Glossary

A

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

Antibody – Y-shaped protein produced against 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

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.

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

C

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)

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.

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.

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; trigger behavioral responses in nearby cells

D

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.

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

E

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

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.

F

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

G

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

H

HLA – human leukocyte antigen; murine homolog :MHC

I

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.

J

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.

K

L

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.

M

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.

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

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

N

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. 

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

O

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

P

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.

Q

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

R

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

S

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

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

T

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.

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’.

V

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.

W

X

Y

Z