Ray Peat Email Advice Depository

[tca300]

Me: I was wondering what your opinion of DMSO was? Thank you!

RP: I think it’s safe for occasional use in small amounts; in the early ‘70s I was interested in it, but I gradually decided that there wasn’t enough known about its metabolism to be sure of its long range safety. People at the Livermore lab suggested some possibly toxic metabolites (in connection with the Gloria Ramirez case), that might depend on a person’s unique redox situation.

 

[paymanz]

On vitamin k

It has many effects, some of them prevent abnormal clotting, others abnormal bleeding, others favor energy production and brain lipid synthesis, calcium regulation.

Perfumes still harmful if only applied to cloths and not to skin?

I don't think they are harmful.

 

[theLaw]

Hey Dr. Peat,

I have recently been trying to prepare the cooked potato juice mentioned on several of your Ask the Herb Doctors shows, but I'm having a bit of trouble understanding how well to filter the juice throughout the process.

After juicing the peeled potatoes, I let it sit for 1hr to settle, and then filter it through a fine mesh strainer.

I then cook it for 1.5 hrs on low heat until it looks like this:

But here is where I need some clarification.
Should the following coagulation (pic below) be thrown out, or is it a healthy part of the amino acids?

My finished product looks like this (pic below):

Am I preparing this correctly?

What kind of potato is it? What kind of juicer? I used a centrifugal juice, that separated a pure white solid (starch) from a slightly viscous clear fluid (free of starch), and the fluid coagulated as soon as it was heated, becoming whitish, the way clear egg white becomes white. It looks like there might not have been a separation of the starch, in which case, it would be similar to eating the whole potato, which is o.k. if there’s no digestive problem.

Hey Dr. Peat,
I'm using russet potatoes and a centrifugal juicer, although I've used golden potatoes before with the same results. After I juice them, there is still starch in the juice as it settles to the bottom over an hour to create a very thick sentiment. If I were to cook it immediately after juicing, I would assume it would still have a significant amount of starch in it.
Haidut, another member of the forum, claims to let his sit for 2-3hrs following juicing to let all of the starch settle.
Should the final cooked juice be free of any visible particles?

They aren’t harmful.

 

[paymanz]

Do you think its possible that some of reported health benefits of dietary fermentable fibers being because of hydrogen thats produced during their fermentation?

Yes, that could have an antiinflammatory effect.

 

[ecstatichamster]

What about a guy who may have heavy metals problems? Can he test his hair? What can he do if he has heavy metals (lead, arsenic, mercury...)


Hair picks up things from water and air, for example lead from gun smoke. If he hasn’t been exposed for a few months, then the short hair would give a clue to the amount that’s stored. Animal studies showed that chelation can increase metal toxicity to the brain and kidneys. Vitamin C and other acids in orange juice reduce the toxicity of mercury and allow it to be excreted safely. At least for some metals, coffee seems to have a similar effect.

 

[Dan W]

In the context of a person trying to manage extreme hunger following eating disorder recovery:

Have you ever tried cooking oat bran as a low calorie food? It's nice as a hot cereal, but when it cools it can be made into slabs to fry in butter.

[concerns about digesting it]

The fiber should be indigestible; bran can be washed, to remove most of the starch so it doesn't feed bacteria. The indigestible fiber stimulates movement of the intestine, while helping to satisfy hunger feelings.

 

[theLaw]

I recently started experimenting with Urea after listening to you mention it on the Ask the Herb Doctor show.

You mentioned in that episode that some people might need 120G per day to reach the proper blood saturation.

If I were to start with a smaller dose, what symptoms/signs should I look for that I'm taking too much?

RP: The big doses were used for major brain injuries, heart failure, and cancer. It’s very non-toxic, but for minor problems a teaspoonful in a glass of juice twice a day is likely to be enough.

 

[Dan W]

Followup to the previous e-mails with a person recovering from an eating disorder:

Safe foods for rebuilding tissues are eggs, scallops, calamari, oysters, orange juice, milk, and cheese, salting things to taste.

 

[goodandevil]

Q: I've almost completed my hemostasis course, and it seems to me that standard textbooks really have no idea what occurs in clotting. Ive more or less committed your article on clotting to memory. It seems to me that complement and clotting factors are essentially the same thing, and i think redox potentials, or electrostatic forces, seem to dominate the mechanism of clotting. I was wondering if you had any more interesting sources for an explanation of clotting than my textbook. The involvement of adp reminds me of danger theory. Also, do you see a practical distinction between PT, aPTT, &c?

Ray: I haven’t seen any use in those distinctions. Have you read any of Melvin Knisely’s work, about 70 years ago, with blood sludging?
I think the most important things to investigate are the effects of metabolites on clotting and fibrolysis, for example hyperventilation, CO2, lactate, aldosterone, sodium, angiotensin.

 

[raypeatclips]

Q. I occasionally eat meals I have made with a tomato passata base, and haven't noticed anything negative that I'm aware of. I recently came across information that tomatoes are very high in glutamate. I wondered if you thought this is an issue? I don't recall you ever mentioning tomatoes and glutamate that I'm aware of.

Thank you.

The amount that occurs naturally in a food is accompanied by balancing factors that prevent excitotoxicity.

 

[goodandevil]

Q: "When exercising for fat loss, so long as it isn't breathless, is an empty stomach better for losing fat?"
R: "I think it’s best to have had some carbohydrate within the hour, to prevent the toxic effects of a large increase in free fatty acids in the blood."

 

[Dan W]

In the context of a person's questions about air purifiers and sources of canned oysters in Mexico:

I use a Mystic Marvel air ionizer near me, it doesn't affect a very big space. I didn't find any good shell fish either in Morelia or other inland areas. I always travel with a few cans.

 

[Dan W]

I think this was in response to a person's H. pylori question:

I think clarithromycin or erythromycin, and pen-V-K or amoxicillin, and olive oil are effective.

Castro M1, Romero C, de Castro A, Vargas J, Medina E, Millán R, Brenes M. Assessment of Helicobacter pylori eradication by virgin olive oil. Helicobacter. 2012 Aug;17(4):305-11.

A recent study conducted by Medina et al. disclosed that virgin olive oil has a bactericidal effect in vitro against Helicobacter pylori because of its contents of certain phenolic compounds with dialdehydic structures. We carried out two clinical trials to evaluate the effect of virgin olive oil on H. pylori-infected individuals.

Two different pilot studies were performed with 60 H. pylori-infected adults. In the first study, thirty subjects who tested positive for H. pylori received 30 g of washed virgin olive oil for 14 days, and after 1 month, the patients took 30 g of unwashed virgin olive oil for another 14 days. In a second study, a group of 30 subjects received 30 g of a different virgin olive oil for 14 days. Helicobacter pylori-infection status was checked by the urea breath test.

Helicobacter pylori was eradicated in 8 of 30 individuals when microorganism status was checked after 4-6 weeks from the first clinical intervention although 12 of 30 individuals did not show H. pylori infection at 24-72 hour of the last oil dose. Eradication rates were 27 and 40% by intention to treat and per protocol, respectively. Moreover, only 3 of 30 individuals were H. pylori negative after 4-6 weeks from the second clinical intervention but 5 of 30 were negative at 24-72 hour of the last oil dose. Eradication rates were 10 and 11% by intention to treat and per protocol, respectively. It must also be noted that 13 subjects withdrew from the studies because of taste and nausea drawbacks.


The administration of virgin olive oil showed moderate effectiveness in eradicating H. pylori. Further studies are needed to confirm these findings, especially with longer periods, different administration conditions, and several types of olive oils.

Full text of the study available here.

 

[Dan W]

I was sent a big ol' collection of Peat's quotes on antibiotics. I tried to track down where they came and link to any discussion of them, but it seems like most of them are new. Since they're from various sources, it's probably worth taking them with a larger grain of salt than usual.

Sometimes the antiseptic foods (raw carrots, cooked mushrooms or bamboo shoots), eaten regularly, will take care of it. I have found, for myself, that small doses of penicillin, such as 200,000 units 3 times a day, are effective in just a day or two. The tetracyclines are more often used for acne, because they have a general antiinflammatory effect, besides the germicidal action. The conventional doses are usually unnecessarily large, based on an assumption that the person has no functional immune system. Large doses of antibiotics have a slight toxic effect on human cells, so I think it's best to use them according to results, rather than formula.

There used to be some products available in health food stores (they are probably still available somewhere) containing B. subtilis and B. licheniformis that produce antibiotics in the intestine (or in milk if you culture them), which are good for people who are afraid of antibiotics in pill form.

I think minocycline is safer than doxycycline, and is very safe. It is antiinflammatory, and has some protective effect against cancer.

(mentioned here, so sometime 2012 or earlier)

People often use minocycline for a long time, but usually 50 or 100 mg in a day. It could possibly make you sensitive to sunlight if it accumulates in your body.

I think penicillin is most effective in such situations when it's used intermittently, 2 to 4 days at a time, at intervals of about a week.

I usually break the tablets up, and use fourths or halves, at intervals according to need. It's important to get some vitamin K1 or K2 when you use an antibiotic (liver or kale, or supplements). Have you checked your thyroid? Low thyroid function is usually behind the dark circles.

My own preference for antibiotics would be in the order Pen-V-K (about 30 to 50 mg at a time, with some carrot), erythromycin, tetracycline, and neomycin (for example Kaomycin). All of the antibiotics are somewhat toxic to people, but at a certain level, they can suppress bacteria without noticeable toxicity for the person. The goal is to establish a better internal ecosystem. Chronic sinus infections are usually the result of chronic irritation of the intestine.

I think it's good to try a small amount of an antibiotic at first, watching for a general effect such as mood; I've noticed that when I first have an odor-like sensation after taking a little penicillin (when it reaches a certain level in the tissues), it comes with a general sense of comfort.

My own preference for antibiotics would be in the order Pen-V-K (about 30 to 50 mg at a time, with some carrot), erythromycin, tetracycline, and neomycin (for example Kaomycin). All of the antibiotics are somewhat toxic to people, but at a certain level, they can suppress bacteria without noticeable toxicity for the person. The goal is to establish a better internal ecosystem.

I think penicillin is most effective in such situations when it's used intermittently, 2 to 4 days at a time, at intervals of about a week.

(above three mentioned here, so sometime 2015 or earlier)

It isn’t habit forming. The antibiotics erythromycin and tetracycline are anti-inflammatory, and might work better than penicillin. An allergy can cause swelling of the surface of the eye, often it’s from something in the air, but it’s possible that something you ate was involved. Vitamin K is involved in some essential chemical processes in the brain, besides helping to produce metabolic energy; I think it might help with relaxation, too.

I use 250 mg tablets of Pen Vi K, which aren’t expensive, and take about a fourth of a tablet at a time, maybe twice a day until a symptom is gone, usually one or two days.

Raw carrots, cooked bamboo shoots, and cooked mushrooms contain antibiotics that are safe to use everyday. Like tetracycline and the macrolide antibiotics, they (especially mushrooms) are also antiinflammatory.

Antibiotics vary in toxicity, but in general I think it’s best to use a minimally effective dose if it’s to be continued very long. I think tetracycline, erythromycin, and penicillin are fairly safe.

Bowel symptoms can affect the heart, maybe you need an antibiotic to reduce the gas.

Antibiotics would be like to help with the gas, but you should test a very small amount of it on your lip a day before you take a dose, to see if you have an allergy to it. Pen-Vi-K, erythromycin, tetracycline, and neomycin are types that can be helpful for gas.

The antibiotics erythromycin and tetracycline are anti-inflammatory, and might work better than penicillin.

Antibiotics vary in toxicity, but in general I think it’s best to use a minimally effective dose if it’s to be continued very long. I think tetracycline, erythromycin, and penicillin are fairly safe.

Silver is just slightly less toxic than mercury. Silver would be about as toxic as the organic antibiotics in the short term, and maybe worse if used chronically. Topically, it's probably not as toxic as mercurochrome; permanganate and copper sulfate might be just a little safer. How does silver kill bacteria? It works pretty much by the same mechanism that makes mercury a powerful antiseptic. Heavy metals are relatively indiscriminate oxidants (potent oxidizing agents). All heavy metals - lead, silver, mercury, nickel, cadmium- are very toxic, potent enzyme poisons and go into the brain, causing diseases like Alzheimer's, ALS, MS, etc.

(found on Lita Lee's page, so it must be sometime prior to 2002)

Antibiotics will take care of the Borrelia organism in a reasonable time. What are the symptoms of the others?

This is following up on the above one, I think:

I think infections of that sort show up when a person’s resistance is low, and the symptoms are likely to be caused mainly by nutritional and hormonal problems, and to disappear when the metabolism is corrected. Low protein diets are a common cause of multiple infections with those things.

2 or 3 weeks of treatment with a couple of the older, safer antibiotics is usually effective.

J Infect Chemother. 2000 Mar;6(1):65-7.
In-vitro and in-vivo antibiotic susceptibilities of Lyme disease Borrelia
isolated in China.
Li M(1), Masuzawa T, Wang J, Kawabata M, Yanagihara Y.
(1)International Center for Medical Research, Kobe University School of Medicine,
7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650, Japan. [email protected]
The antibiotic susceptibilities of seven Borrelia burgdorferi sensu lato isolates
from Ixodes persulcatus in China were examined by in-vitro microdilution minimum
inhibition concentration (MIC) and macrodilution minimum bactericidal
concentration (MBC) methods. All isolates tested were susceptible to amoxicillin,
erythromycin, and minocycline. The MICs of these drugs for the Chinese isolates
were 0.025-0.1 microg/ml, <0.012-0.05 microg/ml, and <0.012-0.05 microg/ml,
respectively. The MBCs were 0.1-0.39 microg/ml, <0.012-0.2 microg/ml, and
0.025-0.39 microg/ml, respectively. The in-vivo antimicrobial susceptibilities of
the Chinese Borrelia isolates to two test drugs, amoxicillin and minocycline,
were evaluated using ddY mice. Mice were infected by subcutaneous inoculation
into the right hind footpad. When infection was confirmed, the mice were treated
by subcutaneous injection of the test drugs into the back. Amoxicillin and
minocycline, which possessed high in-vitro activities against Lyme disease
Borrelia, provided good protection against borreliosis in this animal model.
Higher doses of these drugs resulted in elimination of the Lyme disease
spirochete from all animals receiving this course of treatment. The 50% curative
doses (CD50) of amoxicillin and minocycline were 8.7 mg/kg and 3.1 mg/kg,
respectively. This suggested that amoxicillin and minocycline could be useful for
the treatment of Chinese Borrelia infection.

Yale J Biol Med. 1984 Jul-Aug;57(4):549-53.
Susceptibility of the Lyme disease spirochete to seven antimicrobial agents.
Johnson SE, Klein GC, Schmid GP, Feeley JC.
The antimicrobial susceptibility of five Lyme disease spirochete strains (two
human and three tick isolates) was determined. A macrodilution broth technique
was used to determine on three separate test occasions the minimal inhibitory
concentrations (MICs) of seven antibiotics. The Lyme disease spirochete was most
susceptible to erythromycin with a MIC of less than or equal to 0.06
micrograms/ml. The spirochete was also found to be susceptible to minocycline,
ampicillin, doxycycline, and tetracycline-HCL with respective mean MICs of less
than or equal to 0.13, less than or equal to 0.25, less than or equal to 0.63,
and less than or equal to 0.79 micrograms/ml. The spirochete was moderately
susceptible to penicillin G with a mean MIC of 0.93 micrograms/ml. All strains
were resistant to rifampin at the highest concentration tested (16.0

Sometimes I notice that a few doses of 50 to 100 mg of penicillin will stop a particular symptom; a few times, for a distinct infection, I have used a standard dose of 250 mg 3 or 4 times in a day, stopping as soon as the symptom is gone, usually by the second day. The antiseptic fibrous foods (raw carrot, cooked mushrooms or bamboo shoots) eaten regularly, and avoiding the very rottable indigestible foods such as green salads, give chronic protection against bacteria. Avoiding excess phosphate lowers stress and inflammation, and getting plenty of calcium and vitamin D helps to balance the phosphate. Some aspirin at bedtime might be helpful.

[Context: Penicillin VK tablets]

I usually suck on it slowly, to avoid the risk of the tablet sticking to my stomach membrane.

[Context: the idea of irreparable damage]

The intestinal flora change along with changes in the metabolism, and have to be taken into account. The changes in the environment have to be greater when the degeneration is more advanced. Antibiotics and antiinflammatories and hormonal supplements become more important when a person is seriously sick. Often, even after the age of 50, just going to a high sunny place and eliminating the worst foods is all it takes to restore good health.

(posted/discussed here)

 

[Dan W]

In response to a question about "malabsorption syndrome":

Slow digestion is very characteristic of hypothyroidism, and it can result in either constipation or diarrhea.

In response to a question about the possible mechanism behind this study about red lentil extract and Parkinsonism:

It could be that the phenolic compounds are restoring cellular oxidative metabolism.

 

[Dan W]

I found that to prevent dandruff when taking thyroid i need to eat at least 100-150 g beef liver everyday. It is safe when i feel better with it(more energy, better skin)?

Increased vitamin A increases your need for vitamin E, phosphate should be balanced with calcium, and it’s important to watch thyroid function.

In one of the interview you mentioned P.Kropotkin books. I read Mutual Aid and it is great source of optimistic view on human possible evolution. Do You have any another examples of such books ? It is possibile or real to develop such a good society conections with all those wild capitalistic (Darwinian like) propaganda of survival of the fittest ? What we could do ?

V.I. Vernadsky, in a more explicitly cosmic context, gives reasons for optimism. We have to be alert to the deception that’s pervasive in “science,” schools, and politics. Have you seen Ivan Illich’s books?

I will look for them and read. Whats your view on a good job or way to earning money?

Jobs that I have enjoyed were teaching, tutoring, translating, and being a park ranger, but now those are usually scarce. I have friends who make a good living painting houses, or doing cement or plaster work as independent contractors.

Do You think that when production, transport etc will be more automatized- the ruling class could want to reduce population in some malthusian way?

Starvation makes people willing to work for almost nothing; with more automation, more will be allowed to starve. I think the experiment in India with the elimination of currency shows how easily they can control starvation/population.

 

[raypeatclips]

Q. I wondered how you cleaned all the cups, plates, cutlery that you use and do you consider standard washing up liquid safe?

I use coconut oil soap or Ivory soap only, with hot water it takes only a very small amount.

 

[michael94]

Is nickel a concern in hydrogenated fats because of the nickel catalysts used?

 

[oriana]

Me: Is my introduction of milk causing my arthritis?

Ray:

Many years ago someone noticed an antigenic overlap of lactobacilli with joint tissue, and suggested that it could explain the high incidence of rheumatoid arthritis during women’s fertile years. Another person noticed an overlap of thyroglobulin with joint tissue. Maybe the milk increased the growth of that kind of bacteria. I think the already increased circulation in your thyroid means that progesterone won’t increase its activity. Have you used a little olive oil on your skin to make it easier to spread? Covering your whole leg would increase the effect on your ankle. Is there enough sugar in your diet? Have you tried breathing in a bag occasionally, to increase your CO2?

Benef Microbes. 2011 Jun;2(2):139-54.
The role of components of Bifidobacterium and Lactobacillus in pathogenesis and
serologic diagnosis of autoimmune thyroid diseases.
Kiseleva EP(1), Mikhailopulo KI, Sviridov OV, Novik GI, Knirel YA, Szwajcer Dey
E.
(1)Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus,
Republic of Belarus. [email protected]
During recent years, researchers have been focusing on the concept of an
infectious etiology of autoimmune diseases. The most discussed theory is
molecular mimicry, i.e. the emergence of autoreactive clones of T- and
B-lymphocytes as a result of cross-immune response to homologous bacterial or
viral antigen. Information on the role of probiotic microorganisms (PM) in the
molecular mechanisms of autoimmune thyroid diseases (ATD) is limited. Using
proteins and immunogenic peptides databanks and relevant computer programs, the
homology between the amino acid sequences of thyroid peroxidase (TPO) and
thyroglobulin (Tg), which are potential B- and T-cell epitopes of these antigens,
and proteins of bifidobacteria and lactobacilli was established. Moreover, we
have found components of cells of Bifidobacterium bifidum 791, Bifidobacterium
adolescentis 94 BIM, Bifidobacterium longum B379M and Lactobacillus plantarum
B-01 that selectively bind human antibodies to TPO (anti-TPO) and antibodies to
Tg (anti-Tg) and compete with natural antigens for the binding of anti-TPO and
anti-Tg in ELISA. Additionally, a three-fold difference was observed between the
probability of detecting antibodies (Abs) to the antigens of L. plantarum B-01
and B. bifidum 791 in serum samples containing and those not containing anti-TPO.
On the whole, our data are arguments in favour of the assumption of the possible
role of PM of the genera Bifidobacterium and Lactobacillus in triggering ATD by
the mechanism of molecular mimicry. The data obtained in silico and in vitro
should be proven by use of animal models and clinical studies for extrapolations
to the whole body. Possible antigenic properties of components/proteins of
bifidobacteria and lactobacilli, selectively binding anti-TPO and anti-Tg should
be taken into consideration. Natural human Abs to these bacterial components are
probably able to cross-react with the TPO and Tg in the ELISA for detection of
anti-TPO and anti-Tg, which are serologic markers of ATD. It can lead to
unspecific false positive results and, hence, to an incorrect diagnosis.

Benef Microbes. 2013 Dec 1;4(4):375-91.
Isolation and structural identification of glycopolymers of Bifidobacterium
bifidum BIM B-733D as putative players in pathogenesis of autoimmune thyroid
diseases.
Kiseleva EP(1), Mikhailopulo KI, Novik GI, Szwajcer Dey E, Zdorovenko EL,
Shashkov AS, Knirel YA.
(1)The Institute of Bioorganic Chemistry, National Academy of Sciences of Belaru,
Acad. Kuprevicha 5/2, 220141 Minsk, Republic of Belarus.
Bifidobacterium bifidum 791 (commercially available as B. bifidum BIM B-733D)
cell-surface biopolymers (BPs) interact selectively with human serum thyroid
peroxidase (TPO) and thyroglobulin (Tg) autoantibodies (anti TPO and anti Tg,
respectively). BPanti-TPO and BPanti-Tg were isolated from the soluble fraction
of B. bifidum BIM B-733D by affinity chromatography with anti-TPO or anti-Tg,
respectively. Homogeneity of affinity eluates (AEanti-TPO and AEanti-Tg) was
tested by size exclusion chromatography. For each AE, the elution profiles
generated on the basis of absorbance at 280 nm do not conform to ELISA data for
functional activity characteristic of BPs. Moreover, high functional activity was
detected in chromatographic fractions that had significantly different molecular
weights and no absorbance at 280 nm, which suggests a non-protein (carbohydrate)
nature of BPanti-TPO and BPanti-Tg. The semi-preparative size exclusion
chromatography of AEanti-TPO and AEanti-Tg with detection by refractometer gave
5,000-7,000 Da fractions containing substances that interact selectively with
either anti TPO (BPanti-TPO) or anti-Tg (BPanti-Tg) according to ELISA data.
Analysis by two-dimensional NMR spectroscopy including a 1H, 13C-heteronuclear
single-quantum coherence experiment indicated that both substances are linear
α-1,6-glucans. For the first time, an immunological similarity (molecular
mimicry) of glycopolymers of B. bifidum BIM B-733D and human thyroid proteins,
TPO and Tg, was shown. On the whole, our data point to a possible role of
bifidobacteria in the pathogenesis of autoimmune thyroid diseases (ATD). The main
requirements for triggering/acceleration or prevention/abrogation of ATD by
bifidobacteria through molecular mimicry mechanism are hypothesised to be (1)
genetic predisposition to ATD and (2) intestinal epithelium penetration by
α-1,6-glucan.

J Bacteriol. 2012 Dec;194(24):6997.
Genome sequence of the immunomodulatory strain Bifidobacterium bifidum LMG 13195.
Gueimonde M(1), Ventura M, Margolles A, Sánchez B.
(1)Department of Microbiology and Biochemistry of Dairy Products, Instituto de
Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas,
Villaviciosa, Asturias, Spain.
In this work, we report the genome sequences of Bifidobacterium bifidum strain
LMG13195. Results from our research group show that this strain is able to
interact with human immune cells, generating functional regulatory T cells.

Immune Netw. 2014 Feb;14(1):7-13.
Potential role of bacterial infection in autoimmune diseases: a new aspect of
molecular mimicry.
Alam J(1), Kim YC(1), Choi Y(1).
(1)Department of Immunology and Molecular Microbiology, Dental research
Institute, Seoul National University School of Dentistry, Seoul 110-749, Korea.
Molecular mimicry is an attractive mechanism for triggering autoimmunity. In this
review, we explore the potential role of evolutionary conserved bacterial
proteins in the production of autoantibodies with focus on granulomatosis with
polyangiitis (GPA) and rheumatoid arthritis (RA). Seven autoantigens
characterized in GPA and RA were BLASTed against a bacterial protein database. Of
the seven autoantigens, proteinase 3, type II collagen, binding immunoglobulin
protein, glucose-6-phosphate isomerase, α-enolase, and heterogeneous nuclear
ribonuclear protein have well-conserved bacterial orthologs. Importantly, those
bacterial orthologs are also found in human-associated bacteria. The wide
distribution of the highly conserved stress proteins or enzymes among the members
of the normal flora and common infectious microorganisms raises a new question on
how cross-reactive autoantibodies are not produced during the immune response to
these bacteria in most healthy people. Understanding the mechanisms that deselect
auto-reactive B cell clones during the germinal center reaction to homologous
foreign antigens may provide a novel strategy to treat autoimmune diseases.

Yale J Biol Med. 2016 Sep 30;89(3):331-337. eCollection 2016 Sep.
Unraveling the Dynamics of the Human Vaginal Microbiome.
Nunn KL(1), Forney LJ(2).
(1)Institute for Bioinformatics and Evolutionary Studies, University of Idaho,
Moscow, Idaho, USA; The Bioinformatics and Computational Biology Graduate
Program, University of Idaho, Moscow, Idaho, USA. (2)Institute for Bioinformatics
and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA; Department of
Biological Sciences, University of Idaho, Moscow, Idaho, USA.
Four Lactobacillus species, namely L. crispatus , L. iners, L. gasseri, and L.
jensenii, commonly dominate the vaginal communities of most reproductive-age
women. It is unclear why these particular species, and not others, are so
prevalent. Historically, estrogen-induced glycogen production by the vaginal
epithelium has been proffered as being key to supporting the proliferation of
vaginal lactobacilli. However, the 'fly in the ointment' (that has been largely
ignored) is that the species of Lactobacillus commonly found in the human vagina
cannot directly metabolize glycogen. It would appear that this riddle has been
solved as studies have demonstrated that vaginal lactobacilli can metabolize the
products of glycogen depolymerization by α-amylase, and fortunately, amylase
activity is found in vaginal secretions. These amylases are presumed to be
host-derived, but we suggest that other bacterial populations in vaginal
communities could also be sources of amylase in addition to (or instead of) the
host. Here we briefly review what is known about human vaginal bacterial
communities and discuss how glycogen-derived resources and resource competition
might shape the composition and structure of these communities.

 

[oriana]

Q: How can we know what other substances/organisms/bits of protein chain might also cross react? How do such homologies arise? I really like your perspective that the immune system isn't confused "attacking itself" and so on that view how do you understand how there "just happen" to be these homologous amino acid sequences between, say, my TPO proteins and some from a lactobacillus? If this overlap is at the level of generality on which all organisms use proteins made of amino acid sequences, then it's not interesting, but if it is more specific-- which apparently it is-- then the match it seems quite random unless there is some kind of complicated co-evolution happening?

RP:
There are lots of areas of similar amino acid sequences in proteins of microorganisms and animals, that are important for shaping the protein and making it fit into its normal place in the cell. Even slight “denaturation” of a protein can expose those areas, so stress, changing normal relationships, can make things antigenic. Someone found that an animal’s own cartilage, normally not antigenic, became antigenic after the cartilage was twisted. Energy depletion of a tissue makes it very susceptible to having its antigenic regions exposed; hypothyroidism, and high estrogen, make tissues swell; our “immune system” helps to correct the damage, removing things that are seriously disrupted. Progesterone and pregnenolone have a stabilizing effect, supported by thyroid and CO2. When the damaged tissues are restored, the antibodies will gradually disappear. Well cooked mushrooms and bamboo shoots are probably more effective than carrots. Small amounts of antibiotics, flowers of sulfur, and aspirin, and bacteriophage can help by reducing bacteria in the small intestine.