Glossary

Adaptive immunity: immune responses mediated by lymphocytes and their products requiring activation
by innate immune mechanisms on first encounter with antigen but acting immediately on subsequent
encounters

Afferent lymphocytes: lymphatic vessels entering lymph nodes from tissue spaces

Affinity: strength of a noncovalent binding reaction; the higher the affinity, the more likely two partners wiil
exist in a complex.

Alveolar macrophages: macrophages in the lung

Antibodies: highly variable proteins produced by B lymphocytes of the immune system and that recognise
antigen and target it for destruction

Antibody-dependent cellular cytotoxicity (ADCG): a process whereby FcR-bearing celts encounter an

antibody-coated target cell and degranulate, releasing contents that kill the antibody-coated cell.

Antigen: any molecule or part of a molecule recognised by the variable antigen receptors of the
lymphocytes

Antigenic drift: (of influenza virus) point mutations, predominantly in hemagglutinin and neuraminidase,
that affect recognition by neutralizing human antibodies. Antigenic drift gives rise to epidemic infections.

Antigenic shift: (of influenza virus) reassortment of independent RNA segments from two different
influenza genomes to generate recombinant virus with new antigenic subtypes. Antigenic shift gives rise to
pandemic outbreaks.

Antigenic variation: (in parasites) clonal expression of members of proteins among parasite progeny;
examples include the major surface glycoproteins of trypanosomes and the red cell adhesins encoded by
malaria parasites; variant expression allows parasites to evade immune recognition

Antigen presentation: the binding of fragments of intracellular molecules, usually peptides derived from
proteins of pathogens, by major histocompatibility complex (MHC) molecules and their presentation on the
cell surface for recognition by T cells

Antigen-presenting cells: cells capable of displaying antigen for recognition by T-celts and of activating
naive T cells

Antimicrobial peptides: peptide antibodies that provide defense against microbes and viruses by
interacting with membranes of infectious agents and increasing their permeability. Human antimicrobial
peptides are members of either the u-defensin, $defensin or cathelicidin families

Attenuation: (of a pathogen) loss of pathogenicity, usually through adaptation to growth in culture in
adverse conditions or in cells irom a species other than that of the normal host. Attenuated pathogens are
the basis of many vaccines

Avidity: increased apparent affinity of a molecule for its ligand due to the presence of multiple binding sites
on both partners

Basophils: circulating myeloid lineage cells that-are characterised by cytoplasmic granules that stain with
basic dyes and contain inflammatory mediators and are believed to be important in defence against
parasites as well as in inflammatory and allergic reactions

C1q: complement component that binds to antibodies in immune complexes and activates the classical
pathway of complement activation. ln addition to activating the complement cascade, Clq is recognised by
a phagocytic receptor of macrophages (C1qRp), and so can mediate phagocytosis directly
C3 convertase: either of two proteolytic enzymes of the complement system that cleave the C3 to generate
C3a and C3b. The C3 convertase of the classical and lectin pathways is a complex of C4b and C2b,
whereas the C3 convertase of the alternative pathway is a complex of C3b and Bb

Gapsular polysaccharide: cell-surface polymers of repeating oligosaccharide units, usually linked through
phosphodiester bonds, that form a capsule on the surface of many pathogenic bacteria and protect bacterial
cells from recognition by phagocytes. For this reason the presence of a capsule is often associated with
virulence

Gathelicidins: family of cationic antimicrobial peptides generated in pre-pro forms that require processing
to generate the active peptide; cathelicidins contain an amino-terminal cathelin-like domain and a carboxy-
terminal antimicrobial domain

Ghemokine: any of a family of closely related small, basic cytokines whose main function is as
chemoaftractants. The name is a contraction of chemotactic cytokine

Classical pathway: complement activation pathway through which antibody-antigen complexes trigger the
complement cascade. This pathway is also activated by the pentraxins

Clonal detection: elimination of potentially self-reactive lymphocytes. lmmature tymphocytes undergo

programmed cell death after binding to antigen; in this way, cells that are bearing receptors that recognise
self are deleted before they are capable of participating in immune responses. This is a major mechanism '

of immune tolerance.

Gtonal expansion: the selective proliferation of mature naive lymphocytes that encounter antigen. Only
those lymphocytes bearing receptors specifically recognizing antigen are activated to proliferate and
differentiate into effector cells

Glonal selection: the process whereby potentially self-reactive lymphocytes are eliminated during
ontogeny whereas mature lymphocytes recognising non-self antigens are selectively expanded

Cluster of differentiation (CD): the basis of a system for identifoing cell surface molecutes of immune cells
by the use of antibodies and in which each molecule is given a speciflc number prefixed by CD to form the
basis of a systematic nomenclature. The term cluster reflects the fact that each molecule is usually
recognised by a group, or cluster of antibodies; and the appearance of the molecules usually reflects
different differentiated states of the cell, hence differentiation. Surface marker molecules of immune cells of
different types and at different stages of differentiation or activation have been identified in this way and can
be used to classifiT cells, or,to follow their progress through development or their activation status.

Gollectin: any of a family of structurally related, carbohydrate-recognising proteins of innate immunity,

including mannose-binding lectin and surfactant proteins A and D.

Complement: serum proteins activated directly or indirectly by conserved surface features of

microorganisms, or by antibody, to destroy microorganisms or induce their destruction through a
coordinated immune response including induction of inflammation, aftraction of leukocytes, stimulation of
phagocytosis and stimulation of antibody production

Complementarity-determining region (CDR): region of a lymphocyte receptor for antigen that participates
in the antigen-binding site and determines its structural complementarity to the antigen

Constant (C) domain: lgJike domain of the type found in lg constant regions

Constant region (C region): region of lymphocyte receptor for antigen that does not participate in antigen
binding and does not vary between cells of different antigen specificities

Goreceptor: (of T lymphocytes) receptor on a T-cell that recognises invariant parts of MHC molecules and
forms a recognition complex with the antigen receptor and contributes to intracellular signalling.

Corticosteroids: natural and synthetic hormones that bind to and activate the glucocorticoid receptor.
Corticosteroids are very effective antiinflammatory drugs and are also immunosuppressive.
 C-type lectin: cell-surface or secreted protein that is characterised by a conserved three-dimensional fold
and somewhat conserved amino-acid sequence and that binds to carbohydrate ligands, typically in a
calcium-dependent manner.

C-type lectin-like receptors: cell-surface proteins containing C-type lectin domains that do not bind
carbohydrate ligands and are thus distinct from Ctype lectin receptors; C-type lectin receptors commonly
mediate phagocytic or endocytic uptake and/or signalling into the cell

Cytokine: polypeptide signalling molecules that participates in immune responses. Cytokines often act
locally (in an autocrine or a paracrine manner) but can act systemically. Most cytokines are secreted
molecules, but membrane-bound versions also occur in most cytokine types

Cytotoxic T cells: T lymphocytes specialised to kill cells infected with pathogens that replicate in the
cytoplasm

Dectin-l: a phagocytic C-type lectin receptor recognising microbial B-glucan polysaccharides

Defensins: any of a family of cationic antimicrobial peptides of vertebrates with three disutfide bonds and a
largely beta-sheet structure.

Dendritic cells: specialised cells that ingest debris and infectious agents in the peripheral tissues and
migrate to lymphoid tissues where they present fragments of the ingested particles for recognition by T
lymphocytes in the activation of adaptive immune responses. Some dendritic cells are resident in ihe
lymphoid tissues and function as phagocytes there before differentiating into antigen-presenting cells

Effector cells: cells that are equipped to activate or destroy other cells direcfly

EnzymeJinked immunosorbent assay (ELISA): a technique for measuring the amount of a molecule in a
sample in which the antigen is put or trapped on a solid support and then an antibody with an attached
enzyme is used to bind to the trapped antigen. Alternatively, an ELISA can be used to measure the amount
of a specific antibody in a sample. The amount of enzymatic activity is direcfly related to the amount of the
antigen or antibody on the plate

Eosinophils: cells containing cytoplasmic granules that stain with a dye eosin and contain inflammatory
mediators that are released on activation by T cells or antibody-coated parasites

Epitope: molecular feature of an antigen that is specifically recognised by a lymphocyte or an antibody.

Fab fragment: fragment of an antibody generated

Fc fragment: immunoreceptors that mediate many of the effects of antibodies. These receptors are so
named because the part of the antibody molecule they recognise is called the Fc region. ic receptors
mediate cellular functions such as phagocytosis, cell killing, and degranulation

Heavy chain: the immunoglobulin heavy chains are the larger of the two kinds of polypeptide chains in the
immunoglobulin molecule. Each light chain has a variable region contributing to'the'antigen-binding site,
and a constant region that mediates the effector function of the molecule.

Hemagglutination: the property by which antibodies binding to red blood cells cause them to agglutinate

Hemagglutinin: influenza homotrimeric envelope piotein that binds to widely distributed host-cell-surface
glycoproteins and glycolipids that are modified by sialic acid additions and is required for virat entry to host.

Hematopoietic stem cell (HSC): self-renewing cellthat gives rise to all the red and white blood cells

'Highly pathogenic avian influenza (HPAI): influenza viruses with high virutence for chickens and other
birds. These viruses commonly express H5, H7, H9 hemagglutinin proteins with an expanded basic amino-
acid repeat that increases the ease of proteolytic diggstion required to activate the fusion domain
Histocompatibility: flexible stretch of amino acids between two domains, Cg1 and'CyQ of an lgG molecule,
that allows the antigen-binding sites mobility relative to one another

Human anti-mouse lg antibody (HAMA): antibody produced by an immune response in humans to

determinants on mouse lg, which limits the therapeutic usefulness of mouse monoclonal antibodies

Humanized antibodies: monoclonal antibodies made by using mouse cells and subsequently manipulated
by recombinant DNA technology to produce a molecule most of which is derived from human sequences,
with only antigen-binding loops of the mouse molecule

lmmunofluorescence: a technique in which fluorescently labelled antibodies are used to determine the
location of the corresponding antigen in a tissue section or in cells

lmmunogenic: able to induce an adaptive immune response. Many antigens are recognised by
lymphocytes of the adaptive immune system fail to elicit immune responses in the absence of adjuvants
that promote adaptive immune responses, often by activating cells of the innate immunity

lmmunoglobulin (lg): a class of proteins produced by B lymphocytes of the immune system and that
recognise and binds to foreign antigens. Also called an antibody.

lmmunoreceptor tyrosine-based activation motif (ITAM): a sequence in the cytoplasmic domains of

inhibitory immunoreceptors that, upon phosphorylation on tyrosine recruits signalling inhibitors

lmmunotherapy: (of illergies) a treatment for atopic diseases in which the allergen responsible for the
condition is injected repeatedly.

lnducible nitric oxide synthase (INOS): one of the three isoforms of NOS, the enzyme that makes nitric
oxide, and that is synthesised by phagocytic cells as part of the microbicidal response

lnflammation: coordinated response to infection or tissue injury recognised since ancient Roman times and
characterised by heat, pain, redndss and swelling

lnflammatory cytokines: cytokines that are released by phagocytes of the innate immune system on the
presence of microorganisms, or by activated lymphoid cells, and that act on blood vessels and cells of the
immune system to induce or amplify immune responses

Innate immunity: immune responses mediated by cells and molecules recognizing conserved features of
microorganisms and activated immediately on encounter with them

lnterleukin cytokine: participating in immune responses and originally thought always to be produced by
leukocytes. Many cytokines have been given a systematic name of interleukin x, wehre x is a number from
one to at least 29. lt is now clear that often the range of ac;tion of interleukins extends to non-hematopoietic
lineage lines

Kupffer cells: macrophages in the liver

Langerhans cells: immature dendritic cells in the epidermal layer of the skin

Lectin: protein that binds specifically to particular polysaccharides or other carbohydrate structures. There
are four major structural groups: C-type lectins, ptype lectins, ltype lectins and galectin-like lectins

Lectin pathway: complement activation pathway through which mannose-binding lectin and ficolins
stimulate the complement cascade

Light chain: the immunoglobulin light chains are the smaller of the two kinds of chains in the
immunoglobulin molecule. Each has a variable region contributing to the antigen-binding site, and a
constant region containing a cysteine by which it makes a disulfide bond with the constant region of the
heavy chain
Lipopolysaccharide (LPS): major component of the outer membrane of Gram-negative bacteria and an
important recognition element for innate immunity

Lymph: fluid drained from the tissues flowing through lymphatic vessels

Lymphatic vessels: system of vessels draining fluid (lymph) from the tissues and in which dendritic cells
and antigens are delivered to lymph nodes

Lymph nodes: secondary lymphoid organs distributed widely in the body but especially in the groin, the
axilla and the neck, and along the small intestine

Macrophages: phagocytic cells resident in tissues th'at detect microorganisms by means of receptors
recognising conserved components and ingest and destroy them, and function in tissue repair and
maintenance

Major histocompatability complex (MHC): cluster of genes encoding the classical and many non-
classical MHC molecules and other structurally unrelated molecules, many with important functions in
immunity

Mannose-binding lectin (MBL): a collectin family member that recognises terminal sugars with equatorial
hydroxyls in the C3 and C4 positions, such as mannose and fructose. Also called mannose-binding protein
(MBP)

M cells: specialised epithelial cells in the small intestine that collect antigen at Peyer's patches

Memory cells: Iong-lived lymphocytes that differentiate during the clonal expansion of antigen-specific
lymphocytes during a primary immune response and provide a rapidly activated effector pool on
subsequent challenge with the same antigen

Metacyclic promastigotes: infectious forms of Leishmania that represent terminally differentiated

promastigotes released from the intestinal epithelia and that migrate to the sandfly proboscis; metacyclic
forms are covered with the lengthened form of surface lipophosphoglycan molecules that renders parasites
more resistant to complement and macrophage oxidant killing

MHC class I molecules: cell surface glycoproteins most of which are encoded in the major
histocompatibility complex and most of which bind peptide fragments of cytoplasmic and secreted proteins
and display them on the cell surface. AN important function of these cells is to signal the presence of viral
infection to CD8 T cells

MHC class ll molecules: cell surface glycoproteins encoded in the major histocompatibility complex and
most of which bind peptide fragments of proteins derived from internalised molecules, including those of
extracellular pathogens, and display them for recognition bu CD4 cells

Monoclonal antibodies: antibodies produced by a single clone of cells and therefore with a single
specificity

Monocytes: circulating precursors of macrophages and some dendritic cells

Natural killer (NK) cells: cytotoxic lymphocytes lacking antigen-specific receptors but with invariant
receptors that detect infected cells and some tumour cells and actiriate their destruction

Neuraminidase (NA): influenza homotetrameric sialidase expressed on the virion that cleaves terminal
sialic acid residues from host glycoconjugates to allow the release of infectious progeny virus

Neutralising antibodies: antibodies that can directly block infection by viruses or attachment by bacteria or
toxins, without need of complement or Fc receptors

Neutrophils: phagocytic cells that circulate in the blood and deteet microorganisms by means of receptors
that recognise conserved components
Opsonin: any soluble molecule that-recognises and coats microorganisms and thereby stimulates
internalisation of the microorganism by phagocytes

Opsonized: bound by soluble recognition elements of the innate or adaptive immune system, such as
antibody, iC3b and collectins, that are recognised by phagocytic receptors

Paracrine: produced by one cell and acting on a nearby cell. ls thought to be the main mode of action of
cytokines, although they can act in an autocrine fashion or systemically in an endocrine fashion

Pathogenicity islands: DNA encoding contiguous virulence genes and found in pathogenic bacteria

Pentraxin: any of a small family of pentameric serum proteins that participate in innate immunity by binding
to membranes of microbes and apoptotic cells and activating the classical pathway of complement.

Peptidoglycan: ridgid polymer of repeating disaccharides cross-linked by short peptides that is a major
structural element of most types of bacterial cell walls

Peyer's patches: organised regions of secondary lymphoid tissue in the wall of the small intestine

Phage display: a technique for isolating proteins with specific binding characteristics whereby the desired
protein is expressed on the surface of a bacteriophage. This allows phage to be selected for binding to a
tissue culture dish coated with the ligand

Phagocytic cells: cells that recognise and ingest molecules and particles including microorganisms and
destroy them

Phagocytic receptor: cell surface motecule of phagocytes that binds microbes, viruses or apoptotic cells,
either directly or through opsonins, and induces phagocytosis

Phagocytosis: receptor-mediated internalisation of cells or other particles larger than 1 pm in diameter

Phagolysosome: phagosome that has fused with lysosomes

Phagosome: vesicle generated by invagination and fusion of the plasma membrane of a phagocyte around
a particle bound to phagocytic receptors

Plasma cells: terminally differentiated B lineage cells secreting large quantities of antibody

Polyclonal antibodies: heterogeneous antibodies against an antigen that are obtained by immunising an
individual

Polymeric lg receptor: receptor meCiaiing transcytosis of immunoglobulin A across epithelial cells to

mucosal surfaces

Primary lymphoid tissues: bone marrow and thymus, in which lymphocytes differentiate and mature

Proinflammatory cytokines: cytokines that act on endothelial cells to induce inflammation. Also known as
inflammatory cytokines

Reactive nitiogen intermediates: highly reactive and toxic compounds generated from L-arginine by
inducible nitric oxide synthase (|NOS)

Reactive oxygen intermediates: highly reactive and toxic compounds generated rom molecular oxygen by
NADPH oxidase, superoxidde dismutase andlor myeloperoxidase

Secondary lymphoid tissues: tissues in which lymphocytes are brought together when antigen and
adaptive immune responses are initiated

Secondary component a chain of secreted lgA that is derived from the polymeric Lg receptor and
remains bound to polymeric lgA after proteolytic cleavage of the transport receptor
 Src-family tyrosine kinases: a family of eight memebrane-linked intracellular protein kinases first
discovered as the product of a viral oncogene causing sarcoma in chickens. Src kinases participate in
lmmune cell function primarily via ITAM and lTlM receptor signalling

Surfactant: any of a number of lung proteins of diverse functions. The collectins surfactant protein A (SP-A)
and surfactant protein D (SP-D) are important molecules of innate immunity

T cell receptor (TCR): The complex of variable chains whereby T cells recognise antigen and signalling
chains whereby antigen recognition is signalled to the cell interior

T helper cells: T lymphocytes that activate other cells of the immune system, including phagocytes, mast
cells, basophils, eosinophils and B cells, which when activated differentiate into antibody-producing cells

Thymus: primary lymphoid organ in which T lymphocytes mature

T lymphocytes: lymphocytes that mature in the thymus and different classes of which mediate cytotoxic
responses against cells infected with viruses, activate B lymphocytes to produce antibodies, and activate
phagocytes to ingest and destroy microorganisms

Toll-like reeeptons (TLR): family of receptors that have leucing-rieh repeats in their extracellular domains
and the TIR domain in their cytoplasmic domains

Type 2 granuloma: granulomatous response orchestrated by TaZ cells, eosinophils, alternatively activated :
macrophages and collagen-secreting mesenchymalcells organised in a dense sphericalstructure around a
central inciting agent, such as a schistosome egg

. Type lll secretion system: mechanism by which Gram-negative bacteria translocate host-modifying
' proteins into the cytoplasrn of the target cells through a syringeJike structure penetrating the host cell
membrane. The type lll secretion gystem is encoded in pathogenicity islands

Variable (V) domain: Ig-like domain of the type found in immunoglobulin variable regions. V domains have
two more beta strands in the beta sandwich than do C domains. ln antigen receptors, the V domain
contains the variable binding site for antigens

Variable region (V region): region of a lymphocyte receptor for antigen that participates in antigen binding
and varies between cells of different antigen specificities

Viral set-point the relatively steady-state level of plasma HIV reached after acute infection becomes
controlled by CD8 T cell responses. Although viral and CD4 T cell levels are relatively stable for prolonged
periods, these levels reflect dynamic turnover in both compartments

Zoonotic infection: an infection that crosses species, from an animal, to infect humans

Zymosan: cefl wall preparation of Saccharomyces cerevisiae composed of B-glucans, mannans,

mannoproteins and chitin