Glossary
Adjuvant: A vaccine component included to increase its potency.
Adoptive cell transfer: A type of immunotherapy in which T cells are removed from a patient's body, forced to proliferate in the lab, and infused back into the patient to fight disease.
Allergen: An antigen that causes allergies.
Anergize: To render non-functional.
Anergy: A state of non-functionality.
Antibody-dependent cellular cytotoxicity: Antibodies form a "bridge" between the target and the cytotoxic cell. Antibody-directed killing by cells of the innate system.
Antigen: A rather loosely used term for the target (e.g., a viral protein) of an antibody or a T cell. To be more precise, an antibody binds to a region of an antigen called the epitope, and the T cell receptor binds to a peptide that is a fragment of an antigen.
Antigen presenting cells: Cells that can present antigen efficiently to T cells via MHC molecules, and which can supply the co-stimulatory molecules required to activate T cells.
Anti-retroviral treatment: Chemotherapy that targets specific aspects of the HIV-1 replication cycle.
Apoptosis: The process during which a cell commits suicide in response to problems within the cell or to signals from outside the cell.
Atopic individual: Someone who has allergies.
Autophagy: A process by which starved cells recycle their components.
β2-microglobulin: The non-polymorphic chain of the class I MHC molecule.
CAR T cell therapy: A type of immunotherapy in which T cells are removed from a patient's body, fitted with an engineered T cell receptor, and infused back into the patient to fight disease.
Central tolerance induction: The process by which T cells with receptors that recognize abundant self antigens in the thymus are anergized or deleted.
Checkpoint proteins: Proteins such as CTLA-4 and PD-1 which help turn off the immune system once an invasion has been repulsed.
Chemokine: A special cytokine used to direct cells to their proper positions.
Clonal selection principle: When receptors on B or T cells recognize their cognate antigen, these cells are triggered (selected) to proliferate. As a result, a clone of B or T cells with identical antigen specificities is produced.
Cognate antigen: The antigen (e.g., a bacterial protein) which a B or T cell's receptors recognize and bind to.
Colon: A synonym for large intestine.
Commensal bacteria: Bacteria that have a beneficial, symbiotic relationship with their host.
Co-receptor: The CD4 or CD8 molecules on T cells, or the complement receptor on B cells.
Cortical thymic epithelial cells: Cells in the cortex of the thymus which are the "examiners" during positive selection (MHC restriction) of T cells.
Co-stimulation: The second "key" that B and T cells need for activation.
Crosslink: Cluster together (e.g., an antigen may crosslink a B cell's receptors).
Cross reacts: Recognizes several different epitopes. For example, a B cell's receptors may bind to (cross react with) several different epitopes.
CTLA-4: A receptor on activated T cells which, when ligated (e.g., by B7), interferes with the reactivation of these cells.
Cytokine profile: The mixture of different cytokines that a cell secretes.
Cytokines: Hormone-like messenger molecules that cells use to communicate.
Cytotoxic lymphocyte: A synonym for killer T cell.
Delayed-type hypersensitivity: An inflammatory reaction in which Th cells recognize a specific invader, and secrete cytokines that activate and recruit innate system cells to do the killing.
Dendritic cell: A starfish-shaped cell which, when activated by battle signals, travels from the tissues to the secondary lymphoid organs to activate naive T cells.
Elite controller: A rare, untreated, AIDS patient whose immune system is able to control his or her viral load so that it remains low for an extended period.
Endogenous protein: A protein that is produced within the cell in question – the opposite of an exogenous protein.
Endoplasmic reticulum: A large sack-like structure inside a cell from which most proteins destined for transport to the cell surface begin their journey.
Endothelial cells: Cells shaped like shingles which line the inside of your blood vessels.
Epithelial cells: Cells that form part of the barrier (e.g., skin) that separates your body from the outside world.
Epitope: The region of an antigen that is recognized by a B or T cell's receptors.
Exogenous protein: A protein that is found outside the cell in question – the opposite of an endogenous protein.
Extracellular bacteria: Bacteria that can multiply outside of their host's cells.
Fas: A protein on the surface of a target cell which, when ligated by a FasL protein on a killer cell, can instruct the target cell to commit suicide.
Follicular dendritic cell: A starfish-shaped cell which retains opsonized antigens in germinal centers, and displays these antigens to help activate B cells.
Follicular helper T cell: A helper T cell which has been "licensed" to provide help to B cells in germinal centers.
f-met peptide: A peptide which includes a special initiator amino acid that is characteristic of proteins made by bacteria.
Germinal center: An area in a secondary lymphoid organ in which B cells proliferate, undergo somatic hypermutation, and switch classes.
Granzyme B: An enzyme which CTLs and NK cells use to destroy their targets.
High endothelial venule: A region in a blood vessel where there are high endothelial cells which allow lymphocytes to exit the blood.
Hybridoma: A hybrid B cell that can produce monoclonal antibodies, and which can be grown indefinitely in the lab.
Hygiene hypothesis: The idea that the increased incidence of allergies is due, at least in part, to improved hygiene.
Inducible regulatory T cells: CD4 + T cells which produce cytokines that suppress the immune response to invaders.
Inflammatory response: A rather general term that describes the battle that macrophages, neutrophils, and other immune system cells wage against an invader.
Interferon alpha and beta: Warning cytokines secreted by virus-infected cells.
Interferon gamma: A battle cytokine secreted mainly by Th1 helper T cells and NK cells.
Interleukin: A protein (cytokine) that is used for communication between leukocytes.
Intestinal microbiota: The sum of all the microbes in the intestines (bacteria, viruses, and parasites).
Invariant chain: A small protein which occupies the binding groove of a class II MHC molecule until it is replaced by an exogenous peptide.
Isotype: A synonym for class. The isotype of an antibody (e.g., IgA or IgG) is determined by the constant region of its heavy chain.
Lamina propria: The tissues that surround the small and large intestine.
Leukocytes: A generic term that includes all of the different kinds of white blood cells.
Ligand: A molecule that binds to a receptor (e.g., the Fas ligand binds to the Fas receptor protein on the surface of a cell).
Ligate: Bind to. When a receptor has bound its ligand, that receptor is said to be ligated.
Lipopolysaccharide: A component of the outer membrane of many bacteria. It serves as a "danger signal" for the innate immune system.
Lymph: The liquid that "leaks" out of blood vessels into the tissues.
Lymphocyte: The generic term for a B cell or a T cell.
Lymphoid follicle: The region of a secondary lymphoid organ that contains follicular dendritic cells embedded in a sea of B cells.
M cell: A cell that crowns a Peyer's patch, and which specializes in sampling antigen from the intestine.
Medullary thymic epithelial cell: A cell found in the medulla of the thymus which expresses tissue-specific self antigens, and which takes part in the examination of T cells for tolerance of self antigens (negative selection).
MHC proteins: Proteins encoded by the major histocompatibility complex (a chromosomal region that includes a "complex" of genes involved in antigen presentation).
MHC restriction: A synonym for positive selection. Survival in the thymus is restricted to T cells whose receptors recognize MHC–self antigen complexes.
Microbe: A generic term which includes bacteria, viruses, fungi, and parasites.
Mitogen: A molecule that can cause the polyclonal activation of B cells.
Monoclonal antibodies: Antibodies produced by hybridoma technology.
Monocytes: White blood cells that are the precursors of macrophages or dendritic cells.
Mucosa: The tissues and associated mucus that protect exposed surfaces such as the gastrointestinal and respiratory tracts.
Mucosal-associated lymphoid tissues: Secondary lymphoid organs that are associated with the mucosa (e.g., Peyer's patches and tonsils).
Naive lymphocytes: B or T cells which have never been activated.
Natural regulatory T cells: CD4 + T cells that are selected in the thymus and which interfere with the activation of self-reactive T cells in the secondary lymphoid organs.
Necrosis: Cell death, typically caused by burns or other trauma. This type of cell death (as opposed to apoptotic cell death) usually results in the contents of the cell being dumped into the tissues.
Negative selection: Synonym for central tolerance induction. The deletion of T cells whose receptors recognize MHC–self peptide complexes in the thymic medulla.
Neoantigen: A "new" antigen that a cell makes as a result of a mutation in the DNA which encodes a normal cellular protein.
Neutralizing antibody: An antibody which can bind to a pathogen, and prevent it from infecting or reproducing in the cells it would like to infect.
Neutrophil extracellular traps: Web-like structures composed of cellular DNA that is decorated with neutrophil granule proteins.
Opsonize: To "decorate" with fragments of complement proteins or with antibodies.
Pathogen: A disease-causing agent (e.g., a bacterium or a virus).
PD-1: A receptor on activated T cells which, when ligated (e.g., by PD-L1), interferes with the function of the T cell.
Peptide: A small fragment of a protein, usually only tens of amino acids in length.
Perforin: A molecule used by CTLs and NK cells to help destroy their targets.
Peripheral tolerance induction: The mechanisms that induce self tolerance outside of the thymus.
Phagocytes: Cells such as macrophages and neutrophils that engulf (phagocytose) invaders.
Plasma B cells: B cells which produce a large burst of antibodies in response to an attack, and then die.
Plasmacytoid dendritic cells: Important cells during a viral infection, because they can produce a ton of type I interferon.
Polyclonal activation: Activation of many B cells with different specificities.
Positive selection: A synonym for MHC restriction.
Primary lymphoid organs: The thymus and the bone marrow.
Proliferate: Increase in number. A cell proliferates by dividing into two daughter cells, which then can divide again to give four cells, and so on. Cellular reproduction.
Proteasome: A multi-protein complex in the cell that chops up proteins into small pieces.
Receptor editing: The process by which B cells in the bone marrow can "draw again from the deck" to try to make a BCR that is not self-reactive.
Secondary lymphoid organs: Organs such as lymph nodes, Peyer's patches, and the spleen in which activation of naive B and T cells takes place.
Secrete: Export out of the cell (e.g., cytokines are secreted by the T cells that produce them, and antibodies are secreted by B cells).
Thymic dendritic cell: A cell found in the medulla of the thymus which tests T cells for tolerance of self antigens (negative selection).
Tolerance of self: Not viewing self as an attacker.
Tolerize: To make B cells and T cells tolerant of our self antigens.
Toll-like receptors: Receptor molecules found on the surface of cells or inside cells. These receptors have evolved to recognize the signatures of common invaders, and to generate signals which alert the immune system to danger.
Tumor infiltrating lymphocytes: T cells that are found in the neighborhood of tumors.
Tumor necrosis factor: A battle cytokine secreted mainly by macrophages and helper T cells.
Virgin lymphocyte: A B or T cell which has never been activated. A synonym for naive lymphocyte.
