Doing this based on memory...
The big variables were looking at here, when looking at high ammonia are gut bacteria and breaking down of amino acids. Proteins get broken down and the amino acids recycled constantly, and that's normal. What doesn't get recycled gets excreted, and that's what we're replenishing when we eat protein. We don't have any way to store excess protein. If we eat and absorb more than our bodies can use, then we break down the excess aminos and use them as fuel. Alternately, in a state of starvation, if there isn't enough glucose or fatty acids to use for fuel, the body will then turn to amino acids. Amino acids are the only of the three that have nitrogen, and so the nitrogen waste from breaking down the amino acid gets turned into ammonia. Gut bacteria can also turn dietary protein into ammonia, or break up the stuff we've marked for excretion so it gets reabsorbed.
Some symptoms of high ammonia are brain fog and/or stimming.
The way we normally get rid of ammonia is in the urea cycle. The rate limiting step - the place it usually gets snagged the most, is a step that uses aspartate and citrulline. Asparagus is an exceptionally rich source of aspartate and watermelon has a lot of citrulline. I'm assuming that's part of why they're common components of kidney cleanses.
What the urea cycle can't keep up with, BH4 can detoxify. It uses two molecules of bh4 to clear one molecule of ammonia, though, so it drains bh4 pretty fast. BH4 is also used to convert tryptophan to serotonin, and to convert phenylalanine to tyrosine. Tyrosine is the precursor for dopamine, thyroid hormones, melanin (not melatonin, that's from serotonin) and one more I'm forgetting. One form of PKU involves low/nonexistent BH4 levels.
When there's not enough bh4 to clear out the ammonia, you start to get some nasty oxidants like superoxide (and one other, I forget, its in the yasko methylation diagram) and you don't make as much nitric oxide. (NO, using the NOS enzyme/gene.). Not enough NO, and you end up with cardiovascular disease and other blood vessel damage. Also, in the chain of oxidative stress and antioxidants, low levels of NO can make things worse while good levels can actually stop the chain of oxidative damage.
Symptoms of low dopamine are (this is my list, not an 'official' one) lack of motivation/interest in the world with the potential exception of one obsession; low blink rate (is that in the guess your genetics thread?), and high prolactin (is that why I have an abundant milk supply, why ds starts choking when I'm getting enzyme die-off, and why I have a bunch of cherry angiomas - little blood red mole-type things?). And in my experience, dopamine levels can change within a day or two of dramatically changing my folate or aluminum levels.
Ammonia, especially in the brain, can combine with alpha ketoglutarate to make glutamine and glutamate. Both of those are less toxic than ammonia, so that's a good thing. But high glutamate can be an issue too, as were talking about in the glutamate/GABA thread. (And aspartate, used in the urea cycle, can activate glutamate receptors)
So now the genetics and such, based on yasko-centric reading.
CBS up regulations (likely if you have unexpectedly low homocysteine levels) cause an increased breakdown of homocysteine. Breaking down amino acids creates ammonia. So if you're breaking stuff down excessively, you're going to tend towards high ammonia levels.
Stuff that affects BH4 levels will also affect how well we deal with ammonia, so mthfr A1298C, along with folate status, niacin and vitamin C. I think those are the three main ones that recycle bh2 to bhp. Aluminum blocks that enzyme, so it effectively lowers bh4 as well.
To add digestion into the mix, there's the protein you eat, then there's what, if anything, your gut bacteria do to it, then there's how well you digest and absorb it (stomach acid and pancreatic enzymes, etc), then there's how much your body needs at the moment (think building muscle or making milk or a baby or healing a wound or making enzymes/fixing an amino acid deficit, etc).
The rda for protein is around 56g, I think. Add in tandem nursing with an abundant milk supply and the requirement ups to 70g-ish, a deficit to make up, and not digesting protein well, and I'm eating probably close to 90-100g/day and my ammonia is still low (as are my aminos), I just had it tested. When there's no die off, at least. I'm ++ for the CBS upregulation and +/- for mthfr a1298c, so my ammonia *should* be sky high with that kind of protein intake.
How's that for a brain dump? I'm sure I missed a bunch, too
