Aging Gut Flora

Diet selects for the bacteria that grow in the GI track and control the development of the immune system.  Diet-based inflammation produces aging symptoms.

Returning to the Subject of Aging

I want to return to the subject of aging.  A year and a half ago I wrote, “You don’t wear out, you flame out.”  I still think that is true, but I need to update that idea of inflammation and aging to include diet, gut flora and immune system development.  So here is my old article with a new focus on the gut.

Wearing Out Only Happens with Inflammation

I don’t think that aging happens -- most symptoms associated with aging are just medically mismanaged chronic inflammation.  The major observations are that older people have more degenerative/autoimmune diseases and they suffer from fewer infectious diseases.  The typical explanation is that the bodies of older people have figured out infections with an experienced immune system and that mechanical damage takes its toll over time -- joints wear out.  I think that there may be a minor amount of truth in this cultural perspective, but there is something more profound at work, sarcopenia combined with a compromised gut flora.

Replacing Muscle with Visceral Fat Is Inflammatory

Sarcopenia (muscle loss) is the gradual loss of muscle and replacement by fat.  Thus, by age fifty most people are physically less active and even if they appear to have the same weight and shape as in their active youth, the muscle of their abdomens and limbs has been partially replaced with fat.  This fat, as in those who are obese, releases inflammatory cytokines into the circulation and the body reacts as if it has a low grade infection.

Chronic Inflammation Taxes Immune System

Senior citizens are constantly expending energy and taxing their immune system by chronic inflammation.  As a result they get fewer infections, but the chronic inflammation provides the foundation for cancer and autoimmune diseases.  Their bodies aren’t mechanically wearing out, but they are wearing out by over use of the immune system.  

Aging Symptoms Are Inflammation Symptoms

Those seniors who are physically active and eat an anti-inflammatory diet, do not appear to age as fast as those who are sedentary, obese and display the typical symptoms of chronic inflammation, the metabolic syndrome.  Most of the characteristics associated with advancing years are merely symptoms of poorly managed chronic inflammation that can be reversed by an anti-inflammatory diet and exercise.

Diet Determines Gut Flora

Diet also contributes to aging, because diet controls development of gut flora and gut flora control development of the immune system.  The gut flora of an individual reflect the bacteria that have entered the GI tract, nutrients available to the bacteria in previous meals, bacterial growth regulators released by the gut, exposure to antibiotics, exposure to phytochemicals and gut transit time.

Gut Flora Is Diverse and Adaptable

Gut flora appears to be amazingly diverse from individual to individual with thousands of bacterial species inhabiting humans worldwide and about 150 species in each individual.  The same species remain in an individual for long periods of time regardless of diet.  The dominance of particular species depends on recent diet.  Major changes can result from antibiotics or gut diseases, e.g. Crohn’s.

Constipation Means Dysfunctional Gut Flora

Bowel stools are made up predominantly of bacteria and not undigested plant parts, i.e. fiber.  Fiber is made up of plant polysaccharides that are not digested by salivary, stomach or pancreatic enzymes, e.g. proteases and amylases that degrade proteins and starch.  Fiber polysaccharides pass into the colon where they are digested by gut flora.  People with constipation usually have disrupted gut flora, e.g. wiped out by antibiotics, and so the minimal volume of remaining undigested fiber is all that passes out in compact, dehydrated lumps.  If gut flora have been exposed to a particular type of fiber and bacteria having the needed enzymes have been brought into the gut previously, then the fiber is digested to sugars that feed the gut bacteria.  The increased population of bacteria is what makes up normal, hydrated bowel stools.

Gut Flora Changes Slowly to New Foods (Polysaccharides)

Bacteria grow quickly and with ample nutrients gut bacteria can double in number in about an hour.  Bacterial species are usually defined by the ability to utilize various carbohydrates or polysaccharides as nutrients.  Depending on the food eaten, nutrients favor the growth of particular bacterial species and the gut flora population changes dynamically.  New species are incorporated into the gut flora only if they find their way into the gut on food, e.g. riding on fresh, uncooked vegetables, and food provides nutrients that can permit the new bacteria to grow.  It will take several meals for new bacteria to reach appreciable numbers.  In the mean time the new fiber may be partially degraded and produce chemicals that disrupt other gut flora and cause bloating symptoms of food intolerance.  This is not an allergic reaction of the immune system.  It just takes time and persistence to permit the gut flora to adapt.  Most people systematically make themselves intolerant to particular foods by over-reacting to initial maladaption of their gut flora to the new food.  If they persisted with progressive exposure to diverse foods, their gut flora would adapt.

Simplified Aging Gut Flora Contributes to Inflammation

People of increasing age who maintain a diverse, anti-inflammatory diet and maintain muscle mass by weight-bearing exercise, avoid age-related inflammation and disease, i.e. they age more slowly.  Conversely, those who simplify their diets by eating processed foods high in starch and vegetable oils, show symptoms normally associated with advanced age, even when young.  The aging diet is inflammatory and it also produces a gut flora which is different from the youthful.

Aging Gut Flora Contributes to Disease

Constipation is an extreme example of dysfunctional gut flora and since gut bacteria are needed for the normal development of the immune system that is located in the lining of the small intestines, constipation is also an indicator of a compromised immune system.  Aging is frequently accompanied by digestive problems with one extreme being constipation.  It should not be surprising that individuals with compromised immune systems also develop numerous degenerative diseases indicative of a lack in the immunological tolerance systems that develop in the gut in response to normal gut flora.  Constipation and digestive problems are not normal signs of aging.

Eliminate Symptoms of Aging by Cultivating Gut Flora

A healthy diet, healthy gut flora, and a competent immune system are all tightly connected.  The typical symptoms of aging merely reflect an unhealthy diet and lifestyle that leads to chronic inflammation, a compromised immune system and disease.  The process of aging can be slowed by attention to the next meal.  Most people who fail to be healthy and active well into their 80’s are simply victims of bad choices (or of bad medical advice.)

Antibiotics, Gut Flora, Food Intolerance and Disease

Cattle Are Finished by Selective Killing of Gut Flora.  The Sickened Animals Store Fat that Grills Great.  People Get Metabolic Syndrome.

The likening of modern humans to potatoes sacked out on a couch is misleading.  The obesity epidemic linked to diets of processed foods more closely resembles the stumbling progression of cattle to abattoir.  Antibiotics and diet systematically lead in both feedlot and food court to gut dysbiosis, immune system failure, hormone disruption, rampant fat accumulation, physical inactivity, depression and the modern suite of chronic diseases.  Healthcare costs escalate, but vet bills, in contrast, are forestalled by a captive bolt pistol.

Background Observations

• Antibiotics kill bacteria and not humans, because the bacteria have different machinery for making proteins, nucleic acids and cell walls.
• Antibiotics kill bacterial pathogens and not viruses or fungi.
• Antibiotics kill helpful bacteria in the gut (gut flora) even more readily than pathogens.
• Antibiotics are used in meat production to alter gut flora to change animal metabolism;  e.g. cattle treated with antibiotics gain fat.  Protection from disease is secondary.
• Simple diet means simple gut flora.  Processed foods are simplified foods that simplify gut flora.
• Probiotics can replace only a small fraction of the gut flora diversity.
• Gut bacteria control the immune system development in the lining of the gut.
• Chronic antibiotic use permanently simplifies gut flora and compromises the immune system.
• The appendix stores gut bacteria as a reserve to replenish gut flora following diarrhea.
• Diseases based on inflammation and immune system intolerance result from gut dysbiosis (inadequate gut bacteria).

Antibiotics Kill Good Bacteria

This is a rant about antibiotics, not about humane actions.  Humane actions are not the point here, since I am talking about health care and not treatment of agricultural animals.  I am pleading for the rights of gut flora everywhere and antibiotics are the casual killers.  Compromised gut flora is collateral damage in attempting to eliminate bacteria characterized as pathogens.  Every time the pediatrician treats the mother by acceding to her pleas for an antibiotic prescription to silence a howling ear ache and get a good night’s sleep, or the dermatologist treats teen acne with antibiotics, billions and billions of domesticated bacteria die.

Constipation Is a Sign

Countless hours are wasted waiting, because antibiotic-depleted gut flora cannot hydrate and form normal stools.  Probiotics are gulped down, but they supply only a handful of the hundreds of bacterial species that are needed for health.  Yeasts and other fungi that are naturally resistant to antibiotics quickly replace the lost beneficial bacteria in the gut, vagina and on other body surfaces.  Surcease for simple sorrows leads to lingering and lasting laminations.  Don’t mess with mother nurture.

Damage of Antibiotic Use Is Slow

Most of the impact of antibiotic annihilation of bacteria normally present in humans is unobserved, because the deleterious effects lag months behind the initial treatment.  After all, cattle treated with antibiotics to restructure their gut flora to induce bovine obesity, appear to thrive as they rapidly gain weight and avoid symptoms of infectious diseases.  Humans on antibiotics also display fewer dental and incidental infections.  Constipation is not a high price to pay for a better mirror image.  

Antibiotics Compromise the Immune System

Unfortunately, allergies, autoimmune diseases, degenerative diseases and cancers are not usually linked to prior use of antibiotics.  There is no evidence that gut flora recovers  after antibiotic treatment, but constipation as a consequence of chronic antibiotic use is a common indicator of gut dysbiosis, collapse of normal gut flora bacterial communities.  The harbingers of inflammatory and degenerative diseases are present, but are usually discounted, because they are a common consequence of the Western diet.

Food Intolerance Reveals Inadequacies in Gut Flora

Food intolerance is a sign of depleted gut flora diversity.  Gut flora have hundreds of genes that can break down a huge diversity of polysaccharides derived from plant cell walls.  Gut flora of Japanese who routinely consume kelp have specialized enzymes to hydrolyze unusual algal sulfated polysaccharides.  Essentially all of the polysaccharides in plant fiber can be consumed by bacteria in the anaerobic environment of the colon.  Inability of individuals to digest particular food components usually results from a deficiency of the gut flora and an indication of a history of dietary simplification and antibiotic use.  Lactose intolerance, for example, results from depletion of lactose-degrading bacteria from the gut flora and can be remedied by simply eating lactose with probiotics for a couple of weeks.  Gut flora can adapt, but they need persistent exposure to diverse, i.e. non-processed, food.

Antibiotic Allergies Are Natural

Allergies develop from a combination of inflammation and compromised immunological tolerance.  Inflammation heightens processing of antigens for presentation to the immune systems, whereas loss of immunological tolerance means that aggressive immune responses are inadequately controlled.  Thus, innocuous environmental molecules are incorrectly recognized as pathogen components.  Allergies to antibiotics, such as penicillin, make sense, because the antibiotic is used to treat inflammatory infections and the antibiotic treatment eliminates the gut bacteria that are needed to develop gut lymphocytes (Tregs) to produce tolerance.  Antibiotics lay the foundation for immune system dysfunction that is central to many chronic diseases.

Healthy gut flora and a healthy immune system require:

• avoidance of antibiotics
• systematic (not simply eating yogurt) rebuilding of gut flora following diarrhea or antibiotic use; lack of an appendix means gut flora reservoir is gone
• eating a variety of vegetables; avoiding processed food
• using herbs and spices
• don’t overdo hygiene; gut flora diversity derives from bacteria that you eat and those that rub off acquaintances
• eat seasonally to increase diversity

Lateral Gene Transfer in Gut Flora

Japanese Gain Ability to Digest Algal Polysaccharides from Marine Bacteria
Gut flora adapt to the food nutrients that are prevalent in different parts of the world.  Bacteria able to digest unusual nutrients, such as the sulfated porphyrans found in seaweed eaten in Japanese cuisine, are also consumed along with algae.  Formation of bacterial biofilms triggers the exchange of genes among gut bacteria and the acquisition of new polysaccharide-degrading enzyme activities.

Gut Flora Adapts to Diet
The million or so genes of the thousands of bacterial species found in the guts of humans around the world are adapted to the diet of each of those individuals.  Each individual gut harbors a couple of hundred different bacterial species and those different types of bacteria increase or decrease in number in response to the composition of each meal. 

Diversity of Plant Polysaccharides Provides Digestion Challenge
Plants provide the greatest challenge for digestion, because plants differ the most in their carbohydrate (sugars, oligosaccharides, polysaccharides) composition.  Some of those carbs, such as sucrose, starch or the components of the plant cell walls, pectins, arabinogalactans and xyloglucans, are present in all vegetables.  Whereas other polysaccharides, such as the sulfated porphyrans from red algae of the same name (Porphyra) are restricted to particular plants.  Each different linkage and sugar requires a different digestive enzyme.

Gut Bacteria of Algae Eaters Have Algae-Degrading Enzymes
A recent report (see ref.) traced genes from marine bacteria that digest marine algae/seaweed, to gut bacteria of people who routinely eat seaweed.  Researchers studying marine bacteria identified genes coding for new enzymes, porphyranases, that hydrolyzed porphyrans.  When they checked gene databases for other porphyranase genes, they found that some gut bacteria had previously unassigned genes that were apparently, based on their nucleotide sequences, porphyranases.  Curiously, these genes were only present in gut bacteria isolated from Japanese sources, i.e. from people who traditionally ate seaweed.  In some of these bacteria there were more than 260 genes for degrading a huge variety of different plant polysaccharides.

Marine Bacteria on Seaweed Release DNA Incorporated into Gut Bacteria
Bacteria recognize that other bacteria are around by a process called quorum sensing.  This signaling system triggers the production of matrix polysaccharides produced by the bacteria to hold the bacteria together in complex communities.  Quorum sensing also mobilizes the release of copies of the bacterium’s genes, which is coordinated with uptake of DNA from the surrounding environment.  [Note that the proteins that take in foreign DNA have basic amino acids arranged in the same heparin-binding domains that are also used by growth factors and their receptors or the numerous proteins that bind to nucleic acids in the nucleus or in ribosomes.]  Thus, biofilm formation is accompanied by enhanced lateral gene exchange that would also enhance the incorporation of porphyranase genes from ingested marine bacteria.

Gut Bacteria Are Made in Guts and Shaped by Diet
Species of gut bacteria are defined in the micro lab by their ability to grow in Petri dishes of agar containing particular combinations of sugar, polysaccharides, etc.  The sugars that different bacteria are able to metabolize for growth reflect sugars available as niches in different parts of the gut.  Thus species are defined in part by the sugars and polysaccharides they can metabolize, i.e. by the enzymes they can produce. 

In each human gut, however, bacteria of the species filling a particular niche will have many other additional genes than those that define the species.  These atypical genes are present as a consequence of serendipitous encounters with genes from other bacteria (lateral gene transfer) and may reflect peculiarities of individual diets.  Different regional cuisines also shape the regional gut flora.  Persistent diet components would be expected to provide selective advantage for bacteria with genes capable of metabolizing new nutrients.  Access to a rich diversity of bacterial genes to augment typical gut flora genomes will facilitate adaptation.  Food processing to refine and simplify nutrient diversity, and hygiene to eliminate bacterial diversity in food, will reduce diversity in gut flora and minimize adaptation to novel foods.  Antibiotics, especially persistent use, can permanently disrupt gut flora.  Decreased diversity in gut flora may eliminate species of gut bacteria that are essential for normal physiological functioning of the gut and associated immune system, and may be major contributors to degenerative and autoimmune disease.

Sources of Personal Gut Flora:

• Exposure to Mother, Breast Milk
• Pathogens from Others
• Pets, Farm Animals
• Environmental Sources
• Ingested with Food
• Appendix Reservoir of Gut Flora

Selection Pressures on Gut Flora:

• Breast Milk Normalizes Flora Development
• Formula Disrupts Flora
• Food Nutrients
• Food Phytochemicals (herbs and spices)
• Antibiotics
• Gut Secretions
• Secretory Antibodies
• Bacteriophages, Bacteriocins
• Lateral Gene Transfer

reference:
Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G.  Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota.  Nature. 2010 Apr 8;464(7290):908-12.

Helminths, Oligosaccharides and Immunotolerance

Parasitic worms reverse allergies and autoimmune diseases using oligosaccharides to mimic self and silence immune over-responsiveness.

Helminth therapy, i.e. infection with parasitic intestinal worms to provide remission from allergies, inflammatory bowel and other autoimmune diseases, has been examined as a potential therapeutic model to rehabilitate immunological dysfunction.  The surface oligosaccharides of these worms have been found to mimic human oligosaccharides and alter immune responses by binding to carbohydrate-binding, i.e. lectin, receptors.

Immune Tolerance
The essence of allergic and autoimmune diseases is a defect in distinguishing between pathogen, innocuous and self molecules.  Heightened immune reactions as a result of inflammation move the immune system toward production of antibody and T cell receptors specific for antigens.  Those antigens respond to unique receptors on the surface of each B and T lymphocyte.  The lymphocyte population has been previously depleted of cells that can produce receptors that will bind to most self antigens.  This depletion makes the lymphocyte population generally non-responsive, or tolerant to self antigens.  Thus, the immune system is blind to the body.

Regulatory T Cells and Tolerance
Most of the immune cells of the body are present in the lining of the gut.  It is in the gut that various immune cells continue to develop for their various roles, including controlling immune reactions to self antigens and to common food molecules.  Immune cells in the gut are exposed to some food molecules and bacteria that leak through the cells of the intestinal villi.  Responding to these common antigens by inflammation can lead to inflammatory bowel disease.  This pathological over-responsiveness is normally avoided by development of regulatory T cells, Tregs, that suppress immune responses to common food molecules and to surface antigens of common bacteria.

Treg Development Depends on Gut Flora
Gut bacteria are needed for the normal function of the immune system.  Oddly, Helicobacter pylori, Hp, the cause of stomach ulcers and cancer, also stimulates the development of Tregs.  Thus, the pathology of Hp may result not from its presence, but rather from how it is growing.  Since Hp uses hydrogen gas produced by Klebsiella in the lower bowel and hydrogen production is dependent on dietary starch, then it follows that the pathological behavior of Hp may be dependent on dietary starch.  A low starch diet may actually result in Treg stimulation from Hp and a reduction in allergies and autoimmune diseases.

Tregs Enhanced by Heliminths
Immunological tolerance is also stimulated by parasitic worms, Helminths.  Helminth infestations, therefore, reduce allergies and autoimmune diseases and may contribute to the hygiene hypothesis to explain the prevalence of allergies, autoimmune and other inflammation-based degenerative diseases in modern societies.  Examination of worms to find the molecules responsible for inducing immunological tolerance has identified complex surface and secreted oligosaccharides (small sugar chains) as the active molecules.  Helminth oligosaccharides mimic human cell surface oligosaccharides and bind to carbohydrate-binding, lectin, receptors on immune cells to stimulate Treg development.

Lectin Receptors Control Tolerance
There are many implications of the modulation of the immune system via oligosaccharides.  Note that related oligosaccharides are components of human milk and prepare the gut and develop the immune system.  This explains why formula, which lacks these unique oligosaccharides, results in aberrant gut flora, contributes to neonatal necrotizing colitis and supports the development of allergies and autoimmune diseases.  In contrast, judicious use of self or Helminth oligosaccharides may provide a means of restoring the function of damaged immune systems and therapy for allergies and autoimmune diseases.  Also note that the critical use of lectins, which have oligosaccharide-binding sites rich in aromatic amino acids to bind the hydrophobic faces of the sugars, will also bind and provide entry into immune cells for allergens and autoantigens that have triplets of basic amino acids.  The binding sites of lectins should also bind many aromatic phytochemicals.  Immunomodulation by phytochemicals may result from interference with or mimicking the binding of oligosaccharides to lectin receptors.

reference:
van Die I, Cummings RD.  Glycans modulate immune responses in helminth infections and allergy.  Chem Immunol Allergy. 2006;90:91-112.

Rosacea: Alzheimer’s of the Face

Is Rosacea Caused by Amyloid LL-37, as Alzheimer’s Is Caused by Anti-microbial Abeta?
A recent article in PLoS One (Thanks Daniel!) suggests that the amyloid beta (Abeta) proteins that aggregate to form fibrous plaques in the brain tissue of Alzheimer victims, function as typical defensive anti-microbial peptides (AMPs), similar to the LL-37 cathelicidin implicated in facial tissue in rosacea.  The structural and functional similarities of Abeta and LL-37 suggest to me that Alzheimer’s and rosacea may also be similar in initiation and treatment.  Let’s compare amyloids and AMPs.

[The figure shows a model protein (from ref.) used to examine stain binding to amyloids.  The stains appear to bind to aromatic amino acids spaced evenly between adjacent proteins, but adjacent basic amino acids (blue) are spaced the same way and provide sites for heparin binding.]

Amyloids:

• Amyloid proteins/peptides align into stacks and fibers
• Stacked beta sheets bind amyloid stains: Congo Red, Thioflavin-T
• Fibers form on anionic polymers: heparin, DNA
• Short amyloid stacks are toxic to cells
• Proteases produce multiple sizes of amyloid peptides

Anti-microbial Peptides:

• AMPS typically contain heparin-binding domains -- basic peptides/ plus charge
• Some AMPs, e.g. LL-37, form fibers on DNA, heparin (stain with amyloid stains)
• Toxic to cell membranes
• Kallikrein stimulated by gut flora migrates to face and clips LL-37 to a smaller peptide that binds to host DNA and stimulates the TLR receptor to produce inflammation
• Stomach pepsin hydrolyzes dietary proteins into anti-microbial peptides (heparin is secreted by mast cells onto to the intestinal surface to protect from any amyloid-like effects)
• Defensins, cathelicidins and other AMPs are under transcriptional control of vitamin D receptor

Abeta Is Anti-microbial Like LL-37

Amyloid beta is the well-known source of the fibrous plaques forming brain lesions in Alzheimer’s disease.  The normal function of Abeta has not been firmly established.  The recent article shows data to support Abeta as an anti-microbial peptide comparable to LL-37 against several pathogenic bacteria and yeast.  Knock-out mice deprived of a gene corresponding to Abeta are susceptible to bacterial infections.  The anti-microbial activity present in extracts from Alzheimer’s disease brains was inactivated by anti-Abeta antibodies.

Implications of Abeta as an AMP Like LL-37

The similarities between AMPs and amyloid peptides suggest some implications for both Alzheimer’s disease and rosacea.  Vitamin D is a hormone that binds to a cytoplasmic receptor and the vitD/receptor complex then acts as a transcription factor that controls the expression of defensins in the intestines, LL-37 in facial skin and perhaps Abeta in brains.

Amyloids form fibers on a scaffolding of heparan sulfate (HS).  There is usually an excess of HS on the surface of cells and the HS is rapidly recycled back into cells.  During inflammation, mast cells release heparin, short fragments of HS, that should also inhibit amyloid fiber formation on HS.   Chronic inflammation, however, reduces HS production and may set the stage for amyloid fiber formation.  HS metabolism of the brain may be vitally important to the development of Alzheimer’s disease, especially since the increasing chronic inflammation of aging people should deplete brain HS.

LL-37 forms complexes with DNA from damaged host cells in rosacea skin.  The LL-37/DNA complexes trigger TLRs and inflammation.  LL-37 may normally bind to cell surface HS and chronic inflammation of the skin may cause the shift to pathogenic autoinflammation.  Topical application or perhaps low dose IV heparin may be effective in disrupting the autoinflammation due to LL-37.  Part of the toxicity of LL-37 in the skin may be due to amyloid like structures that could form with inadequate HS and overabundant LL-37 production.  Vitamin D metabolism should also be very important, since LL-37 synthesis is controlled by vitamin D.  This is consistent with the benefits that some rosaceans observe with high doses of vitamin D3 supplements.

references:
Soscia SJ, Kirby JE, Washicosky KJ, Tucker SM, Ingelsson M, Hyman B, Burton MA, Goldstein LE, Duong S, Tanzi RE, Moir RD.  The Alzheimer's disease-associated amyloid beta-protein is an antimicrobial peptide.  PLoS One. 2010 Mar 3;5(3):e9505.

Abedini A, Tracz SM, Cho JH, Raleigh DP.  Characterization of the heparin binding site in the N-terminus of human pro-islet amyloid polypeptide: implications for amyloid formation.  Biochemistry. 2006 Aug 1;45(30):9228-37.

Biancalana M, Makabe K, Koide A, Koide S. Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies.  J Mol Biol. 2009 Jan 30;385(4):1052-63. Epub 2008 Nov 14.

Heparin, Growth Factors and Rosacea

Knock-out Mice and FGF Receptor Inhibitors Mimic Rosacea
Heparin Nanofibers Loaded with VEGF and FGF Mimic Stem Cells

In previous articles, I have emphasized the mediation of extracellular signaling by heparan sulfate proteoglycans (HSPGs, polysaccharides attached to proteins) and heparin (HS fragments, oligosaccharides) and the sensitivity of HSPG expression and HS degradation by inflammation.  I return to that subject, spurred on by reading two articles that together show both the significance of heparin-mediated growth factors in general and in the specific case of symptom development in rosacea.

FGF Receptor Inhibitors Cause Symptoms Like Rosacea
Fibroblast growth factors stimulate the development of cancers, and antibodies against FGF receptors block cancer growth (see ref.)  FGF receptor inhibiting antibodies are now being used to stop cancers.  Unfortunately,  FGFR antibodies (e.g. cetuximab, panitumumab) also cause symptoms in the skin (telangiectasia, acneiform eruption) similar to the facial inflammation of rosacea.  Similarly, in knock-out mice, that lack the ability to produce FGFR, there are related symptoms.  It appears that lack of some FGF signaling may produce the symptoms of visible blood vessels and pus-filled (though lacking bacteria) follicles of rosacea.

FGF Mediated by HSPG
FGF binds to the heparan sulfate of membrane bound HSPG in pairs and these FGF dimer/heparan sulfate complexes activate a pair of FGF receptors.  The result is activation of protein phosphorylation activity (tyrosine kinase) and normal skin development.  HSPG synthesis is modified by inflammation and heparanase activity is increased.  This suggests that inflammation will decrease FGF signaling and could lead to symptoms of rosacea.

Growth Factors (VEGF, FGF) Bind to Heparin Nanofibers that Mimic Stem Cells
Stem cells produce lots of different growth factors and when stem cells are introduced into damaged cardiovascular tissue, more healing results (see ref.)  To determine if the growth factors produced by the transplanted stem cells was sufficient for the improved healing, fibers made of heparin were dipped into stem cell cultures and the resulting growth factor-coated fibers were injected into damaged tissue.  The heparin-binding growth factors were just as effective at enhancing healing as were the stem cells in previous experiments.  This demonstrated that heparin-binding growth factors were the key to normal repair/revascularization and function.

Rosacea Results from Inflammation and Aberrant Vascularization
Rosacea is poorly understood and is probably numerous diseases that have related symptoms and complex development.  As I indicated in previous articles, neurotransmitters from stimulated facial nerves, enzymes (kallikrein) and cytokines from intestinal interactions with gut flora, mast cell products (heparin, protease) and modified antimicrobial peptides (cathelicidins), as well as cryptic bacteria in facial tissues, may all be involved.  Inflammation in the skin of the face and in the intestines is involved.  Vitamin D, omega-3 fatty acids and anti-oxidants have a variety of responses (sometimes paradoxical) that differ from individual to individual and at different stages in the development of the disease.  Facial inflammation leads to abnormal development of blood vessels (telangiectasia) and in accumulation of lymphocytes and neutrophils (papulopustular rosacea).

Facial Inflammation May Depress HSPG Production and Disrupt FGF Function
One of the key ramifications of persistent facial inflammation may be the depletion of of HSPGs that normally coat cells.  HSPGs are continually produced, reabsorbed and degraded.  The half-life for HSPGs, even those that surround the cells that produce cartilage in connective tissue, is six hours.  HSPGs are also the source of heparin, that is produced as a counter ion bound to histamine and proteases in the secretory granules released by activated mast cells.  Thus, inflammation-based depression of HSPG production, which is also accompanied by heparanase activation, will remove the HSPG coating of cells.  This HSPG coating is needed for normal growth factor function.  Lack of an HSPG matrix on the surface of cells will also result in the migration of growth factors away from where they are normally functional and into adjacent tissue where they may stimulate aberrant development of blood vessels.  This may explain telangiectasia.

Is Topical Heparin a Rosacea Treatment?
Topical heparin does penetrate the skin.  It would appear to be a logical treatment, if HSPG depletion is contributing to symptom development in rosacea.  The length of the heparin fragments may be important.  I am unaware if anyone has tried the heparin lotions that are available for treatment of wounds to minimize scarring, on rosacea.  Heparin may be useful in combination with vitamin D3 and remediation of gut flora in a general scheme to treat rosacea.

refs:
Segaert S, Van Cutsem E.  Clinical signs, pathophysiology and management of skin toxicity during therapy with epidermal growth factor receptor inhibitors.  Ann Oncol. 2005 Sep;16(9):1425-33. Epub 2005 Jul 12.

Webber MJ, Han X, Prasanna Murthy SN, Rajangam K, Stupp SI, Lomasney JW.  Capturing the stem cell paracrine effect using heparin-presenting nanofibres to treat cardiovascular diseases.  J Tissue Eng Regen Med. 2010 Mar 10. [Epub ahead of print]

Human Gut Flora Genes

Thousands of Species, Millions of Genes

A research paper in this week's Nature shows a major advance in the study of the role of the human gut flora in disease and health.  Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium examined the role of gut flora in health by a massive project (ref. below) to determine the DNA base sequence of the majority of the millions of genes in the thousands of species of bacteria that abide in human feces.  Gut flora have been linked to many human diseases, as well as the normal function of the human immune system.

Major Findings:

• 576.7 gigabases sequenced (150 times larger than human genome)
• Identified 3.3 million gut flora genes
• Represents more than 1,000 bacterial species
• Each individual harbors approx. 160 different species
• Most prevalent species are identified and shared by everyone

Feces from 124 Europeans

Feces samples (124 individuals total) from a Danish project to determine the role of gut flora in obesity and from a Spanish project to determine the role of gut flora in Crohn’s disease and ulcerative colitis, were extracted for total DNA.

Illumina Multiplex Sequencing of PCR Amplified Fragments

DNA samples from each individual were fragments (<800 bp) and amplified to include indexing information and sequencing primers.  The sequences of a dozen of the fragments at a time was determined using a dozen different dyes (Illumina multiplexing).  Sample preparation and analysis was fully automated to permit identification of overlapping contiguous sequences and assembly of bacterial genomes (1,000-1,150 most common).  The sequence data in this study represents most of the bacterial species of the gut.

Comparison to 89 Existing Human Gut Bacteria Genome Sequences

The new study represented more than 200 times the sequence information than in all previous studies combined.  Existing genome sequences could be identified among the bacterial genomes assembled from the new data.  The identified and sequenced bacterial species represent approximately a tenth of the common bacteria in the gut.

Polysaccharide/sugar Metabolism Common among Gut Flora

Genes coding for enzymes needed to metabolize pectin, sorbitol, mannose, fructose, cellulose and sucrose, were common among the gut flora.  Bacteriophages were also significantly (5%) represented in the total gut metagenome.  Most of the genes were assigned recognizable bacterial functions, but many genes, presumably involved in interactions among the bacterial community or in modification of gut function have not been characterized.

Obese, Crohn’s Disease, Ulcerative Colitis, Compared to Healthy

The bacterial gene compostion of individuals diagnosed with Crohn’s Disease and ulcerative colitis were different and distinct from healthy individuals.  Individuals with Crohn’s disease had 25% fewer species of gut flora than comparable healthy controls.

This study demonstrates the feasibility of using current techniques to examine in detail the interactions between gut flora and tissues of the gut that are involved in health and disease.  This also suggests the risks of antibiotics in altering critical functions of the gut flora, as well as the alteration of gut flora to support health and cure disease.

reference:
Junjie Qin, et al.  2010. A human gut microbial gene catalogue
established by metagenomic sequencing. Nature 464, 59-65.

ABO Oligosaccharides, RBCs, VWF, Endothelial Cells, Megakaryocytes

Blood Group Antigens Are Synthesized in the Golgi by Glycosyl Transferases A or B

This is another rant about poor teaching and false text book information.  I have been trying to summarize some of the key points of genetics and cell biology that I think should shape the minds of young biologists.  To make my point, I want to outline where the common ABO blood group antigens are made and displayed.

ABO Antigens Are Oligosaccharides, Not Proteins

Red blood cells that are type A will clump together with antibodies that bind to A antigens.  At this point many instructors leap ahead and say that the expression of the A gene results in the production of the A protein, that is displayed on the surface of RBCs.  Wrong.  The antigens are carbohydrates, short chains of sugars called oligosaccharides, attached to a lipid embedded in the RBC membrane.

Glycosyl Transferases - Enzymes that Assemble ABO Oligosaccharides

Oligosaccharides are synthesized by adding one sugar at a time onto a growing chain.  Information-rich oligosaccharides, such as the ABO antigens, are made of several different sugars and are linked in a variety of ways to other sugars, so each sugar is added by a different enzyme.  The sugar-adding-enzymes are called glycosyl transferases.  Similar to other macromolecular polymerizations, e.g. protein and nucleic acid synthesis, the monomer sugars are first activated by bonding to a nucleotide phosphate (typically UDP) and the sugar is transferred from this activated intermediate to the growing sugar chain, in this case the H antigen. 

The glycosyl transferase coded by A allele transfers an N-acetylgalactosamine to the end of the H antigen oligosaccharide, whereas the glycosyl transferase coded by the B allele transfers a galactose residue.

Dominance Means Functional Enzyme, Recessive Means Dysfunctional

The ABO blood group system provides a simple molecular interpretation of genetic dominance.  An allele is dominant if it produces a functional enzyme that gives the phenotype, in this case a particular glycolipid attached to an RBC.  A or B alleles that have mutated to yield dysfunctional proteins that no longer function as glycosyl transferases are recessive.  Recessive alleles don’t impact phenotype.  O antigen is nothing more than the original unmodified H oligossacharide.

ABO Is Bizarre because A and B Code for Two Alternative Functional Enzymes - Codominance

Multiple mutations converted an allele that coded for a glycosyl transferse into a second allele that transferred a different sugar.  A and B alleles code for two different glycosyl transferases that transfer two different sugars.  The result is codominance.  AB individual have both enzymes and produce both A and B antigens on their RBCs.  This is very unusual and inconsistent with Mendelian genetics.

AB Glycosyl Transferases Are in the Golgi to Produce Oligosaccharides for Export

Part of the peculiarity of the ABO system derives from the action of the A and B glycosyl transferases in the Golgi.  Proteins destined for secretion have a hydrophobic group of amino acids, the signal peptide, that is synthesized first as a messenger RNA is translated into protein on a ribosome.  The signal peptide orchestrates binding of the ribosome to the endoplasmic reticulum (ER) and the growing polypeptide is extruded into the ER.  A series of vesicle budding and fusing events transfers proteins to the lamina of the Golgi apparatus and a final fusion event with the cytoplasmic membrane results in secretion.

Specific enzymes retained in the ER and the Golgi recognize particular amino acid sequences and attach sugars to exposed hydroxyl of amino groups (O or N glycosylations).  The ABO antigens are a little unusual in that the oligosaccharide is attached to a lipid anchor, so that the A and B glycosyl transferases localized in the Golgi attach terminal sugars and the glycolipid remains bound to the cytoplasmic membrane and is displayed on the surface of the RBC.

RBCs Don’t Have Nuclei, ER or Golgi, but Normoblasts Do

Mammalian RBC’s don’t have nuclei, because the nuclei were expelled during RBC development.  Since the ER is an extension of the outer membrane of the nucleus and the Golgi is derived from the ER, it follows that RBCs don’t have any of these structures.  RBCs are just collapsed bags of ribosomes, hemoglobin mRNA, cytoplasmic enzymes, a few mitochondria, lots of hemoglobin and stiffened membranes displaying ABO oligosaccharide antigens.  The ABO antigens were assembled and displayed on the membrane before the loss of the nucleus.

ABO Antigens Are Also on von Willebrand Factor of Endothelial Cells and Platelets

I have never heard a good explanation of why a transfusion from a universal, type O donor to recipients with type A, B or AB blood doesn’t cause clumping of RBCs.  The galactose and galactosamine sugars that decorate B and A RBCs also commonly decorate the surfaces of bacteria.  The immune system is prevented from making antibodies against its own antigens and so it only produces antibodies against A or B antigens found in bacteria, if they are not own self RBCs.  Type O individuals lack A and B antigens of their own, so they produce anti-A and Anti-B against bacterial oligosaccharides.  So why don’t the anti-A and anti-B antibodies in type O blood serum clump type A or type B blood?

The answer is that a serum protein, von Willebrand Factor (vWF) is also decorated with the ABO oligosaccharides.  A type A person has type A vWF and a type B person has type A vWF.  Thus, the antibodies against A and B oligosaccharide antigens that are present in type O blood will be inactivated by binding to the A or B oligosaccharides of the recipients vWF.

vWF is synthesized by endothelial cells that line veins and arteries.  It is present in the secretory Weibel-Palade bodies of endothelial cells.  It is also present for secretion by platelets.

So, the ABO blood group antigens are very strange examples that are not protein, not Mendelian and are not even predominantly found on RBCs.  The AB oligosaccharides do provide good examples of the use of activated intermediates in macromolecular synthesis, the origin of organelles, secretion, erythropoiesis and immunology.

Last Week of the Eades Cure

Week 6 of The 6 Week Cure for the Middle-Aged Middle

It feels like I have established a new set point ten pounds lower than my start.  I dropped ten pounds easily in the first two weeks and then bounced around plus or minus two pounds for the next month.  The Cure is simple and effective.

The First Weeks of The Cure

The 6 Week Cure for the Middle-Aged Middle was written by Drs. Mary Dan and Michael Eades to efficiently lose abdominal visceral fat and tone the abs.  It starts with two weeks of three whey protein/cream/leucine shakes and one high fat/protein-low carb veggie meal per day.  This surprisingly tolerable regime (without all but essential medications, no alcohol and no grains) helps to reduce fatty liver and use up visceral fat around the abdominal organs.  I noticed the impact immediately and lost about a pound a day.  This also eliminated hunger and exposed snacking habits.

The Middle Weeks of The Cure

The second two weeks of The Cure permits occasional alcoholic beverages and three low carb meals per day, but without dairy.  That is basically meat/fish/eggs and low carb veggies for each meal.  Most calories were from fat rather than carbs.  Portion control became a new issue, but hunger was still not a problem.  The meals were very satisfying.  Energy for exercise returned, but weight loss ebbed.  It was harder to stay away from old snacking habits, since meals were back to a more normal pattern.

The Last Weeks of The Cure

During the last weeks of The Cure there is a final turn to what may be for some a new, low carb, higher fat eating style.  I chose The Cure, because I already knew that the eating philosophy of the Drs. Eades was consistent with my own anti-inflammatory diet and lifestyle.  I did not expect to be surprised by The Cure, but I was.  I learned a lot about my own eating habits.

Gut Flora Matter

I started The Cure, because I thought that the progression of dietary components would destabilize my gut flora and simultaneously destabilize my weight set point.  I anticipated that my gut flora would reorient, and they did.  There were all kinds of changes and some of the weight loss and gain was probably elimination of a pound of gut flora and reestablishment of a new bacterial order.  The new order also came with a lower body weight.

Hunger Comes with Carbs

For the first month of the diet, I was only hungry if I went longer than six hours without eating or if I slipped on the diet and introduced some extra carbs.  Straight protein early in the morning can cause an insulin rise and a blood sugar dip that leads to a little hypoglycemia, but it produces dullness, rather than hunger.  The only problem with the easy weight loss first two weeks, was that there was less energy with the protein shakes.

BMs Are Bacterial Motivated

The noticeable changes in bowel movements during The Cure, should have been expected, but they forced me to contemplate stools.  When I first realized the absurdity of eating breakfast cereals, because of their high carb/grain content, I went in search of alternative day-starters in other cultures.  At that time, I was still hesitant to embrace saturated fats, so I ran across salsas and stewed tomatoes.  The addition of stewed tomatoes to my breakfast (usually stewed tomatoes on a poached egg) made my gut happy and regular. 

The point in this context, is that my studies of BMs and constipation brought pectin to my attention again.  I had previously considered pectin (poly galacturonic acid) as a competitor for biofilm acidic polysaccharides, but in this context pectin is also recommended to aid the development of probiotic biofilms.  Thus, I added apples to The Cure, to help the establishment of a new bacterial order.  The rapid result was a return to a happy, regular gut.  This was the duh moment.  Apples = pectin, tomatoes = pectin, and pectin = happy gut flora.  Adding either apples or tomatoes to your diet can make your gut flora happy.  An apple (or tomato) a day keeps the antibiotics away.

The Cure Works

The Cure did what I expected and more.  My wife was also pleased with the rapid initial weight loss and an ongoing loss of about a pound per week.  The continued loss is due to alteration of diet with a further reduction in carbs.  The Cure makes the connection between weight retention and a high carb diet.  Elimination of grains/starch makes weight loss much easier.  Absence of sugar, high fructose corn syrup and other sources of fructose also makes weight loss easier.  The inclusion of saturated fats and elimination of omega-6 vegetable oils is anti-inflammatory and provides an improved sense of well being.  I recommend The Cure, because it simply works.

Arthritis, Autoimmunity and Arginine Deimidation

Celiac and Antibody Production Against Tissue Transglutaminase as a Model

Arthritis is an autoimmune disease in which the immune system attacks and degrades the connective tissue of joints.  Antibodies against modified amino acids, arginine converted to citrulline, and proteins commonly found in joints, mediate the arthritis disease process.  The development of arthritis mimics the development of gluten intolerance, celiac, in which another enzyme, transglutaminase ( tissue transglutaminase, tTG or TG2) modifies the major gluten protein, gliadin, and antibodies are produced against both modified gliadin and TG2 autoantigen.

Arthritis of Joints Is Like Coeliac of Intestines;  Autoantibodies to Protein Modifying Enzymes

In other articles, I outlined the pathology of gluten intolerance:

• The major protein of wheat gluten, gliadin, contains long stretches of glutamines.
• An intestinal enzyme, TG2, converts the glutamines to glutamates by deamination.
• As TG2 works it binds to gliadin.
• In celiac, the TG2-gliadin complexes are internalized and fragmented to stimulate antibody production against both TG2 and gliadin.
• I think that the internalization and processing for antibody stimulation is dependent on the basic triplet found in TG2.

Arthritis Is Mediated by Autoantibodies to Peptidylarginine Deiminase and Citrullinated Proteins

Parallel to the celiac example, in some forms of arthritis, antibodies are produced against an enzyme that modifies proteins.  In arthritis, the enzyme involved, peptidylarginine deiminase (PAD) removes the terminal nitrogen from arginine (deimination) to produce citrullinated proteins.  Antibodies are produced to both PAD and citrullinated proteins.

PAD Also Has a Triplet of Basic Amino Acids for Internalization

I of course wondered if PAD had the same triplet of basic amino acids, e.g. RRK, that I had found on all other autoantigens and allergens.  Examining the sequence of human PAD in the NCBI sequence databases and comparing to other sequences, I found the basic triplet near the carboxy terminus.  The same or an alternative basic triplet was found in PADs from other mammals.

Autoantigens and Predicted Basic Triplets of Amino Acids Reveal the Cause of Arthritis

Arthritis is an inflammatory disease.  That means that without inflammation, arthritis cannot start and if inflammation is inhibited, arthritis cannot progress.  It is likely that arthritis is the result of chronic inflammation plus a precipitating event, such as joint injury or joint infection.  Alternatively, in a manner similar to Hashimoto’s thyroiditis, in which celiac produces anti-TG2 antibodies that attack the TG2 also produced in the thyroid gland, arthritis may be produced by autoantibodies stimulated in the inflammation of other tissues and spreading to the joints.  Celiac is also a risk factor for arthritis.  Trauma-based inflammation of a joint can also result in migration of Clamydia pneumonia (Cpn)-infected macrophages to the site of inflammation.  Cpn could contribute to joint inflammation and promote immunological presentation of autoantigens and autoantibody production.

reference:
Stenberg P, Roth B, Wollheim FA.  Peptidylarginine deiminases and the pathogenesis of rheumatoid arthritis: a reflection of the involvement of transglutaminase in coeliac disease.  Eur J Intern Med. 2009 Dec;20(8):749-55. Epub 2009 Sep 19.

The Eades Cure Week 4

Meals, Alcohol, Caffeine, but no Dairy

I embarked on The 6 Week Cure for the Middle-Aged Middle to drop ten pounds and reveal my 6-pack.  Now in week 4, I am half way there.  I lost ten pounds (from 188 to 178 lbs) and the visceral fat under the muscle of my belly is greatly diminished, but my 6-pack is yet to be revealed.  My wife dropped a couple of more pounds.  Her blood stats also improved: glucose dropped 10, total cholesterol dropped 30, LDL dropped 20 and triglycerides dropped 26.

The Cure Weeks 3&4
The middle third of The 6-Week Cure is more like a normal low carb diet.  There are three meals a day, but dairy is excluded.  Alcohol, limited to two drinks a week and caffeine (dash of cream, no sugar) are OK.  Plenty of no/low carb veggies, but minimal fruit.  I enjoyed the eggs and bacon for breakfast and popped a whole chicken in the crock pot, after slipping some herb-saturated butter under the skin of the breast.  The second day I pierced the surface of a couple of thick steaks with slivers of garlic and grilled them to produce some lusciously browned edges of fat.

Bad Habits and Portion Control
Alas, I had forgotten that the main reason for going on this gut transition diet, was to destabilize my gut flora, so that I could more easily change my metabolic set point to lose some visceral fat.  I apparently succeeded, because after a couple of days my weight had very easily increased again.  I was clearly taking in too many calories and there was little resistance to weight loss or gain.  During the first two weeks on protein shakes, it was easy to eliminate bad snacking habits and carbs, but the return of normal meals in the 3rd and 4th weeks, made portion control harder.  Before the diet, I would have a poached egg with two strips of bacon.  The Cure version had crept up to two fried eggs, two strips of bacon and a sausage patty.  I was satisfied, but it wasn’t a cure for the middle-aged middle.  The harsh lesson, was that portion sizes still matter.

Energy for Exercise
More normal meals also meant a return of energy and an interest in exercise.  I had only a few times when I felt that my low carb/ high protein & fat meals, stimulated some insulin and lowered my blood sugar.  Common sense prevailed.  I limited my portion sizes, enjoyed coffee and occasional drinks.  I also started walking three miles a day watching the construction for the new community college along Indian Creek.  Another interesting result was my weight training.  I started testing my strength and found that for the first time in forty years I could bench press and crunch my weight, and I could squat twice my weight.  Hand stands and pull ups were also much easier with less weight and more strength.

Altered Gut Flora
Absent PCR tests of my gut flora rRNA genes, I have to settle for empirical changes.  My diet is still predominantly protein and fat, and I haven’t put back as many veggies as The Cure recommends.  [It is winter in Idaho and the veggies in the market are not that appealing.]  That also means that my gut flora are not getting very large meals either, so my stool volume has been cut about in half, compared to before The Cure.  The largest impact is the impression that I can gain or lose weight with each meal.  That makes further weight loss to remove the baby fat covering my 6-pack very approachable.  Unfortunately, I can just reach out and ... feel it jiggle.

Constipation, Gut Flora and Health

“If you notice your bowel movements, they are unhealthy.”

Scatological jokes are common. The guide on my Swedish language tour of Moscow in 1976, told a joke about Russians.  She described Russian toilets that are dry, with a shelf for stools to drop upon and a lower hole in the back into which the stool is swept with water.  This was contrasted to Western toilets that partially concealed the stools as they dropped into water.  The joke was that Russians had no art, because they could easily observe their creations each morning.

You Are What You Eat and the Proof Is in the Toilet

Refer to Mr. Monastyrsky for a broad discussion of constipation and stool characteristics.  This web site has lots of information about stool types, how to get them and how to change them.  His recommendations to avoid constipation center on a healthy diet, like my Anti-Inflammation Diet, plus glutamine to help the gut heal.

Another useful perspective on gut flora is provided by a Nature web site on gut flora genomics. This site describes genomic research to show that changing diet changes relative proportions, but not the types of bacteria in gut flora.  Each person has a recognizable, individual composition of gut bacteria.

Feces Is Primarily Bacteria

What you eat and your eating/health history determines your gut flora, and feces is made up of gut flora and some undigested food.  Healthy bowel movement stools are made up of more than 50% bacteria and the consistency of the stools is determined by the bacterial content.  Less bacteria means drier, harder stools.  Bacteria hydrate stools and prevent constipation.

Pathogenic Gut Flora

Why does a total bowel irrigation with PEG, polyethylene glycol, make people with chronic diseases feel as good as if they had an antibiotic treatment (barring die off)?  I think that the answer is that both disrupt and change the gut flora and in many cases disease symptoms are supported by an unhealthy gut flora/biofilms.  In many cases, the antibiotic cannot have a lasting impact, because it is hard to kill bacteria in biofilms.  PEG may actually clean out more of the biofilms, because it should also disrupt the polysaccharide matrix of the biofilms.

Disruption of Gut Flora Leads to Disease

Babies fed breastmilk vs. formula display very large difference in inflammation and susceptibility to disease.  Formula causes gut inflammation and susceptibility to intestinal and respiratory diesease.  Formula also causes a dramatic shift in gut flora from a simple flora dominated by Bifidobacter to a complex adult gut flora. 

Gut Controls Immune System

The impact of the two different gut flora on development of the GI tract and on the newborn immune system is dramatic also.  Remember that most of the immune system of the body is located in the lining of the gut and immune organs, such as the tonsils, are outgrowths of the GI tract.  The thymus, which is responsible for producing T lymphocytes, is twice as large in breastfed babies.  Thus, feedback from the gut of formula fed babies inhibits thymus and immune system development.

Change Your Gut Flora and Change Your Health

Experiments in mice, and I think in humans, have shown that changing the bacteria in the gut changes interactions with food.  Exchanging gut bacteria between fat and lean individuals, causes fat people to lose weight and lean people to gain weight.  I think that this indicates that gut flora participate in the so called metabolic set point, that determines if it is going to be easier to gain or lose weight.  These experiments suggest that a powerful approach may be to eliminate the gut flora of individuals with chronic disease and replace it with healthy gut flora.  This healthy gut flora, along with a healthy diet may make a powerful contribution to elimination of chronic diseases.  Rosacea, which involves both the face and gut, might best be treated by topical antibiotics and anti-inflammatory agents, after the gut contribution has been eliminated by a fecal transplant with healthy gut flora/diet.

Anti-Inflammatory Diet Should Support Healthy Gut Flora

The efficacy of an anti-inflammatory diet (AID) should be displayed in reversal of inflammatory symptoms and unmemorable bowel movements.  A gut and gut flora that resist inflammation as a result an AID, should also produce a healthier immune system and contribute to a reduction in chronic inflammation and disease.  The gut may also have an impact on gut flora and a diet that does not contribute to inflammation in the body, e.g. lacks fructose and vegetable oils, may also support an anti-inflammatory gut flora.

Cure for Middle-Aged Middle

My First Two Weeks with the Drs. Eades Diet

The Drs. Eades (Mary Dan and Michael) see eye to eye with me on the health benefits of a low carb diet for avoiding chronic inflammation, the foundation of most degenerative and autoimmune diseases and cancers.  Recently they applied their clinical experience with the diets they developed to combat obesity to produce a book that focused on the protruding gut:  The 6-Week Cure for the Middle-Aged Middle:  The Simple Plan to Flatten Your Belly Fast!  That book seemed to be a great way to introduce most people to a healthy diet based on obtaining calories from fat rather than carbs, so I featured it as the recommended book on my blog for the last several months.  Two weeks ago my wife and I decided to practice what I preach and started The Cure.

The Cure Reduces Visceral Abdominal Fat

"The Cure” consists of three, 2-week blocks, that adapt the body metabolism to a new low carb, higher fat diet.  The focus is to reduce visceral fat stored primarily in the abdomen.  Equally important, from my perspective, are the changes that take place in the gut flora -- The Cure changes the composition of the gut flora to facilitate change in body fat and to restore complete function to the immune system.

Basic Outline of The Cure

The first two weeks of The Cure consist of three protein shakes (low carb flavored whey plus cream) and a very low carb meal each day.  Weeks 3 and 4 are no-carb, dairy-free meals of meat/fish/eggs with calories from fat and protein only.  The final two weeks are the new low carb, higher fat diet.  Research on diet and gut flora would predict that the bacterial species in the gut stay basically the same and provide a recognizable individuality, but the relative quantity of each species in the gut changes to maintain body fat.  The efficiency of the total gut flora would increase, if the diet resulted in weight loss and become less efficient, if there was increased fat deposition.

After the First Two Weeks of Protein Shakes

A diet of protein shakes changed my view of food.  I was simply not hungry and cravings disappeared.  My wife was shocked that she felt satisfied after drinking a shake and did not panic without snacks or seconds.  It was relatively easy to eliminate most of the bad eating habits associated with weight gain.  There was no problem about portion sizes or eating outside of meals.  All of the bad habits became noticeable and I could see when I normally reached for some food out of boredom.  There was simply no physiological support for snacking.  Hydration is important and bowel movements were irregular as gut flora adapted to the severe change in diet.  [Also note that the milk whey protein used in the shakes is high in lactoferrin, a protein found useful in controlling bacterial pathogens, e.g. Clostridium dificil, and intestinal candidiasis.]

Weight Loss Was Effortless

It was easy to drop some weight on the protein shakes.  My wife (15 lbs) and I (5 lbs) both lost weight easily.  This is significant, since neither of us was able to reduce our weights in the last several years.  My weight at the start was 20 lbs over what I weighed as a high school gymnast.  I didn’t feel like I had a lot of energy in the first two weeks of The Cure, so I slacked off on walking and weight training.  Now that I am into the luxurious second phase with lots of meat, gaining strength by exercising is a pleasure.

Reduced Need for Fish Oil with Altered Gut Flora

Something that I need to highlight and that I attribute to the change in my gut flora, is a lowered need for fish oil.  I was taking four fish oil capsules per day, to eliminate minor aches in my fingers.  After the first two weeks of The Cure, without vitamin D supplements or fish oil, I still don’t have any finger aches. My wife, also no longer needs fish oil to make our 3-mile hikes along Indian Creek painless for her knees. The Cure seems to have uncovered a remaining source of inflammation in my previous diet.    The most likely inflammatory candidate was the small amounts of grain and starch still in my old diet.  It will be very easy for me to transition to a new anti-inflammatory diet more consistent with the one I have been advocating on this blog.  I think that the anti-inflammatory diet would be a simple, healthy and enjoyable way to avoid most diseases or as an essential part in the treatment of most degenerative and autoimmune diseases and cancers.

My thanks go to the Drs. Eades for creating a smart diet sequence that alters gut flora for loss of visceral abdominal fat and provides a transition to a healthy low carb, increased fat diet.  The diet sequence may also be useful in restoring gut flora destroyed by antibiotic use or dysbiosis indicated by constipation.

Rosacea, Brain Cooling and Niacin Flush

Other players include:  Cathelicidins, Prostaglandins, Cryptic Bacteria, Nerves, Gut

What does it take to make your face red?  Excessive solar exposure can lead to apoptosis of skin cells overloaded with DNA damage and trigger inflammation: vasodilation, recruitment of neutrophils, swelling, etc.  Similarly, a local infection can cause inflammation and the accumulation of neutrophils (see The Inner Life/Extravasation for slide show), lymphocytes, etc., that is observed as pus.  These are general responses that occur in skin anywhere, but the face also blushes in response to emotional cues and flushes with exercise.  Rosacea seems to involve all of these reactions to produce a variety of symptoms of wide severity.  Here I try to provide an overview of the complex physiological interactions involved in rosacea.

Rosacea is Persistent Vasodilation of the Face with Accumulation of Neutrophils

The nervous and circulatory systems of the face are unique and provide numerous triggers for inflammation.  Emotional blushing is a common trait among those who progress to rosacea, even though this type of vasodilation is not easily observed with some facial characteristics.  Thus, many rosaceans claim to have never flushed before their first outbreak, but tests of skin circulation indicate that these individuals had skin types that prohibited display of the blushing.  The face is also adapted to control brain temperature, so changes in body temperature, physical activity, etc. can also trigger flushing.

Facial Blood Circulation to Cool the Brain

The cooling of the blood as it traverses the facial skin is used to cool the brain during extensive exercise or in warm environments.  This unique adaptation also means that control of facial vasodilation can potentially be disrupted in disease and cause symptoms of pathology.  In rosacea,  the brain cooling response is disturbed (see reference below), resulting in persistent vasodilation and suggesting that the unique control of inflammation in the face is why rosacea is limited to the face.  The pattern of blood circulation in the face, however, only roughly approximates the inflammation pattern in rosacea.

Nerves to the Face

The face receives sensory branching from the trigeminal nerve.  The enervation pattern of the branches matches emotional blushing, but they also appear to approximate the pattern of reddening in rosacea.  It makes sense that rosacea involves nerve-triggered dilation of the blood vessels of the face.  One contrast between emotional blushing and rosacea is that emotional blushing does not lead to the offloading of lymphocytes, whereas rosacea produces localization of neutrophils that exacerbate and prolong inflammation.

Cathelicidin, Vitamin D Receptor, DNA Complexes, Autoinflammation

A major component of the innate immune system is the group of basic antimicrobial peptides, cathelicidins.  Cathelicidins are effective against bacteria and they are produced during inflammation and are partially controlled by the vitamin D receptor acting as a transcription factor.  Thus, part of the action of vitamin D in providing protection against disease is by enhancing cathelicidin production.  Cathelicidin action in the skin parallels the control of intestinal villi development by defensins, that are also basic antimicrobial peptides under the control of vitamin D.  Cathelicidins also form complexes with host DNA from damaged cells.  These cathelicin/DNA complexes bind to toll-like receptors (TLRs) and trigger inflammation.  This reaction has been associated with psoriasis and may explain how neutrophil damage can perpetuate inflammation in rosacea.

Niacin Flushing Implicates Arrestins

The unique circulatory system of the face also makes it susceptible to flushing with niacin, a.k.a. nicotinic acid or vitamin B3.  Niacin is cheaper and much more effective at raising HDL and lowering triglycerides and LDL than statins, but is not fully utilized because it also produces intense facial flushes.  A recent article (below) has demonstrated that the lipid benefits can be separated from the flushing and implicated beta-arrestin 1 activation by niacin binding to GPR109A (G-protein-coupled receptor) as the triggering event.  Arrestin, which is involved in clathrin-mediated endocytosis, activates phospholipase A2 that in turn releases arachidonic acid (ARA) from phospholipids.  The ARA (that got into the phospholipids as the omega-6 fatty acid in vegetable oils) is converted by COX-2 into the inflammatory prostaglandin D2.  This prostaglandin is what stimulates vasodilation.  It is possible to produce chemicals that will stimulate the lipid metabolism alterations of niacin, without producing the arrestin activation and inflammation.  Aspirin can be used to inhibit COX-2 and other parts of NFkB-mediated inflammation and eliminate the niacin flush.  It is also interesting that the modified lipid metabolism of schizophrenics also eliminates niacin flushing.  Salicylic acid, the same as the acetylsalicylic acid of Aspirin without the acetate, is also used in some topical applications to quiet the symptoms of rosacea.  Arrestin activation may be involved in rosacea.

Gut Flora, Biofilms and Cryptic Bacteria

The gut is probably involved in most cases of rosacea and bacteria are also implicated by the modification of rosacea symptoms by antibiotics.  This area has not been explored, but I suspect that gut flora controlled by diet, as well as pathogenic biofilms and cryptic bacteria, e.g. Clamydia pneumoneae, in facial tissue are involved in varying degrees in the panoply of pathologies called collectively, rosacea.  Since the bacteria in contact with the gut determine the development of the lymphocytes in the lining of the gut, e.g. Tregs vs. T cells that fight infections, pathogenic gut biofilms may disrupt the normal function of the immune system and support rosacea.  Die off and release of cell wall endotoxin from cryptic bacteria could explain the paradoxical inflammation in response to many treatments that are normally anti-inflammatory.  I have discussed in another article potential approaches to strip off biofilms.

Treatment with Anti-Inflammatory Diet

The Anti-Inflammatory Diet (AID) and Lifestyle that I advocate on this blog would seem to be a natural cure for rosacea.  It should eliminate the inflammatory background that supports rosacea and was probably essential for its development.  This diet also eliminates acne, which is directly related to the accumulation of lymphocytes to make pus.  Inflammation is also needed for the offloading of neutrophils that exacerbate inflammation in rosacea.  Vitamin D is instrumental in cathelicidin production to eliminate cryptic bacteria. 

In most cases of rosacea, the AID should be helpful.  Eliminating dietary sources of inflammation, especially vegetable oils (the source of omega-6 fatty acids that are converted into inflammatory prostaglandins), should reduce rosacea symptoms.

In advanced, severe cases, however, it appears that maintenance of the suppression of the response to cryptic bacteria is required to prevent endotoxin-based inflammation.  Thus, most treatments that decrease inflammation, e.g. omega-3 oils, vitamin D3, Vagal maneuvers, can paradoxically produce elevated inflammation.  These treatments may also inadvertantly contribute to inflammation by upsetting pathogenic interactions between bacteria and intestinal cells.  I have discussed these paradoxical ramifications in another article.

references:
Brinnel H, Friedel J, Caputa M, Cabanac M, Grosshans E.  1989.  Rosacea: disturbed defense against brain overheating.  Arch Dermatol Res. 281(1):66-72.
Walters RW, Shukla AK, Kovacs JJ, Violin JD, DeWire SM, Lam CM, Chen JR, Muehlbauer MJ, Whalen EJ, Lefkowitz RJ.  2009.  Beta-Arrestin1 mediates nicotinic acid-induced flushing, but not its antilipolytic effect, in mice.  J Clin Invest. 119(5):1312-21.

2009: What I Learned Last Year

This year followers of this blog checked in more than 100,000 times to read my 150 articles on diet, inflammation and disease.  I learned a lot and I hope that my readers gained some insights into anti-inflammatory food choices that are helpful in pursuing enhanced health.  Here is a status report.

What We Eat Contributes More to Disease Risk than Genetics

I started this blog to try to understand how food, exercise, sun exposure, etc., contribute to health and disease, because I was shocked that recent, comprehensive studies demonstrated that genetic defects were only minor contributors.  I am trained as a molecular biologist and I search for explanations of disease in terms of the interactions of the proteins coded by the genes in our cells.  History of defective genes that code for defective proteins in sickle-cell anemia, Huntington’s disease or ALS, suggested that personal genetic defects might explain personal diseases.  Fortunately, it appears that in most cases genetic defects only matter when our actions produce chronic inflammation.  What we eat is far more important than our genetics in determining if we are going to suffer from allergies, autoimmune diseases, degenerative diseases, various forms of mental illness or cancer.  If we eat to avoid inflammation, in most cases it doesn’t matter how genetically defective we are.

Diet-Based Inflammation Is the Major Risk

Modern diets rich in starch/sugar/fructose and polyunsaturated fats (omega-6 oils), and deficient in saturated fats and omega-3 oils produce the chronic inflammation that forms the foundation of most diseases.  Vegetable oils, such as corn, soy or safflower oils are inflammatory and should be eliminated from our kitchens.  We should only use olive oil, butter or lard.  Saturated fats from meat, dairy and eggs are healthier than polyunsaturated vegetable oils.  There was never adequate scientific data to justify the shift from saturated fats to polyunsaturated vegetable oils.  That was a tragic, unscientific medical error that contributed significantly to deteriorating health in the developed/developing world.

Anti-Inflammatory Diet and Lifestyle Is the Cure

It came as a surprise to me that simply eliminating inflammatory foods could prevent most diseases.  After diseases have developed, it is harder to reverse the process and return to health, but even in that case, diet is of paramount importance.

Back to Basics of a Healthy Diet (the Food Pyramid Is Wrong)

•   Starch/sugar/fructose are inflammatory.  Low carbohydrate is the healthiest diet.
•   Grains, even whole grains, and especially cereal are a big part of the problem and should be avoided.
•   Fat and not carbohydrates, should be the major source of dietary calories/energy.
•   Saturated fats are healthier than vegetable oils -- use olive oil and butter.
•   Meats/fish (not fed on grains) are healthy.  A healthy vegetarian diet is difficult.
•   Leafy vegetables are a good source of healthful antioxidants.
•   Fruits and fructose are inflammatory and should be eaten sparingly.
•   Healthy gut bacteria are important.  Eat fermented foods with live bacteria, e.g. yogurt.

Living with Inflammation

Chronic inflammation can lead to many problems that diet and supplements can help to remedy.  For example, vitamin D deficiency is an epidemic in America, because chronic dietary inflammation appears to compromise the ability to make vitamin D in the skin with sunlight.  Most individuals eating a diet high in polyunsaturated fats, starch and high fructose corn syrup, are deficient in vitamin D and would benefit from a vitamin D3 supplement of at least 2,000 IU per day.  Vitamin D deficiency also contributes to inflammation.  Fish oil supplements can also help to reduce dietary inflammation and should always be taken with at least equal amounts of saturated fats in the same meal.

Resolve to Eat Your Way to Health

It is easy to avoid most diseases by avoiding dietary inflammation.  Since chronic dietary inflammation produces depression, lethargy, obesity and a lack of energy, a healthy anti-inflammatory diet will also lead to weight loss, increased energy and reduced symptoms of aging.  Most symptoms of aging and disease are actually poorly managed inflammation that exposes genetic defects.  Most people increase in inflammation with age, but proper diet can avoid this risk to health and prolong youthful activity.    The healthiest resolution for the new year is to stop eating blatantly inflammatory foods (starch and vegetable oils) and start eating more spicy meats, fish and leafy vegetables.