Definitions of key terms used in: Arthritis and Autoimmune Disease: The Infection Connection

by Katherine M. Poehlmann, PhD.



Adaptogenic: pertaining to the natural selection of the offspring of a mutant organism better adapted to a new or changed environment, particularly applicable to drug resistant microbes.

Adjuvant: a substance which, administered with a drug or antigen, enhances its pharmacological effect or its antigenicity.

Absorption: the uptake of substances into or across tissues.

Adsorption: the action of a substance in attracting and holding other materials or particles on its surface.

Allergen: a substance capable of triggering an allergic state when introduced into the body. Major categories of allergens are cellular, viral, bacterial, food, chemical, and mycoplasmal. An incoming allergen produces a histamine reaction that prompts the body to generate hydrogen peroxide, which initiates the body’s cell-destruction process, leading to inflammation at the site of the invasion.

Anaerobe: an organism that lives and grows in very low levels of molecular oxygen.

Anaphylaxis: a serious allergic reaction accompanied by shortness of breath, loss of consciousness, even death. Can be triggered by venom (e.g., bee, hornet, jellyfish) or foods (e.g., peanuts).

Antibody: a soluble protein molecule with disease-fighting properties. Antibodies are produced and secreted by B-cells in response to antigenic stimulus. These molecules are capable of binding to a specific antigen, so they are shape-related to the sugar coat of the cells or microorganisms they are intended to attack.

Antigen: a substance consisting mainly of proteins (but which can also consist of carbohydrates, lipids, and sometimes nucleic acids) that is recognized as foreign and gives rise to an immune reaction, i.e., production of antibodies or immune cells. It can also be the toxin secreted by mycoplasmas.

Apoptosis: programmed cell death.

Arbovirus: a viral disease spread by the bite of an arthropod. E.g., mosquito-transmitted Dengue fever.

Ayurvedic: pertaining to Ayurveda, a holistic system of medicine indigenous to and widely practiced in India for more than 5,000 years. Ayurveda was first recorded in the Vedas, said to be the world’s oldest extant Sanskrit literature.

Bacteria: any of numerous widely distributed unicellular, pleomorphic microorganisms that exhibit both animal and plant characteristics. Their three main varieties (bacillus, coccus, and spirillum) range from the harmless and beneficial to the intensely virulent and lethal.

Basophil: a granular blood leukocyte with an irregularly shaped nucleus. A basophil is also considered to be any structure, cell or histologic element staining readily with basic dyes. A high number could be an indicator of malignancy such as cancer or leukemia.

Blood/brain barrier (BBB): the biochemical partition that separates the brain and central nervous system from the blood stream so that only certain biochemicals can cross over. This complex physiologic filtering mechanism keeps many of the large molecules that circulate in the blood out of the central nervous system. The BBB blocks some drugs.

B-lymphocyte or B-cell: small white blood cells crucial to immune system defenses. B-cells originate in the bone marrow and develop into plasma cells, which produce antibodies.

Bone marrow: soft tissue located in the cavities of the bones. Bone marrow is the source of all blood cells in the healthy adult.

Bone Spur: calcium nodule growth produced by an infection.

Budding: the process by which microbes pull a portion of invaded cell membrane around their inner envelope and chromosomes, creating an outer protective coating and tethering the new “bud” to the parent cell.

Bursa: a pouch or sac-like cavity containing synovia and located at the points of tendon friction in the bodies of vertebrates.

Carcinogen: any cancer-causing agent or substance.

Cartilage: a fibrous elastic connective tissue forming most of the temporary skeleton of the embryo, providing a model for development of bones; also denotes a mass of such tissue, composed of collagen fibers and proteoglycans, at any particular site in the body.

Chelation: a medical treatment administered intravenously to bind toxic metals and minerals so they can be excreted from the body. EDTA chelation is the most common type of therapy offered, usually for vascular diseases.

Chemotactic: acting in response to chemical stimulation by initiating the inflammatory reaction, attracting leukocytes to the site of tissue damage.

Chemotherapeutic: pertains to the treatment of certain malignant diseases (e.g., cancer) by the disinfection of affected tissues through the use of chemically synthesized drugs having a specific action against certain pathogenic microorganisms.

Cholesterol: an alcohol compound (C27H45O) found in animal fats and oils, bile, blood, brain tissue, milk, egg yolk, myelin sheaths of nerve fibers, liver, kidneys, and adrenal glands.

Chondrocytes: cells that can produce cartilage by increasing the synthesis of proteoglycans.

Co-factor: an element or principle, e.g., a coenzyme, with which another element must unite in order to function. Also, a related causal element when both bacteria and viruses working together produce pathogenic symptoms. A cooperative element of a compound.

Collagen: a protein substance of the white fibers of skin, tendon, bone, cartilage, and nails.

Commensal: An organism participating in a symbiotic relationship in which one species derives some benefit while the other is believed to be unharmed.

Complement: a complex series of blood proteins whose action “complements” the work of antibodies. Complement destroys antibody-coated cells, produces inflammation, and regulates immune reactions.

Conjugation: the mating process in bacteria by which genetic information is exchanged between two genetically distinct organisms.

Contractures: the chronic loss of joint motion due to structural changes in non-bony tissue.

Cytokines: chemical messengers that help regulate the immune response by mobilizing white blood cells as necessary.

Cytopathic: pertaining to pathologic (unhealthy or diseased) changes in cells.

Cytotoxic T-cells: a special category of T-cells (lymphocytes) that kill other cells infected by viruses, fungi, or certain bacteria, or cells transformed by cancer.

DNA: genetic material (deoxyribonucleaic acid) that carries the directions a cell uses to perform a specific function, such as making a given protein using an RNA template made from the DNA.

Dystrophy: a degenerative disorder caused by inadequate or defective nutrition, toxins made by microbes, or drugs that block chemical pathways.

Edema: excessive fluid retention in intercellular spaces of the body.

ELISA (Enzyme Linked Immuno-Sorbant Assay): a highly accurate testing and diagnostic protocol used to identify specific antigens using IgG or IgE antibodies in a person’s blood sample. 

Endemic: a disease of tolerated morbidity present in a human or animal community at all times but clinically recognizable in only a few individuals. Lyme Disease and Dengue fever are two examples.

Endospore: a dormant, tough, temporarily non-reproductive structure produced by certain bacteria.

Enzyme: an organic compound that acts as a catalyst (an element that is essential) to the change in chemical composition of a material. Certain types of enzymes are required for the proper digestion and metabolism of food in the body. Enzymes break down the agent(s) causing inflammation.

Eosinophil: a granular leukocyte having a nucleus with two lobes connected by a thread of chromatin, and cytoplasm containing coarse, round granules of uniform size. An increase in abundance is usually associated with an allergic condition such as asthma or intestinal worms.

Epidemic: a disease of high morbidity only occasionally present in a human community, attacking many in a region at the same time and spreading rapidly. Hepatitis C is an example.

Epithelial cells: single or multiple layers of cells that line hollow organs and glands and that make up the outer surface of the body to protect or enclose organs. Most produce mucus or other secretions. Certain types of epithelial cells have tiny hairs called cilia that help remove foreign substances, e.g., from the respiratory tract.

Epitope: A localized region on the surface of an antigen that is capable of eliciting an immune response and of combining with a specific antibody to counter that response.

Etiology: a theory of the cause(s) of a disease.

Etiopathogenesis: the origin of the cause(s), development of cellular events, reactions and other pathologic mechanisms occurring during the development of disease.

Eucaryotes: organisms made up of complex cells that have organelles and a membrane-bounded nucleus. These organisms comprise four of the five Kingdoms of species taxonomy—Protista, Plantae, Fungi and Animalia. The remaining and most primitive is Kingdom Monera, which includes bacteria and other prokaryotic cells.

Exanthematic: pertaining to an eruptive disease or fever.

Exudates: materials that have escaped from blood vessels and been deposited in tissue or on tissue surfaces, usually the result of trauma or inflammation. The product is usually fluid, cells, or cellular debris.

Fastidious organism: a microorganism with unusual and/or complex nutritional and environmental requirements.

Gram-negative: bacteria that lose the primary Gram stain (a violet colored chemical) and pick up a counterstain, usually carbolfuchsin or safranine.

Gram-positive: retaining the color of the gentian violet stain in Gram’s method of staining.

Gram stain (Gram’s method): a process developed by Danish physician Hans Gram (1853-1938) for staining bacteria; the stain used to identify broad classes of bacteria based on their cell coat or capsule’s ability to pick up specific dyes.

Helper T-cells: a subset of T-cells that typically carry the CD4 marker and are essential for turning on antibody production, activating cytotoxic T-cells, and initiating many other immune system responses.

Heme [short for hematin]: the deep red, iron-containing non-protein, component of hemoglobin and some other biological molecules.

Hematopoietic: pertaining to the formation of blood cells.

Heparin: An acidic glycosaminoglycan found especially in lung and liver tissue that prevents the clotting of blood.

Histamine: an active chemical, released from mast cells, that causes smooth muscle contraction of human bronchioles and small blood vessels, increased permeability of capillaries, and increased secretion by nasal and bronchial mucous glands.

Homeostasis: the ability or tendency of an organism or cell to maintain internal equilibrium by adjusting its physiological processes

Hydrogen Peroxide (H2O2): a natural chemical compound that can be generated by the histamine reaction, or by certain microorganisms when they are attacked, or by leukocytes in the process of developing killer T-cells.

In vitro: observable in a test tube or other artificial lab setting.

In vivo: within the living body.

Iatrogenic: Caused or precipitated by physician intervention.

Immune system types: Innate is composed of the cells and mechanisms that defend the host from infection by other organisms in a non-specific manner; Adaptive is composed of highly specialized, systemic cells and processes that eliminate or prevent pathogenic growth.

Immunoglobulins (Ig): These antibodies are Y-shaped protein molecules produced by the B-cells. There are five classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM.

Immunosuppressive: capable of reducing normal immune responses, e.g., drugs given to prevent transplant rejection

Interferon: a molecule produced by cells (most often white blood cells) that can inhibit cell division and which has a variety of effects on the immune system.

Interstice: a small interval, space, or gap in a tissue or structure.

Jarisch-Herxheimer reaction: a short-term hypersensitivity response that is often mistakenly interpreted as antibiotic sensitivity.

Killer T-cells: see Cytotoxic.

Krebs cycle: The sequence of reactions by which most living cells generate energy during the process of aerobic respiration.

L-Form: also called the L-phase variant; a bacterium that has partially or entirely lost its cell walls. The “L” is for the Lister Institute in France where it was first discovered. Mycobacteria and other bacteria transform to the L-form when attacked by penicillin and related antibiotics. L-forms and mycoplasmas are of similar size and usually reproduce more slowly than bacteria. L-forms can regrow their cell walls, and therefore have a means to escape attack by antibiotics and emerge later.

Leukocyte: a white or colorless blood corpuscle, constituting an important agent in protection against infectious diseases.

Lipid: any of a group of organic substances, including fatty acids, neutral fats, waxes, steroids, and phosphatides, which are insoluble in water but soluble in alcohol, ether, chloroform, and other fat solvents; lipids are a source of body fuel and an important constituent of cells.

Lipoprotein: a combination of a lipid and a protein, having the general solubility property of proteins.

Lymphatic system: a bodily system composed of channels whose principal function is to maintain blood volume by returning to the general circulation those fluid and protein molecules that leak from the capillaries into interstitial spaces. The lymphatic system includes circulating lymphocytes and lymphoid organs, which are important in defense against infection and tumor growth as well as removal of wastes from the body.

Lymphocyte: white blood cells that are the smallest of the leukocytes, producing cytokines in the bone marrow and thymus, and that are essential for immune defense.

Lysis: destruction or decomposition, as of a cell or other substance, under influence of a specific agent. In context, can also mean gradual abatement of the symptoms of a disease.

Macrophages: enlarged, amoeba-like cells that entrap microorganisms and particles of foreign matter by phagocytosis. They usually arrive after the neutrophils to clean up the debris of dead cells and bacteria.

Mast cells: specialized immune cells found in the skin and nasal passages and in the gastrointestinal (GI) and respiratory tracts.

Mesenteric: Any of several folds of the membrane (peritoneum) lining the abdominal and pelvic walls connecting to the intestines.

Metabolism: the sum of all the chemical and physical processes by which elements of a living organism are produced and maintained; also the transformation by which energy is made available to the organism.

Metalloenzyme: any enzyme that contains tightly bound metal atoms, e.g., the cytochromes, a class of hemoproteins that are widely distributed in plant and animal tissues and whose main function is electron transport.

Microbe: a microscopic organism, especially one of the disease-causing bacteria or viruses.

Microbiome: the totality of microbes, their genetic elements (genomes), and environmental interactions within a particular environment.

Microbiota: microbial flora, the great majority of which are bacteria and fungi, harbored by normal, healthy individuals.

Microglia: small non-neural cells forming part of the supporting structure of the central nervous system. They are migratory and act as phagocytes at sites of neural damage or inflammation.

Microorganism: a general term for protozoa, fungi, bacteria, and viruses.

Mollicutes: from the Latin for “soft” and skin,” the class of cell wall-less prokaryotes to which mycoplasmas belong.

Motility: the ability to move spontaneously.

Mutagen: an agent that induces genetic mutation.

Mutate: to change a gene or unit of hereditary material that results in a new inheritable characteristic.

Mycobacteria: a slender, typically aerobic bacterium difficult to stain. Examples are tuberculosis and leprosy.

Mycoplasma: from the Latin base words for “fungus” and “fluid”; of intermediate size between bacteria and viruses, are characterized by the absence of a cell wall and pleomorphism; the smallest and simplest self-replicating organisms phylogenetically related to gram-positive bacteria, especially to mycobacteria, which have affinity for synovial tissue and cholesterol.

Myelin: the lipid substance surrounding the axis of a group of nerve fibers.

Neurogenic: originating in the nervous system, to form nervous tissue or to stimulate nervous energy.

Neuropeptide: a peptide synthesized within the body that influences neural activity or functioning.

Neutrophils: cells that migrate to the site of an injury and stick to the interior walls of the blood vessels. They then form projections that enable them to push their way into the infected tissues where they engulf and devour (phagocytize) microorganisms and other foreign particles.

Nosocomial: a secondary disorder (e.g., infection) related to a hospital that is unrelated to the patient’s primary condition.

Nucleophilic: having an affinity for the nucleus of a cell.

Palliative: affording relief; also a drug that acts to do so.

Pandemic: occurring over a wide geographic area and affecting an exceptionally high proportion of the population; e.g., malaria.

Parasite: a plant or animal that lives on or within another organism, from which it derives sustenance or protection without making compensation; applies to all infectious microbes, from viruses to ringworms. Parasites can be symbiotic, i.e., adapting and providing beneficial effects on the host. Some parasites can kill the host but others evolve into forms that do not.

Pareto Chart: a method used by economists to show allocation of resources in an economic system; a histogram to illustrate comparative values in a bar chart format.

Parvovirus: a group of extremely small, morphologically similar DNA viruses resistant to fungicides and sporicides.

Peptide: any of various amides derived from two or more amino acids by combination of the amino group of one acid with the carboxyl group of another; usually obtained by partial hydrolysis of proteins.

Peyer's patches: a collection of lymphoid tissues in the intestinal tract.

Phagocyte: any cell that engulfs and ingests microorganisms or other cells and foreign particles.

Pharmacodynamic: pertaining to the action of drugs on living systems.

Pharmacokinetic: pertaining to the study of drug activity or effectiveness for a certain purpose.

Physiology: the sum of all basic processes underlying the functioning of a species or class of organism.

Phytochemicals: plant-derived chemical extracts. There are tens of thousands of these, with varying bioactivity. Some have protective and antibiotic effects, e.g., allicin obtained from garlic.

Planktonic: free-floating microorganisms whose movements are controlled by water movement (not attached to surfaces).

Plasmids: extrachromosomal circular DNA molecules capable of independent replication and carrying genetic information for a variety of different functions, such as drug resistance.

Pleomorphism: exhibiting a variety of shapes.

Polymerase Chain Reaction (PCR): an extremely sensitive means of amplifying small quantities of DNA to detect low-level bacterial infections or rapid changes in transcription at the single cell level. It can also be used in DNA sequencing, screening for genetic disorders, site-specific mutation of DNA, cloning (or sub-cloning), and forensic science applications.

Prokaryote: an organism without a true nucleus, the nuclear material being scattered in the cytoplasm of the cell, and which reproduces by cell division. A bacterium is an example.

Prophylaxis: a measure taken to maintain health and prevent the spread of disease.

Prostacyclin: A prostaglandin produced in the walls of blood vessels that acts as a vasodilator and inhibits platelet aggregation.

Prostaglandins: naturally occurring fatty acids found in various tissues that work to stimulate the contraction ability of smooth muscle, to lower blood pressure, and to affect the action of certain hormones.

Proteinase: any enzyme that catalyzes the splitting of interior peptide bonds in a protein.

Proteoglycans: the component of cartilage that gives it elasticity.

Proteolysis: the splitting of proteins by hydrolysis of the peptide bonds with formation of smaller polypeptides.

Reactive nitrogen species (RNS): a family of antimicrobial molecules derived from nitric oxide (NO) and superoxide (O2) produced via enzymatic activity. RNS and reactive oxygen species (ROS) act together to damage cells.

Reactive oxygen species (ROS): chemically reactive molecules containing oxygen. Examples include oxygen ions and peroxides. They can be either inorganic or organic.

Retrovirus: an RNA virus that gains entry into cells, making mirror-image copies of their RNA to produce a DNA version of their genes, then exploiting vulnerable locations along the host’s DNA to insert themselves, like a transposon, into the cell’s genetic material.

R-factors: genetically coded Resistance Factors possessed by an organism to withstand chemical assaults by one or more chemotherapeutic agents. An example is a transferable plasmid found in many bacteria in the small intestine.

Rheumatoid factor (often called R-factor): a protein in the blood, found by tests that measure the ratio of antibody to gamma globulin. The test reveals IgM antibodies produced by some RA patients against their own IgG.

Salmonella: a gram-negative bacterium causing mild to severe gastroenteritis, occasionally leading to death, e.g. in the case of S. typhus.

Sclerosis: a thickening or hardening of a body part, e.g., an artery, especially from excessive formation of fibrous interstitial tissue

Streptococcus: the genus of gram-positive bacteria, usually occurring in chains, that includes species pathogenic to humans, especially children. A typical chain would include one or more of the following: S. pneumonia, S. synovium, S. aureus, S. hemophilia, scarlet fever, and/or rheumatic heart disease. This initial bacterial infection could lead to production of mycoplasmal microorganisms and L-forms and in turn to rheumatic diseases.

Streptomyces: a genus of bacteria, usually soil forms, but occasionally parasitic on plants and animals.

Subacute: a condition between acute and chronic.

Synovia: pertaining to the transparent, albuminous fluid secreted by the inner layer of the synovial membrane and found in the joint cavities, bursae, and tendon sheaths where lubrication is necessary. This fluid provides nourishment to the cartilage covering the bone and contains white blood cells that battle infection.

Synovial joint: a freely moveable joint where cartilage covers the ends of the bones and the entire joint is encapsulated in a double layer of connective tissue with the joint cavity and its synovial fluid lying in-between the two layers. The outer layer of the capsule is made up of dense connective tissue holding the bones of the joint together. Some of these tissues are bundled together as ligaments. Tendons join muscles to bone. The inner layer of the capsule is made up of loose connective tissue including elastic fibers and fat. 

T-cells: disease-fighting, thymus-derived (“T”) lymphocytes (white blood cells) of the immune system that have the ability to recognize foreign substances (antigens).

Teratogenic: an agent or influence causing a physical defect or deformity in a developing embryo.

Tetracyclines: a family of broad-spectrum antibiotics that inhibit bacterial protein synthesis; tetracycline (C22H24N2O8) is derived from certain species of the bacteria genus Streptomyces; the base and hydrochloride salt are used as an antiamoebic, antibacterial, and antirickettsial.

Thymus: one of the primary lymphatic system organs, located high in the chest, where T-cells proliferate and mature.

Tolerance Induction: A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.

Transposons: genes which move from one position to another on chromosomes; at the bacterial level, movable bits of DNA that generate helpful/harmful chemicals, enzymes, or other substances that confer the ability to resist chemotherapeutic agents.

Vector: a carrier, usually a biting insect (tick, flea, fly, spider, chigger, mosquito) that transfers an infectious agent from one host to another.

Virulence: the capacity to injure an organism and/or produce disease by invasion of tissue and generation of internal toxins. Invasiveness and toxigenicity are measured with reference to a particular host.

Virus: any of a class of filterable, submicroscopic pathogenic agents, chiefly protein and nucleic acid in composition but often reducible to crystalline form, and typically inert except when in contact with certain living cells.


[Return to Home Page]


[Return to Endnotes Page]