Advanced Immunology

cytotoxicity

-NK cells, CD8 T cells -elimination of virally infected and metabolically stressed cells

T cell signaling

-phosphorylation of ITAMs on CD3 -recruitment of ZAP 70 both ITAMs and ZAP 70 are phosphorylated via Lck -co-stimulation of B7 and CD-28 - activates PIP3K - PIP3 - PLC-y - IP3 - opens ER to Ca++ channels that actiavte NFAT via calmodulin and calcineurin activation that leads to the transcription of IL-2 cytokine genes.

Activation of the inflammasome

triggered by the activation of NFkB - leads to the upregulation of the NLR NLRP3 - primed by deubiquitination -cleavage of pro-caspase 1 into caspase 1 which produces IL-1b and IL-18, Can also induce cell death. different types of inflammasomes can be produced in response to different antigens the goal is to cleave procaspse 1 into caspase 1 to either induce cell death or the production of il-1b.

peptide editing

In the context of antigen processing and presentation, the removal of unstably bound peptides from MHC class II molecules by HLA-DM.

lectin pathway

Induced by infection and needs some time to develop The lectin pathway is initiated by soluble carbohydrate-binding proteins—mannose-binding lectin (MBL) and the ficolins—that bind to particular carbohydrate structures on microbial surfaces. Speciic proteases, called MBL-associated serine proteases (MASPs), that associate with these recognition proteins then trigger the cleavage of complement proteins and activation of the pathway. C3 convertase:C4b2a C5 convertase:C4b2a3b

IL-12

Induces differentiation of T cells into Th1 cells. Activates NK cells. important for viral infected cells.

Inflammatory cytokines

Induces fever which slows infection, and activate different tissues to make acute-phase proteins.

Phagocytic receptors

Lectins: recognize carbohydrates • Mannose receptor • Glucan receptor • CD14 (LPS receptor) Scavenging receptors: - LPS -CpG-rich bacterial DNA (mammalian DNA has low frequency of CpG and is mostly methylated) Complement receptor: CR3 and CR4 - Recognize several components of bacteria and yeast

Spleen

Lymphoid organ that serves as a filter of the blood Captures antigens from the bloodstream Lymphocytes in circulatory system meet antigens Remove aged red blood cells

b-Defensins

Made by epithelial cells of the skin, respiratory and urogenital tract • There are 4 different types

How inflammasomes work and what they are, why do we need them?

Needed to activate IL1B

classical pathway

Needs binding of C-reactive protein (innate) or antibody (adaptive) Antibodies bind to antigens, activating C1 C1 splits and activates C2 and C4 C2a and C4b combine and activate C3 C3a functions in inflammation C3b functions in cytolysis and opsonization.The classical pathway is initiated when the complement component C1, which comprises a recognition protein (C1q)-which actually binds proteins, associated with proteases (C1r and C1s), either recognizes a microbial surface directly or binds to antibodies already bound to a pathogen C3 convertase:C4b2a C5 convertase:C4b2a3b

TLR mechanism and END cytokines

Outter membrane:TLR 4(MD-2, CD14) - LPS , TLR-1,2 heterodimer - lipoteichoic acid(lipopeptide), TLR-2,6 heterodimer - cell-wall b-glucans, TLR 5 - flagellin MyD88 - IRAK - TRAF - generates scaffold - leads to actiavtion of NFkB - transcription of cytokine genes occurs - TNF-a, IL-6, IL-1 Endosomal: TLR 3 - DS RNA, TLR-7 - ssRNA , TLR-8 - ssRNA, TLR - 9 DNA with unmethylated CpG. TLR-3 - TRIF - IRF3 - type 1 interferons. TLR 7,8 - MyD88 - IRAK - IRF7 - type 1 interferons

TLRs (toll-like receptors)

Receptors that span the membrane of a phagocyte that allow it to find and bind to the PAMP receptors of various microbes. 1st the exposed end of one TLR hooks onto the PAMP and then joins/merges w/ a second TLR to trap the molecule. This sends a signal to the phagocyte nucleus that stimulates the phagocytic processes & releases chemical mediators. TLRs can recognize gram - and + bacteria, fungi and viruses. The TLR which can detect inter and extra cellular pathogens(bacterial and viral) that trigger the production of type 1 interferons, (INF-a, INF-b), as well as pro-inflammatory cytokines. TLR1,2,5,6 - extracellular pathogens excluding viral. TLR3,7,8,9 - endosomal extracellular viruses.

How do we test that T-cells have been activated

Research paper, packabck- load cells with dye to see if dye is diluted to see how many rounds of t-cell replication have gone through.

How are the mechanisms of BCR and TCR antigen recognition different?

The T-cell receptor recognizes a peptide epitope derived from a partially degraded protein, but only if the peptide is bound to specialized cell-surface glycoproteins called MHC molecules. the antigens recognized by T cells can be derived from proteins arising from intracellular pathogens, such as a virus, or from extracellular pathogens.Antibodies and B-cell receptors directly recognize the epitopes of native antigen in the serum or the extracellular spaces. It is possible for diferent antibodies to simultaneously recognize an antigen by its diferent epitopes; such simultaneous recognition increases the eiciency of clearing or neutralizing the antigen.

Regulation of MHC class two molecules

The invariant chain in the ER prevents binding in the ER. The CLIP small fragment stays bound in the variable region of the MHC as it moves into an acidified endosome. HLA-DM displaces the CLIP and the antigen peptide with a higher affinity becomes presented on the cell membrane. MARCH-1 E3 Ligase degrades MHC class 2 when the cell is not activated by a receptor. TLR signaling prevents MARCH-1 E3 increasing the life span of MHC two.

12/23 rule

The spacing and arrangement dictates that a 12 bp recombination signal sequences(RSS) must pair with a 23 bp RSS for recombination to occur. This prevents two V or J segments from joining.

From all antigen presenting cells, why are dendritic cells considered of crucial relevance and defined as the bridge between innate and adaptive immune responses?

They are the only ones that have the capacity to move into the tissue and move to the secondary lymphoid organs.

RLR mechanism and end cytokines

Viral RNA - induces aggregation of MAVS - recruit TRAFs - activates IRF and NFkB - produces Type 1 interferons and cytokines

alternative pathway

Works at the start of infection C3 present in the blood combines with factors B, D, and P on microbe surface -C3 splits into C3a and C3b, functioning the same as in the classical pathway, the alternative pathway can be initiated by spontaneous hydrolysis and activation of the complement component C3, which can then bind directly to microbial surfaces C3 convertase:C3bBb C5 convertase:C3b2Bb

TNF-alpha

activates vascular endothelium and increases vascular permeability, which leads to increased entry of IgG, complement, and cells to tissues and increased fluid drainage to lymph nodes, fever, shock

T-cell activation requires ________.

antigen binding, MHC recognition and co-stimulation. and the transduction of T-cell activation IL-2.

Cathelicidins

antimicrobial proteins found in neutrophils and other cells. are made constitutively by neutrophils and macrophages, and are made in response to infection by keratinocytes in the skin and epithelial cells in the lungs and intestine

BCL2

cellular survival

Skin barrier

chemical;b-defensins, fatty acids, cathelicidins, lamellar bodies. mechanical: flow of air, fluid

CXCL8

chemotactic factor recruits neutrophils, basophils, and T cells to site of infection

inhibatory receptors on lympocytes

downregulate immune response

Calcineurin

enough IP3 increases cytoplasmic Ca calcineurin

CDR3 region

exhibits the greatest variability Contributes the most to antigen binding. complementarity-determining regions.

RIG-like receptors (RLRs)

found in cytoplasm, detect intracellular viral RNA indicating infection, produce interferons. sensors. The RIG-I like receptor which helps detect intracellular viral infections which, like the TLRs, leads to the production of type 1 interferons and pro-inflammatory cytokines.

variable and constant regions

include Fc and FaB regions Fab has both variable and constant. the light chain has one constant and one variable and the heavy has one variable and 3 to 4 constant.

NLR mechanism and end cytokines

intra-cellular bacteria - RIP2 - TAK1 - NFkB - IL-6, IL-1b, TNF-a

Protein kinase C

is required for the activation of NFkB and AP-1 in T-cells

IL-2

key cytokine for t-cell to proliferate

LCK

kinase unique to T-cells

transduction pathway

know how it starts the main ideals the middle man and the end results. tlr 3 viral infections - IRK 3 - production of type 1 interferon's what do they do.

Ca++ signaling

leads to activation of NFAT - leads to production of IL-2, activates naive t-cells

G-protein-coupled receptors on phagocytes:

link microbe recognition with increased efficiency of intracellular killing - ligand binds to receptor - receptor associates with G-protein - G protein dissociates into sub units which activate other proteins - subunit cleaves GTP to GDP - sub units re-associate - signaling terminates

IL-6

lymphocyte activation and increased antibody production, fever, acutce-phase protein production

What specific receptors and features of cellular localization make DCs important to induce adaptive immune responses?

lymphoid organs and in peripheral tissues. Classical Dendritic cDCs cells have TLRs but they have MHC -2 which allows them to present antigens to CD-4 t cells in the secondary lymphoid tissues which active the adaptive immune response creating the bridge between the adaptive and innate immune systems. Dendritic cells are the only APCs that are able to present in the secondary lymph to activate the adaptive immune system. Dendritic cells express Dectin-1 as wells as other types of C-type lectin like phagocytic receptors. they express mannose receptors

mTOR signaling pathway

main goal is metabolism increase of lipids, mRNA and proteins

three functions of antibodies

neutralization, opsonization, complement activation

Clonal selection

only those lymphocytes that recognize the particular pathogen and respond to it are selected to participate in the immune response

variability of MHC molceules

polymorphisms that mainily afffect the binding area, also the potential of polymorphisms in multiple genes. This allows us to evolve a type of herd immunity, overtime we select based on survival due to the efficiency of the MHC molecules.

Clonal expansion

proliferation and differentiation of these few original lymphocytes to provide large number of effects cells

Three main effects of complement activation

1. inflammation via C3a, C4a and C5a. phagocytic cells to the site of infection and promote inflammation. Also IgG and IgM. also promote contraction of smooth muscle, vascular permeability, release of histamine, increase of TNF-a, increase speed of adaptive immune response. potential death from swelling and suffocation 2. promote Phagocytes with receptors for C3b engulf and destroy the pathogen 3. Completion of the complement cascade leads to formation of a membrane-attack complex (MAC), which disrupts cell membrane and causes cell lysis

B cell signal cascade

1. receptor clustering 2. receptor-associated tyrosine kinases(Blk, Fyn or Lyn) phosphorylate the ITAMs on the Ig-alpha and Ig-beta cytoplasmic tails 3. Syk binds to the phosphorylated ITAMs of the Ig-beta cytoplasmic tail needs co-stimulation of CD21 and C3dg. CD19 binds to CD21.

ANTIBODY DIVERSITY IS GENERATED BY WHICH THREE MAIN MECHANISMS?

1.Multiple different copies of each type of gene segment, and different combinations can be used in different rearrangement events 2. Association of different combinations of H and L chains 3. Junctional diversity - N and P nucleotide addition (contribution of P and N nucleotides results in aminoacid sequence diversity in the CDR3)

How does the B cell receptor (BCR) and T cell receptor (TCR) differ in their structure and the way their interact with antigens?

A TCR is never soluable and does not have a Y-shape making it less flexible. The TCR has evolved to bind to MCH complexes (self-molecules) and not free antigens. BCR can be soluable(antibodies) they have a Y-shape and are more flexable allowing them to bind to multiple eiptopes at once. TCR can recognize epitopes that are buried within an antigen through the protease breakdown of the antigen presented on MHC molecules. BCR only recognize exterior epitopes.

IL-1beta

Activates vascular endothelium Activates lymphocytes Local tissue destruction Increases access of effector cells leads to fever and production of IL-6

TCR and costimulation

Activation, Survival and differentiation. required to activate naive T-cell. IP3 releases calcium

What type of antigens can be recognized by an antibody versus a typical alpha-beta T cell receptor?

Antibodies and B-cell receptors directly recognize the epitopes of native antigen(proteins, glycoproteins, and polysaccharides) in the serum or the extracellular spaces. It is possible for diferent antibodies to simultaneously recognize an antigen by its diferent epitopes; such simultaneous recognition increases the eiciency of clearing or neutralizing the antigen.Whereas antibodies can recognize nearly any type of chemical structure, T-cell receptors usually recognize protein antigens and do so very diferently from antibodies.

septic shock

spreading of bacterial infection to blood. Macrophages are activated to release to TNF-a causing dilation of blood vessels. Blood supply is perturbed compromising vital organs (kidney, heart, lung, etc

Histatins

Antimicrobial peptides constitutively produced by the parotid, sublingual, and submandibular glands in the oral cavity. Active against pathogenic fungi such as Cryptococcus neoformans and Candida albicans.

Antigen

Any substance recognized by the adaptive immune system Protein, glycoproteins, polysaccharides, metals (nickel), organic chemicals (urushiol: poison ivy)

Superantigens

Bind directly to MHCII and T-cell receptor simultaneously, activating large numbers of T-cells to stimulate release of IFN-gamma and IL-2

CD28 verses CTAL4 and PD1

CD28 actiavtes naive t-cells CTLA4 inhibits them. PD-1 is programmed death also an inhibitor binds to B7

lung barriers

Chemcial:pulmonary surfactant, a-defensins, cathelicdins mechanical: movement of mucus by cilia

Gut Barrier

Chemical: a-defensins (cryptdins), low ph, enzymes(pepsin), reg111(lecticidins), cathelicdins, lectins mechanical: air flow, fluid

eyes/nose/oral cavity barriers

Chemical:enzymes in tears and saliva(lysozymes) histatins, b-defensins mechanical: nasal cilia, tears

Leukocyte transmigration, steps

Chemoattraction - chemokines slow cells down Primary adhesion - selectins(ICAM-1) stop cells secondary adhesion - integrins Diapedesis and transmigration

MHC restriction

the property that a given T-cell receptor recognizes its peptide antigen only when the peptide is bound to a particular form of MHC molecule.

Cross presentation

Cross-presentation of extracellular antigens by MHC-I molecules enables professional antigen presenting cells to stimulate CD8 T-cell response against viruses that do not infected them directly

How are the actions of the DCs related to effector functions of other innate immune cells and lymphotcytes?

Dendritic cells are phagocytes like macrophages and neutrophils

Lysozymes

Enzymes that attack peptidoglycans found in the cell wall of bacteria. Found in tears, saliva, breast, milk, and mucus. found in neutrophil granules.

How RIG 1 and RIG 2 work

they are enzymes that recognize and bind RSS for cutting and rejoining

Neutrophils

First leukocyte recruited to site of infection, most common leukocyte in blood. low neutrophils in the blood means they are moving into the tissues - sign of infection. phagocytic receptors, CD-14, mannose receptors. Azurophillic(lysozyme, defensins, proteases) and specific granules(NADPH ozidase, lactoferrin). Respiratory bursts(formed by conversion of azurophillic and specific granules) - NADPH and oxygen to generate superoxide - very harmful to bacteria - superoxide dismuatase - hydrogen peroxide - very harmful to bacteria - catalase regulator - hydrogen peroxide to water and oxygen. After respiratory bursts neutrophils die via netosis(production of NETs that trap pathogens) or apoptosis(packaging into vesicles that become engulfed) -formation of pus capsules. In absence of infection antimicrobial proteins and peptides in neutrophil granules are kept inactive at low pH Granules fuse with phagosome and NADPH and superoxide dismutase reactions raise pH Hydrogen peroxide has potential to damage human cells Catalase efficiently gets rid of hydrogen peroxide Neutrophils die by apoptosis Netosis. Killing via neutrophils - azurophillic + specific + phagosome = ph rises = ph lowers (lysozymes are added) = hydrolysis = cell death = macrophage cleanup

NOD-like receptors

Free floating intracellular receptor. can form inflammasomes. NOD-like receptors(NLR) are slightly different. They are kind of confusing. They can detect gram positive and negative bacterial infections. Some have CARD domains and others have NLRP domains. From my understanding its the NLRP domains of NLRs are responsible for the inflammasome and the end result is IL-1b and IL-18.

CTLA-4

High-affinity inhibitory cell-surface receptor on T cells that interacts with B7 co-stimulatory molecules to regulate T-cell activation

Type 1 interferons

IFN-alpha and IFN-beta, Type I interferons inhibit viral replication and activate NK cells. induce resistance to viral replication in cells, increase expression of ligands for receptors on NK cells, activate NK cells to kill virus infected cells

Type 2 interferons

IFN-gamma

intracellular immunity type 1

ILC1, Th1 cells , elimination of intracelluar pathogens, activation of macrophages

mucosal barrier

ILC2, Th2 cells, elimination and expulsion of parasites, recruitment of basophils, eosinophils and mast cells

extracellular immunity

ILC3, Th17, elimination of extracellular pathogens and bacteria, recruitment and activation of neutrophils

Type 1 interferon response

INF-a, INF-b - type 1 interferons up regulate receptors activate NK cells to kill viral infected cells

Impact in the compliment system if C3 or C5 were not activated?

If C3 is not formed then C3 and C5 convertase is not formed the MAC is not formed. people who have mutations in this they suffer from prevalent infections

a-Defensins

• Made by neutrophils and Paneth cells (epithelial cells in the small intestine) • There are six different types