Glossary

1,25-dihydroxyvitamin DPrimary biologically active vitamin D hormone. Activates the vitamin D nuclear receptor. Produced by hydroxylation of 25-D. Also known as 1,25-dihydroxycholecalciferol, 1,25-hydroxyvitamin D and calcitirol. (1,25-DPrimary biologically active vitamin D hormone. Activates the vitamin D nuclear receptor. Produced by hydroxylation of 25-D. Also known as 1,25-dihydroxycholecalciferol, 1,25-hydroxyvitamin D and calcitirol.) – Primary biologically active vitamin D hormone. Activates the Vitamin D Nuclear Receptor. Produced by hydroxylation of 25-DThe vitamin D metabolite widely (and erroneously) considered best indicator of vitamin D "deficiency." Inactivates the Vitamin D Nuclear Receptor. Produced by hydroxylation of vitamin D3 in the liver. . Also known as 1,25-dihydroxycholecalciferol, and calcitriol.

25-hydroxyvitamin DThe vitamin D metabolite widely (and erroneously) considered best indicator of vitamin D "deficiency." Inactivates the Vitamin D Nuclear Receptor. Produced by hydroxylation of vitamin D3 in the liver. (25-D) – The vitamin D metabolite widely (and erroneously) considered best indicator of vitamin D “deficiency.” Inactivates the vitamin D nuclear receptorA nuclear receptor located throughout the body that plays a key role in the innate immune response.. Produced by hydroxylation of vitamin D3Form of vitamin D made in the skin when exposed to light. Also available in fish and meat. This secosteroid is sometimes converted into 25-D. Also known as cholecalciferol and activated 7-dehydrocholesterol. in the liver.

7-dehydrocholesterolA cholesterol precursor manufactured by humans; when exposed to ultraviolet light converted into vitamin D3. Also known as previtamin-D3. – A cholesterol precursor manufactured by humans; when exposed to ultraviolet light, converted into vitamin D3. Also known as previtamin-D3.

acute bacteria/infection/disease – The term acute does not indicate the severity of the disease. Instead, it indicates how long the disease lasts and how quickly it develops. An infection causing disease with a sudden onset, severity and (often) short course - usually 3 months or less - is an acute infection. Examples of acute diseases include colds, influenza, and strep throat. Acute infections do appear to predispose a person to later chronic disease. See chronic infection.

anti-TNF drugsDrugs which interfere with the body's production of TNF-alpha - a cytokine necessary for recovery from infection – Drugs which interfere with the body's production of TNF-alpha, a cytokineAny of various protein molecules secreted by cells of the immune system that serve to regulate the immune system. necessary for recovery from infection.

antimicrobial peptidesBody’s naturally produced broad-spectrum antibacterials which target pathogens. (AMPs) – The body’s naturally-produced broad-spectrum antibacterials which target pathogens.

autoimmuneA condition or disease thought to arise from an overactive immune response of the body against substances and tissues normally present in the body – A condition or disease thought to arise from an overactive immune response of the body against substances and tissues normally present in the body.

Autoimmunity Research FoundationNon-profit foundation dedicated to exploring a pathogenesis and therapy for chronic disease. – Non-profit foundation dedicated to exploring a pathogenesis and therapy for chronic disease.

azithromycin (Zithromax)Bacteriostatic antibiotic used by Marshall Protocol patients. Has relatively long half-life. – Bacteriostatic antibiotic used by Marshall ProtocolA curative medical treatment for chronic inflammatory disease. Based on the Marshall Pathogenesis. patients. Has relatively long half-life.

Bactrim DSSulfa antibiotic used by patients on the Marshall Protocol. Combination of sulfamethoxazole and trimethoprim. Works by blocking bacterial folic acid synthesis. – Sulfa antibiotic used by patients on the Marshall Protocol. Combination of sulfamethoxazole and trimethoprim. Works by locking bacterial folic acid synthesis.

beta-Defensin An antimicrobial peptide found primarily in immune cells and transcribed by the Vitamin D Receptor. – An antimicrobial peptide found primarily in immune cells and transcribed by the Vitamin D ReceptorA nuclear receptor located throughout the body that plays a key role in the innate immune response..

biofilmA structured community of microorganisms encapsulated within a self-developed protective matrix and living together. – A structured community of microorganisms encapsulated within a self-developed protective matrix and living together.

CYP24A1 – Enzyme transcribed by the Vitamin D Receptor. Acts to break 1,25-D down into 25-D. Sometimes referred to as CYP24.

CYP24 – Enzyme transcribed by the Vitamin D Receptor. Acts to break 1,25-D down into 25-D. Sometimes referred to as CYP24A1.

CYP27A1 – Enzyme which inhibits conversion of pre-vitamin D to 25-D.

CYP27B1 – Enzyme activated when immune system is challenged by pathogens. Activity causes 25-D to be converted into 1,25-D.

CYP3A4 – Enzyme which breaks down 1,25-D. Transcribed by the PXR (Pregnane X Nuclear Receptor).

cardiac immunopathologyAn exacerbation in symptoms of the heart muscle. Requires careful management by physicians. – An exacerbation in symptoms of the heart muscle. Requires careful management by physicians.

cathelicidins Family of antimicrobial peptides found primarily in immune cells and transcribed by the Vitamin D Receptor. – Family of antimicrobial peptides found primarily in immune cells and transcribed by the Vitamin D Receptor.

chlorogenic acidAn antioxidant and phenolic compound which in ways that are not yet fully clear can modulate and/or suppress the immune response – An antioxidant and phenolic compound, which in ways that are not yet fully clear, can modulate and/or suppress the immune response.

chronic bacteria/infection/disease – In the context of the Marshall PathogenesisA description for how chronic inflammatory diseases originate and develop., the term chronic is often used to refer to bacterial infections which persist over a long period of time, often decades. Chronic bacteria are harder to detect and, according to the Marshall Pathogenesis, play a central role in driving chronic inflammatory disease. Examples of chronic diseases include kidney disease, cancer, diabetes, and any of the other dozens of diseases which the MP addresses. See acute infection.

clindamycinBacteriostatic antibiotic used by patients on the Marshall Protocol. – Bacteriostatic antibiotic used by patients on the Marshall Protocol.

cognitive dysfunctionThe loss of intellectual functions such as reasoning; memory loss; and other neurological abilities that is severe enough to interfere with daily functioning. – The loss of intellectual functions, such as reasoning, memory loss, and other neurological abilities, that is severe enough to interfere with daily functioning.

corticosteroidsA first-line treatment for a number of diseases. Corticosteroids work by slowing the innate immune response. This provides some patients with temporary symptom palliation but exacerbates the disease over the long-term by allowing chronic pathogens to proliferate. – A first-line treatment for a number of diseases. Corticosteroids work by slowing the innate immune responseThe body's first line of defense against intracellular and other pathogens. According to the Marshall Pathogenesis the innate immune system becomes disabled as patients develop chronic disease.. This provides some patients with temporary symptom palliation, but exacerbates the disease over the long-term by allowing chronic pathogens to proliferate.

cytokinesAny of various protein molecules secreted by cells of the immune system that serve to regulate the immune system. – Any of various protein molecules secreted by cells of the immune system that serve to regulate the immune system.

demeclocyclineBacteriostatic antibiotic used by patients on the Marshall Protocol. – Bacteriostatic antibiotic used by patients on the Marshall Protocol.

endotoxin – A toxin associated with the outer membranes of bacteria, especially gram-negative bacteria. When these bacteria are destroyed, as will happen during the MP, endotoxins are released, causing a spike in symptoms known as the immunopathological reactionA temporary increase in disease symptoms experiences by Marshall Protocol patients that results from the release of cytokines and endotoxins as disease-causing bacteria are killed..

familial aggregationOccurrence of a given trait shared by members of a family (or community) that cannot be readily accounted for by chance. – Occurrence of a given trait shared by members of a family (or community) that cannot be readily accounted for by chance.

high-dose antibiotic therapy – Any treatment which uses antibiotics at a large enough dose that the immune response is suppressed more than it is not.

horizontal gene transferAny process in which a bacterium inserts genetic material into the genomes of other pathogens or into the genome of its host. – Any process in which a bacterium inserts genetic material into the genomes of other pathogens or into the genome of its host. Also referred to as lateral gene transferAny process in which a bacterium inserts genetic material into the genomes of other pathogens or into the genome of its host. Also referred to as horizontal gene transfer..

human microbiotaThe bacterial community in the human body. Many species in the microbiota contribute to the development of chronic disease. – The bacterial community in the human body. Many species in the microbiotaThe bacterial community which causes chronic diseases - one which almost certainly includes multiple species and bacterial forms. contribute to the development of chronic disease.

immunopathological reaction – Reaction characterized by damage caused by immune activity. Immunopathology is an increase in one's symptoms of disease and is an indication of progress on the Marshall Protocol.

immunopathologyA temporary increase in disease symptoms experienced by Marshall Protocol patients that results from the release of cytokines and endotoxins as disease-causing bacteria are killed. – A temporary increase in disease symptoms, experienced by Marshall Protocol patients, that results from the release of cytokines and endotoxins as disease-causing bacteria are killed.

in silicoExperiment technique performed on computer or via computer emulation. – Experimental technique performed on computer or via computer emulation.

in vitroA technique of performing a given procedure in a controlled environment outside of a living organism - usually a laboratory. – A technique of performing a given procedure in a controlled environment outside of a living organism, usually a laboratory.

in vivoA type of scientific study that analyzes an organism in its natural living environment. – A type of scientific study that analyzes an organism in its natural living environment.

inflammationThe complex biological response of vascular tissues to harmful stimuli such as pathogens or damaged cells. It is a protective attempt by the organism to remove the injurious stimuli as well as initiate the healing process for the tissue. – The complex biological response of vascular tissues to harmful stimuli, such as pathogens or damaged cells. It is a protective attempt by the organism to remove the injurious stimuli, as well as initiate the healing process for the tissue.

innate immune response – The body's first line of defense against intracellular and other pathogens. According to the Marshall Pathogenesis, the innate immune system becomes disabled as patients develop chronic disease. Also known as innate immunityThe body's first line of defense against intracellular and other pathogens. According to the Marshall Pathogenesis the innate immune system becomes disabled as patients develop chronic disease..

Interferon-gammaAn inflammatory cytokine which causes extra mast cells to differentiate to monocytes and then to further differentiate into macrophages and dendritic cells. These phagocytes are the most active cells of the immune system and are charged with digesting bacterial pathogens. (IFN-γ) – An inflammatory cytokine which causes extra mast cells to differentiate to monocytes (primitive white cells) and then to further differentiate (grow) into macrophages and dendritic cells. These phagocytes are the most active cells of the immune system and are charged with digesting bacterial pathogens.

intolerable immunopathologyAn unbearable or unsafe severity of bacterial die-off reaction. – An unbearable or unsafe severity of bacterial die-off reaction.

Koch's postulatesCentury-old criteria designed to establish a causal relationship between a causative microbe and a disease. Koch's belief that only one pathogen causes one disease has now been called into question as multiple postulates are increasingly considered out of date. – Century-old criteria designed to establish a relationship between a causative microbe and a disease. Koch's belief that only one pathogen causes one disease has now been called into question, as multiple postulates are increasingly considered out-of-date.

L-formDifficult-to-culture bacteria that lack a cell wall and are not detectable by traditional culturing processes. Sometimes referred to as cell wall deficient bacteria. – Difficult-to-culture bacteria that lack a cell wall and are not detectable by traditional culturing processes. Sometimes referred to as cell wall deficient bacteria.

lateral gene transfer – Any process in which a bacterium inserts genetic material into the genomes of other pathogens or into the genome of its host. Also referred to as horizontal gene transfer.

Marshall Pathogenesis – A description for how chronic inflammatory diseases originate and develop.

Marshall Protocol – A curative medical treatment for chronic inflammatory disease, based on the Marshall Pathogenesis.

metagenomics - The study of genetic material recovered directly from environmental samples, as opposed to traditional microbiology and microbial genome sequencing, which rely upon cultivated clonal cultures.

metagenomic microbiotaThe community of bacterial pathogens including those in an intracellular and biofilm state which cause chronic disease. – The community of bacterial pathogens, including those in an intracellular and biofilm state which cause chronic disease.

microbiota – The bacterial community which causes chronic diseases; one which almost certainly includes multiple species and bacterial forms.

minimum inhibitory concentrationThe lowest concentration of an antimicrobial that will inhibit the visible growth of a microorganism after overnight incubation. Dosing at well below the MIC improves the MP's effectiveness against slow-growing chronic pathogens and reduces the likelihood of resistance. (MIC) – The lowest concentration of an antimicrobial that will inhibit the visible growth of a microorganism after overnight incubation. Dosing at well below the MIC improves the MP's effectiveness against slow-growing chronic pathogens and reduces the likelihood of resistance.

minocyclineBacteriostatic antibiotic used by Marshall Protocol patients. – Bacteriostatic antibiotic used by Marshall Protocol patients.

murine modelA model of disease which uses rats or mice to mimic human conditions. – A model of disease which uses rats or mice to mimic human conditions.

neurological immunopathologyA temporary exacerbation of neurological symptoms due to bacterial death. Requires careful management by physicians. – A temporary exacerbation of neurological symptoms due to bacterial death.

NoIRSpecial sunglasses worn by Marshall Protocol patients to block light. – Special sunglasses worn by Marshall Protocol patients to block light. The name comes from the phrase “no infrared.” Sometimes called NoIRsSpecial sunglasses worn by Marshall Protocol patients to block light. or NoIR glasses.”

Nuclear Factor-kappa BA protein that stimulates the release of inflammatory cytokines in response to infection (NF-kappaBA protein that stimulates the release of inflammatory cytokines in response to infection) – A protein that stimulates the release of inflammatory cytokines in response to infection. Olmesartan (Benicar) blocks the Angiotensin Receptor, and in the process decreases levels of Nuclear Factor Kappa B. Also known as NF-kBA protein that stimulates the release of inflammatory cytokines in response to infection.

nuclear receptorIntracellular receptor proteins that bind to hydrophobic signal molecules (such as steroid and thyroid hormones) or intracellular metabolites and are thus activated to bind to specific DNA sequences which affects transcription. – Intracellular receptor proteins that bind to hydrophobic signal molecules (such as steroid and thyroid hormones) or intracellular metabolites and are thus activated to bind to specific DNA sequences which affect transcription.

olmesartan (Benicar)Medication taken regularly by patients on the Marshall Protocol for its ability to activate the Vitamin D Receptor. – Medication taken regularly by patients on the Marshall Protocol for its ability to activate the Vitamin D Receptor. Also known by the trade name Benicar.

Pea Soup – The unique combination of bacterial pathogens (and co-mingling of bacterial genes), which accounts for each individual’s disease presentation.

photosensitivityAbnormal sensitivity to sunlight and bright lights. Also referred to as "sun flare" or "light flare." – Abnormal sensitivity to sunlight and bright lights. Also referred to as “sun flare” or “light flare.”

previtamin D3Largely inactive vitamin D metabolite naturally occurring in the human body. When exposed to ultraviolet radiation converted into 25-D. Also known as 7-dehydrocholesterol – Largely inactive vitamin D metabolite, naturally occurring in the human body. When exposed to ultraviolet radiation converted into 25-D. Also known as 7-dehydrocholesterol.

pulsed low dosingAdministration of an antibiotic periodically such as every 48 hours and in amounts small enough that the immunosuppressive effects of the antibiotics are minimized. – Administration of an antibiotic periodically, such as every 48 hours and in amounts small enough that the immunosuppressive effects of the antibiotics are minimized.

Pregnane Xenobiotic Receptor (PXR) – Nuclear receptor which inhibits conversion of pre-vitamin D to 25-D, causing 25-D levels to drop via the CYP27A1 pathway. More significantly though, it transcribes CYP3A4, an enzyme which breaks down 1,25-D.

quercetin – Antioxidant supplement taken by some Marshall Protocol patients to limit intolerable immunopathology. Quercetin inhibits production of Nuclear Factor-kappa B, an inflammatory cytokine.

respiratory immunopathologyA temporary exacerbation in symptoms of the lungs due to bacterial death. Requires careful management by physicians. – A temporary exacerbation in symptoms of the lungs due to bacterial death. Requires careful management by physicians.

Robert KochAuthor of Koch’s postulates – Author of Koch’s postulates, a set of rules for establishing a causal relationship between a microbe and a disease.

spontaneous remissionTheory that diseases go away of their own accord. – Theory that diseases go away of their own accord.

successive infection – An infectious cascade of pathogens in which initial infectious agents slow the immune response and make it easier for subsequent infections to proliferate.

Th1 DiseasesThe chronic inflammatory diseases caused by bacterial pathogens. – The chronic inflammatory diseases caused by bacterial pathogens.

Th1 inflammationThe complex biological response of vascular tissues to harmful stimuli such as pathogens or damaged cells. It is a protective attempt by the organism to remove the injurious stimuli as well as initiate the healing process for the tissue. – The complex biological response of vascular tissues to harmful stimuli, such as pathogens or damaged cells. It is a protective attempt by the organism to remove the injurious stimuli, as well as initiate the healing process for the tissue.

Th1 PathogensThe community of bacterial pathogens which cause chronic inflammatory disease - one which almost certainly includes multiple species and bacterial forms. – The community of bacterial pathogens which cause chronic inflammatory disease; one which almost certainly includes multiple species and bacterial forms.

Th1 Spectrum DisorderThe overlap of different disease symptoms in different patients with similar diagnoses - caused by the fact that any one bacterial species can contribute to numerous disease states. – The overlap of different disease symptoms in different patients with similar diagnoses–caused by the fact that any one bacterial species can contribute to numerous disease states.

tetracycline antibiotics – Family of bacteriostatic antibiotics, a few of which are used by the Marshall Protocol, including clindamycin, azithromycin (Zithromax), demeclocycline, and minocycline. So-called bacterial resistance to the tetracyclines is overcome with the concurrent use of a Vitamin D Receptor agonistA substance such as olmesartan (Benicar) or 125-D which activates the Vitamin D Receptor and transcribes the genes necessary for a proper innate immune response., olmesartan (Benicar).

therapeutic probeA brief trial of the Marshall Protocol to see if it will generate an immunopathological response. The "gold standard" for testing whether a patient is a good candidate for the MP. – A brief trial of the Marshall Protocol to see if it will generate an immunopathological response. The “gold standard” for testing whether a patient is a good candidate for the MP.

TLR2a receptor which is expressed on the surface of certain cells and recognizes native or foreign substances and passes on appropriate signals to the cell and/or the nervous system. – A receptor which is expressed on the surface of certain cells and recognizes native or foreign substances and passes on appropriate signals to the cell and/or the nervous system. Part of the body's innate immune response.

tolerable immunopathologyA state in which a patient has maintained an acceptable intensity of bacterial die-off reaction. The primary goal of the Marshall Protocol. – A state in which a patient has maintained an acceptable intensity of bacterial die-off reaction. The primary goal of the Marshall Protocol.

transmissionAn incident in which an infectious disease is transmitted. – An incident in which an infectious disease is transmitted.

tumor necrosis factor-alphaA cytokine critical for effective immune surveillance and is required for proper proliferation and function of immune cells. (TNF-alpha) – A cytokine critical for effective immune surveillance and is required for proper proliferation and function of immune. Anti-TNF drugs block production of TNF-alpha cells.

Vitamin D Receptor (VDRThe Vitamin D Receptor. A nuclear receptor located throughout the body that plays a key role in the innate immune response.) – A nuclear receptor located throughout the body that plays a key role in the innate immune response.

vitamin D2Form of vitamin D created by plants and fungi. When ingested the secosteroid is (sometimes) converted into 25-D. Also known as ergocholecalciferol. – Form of vitamin D created by plants and fungi. When ingested, the secosteroid is (sometimes) converted into 25-D. Also known as ergocholecalciferol.

vitamin D3 – Form of vitamin D made in the skin when exposed to light. Also available in fish and meat. This secosteroid is sometimes converted into 25-D. Also known as cholecalciferol and activated 7-dehydrocholesterol.

VDR agonistA substance such as olmesartan (Benicar) or 125-D which activates the Vitamin D Receptor and transcribes the genes necessary for a proper innate immune response. - A substance such as olmesartan (Benicar) or 1,25-D which activates the Vitamin D Receptor and transcribes the genes necessary for a proper innate immune response.

VDR antagonistA substance such as 25-D or certain bacterial ligands which inactivates the Vitamin D Receptor the receptor which transcribes the genes necessary for a proper innate immune response. - A substance such as 25-D or certain bacterial ligands which inactivates the Vitamin D Receptor, the receptor which transcribes the genes necessary for a proper innate immune response.