Saturday, June 28, 2008

Mechanism for mitochondria failure during immune system activation

The roots of autism: How immune system activation can cause regression with/without autism and with/without mitochondrial failure. Non-immune system mediated mitochondrial failure. The connection of mitochondria to autism and regression.

This has gotten longer and more complicated than I intended, but I felt it was necessary to include a fair amount on how low NO causes the acute behavioral effects associated with immune system activation and how those effects can become self-sustaining.

The first third of this is devoted to neural connectivity, how that changes, and how those changes matter. Neural connectivity is the fundamental "cause" of all properties of neural networks. That includes all neural activity and all behaviors. This is true in the same sense that the meaning of a book is tied up in how the letters are arranged. That arrangement of letters determines the words, the phrases, the sentences, the paragraphs, the pages, the chapters, and the sections, everything that is "important" about the book. The devil is in the detail, and there are a lot of details. Virtually all of those details (more than 99.999%) remain unknown. This is not a measure of how little we know; rather it is a measure of how complicated physiology and the brain actually are. Most researchers do not appreciate how complicated physiology is.

There has been some discussion about vaccines causing mitochondria failure. There is nothing special about vaccines that cause mitochondria failure; any sufficiently severe immune system activation can/will cause mitochondria failure even in completely healthy individuals even with completely healthy mitochondria. The turning off of mitochondria under conditions of extreme immune system activation is a completely normal, important, and necessary regulatory feature of mitochondria. It can occur with or without neuropathy or regression. In no case is this mitochondria failure due to "toxins" or toxic effects of exogenous materials on mitochondria. This is the cause of death in sepsis, failure of mitochondria leading to multiple organ failure. If too many mitochondria fail, there is nothing that can be done to prevent death. Any successful treatment can only be to prevent too many mitochondria from failing.

This turn-off has nothing to do with any toxic components in vaccines. It is easy to see that the mitochondrial failure following vaccination has nothing to do with "toxic" components in vaccines. If it did, we would expect to see a dose-response effect; that is that mitochondria subjected to the highest dose of "toxins" would be expected to be killed the fastest and the most. If "toxins" in a vaccination cause mitochondrial failure, that failure should be greatest at the site of injection (which is never intravenous, it is either IM or IP) where the dose is many orders of magnitude higher than in a remote site such as the brain. We would expect to see acute necrosis at the site of injection. Acute necrosis at the site of injection is virtually never observed, therefore there is not acute mitochondrial toxicity from "toxins" in vaccines. In other words, every person injected with a vaccine has their mitochondria at the site of injection exposed to many thousands of times higher levels of "toxins" than is the brain of anyone who has ever developed mitochondrial neuropathy following vaccination. If the vast majority of vaccinated individuals don't have toxic effects at the site of injection it is virtually impossible for mitochondrial neuropathy effects observed in some individuals to be due to any kind of "toxicity". I discuss this more later.

Regression (with or without neuropathy) can occur as a consequence of an immune system activation, where transient high NO due to iNOS reprograms the basal NO level slightly lower by feedback inhibition of nNOS and eNOS expression, which then decreases the range of the NO release during neuronal activation (the cause of the BOLD fMRI signal), which lowers the functional connectivity of the brain which then drops below the percolation threshold and the functionality of the neural network drops exponentially especially in regions using NO to mediate social behaviors. Many social behaviors are mediated through neurotransmitters utilizing NO effects, including oxytocin, and steroids. There is positive feedback, where increased social isolation programs the brain to be less social and more on the ASD spectrum. There will be a future blog about that.

The root cause of autism: decreased actual and functional connectivity in neural structures mediating communication

Some of the mechanism(s) by which regression occurs is discussed in the blog on how there is acute resolution of autism symptoms during fever in the section on the "low NO ratchet". The regression of autism is called regression because children so affected lose behaviors mediated through the brain that they previously had. In that sense, any loss of any neuronally mediated function could be called "regression". The regression of autism is similar (my hypothesis) to the "regression" of neurosyphilis (which isn't called that, it is called paresis or paralysis), but depending on which part of the brain is affected the symptoms of paresis would mimic "regression". It is similar to the "regression" of Alzheimer's, which can be resolved acutely by the injection in the spine of agents which block TNF (and so acutely stop neuroinflammation). I see these different types of "regression" as being due to neuroinflammation which raises superoxide levels and so lowers NO levels. It is the low NO that accompanies neuroinflammation that causes the characteristic "regression". With low NO, the range of the neurogenic NO produced to regulate neuronal function is reduced. It is neurogenic NO that produces the vasodilation observed in the fMRI BOLD signal. Low NO in the brain, reduces the range of those NO signals, reduces the functional connectivity, reduces the ability of that brain to engage larger volumes of brain to achieve complex computations. Social computations are the first affected because many of the neural structures involved in social computations have effects mediated through NO, they are also extremely complex high-level responses requiring large computation volumes, so low NO is going to affect them a lot.

The brain is actively rewired to modify functionality. This is observed following stroke and other trauma to the brain. It must happen during development and learning. This remodeling occurs over the entire life span. The many details of how that wiring and rewiring occurs over the lifespan are virtually all unknown. If the brain is able to accomplish a computational task, it must have the neural structures to accomplish that task. Once the task is accomplished, those neural structures may not be needed any more. An example I give later is the ability of children to learn or synthesize new languages. Once the language is incorporated into hardware (i.e. the neural networks comprising those parts of the brain mediating communication), the ability to synthesize a new language isn't needed any more, and that ability is lost. Adults have "regressed" in that they have lost the ability they had as children to learn and synthesize new languages. It is not called "regression" and is not appreciated as "regression" because it happens to virtually all humans, and the lost abilities are not missed, and had no significant utility in evolutionary time (which is why evolution configured development to lose those abilities). Humans didn't need to acquire multiple new languages as adults 100,000 years ago. Once the language synthesizing scaffold generates the neural hardware to use language, the scaffold isn't needed any more and can be taken down and those resources (brain volume, neurons, blood supply, glucose, etc.) can be used for more important things, what ever those things might be.

The meta-programming of the brain occurs via modulation of functional connectivity. The details of how this happens are mostly unknown. It is known that it does happen, so there must be mechanisms that make it happen. These mechanisms cause functional connections to occur between parts of the brain such that activity in one part can then stimulate activity in another part which can then stimulate activity in another part.

I think a large part of that meta-programming of functional connectivity occurs through NO, through the same NO that causes the vasodilation observed by fMRI BOLD imaging. That NO is coupled to NO from each and every other source. That coupling is what modulates brain activity in sync with the physiology of the rest of the body. When the body experiences metabolic stress, NO is lowered, and this modulates the activity of the brain accordingly. There is nothing "abnormal" about this. Usually it takes extreme changes in physiology to produce extreme changes in brain activity. How "extreme" is a matter of degree. Low NO is going to change what counts as "extreme". Superoxide from inflammation or from metabolic stress is going to lower NO levels and reduce the functional connectivity.

I am necessarily describing a schematic cartoonish simplification. The details to go beyond a cartoon are not known. We know that there are lots of details we just don't know what they are yet. There are many details that I am leaving out of what I have written here. There is lots of stuff that connects what I am saying together. The "big picture" is very big, very complex and hard to get even a simplified cartoon of it to fit in something that anyone has even a small chance of reading, much less understanding ;)

Types of autism: Chronic via neuroanatomy vs. Acute via functional connectivity

As I see it, there are fundamentally two types of autism. The distinctions that I make are not precisely the same ones that other people make and there is considerable overlap. One can have either, both, or neither and to very different degrees. Both result from low NO, and are consequences of the fundamental programming of the brain to adapt to the environment the person is being born into, or is living in. The main difference is when the low NO happens, and for how long and does it come back up again and where one is in their development, in utero, infancy, childhood, puberty, early adult, middle age, or elderly.

First, there is autism due to neuronal development in utero. This results in the characteristic brain structures that are visible on MRI. The most notable characteristic is smaller and more numerous minicolumns, increased brain size and increased asymmetries. This fundamentally programs the brain for Asperger's and autism. Depending which particular part of the brain is affected by this neurodevelopment determines the spectrum of positive and negative mental abilities. There is a fundamental trade-off in brain function. The two main characteristic traits of humans are tool use and communication via language. Both of these require large brains. Since the size of the brain at birth is limited by the mother's pelvis, evolution has forced a compromise, an optimization of brain function, depending on the environment the fetus expects to be born into.

Social isolation in early life does cause low NO in the brain in later life. This occurs due to fewer NO producing neurons. This makes sense because if the brain doesn't need pathways to do social-type stuff (because there are no other individuals around to be social with), it is better to divert those resources to non-social-type stuff. This is the fundamental tradeoff along the autism spectrum.

As I see it, autism that develops in utero is more complicated because it depends on the idiosyncratic neurodevelopmental pathway of each individual. Which brain regions are affected and in what ways will determine the spectrum of positive and negative mental abilities and attributes. Autism that develops later in life is more simple because the underlying neuroanatomy is already fixed and isn't as malleable (it can still be extremely malleable, but the time scale is longer). The prompt behavioral effects discussed in the blog on fevers are due to resolution of the prompt and acute aspect of autism (lower functional connectivity). There is plasticity in that the brain can remodel itself even in adults but remodeling takes time, time that was not available during the acute fevers. My own experience is that increased NO has shifted my position on the autism spectrum making me more social. I still have Asperger's, but I am more aware of thing social, less anxious and aware that I am missing a lot that I was unaware of before. Those changes have taken years and are still ongoing. I am quite sure that this has involved neuronal remodeling. I will blog about this in more detail later.

The breakdown of ability to communicate that occurs later than in utero mimics some aspects of the autism which develops in utero but is fundamentally different and more mutable (to some extent). It is when the parts of the brain that deal with communication of certain types are forming (and remodeling) during early childhood that the communication aspects of autism occur. They can only occur when the brain is developing those structures.

It is wrong to think of "autism" as something extra that is added on or taken away from someone who is NT. To some extent, an individual's location on the autism spectrum will be shifted by their NO/NOx status. They can never be "cured". "Cure" is the wrong term to apply to autism. Autism is a range of neurodevelopment, the same way that muscle strength occurs in humans in a range (but neurodevelopment is much more complex). One can move in the muscle strength spectrum, but only to an extent. Autism is like the trade-off between fast-twitch and slow-twitch muscle. Most people have a mix, which lets them do a mix of different things. If you had only fast twitch, you would be a good sprinter but terrible at long distance. If you had only slow-twitch you would be good at long distance but terrible at sprinting. The trade-off on the autism spectrum is similar, a trade off of social skills useful for understanding and manipulating people for skill at understanding and manipulating non-social concepts. "Curing" a sprinter so they can no longer sprint is a wrong concept.

Autism is a complete spectrum in many dimensions. The most visible decreased ability is in social interactions, the most visible increased abilities are in the savant abilities. Usually savant abilities are different in different individuals. These are different dimensions of the autism spectrum. Everyone has some ability at calendar. People with savant calendar are just really good at it. NTs have communication abilities with other NTs that are "savant" compared to the communication abilities of people on the autism spectrum.

The fundamental problem of autism is that some people who are NT are unable to "connect" with people who have autism and that inability to "connect" is intolerable to those NT individuals. This is not a problem of people with autism; it is a problem of some people without autism. This is not to minimize the real difficulties that people with autism have, but those problems are greatly amplified by being treated badly by NTs. The distress that NTs feel when around people with autism is about the NTs, not the people with autism. A fundamental problem that many NTs have is a tendency to project human attributes on non-human things, as for example in Uta Frith's work on the emotional states and motivations of triangles. Communication between individuals requires those individuals to transmit information (i.e. language) allowing each of them to construct (to some fidelity) a representation of the mental state of the other. Projecting one's own mental state onto another is common. When two people are able to map their mental states onto each other, they are able to "connect".

Mapping a mental state from one individual to another individual requires neuroanatomy that can accomplish this. If the mental state cannot be mapped from one individual to another, those two individuals cannot communicate that mental state and cannot "connect" on that level. I think this is a reason for some of the fundamental difficulties in communication that NTs and ASDs have with each other. There are dissimilarities in neuroanatomy that make mapping of mental states between them difficult.

I think (and this is perhaps the most controversial idea in this blog entry) that all NTs have very complex neural net "hardware" that allows NTs to communicate easily and effectively with other NTs. This NT neural net hardware is what NTs use to think their NT thoughts. ASDs lack that neural net "hardware", but can emulate a facsimile of it (to some extent) in the neural net "hardware" that ASDs use for thinking their ASD thoughts. The emulation that ASDs can do is not as high fidelity as the hardware that NTs have and this bothers NTs a lot. Most NTs can't emulate ASDs at all and this doesn't bother those NTs at all, or rather any discomfort those NTs feel is attributed to and projected onto the ASDs and the ASDs are blamed for it (and bullied) as a consequence.

It is the NT neural network that gives NTs the "savant" ability to communicate with other NTs. They don't know how they do it, they can't imagine not being able to do it, they can't imagine anyone else not being able to do it. That is the problem.

Genetic abnormalities: What is the final common pathway? Low NO phenotype (my hypothesis)

There have been many single gene mutations and some more complex mutations associated with autism. I think that most of the single mutations and deletions that are associated with autism "cause" autistic symptoms by invoking metabolic stress and shifting metabolism to a low NO state where the low NO phenotype is invoked and which has more autism-like symptoms. It is the low NO state which triggers the epigenetic development (controlled by many genes), not the simple genetic abnormality per se. If the low NO state can be reversed, I think it is likely that many of the autism-like symptoms can be reversed also. I think this is what happens in Rett Syndrome. The MeCP2 single gene defect puts metabolism under substantial stress by greatly interfering with methylation signaling. Metabolism responds by invoking low NO (my hypothesis), the low NO skews ongoing function and continuing neurodevelopment onto the low NO autism path. In the MeCP2 mouse model, restoring MeCP2 function restores normal physiology, removes the stress, allows NO levels to return to the non-stressed state and restores the non-Rett neurological phenotype. This demonstrates that the "autism" of Rett Syndrome in the mouse model is fundamentally not an issue of neurodevelopment. The neurological phenotype of mature adult mice is restored by restoration of MeCP2. In humans it is more complex because lots of neurodevelopment has occurred under conditions of low NO produced by the MeCP2 defect. People with RS don't have the larger brains that people who develop autism in utero typically do.

The autism phenotype is caused by low NO (my hypothesis). How that low NO occurs doesn't matter. NO can diffuse everywhere, there are no barriers to NO, and each NO sensor only senses the sum of NO from all NO sources. The NO sensor sums and integrates NO from all sources and then produces an output which evolution has determined is likely to be the most suitable. Sometimes it isn't. That is why anaphylaxis sometimes kills people and sometimes saves their life. Physiology has to respond before it "knows" exactly how strong a response is necessary.

There are multiple ways for low NO to occur. The main focus of this article is on the generation of superoxide by mitochondria under high NO levels causing mitochondria depletion which causes high superoxide due to higher mitochondrial potential. Inflammation also generates superoxide from activated immune cells. Metabolism of normal and xenobiotic chemicals by the cytochrome P450 enzyme system also makes superoxide. Xanthine oxidoreductase also makes superoxide.

I think it is better and more correct to call autism-like behavioral symptoms associated with metabolic stress due to genetic abnormalities as "autism-like" syndromes. The "degree" of autism is purely an arbitrary definition. I agree with Michelle Dawson that terms such as "high functioning" and "low functioning" are not useful and should be discouraged. The behaviors characterized as affected in autism are multi-factorial, diverse with a great deal of variability within and between individuals. "Functionality" doesn't correlate well with any traits that can be easily characterized. The largest factor in an individual's ability to cope is likely the other people in that individual's environment. Are they helpful and supportive or hurtful and non-supportive. I think that much of the variability observed in individuals relates to their acute NO status. During fevers the NO level is raised acutely by expression of iNOS and I think that increased NO is the mechanism for the resolution of autism symptoms during fever. Any mechanism to raise NO levels will have similar effects. Raising NO levels during childhood puts the child back on the high NO development paradigm which leads to a more NT phenotype. Maintaining a low NO level causes development on the ASD developmental paradigm and results in the ASD phenotype. There is some degree of movement on the ASD spectrum at any age.

Smaller and more numerous minicolumns are also observed in the brains of distinguished scientists. I suspect they were exposed to low NO in utero and early childhood, developed the characteristic neuroanatomy, and then had high NO levels restored later which allowed for more normal social and communication abilities. My expectation is that if the appropriate NO levels are restored sufficiently early during neurodevelopment in childhood this is how people with autism in utero will turn out.

The diagnostic criteria for autism are all behavioral. The behaviors are mediated through neuronal structures that develop over time. Until those neural structures have or have not developed, a diagnosis as to how they behave once they do develop cannot be made.

What are Mitochondria?

Mitochondria are major energy sources of cells. Each cells has many mitochondria, some have many thousands, some have many more. All the mitochondria are essentially identical. There are some differences in different tissue compartments but the basic mitochondrial DNA in an individual is all identical and inherited 100% from your mother. They produce ATP by oxidizing substrates (the only site in the body that does so). They also produce superoxide where usually a few percent of O2 consumed ends up as superoxide. This superoxide production is a normal, necessary and irreplaceable part of mitochondria regulation. Mitochondria cannot function properly unless they produce superoxide. That superoxide is an important part of very important signaling pathways. Superoxide is confined to the mitochondrial matrix where it is dismutated into H2O2 which can diffuse through the two mitochondrial membranes. Mitochondria are also important in a number of chemical synthesis steps. Urea is produced from ammonia to detoxify it. All urea synthesis occurs in mitochondria in the liver. Heme is made (in part) in mitochondria as are the iron-sulfur clusters which are also used in oxidation enzymes. Hemoglobin is made using mitochondria (to synthesize the very large quantities of heme) and then the mitochondria are removed from red blood cells during their maturation.

Nitric oxide regulates mitochondria at multiple levels, by multiple mechanisms, at multiple time scales, for multiple different reasons in multiple different tissue compartments at multiple different sites on multiple different enzymes in the respiration chain and elsewhere. None of this simple, or is even close to being well understood. Much of this regulation is in synergy with production of superoxide. Mitochondria generate superoxide which is confined to the inner matrix, the local NO level communicates the effects of that superoxide to neighboring mitochondria (and elsewhere) so all the mitochondria can operate "in sync" and so that all of physiology can work "in sync" too. This is an extremely important regulatory function of NO diffusion, keeping mitochondria "in sync" in each cell, in each tissue compartment, in each organ, and in the entire organism. Mitochondria not being "in sync" is a source of reduced efficiency and can lead to dysfunction or even death.

Acute mitochondria failure

In a nutshell, mitochondria failure during immune system activation results from mitochondria being pushed to a high potential (where they generate a high superoxide flux) under conditions of high NO. This generates a high peroxynitrite flux in the inner matrix which eventually deactivates MnSOD causing superoxide levels to increase further which accelerates the production of peroxynitrite. This causes respiration chain inhibition and eventually mitochondria turn-off. Some early steps in this inhibition by this regulation are reversible; eventually a point is reached where the inhibition depletes ATP production in the cell so severely that the inhibition is irreversible. That is, the cells become so depleted in ATP that they do not have enough ATP to repair the damage and recover.

This is not a "disorder" per se; rather it is the normal regulation of mitochondria causing a bad outcome, sort of like the way anaphylaxis can cause a bad outcome. Is anaphylaxis a "disorder"? No, if you had bacteria in your blood stream you want an enormously powerful immune system response because in "the wild", that is the only thing that has a possibility (however remote) of saving your life. Evolution has configured the immune system to minimize the sum of deaths from too strong an immune response (death from anaphylaxis) and from too weak an immune response (death from infection). In an attempt to avoid death from infection, some risk of death from anaphylaxis is acceptable.

Destruction of too many mitochondria under the extreme NO production that occurs during sepsis occurs for the same (ultimate) reason that anaphylaxis occurs. Evolution has configured mitochondria to be turned off under certain conditions so as to minimizes the sum of deaths from mitochondria not turning off enough and from mitochondria turning off too much. It is a balance between two extremes, the way that most things in physiology are. This is not to suggest that there is only one "switch" that determines mitochondrial fate, no doubt there are many. NO happens to be an important one in the context of immune system activation.

This effect is related to the resolution of autism symptoms during fever which I discussed before. It is related in that both effects are caused by high NO, but the level of NO is considerably higher for mitochondria destruction compared to the resolution of autism symptoms. These levels are still quite low (and difficult to measure). Normally the basal NO level is less than the order of a nanomole per liter. That is less than 30 parts per trillion by weight. If the NO level gets up as high as 300 parts per trillion, guanylyl cyclase is about 50% activated and there is massive vasodilation. This does happen in septic shock. It doesn't happen in a simple fever except perhaps locally where there is a local infection, local inflammation and local vasodilation. Locally this is a healing mechanism to bring more blood flow, more immune cells which then generate more NO and more H2O2 to fight the local infection. When the infection becomes systemic, then there is a life-threatening crisis. In the "wild", such a life threatening infection was likely to be fatal and extreme desperate measures are called for by physiology. This is the extreme desperate measure of septic shock.

This paper has a cartoon that shows the mitochondria respiration chain and its regulation by NO and NOx. The point of the cartoon is that there are many different parts of mitochondria that are known to be regulated by NO and NOx, and that regulation is complex in time, space, and under diverse metabolic conditions only some of which are known. The "details" of none of these mechanisms are well understood and are the topics of intense and ongoing research (which is quite challenging). The regulation of mitochondria by nitration occurs in seconds to minutes under conditions of hypoxia, and then is reversed (to some extent) also in a few minutes. Isolating mitochondria so they can be analyzed but without perturbing what is going on (and then demonstrating there has been no perturbation) is very challenging. Mitochondria turn-over; that is they have a finite lifetime and some are replaced each day, usually at night when humans are least active. So when mitochondria are isolated from experimental animals, the entire mitochondria population is isolated, which includes mitochondria of all different life spans (that is time since created).

Mitochondria in neurons

It is loss of ATP from mitochondria in neurons that causes neuron death and neuropathy. Mitochondria in neurons are simpler than in the rest of the body because they don't oxidize lipids. Neurons also don't generate ATP via glycolysis, it is pretty much only generated by mitochondria through oxidation of substrates, lactate, ketone bodies, small acids such as acetate, aspartate. Mitochondria are small organelles that have a few thousand proteins, only 13 of which are coded for by mitochondrial DNA, all the others are coded by nuclear DNA. Mitochondria have 2 lipid membranes, inside the inner one is where the DNA is and the protein manufacture stuff (the mitochondria matrix). Mitochondria work by generating an electrical potential and a pH gradient across that inner membrane. The different respiration complexes take electrons and protons from chemical compounds and extract energy from the chemical reactions as those electrons and protons are moved across the membrane and store that energy in the electrical and pH gradient. That energy gradient is then used to make ATP. Eventually those electrons are added to protons and added to O2 making water. Four electrons and four protons are added simultaneously to make two molecules of water. Doing a four electron reaction is very tricky.

The 13 proteins are all parts of the respiration chain, usually the part containing the active site. All animals (except for a few invertebrates) have these same 13 proteins coded in their mitochondria. Plants have a few extra. These proteins are all large and quite hydrophobic. Why these (and only these) proteins are coded in mitochondria is not understood. I think it has to do with the necessary regulation of mitochondria, some of which has to be local to each mitochondrion and sometimes that regulation means turning off part of the respiration chain and then turning it back on which means making the protein again. In most cells mitochondria are close to the nucleus so that proteins can be made from DNA in the nucleus and then transported to mitochondria (in principle, whether this happens or not is unknown). In neurons that can't happen because the distance between the cell body (where the nuclear DNA and the protein synthesis capacity is) and mitochondria can be inches or even a meter in motor neurons. There simply isn't time for a signal to propagate from mitochondria to the cell body, trigger protein synthesis and then transport proteins out to mitochondria in need of them. If protein synthesis is needed for control of mitochondria, that synthesis must occur locally using locally available DNA. There is pretty good evidence of local regulation of mitochondria activity by the de novo synthesis of proteins in mitochondria. The ability of mitochondria to synthesize the active site of respiration chain enzymes allows irreversible inhibition of the active site to be an acceptable control scheme. If the active site is inactivated it can be replaced in situ by de novo synthesis from mtDNA. The active site is the parts of the respiration chain most exposed to oxidative damage. No other proteins can be replaced in situ. Mitochondria do have the capacity to degrade individual proteins with ATP powered proteases. Amino acids can be degraded and fed into the citrate cycle and oxidized to CO2. Use of highly reactive agents (superoxide derived peroxynitrite) to regulate the active sites of the respiration chain, allows the more distant non-active regulatory sites to be spared contact with the inhibiting agent (because it reacts before it reaches them). The sparing of regulatory components from oxidative damage increases their lifetime and so prolongs the time that mitochondria can survive solely using mtDNA. It think this is also part of why neuronal mitochondria are more simple, fewer proteins to carry means the lifetime of functional mitochondria can be longer while remote from the cell body.

Motor neurons are long, up to a meter in length. Mitochondria can only be made in the cell body, which is in the spine, because that is where the nucleus is and the only place that 99% of the proteins in the mitochondria can be synthesized. Once made, mitochondria are carried out via ATP powered motors to the tippy end of the axon, and when they get "tired", they are carried back for reprocessing via autophagy. In the rat CNS, mitochondria have a half life of about a month. That is in rats, it is likely somewhat longer in humans, but probably only a few months, likely not years.

As the largest cells in the body, neurons are unique. Virtually all of the metabolic load is in the axon far from the cell body. Because the metabolic load depends on the axon length, and the axon length can vary from less than a mm to a meter, the metabolic load (and hence the number of mitochondria must also vary by more than 3 orders of magnitude. A very important question is how does the cell regulate the mitochondria number in neurons over multiple orders of magnitude? The answer is: extremely well. The only type of regulation that would be able to work with such fidelity is feedback control. I suspect that some of the peculiarities of neurons as cells (such as absence of glycolysis and lipid oxidation) reflect physiological constraints imposed by the need for this regulation.

The time constant of that mitochondria feedback control has to reflect the time constant of the lifetime of the mitochondria in the neuron. The neuron needs to control both the number of neurons and also the age distribution of those mitochondria. This is an important point. If the age distribution gets too far out of whack, then at some point too many mitochondria will get old simultaneously and ATP production drops. If ATP demand exceeds the ATP that the remaining mitochondria can supply, the neuron becomes ATP depleted and either sheds metabolic load or dies. I suspect that maintaining the age distribution of mitochondria is one reason why regrowth of nerves is so slow.

Normally cytochrome c oxidase (the enzyme that consumes O2) is tonally inhibited by NO, which blocks O2 from binding and is the major regulatory pathway by which mitochondria regulate their O2 consumption. The only reason that mitochondria can regulate their O2 consumption is because NO "poisons" cytochrome c oxidase and inhibits O2 consumption. Remove that inhibition and mitochondria consume O2 to very low partial pressure, an order of magnitude below what is the "normal" basal O2 level at the location of the mitochondria. At "rest", the O2 flux to a mitochondria in the heart is 1. The O2 consumption by that mitochondrion can increase by 10x. The flux of O2 from the blood vessel to the mitochondrion is purely passive down a concentration gradient. For the flux to go up 10x, either the gradient has to go up 10x, or the distance has to go down by 10x because the concentration at the blood vessel stays the same. For the gradient to go up by 10x, the concentration at the mitochondrion has to go down, and go down a lot, by a factor of 10x. It has to go down while the mitochondrion is increasing its O2 consumption by 10x. The specific O2 consumption by that mitochondrion, moles O2/mg protein/Torr O2 has to go up by a factor of ~100. This is only achieved by removing the "poisoning" of cytochrome c oxidase by NO. This removal is accomplished by the generation of superoxide. The ATP production of neuronal mitochondria probably doesn't change by an order of magnitude. The mitochondria in heart muscle can.

The capacity of mitochondria to generate superoxide is limited only by the supply of O2 and reducing equivalents. The same substrates that mitochondria use to generate ATP.
Superoxide is generated vectorally into the inner matrix. It is charged, so it can't pass through lipid membranes except through anion channels. There is also a pretty high potential, ~140 mV across the inner mitochondrial membrane that tends to keep anions inside. Superoxide is dismutated to H2O2 which is uncharged and so can diffuse through lipid membranes. Normally a few percent of O2 consumed is converted into superoxide (O2-). Superoxide is generated when the mitochondria potential gets high; it is also generated if the respiration chain becomes too reduced, such as when cytochrome c oxidase is blocked. When cytochrome c oxidase is blocked by NO, that blocking is reversed when superoxide is generated (this destroys NO resulting in disinhibition).

What happens when there is insufficient cytochrome c oxidase activity? The respiration chain becomes reduced and superoxide is generated, but the NO level can only go to zero where there is no more inhibition of cytochrome c oxidase. Before that happens other parts of the respiration chain start to be inhibited in many cases also by NO and NO metabolites; including complex I, which introduces reducing equivalents into the respiration chain from NADH, and also complex III which takes reducing equivalents from succinate (from the citrate cycle). There are a couple of different pathways by which that inhibition occurs, some critical thiols become S-nitrosated, and some tyrosines become nitrated. The S-nitrosation is pretty much reversible, some of the nitration is reversible too. The details of this regulation are not well understood and involve NO, superoxide, glutathione, CO2 and no doubt other things. There are over a thousand different proteins in mitochondria. Which ones are regulated by NO and by what mechanisms, in what order and for what purposes under what conditions are mostly unknown. It is obvious that all of those proteins are regulated to work together and "in sync".

Cells can't allow the regulation of mitochondria to break down.

What happens if that regulation were to break down? If the regulation of the mitochondria were to somehow fail such that production of superoxide was not limited? Making superoxide from O2 requires only a single electron, reducing that O2 to two H2O requires 4 electrons. Mitochondria have the theoretical capacity to make at least 4 times more superoxide than they do to consume O2 to make ATP. Mitochondria can increase their metabolic rate many times over the basal rate, some as much as 10x. A few "bad" mitochondria could consume O2 and substrate and produce high levels of superoxide and/or H2O2. Cells cannot afford to have even a few mitochondria running out of control. They could easily kill the cell. Mitochondria generating superoxide at maximum rate could consume the O2 that 30 or 40 times more mitochondria could use at rest. To stop a few bad mitochondria from killing the cell, there must be a "fail-safe" mechanism that reliably turns mitochondria off.

Turning off mitochondria when they produce too much superoxide is easy to observe. and there are multiple mechanisms to decrease superoxide levels when there is too much, including inhibition of the respiration chain, and also expression of uncoupling protein which short circuits the membrane potential dissipating it as heat. Uncoupling protein is from nuclear DNA, so it can't be used in neurons. Mitochondrial uncoupling is a major factor in the heat production during malignant hyperthermia. The problem of malignant hyperthermia isn't just temperature; it is the consumption of substrate and the turn-off of mitochondria which causes a profound reduction in ATP levels and in ATP production capacity. If ATP levels in cells drop enough, the cell will die. Cell death due to ATP depletion in irreversible. There is no way to supply ATP from outside cells. Either a cell has the metabolic machinery to generate sufficient ATP and survives or it does not survive.

Superoxide, a necessary evil.

Because much of the regulation of mitochondria depends on the interplay between NO and superoxide, what happens when mitochondria don't make enough superoxide? Because the regulation requires superoxide, there need to be mechanisms to increase superoxide when the level falls too low. These have not been as well described in the literature. I think largely because there are no good experimental techniques that are well recognized for reducing the superoxide production in part because the physiological pathways are so well regulated. There is a technique which I think does this, but which isn't well appreciated as such, that is the use of near infrared light to photodissociate NO from cytochrome c oxidase. I mention this technique in my blog on the magic light helmet for Alzheimer's.

What does chronic lack of mitochondria biogenesis look like?

I suspect the symptoms will mimic the delayed symptoms of mercury poisoning such as the dimethylmercury poisoning experienced by a woman heavy metals researcher where she had a lethal body burden of dimethyl mercury following acute exposure (estimated at 1,344,000 micrograms at exposure) with no symptoms for 5 months. At 5 months (time of diagnosis) she had a measured blood level of 20,000 nM/L, and a body burden of 336,000 micrograms. This has nothing to do with the non-existent mercury poisoning that the quacks and frauds attribute autism to (which they assert occurs promptly (days) following vaccination with a trivial quantity of mercury (~15 micrograms). These delayed symptoms are for real mercury poisoning, which occurs at levels that are unmistakably diagnosed via testing of any specimen, blood, urine or hair. The level she was exposed to was roughly 100,000 times the level in vaccines.

The very long symptom free period (5 months) demonstrates that even these extremely high mercury levels are not acutely toxic to mitochondria. If they were acutely toxic, she would have died much sooner. Nerve cells can only function for a few seconds without mitochondria. Cells that can do glycolysis can function longer, perhaps minutes. There are essentially no cells that can function indefinitely only on glycolysis. Red blood cells can, but they have a finite lifetime. The major important tissues, muscle, liver, kidney, gut, skin, etc. all require mitochondria. Mitochondria are required to make heme and also to make the iron sulfur complex that is the active site of many proteins. Since the exposure was through essentially a point contact, a spill of pure material on her gloved hand, the local dose to those skin cells was absolutely gigantic. Essentially pure dimethylmercury ended up on her skin. There was no report of acute necrosis of the skin, presumably it didn't happen. If it had happened, perhaps her exposure would have been recognized and she would have been treated. That treatment might have saved her life. I think the five month delay was due to the normal turnover of mitochondria without replacement due to a blockage of mitochondria biogenesis due to the extremely high levels of mercury. I think this relates to the interference with the recycling of mitochondria during autophagy, and specifically in the blunting of the NO/NOx signal that occurs during autophagy. What is interesting is that the organ that failed was the brain, not the other organs. My explanation of this is that these levels of mercury disrupted the normal feedback regulation of mitochondria biogenesis, but only in neuronal tissue. The mechanisms that regulates mitochondria turnover in neuronal tissue (or in any tissue) have not been identified. That there must be such mechanism(s) is certain. With zero mitochondria biogenesis in neurons I would expect the onset of symptoms of failure of the CNS to occur pretty abruptly as observed in the dimethyl mercury poisoning. There is significant redundancy and fewer mitochondria running at high potential can produce the same ATP as many running at low potential. I would expect the abruptness of the transition from essentially no symptoms to death to be pretty rapid (as observed). The abruptness relates to the average of the mitochondria and the number that fail at any one time. The higher the metabolic load each mitochondria experience, the faster it will age and ultimately fail. The longest nerves are the ones affected first, as experienced by peripheral numbness. This is typically the same pattern observed in other neurodegenerative diseases such as amyotrophic lateral sclerosis. The peripheral nerves are (typically) the ones that go first. Mitochondria biogenesis likely doesn't go to zero in ALS the way it likely did in the mercury poisoned woman.

The fundamental control paradigm of mitochondria is for them to produce more superoxide when they require producing ATP at a higher rate. Mitochondria biogenesis can only occur when the superoxide level is low. If the number of mitochondria drops below the level where they can produce sufficient ATP while maintaining a superoxide level sufficiently low for mitochondria biogenesis to happen, then mitochondria biogenesis will stop and cannot be resumed. This is the point of no return beyond which the cell it occurs in is doomed.
The first symptoms this woman noticed were neurological. The CNS has the longest lived mitochondria. For mitochondria depletion to be observed in the CNS first, it must have been essentially non-existent in other tissue compartments. That the disruption is only in neuronal tissue puts quite severe constraints on what the mercury could be doing. It is likely not due to inhibition of key mitochondrial enzymes (that would lead to acute mitochondrial inhibition in many tissues and prompt death) or even inhibition of enzymes that make key mitochondrial enzymes (that would lead to reduced mitochondria biogenesis in all tissues and multiple organ failure on the time scale of mitochondrial turnover for that organ). Mitochondria in neurons are the simplest mitochondria. They don't oxidize lipid or transaminate most amino acids so they likely have only a subset of the enzymes that all other mitochondria have. They should be the most resistant to toxicity because they have fewer enzymes to be disrupted. In some cases of mitochondrial toxicity, the first mitochondria to be damaged are those in the liver with mitochondria in muscle and brain being spared, as for example in Reye's Syndrome. Salicylate increases superoxide production in liver mitochondria and this is what causes Reye's syndrome. Reye's syndrome is characterized by fatty liver and encephalopathy. It would make sense for liver mitochondria to be the most susceptible to toxicity. The liver has the greatest capacity for detoxification, the liver can regenerate itself, a lot of the toxicity of xenobiotics is actually due to the xenobiotic metabolites, not the parent compound.

Since the mitochondria in neurons are the simplest, mitochondria in other tissue compartments have more proteins and enzymes to do more complicated things. The disruption of mitochondria biogenesis in neurons is likely not due to disruptions in transcription because transcription of mitochondrial proteins in other tissue compartments is continuing. Since those mitochondria are more complex than neuronal mitochondria, the loss of neuronal mitochondria biogenesis is likely not due to blocking transcription.

That leaves the signaling upstream of transcription. This relates to a poster I presented at the NO conference 2 years ago, where I hypothesized that the long term regulation of mitochondria number in neurons was mediated through NO/NOx generation during autophagy of dead or dying mitochondria from nitrated proteins. The concentration of nitrated proteins in recycled mitochondria is dependent on the level of metabolic stress that mitochondrion experienced over its lifetime. In other words, the degree of metabolic stress a mitochondrion experiences regulates its membrane potential which regulates its superoxide production which regulates its peroxynitrite production which regulates how many proteins get nitrated by how much. Autophagy reads back that signal and generates the appropriate number of new mitochondria to meet the need. I will discuss the details in a later blog. Autophagy is the only way by which mitochondria are recycled, and recycling of mitochondria is "tricky". Mitochondria are quite dangerous. They contain Fenton active metals, Fe, Cu, and Mn, which can produce hydroxyl radical from H2O2. Hydroxyl radical is extremely reactive. It is so reactive that antioxidants are ineffective against it. Virtually any organic molecule is reactive enough toward hydroxyl that the first molecule hydroxyl hits is damaged.

Inhibition of mitochondria by NO/NOx a critical regulatory feature

There must be a fail safe mechanism that turns off dysfunctional mitochondria to prevent the useless (and dangerous) consumption of O2 and substrates. I suggest that mechanism occurs by the simultaneous generation of too much superoxide in an environment of too much nitric oxide. Normally this mechanism protects cells from a few aberrant mitochondria, the loss of which is of no serious consequence. Under conditions of very high immune system activation many mitochondria can be turned off such that normal metabolism of the cell becomes impossible and the cell dies. When many cells in an organ die, this leads to organ failure, and eventually to multiple organ failure.

The normal regulation of O2 consumption of cytochrome c oxidase is via the destruction of NO by superoxide by a reduced respiration chain. One of the most important targets for regulation by NOx is MnSOD, manganese superoxide dismutase. This enzyme is only found in the mitochondrial matrix, but it is coded for in nuclear DNA, not mtDNA. This means that the total amount of MnSOD a particular mitochondria has is finite and can't change over that mitochondria's lifetime except by going down as it is either inhibited or degraded. MnSOD dismutates superoxide into H2O2 at near diffusion limited kinetics. Those kinetics are close to the rate that superoxide reacts with NO. Superoxide is vectorally generated in the mitochondrial matrix, where there is competition between reaction with MnSOD and with NO. When NO reacts with superoxide it forms peroxynitrite (ONO2-). What happens then depends in part on the CO2 level but we will ignore that complexity.

Peroxynitrite can nitrate proteins, it can also decompose generating NO2 which can also nitrate proteins. The amino acid most susceptible to nitration is tyrosine forming nitrotyrosine. Human MnSOD is inhibited by nitration of a single tyrosine. Bacterial FeSOD (which is highly homologous with MnSOD) is not inhibited when 8 of 9 tyrosines are nitrated. That the two enzymes are homologous demonstrates that they derive from a common ancestor. That the bacterial FeSOD is virtually totally resistant to inhibition due to nitration demonstrates that inhibition by nitration is not an intrinsic property of SOD enzymes. If bacteria evolved SOD enzymes that are highly resistant to inhibition due to nitration, then organisms with mitochondria could too. They haven't, implying that inhibition due to nitration is a "feature" that has been positively selected for by evolution. I think it is, and the very important feature that that nitration accomplishes is the feature of turning off mitochondria when they become damaged, a function that is not necessary for bacterial SOD enzymes. I think this nitration is also important in transducing and integrating the degree of metabolic stress that each mitochondria has experienced over its lifetime, so that during autophagy that signal can be read out and the appropriate number of mitochondria generated to match the load. I think this occurs by the nitrated tyrosine being converted to NO/NOx by conditions during autophagy.

When mitochondria generate ATP, it is always very important that all the mitochondria work "in sync" that is that all the mitochondria generate ATP in concert. If there were differences in how the load of ATP generation were distributed among the mitochondria, then the ones generating more would be overloaded (relatively) and those generating less would be underloaded (relatively). That represents inefficient allocation of resources. Fewer mitochondria efficiently loaded could generate more ATP and at a lower metabolic cost than more mitochondria inefficiently loaded. Over evolutionary time organisms with efficient mitochondria loading will out reproduce organisms with inefficient mitochondrial loading. I suspect this may be one of the primary reasons that all mitochondrial inheritance is only through the maternal line. It is extremely important that all mitochondria in a cell be as identical as possible so they are controlled in sync. If the mitochondria were not identical, then the regulatory mechanisms to share the load could not affect them uniformly. If mitochondria were not reset to all identical in each oocyte, then over multiple generations there would end up being considerable variation in mitochondria. A variation that would preclude precise regulation of all the mitochondria in a cell in sync. I think this is especially important in organs such as the brain where NO regulation of mitochondria is required to be extremely precise and synchronous in both time and space for good function.

It needs to be remembered that there are mitochondria of different ages in each cell. Mitochondria have a finite life time, the longest is about 30 days in rat CNS. Each mitochondrion is "born" in the cell body, loaded with proteins coded in nDNA and then transported out the axon by ATP powered motors.

When a cell needs more ATP, the ATP level drops and the mitochondria "turn on". The details of that process are not important for our discussions. One of the things that regulates the NO level is sGC which is also controlled by ATP. The sensitivity of sGC to NO is modulated by ATP, with low ATP causing greater sensitivity. This is the mechanism by which cells control their ATP level, and via NO how they communicate that ATP level inside the cell and between cells. Communication of ATP levels between cells is very important so that entire organs (and the entire organism) can be regulated "in sync". In the heart for example, different muscle cells need to be equally loaded, to maintain efficient allocation of the resources needed by the heart, glucose, insulin, lipid, O2, hormones, etc.

Normally, the basal NO level is modest, ~1 nM/L, and the mitochondria work together in sync to consume O2, generate and consume NO to regulate cytochrome c oxidase and generate ATP. With all the mitochondria working together, they all experience about the same ATP, O2, and NO levels, and the proportionality of ATP and NO is maintained via sGC. In the brain, this synchronicity is important because NO is a neurotransmitter, one of the very few that passes through cell membranes without requiring a receptor. NO signaling could (conceivably) even occur in the white matter where NO could generate "cross talk" between axons.

Under such circumstances if one mitochondrion begins producing superoxide at a higher rate than all the others, it generates more superoxide, pulls the NO level down locally to itself. This reduces the local ATP level via sGC which accelerates mitochondria ATP production. A period of positive feedback ensues where the mitochondrion generates more superoxide and more peroxynitrite than its neighbors and the mitochondrion begins to down regulate different parts of the respiration chain. Either the mitochondria achieves a new stable operating point where the consumption of O2, NO and generation of superoxide and ATP matches that of its neighbors, or it becomes irreversibly inhibited.

The critical parameters for this regulation are the ATP production rate by the mitochondria and the NO concentration. High ATP production requires a high mitochondria membrane potential and so generates a high superoxide flux. That superoxide flux pulls down the NO level and is dismutated to H2O2. If ATP production or superoxide production is high in the presence of high NO, then there is inhibition of the respiration chain.

If all the mitochondria in a cell are operating at the same level, then the NO and superoxide levels go up and down in sync. The ATP demand is shared between the mitochondria. If one mitochondria gets overloaded, then that mitochondria has a superoxide level that is out of sync with the NO level that all the other mitochondria are experiencing. That overloaded mitochondria makes more peroxynitrite which down regulates that mitochondria. Reversibly at first and then irreversibly. If this happens to one or a few mitochondria, there are plenty left to support the ATP demand of the cell.

With this understanding of mitochondria regulation, the life cycle of mitochondria becomes clear. Mitochondria are made in the cell body, they migrate out the axon carried by ATP powered motors. When mitochondria have a high potential, they move out away from the cell body. When they have a low potential they move back toward the cell body. The sorting of mitochondria by potential, keeps active mitochondria out in the axons and returns dead, dying and dysfunctional mitochondria to the cell body for reprocessing.

In neurons essentially all the metabolic load is out in the axons, and the axons can be different in length by 3 or 4 orders of magnitude. This means the mitochondria number must also be variable by 3 or 4 orders of magnitude. This variability occurs in each cell. When a cell first divides, it is small and then grows larger. The number of mitochondria must be matched to the cell's metabolic demand at every stage in that cell's lifetime, which for a human is the entire lifespan (because many CNS neurons do not divide).

In the cell body mitochondria are reprocessed by autophagy. Cytoplasm including mitochondria is engulfed in a vacuole, protease and other lyase enzyme precursors are ported in, and a pH gradient is set up by the ATP powered proton pump VH-ATPase. The pH gradient is then used to power the transport of other things too. There are a pretty large number of proteases, the cathepsins and they catalyze the breaking of peptides into smaller ones some of which are sorted out and recycled.

The details of autophagy remain mostly unknown. It is the only mechanism by which organelles can be recycled. It is something that all eukaryotes do. It is the only way to recycle mitochondria.

The recycling of mitochondria occurs regularly. In rats, it occurs during the period of low activity, during the day. This makes perfect sense. Mitochondria biogenesis requires a high NO level, and also first requires the destruction of the mitochondria being recycled. This temporarily reduces the ATP production capacity of the cell, so it is not something that the cell can allow to happen if there isn't enough ATP to start with, or to complete the process. The period of lowest ATP demand is during sleep, when activity is lowest. With the highest NO level during sleep, the highest ATP level would be during sleep also.

This is a very important point. The number of mitochondria in a neuron is adjusted every day. Some are disposed of through autophagy, and new ones are made. Disposing of mitochondria takes ATP, as does making new mitochondria. During times of low ATP, this is put off until later. Even crappy dysfunctional mitochondria make ATP. Completely dead mitochondria don't consume ATP until they are reprocessed. If there isn't enough ATP, it is better to put those things off until later when more ATP is available.

How the mitochondria number changes over time demonstrates the mechanism for mitochondrial dysfunction.

If there is mitochondrial "toxicity", the number of mitochondria changes acutely, in a single day. That produces an acute effect on physiology. If that is a severe effect, the consequence is immediate death. This is what causes death from sepsis, hyperpyrexia, malignant neuroleptic syndrome, cyanide poisoning, CO poisoning and a few others.

If there is a change in physiology that is not abrupt, it cannot be due to mitochondrial toxicity. If there is slow mitochondria depletion, that is a problem with mitochondria biogenesis, with the ongoing replacement of mitochondria. If that replacement goes to zero, the result is death with the time scale depending on the tissue compartment. The longest living mitochondria are in the CNS, lack of replacement of mitochondria there would follow the clinical course of the woman with dimethyl mercury poisoning (discussed earlier), essentially no symptoms until the mitochondria depletion reaches a certain level then very rapid decline and death.

If someone has survived for a year, they are replacing mitochondria in their CNS. They might not have "enough" mitochondria, but not enough mitochondria is due to a disruption of the regulation of mitochondria number, not due to blocking mitochondria biogenesis. Mitochondria biogenesis is triggered by NO. Low NO is going to skew the mitochondrial number to a lower value. This is one fundamental cause of insufficient mitochondria, too low a basal NO level. This is what causes physical detraining and also chronic fatigue (which is just an extreme form). If the background NO level is too low, exercise may not be able to raise it enough to trigger sufficient mitochondria biogenesis. In that case there isn't a way to increase mitochondria levels.

That clinical course, no symptoms and then rapid decline and death could occur in any organ. When it happens in the liver it is called fulminate liver failure.

So what happens during sepsis?

During sepsis the level of NO can become very high. The mechanism for the NO increase is that activation of NFkB causes the expression of iNOS, which generates NO via open loop control, that is, the NO generated is not regulated other than by the amount of iNOS produced and the availability of substrates and the presence of inhibitors. This NO inhibits NFkB and prevents the expression of more iNOS. Thus the level of NO before NFkB activation determines in part the amount of NO after NFkB activation. However it is an inverse regulation. The lower the initial NO level, the higher the iNOS expression and the higher the ultimate NO level. This high NO level then reduces the expression of eNOS and nNOS, lowering the basal NO level when the iNOS is degraded in a day or so.

The high NO in acute sepsis from expression of iNOS leads to high ATP concentration. This is not generally appreciated. During acute sepsis, ATP levels are actually higher (if the patient survives) than normal controls. It is my interpretation that the authors of this last report don't appreciate what their own data clearly shows. They show higher ATP levels in skeletal muscle during sepsis than in uninfected controls (p =0.05). ATP is higher because NO is higher. High NO blocks cytochrome c oxidase, so mitochondrial ATP generation is shut down (mostly). This is why septic shock causes cachexia. The body is generating ATP via glycolysis. The mitochondria are shut off by the high ATP, so the body needs to make glucose without using ATP, so it does so by turning the muscles into alanine which the liver can turn into glucose without consuming ATP. All of this glycolysis generates a lot of lactate, which can't be turned back into glucose because the mitochondria are shut down. So the body turns it into fat. That is what septic shock does, it turns muscle into fat. Turning protein into fat and carbohydrate liberates a lot of ammonia. If that is sweated out to the skin, a resident biofilm can turn it into NO/NOx while conserve NOS substrates arginine, NADPH and O2.

Note this ATP measurement during sepsis was in muscle, however the ATP levels of all the cells in the body have to go up and down in sync for physiology to be regulated in a stable way. There has to be a "signal" that communicates the ATP level in cells, so that level can be regulated up and down in sync. This "signal" has to be uncharged to penetrate lipid membranes, and rapidly diffusible to communicate the signal quickly. There are hundreds of different cell types; it is implausible that they would use different signals. It is pretty clear that the signal has to be NO. The coupling of NO and ATP via sGC makes perfect sense in this light. NO is the diffusible signal that causes all cell to regulate their ATP levels up and down "in sync". This is especially important in the brain, where everything really does need to operate "in sync" for the brain to function properly.

When basal NO is low, any immune system activation raises NO levels higher (due to less inhibition of NFkB) than if NO was higher before immune system activation. I hypothesize that this can lead to what I call the low NO ratchet, where activation of the immune system under conditions of low basal NO causes basal NO levels to ratchet lower each time the immune system is activated. When NFkB is activated, more iNOS is expressed under conditions of low basal NO, leading to higher NO levels following immune system activation. That high NO level then causes the feedback inhibition of the expression of eNOS and nNOS, which add to the normal basal NO level. When the iNOS is degraded, the basal NO level falls to below the level where it was before the immune system activation.

I discuss some effects of NO/NOx on bacteria earlier. NO is used as a quorum sensing agent by bacteria, low NO is the trigger for bacteria to form a biofilm. As bad as bacteria floating around in your blood stream is, those bacteria coming out and forming a biofilm is much worse. Much much worse. I think this is the reason that the body cranks the NO level up so high, the attempt is to suppress bacterial quorum sensing for a day or so, so the immune system can knock out the bacteria and prevent them from forming a biofilm which makes them much much harder to get rid of. Preventing a biofilm from forming is so important that it is worth a significant risk of death from the preventative response.

Regressive autism and chronic fatigue syndrome

I think high NO induced switching of physiology (the low NO ratchet) is one of the fundamental causes of regressive autism, and also of low basal NO in adults as characterized in chronic fatigue syndrome (CFS). Many people with CFS can identify when they acquired it, and it corresponded with an acute serious infection other causes include trauma of surgery or accidents. Similarly, many parents anecdotally identify the immune reaction of a vaccination as a precipitating event leading to regression. However the large scale epidemiology shows no change in incidence of autism with changes in vaccination. My hypothesis is that in susceptible individuals, any immune system activation is sufficient to activate the "low NO ratchet", a vaccination, or one of the zillions of infections of childhood. It is the low NO ratchet that (I hypothesize) causes Gulf War Syndrome. Receiving multiple immune system activations (vaccinations) during a high stress period (being deployed to a war zone) causes basal NO to ratchet lower with each immune system activation until it saturates and produces chronic fatigue. This takes a few weeks, while the mitochondria turn-over and are not replaced (due to the low NO level from the chronic stress). Once mitochondria numbers are low, the low NO state is perpetuated due to superoxide from too few mitochondria being pushed to higher potentials to supply the same ATP. With continually low NO, mitochondria biogenesis can't occur enough to get back to the level that is "normal".

Simple oxidative stress alone can cause low NO, and if that low NO persists for long enough, then chronic fatigue will be induced by insufficient replacement of mitochondria.

Mitochondria depletion need not be so severe as to cause neuropathy for "regression" or chronic fatigue to occur. All that is necessary is for mitochondria depletion to exceed a threshold such that they achieve a new operating point with fewer mitochondria working at a higher potential. The higher potential generates more superoxide which lowers NO levels and if not enough mitochondria biogenesis occurs, that state can be perpetuated.

Only rarely is regressive autism or even any type of autism characterized by neuropathy as in the case of Hannah Poling. I think it is more appropriate to call such cases "neuropathy with autism-like symptoms". Normal "autism" is not characterized by neuropathy. Sufficient neuropathy will cause symptoms of the lack of communication. Lack of communication is also exhibited by some people with autism. Neuropathy is neuronal damage. Autism can occur with zero neuronal damage. I consider it fundamentally wrong to call any disorder characterized by neuropathy "autism". People with autism can experience neuropathy unrelated to their autism and again that is fundamentally wrong to connect that neuropathy to autism.

Whether mitochondria depletion progresses to neuropathy depends on how severe the mitochondria depletion is. Perfectly healthy and normal mitochondria can be turned off by this mechanism, which can result in failure of any organ where too many mitochondria are turned off, or in death, or anything in between. The critical factors are how much ATP mitochondria are called on to produce during the high NO state of sepsis (and so how much superoxide they produce), and how high the NO is level during that time.

This irreversible turn-off of mitochondria has been demonstrated in rats by injection of lipopolysaccharide, a component of Gram-negative bacteria which causes an extremely robust immune system response. This is also known as LPS, and endotoxin. This material can cause anaphylaxis, and it is thought that LPS from bacterial contamination in vaccines in 1928 (before thimerosal was used) that killed 12 of 21 children inoculated from a vial that (obviously) became contaminated a few days after 21 children were vaccinated from the same vial without ill effects.

The acute turn-off of mitochondria by LPS was accompanied by damage to mtDNA; that is a reduction in copy number of mtDNA and also the presence of deletions. Later the mtDNA copy number was restored and the presence of deletions greatly diminished. This decline and then increase in mtDNA copy number reflects the number of mitochondria present in the cells. As the number of mitochondria go down, so does the DNA they contain. As mitochondria biogenesis restores mitochondria the number goes back up, and the new mitochondria have intact mtDNA. This reflects the intact DNA required for mitochondria biogenesis. A cell can tolerate some damaged mitochondria, provided sufficient mitochondria remain to maintain the cell while it makes more mitochondria. If they are all damaged, the cell is going to die and be cleared.

This turn off of mitochondria during sepsis occurs in multiple organs including heart, liver, diaphragm and others. Because the cells in an organ communicate (via NO), they tend to fail in sync. If sufficient mitochondria remain viable to support the organ, the organism doesn't die and can recover from the sepsis. How likely mitochondria are to fail depends on the ATP load they are called upon to produce and how many mitochondria there are to share that load. Reducing the ATP demand by being immobile is the primary reason that people feel so crappy and lethargic during illness. That feeling of weakness is to prevent consumption of ATP which turns on mitochondria and can cause them to fail. This is also why putting people on a respirator helps. It reduces the load on their diaphragm muscles which improves the survival of the mitochondria and the survival of the muscle and the survival of the organism. This is also why masking symptoms of fatigue and weakness during immune system activation can be dangerous. Those symptoms of weakness and fatigue are important warning signals that ATP supplies are low, even dangerously low. There are times when overriding those danger signals are useful and lifesaving, such as when running from a bear. There are few instances in modern life where overriding weakness and fatigue are lifesaving. It may be convenient and more comfortable to block pain signals, but it always needs to be remembered that usually pain signals indicate overload, and continued overload will eventually lead to damage, eventually irreversible damage, and eventually death.

What turns off mitochondria is a superoxide level that is too high for the NO level that is present. Very high superoxide can do it, even if the NO level is not that high. That is what causes mitochondria failure during malignant hyperthermia, malignant neuroleptic syndrome or due to a hypermetabolic state from other causes such as surgical trauma. The details of how this happens are not understood. NO levels are low at those times to disinhibit the mitochondria. But the NO level can only go to zero. If at zero NO level the activity of cytochrome c oxidase isn't high enough to fully oxidize the electrons being put into the respiration chain, superoxide will be generated.

Excitotoxicity, seizure induced neuropathy, and delayed neuropathy following stroke

Following ischemic stroke, there are complex responses of the brain to the acute ischemia due to the stoppage of blood flow. First there is the acute death of the neuronal tissue where the blood supply was stopped. This is followed by release of glutamate which leads to excitotoxic death of the affected neurons. There is also death of neurons that have lost the "upstream" neurons that produce the signals for them to process.

It is not clear how much of this ongoing neuronal death can strictly be called "pathological", it is pathological in the sense that it causes greater long term dysfunction, but it may be non-pathological in the sense that it is a programmed physiological function which has understandable benefits in the shorter term. It may be thought of as pathological in the same sense that anaphylaxis is pathological. The neuronal "wiring" of the brain is extremely complex and mostly not understood. Fortunately it occurs and is regulated spontaneously. Occasionally there are disorders such as epilepsy, where seizure activity initiates in one area and propagates to other areas causing disruption of normal brain activity. During a seizure, the seizing part of the brain is disabled and bodily functions depending on that part cannot be performed properly. If that occurred in motor areas while "running from a bear", it is easy to understand how a seizure could prevent escape from the bear and result in death. If inhibitory pathways in the brain are damaged, such that a seizure threshold is reduced, ablating the pathways that may cause seizure later would be a near term benefit, even if there was significant loss of function in the long term. The "gain in function" of a lower seizure threshold can be so life-threatening (under some circumstances) that the immediate benefit of ablating those pathways would be worth the long term reduction in neuronal function. The precise balance of ablation vs. preservation over what period of time is obviously an extremely complicated instance of neuronal remodeling. Presumably the balance depends in part on the organisms' perception of the immediacy of the need to avoid near term seizures vs. preservation of long term cognitive function.

Once mitochondria depletion has occurred, neurons affected are more susceptible to excitotoxic injury. They have reduced metabolic resources to draw on and those most susceptible neurons will be the ones to be "pruned" first in the event of excitotoxic injury.


Many cases of autism are characterized by neuroinflammation. This is discussed in the blog on how acute fevers can temporarily resolve the symptoms of autism. That autism symptoms can be acutely resolved during fever conclusively demonstrates that those symptoms are not caused by damage or by other permanent alterations to neuroanatomy, but rather are caused by the acute regulation of brain function. We know that people with ASDs do have alterations in their neuroanatomy. The alterations that are observed, minicolumn morphology, increased asymmetries occur during early brain development in utero. There isn't time during a fever for that anatomy to remodel. If neuroanatomy did remodel during the fever, it wouldn't change back when the fever resolves. I conclude that any changes observed during a fever must be from changed regulation, not changed in anatomy.

Regulation of active tissue

The brain is "active" tissue in that it can sustain self-perpetuating activation. All self-activating systems have the potential for positive feedback and collapse from a state of meta stable dynamic equilibrium to one extreme state or another. A seizure is one extreme state where all nerves are activated, a state of zero activation is the other extreme state. Neither of these brain states is functional, proper neuronal function requires very delicate control of the balance between activation and deactivation. When this balance is perturbed by the loss of nerves that produce either activation or deactivation, the balance needs to be restored ASAP. Restoration of the balance and immediate function is likely to have been more selected for because the brain is such a critical system that cannot be "offline" for even short periods of time. If the loss of inhibitory or excitatory neurons causes an imbalance that balance can be restored most rapidly by "pruning" which ever type of neuron is in excess. Speed of restoration of balance is probably more important than ultimate restoration of maximum function.

Following a stroke, death of neurons continues for a considerable period of time, even after normal brain vascular dynamics have been restored. Much of this neuronal death is due to excitotoxicity injury. Mitochondria depletion makes neurons particularly sensitive to excitotoxicity induced cell death and there is considerable thought that cell death is due to ATP depletion and not due to oxidative stress. Neuropathy due to acute mitochondrial depletion occurs quickly. That is what causes the neuropathy of stroke, the acute ischemia causes the death of neurons due to ATP depletion, and due to mitochondria depletion.

The brain doesn't have the metabolic capacity for all nerves to fire simultaneously and continuously. That would quickly lead to exhaustion of the supplies of glucose and O2, and likely exceed heat dissipation capacity. Preventing run-away metabolic overload is an absolutely necessary control function.

The brain matches its metabolic requirements with the metabolic resources supplied by the blood stream exquisitely well. That regulation can only occur via feedback and active control. That necessarily includes regulation in both directions, angiogenesis when there is insufficient blood supply and ablation of blood vessels when there is too much.

The same goes for regulation of cognitive functions. When more cognition is needed in a certain area, the brain increases neural connections in that area, recruits more connections in that area and so allocates a greater volume of neuronal resources to whatever computation function is required.

Total brain volume is fixed by the size of the skull. If local brain volume is going to be increased in one region, it must be decreased in another. This is a necessary trade-off. Precisely how this happens is unknown, that it happens is virtually certain. It is well known that brain size does decrease during normal aging, and that this decrease is accelerated in many types of neuronal atrophy.

All individuals "regress" to some extent. Infants and children have the ability to learn any human language. If a group of children is raised without a "well formed" human language (as in societies formed by mixes of immigrants speaking only pidgin versions of multiple languages), the children will synthesize a new language, a Creole, with its own well-formed syntax and grammar. Adults cannot do this. Adults can learn new languages, but it is difficult and they can only (for the most part) learn languages that are already well-formed, or pidgin languages. Adults cannot synthesize a new Creole language. Adults have lost this ability, they have in effect "regressed". My presumption is that this "regression" produced during normal neurodevelopment is to free up brain volume for other purposes that are more important, such as being a parent.


There are several implications from this analysis of mitochondrial dysfunction during immune system activation. Any activation will do it, a vaccine, a cold, an infection, a vaccine preventable disease. It is not possible to produce vaccines that do not produce an immune response. The immune response is the reason for the vaccine in the first place. It is the immune response itself that causes the mitochondria turn-off.

An important factor is the magnitude of the immune response and that depends on the NO/NOx status of the individual before the immune system stimulation.

A high NO/NOx status before immune system stimulation has several protective effects. Probably the most important one is the increased mitochondria number before any immune stimulation happens. NO is what triggers mitochondria biogenesis, with a greater basal NO level you will have a greater basal mitochondria level. That leaves more mitochondria to share the ATP production load, increasing ATP then requires less superoxide production, and there are more mitochondria available in case some get deactivated by this mechanism.

A high NO/NOx level will also reduce immune system activation by reducing the activation of NFkB. So far there are no generally approved methods for raising NO/NOx levels. What about unapproved methods? Meditation will work, but infants don't know how to meditate. Consuming nitrate, as in lettuce (lettuce is ~2000 ppm nitrate) has been shown to increase plasma nitrate, nitrate is concentrated ~10x in saliva and nitrate is reduced to nitrite on the tongue in adults. I have been told that children don't develop the characteristic bacteria on the tongue that do this until they are ~1 year old. I haven't seen any published data on this.

The method I am working on is a topical biofilm of ammonia oxidizing bacteria. I think this is how people lived in "the wild", before the modern era of frequent bathing. Before modern indoor plumbing, humans couldn't bathe every day. In Africa people probably never bathed in their entire lives. It was too dangerous to go into parasite and predator infested natural bodies of water.


Lynn Alexander said...

Well it's a bit more technical than what I typically read on a blog- but clearly you have put a great deal of time into this and I applaud that!

The diagnosis as "high or low functioning" seems to reflect the jargon of a few years ago. We now use "spectrum" and look at clusters of behavior. Not extreme functioning of high or low. We know that skills are uneven- a child might not speak but might have another ability, etc. So high or low is seen as too general and not reflective of multiple skill sets.

I agree with the comments you made at my blog about the connection, or lack of, with vaccines- although I reserve a bit of uncertainty still. I have not been convinced of the relationships but can't claim to know enough to PERSONALLY weigh in- see? I don't really know, and I was more interested in the predicament of parents with an understandable distrust. I don't think we should belittle parents who worry after all the fraud and corruption.

Anyway I think that one problem I see with the spectrum approach is that children are diagnosed with autism with fewer symptoms as a "catch all" diagnosis, or in place of mild retardation. They are often used interchangeably by many clinicians, and I have seen the diagnosis applied to children more readily. I think that the age of observation, the age when many social skills and other indicators might be looked at is also the age where many vaccines are given and this prompts many to believe that it happened after the shots.

daedalus2u said...

Lynn, there is not a shortage of good and reliable information on vaccines on the web. There is too much disinformation put out by anti-vaccine advocates.

Dr. Steve Novella at Neurologica had a good post on the "Green our vaccines" issue.

Orac (who is an MD too), at Respectful Insolence has many good posts on vaccines including the latest celebrity "green our vaccines" nonsense.

Epi Wonk has many good posts also

Denialism is very good too.

Science Based Medicine is very good.

For good information on autism, I would highly recommend the Autism Hub. LB/RB is very good, Autism Vox, and of course Neurodiversity is probably the most complete web resource on autism, run by Kathleen Seidel who has a blog also. She has focused a lot on the politics and the business interests that are pushing the anti-vaccine controversy. It is pretty clear to me that there is a conspiracy, on the part of the anti-vaccine advocates. She was attacked by that anti-vaccine conspiracy, the lawyer leading it issued a breathtakingly broad subpoena for which he was sanctioned by the court.

The "controversy" about vaccines is not a close call. It is all manufactured, starting with Andrew Wakefield who was hired by lawyers to find a connection between MMR and autism. He did "find" a connection, by manufacturing data. He committed fraud. He lied to his co-authors (who have retracted the paper). Children have died because they got measles due to the hysteria Wakefield generated to enrich himself.

I appreciate that non-technical parents may have great difficulty in sorting through some of the highly technical material. It is not at all a close call. The anti-vaccine advocates have put up nothing that is credible or compelling to make their case. It is all smoke and mirror, all marketing hype.

There is a large trial going on, the Autism Omnibus. There are something like 5,000 families claiming that vaccines caused their child's autism. So far there have been 4 hearings on it, I have only read the transcripts from 3 of them, and there is nothing in them to suggest vaccines cause autism. In one of them there was testimony (under oath) that the researcher working with Wakefield sequenced every supposed "positive" measles virus result and in each and every case found them to be a false positive and that he told this to Wakefield before Wakefield published his paper "finding measles virus".

This is not a close call. Many anti-vaccine advocates have businesses selling "alternative" treatments.

The world that the anti-vaccine advocates live in is scary. I am not sure which I find scarier, their breathtaking ignorance or their imputation of enormous monstrosity on the part of MDs and pharmaceutical company employees sacrificing children to make a few pennies profit. I don't know anyone who would do that, apparently the anti-vax people do, so many they think it is SOP. To me, that is very scary.

Lynn Alexander said...

When I say distrust of information, I mean that parents are not sure what information to trust. I am talking about a pattern of deception by the regulators and drug makers to market drugs that are not adequately tested.

Does this mean that vaccines are bad? No. But I am saying that when parents are unsure of who to trust or what to believe, it becomes very difficult. Especially when "experts" are often industry insiders and are far from objective.

The lack of information is not the problem, its the trust we have in that information because we know both sides lie to fit their agenda. parents are often blamed when they are caught in the middle.

daedalus2u said...

I completely agree it is difficult to tell who is lying and who isn't when you don't understand the science behind it. Parents are put in a very difficult position. The anti-vax movement has some serious marketing and serious money behind it. What they don't have is science. The non-scientific media does a terrible job of reporting these issues. They pick the two extremes and call their coverage "balanced". When the media itself is biased (such as Fox news and HuffPo) it is very difficult. The Huffington Post screens comments and doesn’t allow comments that contradict their "party line".

Some of the anti-vax rhetoric about "toxins" is clearly and flat-out wrong. It isn't a close call. There are only a handful of "researchers" who are anti-vaccine. Some of them (such as Wakefield) have clearly (to me) been shown to have committed fraud and lied about adverse effects of vaccines.

You are right, there has been fraud put out there by some pharmaceutical companies regarding some "blockbuster" drugs. Vaccines are not "blockbuster" drugs. I don't think there has been any fraud regarding vaccines by pharmaceutical companies. I can't think of what their incentive to do so would be. The vaccines are already FDA approved, they are not big money makers, they can't be big money makers. There is only a problem if they screw up. They have been making them for many years, so they know how to do it without screwing up.

Many western countries have an indigenous pharmaceutical industry for childhood vaccines. They consider it too important to outsource it. There is essentially nothing proprietary about vaccines. They are "the same" and have been "the same" for many years in virtually every country. If one country had vaccine experiences far different than any other, it would be obvious.

I don't know how to communicate very effectively. I know how to do science, I know how to understand and write about it, but not in ways that people can understand. I think it is because I am out there on the edge, and people don't have the time to learn the background to understand what I am saying. There are a lot of scientists on blogs that are trying to write in ways that are accessible to non-scientists but it is difficult. There is a tremendous amount of disinformation out there.

I don't know how to counter the disinformation.

Lynn Alexander said...

I think vaccines are also a cost-benefit issue. The diseases they prevent are pretty serious.

I know a lot of people who listen to some alternative health gurus who argue against them in books, radio, etc. and I see a lot of confusion there too. I know some people who send money and buy products like they are following a cult or something!

Anyway, it's tough and many Americans don't have the ability to really look at information in a discerning way. They don;t look at bias either or even think about questioning who benefits and what their stake is.

I've been away a lot this summer, my friend! But I will pop in when I can. Keep in touch.

passionlessDrone said...

Hi Deadulus2U -

Very comprehensive stuff; I'll need to read through it a few times to try to digest it to the best of my abilities.

Anyways, I understand your focus is on NO; I'm curious as to your opinion on if increased tnf alpha could be responsible for some biomarkers of mitochonrdial problems in autism? Increased tnf alpha, especially in the CNS has been observed, and I recently ran into this paper that got my gears turning.

Your section on neruoinflammation and / or immune systam activation didn't mention cytokines as a mechanism by which mitochondria function could be affected, or if it did, I missed it.

What do you think?


- pD

daedalus2u said...

I have only seen the abstract, but I don't think it is correct. TNF may do exactly what they say, but I don't consider that to be any sort of "malfunction" or "defect" or "disorder", or "damage".

First of all, a 60% reduction in cytochrome c oxidase activity is a small decrease.

Second, poor O2 extraction is a feature. Mitochondria can't operate in the high NO environment that sepsis produces. If they try to, they fail. That is the generic failure mechanism for mitochondria. It isn't a defect, it is a feature. Mitochondria have to function that way. There has to be an "off" switch for mitochondria. That "off" switch has to be fail safe because a few mitochondria gone bad could kill the cell. That is why mitochondria "fail" via pathways that irreversibly disable them. That is how you want mitochondria to fail. You don't want mitochondria to fail via a pathway that generates unlimited superoxide.

So if TNF does inhibit mitochondria, that is likely a feature and a part of normal mitochondria control. Disabling that normal part of mitochondria control is likely to cause more problems than it will fix.

Preventing the problems of too much TNF inhibiting mitochondria is best solved by increasing the number of mitochondria present in the first place. That is done by increasing NO levels in the basal state, so there is more mitochondria biogenesis so there are more mitochondria to start with, so if/when some of them fail, there are enough to share the load and maintain cellular viability.

TNF does reduce nitric oxide production by a couple of mechanisms, by reducing NOS expression, by generating superoxide, and I think also by phosphorylation.

Cytokines by themselves are not going to turn off mitochondria irreversibly. The only thing that can do that is oxidative and nitrosative damage. Cytokines might cause that to happen, but only through the final common pathway of mitochondrial activation in the presence of too much NO.

Cytokines usually have most of their effects on cells of the immune system. Usually immune cells are mostly powered by glycolysis and not by mitochondria. I think that is because they have to work even in anaerobic tissue. If they relied on mitochondria they would have an absolute need for O2.

passionlessDrone said...

Hi Daedulus2u -

Thanks for your response. I noticed right after I posted that you had mentioned tnf in your inflammation area. Sorry.

I'm re reading and trying to understand what you have here. Can you help me out some more?

There are multiple ways for low NO to occur. The main focus of this article is on the generation of superoxide by mitochondria under high NO levels causing mitochondria depletion which causes high superoxide due to higher mitochondrial potential. Inflammation also generates superoxide from activated immune cells. Metabolism of normal and xenobiotic chemicals by the cytochrome P450 enzyme system also makes superoxide. Xanthine oxidoreductase also makes superoxide.

I'm struggling a bit, because we seem to have low NO attributed as the big problem, but that it can be started off, by high NO and a resultant increase in supoxide the mitochondria. I having trouble sifting through all of this and identifying a reason why you believe in some cases, high NO leads, high superoxide, and eventually to low NO and a consequent inability to get back into synch.

What are your thoughts on why specific individuals and/or specific insults are able to initiate this cascade, but the vast majority of individuals and insults do not?

I apologize if this was in your entry and I couldn't find it.

- pD

daedalus2u said...

High NO doesn't necessarily lead to high superoxide. That is why only in some cases does extreme immune system activation cause mitochondrial failure. Whether there is mitochondrial failure or not depends on whether the mitochondria become activated.

Normally during a high fever mitochondria are mostly off. This greatly reduces potential ATP production in cells, because they are limited by glycolysis (which only makes 1/19 as much ATP per molecule of glucose than does oxidation). Also, glycolysis is limited to using glucose not lipid. If the mitochondria are off, they are not damaged by high NO levels. During sepsis, NO levels become very high. So high that there is systemic vasodilation and systemic hypotension because the very high NO levels have activated sGC in all the vasculature and made it open up wide.

One of the very key papers to look at is this one, where they took muscle biopsies during sepsis and showed ATP levels (among survivors) higher than in normal controls not in septic shock. The ATP levels of those in sepsis who did not survive was lower than normal controls. This is an absolutely key finding. I don't think the authors appreciate how important their data is because they don't even mention it in the abstract. Their hypothesis that there is mitochondrial dysfunction in sepsis is wrong. In the survivors there was no, or minimal mitochondria damage. The high ATP level turns off the mitochondria. Mitochondria turn on to produce ATP. If there is plenty of ATP, mitochondria don't need to do anything, and so they don't, they just sit there, ready to produce ATP at a moments notice.

The high ATP level occurs because high NO raises the ATP setpoint. ATP and NO co-regulate sGC, with high levels of either raising the level of the other. In sepsis, the high ATP is produced by glycolysis. To generate the gigantic amounts of glucose needed during sepsis, the body induces cachexia. The muscles get turned into amino acids, the liver turns those amino acids into glucose, the cells use that glucose and make ATP and lactate, and then the lactate gets turned into fat to get rid of it. In sepsis you lose muscle and gain fat by this mechanism.

Under normal conditions lactate is turned back into glucose by the liver and kidneys. In sepsis the lactate gets turned into fat because it takes mitochondria to turn it into anything else and the mitochondria are turned off because of the high NO and the high ATP levels.

It is only when cells can't keep ATP levels up via glycolysis that problems happen. It is when the ATP level falls below the threshold where mitochondria turn on that the problems happen. To turn on, the mitochondria respiration chain becomes reduced, and forms superoxide at complex I and III. This is a "feature". That superoxide destroys NO, which pulls down the NO level on complex IV and disinhibits it so it can bind O2 and remove electrons from the respiration chain by reducing one O2 to 2 H2O. Mitochondria have an unlimited capacity to produce superoxide. It is limited only by the supply of O2 and reducing equivalents.

The mitochondria can produce enough superoxide to pull down the very high NO level during sepsis, but doing so kills them. There is a balance between superoxide, NO and MnSOD which is only in the mitochondrial matrix. MnSOD dismutates superoxide at near diffusion limited kinetics. The kinetics of NO and superoxide is near diffusion limited too. When superoxide and NO react they form peroxynitrite which can nitrate tyrosine. On MnSOD there is one tyrosine that when nitrated irreversibly inhibits MnSOD. This isn't "supposed to" happen, except when mitochondria have "gone bad" and are producing too much superoxide. This is the "fail-safe" circuit interrupter that all low impedance power sources must have for reliable operation. There is an analogous FeSOD that bacteria use, that has high homology with the MnSOD that mitochondria use. In E. coli, the FeSOD can withstand nitration of 8 of 9 tyrosines with essentially no loss in dismutation activity. Inhibition by nitration is not a necessary defect inherent in that type of SOD. If bacteria could evolve an SOD resistant to nitration, so could eukaryotes. It is a feature. A feature that is necessary for safe mitochondria operation.

When mitochondria are called on to produce more and more ATP (per mg of protein), they do so by pushing the mitochondria potential higher and higher. This has the effect of generating more superoxide, which lowers the NO level, which disinhibits more and more cytochrome c oxidase which can then reduce more and more O2 at lower and lower O2 partial pressures. In muscle, mitochondria can increase their ATP production by 10x. This requires a 10x higher flux of O2 which requires a 10x higher driving force (or a 1/10x diffusion distance). The O2 level at the blood vessel remains constant. It is the O2 level at the mitochondria that drops to increase the O2 concentration gradient so that 10x more O2 can diffuse down it and be consumed at the mitochondria.

When mitochondria start to fail, by too much superoxide and too much NO, they stop producing ATP, and can even start to consume ATP to maintain a membrane potential. This increases the ATP generation load on the remaining mitochondria, and they respond by increasing their membrane potential which makes more superoxide, more peroxynitrite and gets them closer to the death threshold where MnSOD gets inhibited.

Because mitochondria can produce up to 10x more ATP, in "theory" a cell can operate with fewer mitochondria than is "normal". But each mitochondrion will be working much harder, producing much more superoxide and pulling down the NO level to allow for a high O2 flux. If instead of having 100 mitochondria, you only have 12, those 12 can produce the "normal" "at rest" ATP flux of 100 by operating at 8x . But if you try to increase that, they can still only go to 10x where they max out at 120. If you had your normal complement of 100, you could go to 1,000. That is what causes chronic fatigue; not enough mitochondria. You are ok at rest because you have enough mitochondria to produce enough ATP to sustain your at rest metabolic rate. But you have no reserve and can't increase your ATP production to increase metabolic activity.

The trigger for mitochondria biogenesis is NO, so if you end up in a low NO state that is kept that way by too few mitochondria operating at too high a potential, there is no way out. Physiology needs an external source of NO to overcome the hysteresis of the superoxide being generated by too few mitochondria.

Inflammation and other sources of superoxide can exacerbate this condition too.

jim said...

Your article really fits well along with the ideas that ive come up with when trying to figure out a treatment for my chronic fatigue syndrome.

There are some theories now about how nitric oxide is involved.

In some people with chronic fatigue , including myself, it seems like there may be a nitric oxide deficit.

Ive been sick for 9 years and ive taken 100's of supplements recommended by different Dr.'s through out the years.

All of the supplements that were beneficial had some effect on nitric oxide. Including l-arginine, folic acid, b12, nac (precursor to glutathione), hormone called relaxin (stimulates nitric oxide).

There are some papers you should read

The dr that wrote this actually recovered from chronic fatigue with this antioxidant regemign:
R-alpha-lipoic acid.
Ultra EPA fish oil concentrate

Ive thought that a nitric oxide deficit might be causing CFS for a while, i wrote an article about how i understand it. I definately learned alot from your article and i wanted to see what you think of what i wrote. Does what i wrote make sense to you? I would love to get some feedback from you, because it seem like you have a really good grasp on this idea
my article is:

jim said...

i think my links might have gotten cutoff, i really want to hear what you think of the first paper. I think that guy is on to something

Martin Pall article

My article of CFS and nitric oxide

jim said...

thanks alot for your response. Ive been sick for nine years and now i feel like its all starting to make some sense.

daedalus2u said...


I looked at your blog and left a comment there. I think that CFS is caused by low NO also. I completely disagree with the Pall hypothesis.

Another way to increase NO/NOx levels is via consumption of green leafy vegetables; a couple hundred grams a day. They have a few thousand ppm nitrate and that nitrate is well absorbed and does couple to NO/NOx physiology. The half life is short, so twice a day is better than once a day. It isn't the "same" as the bacteria that I am working on, but my bacteria are not yet ready to distribute. (but I am working on getting there).

The mechanism of mitochondria failure that I talk about here is what I think causes CFS. Then not enough NO perpetuates the low NO state by inhibiting mitochondria biogenesis. Too few mitochondria generate the same ATP by operating at a higher potential where they make more superoxide. A feature that lowers NO level and allows consumption of O2 to lower levels. Good in the acute short-term, bad in the chronic long-term.

jim said...

hi daedalus,
i have a couple more question, i hope you dont mind. Thanks for the help. I wanted to know what effect you think these supplements might have on nitric oxide.

I take hydroxycombalin b12 shots, this is one of the most helpful supplements for me. Ive been doing some reading about it and the articles that ive come across say that it is a nitric oxide scavenger. Im not so sure about that, as it clears my concentration problems, which im sure are the result of reduced blood flow in the brain. I just put up my PET scan which showed a generalized low blood flow throughout.

My Brain Scans

It seems like increasing nitric oxide would help restore the blood flow, and help my concentration issues.

Also do you know what effects coq10 might have on nitric oxide?

Ive come across some articles that say it would increase nitric oxide, while others say it is a nitric oxide scavenger.

I tried taking it, and initially my concentration improved alot, but after a 5 days i had no energy and i discontinued it. I wasnt sure if i should continue it and see if my symptoms would improve in the long run.

Also I was considering taking some of the supplements that martin pall had suggested, just to see if they would have a positive or negative effect on me.

Dr. Martin Pall who wrote the article i linked to, had CFS, but recovered after taking high does of antioxidants.
He recommends these:
CoQ-Gamma E with Tocotrienols & Carotenoids
Fish Oil
R-alpha-lipoic acid

I was going to try that supplement FlaviNOx, and see if it had a positive or negtive effect.

What do you think of the ingrediants in it?

Do you think it would be worth it to try these out as a guage to see what i should try next?

thanks alot

daedalus2u said...

I don't disagree with any of the data that Pall bases his ideas on, I do disagree with his explanation and hypothesis (as I understand it).

There are no large, long term, placebo controlled trials showing that supplemental antioxidants do anything positive. My interpretation of this data is that a state of oxidative stress is a state deliberately chosen and regulated by physiology independent of the consumption of dietary antioxidants. A state of oxidative stress is too important to allow it to be regulated by random consumption of antioxidants.

I consider that people in a state of oxidative stress are in that state because their physiology has an oxidative stress setpoint. Free radicals and highly reactive compounds such as peroxynitrite are important signaling compounds in physiology. Antioxidants destroy those compounds and so physiology needs to regulate the level of antioxidants. Physiology can destroy antioxidants by generating more superoxide (which physiology has an unlimited capacity to produce). Consuming excess antioxidants simply forces physiology to destroy them at some metabolic cost. Many of the very large trials of supplemental antioxidants show increased damage when consuming antioxidants. This is consistent with a setpoint hypothesis and is inconsistent with the idea that supplemental antioxidants are reducing oxidative stress.

I looked at the FlaviNOx label, and there is nothing in it that I consider to be of value. I don't know much about herbs. Herbs are so complex that they could have all sorts of physiological effects, positive and negative. The only way to determine what those effects are is via measurement and herbs simply are not well documented enough, grown under controlled enough conditions and subject to enough quality control procedures to be what I would consider something known to be safe and effective. Without knowing the mechanisms that are involved, a particular herb might be acting as a placebo, or it may have short term positive effects and long term detrimental effects.

How you feel in the short term is a poor measure of what is going on with your mitochondria. ATP production is so well regulated and how you feel is so well regulated that feelings can be quite unreliable indicators. Under emergency overload conditions, the body will actually induce euphoria, so you feel great while irreversible damage is being done to your body. Physiology does that so you can survive emergencies such as running from a bear, where any damage short of death is infinitely better than being caught which is certain death.

There are only 3 ways that I know to raise NO levels, meditation and relaxation of certain types, consumption of green leafy vegetables (because they contain nitrate which is used in NO/NOx physiology), and the bacteria I am working with. The bacteria I am working with are not yet available, so that leaves the other two. Getting sufficient rest and avoiding stress is pretty important, especially at night. I would suggest eating a couple hundred grams of lettuce per day. The lifetime of nitrate in the body is pretty short, so eating lettuce twice a day is better than once a day.

The nitrate is absorbed, concentrated from the plasma into saliva (about 10x) and then bacteria on the tongue reduce that nitrate to nitrite. When that nitrite is swallowed, it is reduced to NO at the low pH of the stomach. NO generated by that mechanism has been shown to have positive physiological effects. The right bacteria on the tongue are important, which means not using things like mouth wash to kill them. Alcohol consumption can kill them too. Alcohol has bad effects on the liver too and is better avoided if you have CFS.

jim said...

thanks alot for your response. I'll try adding in some leafy greens, at the moment i dont really eat alot of vegetables.

take care

jim said...

hi daniel,
i not sure if you would be interested or not. But i wanted to see if you would want to write an article about nitric oxide and cfs for $200, that i could use on my website. I would also give you credit and a link to your blog.

Maybe something simple and short that would be easier to understand. More in laymens terms and could show the differences you have with martin palls theory.
I think youve got some great ideas.

Just wanted to run that by you and see if you are interested.


leave me a comment here or on my site chronicfatiguetreatments.comif interested

Junto said...

I love your blog! Interesting stuff.

I've had 1-2 bouts of shingles outbreaks per year since I was 8 years old. My understanding is that this is abnormal for someone with a presumably healthy immune system. I also have severe chronic allergies.
Question: Could the "fact" that my immune system is in a state of constant dystress due to allergies and a less than dormant viral infection cause "chronic fatigue syndrome" or mitochondrial "dysfunction"?

Anonymous said...

I came across your blog while researching my health issues, which include chronic fatigue, anorexia and neuroinflammation (with a family history of Alz) -- I am interested in the parallels with autism. I would say that while I had more negligible social deficits as a child (they were there - I am a woman - these things were not labelled as such at the time), periods of very high neuroinflammation have left their mark.

I realized that you are the same person behind AOBiome, which is marketed as a cosmetic. I am wondering if you believe that AOBiome could raise nitric oxide systemically. I know that you can't prove it in an FDA-supported way at this point, but I am interested more in your theories/thoughts on this matter.

daedalus2u said...

Thank you for your interest in AOBiome and AO+ Refreshing Cosmetic Mist.

AO+ is our cosmetic formulation of stabilized Ammonia Oxidizing Bacteria (AOB). Because we are marketing AO+ as a cosmetic, FDA guidelines strictly prohibit us from making any therapeutic claims or discussing possible health benefits.

AOBiome scientists are engaged in an active scientific research program investigating multiple pharmaceutical applications of medical-grade ammonia oxidizing bacteria. We will report the results of this research on the AOBiome company website and on our mailing list.

For those seeking fresh and healthy appearing skin today, AOBiome is pleased to offer AO+ Refreshing Cosmetic Mist, a cosmetic formulation of ammonia oxidizing bacteria.