Anti-Inflammatory Diet

All health care starts with diet. My recommendations for a healthy diet are here:
Anti-Inflammatory Diet and Lifestyle.
There are over 190 articles on diet, inflammation and disease on this blog
(find topics using search [upper left] or index [lower right]), and
more articles by Prof. Ayers on Suite101 .

Monday, September 28, 2009

Paradoxical Inflammation

Anti-inflammatory Treatments Cause Inflammation in Some Diseases, e.g. Rosacea

I thought that the anti-inflammatory diet and lifestyle I outlined on this blog would be a general purpose starting point for the treatment of all diseases. Inflammation is the foundation for allergies, autoimmune diseases and cancer. Inflammation is a basic defense against infectious diseases and many tissues require signaling components integral to inflammation for their normal function, so it is possible to overdo anti-inflammatory treatment and produce immuno-suppression. But that is unusual. What I am talking about here is inflammation caused by vitamin D, omega-3 oils, potentially low carbs and inhibitors of NFkB, such as tumeric. This is Paradoxical Inflammation.

Rosacean Inflammation Is Paradoxical

The obvious example of a paradoxical inflammatory disease is rosacea. Rosacea seems to be a large group of diseases that manifest in facial inflammation. Excessive flushing of the face can become persistent and form pustules and swelling. The triggers for rosacean inflammation are legion and idiosyncratic. They include mundane social interactions, numerous foods, temperature extremes and, paradoxically, just about everything that I recommend to decrease chronic inflammation.

Bacteria in Tissue and Gut Biofilms Are Candidates

Why do otherwise anti-inflammatory foods and exercise make rosaceans red in the face? Even vagal stimulation that is uniformly calming to inflammation, can make a rosacean flush. This is very inconvenient. I can only invoke the typical players: cryptic bacteria, biofilms, vagus nerve stimulation and response, lymphocytes/macrophages, cytokines and neurotransmitters.

All rosaceans have demonstrated facial inflammation and have had long term exposure to antibiotics and NSAIDs. That combination suggests that bacteria have been transported from a leaky gut (NSAIDs) to the site of inflammation (the face). It is likely that cryptic bacteria inhabit the dermis near the blood vessels and resident lymphocytes/mast cells. This is also the location for axons from vagus nerves. Thus, vagus stimulation may result in the release of neurotransmitter acetylcholine to stimulate lymphocytes/mast cells with subsequent release of cytokines. In this case the cytokines are inflammatory.

Other sources of inflammatory cytokines are lymphocytes/mast cells activated by endotoxin release from cryptic bacteria triggered by immunological attack. In this case, the immunological attack can be initiated by disruption of the stasis invoked by the cryptic bacteria.

Activated Cryptic Bacteria Are Source of Inflammation

It is hypothesized that the cryptic bacteria remain in tissue, because they are able to induce a hibernation-like physiology in the tissue. Disruption of the hibernation would initiate an immunological assault. Disrupting agents typically include vagal stimulators, such as activators of the hot or cold sensors, e.g. capsaicin, castor oil or menthol. Interestingly, the cryptic bacteria require a residual level of inflammation to acquire nutrients from the host. Anti-inflammatories that inhibit NFkB may destabilize the bacterial/host interaction and result in an immunological attack on the bacteria. All of the attacks on the cryptic bacteria release inflammatory endotoxin.

Gut Biofilms Store Bacteria Recruited to Become Cryptic in Inflamed Tissue

During the course of the disease and following numerous antibacterial treatments, bacteria can be continually recruited from safe havens, such as gut biofilms. Antibiotic treatment of biofilms converts the biofilm community to antibiotic resistance through activated horizontal gene transfer. Moreover, harsh treatment of biofilm communities initiates shedding of bacteria that could migrate across the leaky gut adjacent to the gut biofilms and provide new emigrants into the inflamed face tissue. A likely resident would be Chlamydia pneumonia, which has been demonstrated to be carried by macrophages and offloaded at distant sites of inflammation.

How the Vagus Becomes Inflammatory

This brings up the question of why vagal stimulation shifts from anti-inflammatory to inflammatory in rosaceans. I don’t think that the vagus nerves change in either their activation or in the neurotransmitters that are released as a result of stimulation. This means that the cells that respond to the vagal acetylcholine must be changed. I think that the change is a depletion of Treg cells and the result is that acetylcholine receptors on the remaining T cells cause a release of inflammatory cytokines. These cytokines cause the release of NO by endothelial cells and vasodilation. Leaking of endotoxin from the resident cryptic bacteria causes persistent dilation and restructuring of the vasculature.

Helminth and Il-2 Therapy Reestablish Tolerance and Reverse Vagal Inflammation

Since I have been forced to explain paradoxical inflammatory diseases, I might as well speculate on exotic approaches that already suggest potential treatments. Ingesting parasitic worm eggs (helminth therapy) has proven successful in the treatment of inflammatory diseases such as asthma, allergies and IBDs. Interleukin 2 (Il-2), usually used as a complex with an anti-Il2 antibody, is also a productive treatment. In both of these cases, the treatment stimulates the proliferation of Treg cells, which appear to be deficient in many of the inflammatory diseases. These treatments should also lead to a lowering of inflammation in the gut and suppression of inflammation as a result of vagal stimulation. Inhibitors of acetylcholine receptors, e.g. scopolamine patches, might also be interesting to test to see if they inhibit rosacean flushes in response to typical vagal stimulants such as castor oil or menthol.

Addendum:  Another possibility associated with the heavy use of antibiotics by rosaceans is intestinal (biofilm?) candidiasis.  Yeast infections are common after prolonged antibiotic treatment.  Interestingly, Candida produces resolvins from omega-3 fatty acids and the resolvins suppress neutrophil activity that would attack the yeast.  Thus, many of the anti-inflammatory treatments would actually aggravate yeast infections and contribute to rosacea.  Treatment for candidiasis (keeping in mind that yeast may be protected by biofilms) helps many rosaceans.  Stripping biofilms may be useful if pro- and pre-biotics are used to displace Candida.

Thursday, September 17, 2009

Vagus Nerve Controls Gut Inflammation II

Inflammatory Mast Cells Silenced

In a previous article, I outlined the role of the vagus nerve in responding to infection/damage signals by producing signals that inhibit inflammation. In a recent article (ref. below), the role of the vagus nerve in gut inflammation was examined using real-time biophotonic labeling. Basically that means that a video camera sensitive to infrared can be used to detect infrared dyes produced when NFkB is activated -- the camera is able to visualize regions of inflammation in living mice. Using this technique, researchers were able to demonstrate that cutting the vagus nerve produced heightened inflammation in gut treated with an irritant. The vagus nerve appears to stimulate regulatory T cells that lower the activity of inflammatory cells.

Inflammation/NFkB Activation Visualized in Live Mice

The studies were performed in a mouse line constructed to express an infrared fluorescent protein in cells in which the inflammation transcription factor, NFkB, is activated. Mice of this strain were prepared with and without the vagus nerve intact leading to the intestines. The mice were then exposed to sodium dextran sulfate (DSS) to simulate inflammatory bowel disease symptoms.

Cutting the Vagus Nerve Permits Inflammation

Mice with intact vagus nerves exhibited much less inflammation in their gut than those without vagus innervation. The cut vagus experiments demonstrated that the vagus nerve was responsible for suppressing inflammation. Further experiments were performed to determine if the inflammatory and anti-inflammatory reactions could be transferred to other mice by transferring cells from the treated mice.

Regulatory T Cells (CD4+, CD25+) Block Inflammation

Transfer experiments showed that inflammatory T cells (CD4+, CD25-) from cut vagus, DSS mice would cause bowel inflammation in other mice, but that did not happen with the same type of cells from mice with intact vagus nerves. Further tests showed that either cutting the vagus or adding inflammatory T cells from a mouse with a cut vagus, reduced the population of regulatory T cells (CD4+, CD25+) in control mice treated with DSS. So, without the vagus stimulation, the regulatory T cell population declined in the presence of inflammatory signals.

Absence of Regulatory T Cells Can Explain Many Inflammatory Diseases

In many inflammatory diseases, e.g. celiac, Crohn’s disease, rosacea, there appears to be a deficiency of regulatory T cells. In the absence regulatory T cells, signals from vagus nerves will no longer produce anti-inflammatory suppression. In fact the same nerve signals may become inflammatory. This would explain why rosaceans will become inflamed by hot or cold stimulation that would normally lead to anti-inflammatory stimulation of regulatory T cells. Similarly, capsaicin, castor oil and menthol, which normally produce an anti-inflammatory response, produce inflammation in rosaceans.

[Vagal stimulation exercise links:  here and here.]

O'Mahony C, van der Kleij HP, Bienenstock J, Shanahan F, O'Mahony L. 2009. Loss of vagal anti-inflammatory effect - in vivo visualization and adoptive transfer. Am J Physiol Regul Integr Comp Physiol. Aug 12. [Epub ahead of print]

Thursday, September 10, 2009

Watson Makes Us Sick

Common Textbook: Molecular Biology of the Cell, Lacks Coverage of Critical Molecular Interactions

One of the major reasons why healthcare practitioners are unable to cure diseases, is that their molecular view of disease is outdated. Their models of key signaling interactions lack critical molecules and fundamental types of chemical bonds are ignored.

The Major Textbook Used to Train Medical Students Lacks Essential Cellular Interactions

The most pervasive and perhaps the best text book on cell biology, The Molecular Biology of the Cell, first authored by James Watson, lacks a discussion of the bonding of aromatic amino acids (tryptophan, tyrosine, phenylalanine) with basic amino acids (arginine, lysine), carbohydrates, and aromatic phytochemicals, e.g. plant antioxidant or alkaloids. As a result, medical school graduates lack familiarity with the prominent interactions that dominate disease and drug treatments.

Hydrophobic Bonding to Aromatic Amino Acids Dominates Cell Molecular Biology

The dominating significance of aromatic hydrophobic bonds is the strength of these bonds, ca. 20 kcal/mol versus, the commonly considered weak bonds (hydrogen, ionic) at 1-2 kcal/mol, the same as the kinetic energy of water at body temperature. Thus, structures, such as alpha helices and beta sheets of proteins, require multiple weak bonds to be stable, but the hydrophobic bonding of tryptophan to a single arginine draped across its surface is stable.


Tryptophan is the most highly conserved amino acid in protein structures (more than cysteine forming disulfide bonds!). This means that tryptophan is the most important amino acid in protein structure, and probably determines how proteins fold.

Carbohydrates have hydrophobic faces to their ring structures and typically bind to lectins, glycosidases and glycanases, via the hydrophobic surfaces of tryptophans or tyrosines in active sites.

Transport of proteins into nuclei is by binding of arginine or lysine residues of nuclear localization signals (basic quartets or neighboring basic pairs) to tryptophan hydrphobic residues projecting from the surface of LRR (leucine-rich repeat) importin molecules.

Heparin binds to basic amino acids in proteins via hydrophobic interactions. Aromatic dyes, such as berberine, bind to heparin through similar hydrophobic interactions.

Heparin binds to the basic amino acids arrayed in stacks of amyloid molecules and berberine blocks these interactions. Congo Red, a diagnostic dye for amyloids, is an aromatic molecule. Similar interactions occur with prions and the plaques of atherosclerosis.

Acidic polysaccharides form the matrix of biofilms. Heparin and nucleic acids can also serve this function. PEG, which disrupts hydrophobic interactions, can be used to disrupt binding of proteins to heparin, nucleic acids and biofilm polysaccharides.

Heparin binding mediates the interaction between most growth factors or cytokines and their cell surface receptors.

Many viruses and bacteria bind to cell surfaces via heparan sulfate.

LDL binds to LDL receptors via heparan sulfate. ApoE in diagram (arg and lys in blue, hydrophobic in pink.)

Antimicrobial peptides, e.g. defensins, have groups of basic amino acids. Heparin binding domains excised from proteins as peptides are antimicrobial.

Stomach proteases cleave around heparin-binding domains to produce antimicrobial peptides. Intestinal proteases cleave within heparin-binding domains and inactivate bacterial and viral agglutinins.

Life starts with heparin, i.e. heparin is leaked into fertilized eggs to remove the small, highly basic proteins used to package the sperm chromosomes.

Heparin is injected experimentally into nerves to silence IP3 signaling based on the binding of the hydrophobic face of inositol to basic amino acids, similar to heparin binding domains, of the IP3 receptors located on the surface of the ER.

The cytoplasmic domains of some receptor proteins have basic regions that interact with the IPs of the membrane surface, but subsequently serve to transport membrane-derived vesicles to the nucleus via importin carriers.

Heparin/heparan sulfate proteoglycans are secreted bound to basic molecules such as polyamines or histamine.

Heparan sulfate proteoglycans are continually secreted and taken up with a half life of six hours. This circulation is a major transport system of most cells. Amyloid/heparan aggregates on the surface of nerves and gliadin/tTG/antibody/heparan complexes on endocytes (celiac) may poison this system.

All allergens and autoantigens have a triplet of basic amino acids that may be involved in the initial aberrant presentation of these antigens as a result of the internalization by the carbohydrate-binding domain of mannose receptors on the surface of inflammation-stimulated immune cells.

Many neurotransmitters bind to their receptors via hydrophobic, aromatic interactions. These same receptors interact with hydrophobic, aromatic phytochemicals, e.g. “anti-oxidants.” Many spices, herbs, alkaloids and other phytochemicals have their abundantly complex interactions via these mechanisms.

Crystals of the tryptophan repressor involved in binding tryptophan and altering the expression of genes involved in tryptophan synthesis, shatter in the presence of tryptophan -- the tryptophan (yellow) strongly binds to basic amino acids (blue) in the tryptophan-binding domain of each repressor protein in the crystal and alters its shape.

Wednesday, September 2, 2009

Cure for Inflammatory Diseases

Destabilizing Gut Biofilms by Simple Remedies

The intercommunication between the gut flora biofilms, the cells of the immune system juxtaposed with the intestinal endothelium and cryptic bacteria/tissue biofilms produces stable chronic inflammatory disease. Disrupting the gut biofilms may permit a resumption of effective immunity and remission.

Disrupting Biofilms to Treat ASDs

Cristian Stremiz brought to my attention the work of Dr. Anju Usman on the treatment of autism spectrum diseases by attacking inflammatory gut biofilms.

A Panacea

This approach, based on the use of common food components, to attack the gut biofilm matrix of acid polysaccharides, cations and proteins, should be generalizable to most inflammatory diseases. The interventions also provide facile explanations for the utility of numerous traditional cures such as vinegar, fiber, glucosamine, pectin, whey, proteases and probiotics.

Cures Act via Gut Flora Biofilms

There are numerous anecdotal reports of traditional, simple remedies working for essentially all diseases. Tantalizingly, many of these diseases are also occasionally successfully treated with antibiotics. The common thread seems to be the involvement of inflammatory gut flora and perhaps cryptic bacteria residing in the tissues displaying symptoms. Glucosamine works sometimes for arthritis, but little of the glucosamine that is eaten reaches the blood stream and the aching joints that seem to become less inflamed. Vinegar, pectin, and fiber have also been attributed with curative powers, yet none is likely to impact inflamed joints directly. Impacting gut biofilms is much easier to explain.

Biofilms of Bacteria Attached to Acidic Polysaccharides and Divalent Cations

Acidic polysaccharides are produced by bacteria and divalent cations cross-link the polysaccharides into a matrix. The bacteria have agglutinins to attach to the matrix. Gut pathogens produce agglutinins that they use to attach to the heparan sulfate (HS), the predominant acid polysaccharide of the intestinal epithelium. Mast cells of the intestines normally release heparin, which is a mixture of HS fragments, to stick to the agglutinins and block attachment to the HS of the epithelium. Numerous bacterial species form complex communities on the polysaccharide matrix and prevent access by antibiotics. Biofilms require 100X the antibiotic concentrations and a cocktail of different antibiotics to eradicate the bacteria.

Biofilms Disrupted by Competing Acid Polysaccharide Fragments and Cation Chelators

The Achille’s heal of biofilms is the ionic interaction between the acidic polysaccharide and divalent cations. This interaction can be attacked by both small fragments of similar acid oligosaccharides, by organic acids that can solubilize the cations, e.g. acidic acid in vinegar, or by chelators, such as EDTA. All of these treatments can remove the calcium, magnesium and iron that is essential to the matrix. Small molecules, such as glucosamine, chondroitin sulfate fragments, heparin, and pectin, can disrupt biofilms. Molecules that bind to heparin or nucleic acids, e.g. berberine, quinine (tonic), methylene blue, should also be effective in disrupting biofilms. [Note that the similarity between amyloid production and biofilms, means that treatments should overlap.] Lactoferrin is effective, since it both binds iron and binds to acidic polysaccharides via its heparin-binding domains.

Proteases Cleave Agglutinins

Stomach proteases, e.g. pepsin, specifically cleave proteins to release heparin-binding, acidic polysaccharide-binding domains that inhibit biofilm production in the stomach. Subsequently, the basic, antimicrobial peptides and agglutinins are cleaved by proteases, e.g. trypsin, that hydrolyze the binding domains. Eating proteases, such as nattokinase present in fermented soybeans, dissolves intestinal biofilms by attacking the agglutinins. The pathogenic E. coli and avian H5N1 also have these agglutinins. It is, therefore, wise to avoid establishing gut biofilms that can immobilize pathogens.

Probiotics Protect Against Biofilms

Resident gut bacteria that produce organic acids, e.g. lactic acid or acetic acid, provide protection against biofilm formation. Examples are the bacteria present in common forms of fermentation and food preservation, e.g. Lactobacillus sp., and the bacterium present in exclusively breastfed babies, Bifidobacter sp. Formula fed babies rapidly develop inflammatory biofilms, which explains their high rates of intestinal and respiratory diseases, as well as increased rates of inflammatory diseases.

Biofilm Inflammation Results in Inflammatory Bowel Disease, etc.

Gut biofilms support system-wide chronic inflammation that leads to allergies, autoimmune diseases, degenerative diseases and probably cancers. This attach on the gut also produces a leaky gut that supplies the bacteria that a moved by macrophages of the gut to all parts of the body. This may be how Chlamydia pneumoniae colonizes sites of inflammation throughout the body.

Attacking Gut Biofilms Is the First Step in the Treatment of All Inflammatory Diseases

Many inflammtory diseases, e.g. chronic lyme disease, rosacea, may be refractory to treatment with antibiotics, because of the reservoir of bacteria in gut biofilms. Attacks on gut biofilms with relatively non-intrusive treatments, such as vinegar, EDTA, lactoferrin and proteases, may lower the total resident pathogen load and make subsequent antibiotic treatment more effective.