AIRE – autoimmune regulator, or AIRE. A thymus-expressed protein tasked with the  expression of many proteins that are not typically expressed in thymic cells IE lung, skin, brain, intestinal, etc proteins.

Acute phase response or acute phase proteins – systemic stimulation and release of a class of innate immune enhancing proteins and peptides in response to injury and infection, promote fever, complement activation, opsonization, coagulation, chemotaxis, etc

Adjuvant – a substance that is added to a vaccine to increase the body’s immune response to a vaccine.

Allograft – a tissue graft from a donor of the same species as the recipient but not genetically identical.

Antibody – Y-shaped protein that recognizes and binds to specific antigens; typically produced by plasma cells

Anti-CD3/anti-CD28 – antibody cocktail frequently used in in vitro and in vivo experiments to activate T cells by crosslinking the T cell receptor and co-stimulatory molecules.

Antigen – any foreign substance (biological or non-biological) that incites an immune response

Apoptosis – a directed process of cell self-destruction marked by the orderly fragmentation of nuclear DNA. Apoptosis is a normal physiological process eliminating damaged (DNA damage, oxidation, infection), superfluous, or unwanted cells also calledo cell suicide, programmed cell death


B cell – adaptive immune cells which arise in the bone marrow and mature in the spleen and/or lymph nodes, are capable of presenting antigen, secrete antibodies and express a B cell receptor.

Basophil – a type of granulocytic innate immune cell that is often involved in allergic responses and asthma.

Bim/BCL2 family – BCL-2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities


CAR – Chimeric Antigen Receptor. A hybrid molecule engineered to express key components of the T cell receptor, most importantly containing a specifically engineered recognition site to target molecules expressed by cancer cells.

Cas 9 – CRISPR-associated protein 9; an enzyme using CRISPR sequences as a guide to recognize and cleave specific strands of DNA  complementary to the CRISPR sequence.

C57BL/6 strain mouse – the most widely-used and best selling strain of mouse for modeling human disease

CD4+ T cell – T helper cells. A T cell co-expressing a TCR and the co-receptor molecule CD4. CD4+ T cells, also known as T helper cells fall into multiple classes (TH1, TH2, TH17, TH13, etc), and are known as “helpers” because of their stimulation, licensing, and activation of B cells and B cell responses (Antibodies)

CD4/CD8 – Proteins on the surface of helper T cells and cytotoxic T cells, respectively, that act as a co-receptors during T cell activation. In order for a T cell to become activated, it must bind antigen with its T cell receptor (TCR), but this is not sufficient for full activation. In addition, the T cell requires other “ON” signals, which are achieved through cytokines and binding of the co-receptors CD4 or CD8 to the MHC molecule that is presenting the antigen to the TCR.

CD40 – a co-stimulatory protein found on antigen presenting cells and is required for their activation. Co-stimulation signal when it binds CD40L on target immune cells

CD40L – CD40 ligand is a protein that is primarily expressed on activated T cells and binds to CD40 (protein) on antigen-presenting cells (APC).

CD8+ T cell – cytotoxic T lymphocytes. T cells which co-express a TCR and the CD8 costimulatory molecules. Responsible for direct cell-cell killing by the release of cytotoxic granules and/or induction of apoptosis in target cells.

cGAS (cGAMP synthase) – an immune “sensor” protein that initiates an enzymatic reaction to produce cyclic GMP-AMP/cGAMP from ATP and GTP upon activation

CRISPR – Clustered Regularly Interspersed Short Palindromic Repeats;  a family of DNA sequences found within the genomes of prokaryotic organisms such as bacteria and archaea.

CRISPR-Cas 9 – A system that acts as an adaptive immune for some bacteria and archaebacteria against phages and viruses,, arming the organisms to eliminate invading genetic material. 

CRISPR-Cas 9 (Applied) – An accurate, low cost, and flexible DNA-editing tool that allows for the introduction or removal of more than one gene at a time. Its applied use is not species-specific and can be used on organisms previously resistant to genetic engineering.

Commensal bacteria – normal microflora that do not harm the host; play a role in host immunity.

Complement – a circulating suite of proteins that enhance the action of antibodies in marking and aiding in the digestion of pathogens by phagocytes.

Costimulation – A second signal typically required to activate immune cells.

Cross reaction, Cross reactivity -A non-cognate reaction between an antibody and an antigen that differs from the original, primary immunogen.

Cytokine – any number of small proteins that act in cell signaling; they trigger behavioral responses in nearby cells or the cytokine-secreting cell itself.


Dendritic cell – antigen presenting cells which process and present exogenous antigen to cells of the adaptive immune system. They act as primary liaison cells between innate and adaptive immune cells.

Degranulation – A cellular process through which inflammatory cytokines, enzymes and other molecules are released from secretory granules found inside certain cell types. Innate immune cells such as neutrophils, eosinophils, and mast cells go through this process.

Disulfide bonds – a covalent bond that forms between two cysteine residues


Endogenous retrovirus (ERV) – genetic fragments from ancient retroviral infections that are now a part of the human genome.

Endothelial cell – cell that forms the sheet of tissue lining the blood vessels

Enzyme – A type of protein that catalyzes biochemical reactions.

Eosinophil – A type of innate immune cell that has roles in infection, allergic reactions, and asthma. These cells contain secretory granules with enzymes that are released during the immune response.

Epigenetic – relating to or arising from non-genetic influences on gene expression.

Epitope spreading – When a specific T or B cell epitope no longer restricts T or B cells, allowing them to interact with and “recognize” other target epitopes.

ex vivoexperiments performed on tissue from a living organism in an external environment with minimal alteration of its natural conditions.


Fas / Fas ligand – required interaction for development of the death-inducing signaling complex required for apoptosis.

Fusion proteinFusion proteins or chimeric proteins (literally, made of parts from different sources) are proteins created through the joining of two or more genes that originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins.


Genome – the complete set of genes or genetic material present in a cell or organism.

Granulocytes – a type of white blood cell that contains small granules in the cytoplasm. These granules contain enzymes that are released during infection and allergy. Neutrophils, basophils, and eosinophils are all examples of granulocytes.


Histamine – A chemical that is released by mast cells during the immune response. Release of this chemical promotes inflammation at the site of infection or allergic reaction.

HLA – human leukocyte antigen; murine homolog :MHC


IFN-γ – a cytokine that comprises the type II class of interferons; activates macrophages and induces class II MHC

IgA Immunoglobulin A – a key component of mucosal immunity

IgD Immunoglobulin D – typically co-expressed with IgM, thought to increase mucosal immunity and may play a role in allergic reactions (still very poorly understood)

IgE Immunoglobulin E – an immunoglobulin strictly found in mammals; plays a key role in parasitic infections as well as type I hypersensitivity reactions

IgG Immunoglobulin G – the most commonly found antibody in circulation (in humans) and the only antibody in humans that is known to cross the placental barrier

IgM Immunoglobulin M – found in all jawed vertebrates and is the first antibody to respond after antigen exposure

IL-4 Interleukin 4 – aids in differentiation of naive T helper cells into T helper 2 cells (Th2); similar function as IL-13

IL-6 Interleukin 6 – pro-inflammatory cytokine secreted by T cells & macrophages to stimulate innate immune cells; mediates fever during acute phase response

IL-12 Interleukin 12 – aids in differentiation of naive T helper cells into T helper 1 (Th1) cells; stimulates growth of T cells as well as production of IFN-γ and TNF-α

IL-13 Interleukin 13 – secreted by Th2 cells and several other immune cells; regulates synthesis of IgE

Immune evasion – a strategy used by pathogens to evade the host’s immune responses in order to continue spreading.

Innate immune cells – macrophages, neutrophils, mast cells, eosinophils.

in vitro – experiments performed in a dish, tube, flask or other vessel; experiments performed outside of a living organism.

in vivo – experiments research performed in a  living organism, such as a zebrafish, nematode, mouse, or rat.

in silico experiments performed using computer modeling or computer simulation.


Janus Kinase (Jak) proteins – A family of non-receptor tyrosine kinases that commonly associate with cytokine receptors and; upon receptor activation, JAKs transduce intracellular signaling cascades via the phosphorylation of downstream targets such as STAT proteins.


Kinase – an enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule.


Leukocyte – blanket term for white blood cells, or cells of the immune system.

Ligand – a molecule which binds to and and alters the behavior of a receptor or enzyme. Typically small molecules.

LIGHT ligand for LTβR – lymphotoxin-like, exhibits inducible expression, and competes with HSV glycoprotein D for HVEM, a receptor expressed by T lymphocytes; TNFSF14

LPS lipopolysaccharide – LPS is an integral part of the outer membrane of Gram-negative bacteria. It is also called “endotoxin” and is a potent PAMP.

LTαβ2 ligand for LTβR – one of two lymphotoxin heteroproteins, LTα1β2 and LTα2β1, which can be formed between LTα and LTβ; bound to membrane via LTβ subunit (TNFSF3)

LTβR lymphotoxin β receptor – the lymphotoxin-β receptor (LTβR, TNFRSF3) signaling pathway activates gene transcription programs and cell death important in immune development and host defense. The TNF receptor associated factors (TRAF)-2, 3 and 5 function as adaptors linking LTβR signaling targets.

Lymph nodesmall, encapsulated organs found distributed throughout the body which monitor and strain lymphatic fluid for pathogenic indicators. Widely distributed, with major constituent nodes found at the base of the neck, in the armpit, groin and along the intestinal tract.


Macrophage – A phagocytic cell of the innate immune system; they are also prominent antigen presenting cells and play an important role in the production of inflammatory cytokines.

Mast cell – A type of innate immune cell that plays a primary role in allergic reactions. These cells are also granulocytes, meaning that their cytoplasm contains secretory granules housing inflammatory cytokines.

MHC – major histocompatability complex; human homolog: HLA (see What is MHC and why does it matter?); MHC proteins present peptides on the surface of cells for surveillance by the immune system. 

MHC class I – glycoproteins expressed on the surface of nearly all cells; these complexes present self-peptides, as well as intracellular peptides derived from an infecting pathogen.

MHC class II – glycoproteins expressed on the surface of specialized immune cells known as antigen presenting cells (APCs); these complexes display immunogenic peptides derived from extracellular sources, such as by a bacteria engulfed by a macrophage.

Microfold (M) cells – specialized antigen-capturing cells found in gut-associated lymphoid tissue and the tonsil tissues. Integral to initiating mucosal (IgA-driven) immune responses. M cells are uniquely capable of transcytosing antigen from the lumen side of an epithelial barrier to the internal side.

MIP-2α Macrophage inflammatory protein 2α – a cytokine secreted at sites of inflammation by monocytes and neutrophils

Molecular mimicry – The theoretical possibility that sequence similarities between foreign and self-peptides are sufficient to result in the incorrect activation (aka cross or non-cognate activation) of autoreactive T or B cells by pathogen-derived peptides.

Monocuclear leukocyte  white blood cells with a one-lobed nucleus; they lack intracellular granules which identify granulocytic

Monocyte – a type of phagocytic white blood cell that is produced in the bone marrow and travels throughout the blood stream; when monocytes leave the blood and enter other tissues, they can differentiate into macrophages

mTOR – The mammalian target of rapamycin (mTOR) is a kinase that in humans is encoded by the MTOR gene. mTOR is a member of the phosphatidylinositol 3-kinase-related kinase family of protein kinases.

Murine – of or referring to mice, mouse cells, or mouse-derived tissues

Myeloid – Cells like granulocytes and monocytes which are differentiated descendants from common progenitors derived from hematopoietic stem cells in the bone marrow


Natural killer (NK) cell – An innate immune cell capable of direct cell killing (cytotoxicity); very rapid responders to viral infection and carcinogenic mutations

Natural killer T (NKT) cell – Thymus-derived immune cells that display characteristics of both NK cells and T-cells. NKT cells display many NK cell markers and have rearranged TCRs with limited diversity that bind to a non-classical MHC molecule. 

Neutrophils – a type of innate immune cell; neutrophils are often one of the first cells to respond at a site of infection and are capable of killing pathogens via both phagocytosis and the release of granules containing toxic enzymes.

NF-kappa-B – five protein family sharing c-terminal homology. Immune “first responder”, rapidly signalis for immune activation. Regulator of DNA transcription, cytokine production, cell survival. Key component of immune regulation. Directly inhibited by IkappaB family proteins


Opsonization – flagging or marking a dead cell, pathogen or other object for phagocytosis and recycling by NK cells, neutrophils, or macrophages.


PAMPS pathogen associated molecular patterns – gross patterns or motifs found on many pathogens which are recognized by PRRs.

Peyer’s patch – specialized immune tissue found in the mammalian digestive tract. Part of immune surveillance of symbiotic and pathogenic microorganisms in the intestines.

Phagocytosis – The process through which a cell internalizes, or engulfs, external particles, including other cells; the engulfed items are stored in membrane bound vesicles, called phagosomes, within the cytoplasm of the phagocytic cell.

Platelet Platelets are cells which are part of the clotting mechanism cut or torn blood vessels. AKA thrombocytes, platelets aggregate to form clots

PRR pattern recognition receptor – an innate immune component composed of Toll-Like receptors (TLRs) and other receptors which recognize gross patterns or motifs on pathogens (PAMPS) and activate innate immune responses. PRR activation is also required to initiate and shape adaptive immune responses.


qPCR quantitative PCR; also “RT-PCR” – a PCR method which allows the real time amplification of a transcript to be assessed, allows determination of absolute quantity/transcript number.


Rapamycin – Sirolimus, also known as rapamycin, is a macrolide compound.

Receptor – A protein on the surface of or within a cell that specifically binds particular substates.


“Self” cells – A person’s (or other organism’s) own cells that should be tolerated by the immune system. When this is not the case, auto-immunity can arise. In contrast, “non-self” cells, like invading bacteria, should be recognized and eliminated by the immune system.

Senescence – The biological aging of a cell or organism.

Signal Transducer and Activator of Transcription (STAT) proteins – A family of cytoplasmic transcription factors that, when tyrosine phosphorylated (often by Jak proteins), dimerizes and translocates to the nucleus to impact gene expression in response to cytokine signaling.

Somatic hypermutation – A B cell process process in which point mutations accumulate in the antibody V-regions of both the heavy and light chains in response to the presence of antigen.

Somatic recombination – An enzymatic process that generates diversity in T- and B-cell receptors by splicing DNA segments together to the exclusion of intervening sequences.

Spleen – Secondary immune organ where B -T cell interactions occur, activating B cell responses, promoting somatic hypermutation


T cell – Adaptive immune cells which arise in the bone marrow, mature in the thymus and express a T cell receptor

TNF – tumor necrosis factor

Tight junctions – connections between adjacent cell membranes that eliminate interstitial space, do not allow the diffusion of molecules

Tolerance – An unresponsive state adopted by the immune system towards substances or tissues that have the capacity to elicit an immune response in given organism. Generally a form of protection against autoimmunity.

Tonsil – compact immune-capable organs found in  the throat (post-sinus); have specialized cells (M cells) which capture and present antigen to tonsil-resident adaptive immune cells.

Transgenic – the result of artificial introduction of genetic material from an unrelated organism into a host system.

Transmission electron microscopy – uses a thin beam of electrons that passes through thin slices of tissue and creates highly magnified images of cells. These images are so sharp that they clearly depict even the tiniest details of cells, like mitochondria.

Tyrosine kinase – A common enzyme responsible for transferring a phosphate group from an ATP molecule to a protein target, usually to turn the function of that protein ‘on ‘ or ‘off’.


Virulence Factor – Molecules made by pathogens (bacteria, fungi, viruses, protozoa and parasites) that make them any of the following: easier to transmit, better at colonizing an evolutionary niche in a host, more capable of evading or suppressing immune reactions or immune cells, subversion of immune reactions, entry into host cells, cell-to-cell transmission, or scavenging of nutrition from the host.