Cpn theory: Effect of pH on Cpn

Cpn theory: Effect of pH on Cpn

For a few years I have considered that lowering intracellular pH (pHi) might be beneficial for treating Cpn. I suspected that this would be a logical signal to induce Cpn into an EB state which should make it more susceptible to antimicrobial agents as it is most vulnerable during its subsequent conversion from EB to RB state and additionally may have to give up its resistance mechanism. The reason I believed that lower pH triggers the EB state was originally based upon observations of the effect of many acidic substances such as ascorbic acid, exercise, NSAIDs, caffeine, ect. And it seemed logical that this would be the trigger that Cpn used as pH would drop in cells where (1) there was an overgrowth of RBs, (2) the cell was undergoing apoptosis, or (3) the cell was dying from necrosis. In all of these cases, it would benefit Cpn to condense down to the EB state.

Interestingly Cpn has Na+/H+ exchangers/pumps. Typically these pumps lower pHi by exchanging hydrogen ions for sodium. IMO it makes little sense for Cpn to have this mechanism as an intracellular pathogen should be able to rely on the host cell's buffering mechanisms. It is also noteworthy that Cpn's genome only has about 36% homology to these pumps. This is surprisingly low as other bacteria average 65% homology. So I suspect these incomplete Na+/H+ pumps actually are used only to monitor pH levels and when it drops to some thresh hold value, produce some other result aside from exchanging hydrogen ions for sodium that induces conversion to the EB state.

For the last couple of years I and a few others have been testing this idea with various agents that help lower pHi. The results have been very good although perhaps not as good as I had originally hoped. This approach seems to work about twice as fast and with about half the side effects as some of the other approaches but it still takes a couple of years for many people.

More recently the lab work has begun to catch up with the clinical testing and Dr. S. has shown in vitro that lowering pH with lactic acid causes an 8 fold decrease in the production of HSP-60. This recovers to the control levels after about 24 hours. The most likely cause of these results seems to be that the lower pH induces the EB state.

There are a variety of ways to lower pHi:

(1) Anaerobic metabolism lowers pH very efficiently. Historically this was thought to be from a build up of lactic acid although that is no longer believed to be true. It is pretty easy to induce anaerobic metabolism in skeletal muscles but more difficult in other parts of the body. However I think that Cpn (like all bacteria) use efflux pumps to remove environmental toxins. I think they pump out most/all antimicrobial agents and this is metabolically expensive. So taking many of the antimicrobial agents can contribute to lowering pH. I also think that it expends energy to pump out nitric oxide as this is the host cell's natural antimicrobial defense. The downside of relying only on this approach is that infected cells are "starved" of ATP for prolonged periods of time. This can cause a number of problems and specifically is probably the cause of secondary porphyria as cells are always producing heme and some of the steps in the process of converting porphyrins to heme require ATP.

(2) Expelling calcium which is a base or buffer is another way to help lower pHi. Caffeine induces this through causing ryanodine receptors to release calcium. This is a very novel way to help lower pH but caffeine does have the drawback of poor penetration in joints and skin. There is a new disease modifying RA drug (tenidap) in the works that appears to also lower pH through expelling calcium. This could be interesting as presumably being used for RA, it penetrates into joints.

(3) Acidic agents can also contribute to lowering pHi although I think there are some caveats. Cells tend to be a little more acidic than the surrounding fluid. So it takes an active mechanism to transport acidic molecules across the gradient. Substances that can contribute to lowering pHi should be ones that cells have a need for (or are molecularly similar to these). Some of the obvious ones are ascorbic acid (pKa 4.17), cobalamin (pKa 2.7), taurine (pKa 1.5), and niacinamide (pKa 0.5). There are a wide range of these that work to some degree or another but I doubt if they can be used alone as it seems unlikely that a cell would just continuously keep taking up something like ascorbic acid. In topical areas it is easy enough to flood cells with an acidic agent which can be very useful. Examples are the various agents used for "peels" such as salicylic acid (pKa 2.98), lactic acid (pKa 3.83), glycolic acid (pKa 3.83), ascorbic acid (pKa 4.17), etc. In sinuses cromolyn (pKa 1.1) (Nasalcrom brand) works well.

As time permits, I will start another forum topic to discuss some possible therapeutic approaches and Cpn's mechanism of resistance.

- Paul


Paul, All very interesting. I just have a question. Where does plaquenil fit into this picture? I herxed terrible with doxy and plaquenil with pretty good improvement after 2 months. Whipple disease is also intracellular and plaq and doxy is one way to treat it. I thought plaq makes the cell more alkaline. They also use it for lyme and its been proven not to be a cyst buster as once thought. Also the work done by Azenabor using l type calcium channel blockers with abx as a direct kill. Where does this fit in?

200mg doxy daily, 500 zithromax mwf,flagyl 1000 m-fri.rifampin 2x daily,chloestryramine 2x daily

Hi Lee,

I think that hydroxychloroquine works by inducing Cpn efflux pumps. It has a very long, 100 hour half life, so it does not get pumped out by human cells and I think it provides a constant level of stress to Cpn. If a typical cell can support 5-6 RB/cryptic Cpn, hydroxychloroquine might reduce this to 3-4 as Cpn's ATP requirements would increase. I would guess that after some initial adjustment to the drug (presumably fatigue and porphyria like reactions) and a new homeostasis is reached, it should provide significant symptomatic benefit by reducing the Cpn population and subsequent inflammatory protein production.

Calcium channel blockers also decrease intracellular calcium although the mechanism of action is different than caffeine. I probably should have included them in the agents that lower intracellular calcium discussion but frankly had forgotten about this. I was not aware that these had been tried with antibiotics but it certainly makes sense. Personally I am not interested in trying these as I would think they cause unwanted side effects by their mechanism of action.

- Paul

Paul, your description of reaching a beneficial homeostasis with hydroxychloroquine fits my experience.  Even off all meds, I find porphyria levels become unbearable after 10 days without hydroxychloroquine.  So that indicates to me that the infection alone is causing porphyrin build up without even the presence of increased die-off from antibiotics. Somehow the Plaquenil is helping keep it at bay.

I'm looking into possible genetic susceptibility/intolerance of lead as a contributing cause of my extra difficult porphyria.  Hopefully chelation will make a dent so I can treat with antibiotics more easily.

I am getting my first batch of Rifabutin tonight and wondering whether to do the caffeine protocol with it based on your latest findings.  Are you still finding it's worthwhile to do, or has a better alternative become available?

Thanks loads for the update on the Vanderbilt research.



I also doubt that hydroxychloroquine lowers pHi. It has a pKa 8.1 which is higher than your bodies pH of 7.4.

- Paul

Hi Marysia,

I think rifabutin and caffeine is probably the best way to go, at least initially. Most of the people I know are doing that although some are adding other acidifying agents like taurine as they near the end of their therapy.

- Paul

When reading Donta's claims about hydroxychloroquine, I assumed he meant that the pH-raising action of the drug wouldn't be by mass action, but rather by messing with the body's own pH regulatory systems: activating some receptor or other, which started up some machinery to cause the body to generate something alkaline and dump it into an endosome.

That's because changing the body's pH via agents which work through mass action is quite difficult, since the body has a desired pH level, and fiercely defends it. If you eat something acidic like ascorbic acid, the body not only does its best to excrete it in the urine, but also responds instantly by creating alkaline substances such as bicarbonate to neutralize it. (Bicarbonate can be made from CO2, which the body is constantly generating. Indeed, part of the problem with control of pH in exercise is a lack of O2 to make CO2 with.) The reason the body does this is that a lot of biochemistry depends on the pH being near the desired value. If you actually did manage to eat enough acids to override the body's responses, you might kill yourself. (I think Paul knows this, thus his references to it being relatively easy to change pH in the skin; the implicit contrast is with the rest of the body, where it's not easy. Even if you just want to make a minor change in pH, which wouldn't damage you, you'll still be fighting all the systems which control pH. Of course eating something that subverts those systems, rather than just fighting them, is another matter entirely; but that can get tricky.)

Endosomes which don't have any cellular machinery in them are an exception to this tight control: their pH can vary widely. They're just trash barrels, and/or places to dump noxious substances into, in order to destroy invading germs. Wikipedia states that "hydroxychloroquine has been known for some time to increase[1] lysosomal pH in antigen presenting cells", citing what looks like a pharmacology textbook.

In any case, as regards the experiments, I'm curious as to how far the pH needed to be reduced, to get that decrease in HSP-60.

Hi Norman,

We agree that changing the pH by ingesting acidic substances is not easy. And it would not be practical or even desirable to change the bodies pH. However I do believe it is possible to effect intracellular pH for a brief time by ingesting larger doses of acidic agents provided they are actively transported into cells.

pH is normally maintained in cells at about 7.4. In the experiments I think 15 mM of lactic acid was used so based upon the literature I think pH was lowered to about 6.0-6.5. This is well within levels muscle cells hit during exercise. And I think this is easily achievable in vivo with a combination of antibiotic(s), caffeine, and acidic agents that are actively transported into cells.

The duration does not seem to matter greatly. Based upon observation it appears that lowering the pH for a couple of minutes (and maybe less) is all that is required. One might speculate that this is because Cpn needs an irreversible mechanism to convert to the EB state. Normally Cpn would grow until the host cell's energy is taxed to the point that anaerobic metabolism begins, and pH would drop. Not long after this other mechanisms of ATP production would begin occurring that increase pH. So the period between low and high pH might not be very long.

Note: Total conjecture below:

I did not discuss what I think the actual mechanism of action to convert to the EB state is as it is just a hypothesis where everything else I wrote is supported to some degree, if only observation. I think that Cpn actually has a complete Na+/H+ exchanger and the reason for differences in homology are because this mechanism is reversed. That is it allows H+ to enter the Cpn cell membrane and pumps out Na+. I suspect that Cpn normally gravitates toward alkalinity and this mechanism helps maintain pH at about 7.4.

When host cell's pH drops substantially this mechanism may continue to lower Cpn's pH to the host cell's level. However I suspect that Cpn's pH does not quickly recover, that is it does not have a buffering systems that increase pH. I think the process of condensing down to an EB state is based upon lower pH (presumably around or below 6.5). Many proteins and enzymes can only be made within a narrow pH range. I think when Cpn's pH drops to some level, it begins making what is needed to convert to an EB.

- Paul

What is meant by "intracellular PH"? PH of different parts of cell is different. PH of cytosol is generally 6,8-7,4 and PH of acidic organells is 4,5-6. What exactly we are going to lower, PH of cytosol? This all is very unclear to me.

Stratton/Wheldon protocol 02/2006 - 10/11 for CFS and many problems 30 years

Thanks for the numbers. A pH of 6.0 is a bit outside the ranges that Google finds for me, when I do a search for pH values resulting from maximal exercise, but a pH of 6.5 is indeed within them. This paper on apoptosis says that acidification in apoptosis "typically amounts to 0.3-0.4 pHi (intracellular pH) units", which perhaps surprisingly means that exercise can involve much more change in pH than apoptosis does. In any case, muscles subjected to maximal exercise hurt; in an experiment like that, I wonder whether the decrease in HSP-60 might be the result of some sort of distress the host cells are suffering, rather than a reaction to pH per se.

Some random thoughts on the theory:

I'm not sure why Cpn would necessarily have to turn into an EB, in order to survive apoptosis. The recent paper on Cpn-infected apoptotic neutrophils being eaten by macrophages and thus infecting them (link) doesn't seem, on a quick scan, to mention the form that the Cpn takes, inside the apoptotic fragments. The EB form is needed for Cpn to survive extracellularly, and particularly during transmission from patient to patient; but being inside an apoptotic fragment doesn't subject the germ to the stresses of the outside world: there is no osmotic shock, no dehydration, and no mechanical disruption. There is a lack of energy, or at least of ATP; but the cryptic form could perhaps handle that (and RBs can easily transition into the cryptic form). The idea that it turns into an EB sounds plausible, but proving it is another matter.

As for the idea that anaerobic metabolism, and thus acidification, would be the trigger for Cpn to decide that it's sucked a cell dry, and needs to turn into EBs and move on, I don't buy that at all. Anaerobic metabolism results from a lack of oxygen; but why would oxygen be the limiting factor? It's the limiting factor in muscles, where every cell in the muscle is straining at once; but in Cpn infection, each infected cell is typically surrounded by uninfected ones, and so is free to use not only its share of the oxygen flow, but also much of its neighbors' shares. (Or, at least, that's how the infection starts out. It may eventually progress to involve a large fraction of the cells; but whatever tactic it uses has to work even at the start, when only a tiny proportion of cells are infected; otherwise the infection can never get established.) Oxygen diffuses across cell membranes very readily. It seems to me that something else would give out first: likely ATP-generating capacity, since each cell only has enough of that for its own use, whereas fuel supply and oxygen supply are shared, and thus get diverted pretty automatically (just by flowing down concentration gradients) to cells that consume more of them. Also, Cpn infections very commonly start in the lungs; good luck getting anaerobic conditions there! That last bit is the clincher, to me: whatever mechanism one proposes, it has to work in the lungs, where oxygen concentration is very high.

To me, the obvious suspect for the trigger by which Cpn decides that it's used up a host cell, and needs to turn to EBs and move on, is lack of ATP.

As regards caffeine activating ryanodine receptors, and thus releasing calcium: yes, there are a lot of experimental papers using that effect in vitro; but the caffeine concentrations they use are awfully high. The paper "Actions of Caffeine in the Brain..." has some numbers on all the various effects that caffeine has at various concentration levels, as compared to the concentration from one cup of coffee, and also to the toxic concentration (see in particular Figure 1), and concludes that of the various effects, the only ones that are "likely to be reached by humans by any form of normal use of caffeinated beverages" are the inhibition of adenosine receptors. I was actually looking up the paper because I was wondering about another of caffeine's effects, inhibition of phosphodiesterase leading to a rise in cyclic AMP levels; I'd spotted some references to that affecting chlamydial growth -- in particular, mention that raising cyclic AMP inhibits chlamydial growth. That occurs at lower concentrations of caffeine than calcium release requires; but even so, it seems like one would have to really push up the dose, to get any effect on cyclic AMP. The sorts of doses that John (farandwide) was packing down -- 1200 mg/day -- might do it, but then they might not. And to hit ryanodine receptors, you'd need another factor of five increase, which pushes you into toxic levels. (Indeed, hitting ryanodine receptors might be why caffeine gets toxic at those levels: that calcium release is used by the body as the signal to contract muscles, and to make the heart beat. Too much of it, and you might end up with fatal cardiac arrhythmia, or killed by having all your muscles contract uncontrollably like a nerve gas victim's.)

Anyway, even if one follows that paper and looks only at caffeine's effects of blocking adenosine receptors, there are still lots of ways for it to affect Cpn treatment one way or another. For one thing, one class of those adenosine receptors (type "A2A") ends up doing the same thing I was looking for information on: raising cyclic AMP levels. But the sign of the effect is different! Adenosine activates those receptors, and raises cyclic AMP levels, while caffeine blocks them, and lowers cyclic AMP levels. Or, at least, it blocks them if there's anything to block in the first place. There may not be any adenosine around to block; adenosine is elevated in response to injury and inflammation, so if you're clear of infection, and haven't been injured, you may not have anything to block, and thus you may report (as you, Paul, indeed have reported) that caffeine doesn't noticeably affect you.

But on to the topic of what cyclic AMP does -- this being the substance that, to summarize the above, is increased by one method of action of caffeine, which only takes place at high doses, while it's decreased by another method of action, which takes place at low doses too, but requires a specific type of adenosine receptor, which is only present in some types of cells (I haven't looked up which), and in any case might only be relevant to infected people. Hmm, not a very short summary, was that? Readers, if they've made it this far, are probably already saying to themselves "You are caught in a maze of twisty little molecules, all different". And we're just getting started. Cyclic AMP is what's called a "second messenger": a messenger molecule that's created by another messenger molecule hitting a receptor, and goes off to convey the message to some other place. And what receptor creates cyclic AMP, and what it does, is different -- very different -- in different types of cells. In one type of immune cell, it may stimulate the immune system; in another it may turn it down; in a brain cell it may do something enabling you to learn a new memory. And in any case adenosine has other receptors, which are also blocked by caffeine, and which use pathways other than cyclic AMP. Hmm, maybe I can do better: "To summarize the summary of the summary: people are a problem" -- especially if you try to figure them out using biochemistry.

To descend to less theoretical levels, where we are at less danger of getting lost in the clouds, another paper I ran across was this one, which is about using caffeine to help cure cancer. Cancers, it says, use adenosine to suppress the immune system, and thereby stop the immune system from destroying them. The paper does not suggest using caffeine by itself, but only as an adjunct to certain specific other types of immune system therapy (although it sounds like it might be useful on its own, too). It's conceivable that caffeine could play a similar role in Cpn therapy; getting the immune system to destroy infected cells is sort of similar to getting it to destroy cancerous cells. But the paper also warns that when this is done in cancer therapy, it increases autoimmunity -- the attack of the immune system on innocent bystander cells. Some of their mice not only eradicated their melanomas but went on to kill many of their normal melanin-producing cells (producing vitiligo). Fortunately, the autoimmunity was only temporary. Still, it's a way by which caffeine might increase the pain of treatment without increasing the gain. Which of these two effects, one good and the other bad, is dominant? Which of them exist at all, to any serious degree? Beats me. That's what experiments are for. Thanks again to Stratton and crew for doing such experiments, and for Paul for generously supporting them. I hope the planned experiments include some with caffeine itself, though; trying to guess what it will do from theoretical principles is an uncertain game at best.

Hi Norman,

As to the pHi level that is needed to induce Cpn into converting to an EB, you are probably correct that that level does not need to go as low as I suggested. We have not yet done any experiments to ascertain if pH in the range of say 7.0 achieves the same result. The 0.3-0.4 that you found that induces apoptosis is very interesting (do you have a link to that BTW?). That could easily be the level that is actually required. Assuming it is, that makes achieving the needed thresh hold even more easily attainable.

As to levels of caffeine that would be required to lower pH enough to convert Cpn, I agree with you. I initially noted most of the effects from caffeine in the GI tract when I was taking it in a more common form of caffeinated beverages. It took about 3-4 months for this to stop producing effects on the GI tract. In the pill form which I now take, I think you can achieve levels necessary to lowering pHi in other cells. I commonly take 500 mg at one time and someone I know takes 1,000 mg in a single dose now.

We do not agree on some of you other statements. I do not know if Cpn has to convert to the EB state to survive outside of cells but I think it does have to if it is going to infect another cell. So on that we will just have to agree to disagree.

You have a very interesting thought on lungs and availability of oxygen. However there is no reason that I can think of that caffeine in high doses would not allow you to reach the desired thresh hold. And there is a viable back up for this as cromolyn (pKa 1.1) is available in forms for inhalation.

I believe that many substances that have been used for treatment and side effects of treatment are going to end up helping lower cellular pH, although perhaps not in the way we think. For example I originally thought caffeine worked because it gets good tissue penetration and has a very low, 0.5, pKa. However you helped catch my error some time ago by correctly arguing that caffeine does not easily give up its proton. And it turns out expelling calcium is a more useful mechanism of action.

Some other substances that are notable are pyruvate and glucose. You did a lot of testing with these some time ago. I would argue that a "typical" Cpn infection is not an isolated cell but a group of infected cells in one area. So if you stress those Cpn with a combination of antibiotics and then ingest a lot of pyruvate or glucose, you would likely cause these cells to have to switch to anaerobic metabolism. If glucose/pyruvate became scarce, cells might have to rely on alternative energy production mechanisms that do not promote acidity.

Another substance that has been used in therapy a lot and has an unexpected mechanism of action is quercetin. It promotes cellular acidity by blocking lactate export. Inhibition of lactate export by quercetin acidifies rat glial cells in vitro.

- Paul

I already linked to the paper with that pH number for apoptosis, but here it is again. (The number I quoted is on the first page, under the heading "Intracellular acidification in apoptosis".)

As for lungs and availability of oxygen, the point was not to say that you couldn't lower pH in the lungs, but rather to argue that lower pH wasn't likely, in the first place, to be the thing that Cpn uses to decide that it's time to convert to EBs and break out of the cell to infect other cells.

The thing about whatever mechanism Cpn uses to sense that a cell is used up, and that it's time to convert to EBs and move on, is that it has to work in all circumstances (or at least all circumstances in which Cpn succeeds). A typical infection may indeed be a group of infected cells -- but that infection still has to start with a single EB infecting a single cell and growing from there; if Cpn's mechanism didn't work in a single isolated cell, it could never grow to establish a typical infection. Also, whatever the mechanism is, it has to work in the lungs. You can hypothesise that the mechanism is something complicated -- that it's pH from anaerobic metabolism in some circumstances, and some other mechanism in the lungs. Having two alternative mechanisms to accomplish the same effect is entirely possible; it happens all the time in biology. But if the mechanism is to be one simple thing, I don't think pH can be the trigger. Lack of ATP, maybe.

Hi Norman,

As always you bring up great arguments. And this time your point was so good, it about gave me a heart attack as I thought of the years, time, and money invested on this track... ;)

However I would not assume that oxygen is plentiful and unlimited just because of the location of cell. The variable here is that while the ability of oxygen to enter these cells is essentially fixed, the number of mitochondria in the cell is not. Lung cells can have thousands of mitochondria. So no matter how much oxygen is available, they are probably capable of exceeding the ability of oxygen to enter cells because of the sheer number of mitochondria. And in fact since these cells are able to produce so much energy, the probability is that they can support MANY more RBs and cryptic Cpn. So I think that lung cells are perhaps one of the best candidates for Cpn infection, which kind of tracks with observations.

BTW I am pretty sure lack of ATP is the signal used to induce the cryptic state. I plan on writing some more of these "Cpn theory" threads and will try and cover that in the appropriate one.

- Paul

Unlike most biological molecules, oxygen diffuses across cell membranes like they weren't even there; it's a nonpolar molecule, so they don't pose any barrier to it. (What oxygen doesn't dissolve very well in is polar solvents, such as water. Augmenting oxygen's ability to dissolve in water is what hemoglobin and myoglobin are for.) For supplying most of the body's cells with oxygen, capillaries come close to them; but "close" means, in most tissues, within something like five to ten cell widths; so their oxygen supply sometimes has to diffuse across five or ten other cells before it gets to them; this works well, despite those other cells consuming their own shares of the oxygen as it crosses them.

As for lung cells having lots of mitochondria, where are you getting this? The first paper Google finds me that says anything definite on this question says that:

"Indeed, the lung is sparsely populated with mitochondria, although a few cell types, such as type II epithelial cells and bronchial and vascular smooth muscle cells, are rich in this organelle."
Of those exceptions, muscle cells are relatively minor players in the lung; epithelial cells are much more numerous, and are the ones I've often read of Cpn infecting. I had to look up what "type II" epithelial cells were; according to this article,
"Type I cells are thin, flat cells that cover pulmonary vascular endothelial cells and comprise 95% of the alveolar surface (56). These cells are important for gas exchange, regulation of alveolar fluid levels, and stretch-induced modulation of surfactant secretion. ... Type II cells, on the other hand, are large, cuboidal cells that contain lamellar bodies and apical microvilli (21). These cells are important for producing surfactant, regulating alveolar fluid levels, and host defense."
So both of these types are alveolar cells (forming the lining that separates the air in the lung from everything else); and in that lining, the Type II ones are only a small proportion of the cells. But as the cells "important for ... host defense", might they, and not the type I cells, be the ones that engulf Cpn, and thus get infected by it? (Does another search...) Not according to the paper "Alveolar epithelial cells type II are major target cells for C. pneumoniae in chronic but not in acute respiratory infection". According to it (or at least according to my rather-hasty reading of it, focusing primarily on its Table I), both types of epithelial cells get infected, with the percentages in acute infection being only a bit higher in Type II than in Type I cells. In chronic infection, as the title of the article indicates, Cpn's preference is much more for the Type II cells. Perhaps, having more mitochondria, they are more hospitable to chronic Cpn infection. Even so, both types do still get infected.

In any case, with those Type II cells being right next to the air in the alveoli, about a sixth of which is oxygen, it'd take a truly stupendous burn rate to produce anaerobic conditions. The more oxygen you burned up, the steeper the concentration gradient would become, and so the faster more oxygen would diffuse in. To overwhelm that increased diffusion, you'd probably need something like the burn rate of a flame, which would also mean the heat generation rate of a flame and the fuel consumption rate of a flame. I don't think any number of mitochondria could do it.

As for the thing that causes Cpn to go into the cryptic form, I've seen various things credited in the literature as being able to produce that form: antibiotics; interferon-gamma; and lack of iron. (The lack of iron, they produce in cell cultures by adding iron-sequestering compounds.) I wouldn't be at all surprised if lack of ATP should be added to that list. But I don't think it would replace any of those three causes. (Of course the first cause, antibiotics, is entirely artificial, so might not be in the realm of what you were considering; and severe iron depletion might also be artificial; but interferon-gamma is definitely something the body makes naturally, and I doubt it works by depleting ATP.)

Hi Norman,

Here are some links to the number of mitochondria in lung cells. Note the second one is from a rabbit.

lung fibroblast cell
800 +/- 24

lung macrophage cell (rabbit)
1720 +/- 162

But I think you may have me on this. After thinking about this further (hadn't really thought about the specifics of lung tissue much before), I suspect that this large number of mitochondria might allow a cell to undergo apoptosis in spite of Cpn attempting to inhibit this. So if this is the case, that would lead to a lower pHi before the cell actually died.

Interferon is the best example of ATP depletion in Cpn I can think of. Interferon induces the production of nitric oxide, the cell's primary defense against intracellular bacteria. It would be highly improbable if Cpn did not attempt to pump nitric oxide out. And I think this leads to depletion of ATP.

- Paul

Those are numbers of mitochondrial DNA molecules, not numbers of mitochondria; to get the latter, according to this paper, one divides by about 2.6.

Even so, those are big numbers. But the mention I ran across of really big numbers was for the liver, with "about 1000-2000 mitochondria per cell making up 1/5th of the cell volume" (according to Wikipedia). With all the energy-consuming chemistry the liver does on behalf of the rest of the body, that's no surprise.


I don't know if I would love or hate sitting next to you two in a coffee shop. ;)lol Great conversation. The parts that I can understand at least. The acid, alkaline balance has always been hard for me to grasp.

200mg doxy daily, 500 zithromax mwf,flagyl 1000 m-fri.rifampin 2x daily,chloestryramine 2x daily

Hi Norman,

I am not sure if this is where you are going but it is interesting that liver and lung cells have such a large number of mitochondria. Observation suggests that both of these these organs seem to have a more significant than typical amount of infection. Which stands to reason since Cpn's growth is energy dependent. I could imagine these cells supporting hundreds of chlamydia before apoptosis or necrosis occurred. The inflammation from HSP-60 production and immune response to cells that undergo apoptosis or necrosis, even from a small amount of infected cells, would be staggering.

- Paul


To update what I wrote earlier, the actual amount of lactic acid used was 13.4 mM. The paper, Inhibitory effect of tumor cell–derived lactic acid on human T cells, discusses using lactic acid at 20 mM lowers intracellular pH from 7.4 to 6.5-6.8. So while speculative, I would guess the actual pH that was attained was perhaps in the 7.0-7.2 range. However that is not factoring in anaerobic metabolism that might be occurring in these infected cell lines.

BTW one thing I took from this discussion was a better explanation for the difficulty in eradicating Cpn from areas such as skin and sinuses using acidic inducing agents that are taken orally. I had assumed that the difficulty in eradicating the infection via oral agents was a result of poor blood flow and challenges with getting a high enough concentration of these agents in these cells. A better explanation would seem to be that the combination of this and having access to unlimited oxygen and as a result, rarely using anaerobic metabolism. In any event, it is surprisingly easy and effective to use topical agents in these areas so while interesting, the point seems mostly academic.

- Paul


Another drug with an unexpected mechanism of action is Sildenafil (Viagra). It helps lower intracellular pH (pHi) by inhibiting Na+/H+ exchangers (NHE). See Decreased Activity of the Na+/H+ Exchanger by Phosphodiesterase 5A Inhibition Is Attributed to an Increase in Protein Phosphatase Activity. Based upon the research this would suggest that it reduces production of the highly inflammatory HSP-60 that Cpn produces. Sildenafil is an anti inflammatory drug that was originally targeted toward and successful for high blood pressure. Unfortunately it has been marketed so heavily for other uses as to become somewhat of a joke.

I can't wait to hear about someone going to their doctor and requesting viagra because they have a chlamydia infection though... ;)

- Paul

Paul, if viagra is what is going to save me, I am going to buy a wagon and ask for prescription at the doctor's office. I no longer care about what doctors think. They already think I am mad, so why shouldn't they think I am impotent too? I am no longer surprised by anything. Last time I saw one doctor, she said chlamydia is spirochete. Well, she herself looked like big fat chlamydia, her brain probably already consumed. And my friend (man) read in his medical card, that he started to have his menses when he was thirteen... That is reality, but I am not going to continue to hitchhike this thread..

Stratton/Wheldon protocol 02/2006 - 10/11 for CFS and many problems 30 years

As regards the skin, that's a different situation from the lungs. The skin has a thick barrier layer of dead cells and collagen and so forth; it's not like the lungs, where there are only three or four cells between the air and the flowing blood in capillaries. The lungs are optimised for gas exchange; the skin is optimized to take mechanical damage. I don't know if useful amounts of oxygen get through the skin; they might not, especially in thickly calloused areas.

In the sinuses, a big challenge is likely to be biofilms -- not that Cpn itself forms them; but coinfections can.

As for Viagra, the abstract you linked to says that it "did not affect basal intracellular pH", and that after an "acidic load" was applied, it decreased proton efflux. Since proton efflux increases pH, this would seem to be the reverse of the effect you want (even apart from the fact that some sort of applied "acidic load" would be necessary to get it).

If you look at Figure 7 of the paper you referenced, it has a graph of intracellular pH versus extracellular lactic acid concentration; your concentration of 13.4 mM results in pH of about 6.4. (Well, that's where the line on the graph is; if one takes into account the error bars, the range would be about 6.2 to 6.6.) However, that's for one specific type of cell (cytotoxic T cells), which the article says are unusual in that they generate lactate themselves even when sufficient oxygen is available. The pH numbers for other types of cells may be very different.

I wasn't going anywhere in particular with the liver mitochondria number, but the ability of the liver to support a big Cpn infestation is indeed something it implies.

Hi Norman,

You and Dr. S both caught me on the sinus/skin thing. As both of you noted, the dead cells create a barrier to oxygen entry. It is not too important but I am happy to have that clarified.

Decreasing proton efflux should increase intracellular pH. It did not decrease pH by itself but I think if you acidify a cell by some other means, it will reduce the cell's ability to overcome this.

The pH range that you used is fine with me. It has always been sort of academic because even if you can pinpoint this, what occurs in vivo will be different than what you are able to test in vitro (the cancer cell example applies here as that is usually the type of cell used for in vitro testing).

- Paul

Hello Paul and others 

Here are some questions and comments 

*How long after taking an antibiotic should I take the caffeine one hour two ?

*Can I use Doxy and caffeine?

*How long after taking antibiotics do I use pyruvate to assist anarobic metabolism ?

Other Comments
It seems that my body kind of knows what it needs because when I am able to  swim I have a desire to do a few laps underwater holding breath until I start starving for air then come up I think this drives the body (cells) acid. Also I like to do partial fasts which I think also drives the body acid
It seems like if I did this with antibiotics and caffeine I may get good results .....,,,,, What do you think?


DAILY:  NAC 2400MG , DHEA sublingual , vit D3 , multi vits,./ Three times  a week: B12 injections (Hydroxycobalamin). Deer antler./  Once every few months methyl B12 Methyl injections

Hi Homina,

I take caffeine with the antibiotic(s). I would think doxy could perhaps work. The idea is to cause Cpn to begin replicating where it is very susceptible to many common antibiotics. It is somewhat susceptible to doxy in this state but less so than others. Tetracyclines like doxy are very useful as they are the only antibiotics that have a known protein synthesis target in the cryptic/persistent state. But for this approach that is not required. I am not sure when the best time to start taking pyruvate or glucose is but I think it is 15-30 minutes after taking the antibiotic(s). Please be cautious and go slowly. While I believe this approach is easier and faster, you can really do a lot of harm by killing too many Cpn at one time with this or any other approach.

The idea is to lower pH in either the host cell (Cpn have NhaD antiporters so even a very brief reduction in pH in the host cell produces a lower pH in the Cpn) or in Cpn itself. Giving it pyruvate or glucose allows persistent Cpn to produce ATP via fermentation with a lactic acid byproduct. This efficiently lowers Cpns's pH. I was going to write a separate thread about this (and still may) but the reason I think it is important to lower persistent Cpn's pH is that this allows them to use their ATP/ADP exchange and begin replicating which allows them to be killed much more easily. ATP/ADP exchange is driven by a proton pump so I think that Cpn's pH must be lower than the host cell for this to operate.

NOTE: I had previously argued that lowering pH induces Cpn into the EB state. In some cases where its pH goes low enough it should. But whether you induce it into the RB or EB state, it is far easier to kill than in CB state. Also this approach has not been proven to work for all cases. It is very possible that this approach might not work as well across the blood brain barrier where acidic agents might not cross as quickly and glucose is more tightly regulated. I have no experience or contact with anyone using this approach for MS although Dr. RS has used caffeine it with some patients. But one could always start with zithromax and use various approaches to lower pH to get the "low hanging fruit" and then add doxy/metro later which would be pretty consistent with the CAP.

BTW I would think that swimming under water is probably one of the best ways to induce anaerobic metabolism in skeletal muscles and to a degree surrounding tissue. Once you no longer get "hammered" by this, you could enhance the effect by taking some of these supplements before swimming. Lots of serious athletes take caffeine, taurine, and glucose/pyruvate before exercise. In fact one of the best places to buy some of these supplements is at sites that cater to athletes. Or you could just drink a bunch of Red Bull or Monster energy drinks ;) Their main ingredients are taurine, caffeine, and sugar...

- Paul

Hi Paul


As I think about your response I will probably have some more questions if you don't mind



DAILY:  NAC 2400MG , DHEA sublingual , vit D3 , multi vits,./ Three times  a week: B12 injections (Hydroxycobalamin). Deer antler./  Once every few months methyl B12 Methyl injections


Would using ph testing strips be of any value? My dr. is having me do a 2 week ph saliva test using these strips.

200mg doxy daily, 500 zithromax mwf,flagyl 1000 m-fri.rifampin 2x daily,chloestryramine 2x daily