaline Balance chapter of book 3, and also the section on undenatured whey in book 3.)
Besides using whey to provide the raw materials to make glutathione, the best way to increase glutathione levels is to take the oxidant strain off the body (eg avoid unsaturated oils) and to improve liver function (eg avoid estrogens).
Glutathione is the premier antioxidant of the body. It also recycles vitamin C, another antioxidant. Dr. Cheney has expressed some concern that lots of vitamin C could lower glutathione levels because the body would be using a lot of the available glutathione to recycle the vitamin C. (Glutathione itself is recycled by NADH and lipoic acid.) Try to keep antioxidants like vitamin C, E, glutathione and coenzyme Q10 in balanced.
Glutathione is a tri-peptide, consisting of three amino acids: glutamic acid, glycine, and cysteine. When ingested, glutathione will break up into these separate amino acids in the stomach. Each of these may pose some problems for different individuals.
Glutamic acid— Although glutamic acid does not release ammonia like glutamine does, it can be a problem for two reasons: glutamic acid will reduce taurine levels, and glutamic acid is considered an excitotoxin.
Cysteine— Excess cysteine has anti-thyroid properties. Cysteine can increase yeast growth in some people. Cysteine will move mercury around, making it difficult to tolerate if you are mercury poisoned.
Glycine— Glycine is generally very helpful. However, glycine can sometimes increase yeast or bacteria growth. (See comments in the Liver Health chapter in book 1 on tri-methyl-glycine, TMG.)
The best supplement may come down to what the body tolerates the best. All three of these amino acids are closely related to each other and to the amino acid serine. (The body removes phosphate from glutamate and can create serine. Serine plus sulfur can be made into cysteine. By removing a methyl group, serine can become glycine.) So it raises the question of what is the most acceptable supplement for the body. Of these separate amino acids, glycine seems to be the least likely to pose a problem.
I know that both glutathione and cysteine supplements used to give me a headache, but they don’ t bother me now. Sorry, I don’ t know why. However, it might have something to do with my starting a thyroid supplement in the interim.
Andy Cutler: People who are mercury poisoned sometimes have a condition where the level of the amino acid cysteine in their blood plasma is elevated. Taking things like whey is very harmful to people in this state.
Regardless of whether people have trouble with the amino acid cysteine, yeast love it and related thiol compounds. These are very nourishing to yeast. Eating too much of these is like giving vitamins to your yeast – they grow big and strong very rapidly. These foods are: eggs, dairy products, bakery products containing whey, cysteine, or “ enzymes,” cabbage, bok choy, cauliflower, broccoli, brussels sprouts, kale, turnips, rutabagas, asparagus, and coffee. When eating these foods it is important to keep a proper balance between what your body needs and what your yeast can use to grow. Onions, shallots, leeks, garlic are “ sulfur foods” that are likely to suppress yeast, but will still cause great problems for people who have “sulfur food” sensitivity.
* I describe how to check for mercury poisoning in my book, AMALGAM ILLNESS: DIAGNOSIS AND TREATMENT.
Polly: Yes, the sulfur containing amino acid cysteine may increase yeast growth. In fact, it is added to bread to make it rise. Yet, pure elemental sulfur (flowers of sulfur) is an antifungal agent. It must be the form of sulfur that is important in yeast growth. I don’ t know if the form of sulfur found in MSM could be a problem; however, no one at our forum has reported that it increased their yeast growth. Most say that MSM has been helpful. A person might experiment to see if they feel better without the sulfur foods that you mention, but I really don’ t like the idea of eliminating them unless necessary. Our body needs the sulfur amino acids and compounds to function properly. Broccoli and cruciferous vegetables in particular are very important to the liver’ s phase 1 detoxification of estrogen. .
Acetylaldehyde’s Effect On Amino Acid Balance
Polly: The first break-down product of alcohol in the body is acetylaldehyde. This chemical is thought to do much of the damage of alcoholism. Yeast also make this chemical. If we have been exposed to this toxin for a long time, it can damage the body. About twenty years ago, Dr. Truss presented the hypothesis that many people with yeast overgrowth were suffering from exposure to this toxin. He found that people with yeast overgrowth were low in the amino acids associated with exposure to acetylaldehyde. These amino acids are glutamine, glutamic acid, glutamate, alpha-ketoglutaric acid, and asparagine (similar to aspartic acid). Dr. Truss did not find that taurine levels were particularly low in the patients in his study. However, in Phyllis Bach’ s book, Prescription for Nutritional Healing, she states that taurine is dumped in the urine by those with yeast overgrowth. Taurine is also dumped in the urine when a lot of alcohol is drunk. Perhaps there is a connection.
Alpha-ketoglutaric Acid And Aspartates
Polly: In Leon Chaitow’ s book on amino acids, he suggests that many ill people do better with some added alpha-ketoglutaric acid and aspartates (aspartates are very closely related to asparagine). These are very important for removing ammonia and for activating the Krebs energy cycle. I tried this combination at one point. It was wonderful. After a few weeks of taking the recommended amount I had much more energy. Fearful of ever overdoing such a product, and realizing that I was not gaining any additional energy after the first month of use, I stopped using the product after two months. After stopping the product, I did not lose the energy boost that it had given me.
The product that I took was Pysician’ s AQC from Advanced Physician’ s Products. (website http://www.nutritiononline.com, phone 805-730-7420 or 800-220-7687) The product has 200 mg of alpha-ketoglutaric acid per pill. The product used to have aspartates, but the company has now substituted malic acid (165 mg) in their formula. They thought the malic acid was safer. (The body can convert malic acid into aspartic acid, and vice versa.) Klaire Labs makes a supplement of just alpha-ketoglutaric acid, website http://www.klaire.com, phone 858-350-7880 or 800- 859-8358. It can also be ordered through Kirkman Labs, which carries many of the supplements people use to treat autism.
Since alpha-ketoglutaric acid is closely related to glutamate, one should be very concerned about taking it for any extended period without good reason. Glutamate and aspartic acid are considered excitotoxins. Too much can induce seizures and can damage brain cells. On the other hand, aspartic acid and alphaketoglutaric acid are very important to the removal of ammonia. This property helps prevent seizures. The proper amount of these amino acids is needed.
Certain substances will help protect you from the ill effects of glutamate and aspartates. Dr. Baylock, author of Excitotoxins: A Taste that Kills, states that various combinations of coenzyme Q10, vitamin C, vitamin E, lipoic acid, B12, B2, B1, pycnogenol, phosphotidylserine and niacinamide can be protective. He also includes acetyl-L-carnitine in his list of protective agents. However, please be careful. A little carnitine is protective, but too much can cause seizures. He mentions that controlling hypoglycemia and hypoxia (lack of oxygen) will provide some protection too. In Braverman’ s book on amino acids, he says that a combination of tyrosine, phenylalanine (a precursor to tyrosine), and methionine can counter some of the ill effects of aspartates and glutamate. Magnesium, B6 and manganese are important too.
Citrulline and Arginine
Polly: Citrulline and arginine will help get rid of the extra ammonia formed when taking glutamine, and normally, when you give glutamine these aminos will increase. Citrulline will be formed in the intestines. Arginine will be formed mainly in the kidneys, except in the very young, where most of it will be formed in the intestines instead.  (The intestines also convert dietary proline into arginine.)
However, there might be a problem with this normal adaptation of the body. Mercury interferes with an enzyme called ornithine transcarbamylase, which converts ornithine into citrulline.  (Citrulline converts into arginine.) This could cause a deficit of citrulline and arginine. Therefore, if you suspect mercury poisoning, you may want to check your citrulline and arginine levels before you try loading the body with glutamine. You are also more likely than most to have low arginine and citrulline if you have fibromyalgia. 
It is possible that the bacteria in your gut have lowered your arginine levels. Braverman mentions a case presented by Stanbury and colleagues from MIT, where the presenting symptom was constipation. The bowel flora contained the bacteria Streptococcus fecalis, a potent source of arginine desaminase. This enzyme converts arginine back to citrulline, and its excess caused a deficiency of arginine in the patient.
If mercury or the bacteria in your bowel are reducing the levels of these amino acids, correcting your bowel flora may bring the situation under control. However, it also makes sense to correct an amino acid deficit if it exists. Correcting an arginine deficiency is very important because arginine supports the immune system and helps your body get rid of bacterial infections. It will also help correct a leaky gut by increasing nitric oxide production in the gut.  Yet you shouldn’ t get too much arginine. Too much nitric oxide may harm the gut by interfering with mitochondrial energy production. High dose B12 shots will mop up nitric oxide and perhaps allow you to tolerate these amino acids.
When using arginine, it should be balanced with lysine in equal portions, or otherwise you may have a flare up of cold sores, or some other virus. If you have a cold or virus, then it may be prudent to go off arginine until your body has recovered. It might also be wise to avoid supplementation of arginine and lysine until after any yeast overgrowth has been reduced by a change in diet and the use of anti-fungals. If there is yeast overgrowth, the level of a sugar called arabinose is likely elevated. This sugar attaches to lysine and arginine and forms pentosidine. Pentosidine causes undesirable cross-linking of proteins, as described in Dr. Shaw’ s book on autism, Biological Treatments for Autism and PDD. You don’ t want to form more pentosidines just by virtue of supplementing lysine and arginine before the arabinose levels are down.
Branch Chain Amino Acids
Polly: The branch chain amino acids of valine, leucine, and isoleucine improve sugar control, support production of the amino acids needed to remove ammonia, and help balance tryptophan and tyrosine. Even though branch chain amino acids may be helpful, there are always precautions for the use of any amino acid. In particular several nutritional deficiencies should be corrected before trying the branch chain amino acids. These are the precautions that I’m aware of.
1. If you supplement branch chain amino acids, do so with a small amount over a long period. (Exposure to ammonia can lower branch chain amino acids, yet curiously, supplementation with branch chain amino acids can increase ammonia levels. You don’ t want to expose your body to more ammonia than it can handle.)
2. Correct a taurine deficiency before experimenting with the branch chain amino acids. (Branch chain amino acids are converted into alanine by the muscles. Alanine inhibits taurine metabolism and causes the loss of taurine.)
3. If you are seriously ill, be especially careful. Those with Lou Gerig’ s disease usually have too much ammonia and they also have some problems with taurine metabolism. These people tend to have trouble with branch chain amino acid supplementation. 
4. To use the branch chain aminos properly, the body also needs B6, magnesium, alphaketoglutaric acid and copper.  I’ d correct any deficiencies of these before trying the branch chain amino acids.
5. Biotin is also needed to use the branch chain amino acids properly.  A lack of biotin can lead to excess ammonia, muscle pain, sleepiness, acidosis, and depression. Biotin is also important because it serves as a carrier of carbon dioxide.  Yeast overgrowth can cause a real and a function deficiency of biotin. However, you might want to wait on biotin supplements until after you have brought any concomitant yeast growth down; biotin can encourage yeast growth. Sometimes rather large doses of biotin are needed, on the order of 1 to 5 mg. Large doses of biotin need to be balanced with inositol to protect the liver.
6. You probably shouldn’ t take the branch chain amino acids during the painful stage of a migraine. This could interfere with the formation of serotonin. Blood serotonin levels are dropping rapidly during the painful stage of a migraine. You wouldn’ t want to speed up the drop in serotonin at this time.
7. To increase absorption, don’ t take the branch chain amino acids at the same time as a high protein meal. Any tryptophan and tyrosine in your meal would compete with the branch chain amino acids for transport/absorption in the intestines. If tryptophan lingered in the intestines, this may lead to increased formation of IAG.
8. If you happen to have pellagra (a fairly rare condition caused by a lack of niacin), you should not be using branch chain amino acids. You need niacin to use the branch chain amino acids properly.
9. In Maple Syrup Urine Disease, an enzyme essential to the proper utilization of branch chain amino acids is either missing or inadequately available. The urine smells like burnt sugar. The branch chain amino acids should not be supplemented in this case. Cofactors for the proper functioning of this enzyme are coenzyme B1, lipoic acid with lysine, NADH, coenzyme A (CoA), and coenzyme B2.