biofilm RNA seed - Holistic Family Dentistry Steven N. Green, DDS


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biofilm RNA seed - Holistic Family Dentistry Steven N. Green, DDS

  1. 1. BIOFILM – OUR SUSTENANCE, OUR SIGNIFICANT OTHER, OUR SOURCE<br /> Bacteria account for much of Earth's biological diversity. These small life forms play essential roles in quite varied environments and we are experiencing an awakening in understanding about the underlying importance of bacterial biodiversity, and how intertwined they (and we) are. <br /> Advances in molecular biology have provided astonishing insights into microbiological pleomorphic variety, considerably improving our knowledge of the ever-changing morphological, physiological and ecological features of our life partners, who mostly exist as colonial bacterial species in interactive community enveloped by a mist of our ever-present shared viral as well as naked viroid DNA and RNA.<br /> Bacteria had been mostly examined and thought of by us as unchanging monomorphic individual free-swimming species, captured and studied in their planktonic form. When these bacteria are grown in culture, growth medium must be freshened daily in order for the organisms to maintain their characteristics. When cultured in unchanged medium, bacteria begin to pleomorphically alter their form and physiology depending on their new environment due to gradient changes in their surrounding waste products and remaining nutrients. <br /> More importantly, 99% of all microbial species from most environments are ordinarily unculturable. Microbiology as a discipline has traditionally focused by necessity on the 1% of cultivable species.  Attempts to culture more species in the lab by manipulating growth media have historically failed.<br />Studying a bacterium in isolation and understanding the biofilm is like trying to study a caged animal in a zoo or defining the human experience by studying a single sperm cell.<br /> In nature, 99% of bacteria live in structured biofilms, a kind of cooperative multi-cellular life form, exhibiting many sophisticated survival strategies. As an organism composed of many integrated microorganisms, it creates a small percentage of low-metabolism ‘persisters’ and exhibits hormetic response to stressors, eliminating the weak cells within via apoptotic signaling, becoming globally more resistant to death. Whatever does not completely eliminate biofilm makes it better able to survive. <br /> Pseudomonas aeruginosa, a biofilm-forming microorganism, is probably the most common life form on the planet, as we animals and plants thrive, blanketed with our characteristic bacterial colonies. <br /> Cultured bacterial biofilm phenotype characteristics cannot be predictably correlated with the clinical virulence of similar phenotypes (for example, E. coli isolates) living in the host within their biofilm. The overriding influence of local environmental conditions provided by the host underscores the challenge in developing better biofilm model systems to copy clinical situations (from cloudy contact lenses to tooth decay, periodontal diseases, bacterial endocarditis, cystic fibrosis lung infections, avascular necrosis and other non-healing wounds or implants as well as infections of joint synovia, nasopharynx, digestive system or urogenital tracts).<br /> The goal of current microbiology research is to understand the molecular nature of uncultivability as well as find new microorganisms. Roughly a third of bacterial domains do not have a single cultivable representative. We know of their existence only from DNA recovered from the environment. Today the latest PCR (polymerase chain reaction) DNA tests imply that most chronic illness is really due to biofilm infection, no matter what the cultures said.<br /> For example, the reverse transcriptase-PCR–based assay system can detect the presence of bacterial mRNA in many culturally ‘sterile’ middle ear effusions. Bacterial mRNAs have a half-life measured in seconds to minutes; therefore, detection of bacteria-specific mRNAs is evidence that metabolically active organisms are present. <br /> Careful adjustment of growth medium composition is an important first step. Incorporation of more adequate attachment surfaces in the experimental design is an added measure; perhaps studying biofilm formation directly on eukaryotic cells will help. <br /> However, since multiple species are present in most natural environments, we also need models that allow monitoring of possible antagonistic or synergistic interactions between community members (and even these copies cannot take the state of an individual host’s immune system into account). <br /> A diffusion chamber has been designed for growing unculturable organisms. A simulated natural environment is provided by growing microorganisms in a chamber that allows exchange of chemicals with the environment, but restricts movement of cells. Many unculturable organisms will grow on synthetic media in the presence of other, neighboring species that release substances that act as growth promoters. Lack of bacterial growth on foreign media seems to be due to ‘choice’, rather than a missing metabolic ability.<br />Biofilm Formation<br /> Biofilm becomes a collaborative community of sessile microorganisms now expressing different genes, becoming metabolically distinct from their free-living, planktonic kindred. First bacteria become attached, and then they accumulate, mature and then eventually detach to reproduce elsewhere. At either extreme, nutrient-rich or very nutrient-poor conditions, greater numbers of cells exist in the planktonic phase where they have greater access to local nutrients or can be distributed to a new environment.<br /> The cryptic bacterial infection hypothesis holds that, many, if not all chronic diseases are initiated by inflammatory events that release bacteria into the blood stream that become carried in phagocytic cells. The cells migrate and take up residence at a region of inflammation. The bacteria produce molecules that produce tissue hibernation and quell local inflammation in response to the bacteria. The bacteria are, however, a source of ongoing irritation to the tissue and a chronic inflammatory disease results.<br /> The compromise of tissue inflammation in response to cryptic bacteria is similar to the physiology of rodent hibernation. In both cases, systemic inflammation is suppressed. At the cellular level, this means that other signaling pathways silence the inflammatory NFkB expression pattern. One of the major nuclear receptors activated in hibernation is PPAR. PPAR is activated by opiods and sulfides (H2S), which also induce hibernation in rodents.<br /> An initial priming step in the biofilm forming process before attachment occurs. This describes an initial interaction of the surface with its environment and is called conditioning. Conditioning happens, for example, when a foreign body is placed in the bloodstream and the natural endothelial surface of the vessel is altered by the adsorption of water, albumin, lipids, extracellular matrix molecules, complement, fibronectin, inorganic salts or toxins. Once a surface has been conditioned, its properties are changed, so that the attraction of a circulating organism for a normal or a conditioned surface can be very different.<br />  Free floating or planktonic bacteria encounter a surface and form a reversible, sometimes transient attachment, often within minutes. This attachment called adsorption is influenced by electrical charges carried on the bacteria, by Van der Waals forces and by electrostatic magnetism (although the precise nature of the pull is still debated). Van der Waals forces include attractions between atoms, molecules and surfaces, differing from stronger covalent and ionic bonding since they are caused by harmonic correlations in the frequencies of fluctuating polarizations of nearby particles (a vibrational effect of quantum dynamics).<br /> In some cases, as in the connection between a pathogen and the receptor sites on cells of its host there may be a stereo specificity which though still reversible, is stronger than that achieved strictly by ionic or electrostatic forces. <br /> A net repulsion between two surfaces can be overcome by specific molecular interactions orchestrated by adhesins located on structures extending from the bacterial cell surface, such as pili (sticky hair-like appendages bacteria use to adhere to surfaces). The longevity of primary adhesion depends on the sum total of all variables, but surface chemistry pushes the equilibrium in favor of binding by predicting that organic substances in solution will concentrate near a surface and that microorganisms tend to congregate in nutrient-rich environs.<br />Viruses change bacteria.<br /> Virus can enter bacteria via their pili. Pili are likely culprits since bacteria that lack them are rarely pathogenic. Viruses then take over the cell and can cause normally benign bacteria to manufacture toxin. Perhaps even pili themselves are expression of transmissible DNA, a viral infection turning a friendly commensal without pili into a potential pathogen with pili, increasing stickiness and opening the door for still more viruses.<br /> If the association between the bacterium and its substrate persists long enough, other types of chemical and physical structures form which transform the reversible adsorption to a permanent and essentially irreversible attachment. The final stage in the irreversible adhesion of a cell to an environmental surface is associated with the production of extracellular polymer substances (EPS). <br /> A glycocalyx is the glue that holds the biofilm fast to the colonized surface and is a complex of exopolysaccharides of bacterial origin and trapped exogenous substances obtained from the local environment, including nucleic acids, proteins, minerals, nutrients and cell wall material. Most of the EPS of biofilms are polymers containing sugars such as glucose, galactose, mannose, fructose, rhamnose, N-acetylglucosamine and others. <br /> Bacteria mostly exist in their attached interconnected form with an altered genetic profile and metabolism as part of the fabric of a highly-structured cooperative microscopic city, organized as a sessile sentient organism with sophisticated forms of communication and a group strategy for survival. <br /> Virtually any surface, animal, mineral or vegetable becomes colonized with biofilm formation, including contact lenses, ship hulls, dairy and petroleum pipelines, rocks in streams, as well as all varieties of biomedical implants and transcutaneous devices. Free-swimming bacteria (which are what we capture and culture) are mostly reproductive cells that are released from an established biofilm community that has become mature, stressed or crowded.<br /> A dispersion-inducing molecule provokes genetic and physiological changes in the biofilm bacteria, causing them to disperse and return to a planktonic state. The dispersion autoinducer now being researched by David Davies (a halogenated furanone) has been effective in dispersing biofilms containing Pseudomonas aeruginosa, Escherichia coli, Streptococcus mutans and Staphylococcus aureus, whether those bacteria exist in a pure or mixed-culture biofilm. A surface protein-releasing enzyme (in Streptococcus mutans) becomes actively involved in the degradation of attachment polymers on tooth surfaces, releasing planktonic bacteria into the surrounding liquid.<br /> This is one of the few known examples anywhere in nature of a communication signal that remains effective across species, family and phyla. Davies predicts the compound may also prove to have communicative effect even across bacterial kingdoms. Since bacteria become easier to kill in their planktonic state, this molecule shows promise in treatment of non-healing wounds.<br /> Biofilm formation relies heavily on virus genes present within the bacteria, some injected by viral bacteriophages. Viruses are made mostly of protein and RNA or DNA and ‘live’ primarily to inject their message into a functioning chromosome, and then take over the cell’s metabolism and make the cell’s physiology start working for the invading virus. <br /> A protein within bacterium called Hha has the ability to control whether virus genes are kept within the organism or unloaded. When Hha is basically “turned on,” bacteria expel virus genes, opting for motility over the ability to form biofilms. Likewise, when Hha is not expressed, bacteria move slower, but grow biofilms at a much faster rate. The viral prophage (CP4-57) helps its host to attach to the surface to form a biofilm, and also helps to generate and promote diversity inside the biofilm community.<br />Viruses participate in biofilm too.<br /> The genes of E. coli have been sequenced and they contain nine or ten viral remnants that no longer function as virus. Usually a bacterium will discard genes that it no longer needs, but in this case this life form did not dump these leftover viral genetic fossils. E. coli has kept these tools that encourage survival of its colony. These tools allow the cell to dismantle itself, preserving useful parts via apoptosis. This allows some planktonic cells to escape threatened biofilm or it can possibly protect itself by partly dismantling, shrinking and entering a spore-like hypometabolic hibernation state for long-term survival.<br /> Bacteria in biofilm are connected to each other by a polymer, DNA, sucrose or protein. In order for some reproductive cells to be released when conditions change, others near the surface must die by apoptotic programmed cell death, where useful cellular parts are reclaimed. <br /> Another reason for the bacterium to keep and utilize viral DNA in order to commit apoptosis (kill itself) is that when another virus attacks that particular cell it can eliminate itself ‘altruistically’ via cell suicide before the infecting virus can take over its cellular machinery, replicate, multiply and spread its viral progeny to the entire biofilm colony.<br /> Perhaps antibiotics do not primarily kill cells; more often metabolic derangements produced by antibiotics actually trigger apoptotic suicide. The strongest argument for programmed death of defective cells comes from the finding of genes (such as hip, vncS and sulA) that dramatically affect survival to antibiotics without changing growth susceptibility.<br /> Antibiotics are low molecular weight products of bacteria and fungi that have long been used as treatments for infectious and other diseases. It seems that these compounds have quite different roles in the environment compared to therapeutic applications. The difference lies in the available concentrations that determine inhibitory activity compared to transcription modulation. Low concentrations may be responsible for cell-cell signaling activity in microbial communities.<br /> In flowing cold mountain streams, there might be only nine bacteria floating in a milliliter of water, but a hundred million live in structured harmony in one square centimeter of biofilm slime covering the rocks over which the water rushes. Attachment is possible because of catch bonds, which are noncovalent biological adhesive bonds with the counterintuitive property that they are longer-lived when mechanical force is applied to pull them apart. <br /> A bacterial adhesive protein called FimH forms catch bonds. Bacteria binding through FimH will only bind firmly at high levels of fluid flow, and will roll across the surface or detach if the flow is stopped. FimH is expressed on most of our intestinal bacteria and is involved in urinary tract infections.<br /> Each person, each animal and every plant or rock provides ecological niches for its own characteristic symbiotic, interactive and mostly beneficial microflora communities. A tree does not stand alone. It is part of a whole ecosystem of virally, bacterially and insect laden soil containing yeasts decaying organic matter as well as supporting the growth of weeds. Oxygen and carbon dioxide is exchanged. The insects, birds and animals that seek shelter in the tree fertilize it and the soil as well.<br />We are not individuals, but cooperative symbiotic ecosystems.<br /> A typical mobile human host (supporting its ecosystems) consists of roughly a trillion cooperative communicating eukaryotic ceils developed and organized by less than 30,000 genes. Each human also hosts a biofilm which is an assemblage of surface-associated microbial cells enclosed in various organized extracellular polymeric polysaccharide matrices consisting of about 10 trillion communicating cooperative prokaryotic cells, with their roughly 300,000 genes. If we add DNA and RNA viruses as well as yeasts to the number of bacteria, our biofilms may total 100 trillion life forms.<br /> Humans may be seen as super organisms in which many bacterial genomes (forming a metagenome) work in tandem with our own. The NIH has estimated that 90% of the cells in Homo sapiens are microbial and not human in origin.<br /> Perhaps the fundamental problem in our thinking is the concept that human tissue is sterile, free from microorganisms, such as viruses, yeast or bacteria, unless there is overt infection. Part of the sterile assumption derives from the intense inflammatory response to some microorganisms. In order for bacteria to survive in tissue, they escape detection or suppress inflammation and the tissue must tolerate the slow leaching of their inflammatory antigenic molecular metabolic markers.<br /> We can no longer assume that antibodies generated in autoimmune disease are created solely as autoantibodies to human DNA. New evidence shows that the human microbiota accumulates during a lifetime, and a variety of biofilm persistence mechanisms are now understood. <br /> In one model, obstruction of VDR nuclear–receptor-transcription prevents the innate immune system from making key antimicrobials, allowing the microbes to persist. Genes from these microbial biofilms must necessarily impact disease progression. Newly directed efforts to decrease this VDR-perverting microbiota in patients with autoimmune disease have resulted in reversal of autoimmune processes.<br /> Commensal and probiotic biofilms in the colonic mucosa act as a prominent stimulus for epithelial cell development and differentiation, and that cross-talk among bacteria, and between bacteria and epithelium provide fundamental signaling in gut physiology. All mammals are adapted to life in a microbial world and are colonized by bacteria on all their body surfaces at birth. <br /> The stimulation by commensal bacterial antigens is critical for normal development of the mucosal immunity and the maintenance of tolerance. In fact, animals that are kept germ-free from birth have dysfunctional immune systems; development is somehow stunted and their energy requirements are abnormally elevated.<br /> 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 gut biofilms may permit a resumption of effective immunity and remission.<br /> The human vermiform ("worm-like") appendix is a 5-10cm long and 0.5-1cm wide pouch that extends from the cecum of the large bowel. The design of the human appendix is unique among mammals, and few mammals other than humans have an appendix at all. <br /> The function of the human appendix has been a matter of much debate (including its function as an escape-valve for flatus). It is often considered a vestige of evolutionary development despite contrary evidence based on comparative primate anatomy. The appendix seems to have some immune function based on its association with substantial lymphatic tissue, and it can help make, direct and train white blood cells. Its removal increases risk to Chron’s disease, an autoimmune disease, in which the body's deregulated immune system attacks its own gastrointestinal tract, causing inflammation; it is classified as a type of inflammatory bowel disease.<br /> Based (a) on a new understanding of immune-mediated biofilm formation by commensal bacteria in the mammalian gut, (b) on biofilm distribution in the large bowel, (c) the association of lymphoid tissue with the appendix, (d) the ability of biofilms to protect and support colonization by commensal bacteria, and (e) on the architecture of the human bowel, it seems that the human appendix functions as a "safe house" for commensal bacteria. It provides support for commensal bacterial growth and for potential re-inoculation of the colon in the event of purging of its contents following exposure to a pathogen.<br />Immune recognition of friend and foe<br /> Innate cellular immunity has generally been considered a non-specific immune response characterized mainly by phagocytosis.  However, we now know that innate immunity has substantial specificity, and is capable of discriminating between individual species of microbes.  Pathogens “seen” as dangerous to the host elicit an inflammatory response capable of destroying the microbes, while commensals do not bring forth such a response and their survival is tolerated or even encouraged by the host. <br /> This immune discrimination is attained through the recognition of multiple microbe-specific surface molecules by pattern-recognition receptors (PRRs) present on mucosal cells.  There are several types of PRRs including the nucleotide binding oligomerization domain family of proteins (Nod1, Nod2), Toll-like receptors as well as the receptors for complement, glucans and mannose.  <br /> Innate immunity specifically recognizes molecular patterns of microorganisms through Toll-like receptors (TLRs) and other pattern-recognition receptors, and use of pattern-recognition receptors helps regulate the development of antigen-specific adaptive immune responses. TLR-dependent recognition of commensal bacteria is required for reducing inflammation and maintenance of immune intestinal homeostasis.<br /> The PRR-recognized molecules on the microbes include surface proteins, nucleic acids and carbohydrates (e.g., lipopolysaccharide, peptidoglycan, lipoteichoic acids) and host factors that bind to the microbial surfaces include complement fragments and salivary components.  Such “patterns” are called microbe-associated molecular patterns (MAMPs) and the innate immune system is thought to recognize at least 1000 MAMPs.  MAMPs include molecular patterns of commensals and pathogens (PAMPs).<br /> Pattern-recognition receptors interactions with pathogen microbe-associated molecular patterns trigger a complex set of intracellular signaling cascades that ultimately result in expression of antimicrobial factors as well as pro-inflammatory molecules.  These responses include activation of complement, coagulation, phagocytosis, inflammation and apoptosis.  <br /> In addition, the innate immune system assists the adaptive immune system in recognition of microbial antigens and production of a robust antibody response.   Dysfunction in the discrimination between oral or digestive commensal and pathogenic microbes could lead to either an ineffective immune response and infection by relatively harmless microbes, or a hyperactive immune response characterized by inflammation and host tissue destruction. <br /> Among the adaptive immune cell populations in the intestinal mucosa, the best-characterized cells are the secretory IgA-producing plasma cells. Normal intestinal mucosa contains abundant SIgA-secreting plasma cells, and the secreted IgA plays a critical role in the host defense against pathogenic bacteria. More importantly, SIgA regulates the ecological balance of commensal bacteria. SIgA and the mucus of the large bowel may actually be involved in pro-microbial activity.<br /> EpiCor (dried yeast fermentate) can boost levels of secretory IgA (the crucial immunoglobulin that coats mucosal pathways like mouth, nose and eyes) thus reinforcing your body’s defense against invaders before they even enter your body. At the same time, EpiCor also enhances circulating natural killer (NK) cells’ ability to destroy harmful pathogens with both speed and efficiency. It also provides significant antioxidant protection and safe, natural inflammation control.<br />Colonizing communication chemistry<br /> Quorum sensing genes respond to signals from numbers of bacteria present and environmental changes as well as respond according to influences from ever-present local RNA’s interpretation of the environment, and cause the bacteria to settle down and organize. Human and microbial cells both genetically respond in order to optimize metabolism to meet current environmental needs based on RNA messaging. Structured biofilm forms our outer protective barrier layer, teaches our immune system tolerance and creates the digestive ‘soil’ that nurtures us. <br /> Furanones were first isolated from marine algae and are thought to be part of the plant’s natural defense against microbial attack. Chemotaxis, motility and flagella gene expression in bacteria is post transcriptionally repressed by furanones. <br /> Brominated furanones block quorum sensing by acyl homoserine lactones, signal molecules used by Gram-negative bacteria (often pathogenic in humans since lipopolysaccharides in their cell walls mimic endotoxin). Furanone-based quorum sensing inhibitors increase sensitivity of Pseudomonas aeruginosa biofilms to antibiotics and improve clearance of these same bacteria from a mouse model of lung infection.<br /> The indigenous, 'normal' microflora can in response to changed surroundings, become pathogenic and then cause localized infectious diseases of the oral cavity (e.g., dental caries, alveolar abscesses, periodontal diseases and candidiasis). This same microflora, when in balance, also protects the host from exogenous pathogens by stimulating a vigorous immune response and providing colonization resistance.<br /> Symbiosis means 'life together.' Symbiosis is capable of continuous change as determined by selective pressures of the environmental milieu. Mutuality symbiosis, where both the host and the indigenous microflora benefit from the association may shift to a parasitic symbiosis, where the host is damaged and the evolved indigenous microflora flourishes.<br /> Complex microbial consortiums, existing as a biofilm, often provide the interfaces that initiate and perpetuate infectious assault on host tissue. The ecological balance of the various microhabitats is critical for the development of the appropriate selecting milieu for pathogens. <br /> The microbiota associated with dental caries progression is largely influenced by immune imbalance and loss of pH buffering capacity, whereas periodontal diseases and pulpal infection appear to be due to reduced energy production or redox potential, thus diminishing cellular immunity and heightening destructive humoral immunity. Candidiasis results from immune-suppression host factors that favor yeast overgrowth (like low vitamin C) or lack of bacterial competition caused by antibiotics. <br /> Oral health or disease as well as adequate digestion depends on microbial adaptation to prevailing conditions; prevention of endogenous oral or digestive disease can occur only when we realize that ecology is the heart of these host-symbiont relationships.<br />Enterohaemorrhagic Escherichia coli (EHEC) colonization will occur if it encounters a favorable signal (e.g., the stress hormone norepinephrine). However, because the gastrointestinal tract nonpathogenic flora is not uniform, it is also likely that the pathogen encounters a signal that inhibits colonization (e.g., indole). If the pathogen encounters both signals simultaneously, the extent of colonization will depend on the dominant signal.<br /> Autoinducer-2 (AI-2) is the signal utilized by E. coli for colonization inside a hot-blooded body. AI-2 helps warm E. coli produce more biofilm by making colonic acid, which is a sugar that forms the ‘mortar’ of the bacterial bedroom.<br /> Indole is used as a signal for biofilm growth outside of the body (for instance on cooler surgical replacement parts yet to be implanted). E. coli can convert tryptophan into indole. A slightly modified indole, 7-hydroxyindole, turns off the bacterium's ability to communicate and organize. <br /> Dehydration initiates exaggerated histamine production as a water-regulating control. Asthmatics have excessive levels of histamines in their lung tissue, causing constriction of the bronchial passages and increased mucus build-up, encouraging biofilm build up. <br /> Inflammation easily clears planktonic bacteria (who try to avoid triggering inflammatory response). In contrast, sessile bacteria in biofilm engender inflammatory exudates for nutrition. Steroids rob biofilms of food by reducing inflammatory exudates, allowing some chronic wounds to heal. <br /> Planktonic bacteria are controlled by the inflammatory response, allowing a clot to seal and heal an open wound. But an established biofilm in a wound creates a proteolytic environment that prevents post-debridement blood clotting, creating a non-healing wound.<br /> Fibrinogen and fibronectin both enhance Staphylococcus aureus binding and inhibit Staphylococcus epidermidis or Gram-negative bacteria adherence, while whole blood promotes Pseudomonas aeruginosa biofilm formation.<br />Body and biofilm are interconnected.<br /> 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. <br /> 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. <br /> Several pathogenic intracellular micro-organisms that attack oral endothelium are now being investigated for triggering the development of cardiovascular disease in the vascular endothelium. Many mechanisms involved in the chronic intimal inflammatory process that is atherosclerosis are mediated by the same cellular mechanisms that are "primed" to protect the body from chronic microbial invasion. <br /> The herpes variant cytomegalovirus (CMV), carried in the body of 60-99 % of people, raises levels of inflammation markers, increases blood vessel inflammation and causes high blood pressure in mice. An enzyme that causes high blood pressure, rennin is elevated in the kidneys of mice and the blood vessels of humans infected with CMV. <br /> Atherosclerosis is a chronic disease of the arterial wall where both innate and adaptive immune inflammatory mechanisms are involved. Inflammation is central at all stages of atherosclerosis. When endothelium is activated, expressing chemokines and adhesion molecules, monocyte/lymphocyte recruitment occurs with foam cell infiltration into the subendothelium, creating formation of early fatty streaks.<br /> It also acts at the onset of adverse clinical vascular events, when activated cells within the plaque secrete matrix proteases that degrade extracellular matrix proteins and weaken the fibrous cap, leading to rupture and thrombus formation. Cells involved in the atherosclerotic process secrete and are activated by cytokines. <br /> New understanding of the mechanisms of atherosclerosis provided evidence that the immune inflammatory response in atherosclerosis is modulated by regulatory pathways, in which the two anti-inflammatory cytokines interleukin-10 and transforming growth factor- play a critical role.<br /> Regulatory (suppressor) T cells play a critical role in the control of the immune-inflammatory response in atherosclerosis and substantially limit lesion development. Measles virus infection or vaccination is associated with immune depression, in part through the induction of an anti-inflammatory response by measles virus nucleoprotein. <br /> Repetitive administration of measles virus nucleoprotein to apolipoprotein E–deficient mice promotes an anti-inflammatory T-regulatory-cell type 1–like response and inhibits macrophage and T-cell accumulation within atherosclerotic lesions. Treatment with measles virus nucleoprotein significantly reduces the development of new atherosclerotic plaques and markedly inhibits the progression of established lesions. The protective effects on lesion size are lost in mice with lymphocyte deficiency.<br /> Gut biofilms support system-wide chronic inflammation that leads to allergies, autoimmune diseases, degenerative diseases and probably cancers. This attachment on the intestinal wall also produces a leaky gut that supplies the bacteria that are moved by GI macrophages to all parts of the body. This may be how Chlamydia pneumoniae colonizes sites of inflammation throughout the body.<br /> A strong association exists between coronary heart disease and Chlamydia pneumoniae, a Gram-negative respiratory pathogen. Viable C. pneumoniae has been isolated from atherosclerotic plaques. Whereas C. pneumoniae can be transported from the lung to the arteries through macrophages, oral organisms are introduced into the bloodstream multiple times daily in individuals with periodontitis through chewing or tooth brushing.<br /> The mouth holds a potentially large reservoir of Gram-negative pathogenic organisms that could readily interact with cardiovascular tissues. P. gingivalis is the predominant species among anaerobic bacteria in bacteremia after dental procedures. P. gingivalis heat shock protein-specific T-cell lines have also been isolated from atheroma lesions.<br /> Invasive periodontal pathogens are present at sites of atherosclerotic disease. Their presence has been demonstrated with DNA levels. Living P. gingivalis and A. actinomycetemcomitans can invade host cells. Either exogenous microbial pathogen-associated molecular patterns and/or endogenous molecules carrying antigenic messaging (heat shock proteins, ß2-glycoprotein-I, oxidized low-density lipoprotein (LDL) and related phospholipids via molecular mimicry) may activate innate immune responses that create the atherosclerotic process.<br /> Accelerated atherosclerosis is associated with herpes viral infection both in transplant patients and after balloon angioplasty. Marek's disease virus (MDV) is a herpes virus that induces accelerated atherosclerosis associated with the development of invasive lymphoma in hyperlipemic roosters. Striking, grossly visible atherosclerotic lesions were seen in large coronary arteries, aortas and major aortic branches of infected normocholesterolemic and hypercholesterolemic chickens, but not in matched uninfected chickens.<br /> Vascular endothelium may be a site of latent herpetic viral infection, and activation of such infection might cause or aggravate atherosclerosis (think of herpetic mouth ulcers or of bubbling, crusting lesions on the lips). There is widespread and persistent infection of human populations with up to five different herpes viruses. Infected endothelium may be damaged by marginated inflammatory cells, and be transformed from an anticoagulant to a pro-coagulant tissue.<br /> The benefit of vitamin D supplementation on reducing atherosclerotic plaque (a biofilm) is substantial. Vitamin D was replaced using gel cap forms (for assured absorption, not obtainable with powder-based tablet forms) as a nutritional supplement at a dose sufficient to maintain a serum level of 25-hydroxy vitamin D of 50-60 ng/ml, requiring a mean dose of 3590 units per day. Participants were instructed to take their dose in the morning with meals. Mean serum D3 levels increased 83%.<br /> Vitamin D has known anti-viral properties. The mechanisms of vitamin D’s action with regards to coronary atherosclerotic plaque are many. Vitamin D exerts suppressive effects at several points in inflammatory pathways (e.g., suppression of matrix metalloproteinase-9, reduced C-reactive protein), reduction in blood sugar and enhanced insulin responsiveness, reduced blood pressure via an angiotensin-inhibiting mechanism. Vitamin D deficiency has been related to increased risk of cardiovascular events and cardiovascular death repeatedly. <br /> Vitamin A helps regulate the immune system, which helps prevent or fight off infections by making white blood cells that destroy harmful bacteria and viruses. Vitamin A also helps lymphocytes fight infections more effectively. Vitamin D also helps maintain a healthy immune system and helps regulate cell growth and differentiation, the process that determines what a cell is to become. Vitamin Es and Ks are both also beneficial to intimal health.<br />Biofilm also houses yeast, a primitive eukaryocyte like us.<br /> Central to yeast infections is the biofilm, a population of microbial eukaryocytes, C. albicans cells, joined together to form structured sheets of cells. Candida albicans is an opportunistic pathogen that infects primarily immune-compromised hosts. <br /> The zinc-responsive regulatory protein Zap1 prevents the production of soluble b-1,3 glucan, a sugar that is a major component of matrix. Other genes have been identified whose expression is controlled by Zap1, called Zap1 target genes. These genes encode two types of enzymes, glucoamylases and alcohol dehydrogenases, which both control the production and maturation of matrix components.<br /> Biofilms are very varied, with some areas being both highly hydrated and hydrophilic and others being hydrophobic. They contain micro colonies of bacterial cells encased in their own extracellular polymeric extracellular polysaccharide matrix and separated from other micro colonies by interstitial voids (water channels). Some internal parts have low oxygen and are anaerobic. Surface areas may be aerobic. Biofilm architecture is diverse both in space and time, constantly changing because of external and internal communicated processes. <br />Biofilm is sentient and our ‘significant other’.<br /> Biofilm in its niche becomes a purposeful ecological community. As cells become sessile, diversification is encouraged, seemingly an expression of altruism for the community. Each cell contributes to a larger cooperative structure forming an organism with the will to survive, exhibiting consciousness and seemingly even freedom of choice. <br /> Both we (and this group of ‘significant others’, our biofilm in its various recesses) meet the requirement of sentience, the ability to feel pleasure and pain as well as the ability to communicate that perception. Our biofilm seems to have its own mind, displaying surprising levels of creativity, intelligence, even wisdom, self-awareness and intentionality. <br /> Biofilm has the ability to communicate its desires to us by making us crave and seek certain foods, thus take action and alter our behavior. In Eastern philosophy, sentience is a metaphysical quality of consciousness in all things (perhaps all surfaces covered by biofilm) that requires our respect and care.<br /> ‘Classification tree analysis’ through DNA samples of saliva microbiological composition showed that 98.4% of overweight women could be identified by the presence of a single bacterial species (Selenomonas noxia) at levels greater than 1.05% of the total salivary bacteria. <br /> Likely the composition of salivary bacteria changes in overweight women, as the median percentage difference of 7 of the 40 bacterial species measured was greater than 2% in the saliva of overweight women. These bacterial species might serve as biological indicators of a developing overweight condition. More intriguing, and the subject of future research, is the possibility that oral bacteria may participate in the pathology that leads to obesity.<br /> Included among the many jobs performed by our intestinal bacteria is that of extracting calories and nutrients from the foods we eat. They also store them for later use, as well as making sure there is sufficient nourishment to produce new bacteria to perform the same job. Differences in our gut microbial ecology may determine how many calories we are able to extract and absorb from our diet and deposit in our fat cells.<br /> Individuals who are prone to weight gain tend to have greater numbers of gut bacteria called firmicutes and fewer numbers of another type of bacteria called bacteroidetes. These two major groups account for the majority of the microbes in the human digestive tract, more than 90%. As folks lose weight, the ratio of bacteria shifts; bacteroidetes becomes more abundant, while the number of firmicutes lessens.<br /> A protozoan, toxoplasma gondii alters brain chemistry of rats so they are more likely to seek out cats. This is a fatal mistake since the parasite (toxoplasma) reproduces in the cat. Roughly 60,000,000 ‘symptom-free’ Americans carry toxoplasmas which are immune-suppressive, and alter neurotransmitter function with effects from subtle shifts in behavior to schizophrenia (especially if there are a lot of cats around). Behavioral changes in humans include slower reaction times and a 6-fold increased risk of traffic accidents among those infected. Ummm, perhaps this explains some of the habits of the ‘cat lady’ we all know. <br /> Geography of T. gondii infection (preference for raw meat in France) shows links with ‘neuroticism.’ In the human host, the parasites form tissue cysts within cells (escaping immune detection), most commonly in skeletal muscle, myocardium, brain and eyes. These cysts may remain throughout the life of the host.  <br /> A high titer of T. gondii antibodies in mothers skews newborn’s sex ratio more strongly to the male (260/100) with normal being (104/100). Congenital infection occurs if mom is infected during pregnancy.  Toxoxplasma gondii tachyzoites can cross the placenta to the fetus which may lead to spontaneous abortion, stillbirths or severe birth defects, especially of the female child.  Early diagnosis and treatment of the mother may reduce the probability of congenital infection.<br /> Fibrin limits hemorrhagic blood loss during infection by the protozoan parasite Toxoplasma gondii, thereby performing a host-protective function essential for survival. Surprisingly, fibrin does not simply protect against vascular damage caused directly by the parasite, but rather, protects against hemorrhagic damage triggered by IFN-gamma, a messenger molecule of our immune systems. <br />Coagulation has a beneficial role during immunity. Fibrin protects our tissue from collateral damage caused by our immune response to infection, by limiting hemorrhagic pathology as well as smothering growth and dissemination of bacteria. Pathological coagulation may result from dysregulation of cytokine pathways that are meant to function protectively.<br /> Fibrin's dense mesh-like structure likely physically traps bacteria, thereby curbing dissemination. Interestingly, this fibrin-mediated restraint of bacterial growth and dissemination applies both to infection by bacteria that predominantly replicate extracellularly (ex. Staphylococcus aureus) and intracellularly (ex. Listeria monocytogenes).<br /> Host resistance to this protozoan parasite depends on a Th1 immune response with potent production of the cytokines interleukin-12 and interferon. Although Toll-like receptor 11 (TLR11) plays a major role in controlling Th1 immunity to this pathogen in mice, this innate immune receptor is nonfunctional in humans, and the mechanisms of TLR11-independent sensing of T. gondii remain elusive. <br /> Oral infection by T. gondii triggers a TLR11-independent but MyD88-dependent Th1 response that is impaired in TLR2xTLR4 double knockout and TLR9 single knockout mice. These mucosal innate and adaptive immune responses to T. gondii rely on the indirect stimulation of dendritic cells by normal gut microflora. <br /> Thus, in humans, gut commensal bacteria serve as molecular adjuvants during parasitic infection, providing indirect immune stimulation that protects against T. gondii in the absence of TLR11. Encouraging the production of our natural gut flora through probiotic use tends to help stimulate our immune systems to protect us against the ubiquitous protozoan parasite Toxoplasma gondii.<br /> When microbes communicate with any of the thousands of sensory nerve cells that lie within the gut walls, either directly or through nearby mobile macrophages, it would influence immune response and the emotions. Supporting evidence has been found in rodent experiments. Beneficial biofilm boosts our general sense of well being due to friendly bacterial communication via ‘toll receptors’ on immune cells and the vagus nerve system. Kefir, the ancient Turkish word for goat milk fermented with beneficial flora, literally means ‘feel good.’<br />Pathogenic biofilm<br /> Virulence characteristics of biofilms that influence infectious disease processes include detachment of cells or biofilm aggregates that may result in bloodstream or urinary tract infections or in the production of emboli; cells may exchange virulence and resistance plasmids, a form of horizontal gene transfer within biofilms; cells in biofilms have dramatically reduced susceptibility to antimicrobial agents; biofilm-associated gram-negative bacteria may produce endotoxins and biofilms are resistant to host immune system clearance.<br /> Variants of the species E.coli are adapted to various host organisms, such as humans, monkeys, horses and birds, in which they belong to the normal intestinal flora. In addition, pathogenic strains (perhaps virally infected) have the capacity to cause sepsis or local infections of the intestines, as well as of the kidney, bladder and brain, in different hosts. <br /> On the other hand, high doses of non-pathogenic E. coli bacteria can function as a strong, direct inhibitor of mast cell degranulation. This suggests a basis for antiallergic treatment (modulating exaggerated humoral immunity) or prevention, with commensal bacteria.<br /> German professor Alfred Nissle, in 1917, isolated a strain of E. coli from the feces of a World War I soldier who did not develop enterocolitis during a severe outbreak of shigellosis. In those days, antibiotics were not yet discovered, and Nissle used the strain with considerable success in acute cases of infectious intestinal diseases (salmonellosis and shigellosis). Escherichia coli Nissle 1917 is still in use (as Mutaflor) and is one of the few examples of a non-lactobacillus probiotic.<br /> Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. Horizontal gene transfer and gene reduction represent two mechanisms contributing to the evolution of prokaryotic genomes “in quantum leaps”. Thus, the acquisition of plasmids and phages, as well as large DNA regions called “genomic islands,” plays an important role in the development of new species, subspecies as well as pathogenic characteristics of known species.<br /> Many microbes can accelerate the rate at which their genes mutate. This allows them to obtain new abilities that may be helpful when conditions get tough. Escherichia coli mutates more rapidly when under stress, and yeast can perform the same trick.<br /> The localization of many virulence-associated genes on mobile genetic elements, such as bacteriophages, plasmids and pathogenicity islands (PAIs), reveals that horizontal gene transfer plays a major role in the evolution of different bacterial pathogenic types. Genetic diversity among pathogenic and commensal E. coli isolates is very high with respect to genomic alterations.<br /> Plasminogen (Plg) is a proenzyme of the serine protease plasmin, which is involved in several important physiological and pathological processes such as fibrinolysis, degradation of the extracellular matrix (ECM), eukaryotic cell migration, tissue remodeling, embryonic development and inflammation as well as tumor metastasis. <br /> Plasmin is central for cell migration as it directly degrades laminin, the major glycoprotein in basement membranes, and indirectly enhances tissue damage by activating latent matrix metalloproteases (MMPs) which are capable of degrading collagens and other constituents of ECM.<br /> Basement membranes form important tissue barriers and also offer a setting where components of the plasminogen system are present and can be activated, thus the proteolytic activity of plasmin is efficiently targeted to these physiological barrier structures.<br /> Invasive bacterial, yeast and parasitic pathogens can intervene with and usurp our plasminogen system by expressing receptor molecules which enable the microorganisms to gain surface-bound invasive proteolytic activity. On the other hand, plasminogen is modified in the presence of beneficial L. crispatus and Lactobacillus johnsonii cells into internal plasminogen fragments which included angiostatin, known to suppress endothelial cell proliferation and tumor metastasis.<br />Really small life forms exist in the biofilm.<br /> Mycoplasmas (L-form or cell-wall deficient bacteria) sometimes originate from bacteria which have shed all or part of their cell wall or had it destroyed by antibiotics. Many chronic diseases may be due to smaller infectious bacteria which transform into the mycoplasma state (kind of small bacteria acting like a virus) and live intracellularly to better survive inside the body (often even infecting our immune cells). <br /> Infected phagocytes circulate in blood and tissues. In the extreme case of sarcoidosis they clump together and form granulomas, clusters of phagocytes without normal supporting structure. They are also capable of accumulating in regions of inflammation such as joints. When a phagocyte becomes infected, intra-cellular bacteria can manufacture a lot more proteins, cytokines and toxins than they could if they had infected a red cell, as the cell nucleus and mitochondria allow them access to Homo sapiens mRNA transcription, and Homo sapiens nutrients.<br /> Regular bacteria stressed with starvation pack their DNA into tight bundles, shut down virtually all their activities & shrink down to about 1/3 normal size. These ultra micro bacteria can remain in this dormant state for decades, or possibly even centuries, floating around in the deep oceans or buried far underground (and they have surprisingly survived years of outer space travel).<br /> These self-mummifying bacteria outmaneuver death by transforming themselves into a metabolically suspended quasi-crystal: the endospore. The endospore is a downward spiral that can go upward, a tautological emergency exit into blissful core energy, a survival strategy that only prolonged boiling can tear apart. Once environmental conditions again favor normal metabolism, the endospores return to life as if the last 60 hours or 6000 years never happened.<br /> The beta-lactam antibiotics (cephalosporins and penicillins) that attack cell walls are deadly to free-swimming blood-borne bacteria but ineffective against Cell Wall Deficient (CWD) bacteria. In fact, they actually promote formation (by destroying bacterial cell walls) of the tiny L-form CWD bacteria which have been seen living inside phagocytes. Because the beta-lactams actually protect the CWD bacteria, they are even used in test tube when culturing and growing the tiny L-forms.<br /> CWD mycoplasmas are associated with many different conditions as chronic fatigue syndrome, fibromyalgia, TB, Gulf War Illness, AIDS, rheumatoid arthritis and even certain forms of cancer. The tests used to identify mycoplasmal infections, Forensic Polymerase Chain Reaction and Nucleoprotein Gene Tracking, are very sensitive and highly specific. Mycoplasmal biofilm infections can explain much if not most of the chronic signs and symptoms found in these challenging, chronically ill, difficult to diagnose patients.<br /> The pleomorphic cancer causative agent has been described as having virus-like and fungus-like, as well as bacterial mycoplasma-like phases. Such a “life cycle” that would allow survival of microorganisms under attack is considered nonsense and microbiologic heresy by conventional approach, but reflects real observations of the biofilm. Could a simple deficiency of friendly commensal microflora caused by taking antibiotics or anti-infective botanicals/minerals, or experiencing overwhelming stress at any point in one's life, promote disease-causing chronic inflammation, biofilm micro bacterial infections and ignite the process of carcinogenesis?<br />Beneficial viruses and childhood diseases<br /> The 3-D structure of Seneca Valley Virus-001, shows that it is different from any other known member of the Picornaviridae viral family. It is dissimilar from other known picornaviruses such as poliovirus and rhinoviruses (which cause the common cold). The ‘new’ Senecavirus has an outer protein shell that looks like a craggy golf ball (one with uneven divets and raised spikes) and the RNA strand beneath it is arranged in a round mesh shaped like a whiffle ball. <br /> The Seneca virus does not affect normal human cells, but can infect certain solid tumors, such as small cell lung cancer, the most common form of lung cancer. Several areas on the viral protein coat likely hook onto receptors on cancer cells in the process of infecting them. This virus has a cancer-killing specificity that is 10,000 times higher than that seen in traditional chemotherapeutics, with no overt toxicity.<br /> Mumps is a common childhood disease which is benign in the in the vast majority of cases. It is preferable that mumps be contracted in early childhood because, when experienced in adulthood, the disease may cause meningitis and/or damage to the testes, ovaries, auditory nerves or pancreas. Also, notably, women are less likely to experience ovarian cancer if they were infected with mumps during childhood.<br /> Adults who had had natural measles with a rash have a decreased incidence of various cancers, including cervical. After contracting measles and other childhood illnesses (e.g.. chickenpox, scarlet fever, whooping cough, rubella, mumps and perhaps others), it has been widely accepted by many health practitioners, including experienced orthodox pediatricians that this is most often beneficial for the general health of our children. Children contracting measles naturally become less likely to suffer later from allergic conditions such as asthma, eczema and hay fever. <br /> An acute inflammatory childhood illness (measles, mumps, rubella, chicken pox, scarlatina or whooping cough) develops the cell-mediated immune system, while a vaccine activates the humoral immune system. The difference is crucial because it is the cell-mediated response that is first line of response to protect from future illness and that provides, in effect, the deeper immunity. Humoral immunity fosters antibodies, allergy as well as auto-immune disease like diabetes, migraine and asthma.<br /> Physicians who practice Anthroposophical medicine foundationally believe that having acute but limited inflammatory diseases as a child helps protect one as an adult against more serious, long-term, chronic illnesses. Not having these childhood illnesses (because of multiple vaccinations) can lead to diminished cellular immunity and a greater incidence of adult health problems. The same result occurs when childhood illnesses are routinely suppressed with antibiotics rather than helping the cell-mediated immune system to eliminate the illness with fever, sweats, rash or mucous discharge.<br />Periodontitis, nanobacteria and immune dysregulation<br /> Periodontitis is thought to arise from complex microflora consisting of putative disease causing bacteria, such as P. gingivalis, T. denticola, Tannerella forsythia (formerly Bacteroides forsythus or Tannerella forsythensis) and Fusobacterium spp. These bacteria have been co-isolated from diseased periodontal sites, and periodontitis is maintained by cooperation between the different species.<br /> Perhaps these oral bacteria are simply attracted to low-oxygen inflammatory sites of auto-immune destruction. These tooth-bound avascular pockets of periodontal devastation are created by uncontrolled upregulated humoral response to antigenic cellular immune messaging left behind on forming root surfaces (neuroectodermal cells called rests of Malasez that remain due to disabled developmentally-planned apoptotic elimination of these enamel-like root guiding cells). <br /> In addition to P. gingivalis, oral treponemes have been implicated in periodontitis and oral malodor. These helically shaped spirochetes (which can also exist in very small cyst or cell wall deficient forms) are present in significantly elevated numbers in plaque samples from deep-pocket sites of patients with severe periodontitis. Most oral spirochetes either cannot yet be grown or are extremely difficult to grow in culture because they have lost the ability to synthesize many essential molecules that they normally obtain from their host.<br /> Even smaller are the mycoplasmas which may have the smallest of the prokaryotic genomes and seem to lack complex gene-regulatory systems. Biofilm formation by Mycoplasma pulmonis is dependent on the length of the tandem repeat region of its variable surface antigen (Vsa) protein. Mycoplasmas that produced a short Vsa protein with few tandem repeats formed biofilms that attached to polystyrene and glass (with an extracellular matrix containing Vsa protein, lipid, DNA and saccharide). Mycoplasmas that produced a long Vsa protein with many tandem repeats formed microcolonies that floated freely in the medium. <br /> Even smaller are the nanobacteria, perhaps the most primitive organisms on Earth. Nanobacteria are structurally and physiologically unique in many ways: they are 20-200 nanometers in size; they have a unique “cellular” and membrane structure. They replicate very slowly (every 3-5 days) and by different methods. In contrast, typical bacteria mitotically double about every 20 minutes.<br /> Nanobacteria are pleomorphic, assuming different life forms and sizes for different phases and activities of their lives; they can go dormant in a self-made calcium shell. They are saprophytic in humans, feeding on dead or decaying organic matter. They are “the toughest of bugs” resistant to being killed both In vitro and In vivo and may be at the root cause of many human diseases. They are structurally and functionally simplistic, unbelievably small and genetically unique.<br /> Nanobacteria excrete a slick calcium biofilm around themselves that subsequently hardens, creating a calcium shell “igloo” around them. They can build upon themselves in this calcified form much like coral formation. <br /> Pathological calcification in humans, like coronary artery heart plaque, vascular plaque, soft tissue calcifications, dental tartar and pulp stones, kidney stones, polycystic kidney disease, arthritis as well as chronic prostatitis and even dermatology disorders (eczema, psoriasis, lichen planus and scleroderma), may be biofilm-generated calcification, plausibly created by nanobacteria or mycoplasma in their microscopically mixed pleomorphic concreted colonies. Nanobacteria have even been found in the calcified debris found in tissue biopsies from ovarian cancer patients.<br /> Biologic nanoparticles (NPs) isolated from human arterial calcifications and kidney stones form an adherent film on the bottom of flasks when placed in standard cell culture conditions. Since NPs have certain features consistent with living microorganisms, perhaps antibiotics and/or RNAse might inhibit this biofilm formation. <br /> NPs isolated from calcified human arterial tissue were cultured onto glass cover slips, plus either no treatment (control), RNase, tetracycline or gentamicin added. At 1, 7 and 14 days after inoculation, cover slips were fixed, mounted and analyzed. In controls, the percent cover slip covered by biofilm increased by 120% from day 1 to day 14, compared to 47% and 35% in wells treated with RNase and gentamicin, respectively. <br /> Wells treated with tetracycline showed a 3% decrease in biofilm by day 14. Since RNase should not enter intact cells, these results indicate that extracellular RNA plays a role in biofilm formation by NPs. Although tetracycline can chelate calcium, it also inhibits ribosomal function, as does gentamicin, indicating that intact ribosomal function is required for NP-associated biofilm growth. Biofilm formation by NPs then consists of biologically driven physicochemical processes.<br /> Nanobacteria can easily cross the blood-brain barrier to cause brain calcification disorders and “brain sand”. Small self-replicating structures containing nucleic acids were cultured from filtered homogenates of two calcified aneurysms. Almost 100% of atherosclerotic patients have anti-nanobacteria antibodies in their serum, while in healthy blood donors anti-nanobacteria antibodies are seen in about 15%.<br /> Nanobacteria cause “apoptosis” or cell-death in tissues they contact. The antigenic properties of the structures identified as Nanobacterium sanguineum might be explained as humoral antibody response to a number of biomolecules simply adsorbed onto the surface of the biofilm’s hydroxyapatite microcrystals. However, arteries without atherosclerotic plaque have 20-50 fold increase in Vitamin K2 concentration over arteries with plaque in the same human body.<br /> Calcium deposits are not random. They aggregate around the remnants of dead (”apoptotic”) smooth muscle cells. Vitamin K2 supports at least two proteins that are likely to protect against atherosclerosis: matrix Gla proteins and growth arrest specific gene product 6 (Gas6). <br /> Gas6 increases cell survival and helps clear away any fragments left behind by cells that do happen to die. When vitamin K2 levels are adequate, two of the Gla-proteins that are activated are: (1) osteocalcin, the protein responsible for anchoring calcium within bone, and (2) matrix Gla-protein, which prevents calcium from depositing in the heart, arteries, breast and kidneys.<br /> Nanobacteria do not grow in standard bacteriologic culture conditions.  They alter RNA and DNA and transcription expression of the cells they grow on or in. Their small size, slow grow rate, and unusual culture requirements explain why Nanobacterium sanguineum has until recently eluded detection, as they can only be visualized frozen under an electron microscope. They are calcifying self-propagating nanoparticles that may be part of a larger bacterial life cycle.<br /> Known ultra micro-bacteria are sized at about 200-300nm. The theoretical minimum size for a free-living organism (capable of holding the minimal molecular group of about 250-450 proteins, genes and ribosomes) would be 250-300nm in diameter, about the same size of the ultra micro-bacteria. Indeed, even a single ribosome, if surrounded by membrane and wall, would occupy a viral-sized sphere of 57nm in diameter<br /> Nanobacteria may represent a primitive Archaea symbiont that requires cell contact or lipids from other cells for growth, and are only about 1/100th the size of conventional bacteria, at 20-150nm. Coincidentally, this is also the standard size of commercially produced hydroxyapatite nanocrystals. Perhaps the particles identified as the living organism Nanobacterium sanguineum might actually be non-living, but self-generating inorganic particles of calcium hydroxyapatite (once they have been complexed with nucleic acids, proteins and other ionic molecules of the biofilm).<br /> Organic materials play key roles as nucleating surfaces, triggering crystal growth in the bio mineralization of apatite, in addition to modulating and finally inhibiting the process. Such crystal growth is enhanced markedly in low gravitational environments (and astronauts returning to earth are very prone to calcific atherosclerosis).<br /> Nanobacteria cause production of human antibodies in response to their biofilm, but when our cellular defense systems arrive, they cannot “see” anything because these bacteria are too small; it’s like fighting a war against invisible men. Nanobacterial biofilm triggers an immune system hyperalert process, which causes chronic inflammation to spread systemically from tissues locally affected by the bacterial antigens.<br /> These parasitic bacteria are also called pleomorphic (many shapes) or L-form (named for the Lister Institute where they were discovered) or Cell Wall Deficient (CWD) or cell wall divergent or cell-wall defective or large bodies or cryptic or nanobacteria, micro bacteria or spores.<br /> We are exposed to CWD pathogens in our food/milk (they are not killed by pasteurization), water (they are not killed by chlorination), intimate contact (spouses are at higher risk), before birth (via sperm), at birth (mother to child transmission) and biologic (injectable) medicines (they are too small to be filtered during the 'purification' processes used in pharmaceutical manufacturing procedures). They have even been cultured from dry soil. L-forms of Bacillus anthracis (Anthrax) are known to survive in dry soil indefinitely.<br /> The Th1 (T-helper) inflammatory response occurs in reaction to the invasion of cells by extremely tiny variant bacteria. The body’s defenses trigger several medical markers of inflammation, including C-reactive protein (CRP). Elevated CRP levels are a major risk factor and harbinger of coronary artery disease and stroke. Many human degenerative disease processes including cancer, have been associated with chronic inflammatory pathological calcification, likely due to biofilm containing nanobacteria.<br /> Dr. Gary Mezo has proposed that anti-nanobacterial therapy might help treat coronary artery disease, as well as other disease states associated with abnormal, extra-skeletal calcification.  His study protocol involves the nightly administration of 1500mg of a rectal EDTA suppository (a calcium and heavy metal chelating agent), coupled with an oral prescription of 500mg tetracycline (an antibiotic with metal chelating and anti-inflammatory properties) taken orally for three to twelve months. (This therapy would be effective at debulking and dismantling most biofilms.)<br />Immune tolerance<br /> The difference between friendly commensal biofilm and harmful pathologic biofilm is its local environment, partly controlled by the host’s individual DNA and RNA heredity with resultant physiology, hygiene habits, stress levels, diet, sleep, daily rhythm, heavy metals and other toxicities as well as onboard viruses. <br /> A newly found gene, pims has been found to be expressed during bacterial infection in the gut. It disrupts the pro-inflammatory Imd pathway, signifying a role in modulation of this pathway. Pims is a negative immune-regulator triggered when specific Imd activation thresholds are reached, after which the immune response is suppressed. It is the existence of this immune-reactivity threshold that allows coincident existence of tolerance to commensal gut microorganisms while maintaining immune-reactivity against infective pathogens.<br /> The mechanism of oral tolerance partly exists because mucosal tissues are replete with a unique subset of antigen-presenting dendritic cells (macrophages) that secrete factors such as, TGF-beta1 and retinoic acid, that induce immunosuppressive regulatory T cells or Tregs (foxp3+ regulatory T cells). <br /> T cell regulation is partly mediated by secretion of soluble IL-10 (Tr1 cells) and/or TGF-b (from Th3 suppressor or regulatory cells) after antigen-specific triggering. Tr1 cells, which suppress colitis and are induced by IL-10, mediate regulation, in part, by secretion of TGF-b. Both Th3 and Tr1 cells are induced via the mucosal route, thru different compartments. IL-10 and TGF-b are important regulatory cytokines (TGF-b-deficient animals have widespread inflammation and IL-10-deficient animals develop colitis).<br /> The primary putative pathogens causing periodontitis are Porphyromonas gingivalis and Bacteroides forsythus. Half of young adults with severe inflammatory periodontitis are seronegative for antigens of their infecting bacteria. In treating inflamed gingiva, removal of bacterial deposits from roots of teeth via scaling and root planning results in marked clinical improvement. <br /> Prophylaxis induces gingival bleeding resulting in bacteremia. This causes seronegative patients to seroconvert and produce higher titers of biologically more effective serum antibody (mostly IgG2 subclass), thus reducing biofilm accumulation and gingival inflammation.<br /> Dietary proteins are taken up preferentially by gatekeeper dendritic cells in the lamina propria of the small intestine. These then migrate to interact with antigen-specific CD4+ T cells in the mesenteric lymph nodes, inducing tolerance to the mucosal immune system under physiological conditions, but being sufficiently responsive to inflammatory stimuli to allow T cell priming and protective immunity when necessary.<br /> Expression profiles of human mucosal gene expression patterns display striking differences in modulation of pro-inflammatory NF-kB-dependent pathways, notably after consumption of living L. plantarum bacteria in different growth phases. These cellular pathways correlate with immune tolerance in healthy adults.<br /> Classically, commensal microbiota establishes tolerance at mucosal surfaces, and invasive pathogens cause stereotypic inflammation. The reality is more complex, marked by three emerging concepts: (1) pathogens take advantage of inflammation to cross the epithelial barrier, (2) pathogens reduce the commensal flora to invade their niche, and (3) pathogens express dedicated effectors that modulate inflammation.<br /> Gut pathogens in combination with stimulation by cytokines such as TNF-alpha (tumor necrosis factor) can cause cells of the intestinal epithelium to respond by releasing more proinflammatory messenger molecules like interleukin-8 (IL-8). On the other hand, probiotic strains, Bifidobacterium longum and Lactobacillus bulgaricus, can suppress IL-8 secretion in intestinal epithelia when stimulated by proinflammatory cytokines, down-regulating inflammation in the gut.<br /> In mice, pre-existing persistent infection with lymphocytic choriomeningitis virus (LCMV) clone 13 prevents the induction of tolerance, mixed chimerism and donor-reactive T cell deletion. Mice continue to be refractory to tolerance induction even after viremia has been resolved and virus is present only at very low levels in peripheral tissues. <br /> Conversely, the full tolerance regimen, or co stimulation blockade alone (CD28 and/or CD40 blockade-based strategies to induce tolerance), specifically inhibits already ongoing antiviral immune responses, leading to an inability to control viremia. Ongoing T cell responses continue to depend on co stimulatory interactions in the setting of a chronic infection and provide insight into potential risks following co stimulation blockade posed by chronic or latent viral infections such as hepatitis C, EBV and CMV.<br /> Innate immune responses and inflammation are regulated in part by neural mechanisms. Innate immunity and inflammation are controlled by the vagus nerve, classically known as a regulator of other vital physiological functions. When vagus nerve function is diminished, inflammation soars, inviting biofilms to grow and become pathogenic. (The relaxation effects of neurally derived NO appear to inhibit ongoing vagal cholinergic activity. The primary site of action of nitrergic mechanisms on gastric fundic tone is at a presynaptic site on vagal cholinergic efferent nerves.)<br /> Activation of vagus nerve cholinergic signaling inhibits TNF (tumor necrosis factor) and other pro-inflammatory cytokine overproduction through ‘immune’ α7 nicotinic receptor-mediated mechanisms. This efferent vagus nerve-based ‘cholinergic anti-inflammatory pathway’ is a critical regulator of inflammation in several experimental models of diseases. <br /> Acupuncture, meditation, hypnosis and relaxation therapies can stimulate vagus nerve activity. Exercise raises vagus nerve firing and decreases inflammatory cytokine levels. Fish oil, soy oil and olive oil increase vagus nerve activity mediated by cholecystokinin. Choline helps to form acetylcholine, the neurotransmitter of the efferent vagus. <br /> Nicotine is anti-inflammatory by acting on the acetylcholine receptors normally responsive to acetylcholine released by the vagus nerve. Macrophages also have receptors for the neurotransmitter acetylcholine that is released by branches of the vagus nerve in the intestines. Nicotine blocks inflammation triggered by LPS. (LPS typically signals a macrophage, NF-kB becomes activated, inflammatory genes are expressed, mediators are secreted and tissue inflammation ensues.)<br />Restore an imbalanced biofilm.<br /> Chrysanthemum tea contains choline, vitamin A, B1, glycosides, adenine, amino acids, flavonoids, pigments and volatile oils. It has an inhibiting effect on bacteria, including Staphylococcus aureus, Streptococcus hemolyticus B, Pseudomonas aeruginosa, Shigella dysenteriae, tubercle bacillus and dermatomycosis. The tea also has antivirus and antispirochete qualities. <br /> Honeysuckle flower is one of the most potent anti-bacterials of nature’s “antibiotics”. Honeysuckle flowers (from what some consider an invasive weed) are effective against bacteria, viruses, fungi and parasites. Honeysuckle is also be used to treat infections caused by staphylococcal or streptococcal bacteria. <br /> Chlorogenic acid, an ester of caffeic acid and quinic acid, found in honeysuckle, is also a major phenolic compound in coffee, and can be isolated from the leaves and fruit of many plants.  This well known antioxidant also slows the release of glucose into the bloodstream after a meal. <br /> Chlorogenic acid can be used as anti-infectious active ingredient, it has wide anti-virus, anti-bacteria effects and has relatively low toxicity or side-effects. Some Japanese health food products include honeysuckle for treating bloating, nausea, and vomiting caused by hepatitis C. It has obvious anti-infectious effects, and unlikely to lead to anti-microbial resistance.<br /> Honeysuckle is best used for acute conditions, and is not generally used in the treatment of chronic illnesses. This herb can be used for all infections and inflammations, including urinary tract infections, respiratory tract infections and some gastrointestinal tract inflammations. It is also used for fevers, the common cold, sore throat and influenza. Honeysuckle flowers act as natural antihistamine, although they are more useful for treating rashes and inflammation than for treating coughing and sneezing. <br /> Honeysuckle is a very useful remedy for persistent acne, and all sorts of skin eruptions. Simply add to a cup of hot/boiling water. Add a little honey if you wish for taste. To eliminate a skin boil, mash honeysuckle flowers into a paste, place on top of the boil with a gauze covering the area.  <br /> In comparison between semi (black tea) and non-fermented tea shoots, biofilm growth inhibitory concentration of oral streptococci was lower for semi fermented Camellia sinensis extract and its antimicrobial activity was better as compared to green tea. Bactericidal effect of both tea extracts was clear. Drinking green tea while taking antibiotics appears to increase the action of antibiotics and reduce the drug resistance of bacteria, even in superbug strains.<br /> Community acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) , necrotizing (“flesh eating") pneumonia, can be fatal in many cases. Besides causing a high fever, CA-MRSA pneumonia can sometimes cause blood pressure to drop and progress to septic shock, requiring patients to be placed on mechanical respirators in order to breathe. Potentially deadly CA-MRSA pneumonia seems to occur most commonly following a flu-type illness, like the H1Ni virus.<br /> When bacteria are exposed to antibiotics, some cells that are resistant to these drugs live on to reproduce. Thus, while antibiotics are important for disease treatment, their use creates stronger, more-resistant strains of bacteria over time. The amount of antibiotics used non-therapeutically in animal agriculture is eight times greater than the amount used in all of human medicine.<br /> Many of the antibiotics used in animal agriculture are also used in human medicine. While overuse in human medicine is a significant part of the problem, 70% of all U.S. antibiotics and related drugs are fed non- therapeutically to livestock, poultry and fish on industrial farms (as a routine feed additive to promote slightly faster growth and to compensate for unsanitary and crowded conditions). This is an idiotic way to encourage bacteria to develop antibiotic resistance that can easily be spread about.<br /> In comparison between non-fermented and semi fermented Camellia sinensis extracts, the black tea (with more volatile components) has faster effect on growth inhibition of oral streptococci. In case of 3 mg mL-1 of black tea extract, after 30 minutes the count of viable cells was below 1 log of cfu mL-1 and this amount achieved by same amount of green tea extract took 40 minutes.<br /> Epigallocatechin gallate (EGCg), the primary polyphenol of green tea, has several antibacterial qualities. Tea catechins can fight or even destroy the bacteria that cause cholera, pneumonia, abscesses, botulism, dysentery and food poisoning, as well as those that cause cavities and bad breath. Catechins can inhibit the action of the flu virus, herpes simplex, polio, HIV and others.<br /> Catechins inhibit the growth of the disease-causing bacteria, especially Clostridium perfringens (a common cause of food poisoning), Clostridium difficile (which is linked to killer diarrhea and colitis), and Bacteroides (which can cause abscesses if bacteria escape from the intestines). But the gut’s “friendly” bacteria, including Bifidobacterium and Lactobacillus, are relatively unaffected by the tea catechins.<br /> EGCg interferes with the polysaccharides that form the glycocalyx, disrupting their interactions either reciprocally or with the cell wall, thus reducing the amount of biofilm slime that accumulates. However, EGCg also binds to peptidoglycan, breaking the integrity of the bacterial cell wall, and could therefore interfere with the initial docking phase of biofilm formation, which requires hydrophobic interactions between the bacterial cell wall and the surface to be colonized. <br />Nature’s acids versus pathogenic bacteria<br /> Lactic acid fermentation is used by some fungi and bacteria. The most important lactic acid producing bacteria is Lactobacillus. The presence of lactic acid, produced during lactic acid fermentation is responsible for the sour taste and for improved microbiological stability and safety of food. <br /> Re-establishing predominance of these bacteria in the biofilm helps return a pathogenic microbial community to its symbiotic commensal role. Breast-feeding can be a significant source of lactic acid bacteria to the infant gut. Lactic acid bacteria present in breast milk has an internal origin (not contamination from the surrounding breast skin).<br /> Lactic acid fermentation is responsible for the sour taste of dairy products such as cheese, yogurt and kefir. Lactic acid fermentation also gives the sour taste to fermented vegetables such as traditionally cultured sauerkraut and pickles. The sugars in the cabbage are converted into lactic acid and serve as a preservative.<br /> One common lichen (which is a symbiosis of algae and fungus) metabolite, usnic acid inhibits carotenoid synthesis. Usnic acid has antihistaminic, antiviral and antibacterial activities.<br /> Usnea (usnea longissima, hair lichen) combines the properties of both lichen and algae. It is anti-viral, antiseptic, antibiotic, antibacterial and anti-tumor. It is more powerful than penicillin against both staphylococcus and streptococcus bacteria and works by changing cellular metabolism. As usnea has no known contraindications or side effects it is a popular herbal antibiotic remedy (often combined with golden seal, wild indigo, myrrh or witch hazel depending on the nature of the problem treated).<br /> Lechenya Meera (a proprietary blend of lichens, mosses, fungi and algae) which is raw harvested and cold-pressed with other natural substances, is a natural anti-septic and disinfectant.  Lichen is a moss-like plant that grows primarily in cold and moist environments. The lichen and other ingredients are blended when the fungus and alga in their dual relationship produce active acids, which create anti-microbial byproducts, effective against various bacteria (staph and strep). It is also effective as a surface treatment for mildew and molds in the more humid areas of the world.<br /> Total Solution 2000 (containing Lechenya Meera) attacks the microbe, bacteria or virus, by suffocating it and especially by depriving it of "biofilm," the primary protection and food source of bacteria.  It affects both bacteria and viruses by stopping their reproductive processes and sterilizes the bacterial spore or the virus so that it cannot reproduce, mutate or cross-contaminate.  With both feeding and reproduction shut down, bacteria are neutralized so that they are no longer harmful and they soon die. <br />RESPIRATORY MIST is a special solution prepared for use on mucous membranes, ears and the eyes. It relieves sinus congestion, bronchial disturbances and stuffed up nose. It is useful for treating filters for furnaces and air conditioners creating a residual effect that acts like an air freshener.  It contains Witch Hazel, Lechenya Meera, Stabilized Oxygen, Citronella and Pennyroyal in an alkaline water base.<br />FIX (2004): is a special fermented Lechenya Meera to be used to relieve upset stomach, diarrhea, protect against toxins in food, counteract indigestion, correct allergic reactions replace and restore electrolytes and beneficial flora to the digestive system. Call Suzy Star, at(541) 736-5150 /<br /> The black seeds of papaya are edible and have a sharp, spicy taste. They are sometimes ground up and used as a substitute for black pepper. Both fruit and seed extracts have pronounced bactericidal activity against Staphylococcus aureus, Bacillus cereus, Escherischia coli, Pseudomonas aeruginosa and Shigella flexneri. After a course of antibiotic therapy, papaya juice rapidly returns intestinal bacteria to normal. <br />Life-threatening sepsis<br /> Lipopolysaccharides (which mimic endotoxin) from the bacterial cell wall are a potent stimulus for Tumor Necrosis Factor-alpha (TNF-α) synthesis. TNF-α acts as a key mediator in the local inflammatory immune response by initiating a cascade of cytokine release, recruiting macrophages to the site of infection, and cause blood clotting to attempt to contain the infection. TNF-α amplifies and prolongs the inflammatory response.<br /> Originally, sepsis was believed to result from invading bacteria itself, but it was later found that the host’s system proteins, like TNF-α and HMGB1, induced sepsis as an exaggerated immune response. Sepsis is caused either when cytokine production exponentially increases to an extent that it escapes the local infection or when uncontrolled infection enters the circulation. Victims of septic shock experience fever, plummeting blood pressure, myocardial suppression, headache, dehydration, kidney failure and respiratory arrest. This exaggerated immune response causes body organs to fail and death may result from lethal septic shock.<br /> Staph aureus is a normal commensal inhabitant of skin and mucus linings. When stressed by a low zinc or magnesium environment, it changes its metabolism, making more lipopolysaccharides to create a thicker cell wall. These cell wall lipopolysaccharides mimic one of our own cytokines, endotoxin, which even at extremely low concentrations is a major immune-system messenger of alarm.<br /> Women whose diets are low in zinc or magnesium or may be a bit bulimic or have diarrhea or be taking mineral-wasting diuretics will have lower tissue levels of these important minerals. If a super-absorbent tampon is used, that further lowers level of zinc and magnesium locally causing the normal commensal staph aureus to change its metabolism in response to this stress and thicken its lipopolysaccharide cell wall, making many more mimics of endotoxin. Such lipopolysaccharide signaling can create an overwhelming crescendo of immune response, sometimes leading to toxic shock syndrome and death.<br />Exhaustion of reduced glutathione is the septic switch that shuts down cellular immunity, while encouraging uncontrolled inflammation, which signals biofilm to become pathogenic triggering responsive unbridled allergic response as well as auto-immune destruction.<br /> Zinc and magnesium are also critical for recreating reduced glutathione (GSH). Lack of GSH, this primary hydrogen ion supplier, reduces energy production dimming the electromagnetic barrier produced by our aerobic cells while at the same time slowing activity of immune white blood cells. <br /> Lack of reduced glutathione shuts down phagocytic cellular immunity since the white blood cell becomes sluggish and can neither turn on its ‘killer’ metabolism nor protect itself from its own purifying oxidative burst. Blocks in the ability to recycle glutathione become the ‘septic switch’ that encourages pathogenicity of one’s resident biofilm. Then, to compound the damage, commonly prescribed antibiotics often further wipe out the friendly flora designed to compete against yeast overgrowth or viral attacks like influenza.<br /> Activation of central (brain) cholinergic transmission by selective muscarinic receptor ligands results in lower systemic TNF levels in rodents and indicates that the efferent vagus nerve provides a functional brain-to-immune system connection. Central cholinergic signaling significantly activates the cholinergic anti-inflammatory pathway. <br />When cellular immunity becomes depressed, humoral immunity is then responsively turned on, (and untethered due to lack of reduced glutathione) with its hypersensitivities and allergies caused by increased antibody production, along with heightened expression of normally suppressed onboard bacteria, yeasts and viruses as well as unbridled auto-immune destruction.<br /> Reduced glutathione is so critically foundational for cellular function that multiple genes and three major chemical pathways create, regenerate and support its production. Multiple toxicities (mercury poisons a key enzyme) or deficiencies must be present before GSH (reduced glutathione) stores are compromised. Vitamins C and E recycle oxidized glutathione. Hardly anybody eats enough fresh fruit or whole grains with vitamin E. ‘Which straw broke the camel’s back?’ <br /> Recycling oxidized glutathione to reduced glutathione is heavily dependent on all methylating B vitamins as well as foundationally on methionine, niacin, riboflavin and pyridoxine. Zinc, selenium or magnesium are also critical cofactors. NAC (n-acetyl cysteine), glutamine, glycine, taurine, selenium, milk thistle, regular and fermented garlic, ginger, turmeric and its curcurmin, balloon flower root, guggal and Hawthorne all help recycle glutathione.<br /> Lipoic acid at (100-200mg/day) independently helps recycle glutathione and increases levels 30%. Take lipoic acid along with biotin for best effect, at 50mcg biotin for every 100mg lipoic acid. <br /> Larger doses of lipoic acid (like NAC) in ranges of 600-3,000mg/day may also mobilize heavy metals and toxins creating irritability, low blood sugars, rashes and cognitive difficulty. Reduce dose to lessen negative symptoms of redistribution; drink lots of water; stoke multiminerals; eat seaweeds, greens, avocados and raw egg yolks; use clays and activated charcoal to sop up poisons. Friendly bacteria and extra fiber detoxify and open up excretion channels.<br />Biofilm life-forms want glutathione and SOD too.<br /> Immunity often weakens due to opportunistic onboard RNA viruses chronically replicating and encoding to produce their own protective glutathione peroxidase, reducing our supplies. Many viruses and bacteria either encode for and make glutathione or acquire (steal) it or its ingredients directly from their host. <br /> Most life forms use glutathione as a universal mechanism for protection from free radicals, toxicity and radiation. Included are HIV 1 & 2, Coxsackie B, Hepatitis B & C, some herpes and other viruses along with many forms of bacteria. <br /> Next among the most important regulators of reactive oxygen species levels are the superoxide dismutase (SOD) enzymes: copper/zinc SOD functioning in the cytoplasm and outer mitochondrial space, and manganese SOD existing exclusively in the inner mitochondrial space. Superoxide is converted to hydrogen peroxide (H2O2) and O2 by SOD. Peroxiredoxins and abundant catalase enzyme then scavenge the hydrogen peroxide, converting it to molecular oxygen and water.<br /> Microorganisms can also hijack SOD for their own use, then making our mitochondria reject the normally sustaining, but now damaging oxygen (due to SOD lack), disabling energy production, creating chronic fatigue, fibromyalgia with compromised detoxification and altered immunity along with multiple environmental sensitivities.<br /> When a phagocytic cell attacks defective cell, virus, bacteria or antigenic food information, its metabolism revs up a thousand fold, using peroxisome produced peroxides to dismantle its foe(s). If short of pivotal glutathione reserves, the white blood cell cannot generate an explosion of energy or protect itself from its own peroxidative burst and cellular immunity shuts down. <br /> The cellularly-undefended allergic or hypersensitive state called humoral immunity then compensatorily switches on. Plaque begins accumulating in the mouth or the yeast itch and/or burning begins; or prodromal awareness starts with a brewing expression of herpes outbreak that may create ulcers in mucus membranes, fissures in the tongue or clusters of painfully bubbling hives on the lips or skin. Next, that injured joint or tooth that was just a minor annoyance begins to add to the inflammatory cacophony.<br /> Virus replication competes for and removes onboard glutathione precursors: selenium, glutamine, cysteine and tryptophan or glycine from the host. This creates deficiencies that disable immune and neuroendocrine function at multiple levels. Virally infected ‘putative’ bacterial periodontal pathogens (also found in arterial plaque) are five times (if Epstein-Barr co-infected) to thirty times (if Herpes-6 co-infected) more pathogenic. <br /> The herpes virus (human cytomegalovirus, HCMV and Epstein-Barr virus, EBV) are often involved in periodontal diseases. Genomes of HCMV and EBV occur at high frequency in aggressive, HIV-associated, ANUG, and advanced type periodontitis associated with medical disorders. HCMV infects periodontal monocytes/macrophages and lymphocytes, and EBV infects periodontal B-lymphocytes. Herpes virus-infected inflammatory cells may elicit tissue-destroying cytokines and thus create diminished ability to defend against bacterial challenge.<br /> Viruses and viroids are the RNA ribosomal world responding to the environment we are both in, choosing various expressions of our species’ DNA and our individual biofilm’s DNA. Virally-induced nutritional deficiency is expressed as spiraling-downward worsening disease. Aggressive periodontal disease is a significant ‘septic’ break down in immunity, not that different from other AIDS-related infections, requiring significant changes in diet and lifestyle to restore rhythm and repair cellular immunity for real reversal.<br />More biofilm control strategies<br /> The therapeutic effect of hyperbaric oxygen (HBO) is related to elevated partial oxygen pressure in the tissues. HBO both alone and in combination with scaling and root planning of the teeth (SRP) reduced the Gingival Index value to zero and gingival health persisted for 3 months at least. Thus, in parallel with the loss of periodontal pathogenic bacteria, a substantial improvement in oral health was observed.<br /> The combination of HBO and SRP substantially reduced (by up to 99.9%) gram-negative anaerobe loads of subgingival microflora. The low values of pathogens persisted for at least two months after the therapy. HBO or SRP alone produced a temporarily more limited effect on periodontal anaerobes. HBO both alone and in combination with SRP reduced the Gingival Index value to zero and gingival health persisted for 3 months at least.<br />Phosphate sequestration theory of dental caries<br /> Both bacteria and we use large amounts of phosphorous to make ATP (adenosine triphosphate), the biochemical currency of energy. We make roughly half our body weight in ATP each day. When we consume large amounts of sugar, lots of ATP is generated, reducing the amount of available needed phosphorous for the benign biofilm plaque living on teeth. Taking large doses of calcium can also deplete available phosphorous. <br /> By changing its metabolism to generate more acid, dental plaque, the mouth’s cooperative biofilm can conveniently release and obtain newly needed phosphorus by dissolving the calcium phosphate hydroxyapatite crystal of adjacent teeth.<br /> Besides lowering available phosphorus, excessive sugar (or just too many calories) fuels the germs while it creates a spiked release of cortisol and other stress hormones. This causes patrolling mobile white blood cells to sequester themselves in the liver and spleen, thus removing them from actively policing the barrier tissues and tubes (arteries, veins, digestive system, ducts, bladders as well as oral and nasopharyngeal membranes). Stress in all of its guises shuts down cellular immunity, responsively encouraging hypersensitivities, auto-immunity and development of pathogenic biofilm.<br />Other anti-plaque strategies<br /> Polyphenols occurring in cocoa, coffee and tea have a role in the prevention of cariogenic processes, due to their antibacterial action. Cocoa polyphenol pentamers significantly reduce biofilm formation and acid production by Streptococcus mutans and S. sanguinis. In the same way, trigonelline, caffeine and chlorogenic acid occurring in green and roasted coffee interfere with S. mutans adsorption to saliva-coated hydroxyapatite beads. <br /> Studies on green, oolong and black teas show that tea polyphenols exert an anti-caries effect via an anti-microbial mode-of-action, and galloyl esters of (-)-epicatechin, (-)-epigallocatechin and (-)-gallocatechin show increasing antibacterial activities. The anti-cariogenic effects against alpha-hemolytic streptococci showed by polyphenols from cocoa, coffee and tea suggest use of these beverages in the prevention of caries.<br /> Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola are three major etiological agents of chronic periodontitis. The strong proteolytic activities of these bacteria are critical to their survival since their energy source is obtained from peptides and amino acids derived from proteins. In addition, proteases are important factors potentially contributing to periodontal tissue destruction by a variety of mechanisms, including direct tissue degradation and modulation of host inflammatory responses. <br /> Non-dialyzable material prepared from cranberry juice concentrate reduces either the proliferation of P. gingivalis, T. forsythia and T. denticola in periodontal pockets or their proteinase-mediated destructive process occurring in periodontitis.<br /> Ethanol extracts from the peels of mangosteen (Garcinia mangostana L.) showed strong inhibition of acid production by S. mutans. Garcinia mangostana L extract in ethanol strongly inhibited the biofilm formation of S. mutans. Its deep purple rind contains fulxanthones and polysaccharides, which have powerful antibacterial effects, with in vitro activity against a range of antibiotic-resistant bacteria. Mangosteen compounds also help inhibit IgE-mediated histamine release and inhibit development of pre-neoplastic lesions.<br />Biofilm survival strategy creates non-healing wounds and cancer.<br /> Once established to critical mass, biofilm infections circumvent the host immune system to promote chronicity in wounds. The biofilm in wounds can actually hijack host immunity to help its pathogens survive and remain in their niche within the wound. In contrast to the most commonly accepted hypothesis of host-centered pathology, it is quite possible that bacteria in an unclean wound, not host dysfunction, cause the chronicity and perpetual inflammation associated with chronic non-healing wounds. <br /> Biofilm formation in wounds is the best unifying explanation for the failure of a variety of chronic wounds to heal.  Clinical evidence has shown improved healing when chronic wounds are treated with the assumption that biofilm is the cause of the failure to heal.<br /> Cancer is a non-healing wound, and shares many characteristics with pathogenic biofilm. It turns out that the promising anti-cancer angiogenesis (VEGF) inhibitors do reduce blood supply to tumors and thus shrink them, extending life a few months. But then the strategies of the tumor changes (just like a biofilm), and it seeds and metastasizes. <br /> Dr. T. Simoncini, an oncologist in Rome, Italy has pioneered sodium bicarbonate (NaHCO3) therapy as a means to treat cancer. The fundamental theory behind this treatment is that, despite a number of variable factors, the formation and spreading of tumors seems simply the result of the presence of an invasive fungal biofilm. Dandruff, yeasty dental plaque, athlete’s foot and nail fungus are common ‘contained’ fungal biofilm infections.<br /> For about 100 years, the fundamental theory behind cancer has been based on the theory that it is a malfunctioning of the genes. This point of view implies that cancer is primarily genetic and intracellular. Dr. Simoncini thinks that cancer is often a chronic fungal biofilm infection, and therefore primarily an extra cellular phenomenon, then triggering genetic changes in responsive stem cells.<br /> Sodium bicarbonate, unlike other anti-fungal remedies to which fungus can become tolerant or resistant, is extremely diffusible and retains its ability to penetrate the tumor, due to the speed at which the sodium bicarbonate disintegrates the tumor. This speed makes fungi’s adaptability impossible, rendering it defenseless. <br /> The sodium bicarbonate solution is administered directly on the tumor, if possible. Otherwise, it can be administered by selective arteriography, which basically means selecting specific arteries through which the solution is administered, which subsequently dissolves the tumor.<br /> Molecular analyses of chronic wound specimens divulge diverse polymicrobial communities and the presence of bacteria, including strictly anaerobic bacteria, rarely revealed by culture. Bacterial biofilm prevalence in s