Immunology and Microbiology Flashcards

Question

T cell activation

Answer 1

T cells are activated when encountering foreign antigen presented on MHC I or II with the co stimulatory signal from CD28 and B7, combined with an array of different cytokines. - It can also happen in a non MHC activating pathway, this is when a t cell is activated by an array of cytokines and an activation by microbes for example TLR and NLR activation. Dendritic cells present antigen and is ´hunted´down by T-cells, which can ´smell´the chemokines CCR7 and CXCR3. Co-stimulation is a 2nd signal for activation of T cells and is only present when the innate immunity has sensed an infection and thus ensure activation of T cells only when there is an infection. - Only dendritic cells, macrophages, and B cells will express co-stimulatory molecules only in the presence of infection so other cells don’t accidentally activate T cells - This is a safety mechanism because selection in thymus is not 100% perfect. An autoimmune cell that sees its antigen in absence of infection will not be activated (in fact, it will be eliminated).

Answer 2

T-cell receptor comlex is made up of a variable antigen-recognition proteins and an invariant signaling protein. - TCR alpha:beta heterodimer, the beta-chain has to reassemble (recognizes MHC molecule) - TCR gamma:delta, both has to reassemble to specifically each other or rearrengement stops (recognizes soluble agents at epithelial surface) - CD3 and zeta chains that mediate signaling in the cells Signaling from the T-cell receptor is initiated by ITAMs (10 ITAMs) Instead of a light and heavy chain, it has an beat and alpha chain - Always reside in the plasma membrane. - 1 antigen binding site

Answer 3

Expression of one of two alternative genes of a gene→ Restricted expression of antigen receptor genes => immunoglobulin and TCR of a single antigen specificity.

Answer 4

- Expressed on all nucleated cells - TCR recognizes MHC I, and CD8 binds to the side of the MHC I 1. MHC class 1 binds to chaperone proteins, and binds to TAP via tapasin 2. Cytosolic proteins are degraded to peptide fragments by the proteasome and is transported through the membrane by TAP 3. TAP delivers peptides to the ER. 4. This is further cut by ERAAP. 5. A peptide binds to the MHC class 1 molecule and completes its folding 6. MHC molecule is released from the TAP complex and exported to the cell membrane MHC’s do NOT discriminate between self and non-self – T cells do

Answer 5

- Peptides translated from introns in improperly spliced mRNA, translation of frameshift, improperly folded cytoplasmic proteins and membrane or secreted proteins that fail to enter ER- Tag with ubiquitin for degradation- Might help to generate peptide substrates from self-proteins and pathogen proteins for presenting by MHC I

Answer 6

- Found on antigen presenting cells (B-lymphocytes, dendritic cells, macrophages)- - CD4 binds to the side of the MHC 1. Extracellular peptides Invariant chain (Li) inhibits the binding of peptides and misfolded proteins, Li is cleaved in the acidified endosome. 2. CLIP is still bound, CLIP peptide blocks the binding of peptides and prevents the migration of MHC II. 3. HLA-DM binds to MHC II releasing CLIP, peptides can then bind to MHC II and MHC II migrates to the cell surface. MHC’s do NOT discriminate between self and non-self – T cells do

Answer 7

MAIT- Present in mucosal immune system- respond to bacterially folate derivates presented by non-classical MHC MR1INKT- Innate-like lymphocyte carries T-cell receptor invariant alpha and beta chain- Recognizes glycolipids presented by CD1 MHC class- Surface marker NK1 (same as NK cells)

Answer 8

IL-7 R is a true marker for memory T-cells that is only expressed on memory cells.Central memory T-cells(TCM): Arise from a primary T-cell response.- Express CD62 and CCR7- Recirculate in blood and secondary lymphoid organs.When antigen is recognized they get a recall response, and undergo rapid effector T-cell proliferation. Slower to acquire other effector functions,Effector memory T-cells (TEM): Arise from a primary T-cell response.- Lack CD62 and CCR7, but express high levels of beta1 and beta 2 integrins.- recirculate in blood and are rapidly recruited into inflammatory tissues where they initiate T-cell responses after restimulation.- express receptors for inflammatory chemokines and can rapidly mature into effector T cells, that secrete effector cytokines (IFN-gamma, IL4 or IL17)Tissue-resident memory T (TRM):Take up longterm residency in various barrier sites- Lack CCR7, but express other chemokine receptors (CXCR3 and CCR9) → allow migration into peripheral tissues- Express CD69, which reduces S1PR1, thereby promoting retention in tissues.- Can be both CD4 and CD8 T cells- Rapid response to TCR signaling or cytokines- surveillance and can initiate a particular immune module response locally

Answer 9

TH1 cells play a crucial role in combating intracellular bacteria through the activation of macrophages, induction of apoptosis, and modulation of immune cell balance. Their cytokine production and effector functions contribute to both antimicrobial defense and autoimmune responses. Activation: Triggered by IL-12, IL-15, and IL-18. in addition INF-gamma Pathogens Targeted: Primarily fights against intracellular bacteria. - IFN-gamma and CDL40 induce and activate M1 macrophages- FAS ligand and LT-beta, produced by Th1 cells, induce apoptosis - Il-2 produced by Th1 cells acts on activated naive CD4 and CD8 → alters balance to favor Th1 cells from TFh and CD8 CTLs and memory. - IL-3 and GM-CSF stimulate production of monocytes in bone marrow - Produce TNF-alpha and LT-alpha acts on blood vessels and induce binding and exit of monocyte Cytokines Produced: IFN-gamma, CD40 Ligand, IL-2, IL-3, TNF-alpha, and LT-alpha. Proinflammatory Responses: Responsible for killing intracellular parasites. Contribute to autoimmune responses by inducing macrophages and monocytes. ## Footnote can also differentiate to TFH cells, that again leads to B cell activation

Answer 10

Activated by IL-25 and IL-33T cells: Th2 cells Pathogens: Helminth infections and parasites Effects: IL-13 induce epithelial cell repair and mucus production → increased turnover and movement, which shreds parasitized epithelial cells. Mucus prevents adherence. - IL-13 induce smooth muscle contraction → enhance infection expulsion - M2 macrophages recruited via. IL-4 and IL-13 → enhance smooth muscle contractions and tissue repair. - IL-5 recruits and activates eosinophils - Mast cell recruitment via. IL-3 and IL-9 and specific IgE mast cell arms against helminths. → produce mediators as histamine, THF-alpha and MMCP → inflammatory response and remodel mucosa. Cytokines: IL-13, IL-4, IL-5,IL-3, IL-9 Effector function: Increases epithelial turnover and mucus production, increase smooth muscle contraction, recruit and activate M2 macrophages → tissue remodeling and repair, recruitment and activation of eosinophils, enhance inflammatory response (mast cells) ## Footnote can also differentiate to TFH cells, that again leads to B cell activation (different from Th1 response

Answer 11

Activated by IL-23T-cells: Th17 cells Pathogens: Infections agianst extracellular bacteria Effects: IL-17 and IL-22 induce production of antimicrobial peptides → kills or inhibts growth of bacteria attached to epithelium - IL-22 increase epithelial turnover - IL-17 activates stromal cells and myeloid cells to produce G-CSF → stimulate neutrophil production - IL-17 activates stromal cells and epithelial cells to neutrophil attracting chemokine production. - CGL20 chemo-attractment of other Th17 cells Cytokines: IL-17, IL-22, G-CSF and CGL20 Effector function:recruitment of neutrophils and the stimulation of epithelial antimicrobial defenses at infection sites

Answer 12

- Activation: Inhibited by IL-6, produced by DCs - Function: Suppress immune responses, 1 and 2, and are able to inhibit T-cell proliferation and cytokine production, plays a critical role in preventing autoimmunity through binding with high-affinity IL-2 receptor and removing IL-2. - Markers: CD25 and CD127, FowP3 intracellular. - Produces: IL-10 and TGF-beta

Answer 13

antigen-experienced CD4+ T cells found in the periphery within B cell follicles of secondary lymphoid organs such as lymph nodes, spleen and Peyer's patches, and are identified by their constitutive expression of the B cell follicle homing receptor CXCR5 Function: Upon cellular interaction and cross-signaling with their cognate follicular B cells, TFH cells trigger the formation and maintenance of germinal centers through the expression of CD40 ligand (CD40L) and the secretion of IL-21 and IL-4. TFH cells also migrate from T cell zones into these seeded germinal centers. - Play a critical role in mediating the selection and survival of mature B cells or germinal center-dependent memory B.

Answer 14

- Resting B-cells: Express CxCR5 and reside in follicles - Activated B-cells: induce CCR7 and EBI2 Antigen presentation to CD4+ helper T-cells in humoral immune responses.

Answer 15

1. Stem Cell Response: Responds to cytokines to coordinate VDJ recombination and B-cell development. 2. Early Pro-B Cell:D-J rearranging of the heavy chain. 3. Late Pro-B Cell: V-DJ rearranging of the heavy chain. 4. Large Pre-B Cell: VDJ rearranged heavy chain transiently expressed on the surface. 5. Small Pre-B Cell: V-J rearranging of the light chain. 6. Immature B Cell: VJ rearranged light chain, expressing IgM on the surface. 7. RAG Activity: High during the rearrangement of light and heavy chains. 8. Testing for Autoreactivity (Central Tolerance) in Immature B Cell: - Multivalent recognition of self-antigen leads to apoptosis or receptor editing. - Weakly cross-linking self-antigen results in apoptosis due to unresponsiveness. - Non-crosslinking antigen leads to immunological ignorance to the antigen. Complete Maturation in Spleen: Tested for BAFF-R, BCR, affinity, and cross-linking. If low affinity and non-crosslinking, the B-cell matures. In summary, B-cell development involves a series of stages from early pro-B cells to the testing of autoreactivity in immature B cells. The process includes rearrangements of heavy and light chains, expression of surface markers, and rigorous testing for self-reactivity to ensure central tolerance. The final maturation in the spleen involves further testing for B-cell receptor parameters, determining the maturity of the B-cell.

Answer 16

- VDJ recombination → Primary diversificationRecombination occurs between gene segments on the same chromosome- RAG1/2 is essential for the recombination and is followed by the NHEJ and DSBR1. - Binding of RAG1/2 to 23 RSS and 12RSS → leads to cleavage of DNA2. Ku70/Ku80 binds DNA endsa. - Artemis:DNA-PK opens hairpin structure, the cut ends are modified which randomly add and remove nucleotides → then ligated by DNA ligase IVb. - DNA ligase IV ligase DNA. - CDR1 and CDR2 reside in the V region, CDR3 is formed by the VJ joining. - - AID → secondary diversificationEnzyme important in secondary diversification- Initiates somatic hypermutation and class switch recombination - AID → MMRTLS → BER → APE1 → gene conversion → class switch recombination - Happens at the immunoglobulin V-region

Answer 17

Mutations in V-region DNA of rearranged immunoglobulin genes that produce variant immunoglobulins, for higher affinity to antigen.-Increases affinity and specificity towards the antigen

Answer 18

- Somatic gene recombination in activated B-cells- Replace a heavy-chain constant region with a different isotype- Switching immunoglobulin isotype (IgI→IgA)

Answer 19

Expression of one of two alternative genes of a gene→ Restricted expression of antigen receptor genes => immunoglobulin and TCR of a single antigen specificity.

Answer 20

First signal required for B-cell activation is delivered through BCR  migrates to germinal center of secondary lymphoid tissue- B-cells take up antigen through BCR phagocytosis and present antigen derived peptides on MHC class II- T cells express CXCR5 and B cells express CCR7- TFH cells recognize MHC II secrete cytokines, to deliver the second signal- CD40L binds to CD40- NF k beta is activated- NFk beta activates NIK, which stimulates pro-survival genes eg. Bcl-2- B cells migrate near the follicular and proliferate into B cell plasmoblasts and B cell memory cells

Answer 21

B1: Secretes IgM (anti polysaccharide antibody) and binds IL-5 without help form T-cells. - Plasmacells: secrete antibodies- Plasmoblasts: Secrete antibodies, but retain surface Ig and MHC II molecules, migrate to bone marrowB2(follicular): B-2 cells are a subtype of B cell. They form part of the adaptive immune response and mediate humoral immunity. B 2 cells can produce high-affinity antibodies and generate immunological memory. B-2 cells are often used synonymously with classical B cells.B-memory cells:B memory cells arise from germinal center reaction during primary response. They express a class-switched surface and reside in the blood. They are poised to generate more rapid and robust antibody.

Answer 22

Bone marrow b cells develop in the bone marrow and is checked for central (self) tolerance before leaving.Thymust cells develop in the thymus, and are also checked for central tolerance before leaving. t cells upregulate S1PR1 to leave thymus

Answer 23

Peyer´s patchesMucosal immune system, gut associated lymphoid lymphoid tissues(GALT) Peyer’s patchesPeyer’s patches = groupings of follicles in the mucus membrane and is covered by an epithelial layer containing M-cells which have ruffels, reside in the small intestineLymph nodeParacortical area (T-zone) → produces T-cell and DC attracting chemokines (CCL21 → CCR7)primary lymphoid follicle (B-zone) → produce a B-cell attracting chemokine (CXCL13 → CXCR5)Germinal center germinal centre (GC) of lymphoid organs is the main structure where antigen-activated B cells diversify their immunoglobulin genes by somatic hypermutation-Follicular B cells in lymph nodes transport antigen to FDC’sThe spleenMarginal zone: Dendritic cells, macrophages, and B-cellsB-cells in marginal zone transport antigens to FDC’sPals: T cells and dendritic cells - B and T-cells both migrate to follicular and interfollicular regions- B and T-cells aggregate at periphery of follicles (B-cells reduce CCR7)

Answer 24

-2 heavy chains -2 light chains-Held together by disulfide bonds-Immunoglobulin fold= One β sandwich of two β sheets folded together and linked by a disulfide bond -Variable regions(fab)= recognize antigen (proteins or haptens) -Constant regions(fc)= dictate antibody class and isotype (effector function) -Paratope= the region of the antibody that recognizes the epitope -Idiotope= amino acid residues that do not have direct contact with antigen, but still contribute to antigen recognition -Antibodies bind antigen via non-covalent interactions (e.g electrostatic forces)-CDR= hypervariable regions that interact with antigen (v-type) CDR3 region is the most critical in antigen recognition and specificity (CDR1 and CDR2 are also important) -C-type=no variability-B-cell receptor can be in soluble or bound within TM domain Functions: - Bind to pathogens and toxins therby neutralize their infection and intoxication of host cell - Promote phagocytosis (opsonization)

Answer 25

Major antibodies in extracellular fluid. Neutralization. Can be secreted as dimer because of J-chain.

Answer 26

Blood, not very abundant, effector function not well characterized

Answer 27

Blood stream, constant region provides strong activation of the complement system. First antibody to be expressed on naive B-cells. Can be secreted as pentamer because of J-chain.

Answer 28

mucosa. Often found in the skin. Associated with allergy. Defense against parasites by recruiting mast cells. Mast cells can secrete toxic compounds towards the parasite.

Answer 29

Sensitization- Der p 1 is taken up by DCs for antigen presentation and T-cell priming- TFH/TH2 cell induce B-cell switch to IgE production- IgE binds to FCepsilonRI on mast cell- Mast cell granule content cause allergic symptomsRe-exposure- Mast cell IgE bound to FCepsilonRI recognizes antigen- Mast cell secrete histamine, prostagladins and leukotrienes- Inflammatory cascade produced by mast cell activation is amplified by eosinophils, basophils, TH2 lymphocytes and B cells

Answer 30

most abundant isotype, in the blood. Several effector functions. Can be transferred to the fetus through the placenta. Activate complement (though not as strongly as igG).

Answer 31

Opzonization, neutralization and vaccines

Answer 32

Allergy:- GeneticMain reason for developing an allergy= Susceptibility loci, these genes make it skewed towards TH2 responseIL4: IgE (promoter mutations high IgE) TIM genes: Th1 and Th2(p40) IL12 IL23: Th17

Answer 33

- EnvironmentalEarly exposure to ubiquitous microorganismsEary depletion of microorganisms by repeated use of antibioticsHelminth infectionHepatitis A virusComposition of gut commensal microbiota.Atopic individual: People who are allergic

Answer 34

Hypersensitivity reactions can be mediated by TH1 and T17 cells and CD8 cytotoxic T cells.

Answer 35

large family of small, secreted proteins that signal through cell surface G protein‐coupled heptahelical chemokine receptors. They are best known for their ability to stimulate the migration of cells, most notably white blood cells - CXCL13 → produced in the follicle and the light zone of germinal centers that bind CXCR5 and attracts more B cells - CXCL12 → produced by stromal cells in dark zone of germinal center binds CXCR4 expressed by centroblasts. - CCL21 → produced by DCs and stromal cells in T cell zones in lymph nodes that binds CCR7, attract naive T cells - CCL19 and CCL18 → produced by DCs attract T lymphocytes to developing lymph node -

Answer 36

Mainly produced by dendritic cells, macrophages and some endothelial and epithelial cells. Pro-inflammatory cytokines: - IL-1 → macrophages and epithelial cells (permeable influence transport of immune components and sticky to leukocytes) - TNF alpha → Macrophage, DCs, NK and T cells (epithel permeable influence transport of immune components and sticky to leukocytes) - IL-6 → macrophages, T-cell and epithelial cells (promotes adaptive immune response) - IL-12 → macrophages and DCs- IFN alpha → DCs and viral infected cells- IFN beta → viral infected cells - IFN-gamma → see type responses above - IL-2 → T cell growth factor - IL-3 → monocyte and mast cell recruitment - IL-4 → B-cell activation and M2 recruitment - IL-7 → marker for memory B-cells - IL-13 → Stimulates turnover and smooth muscle contraction - IL-17 → induce activation of antimicrobial peptides and stimulate neutrophil production and attachment. - IL-21 → germinal maintenance- IL-22 → production of antimicrobial peptides - IL-25 → TH2 cytokine production, activates TH2 response and ILC-2 - IL-33 →TH2 cytokine production, activates TH2 response and ILC-2 - LT-beta → induces apoptosis - TNF-alpha → promotes inflammation - FAS and FAS ligand → cationic independent toxicity and apoptosis - TRAIL → apoptosis of tumor cells and activated T cells - APRIL → B cell proliferation

Answer 37

Cytokines affecting behavior of the cell that releases the cytokine

Answer 38

Cytokines affecting adjacent cells

Answer 39

Cytokines affecting distant cells, depends on their ability to enter circulation and half-time in blood.

Answer 40

- CCR7 → Expressed by all naive T and B cells, binds CCL19 and CCL21 made by DCs and stromal cells in lymphoid tissue.- CCR9 → expressed by DCs, T cells, thymocytes and binds CCL25 and mediates recruitment of gut-homing cells- CXCR5 → Expressed by circulating B cells and activated T cells, bind CXCL13 and direct cell migration into follicle- CD40 and CD40L → CD40 on B-cells and CD40L on TH cells, co-stimulatory molecules required for the proliferation and class switching. Also expressed by DCs and CD40-CD40L interaction provide co-stimulatory signals to naive T cells- CXCL8 → produced by monocytes, macrophages (under inflammatory response) attract neutrophils and naive T cells.- P-selectin → Reside on activated endothelial cells- LFA 1 (integrins) → Reside on leukocytes binds to I-CAM 1- I-CAM 1 → reside on activated endothelial and leukocytes, binds to LFA 1- G-proteins → act as molecular switch in signal pathways (GPCR) to induce high affinity with LFA 1.- CD28 → activation receptor on T cells that binds to the B7 co-stimulatory molecules present on APCs.- BAFF → acronym for B-cell activating factor, binds to BAFF-R and TACI promote B cell survival.

Answer 41

Consists of cas genes, leader and repeat-spacer array- Class 1 is a multiprotein complex- Class 2 is a single proteinPAM adjacent protospacer motif and CRISPR protospacer is required for cas nuclease to recognize target and cut1. Short viral DNA is incorporated as a novel spacer into CRISPR array2. During expression CRISPR array is transcribed into pr-CRISPR RNA → mature crRNA with unique CRISPR spacer3. During interference, crRNA guide CAS effector nuclease → sequence-specific cleavage- Class 1, Cas 3 nicks DNA and Cas 10 cleaves- Class 2, Cas 9 nicks DNA and Cas 12 offset two nicksAltering CRISPR spacer or PAM → gain or loss of function→ Can be used in antimicrobial, anti-infective and genome editing systems

Answer 42

Caspase 1 is a hallmark for NLRP3 activation and NOS2 is a hallmark for classical activated M1 (inflamasome deficient mice)- NLRP3 form oligomers, which brings multiple NLRP3 pyrins together- Interacts with ASC pyrine domain- Aggregates ASC CARD domain- Aggregates Caspase 1 CARD domain, including proteolytic cleavage of caspase 1 => caspase 1 activation- Cleavage of IL-18 and IL-1 => cytokine releaseReduce amyloid-beta phagocytosis, which inhibit long term protentiation (LTP) and therefore contributes to ALZ

Answer 43

Essential for CD8 T-cell recruitment and effector functions.- Neutrophils are important in initiating and maintaining immune reactions- Leave CXCL12 trails on ICAM-1 coated surfaces- Neutrophils leave behind membrane trail, containing CXCL12- CD8 T-cells become more localized, with lower velocity and displacement

Answer 44

Pou2f3 gene is essential for tuft cell specification- Produce IL-25 upon infection of helminths and percentage of proliferating tuft cells in crypts increase- Regulate ILC2 and TH2 production- Induces production of IL-4 and IL-13 which initiates a type 2 response, IL-13 also acts as a positive feedback loop, as they amplify tuft cell lineage- Epithelial remodeling → goblet cell hyperplasia and changes in mucus composition

Answer 45

RNF 213 acts as a E3 ligase and require the presence of ATP as well as E1 and E2 enzymes. RNF213 starts focally and spread around bacteria- Independent of RING domain in autoubiquitination1. RNF213 mediated ubiquilation2. LUPAC recruitment- Required for NEMO and Optn recruitment- p62 and NDP52 only require RNF2133. Addition of M1-linked ubiquitin chains4. Recruitment of NEMO (induce inflammation) and Optn, p62 and NDP52 (induce autophagy)RNF213 restore recruitment of autophagy marker LC3

Answer 46

RNF 213 acts as a E3 ligase and require the presence of ATP as well as E1 and E2 enzymes. RNF213 starts focally and spread around bacteria- Independent of RING domain in autoubiquitination1. RNF213 mediated ubiquilation2. LUPAC recruitment- Required for NEMO and Optn recruitment- p62 and NDP52 only require RNF2133. Addition of M1-linked ubiquitin chains4. Recruitment of NEMO (induce inflammation) and Optn, p62 and NDP52 (induce autophagy)RNF213 restore recruitment of autophagy marker LC3

Answer 47

Increased CD44 and decrease of CD62L and CD127 indicate activated CD8 and CD4 T-cells- CD44 is an activation and maturation marker for T lymphocytes and correlate with increased lymphocytes in bloodEBOV suggest an late adaptive immune response, due to INF-gamme production in CD8 T-cells and the protection of recipients from EBOV challenge

Answer 48

- Tunnel assay detects DNA breaks in apoptosis.- Flow cytometry is a technology that provides rapid multi-parametric analysis of single cells in solution. Flow cytometers utilize lasers as light sources to produce both scattered and fluorescent light signals that are read by detectors such as photodiodes or photomultiplier tubes.

Answer 49

-Trimeric Fas ligand (FasL) binds to and trimerizes FAS-Clustering of the death domains (DDs) in the Fas cytoplasmic domains allows Fas to recruit FADD via it domain-The clustered death effector domains (DEDs) of FADD recruit and activate pro-caspase 8 via similar DEDs in the pro-caspase-Activated caspase 8 cleaves pro-caspase 3, which then cleaves I-CAD, releasing CAD to enter the nucleus and cleave DNA

Answer 50

Cytochrome C, specific for mitochondria is released into cytosol, and binds to Apaf-1. This complex binds to pro-caspase 9 and form a complex that activates pro-caspase 3. Pro-caspase 3 cleaves I-CAD, which activates CAD to enter the nucleus and cleave DNA.

Answer 51

- B cell, gives rise to plasma cell - T cell, gives rise to effector cell: These two are considered as the adaptive immunesystem - NK cell (Innate immunesystem)

Answer 52

- The monocyte gives rise to macrophages - Dendritic cells These cells is a part of the innate immunesystem

Answer 53

- Neutrophils - Eosinophils - Basophils - Mast cells These cells is a part of the innate immunesystem

Answer 54

Monocytes are white blood cells that derive from the bone marrow. A monocyte is part of the innate immune response and functions to regulate cellular homeostasis, especially in the setting of infection and inflammation - precurser cell to macrophages

Answer 55

- Produced by microbes and not the host - invariant in pathogens of a given class and serves a vita function. Examples such as LPS can however be phosphorylated and acetylated, to hide from the immunesystem.

Answer 56

Important mediators of inflammatory pathways in the gut which play a major role in mediating the immune responses towards a wide variety of pathogen-derived ligands and link adaptive immunity with the innate immunity. Can lead to an intrinsic signalling pathway - Type I: recognize bacteria, parasites and fungi - Type 2: recognize single-stranded viral RNA, DNA vira and bacteria - Type 3: recognize dobble-stranded viral RNA - Type 4: recognize Bacteria flagellin Induces gene expression leads to production of pro-inflammatory cytokines, with Systemic effects on: - Neutrophil mobilization - Fever and catabolic state - Acute-phase protein release from the liver

Answer 57

cytoplasmic PRRs that are unrelated to the transmembrane PRRs. NLRs mediate detection of intracytoplasmic bacterial products. Among the NLRs are five members of the NOD family, 14 members of the NALP family, CIITA, IPAF, and NAIP

Answer 58

The IFN-α/β response consists of an inductive phase in which virus infection stimulates infected and possibly uninfected cells to produce and secrete IFN-α and IFN-β proteins that signal through the dimeric IFN-α/β receptor and cause the transcriptional upregulation of antiviral effector genes - Feedback in viral response and positive feedback.

Answer 59

- Senses Z-nucleic acid. Z-DNA binding protein 1 (ZBP1) functions as a central regulator of programmed cell death and inflammatory responses in diverse conditions through RHIM domain-dependent interactions with the kinases RIPK1 and RIPK3. 1. Induce inflammatory responses 2. Thereafter it induce apoptosis or necroptosis

Answer 60

pattern recognition receptors (PRRs) is a group of cytosolic RNA helicase proteins that can identify viral RNA as nonself via binding to pathogen associated molecular pattern (PAMP) motifs within RNA ligands that accumulate during virus infection. - dimerize and form signalling complex, leading to inflammatory of cell death response.

Answer 61

prevents pathogen dissemination by * Trap within thrombi * Limit pathogen movement * Recruit leukocytes * Increase local concentration of antimicrobial peptides

Answer 62

- Regulate blood pressure and inflammatory reactions - Increases permeability of blood vessels - Released by immune cells during tissue damage

Answer 63

Pathogens use protease: * Increase dissemination (tissue damage) * Inactivate antimicrobial proteins Protease inhibitors inactivates protease through eg. α2-Macroglobulins: 1. Cleavage of bait regions -> activate α2-M 2. Covalent binding of protease by thioester 3. Conformation change of α2-M 4. Phagocytosis of complex

Answer 64

an evolutionarily conserved protein found in nearly all eukaryotic organisms. The main features of ubiquitin are its seven lysine (Lys) residues and the N-terminus. - Depending on binding it can vary structurally, giving it different functions such as immune signalling, degradation tag or vesicle traficking.

Answer 65

Encodes peptide presenting MHC proteins; - Class I: B, C, A Activates CD8 cytotoxic T-cells and is "one flavor" - Class II: DP, DM, proteasome genes (TAP1 and 2), DQ and DR activates CD4 heper T-cells and is "two flavor" - Class III: Complement proteins (C4, factor B, C2) and cytokines (LT-beta, TNF-alpha and LT-alpha) MHC proteins have a broad specificity and a very stable interaction. Co-dominant expression of parantal alleles

Answer 66

In the presence of infection, NK cells enter the infected tissue and secrete the inflammatory cytokine interferon-γ (IFN-γ), which induces the tissue cells to assemble and use the immunoproteasome for protein degradation. IFN-γ, also called type II interferon, is structurally and functionally unrelated to the type I interferons.

Answer 67

1. Crystal Violet Staining: The bacterial cells are initially stained with crystal violet, a purple dye. This step colors all cells uniformly. 2. Iodine Treatment: Iodine is then applied as a mordant, forming a complex with the crystal violet. This helps to fix the dye within the cells. 3. Alcohol or Acetone Decolorization: The stained cells are then exposed to either alcohol or acetone. This step differentiates between Gram-positive and Gram-negative bacteria. Gram-positive bacteria retain the crystal violet-iodine complex and remain purple, while Gram-negative bacteria lose the stain and become colorless. 4. Counterstaining with Safranin: The colorless Gram-negative bacteria are then counterstained with safranin, a red dye. Gram-positive bacteria retain the purple color from the initial staining. After the entire process, Gram-positive bacteria appear purple under the microscope, while Gram-negative bacteria appear red. This staining method is valuable in bacterial identification, as the differences in cell wall structure between the two groups have implications for treatment and susceptibility to certain antibiotics.

Answer 68

Cell wall structure: These bacteria have a thinner peptidoglycan layer in their cell wall, and it does not retain the crystal violet stain. Instead, they have an outer membrane composed of lipopolysaccharides (LPS) in addition to the peptidoglycan layer. Outer Membrane (Gram-negative bacteria only): additional layer outside the thin peptidoglycan layer and contains lipopolysaccharides (LPS). LPS has lipid and polysaccharide components and plays a role in the structural integrity of the outer membrane and can also act as an endotoxin. Periplasmic Space: larger periplasmic space between the cytoplasmic membrane and the thin peptidoglycan layer, and this space includes the outer membrane in addition to the peptidoglycan layer.

Answer 69

Cell Wall Structure: thick peptidoglycan layer in their cell wall, which retains the crystal violet stain used in the Gram staining process. This thick layer provides structural support and protection to the cell. Periplasmic Space: narrow periplasmic space between the cytoplasmic membrane and the thick peptidoglycan layer.

Answer 70

- MALDI-TOF mass spectrometry, particles are ionized, separated according to their mass-to-charge ratio, and measured by determining the time it takes for the ions to travel to a detector at the end of a time-of-flight tube - 16s RNA sequencing - Serotyping: agglutination of the bacteria with specific antisera to identify variants of somatic (O) and flagella (H) antigens. This provides the antigenic formula of the strain associated to the name and subspecies of the serotype

Answer 71

- CR1: a membrane receptor for C3b and C4b expressed on erythrocytes, leukocytes and podocytes. It plays an important role in removal of immune complexes and pathogens coated with C3b and C4b. - DAF: acts to accelerate the decay of the classical and alternative C3 and C5 convertases, the central amplification enzymes of the cascade. - MCP: C3b/C4b-binding cell surface glycoprotein which serves as an inhibitor of complement activation on host cells - Protectin: complement regulatory protein which blocks the membrane attack complex during complement activation - Factor H: regulates complement activation by (i) inhibiting the assembly of the alternative pathway C3 and C5 convertase enzymes via competition with factor B for C3b binding; (ii) facilitating the disassembly of the convertases by displacing bound factor Bb ('decay accelerating activity')

Answer 72

process by which T cells and B cells randomly assemble different gene segments – known as variable (V), diversity (D) and joining (J) genes – in order to generate unique receptors (known as antigen receptors) that can collectively recognize many different types of molecule.

Answer 73

Results from the imprecise joining of gene segments and from the addition of nucleotides to the DNA sequence at splice sites. TdT adds up to 15 nucleotides to the DNA sequence of human VH and JH regions.

Answer 74

* Many different V, D, and J genes * Random combination between α and β chains * Junctional diversity by the N and P (palindromic) nucleotide insertion * D segment can be read in all 3 reading frames

Answer 75

* With positive selection, it is ensured that T cells are able to recognize peptide-MHC molecules with a low affinity. * Without positive selection, the T cell will not be able to interact with the MHC on the APC (so, T cell is killed). * In negative selection, if the T cell binds the peptide-MHC complex with a very high affinity, then there is a risk for autoimmunity (so, T cell is killed).

Answer 76

* AutoImmune REgulator (AIRE) is a protein that regulates hundreds of other genes and ensures expression of all “self” molecules in the thymus * If there is a mutation in Aire, then there is autoimmunity. Aire KO mice express fewer tissue specific antigens on the thymic medullary epithelium and fail to negatively select tissue specific thymocytes efficiently

Answer 77

T cells are recycled; this recirculation of T cells is controlled by adhesion molecules that are expressed at different stages dependent on T cell activation - T cells are ‘homed’ to secondary lymphoid tissues by chemokines and cell adhesion molecules

Answer 78

Selectins can control their affinity to a ligand. In this way, the T cell can control if it binds poor/well to the APC. This gives T cells the opportunity to move from cell to cell.

Answer 79

- Granule exocytosis model (Ca2+-dependent) - Perforin (a membrane disrupting protein) - Granzymes (serine proteases) - Fas/Fas-L (Ca2+-independent) CD8 T cells will only kill antigen-containing cells. After adequate recognition, CD8 T cells will release lytic granules and induce the target cell to die by apoptosis (via JAK-STAT signalling to affect gene expression).

Answer 80

Th1/Th2 balance is crucial for the development of fibrosis as IL-4 producing Th2 cells induce fibrosis while IFN-γ producing Th1 cells inhibit fibrosis in experimental models of fibrosis Th1 cells promote cellular immunity and are involved in the development of autoimmune diseases; Th2 cells mediate humoral immunity and are involved in allergic immune

Answer 81

PTMs (Post-Translational Modifications): - Ubiquitination - Phosphorylation Second Messengers: - PIP2 cleavage into IP3 and DAG - Ca2+ - cGAMP

Answer 82

Location: Plasma membrane at lipid rafts. Receptors: TCR and BCRs rely on Immunoreceptor Tyrosine Activation/Inhibition Motifs (ITAMs and ITIMs). T-Cell Receptor Signaling: - CD3 and zeta chains contain ITAMs. - LCK phosphorylates ITAM. - ZAP-70 binds P-ITAM to propagate the signal. - PLC cleaves PIP2 into IP3 and DAG. - ITAM phosphorylation facilitates the assembly of the Immune Synapse. B-Cell Receptor Signaling: - SRC kinases phosphorylate ITAM in Igα/β. - SYK binds P-ITAM to propagate the signal.

Answer 83

Draw yourself

Answer 84

- SHP phosphatases dephosphorylate Tyr residues on P-ITIM, limiting activation. - CBL-b (E3 ubiquitin ligase) ubiquitinates TCR and ZAP-40, targeting them for proteasomal degradation.

Answer 85

- Type I IFNs induce cGAS expression. - cGAS binds nucleotides, stimulating cGAMP. - cGAMP promotes NF-kB signaling and proinflammatory cytokine production.

Answer 86

Definition: - Large group of small signaling proteins (~25 kDa) that are secreted by various cells (all immune cells) in the body - Bind specific receptors - Regulate and coordinate many activities of the cells of innate and adaptive immunity (growth, differentiation, activation, cell recruitment) Sub-groups: - Interleukins (IL-1,-2,-4,-5,-6...etc.) - Colony-stimulating factors (G-, GM- & M-CSF, progenitor differentiation) - Interferons (IFN-α,-β,-γ) - Tumor necrosis factors (TNF-α, Ltα/β) - Transforming growth factors (TGF-β) - Chemokines (chemotactic cytokines)

Answer 87

- Type I and II Cytokine receptor (JAK-STAT) 1. L-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-9, IL-11, IL-13, IL-15, IL-21), interferons (IFN-α, IFN-β), and colony-stimulating factors. 2. interferons (IFN-γ), IL-10, IL-20 family, and IL-22. - TNF Receptor family TNF-alpha, TNF-beta, LT, CD40, FasL, BAFF, April, OX40, GITR, nerve growth factor - IL-1 receptor family IL-1, IL-18, IL-33

Answer 88

- IL-1B activates vascular epithelium, activates lymphocytes, local tissue destruction and increases acces of effector cells - 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 lymphnodes - IL-6 activates lymphocytes and increase antibody production - CXCL8 recruits neutrophils, basophils and T cells to site of infection - IL-12 activates NK cells and induces the differentiation of CD4 T cells into Th1 cells IL-1B, TNF-alpha and IL-6 acts on the liver (complement system), bone marrow, hypothalamus, fat/muscle and DCs.

Answer 89

- MHC class (activation) - CD28 (co-stimulatory binding factor) (survival) - Cytokines (differentiation)

Answer 90

Inflammasomes are cytosolic molecular factories that typically consist of a sensor protein, the adaptor protein apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC), and the proinflammatory caspase, caspase-1

Answer 91

Autoimmune and allergic reactions are the same in that they are both inappropriate immune responses, but result from different antigens (autoimmune is self, allergy is foreign). - Type I: are triggered by the interaction of an allergen with allergen-specific IgE bound to the FcεRI receptor of mast cells, basophils, and eosinophils. This interaction causes these cells to degranulate and release a potent mixture of inflammatory mediators. Cells that can bind IgE are mast cells, eosinophils, and basophils - Type II: IgG response to chemically reactive small molecules that become covalently bound to the outside surface of cells. The chemical reaction modifies the structures of human cell surface components, which are now perceived as foreign antigens by the immune system. - Type III: small soluble immune complexes of antigen and specific IgG that form deposits in the walls of small blood vessels or the alveoli of the lungs. At these sites, the immune complexes activate complement and an inflammatory response that damages the tissue and impairs its function. - Type IV: mediated by antigen-specific effector T cells, and in most instances by CD4 TH1 cells (e.g. nickel allergy). Some are due to CD8 T cells (e.g. poison ivy).

Answer 92

- Anti-histamine (won’t help for T cell reactions because histamine mediates the immediate phase) - Cortisol/steroid crème - Adrenaline

Answer 93

The immune system has two main responses: 1. Early (Innate) Response: - Rapid and non-specific. - Involves physical barriers, inflammatory cells, and quick, general defenses. 2. Late (Adaptive) Response: - Specific and memory-based. - Takes longer to develop but provides targeted and lasting protection. - Involves B cells, T cells, and the production of antibodies. - Creates immunological memory for faster future responses.

Answer 94

Genetic factors: - Inherited traits influence immune system development. - Genetic diversity contributes to variable immune responses. - Genetic mutations can lead to immunodeficiencies. Environmental Factors: - Pathogen exposure shapes immune system responsiveness. - Nutrition, lifestyle, and stress impact immune function. - Vaccinations prime the immune system against specific pathogens. Gene-Environment Interactions: - Epigenetics modulates gene expression in response to the environment. - The microbiome, influenced by diet and antibiotics, affects immune system function.

Answer 95

Central tolerance: develops in the primary lymphoid organs (Bone Marrow for B cells and Thymus for T cells) - Negative selection of high-avidity leading to apoptosis , mediocra avidity leading to receptor editing and low-avidity leading to anergy (total strengt required for interaction) (B cells) - Positive and negative selection of self-reactive cells (T cells) - Receptor editing (Only in B cells) - Anergy (B cells) (absense of normal immune response) Peripheral tolerance: mechanisms that inhibits self-reactive cells in the periphery. - T cell provide signal for B cells (or other source eg. complement or PAMPs) - Requirement of co-stimulation for activation of naive T cells - Treg cells suppres T cells and other immune cells - require self-reacting T- and B-cells (2 signals)

Answer 96

- Common antigens - Low expressed antigens - Tissue-restricted antigens AIRE allows expression of many different genes that are not present in the thymus to allow for selection of tissue-restricted antigens (basically all self-antigens in the body). and self-types specific for some organs. Self-tolerance + self antigen leads to: - Regulation by inhibitory receptors - Anergy - Suppression - Deletion

Answer 97

Infection can cause autoimmunity through: - Self tolerance - Induction of co-stimulatory signals - Molecular mimicry

Answer 98

Type II, III, or IV hypersensitivity reactions: - Type II: IgG response to chemically reactive small molecules that become covalently bound to the outside surface of cells. The chemical reaction modifies the structures of human cell surface components, which are now perceived as foreign antigens by the immune system. - Type III: small soluble immune complexes of antigen and specific IgG that form deposits in the walls of small blood vessels or the alveoli of the lungs. At these sites, the immune complexes activate complement and an inflammatory response that damages the tissue and impairs its function. - Type IV: mediated by antigen-specific effector T cells, and in most instances by CD4 TH1 cells (e.g. nickel allergy). Some are due to CD8 T cells (e.g. poison ivy). No autoimmune reaction is mediated through IgE.

Answer 99

- Negative selection in thymus - Expression of tissue specific protein in thymus - Lack of lymphocyte acces to some tissues - Restriction of HLA class II - Supression of autoimmune response by Treg - Induction of anergy in autoreactive B and T cells - Requirement of B cell responses for T cell help - Requirement of co-stimulation in naive T-cells - Oral tolerance to food and commensal organisms

Answer 100

- HLA polymorphism (genes encode MHC proteins involved in the regulation of the immune system) - CTLA-4 polymorphism ( regulates immune responses by downregulating T-cell activation) - PTPN-22 polymorphism (is involved in T-cell signaling and regulation.) - Polymorphism of autoantigens (Autoantigens are self-antigens that trigger immune responses in autoimmune diseases.) - AIRE deficiency (gene responsible for maintaining self-tolerance by promoting the expression of tissue-specific antigens in the thymus.) - FoxP3 deficiency (crucial regulator of regulatory T cells (Tregs) that maintain immune tolerance)

Answer 101

Autoimmune Hemolytic Anemia: - Targets erythrocyte surface. - Antibodies activate complement, leading to hemolysis. Myasthenia Gravis: - Impairs signaling at the neuromuscular junction. - Autoantibodies target acetylcholine receptors. Graves' Disease: - Affects the thyroid gland. -Agonist autoantibodies stimulate TSH receptors, causing hyperthyroidism.

Answer 102

Systemic Lupus Erythematosus (SLE): - IgG against various self-antigens. - Immune complexes deposited in tissues cause inflammatory reactions.

Answer 103

Hashimoto's Disease: - CD4 TH1 response leads to hypothyroidism. - Progressive destruction of thyroid tissue. Multiple Sclerosis: - Autoimmune attack on myelin sheath. - TH1 CD4 cells and IFN-γ secretion cause demyelination. Type 1 Diabetes: - CD8 T cells mediate β-cell destruction. - Gradual reduction in insulin-secreting cells. Rheumatoid Arthritis (RA): - Systemic autoimmune disease. - Production of antibodies against Fc region of human IgG. - Synovium infiltration leads to tissue damage.

Answer 104

1) ESCAPE OF THE MICROBES FROM IMMUNITY - Antigenic variation -> mutations, recombination and gene re-arrengement. - Hide/camouflage - Suppression of immunity 2) MICROBES leading to IMMUNO-DEFICIENCY - HIV/AIDS 3) INBORN/ACQUIRED IMMUNODEFICIENCY - Example: Severe Combined Immunodeficiency (SCID) often involves mutations in IL-2 receptor gamma or IL-7 receptor alpha chain. - Genetic defects in RAG1, RAG2, and Artemis, related to antigen receptor recombination, can cause immunodeficiency. - Deficiencies in IFNγ, IL-12, and their receptors prevent mutual activation of macrophages and NK cells, allowing infection persistence. - Complement component (Classical, MLB and Alternative) defects lead to infections and immune complex accumulation. Bone marrow transplant can reverse inherited/acquired immunodeficiencies.

Answer 105

- Mechanisms by Herpes and Pox viruses to subvert the host immune system are employed. - Cancer-induced immunodeficiency can result from malignant T cell cytokines inducing skin barrier defects.

Answer 106

Parasites encode multiple genes with similar functions, providing redundancy. Examples include EBA1-3 and PfRh1-4 in malaria.

Answer 107

Parasites exhibit allelic diversity in genes, making them elusive targets for the immune system. Examples include AMA-1 and MSP-1 in malaria.

Answer 108

Multicopy gene families, like PfEMP1 in malaria, enable parasites to vary antigens within the same clone.

Answer 109

Parasites use molecular mimicry or hiding. In malaria, infected erythrocytes (IEs) sequester, and IgM masking prevents specific IgG binding to Duffy binding-like domains.

Answer 110

Malaria parasites, like MSP1, can subvert immune functions, destroying the immune response.

Answer 111

Parasites can increase virulence under host pressure. Vaccines offer imperfect protection, and many people remain unvaccinated.

Answer 112

- Injection to Liver: Sporozoites injected into the skin migrate to the liver. - Parasite Development in the Liver: Sporozoites invade hepatocytes, undergo asexual reproduction, and release merozoites. - Erythrocyte Invasion: Merozoites infect erythrocytes, leading to asexual replication and release of more merozoites. - Sequestration: Infected erythrocytes adhere to endothelium, causing pathology. - Completing the Cycle: Mosquitoes ingest gametocytes during blood feeding, and the cycle continues.

Answer 113

- Protective Immunity: Innate and adaptive immunity, including CD4+, CD8+ T cells, and antibodies, contribute to protection. - Antigens of Importance: PfEMP1 is a key antigen involved in sequestration and immune evasion. - Antigenic Variation Mechanisms: "Mutually exclusive" expression of var genes, sequential immunological gap-filling. * CSP is main pre-erythrocytic stage antigen that is recognised by protective immune cells in the immune system and is also the target of the current malaria vaccine. * TRAP is the main sporozoite ligand for hepatocyte invasion, and by using TRAP is how the sporozoites move.

Answer 114

Characterizes eneveloped viral responses; Regulates downstream pathway, as fucose eg. inhibits binding of FabetaIIalpha receptor on NK cells.

Answer 115

- Innate immunity activation DC , macrophages , and NK cells - Adaptive immunity activation CD4+ , CD8+ , and ( gd ) T cells IL-10 TGFβ - Activation phagocytic cells TNFα Important parasite killing - Regulation inflammation - B cell, antibodies

Answer 116

- Transmission and Life Cycle: Leishmania is transmitted by sandflies, with various species causing different diseases. Promastigotes in sandfly saliva transform into amastigotes in host cells, causing disease. - Immunology: Neutrophils respond to sandfly bites, and Th1 responses are associated with leishmanicidal activity. IL-10 may contribute to immune suppression, favoring parasite persistence. - Genome and Surface Molecules: Leishmania has a unique genome with 36 chromosomes. Surface molecules like LPG, gp63, and GPI-anchored proteins play roles in infection. - Diagnosis and Treatment: Diagnosis involves identifying parasites in biopsy specimens. Sodium stibogluconate is the primary drug, but drug resistance is a concern. - Control Strategies: Control involves targeting sandflies, reservoir animals, treatment, education, and vaccine development. Clearing the parasite depends on the type of macrophage response, with M1 being leishmanicidal.

Answer 117

- Disease Overview: Schistosomiasis is a parasitic infection transmitted by freshwater snails. It exhibits focal distribution and affects various organs based on the schistosome species. - Life Cycle: Infection occurs when cercariae penetrate the skin, leading to various forms of the disease. Immunity develops slowly, with Th2 responses associated with resistance. - Immune Responses: Th2 responses and specific antibodies (IgE, IgG1, IgG3) correlate with resistance. IL-10 may play a role in promoting parasite persistence in visceral leishmaniasis. - Pathogenesis: Disease results from the host's immune response to schistosome eggs. Granuloma formation and fibrosis occur, leading to various symptoms. - Treatment and Vaccine Considerations: Praziquantel is used for treatment but does not prevent re-infection. An ideal vaccine should induce strong, long-lasting immunity without worsening morbidity.

Answer 118

- Pre-erythrocytic vaccines target sporozoites and liver stages. - Erythrocytic vaccines aim to block red blood cell invasion. - Transmission blocking vaccines use antibodies to hinder parasite transmission via mosquitoes

Answer 119

Transmission Routes: - Infections can be transmitted through airborne particles, direct contact, and indirect contact (utensils). - Two infection routes: endogenous (from the patient's own body) and exogenous (from other people or objects). Contamination Routes: - Sneezing, inoculation (cuts or punctures with contaminated needles), and alimentary routes (e.g., contaminated water or food). - Bacteria localize on skin and hair follicles, and hand hygiene suppresses but does not eradicate skin flora.

Answer 120

- Streptococcus pyogenes: Gram-positive cocci causing various diseases in different body parts. - Clostridium tetani: Gram-positive rods forming spores, producing toxins affecting neurons (tetanus). - Bacillus anthracis: Gram-positive rods forming spores, causing anthrax through cutaneous, pulmonary, or gastrointestinal routes. - Pseudomonas aeruginosa: Gram-negative rods, associated with hospital-acquired infections, especially in burn wounds. - Staphylococcus aureus: Gram-positive cocci causing a range of diseases, including toxic shock syndrome (TSS). - Escherichia coli: Gram-negative rods, typically harmless in intestines but can cause infections outside.

Answer 121

- Biofilms are characteristic of chronic, long-term infections. - Often unresponsive to antibiotic treatment and resistant to host defenses, including phagocytosis. - Common in non-healing wounds and medical implant infections. Difficult to diagnose and may require implant removal for a cure.

Answer 122

Animal Models: - Various animal models (C. elegans, zebrafish, non-human primates, rodents) used to study biofilm infections. - Rodents, especially mice, commonly used in laboratory settings for different infection models. Novel Treatment Strategies: - Challenges: Multidrug-resistant bacteria, lack of new antibiotics, and biofilm implications. - Strategies include prevention of biofilm formation, killing/removal of biofilms, weakening biofilms by QS inhibitors, c-di-GMP manipulation, and surface coatings. Three R’s Principle: - Refinement, reduction, and replacement guide ethical use of animals in research.

Answer 123

Quorum Sensing (QS): - Collective decision-making by bacteria, leading to the expression of QS-controlled target genes. - QS inhibitors (QSI) target the signaling molecules to disrupt biofilm formation. C-di-GMP Manipulation: - Bacterial second messenger regulating biofilm formation. - Manipulation using drugs that disperse biofilm bacteria, followed by conventional antibiotic treatment. Potential Treatment Strategies: - Single treatment with QSI drugs may not be beneficial for immunocompromised patients. - Treatment with c-di-GMP lowering drugs alone might lead to severe systemic infection. - Prophylactic treatment to avoid or delay biofilm establishment. - Combination treatment with QSI drugs/c-di-GMP lowering drugs and conventional antibiotics is considered the best strategy.

Answer 124

Efflux pumps, low permeability of bacterial cellular envelope, genetic changes, antibiotic degradation, and slow metabolic activity contribute to chronic infection.

Answer 125

- Activation of inflammatory responses can cause tissue and systemic damage. - Bacterial evasion mechanisms include inhibiting phagocytosis, inactivating complement, and changing antigenic appearance.

Answer 126

- The virion is the virus particle, consisting of a nucleic acid genome and a protein coat (capsid) or membrane envelope. - Viral attachment proteins (VAPs) mediate interaction with host cells. - Capsids are rigid structures, and enveloped viruses have a membrane composed of lipids, proteins, and glycoproteins. - Matrix proteins within the envelope facilitate virion assembly. - Viruses can have helical or icosahedral structures.

Answer 127

Classification is based on physical and biochemical characteristics, including size, morphology, presence of an envelope, type of genome, and means of replication.

Answer 128

- Viruses must address three challenges: reproduce inside host cells, spread from cell to cell, and counteract host defense systems temporarily. - DNA viruses replicate in the nucleus, while RNA viruses replicate in the cytoplasm. Viral Protein Synthesis: - Viruses depend on host cell ribosomes, tRNA, and posttranslational modification mechanisms for protein synthesis. mRNA binding to the ribosome is mediated by a 5’ cap structure or IRES. - Different viruses acquire the cap structure in various ways. - Bacterial ribosomes can translate polycistronic mRNA, while eukaryotic ribosomes make only one continuous protein. - Polyprotein synthesis occurs in positive-strand RNA viruses and is cleaved into functional proteins. - Different tactics are employed to promote viral mRNA translation over cellular mRNA. Virion Assembly: - Virions are assembled from small parts with recognition structures. - Assembly involves synthesis of necessary pieces and sufficient concentration of structural proteins. - Assembly may be facilitated by scaffolding proteins. - Assembly sites and mechanisms depend on genome replication and final structure. - Enveloped viruses acquire their envelope through budding from cellular membranes. Release: - Viruses can be released through cell lysis, exocytosis, or budding from the plasma membrane. - Naked capsid viruses are typically released after cell lysis. - Enveloped viruses are released after budding from the plasma membrane without killing the cell. - Some viruses prevent clumping within the cell by removing potential sialic acid receptors.

Answer 129

Recognition and Attachment: - Viral attachment proteins (VAPs) or structures on virions bind to receptors on host cells. - Receptors can be proteins or carbohydrates on glycoproteins or glycolipids. - Host range and tissue tropism are determined by specific receptors on target cells. Penetration and Uncoating: - Penetration can occur through endocytosis, viropexis, or fusion with the host cell membrane. - Uncoating involves removal of the capsid or envelope, exposing the viral genome.

Answer 130

- Mutations in viral genomes lead to new strains with different properties. - Viral polymerases are error-prone, resulting in a higher mutation rate for RNA viruses. - Different types of mutants include lethal, deletion, plaque, host range, and conditional mutants. - Recombination, reassortment, complementation, marker rescue, and trans-capsidation contribute to genetic diversity. - Viruses are selected based on their ability to use host cell machinery and withstand various conditions.

Answer 131

- Potential outcomes of viral infection include failed infection, lytic infection, persistent infection, replication without cell death, and immortalization. - Lytic infections result in cell death, while persistent infections may be chronic, latent, recurrent, or transforming. - Nonpermissive, permissive, and semipermissive cells play roles in viral replication.

Answer 132

- Innate and immune responses aim to prevent, limit, and eliminate viral infections. - Innate responses involve fever, interferons, macrophages, dendritic cells, and natural killer cells. - Antigen-specific immune responses, involving antibodies and cell-mediated immunity, play crucial roles. Immunopathology: - Hypersensitivity and inflammatory reactions initiated by antiviral immunity can cause pathologic manifestations. - Prodrome symptoms are induced by interferons and cytokines. - Inflammatory responses may cause immunopathologic conditions and immune complex hypersensitivity reactions. - Immunopathology can be a major cause of the symptoms of viral diseases.

Answer 133

- Some DNA viruses and retroviruses establish persistent infections that stimulate uncontrolled cell growth. - Characteristics of transformed cells include continued growth, alterations in morphology and metabolism, increased growth rate, and loss of contact inhibition. - Immortalization occurs through various mechanisms, including activation of growth-stimulating genes.

Answer 134

- Genetically manipulated viruses can serve as delivery systems for foreign genes. - Advantages include easy amplification, tissue targeting, and use of defective or attenuated viral vectors. - Viral vectors may be used for gene replacement therapy, vaccines, and targeted tumor killing.