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Understanding the Model / Updated disease model [WIP]
« on: September 25, 2022, 03:08:47 PM »
This is a preview of the hypothetical disease model being described in the upcoming paper.

[Click here to download a PDF version of the experimental intervention protocol based on this work.] (v3.65 RC3 7th March 2024)

These figures are a draft and may contain errors. An interactive version for some of these diagrams is being actively developed and a beta version can be found here, which is currently not working on mobile browsers; however, you can also right-click on the images below and open them in a new tab / save them for high resolution and/or easier navigation.

Questions / discussions - please join our Discord server - (the forum previously hosted here was relocated to Discord in 2021). 

A recorded presentation of the model, as of February 2023 can also be found here:

Errata in video dialogue / content:
2:35 - Interferon-gamma inhibits Complex I and Interferon-alpha inhibits Complex II, not the other way around.
51:50 - NOS reaction should have NADPH as the acceptor and is reversible. See updated diagrams.
59:20 - The "Chief Science Officer" referred to was from Oligolab, not to be confused with Oligoscan, as these are separate companies which both offer this technology. [English subtitles are now corrected. Auto-translation to other languages will be checked.]

An updated presentation of the model, as of August 2023 can be found here:

Figure 1:

Figure 2 (legacy material - being retired/superseded by Figure 3 and will be replaced soon):

Figure 3:

Figure 4:

Figure 5:

Here is a highly simplified description of the pathophysiology key-points:

1.      Biofilms are a protective 3D extracellular matrix surrounding microorganism and are a normal feature of the microbial lifecycle and our microbiomes - which can largely be found in any/all mucosal tissues

A blind spot in the human immune system exists around the contents of these biofilms, allowing for “pathogenic” species to create hidden reservoirs.

Pathogenic species of particular interest to this disease model include acetaldehyde producing species, such as H. pylori, S. aureus, Streptococcus spp., Klebsiella spp., E. coli, Candida spp., Aspergillus spp. and others.

The contents of biofilms are not inspected and therefore an immune checkpoint is only provided during the planktonic and yeast stages of the microbial lifecycles, preventing biofilm surface area expansion.

These biofilms are also degraded by helpful microorganisms (various Lactobacillus spp., Bifidobacterium spp., Bacillus spp. and other species), stomach acid, dietary intakes of biofilm degrading compounds and lifestyle choices.

2.      Through environmental exposure, small amounts of pathogenic biofilms will form in very early childhood. Moreso, if the microbiome has been compromised by a lack of protective species, such as Bifidobacterium spp. and Lactobacillus spp.

These protective species are abundant in human breast milk and can make up 80% of a neonate’s gut microbiome and 20% of a “healthy” adult human’s gut microbiome. Conversely, low populations of bifidobacterium are routinely found in chronic disease.

These protective microorganisms metabolise acetaldehyde into acetate, degrade biofilms and inhibit pathogenic species.

Breast milk contains calcium and phosphorus to help buffer stomach acid pH and allow survival of these protective species through the stomach and small intestine. Breast milk contains selective prebiotics such as lactose and human milk oligosaccharides, supporting colonisation of these species. Milk also contains colostrum, lactoferrin, xanthine oxidase and IgG, supporting mucosal immunity.

Antibiotics have broadly deleterious effects on microbiome diversity and abundance.

3.      An ongoing slippery slope of microbiome dysbiosis is created by events which allow the surface area expansion of pathogenic biofilms. These events may include introduction of a catalyst or antigen which distracts/dysregulates immune activity or decreases the diversity and counts of protective microorganisms;

eg. Immune system dysregulation caused by malnutrition, low NK cell counts, medications that alter Interferon signalling bias / cascade regulation, antibiotics, biotoxins, IFN-alpha promoting antigen dominance (eg. SARS-CoV-2 spike protein / infection, influenza, reactivated herpesviruses, isocitrate lyase expressing microorganisms, lipopolysaccharides, medical interventions which provide antigens for immune imprinting), and chronic stress (as elevated cortisol, dysregulation of cytokines) can each provide a window of opportunity for unimpeded biofilm growth, increased endo/mycotoxin production and net acetaldehyde increase.

Acetaldehyde is well-known in chronic alcoholism for causing T-cell exhaustion, inhibiting glycolysis, inhibiting methylation, inhibiting collagen synthesis, dysregulating thiamine pyrophosphate metabolism and having a higher affinity for various aldehyde dehydrogenase (ALDH) isoenzymes required for eg. neurotransmitter degradation, histamine degradation and many other pathways.

Gliotoxin, other mycotoxins and endotoxins are also relevant to this cascade.

4.      These and other factors can lead to degradation of the epithelium, chronic low-level infection / bacteraemia / fungaemia and chronic innate immune response + mast cell activation, as the pathogenic reservoirs are hidden from the immune system.

An inflammatory cascade involving TNF-alpha, IL-1beta /6/10/22 promotes hepcidin. Hepcidin is a peptide-hormone which inhibits divalent metal transporter-1 (DMT-1) and ferroportin. These 2 transporters are well-known for regulating systemic iron homeostasis, however the literature shows they are also responsible for 8 other metals required in energy metabolism, neurotransmission, collagen synthesis and other relevant pathways.

Enterocytes in the gut express both DMT-1 and ferroportin. Cells in the brain, liver and kidneys only express ferroportin. This means that while the absorption of dietary minerals is blockaded in the gut, circulating minerals are sequestered in brain, liver and kidney tissues until the inflammatory cascade subsides.

This mineral transport blockade appears to benefit the host in an acute infection by limiting available minerals for pathogen proliferation, however in chronic infection leads to induced malnutrition / mineral depletion.

5.      The IFN-gamma innate immune response alters transcription factors and NAD+ metabolism in specific ways which favour immune activity against microbial and other pathogens.

An elevation of IFN-gamma signalling can result in reactive oxygen species (ROS) generation by at least 3 enzymes – xanthine oxidase (XO), NADPH oxidase (NOX) and nitric oxide synthase (NOS).  NOS is also a reactive nitrogen species generator when tetrahydrobiopterin (BH4) is low.

IFN-gamma inhibits mitochondrial complex I / NADH dehydrogenase, inhibiting the NAD+ redox and allowing the NADH pool to increase.

Increased NADH pool status from TCA cycle flux created by exertion / metabolic activity promotes NADP transhydrogenase activity in converting NADP into NADPH, returning one NAD+.

NAD+ biosynthesis is simultaneously upregulated at IDO1/TDO, enhancing catabolism of tryptophan through the kynurenine pathway, however this is limited by a number of factors, some highlights for which include (endogenous and microbial synthesis of) tryptophan, P5P pool status and oxidative stress.

NAD+ and NADPH are used by a number of pathways to benefit host response to infection and tissue repair / adaptions:

For IFN-gamma activity’s ROS generation and oxidation of pathogens – XO requires elevated NAD+:NADH. NOX requires elevated NADPH: low NADP. NOS requires elevated NADPH:low NADP.

For methylation – methylenetetrahydrofolate reductase (MTHFR) and dihydrofolate reductase (DHFR) are promoted in one direction by elevated NADPH: low NADP, increasing 5-MTHF and BH4 recycling, respectively.

Hormone and cholesterol biosynthesis are promoted by elevated NADPH:low NADP and elevated NAD+: low NADH. Cortisol is decreased.

Conversely, cortisol inhibits IFN-gamma signalling / activity and is promoted by elevated NADH: low NAD+, low pyridoxal 5-phosphate (P5P) and low glycolytic flux. Cortisol appears to be the primary regulator for IFN-gamma activity, promoting catabolic energy pathways and allowing the various pool status to reset / replenish. The model predicts inversion of the diurnal cortisol release profile where cofactor pool status is not well-supported.

6.      Excessive or dysregulated IFN-gamma activity depletes NAD+ and causes oxidative stress, relative to exertion and/or immune activity.

The model describes oxidative stress as a key factor in post-exertional malaise (PEM).

Various mineral and electrolyte deficiencies, caused by dietary insufficiency, renal dysfunction and/or the described mineral transporter blockade impairs metabolism of ROS.

During upregulated IFN-gamma activity, metalloenzymes which metabolise reactive oxygen species are promoted to protect cells against the innate immune response.

These metalloenzymes include CuZnSOD (requiring copper and zinc), MnSOD (requiring manganese), catalase (requiring heme), glutathione peroxidase and reductase (requiring selenium + cofactors for riboflavin -> adeflavin (FAD) metabolism – Zn, Mo, Ca, I, Se, Heme and Mg.)

These mineral deficiencies create or exacerbate oxidative stress during IFN-gamma activity and leads to exhaustion of available antioxidants – ascorbic acid, tocopherols / tocotrienols,  BH4, cobalamin II, melatonin,  glutathione, alpha-lipoic acid and dietary sources of antioxidants.

7.      Oxidative stress and insufficiency of these antioxidants has a significant impact on tissue damage, energy metabolism and neurotransmitter homeostasis.

Glycolysis is inhibited by oxidative stress at pyruvate kinase and other reactions.

Carnitine biosynthesis is inhibited by oxidative stress. Carnitine is required to shuttle longer chain fatty acids in fatty acid oxidation.

The TCA cycle is inhibited in multiple places by oxidative stress.

Tissue damage from oxidative stress and other influences leads to promotion of transforming growth factor beta-1 (TGF-b1) and inhibition of vitamin B6 -> P5P metabolism, with a broad impact on neurotransmitter metabolism and 140+ other pathways.

Specific influences affecting prolyl hydroxylase activity leads to Hypoxia Inducible Factors (HIF-1a) stabilisation / promoting, triggering anaerobic glycolysis (lactic acid metabolism) and reactivation of human herpesviruses, human papilloma virus, HIV, etc

These influences include:
Impaired glycolysis / fatty acid oxidation, low Mg and other factors leading to low alpha-ketoglutarate.
Low riboflavin -> FAD and/or elevated IFN-alpha -> itaconate, affecting succinate dehydrogenase activity, leading to elevated succinate.
Insufficiency of prolyl hydroxylase cofactors – low Fe/Si  | low Zn | low vitamin C (caused by oxidative stress from IFN-gamma activity) | hypoxia.

8.      A significant conflict exists between IFN-gamma activity, leading to low NAD+, the mineral and electrolyte deficiencies and ALDH activity. ALDH requires NAD+ as a cofactor, along with Mo, Zn and Mg. This creates / exacerbates aldehyde toxicity and especially acetaldehyde toxicity.

Overall, this is only a brief outline for key-points in the disease model.

The sum of the alterations outlined here and numerous others detailed in the disease model leads to dysregulation of aldehyde metabolism, histamine metabolism, B6 degradation, mitochondrial and other energy metabolism, neurotransmitter metabolism, renal function, blood volume and temperature regulation, immune functions and more.

Variables inside the cascade, such as mineral and nutritional status, biofilm locations, microbiome dysbiosis and pathogenic species involved predict feature presentation and severity.

The disease model suggests this cascade could be loosely described as microbe-mediated scurvy and alcoholism, with extras. It has further implications for aging and longevity.

General Mitochondrial and Wellness Protocol
Author: Joshua Leisk,
Based on:

[25th September 2023]: 
Apologies, this page has moved -
The latest downloadable PDF version of this protocol is now located in
the [disease model] page, for efficiency and ease of access.


[This article is being regularly updated.]

Under normal human metabolism, blood pH is tightly regulated between 7.35-7.45.

Interstitial fluid pH (an extracellular fluid) also starts around 7.4 and for the general population, with intense physical activity, can often drop to 7.0 for brief periods, thanks to elevated activity by our muscle cells. In chronic disease the interstitial pH can shift towards acidosis. This can be accelerated and exacerbated by an impaired lymphatic system, which plays an important role in connecting our extracellular fluid compartment back to our circulatory system and modulating immune function. From there, blood transport efficiency, pulmonary respiration, hepatic and renal function are also critical.

This pH shift can be caused by mitochondrial fragmention / HIF-1a alterations / Warburg metabolism seen in various infections / cancers / senescent cells. pH shift caused by various molds - notably many aspergillus and penicillium species. Mitochondrial fragmentation can also be caused by the spike protein seen in SARS-CoV-2 infections AND the current vaccines which produce analogues of this spike protein.. outcomes can benefit from preventing the pH shift.

A "somewhat normal" blood smear on a brightfield microscope may look something like this.
(Note the red blood cells are repelling each other and are maintaining a healthy round shape.)

When systemic pH is not tightly regulated, cellular metabolism is severely impaired.
Red blood cells no longer repel each other, clumping together and forming rouleaux.
These effects can be further impacted by the presence of biofilms, such as the ones visible in this next image.

When the red blood cells are extremely stressed, they display a "crowning effect", indicating membrane damage and impaired functionality.

These features can also be seen in the presence of pH-shifting molds, such as Aspergillus and Penicillium-

and have been observed in both COVID-19 infections and vaccinations, owing to induced mitchondrial fragmention and Warburg metabolism by both the wild-type and vaccine-induced spike proteins -

Ultimately, these features may lead to hypercapnia and/or hypoxia, while also preventing red blood cells travelling in single-file through tight places.

With haemoglobin's primary activity impaired, this places undue stress on bicarbonate levels to help maintain systemic pH.

Measuring blood pH has complications, however taking a first-morning sample of both saliva and urine with a high resolution digital pH meter or pH test strips may be beneficial in monitoring trends in pH over time and making adjustments. The morning sample should normally be the most alkaline sample of the day.

As these measurements do not show interstitial pH or blood pH, the data has limited uses. More research into practical ways to sample those fluids is being explored. Sweat may be a suitable inference for interstitial pH, however this has not been fully explored.

(A portable device used by athletes for measuring blood lactate may be an better option, however there may be some additional difficulties, also. L-lactate is produced by our metabolism and D-lactate is produced by microbial metabolism. Testing only L-lactate levels may show a false negative, if the source of the lactate problem is microbial D-Lactate. A solution could be to first perform a Genova Diagnostics Organix test or various others that sample both L and D lactate levels. If D-Lactate can be excluded, then L-Lactate may be a viable at-home marker to track, using a finger-prick test.) 

Depending on the level of pH, a pH imbalance can be labelled as -

Alkalosis (common types/causes):
- Nitrogen metabolite excess

Acidosis (common types/causes):
- Lactic acidosis
- Respiratory acidosis
- Renal tube acidosis
- Metabolic acidosis

The critical blood pH regulators are hemoglobin, bicarbonate, gas exchanges from respiration and normal renal function.

If hemoglobin count or morphology is unfavourable, this transfers considerable burden to bicarbonate to maintain homeostasis. If kidney function and alkaline blood flow is impaired, this can be catastrophic. If additional gas exchange from breathing is unable to maintain the balance, a poor outcome is expected.

Other pH influences are digestion end products, microbiome influence, mineral deficiencies including electrolytes, ferritin and related mineral metabolism substrates / cofactors.

Downstream effects of pH abnomalities include systemic ion channel disturbances and membrane inflammation. Most noticeably, these could be sodium/potassium related and rely on eg. Na+/K+/-ATPase for gradient regulation. Intracellular calcium accumulation may occur.

This could cause some of the symptoms relating to ME/CFS - post-exercise malaise, muscle contraction impairment and inflammation, dopamine transport / metabolism, major depression, pseudo-parkinsonism, encephalopathy, renal function abnormalities and calcium channel irregularities such as NMDA overexcitability.. and more.

This is very much a "tip of the iceberg" list, as this would be expected to create a catastrophic and familiar cascade of symptoms, and even prevent medication from working.

Identifying if someone may benefit from exploring this further would involve some testing.

Related biomarkers:
- Blood CO2 high / low, bicarb
- 24h urine electrolytes
- Anion gap, etc

Pulmonary function tests may be appropriate, including peak flow:

If either respiratory or renal functions are impaired, pH balance becomes problematic. If both functions are impaired, pH can become very problematic.

My suspicion is that dysautonomia and/or airway obstruction, including nasal inflammation may cause poor gas exchange and pH management. This could be further compounded by sleep-related breathing disorders.

Where the issue is CO2 accumulation / incomplete gas exchange, these effects could be transient over the day, or longer phases, with symptoms similar to hypercapnia. Increasing oxygen intake via an oxygen bottle is unfortunately not very helpful for removing carbon dioxide buildup.

(More details here -

As of v3+, the experimental protocol addresses pH shift from HHV-related mitochondrial impairment around ammonia metabolism, removal of some microbial nitrogen influences, as well as the lactic (acidosis) downstream from mitochondrial fragmentation / HIF-1a and impaired hepatic gluconeogenesis. Dietary inputs to metabolic acidosis are managed by vegetables and other foods in the example diet in v3.31, including the electrolyte intakes.

What is not currently covered in v3 and may require individual assessment, remediation:
- Other pathogens - these may still benefit from antioxidants / glutathione precursors and HIF-1a modifiers, eg. very high dose [thiamine, benfotiamine, sulbutiamine, fursultiamine (thiamine tetrahydrofurfuryl disulfide) or allithiamine] / resveratrol / dichloroacetate to prevent lactic acid metabolism.
- Breathing sufficiency / efficiency. With chronic shallow breathing, it's possible that over time that a person could need to 'retrain' their breathing habits to restore normal gas exchange.
- Sleep breathing disorders.
- Kidney function (eGFR is not a comprehensive evaluation of renal sufficiency).
- Specific intracellular mineral deficiencies (such as magnesium, manganese, lithium, copper and zinc).
  Serum tests are not very helpful as they are also tightly regulated by the kidneys.
  White blood cells (SpectraCell tests) are a useful indicator for intracellular levels of vitamins, minerals and various metabolites.
  This may be combined with Hair Toxin Mineral Analysis (HTMA) reports and due to the nature of HTMA, need to be interpreted appropriately for obtaining actionable data. Trace elements often labelled as 'toxic' often have important function, but become toxic in excess. Rubidium, strontium and cobalt are good examples of these and may need resolving by diet and/or supplements, in balance.

Considerations and interventions:

In some circumstances, dietary interventions such as adding an appropriate amount of potassium bicarbonate to water, consumed between meals could be a useful way to temporarily alleviate or reduce symptoms of some pH imbalances.
Up to 1 grams / hour of potassium bicarbonate, dissolved in a glass of water, could be appropriate, with a daily limit of 3 grams.
Alternatively, up to 1 gram / hour of sodium bicarbonate, dissolved in a glass of water, could be appropriate, with a daily limit of 3 grams.

Controlled deep breathing exercises may be highly appropriate. Correcting a bicarbonate deficiency allows for improved pH buffering, however this is still dependent on respiration.

Medical devices for improving breathing efficiency during sleep, such as a bipap machine, can be discussed with an appropriate medical professional.

Some intracellular mineral deficiencies (and excesses), particularly electrolytes, can be problematic to remediate. According to widely available (anecdotal) evidence, it can often take many months for a chronic magnesium deficiency to be corrected. I suspect this can be improved on.

Additionally, creating serum spikes of an electrolyte by consuming supplements are known to cause rapid corrections via renal excretion, whereas taking small amounts over the day can prevent this. Studies have shown as little as 11% of supplemented magnesium is retained. For this reason, adding magnesium to your daily water intake is superior to taking a tablet.

Special forms of electrolyte supplements, such as acetylated electrolytes, including magnesium acetyltaurinate may also be very helpful in bypassing this issue.

Lithium has many important biological functions. A deficiency can cause renal magnesium wastage by altering the retention ratio. Unlike clinically relevant "therapeutic overdoses" of lithium (20mg-1800mg/day), 0.5-1mg has been suggested as a daily value for lithium / as an essential nutrient and is associated with longer lifespans and quality of life in the literature.

Some further complications are that due to compensations and altered homeostasis, increasing these depleted minerals could also cause paradoxically opposite effects, eg. supplementing or increasing magnesium may initially cause sleep disturbances and increased adrenergic signalling, until a new homeostasis is achieved.

Magnesium is directly involved in 300+ reactions and along with zinc, is a key cofactor for metabolising any/all dietary forms of Vitamin B6 into P5P. A deficiency of either can lead to B6 toxicity symptoms, such as small fiber peripheral neuropathy.

Dietary P5P supplements are less helpful than they appear, as digestion of any P5P supplements cleaves the phosphate group, thus requiring magnesium and zinc for later reassembly. P5P is responsible for 150+ reactions, including dopamine synthesis, so an intracellular magnesium deficiency can impair 450+ reactions.

Manganese is often overlooked and a deficiency can create issues with Vitamin B and C metabolism, along with creating further oxidative stress via decreased MnSOD.

Zinc also has important roles in Vitamin B6->P5P, neurotransmitter and catecholamine metabolism. Copper is also important and the intake of copper, zinc needs to be balanced. Excessive intake of either can also create symptoms of deficiency.

Magnesium and zinc are the primary inhibitors for NMDA receptors and the literature suggests their deficiency can cause excitotoxicity.

DBH and BH4

Our ongoing research strongly suggests that at a fundamental level, one of the key differences between mild, moderate and severe ME/CFS is dopamine metabolism.

Specifically, impaired dopamine beta hydroxylase (DBH) and Tetrahydrobiopterin (BH4) - the latter being a cofactor for tyrosine hydroxylase and L-DOPA synthesis, further acting to rate-limit dopamine synthesis. This may be an important feedback loop when dopamine synthesis exceeds release / metabolism, as mediated by a DBH insufficiency.

There are a multitude of ways that DBH can be impaired. It's expected that multiple influences may be exerted at the same time to create a 'perfect storm'.

For example, a number of Clostridia species are capable of creating "gaseous mycotoxins" which inhibit DBH, with catastrophic results. T.gondii is able to impair DBH. Excess agonism of alpha-adrenergic receptors can impair DBH. Polymorphisms for DBH related genes can impair DBH. Potassium and or magnesium deficiency can impair DBH. Low vitamin C and/or copper can impair DBH. Further, low manganese and/or excessive oxidative stress can cause intracellular vitamin C deficiencies.

Low fumarate, chloride and acetate can cause DBH abnormalities. This may be suggestive of problems with mitochondrial fragmentation with impaired methylation and/or impaired succinate dehydrogenase (SDH). SDH and methylation both rely heavily on a riboflavin metabolite - flavin adenine dinucleotide (FAD). SDH also requires ubiquinone as a cofactor. Impaired pulmonary respiration and/or hemoglobin transport function may also be causal for low fumarate.

Sustained neural and neuromuscular activity with mitochondrial fragmentation, impaired methylation and HIF-1a alterations could lead to interstitial lactic acidosis, which by nature means a low pH state. This can be further mediated by insufficient lymphatic clearance.

Low pH, impaired Na+/K+-ATPase and high intracellular calcium levels are able to completely impair DBH. In this way, exercise intolerance and the sterotypical ME/CFS "crashed" state can be reached by low levels of metabolic activity. Resting is required to partially revert this state.

Research is continuing towards quantifying all other known DBH influences.

DBH has multiple roles. Its key role is to metabolise dopamine into norepinephrine, thereby facilitating fatty acid oxidation and other adrenergic signalling. In presynaptic neurons, DBH also behaves as a critical membrane transporter for releasing noepinephrine outside the cell.

Dopamine circulates systemically and has many functions beyond activating post-synaptic neurons. A systemic dopamine deficiency, or insufficient D1 receptor agonism can easily create inflammation via increased NLRP-3.

NLRP-3 can cause anxiety, hypertension in a sodium-rich environment and catabolism of norepinephrine. Insufficient dopamine and/or norepinephrine can impair blood flow in key tissues, cause neurological disorders and is well-known for causing debilitating movement disorders / muscle paralysis, including gastrointestinal tissues.

Dopamine transport and binding events through cells membrane can also become catastrophically impaired when the cell is suffering from abnormally high/low extracellular pH and/or when electrolytes required to operate ion channels, transports and pumps are either low, or the gradient between the intracellular and extracellular pools are not being maintained by the ATP-dependent "pumps" or ATPases. This can directly affect systemic dopamine metabolism in a similar manner to DBH deficiency, only potentially much, much worse - as numerous other transporters, receptors and pathways will be similarly impaired by these abnormalities.

If presynaptic intracellular dopamine levels are excessively high due to low DBH and/or impaired dopamine transport, this may be rate-limited by biopterin recycling / low BH4. BH4 is responsible for synthesis of key neurotransmitters. Without BH4, tyrosine hydroxylase is impaired, reducing the conversion of tyrosine to L-DOPA and thus dopamine.

BH4 can be impaired by peroxynitrites, low ferritin, low riboflavin, low niacin and low 5-methyltetrahydrofolate (5-MTHF).

If excessive dopamine metabolism is combined with a DBH deficiency, the subjective experience could resemble the horrible "disulfiram effect" - custodially imposed on some cocaine users - any increase of dopamine and/or alcohol metabolism does not cause pleasure, instead causing anxiety, nausea, potential seizures and/or severe sensory-motor polyneuropathy.

An imbalanced GABA:glutamate ratio can lead to excessive dopamine metabolism, excitotoxicity and oxidative stress. This can sometimes be caused by insufficient NMDA inhibition (further relating to magnesium and/or zinc deficiency).

Another cause for GABA:glutamate imbalance may be P5P deficiency - further relating to a deficiency of magnesium and/or zinc and/or riboflavin - this is often caused as a downstream effect of high oxidative stress / mitochondrial fragmentation / Warburg metabolism, where P5P and methylation cofactors B9, B12 are ultimately converted into "mitochondrial fuel" as a backup pathway to maintaining Succinyl-CoA). Hormonal imbalances have also been previously discussed as causal. Damaged cell membranes and ion channels from pH imbalance are another possible cause. A less common cause may also include antibodies to glutamate decarboxylase.

This altered metabolism can be "somewhat patched" by benzodiapines and related pharmaceuticals, however this comes with an additional well-known set of problems and some benefits. 

A preferred approach (after confirming noradrenaline is low and/or vanillylmandelic acid is low on urine tests), is to normalise DBH, thereby correcting the downstream cascade. This would be best mediated by removing any/all "low-hanging fruit", such as:

1. Quantifying and remediating deficiencies of vitamin C, copper, manganese, magnesium, zinc, lithium, riboflavin and potassium. (PQQ may also be helpful.)
2. Quantifying and remediating interstitial and blood pH. Confirming by blood smear that red blood cell morphology is normal. Any clumping or rouleaux may act to limit other interventions.
3. Quantifying and remediating pulmonary respiration function.
4. Antagonising a2-adrenergic receptors, using a suitable intervention. (At this time, appropriate a2-antagonists may include small doses of yohimbe / yohimbine, rauwolscine and phenoxybenzamine. This is a WIP)
5. Further reducing NLRP-3 using eg. hesperidin.
6. Removing / remediating any detected pathogens that impair DBH - this can be a long process.
7. Investigating a BH4 deficiency - this is difficult to measure directly. This may appear as low levels of neurotransmitters, low ferritin, low intracellular riboflavin, low 5-MTHF / folinic acid, low citrulline.   

To summarise -

It appears that different pathogens affect specific energy metabolism pathways, often via neurotransmitters:
Low BH4 affects glycolysis, nitric oxide synthesis / blood volume, neurotransmitter synthesis / recycling and downstream of dopamine, adrenergic signalling and therefore fatty acid oxidation (FAO). It may also lead to low NAD+ and immunosuppression.
    Common BH4 insults may include lipopolysaccharides (LPS) and potentially low trace elements, such as rubidium.

Low DBH reduces norepinephrine synthesis, affects fatty acid oxidation and can cause obesity, malaise and impaired hepatic gluconeogenesis / lactic acidosis.
    Impaired DBH can also cause intense anxiety instead of pleasure when dopamine is increased.
    Common DBH insults may include: T.gondii, various clostridia species, low copper, low vitamin C, low potassium.

Low SAM-e will further impact FAO at conversion of norepinephrine to epinephrine, while also impacting serotonin metabolism.

Elevated glutamate dehydrogenase (GDH) upsets nitrogen metabolism, causing uremia and potentially hyperinsulinism, where GDH is high in pancreatic tissue.
    Hyperinsulinism, and/or insulin resistance cause by a low pH environment can readily impair glucose metabolism and glycogen storage.
    Common insults: The 9 HHV family members or tick-borne cousins, MHV-68 or MHV-72. HIV also increases GDH.

High levels of oxidative stress or mitochondrial fragmentation will further exacerbate nitrogen metabolism, while altering hypoxia inducible factors and triggering lactic acid metabolism / pH shift down, blood clotting / rouleaux, hypoxia / hypercapnia, while rapidly depleting B12, folate (impacting BH4), B6->(magnesium, zinc, riboflavin/FAD)->P5P.
    This may also prevent collagen synthesis, leading to tissue degradation and ageing (see CFS/ME: A New Hope, figure 6.).
    Common insults: NMDA over-excitability, rampant viral protein synthesis, SARS-cov-2, all known COVID-19 vaccines and a long list of pathogens that trigger Warburg metabolism. Low trace elements such as manganese. Low dietary antioxidants. Gut microbiome dysbiosis. Heavy metal toxicity. Poisoning.

Low magnesium and zinc may lead to NMDA over-excitability, further altered by acidosis and intracellular calcium accumulation. This can overdrive dopamine synthesis, creating a very unpleasant situation, if DBH is low. This may be limited if/when this or low riboflavin causes P5P to run low, or if BH4 runs low.

Low riboflavin/FAD may lead to impaired succinate dehydrogenase and other mitochondrial reactions, elevated succinate and low fumarate, especially if combined with poor hemoglobin function / respiration.

Low P5P metabolism caused by the previous 3 points can readily cause toxic B6 accumulation and peripheral neuropathy.

When glucose, glycolysis and fatty acid metabolism are all impaired, with low pH and/or insulin resistance, this forces these cells to survive via HIF-1a and lactic acid metabolism, contributing to systemic load and can be fairly catastrophic, if lymphatic, hepatic, blood transport or renal function are insufficient.
    This may also lead to high levels of cortisol being generated in an attempt to trigger gluconeogenesis and recover. Edema response to androgens and estrogens may become apparent.
    NB. Rapidly disabling HIF-1a / Warburg metabolism in this state will cause acute energy loss to these cells and this may be observed by an intolerance to NAC, R-ALA, resveratrol and/or any other antioxidants. Conversely, increasing oxidative stress via eg. opiate use may be reported as beneficial.

Low pH and acidosis is expected during these conditions, further impairing all cell membranes, ligand binding, ion channels, electrolytes.

Any other cause for lymphatic, renal or hepatic impairment can also lead to this state.

[To be continued..]

Understanding the Model / The origin of this discovery
« on: June 14, 2021, 04:46:25 AM »
(This backstory was first shared at S4ME and then Phoenix Rising, in early 2021. Minor edits/updates have been made.)

I'm an anomaly.

I'm a fully recovered CFS/ME sufferer (25 years free and clear) with a strong background in IT and and interest in bioinformatics. I "retired" at 38 and got bored. I like puzzles, pathways and systems. This was a puzzle that had bothered me for a few decades, so I thought it was worth helping people solve.

Here are our three most recent papers, currently in preprint -

For CFS/ME, our primary research focus is the liver (and now also the brain).

My original research strongly suggested that it's a combination of the antibodies from the lytic phase, PLUS the primary issue of latent viral hepatitis - the metabolic burden of the latent cell activities, hard-wired by GLS1 - KGA, GAC + GDH, etc., for protein-synthesis tasks, glutaminolysis and lactate production interfere by the behaviour of the neighbouring hepatic cells. eg Lactate cycle metabolism. Arresting the lytic phase does not solve CFS/ME, but it will reduce the antibodies.

Checking eg. EBV EBNA,VCA IgG counts for systemic latent infection and then inferring localised hepatic infection by performing the 'succinate challenge' I mentioned in the paper gives us an understanding of the pathophysiology, where hypoxia is present. For other disorders and diseases, it's largely tissue specific.

We would happily perform more experiments ourselves, but we're a pair of researchers without a lab facility.

We would love to run a clinical trial based on some robust preliminary test results, however we are reliant on others for properly testing this hypothesis. We are currently engaging with some existing parties to make that happen here in Australia, although are open to assistance from any other parties.

We're happy to work with others. In case we have misinterpreted any cited papers, we're open to any discussion and correction.

The background on this discovery is that in the course of my normal consulting, I had a cluster of 5 diet coaching clients over roughly one month presenting for a number of different goals, yet similar issues - with a common complaint of daytime fatigue.

Most had joint pains and involuntary muscle contractions. The male and female clients had endocrine, sleeping and neurological disorders, such as acute anxiety. The males and females exhibited signs of alopecia. All had extensive pathology data, spanning more than 10 years and a history of symptoms longer than 15 years. Only one client had ever been officially labeled as a "CFS/ME" patient.

I compiled and analyzed their pathology data and saw a common pattern of urea cycle abnormalities, cortisol / adrenal cortex dysregulation and mild leukopenia - specifically, borderline subclinical lymphocytes. ANA, CK, cRP, ESR, thyroid markers all unremarkable. Some minor liver enzyme elevations in some clients, which appeared to match their body composition and life choices. I thought the overall pattern was interesting, so I kept investigating.

Most clients had acute eating disorders. Ear/nose/throat infections were common. Environmental allergies were common. There was a history of GI issues and all had a specific pattern of food intolerances. Eggs and lecithin were consistently mentioned. I found that even more interesting.

I assessed their dietary habit using one of my favourite nutrition tracking tools, "Cronometer". The observed protein intake was very low - typically less than 40 grams per day, which did not match the unusual serum urea also being observed - BUN was typically high range, or in one client, very low range. This was interesting, because it suggested that either glutaminolysis was being used, and / or the urea cycle was impaired at different times.

3 of the clients had reported some benefits from ketogenic diets. 1 of them was currently employing a ketogenic diet. The others had not attempted this. This 1 client chose to discontinue their ketogenic diet and had an acute worsening of symptoms. This was interesting because it demonstrated a pattern of mitochondrial impairments.

All clients had a habitual lifestyle that obsessively revolved around dietary supplements. This was also interesting and it allowed me to ask them what supplements they took regularly and why.

Importantly, I also asked them what they didn't take and why - "what had they experienced negative reactions to?"

A common list of "problem" supplements for all clients was acetyl-l-carnitine, EGCG, choline, arginine, citrulline. Some of them reported that acetyl-l-carnitine caused acute edema and myopathy. I found that very interesting, also - suggesting influences to fatty acid oxidation / PDH, GDH, acetylcholine receptors, respectively.

All of the clients had exercise intolerance to even the mildest exertion levels, with suboptimal lactate threshold and oxygenation, even beyond my expectations for a sedentary lifestyle.

3 of the clients had prescriptions for salbutamol inhalers.

From this combined data, I saw more patterns forming. I analyzed other data they had captured, including HTMA tests, which excluded heavy metals, etc as a source of hypoxia.

At this point, I decided to take a personal interest in these cases and chose to work closely with 2 of these clients on a daily basis, exploring published literature and talking with them for typically 5-8 hours a day over many months, observing and analysing high levels of detail about their diet, daily activities, symptoms, influences / triggers / responses, while assembling connections between individual data points. This was a performed without any financial consideration. Being "retired" made this level of dedication and focus possible.

Dietary intervention of adding 2 eggs and some soy lecithin to every meal and 2 more before bed improved or resolved involuntary muscle spasms, with some not-unexpected discomforts. This was partially replaced by choline bitartate.

Pathology for Plasma Amino Acids found some common abnomalities with elevated glutamine, glutamic acid, low 1-methyl-histidine.

Exploring the literature and looking at the published CFS/ME metabolomics data, I saw many parallels between client data and published data. I explored this further, creating new connections along the way.

Serology markers showed high titre active EBV in both cases. There were differences in testing method availability, due to geographical location.

(Shared with full consent / expressed permissions.)

Client 1 -
EBV VCA IgG+++ (exceeded reporting thresholds)
EBV EA was not provided

Client 2 -
EBV EBNA was not provided
EBV EA was not provided
CMV IgG ++

At this point, I considered that we had maybe progressed beyond "smoke", to "fire".

[QUESTION - "Perhaps the impact from lytic EBV infection or CMV was the source of the symptoms?"]

I reached out to those 2 clients' physicians and requested assistance. Under their care, off-label spironolactone (aldactone) was initiated at 25mg/day (Campo et al.) and client 1 increased to 2 x 25mg/day after 1 month. Client 2 also chose to self-administer nigella sativa for their CMV infection.

Over 3 months of close interactions, I observed many patterns in triggers / responses and durations, including associations between both clients' reported salbutamol usage vs timing of and cessation of upper-right abdominal pain, with increased energy levels.

The abdominal pain followed periods where they had been feeling better, with improved energy levels and decided to make use of them. Due to concomitant hypoxic symptoms, they self-administered salbutamol and this demonstrated a pattern of resolving their abdominal pain and also a reduction of the duration and intensity of post-exercise malaise. It also increased their energy levels. I found this very interesting.

The location of the pain and the relationship to the salbutamol dosage suggested strongly that beta-oxidation pathways were involved and the lactic acid cycle was impaired at hepatic gluconeogenesis. It didn't explain the cause of the high lactate, which I considered to be related to the impairments surrounding energy production.

Via close observation of client myopathy vs activity, I could see that unusual amounts of lactate were being generated, in addition to impairments in hepatic conversion back to glucose.

Combined with the noted urea cycle abnormalities and hypoxia, this was pointing strongly to a deficit in succinate and fumarate. The general lack of energy was suggesting an insufficient amount of ATP was being generated. This pointed to Complex V.

Gradually, over these months, I collected enough information from observations and literature searches to collectively create a hypothetical map.

Client 1 obtained a high result for EBV PCR roughly 1 month after starting spironolactone and flow cytometry, from the same sample showed low CD4. At 2 months, returned negative on PCR tests. WBC / flow cytometry all amazingly unremarkable.

Client 2 obtained negative results on both EBV and PCR test at roughly 6 weeks.

This was a strong suggestion that spironolactone has efficacy for arresting EBV, CMV lytic phase. Only expected side-effect being increased urination, requiring increased hydration and electrolytes.

Both clients had some tangible improvements to many symptoms, but were still showing all of the hallmark CFS/ME pattern of impairments I had personally experienced all those years ago.

[ANSWER - "The lytic phase is only partially responsible for CFS/ME. (n=2)"]

[QUESTION - "Wonderful, so what does this mean?"]

Looking at the pathway map I had created, three "hot-spots" were a-KGDH, PDH and selective beta-oxidation pathway insensitivity.

NutraEval reports are incredibly useful for identifying these abnormalities, however these need to be interpreted based on the level of activity prior to sampling, in much the same way that metabolomic studies need to be controlled against time of day and prior activity levels to provide any meaningful data.

Further to this, my research into the behaviour of HHV-infected cells revealed a metabolic preference for glutaminolysis (Krishna G et al), just like many cancer cells (Song Z et al.) and an ability to replicate via transcytosis (Hutt-Fletcher L et al.). This suggested a number of things, not the least of which was that these infected cells would be susceptible to the same metabolic influences as those cancer cells (Saunier E et al.). I considered that just like in certain types of cancer cells, the location and behaviour of the latent cells would have influence on the neighbouring cells. Where these are hepatic cells, this would unduly influence the hepatic function, in particular with regards to lactate metabolism / gluconeogenesis. In other tissues, many other disorders would be expected, where collagen synthesis and other tasks downstream of prolyl hydroxylase activities are degraded, leading to various states of inflammation and cortisol dysregulation. This has implications for Ehlers Danlos Syndrome and others.

As such, in my capacity as a diet and health coach, I educated Client 1 and Client 2 on the benefits of specific over-the-counter dietary supplements which are known for addressing these pathways, with advice to verify with their physician if contraindicated in their illnesses.

In the general population, like most dietary supplements in general, these specific dietary supplements would have little to no noticeable effects or benefits beyond those provided by a normal, balanced diet. They chose to purchase these from their local health food store or supplement vendor and self-administer them. They further chose to provide me with reports on their experiences with this self-experimentation.

Unlike the typical 'non-response' expected in the general population, the effects from these specific supplements were reported as both rapid and acute in both clients. Their energy levels returned to normal and they regained normal daily functionality and lifestyles. Due to their natural curiosity and a long history of experimentation with supplements, they also tried different combinations and dose schedules of these supplements and reported the effects. I analysed their reports and noticed a pattern, where failure to address any one of these "hot-spots" I had educated them on led to a consistently repeatable pattern of initial impairments and a resumption of full CFS/ME symptomology.

Using the combination of dietary supplments, viral EBNA IgG has been demonstrated to have decreased by 25% over 2 months, suggesting reduced systemic burden.

[ANSWER - "We are long past 'smoke', well past 'fire' and currently 'discussing the merits of different coloured fire extinguishers.'"]

[QUESTION - "This needs robust testing - how do I share this information with people who are in a better position to make use of it and without creating problems associated with communicating this around a demographic of patients who are desperate for early answers?"]

At this point, although having read perhaps 900 papers, I thought it would probably be best if I studied the literature further, wrote a review and shared it with the community. This presented some new difficulties, as although demonstrated by my recent manuscript, through personal interests my understanding of metabolism, rheumatology, cellular biology, immunology, endocrinology and biological pathways could be considered with some equivalencies to a PhD level education, due to my life choices and preference for self-education, usually by intense reading, I lack the credentials required to present these findings to a wider audience, in the format they would normally be inclined to appreciate and give due consideration.

I prefer to learn things in my own way and explore topics in an organic way, where my brain absorbs them efficiently. I find structured education traditionally 'grinds my gears' by causing frustrations and inefficiencies, therefore I limit any formal education and certifications to the barest minimum required to permit me to work in any specific field. This is also likely why I left school at 14 and "retired" at 38. Overall, I have lived an unusual life.

A self-taught "diet and health coach" traditionally does not write medical journal articles on complex metabolic disorders and virology. This is a significant anomaly, although my life to-date has been one long anomaly. Importantly, I also lacked a full understanding of the nuances and expectations of academia, with regards to publishing material for peer-review.

[ANSWER - "Fortunately, through fate and/or luck, my life-partner and co-author happens to be a brilliant scientist, holding a PhD in Neuroimmunology, with a Masters in Biochemistry. Keeping in line with my usual preference for organic learning, she helped me understand the normal requirements for publishing a paper, assisted and answered questions about lab methodology, where I found criticisms of papers I was reading, edited and helped proof the manuscript, along with many other key aspects of the journey towards where we are today. I'm always thankful for having her in my life." ]

In the process of continuing to map the pathophysiology, draw the diagrams and write the paper, my research connected the dots with a broader array of disorders and diseases. I realised that my research had significantly greater implications for many diseases and disorders. During the many weeks that was required to author the paper, I was was also contacted by some other clients and friends who had a number of different diseases / disorders - including bipolar disorder, schizophrenia, ehlers danlos syndrome, IBS, lupus and rheumatoid arthritis, which were already strongly hinted at having a common origin, by the growing manuscript and diagrams.

Consequently, I found the same signature of metabolic alterations and serology markers in those clients and they show an acute response to the same dietary supplement advice, although there are variations and further optimisations possible where hepatic impairment cannot be demonstrated or where lytic phase cannot be detected in serology. For each of these disease model sub-types, I have drafted early specifications that can be used for testing in clinical trial research around these disorders.

In v1, there were two small mitochondrial "leaks" to resolve regarding a-KG accumulation and ROS. They're now fixed in v2 and provide a treatment which allows normal daily life, however this can be further improved.
v2 was demonstrated in small numbers to provide symptomatic remission, with gradual improvements to latent cell burden, if combined with a prescription for eg. spironolactone.
v3 is being actively tested.

At this point, we have also filed a patent for the formula, to also aid later discussions with pharmaceutical companies.
We are not selling any products. We are not selling any services.

The treatment involves items that can be bought at vitamin stores and supermarkets.
If people need help, I've been offering my time and assistance without any thought of financial gain. This is real and my aim is to help people.

However, this is also where WE need help in continuing this journey.

"Can you please assist us in making this a success for everyone?"

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