Bact Path – Microbiology – Flashcards
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| Sec Proteins |
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| SecB - chaperone SecA - ATPase SecYEG - transporter |
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| SecA Functions (4) |
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| 1. Recruit Protein to SecYEG 2. Provide energy (ATP) 3. Push peptide through 4. Prevent back sliding |
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| Sec Signal Peptide Structure |
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| Small (7-15 amino acids) Basic N terminal Hydrophobic Middle SXS Cleavage Site |
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| SRP "Proteins" |
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| FtsH - Particle - chaperone (co-translational) FtsY - Bring to SecYEG Both have GTP activity |
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| Topology Rules |
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| 1. Positive Inside 2. IM - alpha helices 3. OM - beta sheets |
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| Topology Experiment Genes |
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| PhoA - periplasm LacZ - cytoplasm *must be C-termninal **wont work if too close to the membrane |
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| TAT Proteins |
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| TATC - 7TM domain - RR recognition TATD - cytoplasmic unknown function All others two helices TATB - help TATC TATA - polymerize TATE - unknown |
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| TAT energy source |
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| Proton Motive Force |
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| Oxidative Pathway vs. Reducing Pathway |
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| DsbA/B and DsbC/D Use second to re-estiablish first using the electron transport chain of the IM |
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| Periplasmic Chaperones |
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| Skp - OM proteins Pilus Specific Chaperones LolA/B - lipoprotiens |
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| PPI (function and location) |
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| Peptidyl prolyl isomerase periplasm (lots of OM proteins have P) |
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| Periplasmic Proteases |
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| DegP and DegS |
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| Sigma E system |
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| OM stress - Temperature and Alcohol RseB bind OM protein Releases RseA RseA releases SigmaE SigmaE promotes: degP, reseABC, fpkA) |
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| CpxA/R system |
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| Stress - pH and composition CpxA gets phosphorylated Relay to CPxR CpxR induces degP, CpxA/R, dsbA |
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| BAM |
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| Beta barrel assembly machine OM proteins |
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| Type II Secretion |
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| Start with Sec/Tat No Anchor Secreton: Secretin (ring) and Piston (pilus-like) Coupled to Cytoplasm for energy (ATP) |
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| Type V Secretion |
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| Autotransporters VacA and IgA1 sec/tat signal, passenger (contains cystines), beta barrel optional cleavage |
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| Type I Secretion |
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| Skip periplasm HlyA (in E. coli) Each have their own translocase (substrate specific) - trimeric IM anchor - ABC transporter Pairs with TolC (alpha helices protect) |
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| Type III Secretion |
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| And Type 4, 6, 7 Nano Syringe ATPase at base (cytoplasm) Vir complex |
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| Parts of Pap Protein |
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| PapG - tip PapF - linker PapE - fimbrillae PapK - linker PapA - rod pili structure PapH - anchor |
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| Non-structural Pap Genes |
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| PapC - usher PapD - chaperone PapI and PapB - regulatory PapJ - unknown |
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| PapD Mechanism |
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| Donor Strand Complementation Ig Fold has 7 Beta sheets Need G1 of PapD to bing to C-terminal of Pilin |
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| Driving Force of Type 1 pili |
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| 4 structure |
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| Regulators of Pilins |
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| CAP Lrp (Leucine response regulator protein) Iron Temperature SigmaE/Cpx |
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| Regulatory mechanisms of pili |
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| 1. Methylation-Dependent (gradient) 2. Inversion-Dependent (on/off) |
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| Twitching Motility Requirements |
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| Flagella-independent Wet Surfaces Population dependent |
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| Type IV Pilus Movement Mechanism |
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| Twitching Motility Extension, Tether, Retract (pilT-dependent) |
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| Type IV Pilus Structure |
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| Pre-pilin: N-alpha helix, 4 beta sheets, adhesion Pentamers: Coiled-Coil Glycoslated |
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| Type IV Pili Genes |
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| PilE -pilin PilQ - secretin PilS - pseudogenes pilD,F,G,T - energy coupling (secreton) |
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| Type IV Aseembly |
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| Homologous to Type II 1. Pre-pilin goes through Sec system 2. Signal Cleaved on cytosolic face 3. Pentamer formation 4. Ogliomerization (DsbA dependent) 5. Secreted by PilQ |
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| Mechanism of Pilin modification (protein) |
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| pilS genes without N termini Combined at random - infinite combinations |
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| LPS Sugars |
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| Core KDO - 8C Heptose - 7C |
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| LPS Assay |
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| LAL Assay Horseshoe Crab |
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| McConkey Plates |
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| Select for Enteric Bacteria due to high bile contents that bacteria need O antigen to withstand |
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| O antigen Functions |
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| 1. Resistance to Complement 2. Resistance to Bile Salts 3. Resistance to Detergents 4. Phase Variation (homopolymeric tracts on enzyme genes) 5. *We used vaccine* |
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| LPS Assembly |
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| 1. Core Sugars with nucleotides 2. Assembled of O antigen and LipidA-Core Separately - O antigen on undecarponal tail 3. Export O (Wzx/Wzy or ABC system)* 4. Expore LipidA-Core (MsbA system)* 5. Add O to LipidA-Core (WaaL system) 6. Transport to OM (Lpt System)* *ATP is the energy source |
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| K host mimicry examples |
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| K1/Niesseria - neural cell adhesion molecule K5 - heprin |
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| Functions of Capsule |
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| 1. Invade Serum (complement) 2. Host Mimicry 3. Phase Variation 4. Prevent dessication 5. Adherence 6. Motility (lube) |
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| Phase Variation of Capsule Example |
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| C. jejuni on/off or gradual population level CPS gene cluster = homopolymeric tract = slipped strand mutagenesis |
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| Glycosylation in H. pylori |
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| Flagella, OM, IM, Cytoplasmic Just O-linked |
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| Glycosylation in C. jejuni |
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| Flagella, Periplasmic O-linked and N-linked |
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| O linked glycosylation - Specificity |
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| Ser/Thr Structrual (surface) |
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| N linked glycosylation - specificity |
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| D/E - X - N - X - S/T Only last three in euks |
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| Glycosylation Sugars |
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| Simple: Heptose (e. coli) Complex: Pse, DAB (C. pylori) Polymeric: Trisaccharides (archaea) |
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| Functions of Glycosylation |
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| 1. Secretion 2. Antigenecity - immunoevasion 3. Stability, solubility, and polymerization 4. Adhesion (invasion of host tissue) |
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| Glycosylation in N. gonorrheae |
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| ptgA gene encodes a glycosyl transferase Complicated strains - polyG tract = not always expressed = migration |
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| Ogliosaccharide production |
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| 1. assembly of nuc-sugars onto undecaprenol phosphate carrier (Und-P) 2. Black transfer to periplasm 3. saccharidyl transferase attaches sugar to protein |
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| Ogliosaccharide example |
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| pgIB in c. pylori N |
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| Treatment of H. pylori |
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| Chlarithromycin, Tetracyclin, Protein Pump Inhibitor, Bismuth High doses - to reach stomach = nasty side-effects |
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| H. pylori animal models |
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| WT Mice (and adapted bug) = infection no inflammation Il-10 KO mice = inflammation but little infection |
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| H. pylori Virulence Factors (7) |
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| 1. Urease 2. Type 4 Secretion - Cog PI (cancer) *not all strains 3. VacA 4. LPS - Lipid A is poorly endotoxic 5. Lewis structures on OMP and O antigen 6. Flagella - glycosylated 7. Hcps |
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| VacA |
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| Autotransporter gene polymorphisms - paleo-microbiology and differences in virulence |
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| Hcps |
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| Heliobacter Cystine-rich Proteins - SLR motif:helix-SS-helix = protein-protein interaction - need dsbK |
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| Regulation of Cytokine Activity (5) |
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| 1. de novo 2. short mRNA halflife 3. Procytokines produced first 4. Short activation radius 5. High affinity receptors |
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| Myristiltated |
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| attaching lipids (usually N terminal) |
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| TACE |
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| TNF alpha converting factor |
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| IL-1 Receptors and Antagonists |
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| IL-RI - normal IL-RII - no signal transduction IL-Ra - antigonist |
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| IL-1 activation |
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| 1. Production of pro-ILB 2. Secondary signal (C3aR or TLR4) - efflux of ATP 3. ATP sensed by p2X7 - ion exchange 4. Caspase-1 activation |
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| Function of IL-8 |
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| 1. Bring neutrphils 2. Neutrophil adherence 3. Neutrophil granular exocytosis 4. Respiratory burst |
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| CXCR1 Structure and Function |
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| 7 TM - G coupled protein receptor IL-8 receptor |
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| CXCR1 alpha pathway |
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| PLC cuts PIP2 into IP3 and DAG IP3 - releases Ca2+ stores DAG - increases NADPH oxidase activity |
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| CXCR1 beta-gamma pathway |
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| PI3 Kinase adds p to PIP2 -> PIP3 chemotaxis, adhesion neutrophil granular exocytosis (by MAPK) |
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| PLC Effect on Phospholipids and Diacylglycerols |
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| Make Arachonic Acid 1. Make Leukotrienes - B4 - neutrophil recruitment and pro-inflammatory 2. Make Prostacyclin - vasodilation and platelet aggregation Thromboxane - platelet activation and vasoconstriction *All have G-coupled protein receptor pathways |
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| Neutrophils - Secretory Proteins |
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| CR1, CR3, FPR, CD14, CD16 (IgG) |
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| Neutrophil - Developmental stages |
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| 1. Blast cell 2. Promyelocyte 3. Myelocyte 4. PMN - wait for 5 days - blood for 10 hours (shorter if used) |
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| Attachment of Neutrophils and Vasculature in Extravasation |
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| P-selectin - PSGL ICAM - LFA1 PECAM-1 homodimers |
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| Oxygen Dependent Killing |
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| b558 Cytochrome (NADPH oxidase) => superoxide anion Superoxide dismutase => hydrogen peroxide Myeloperoxidase + Halide => HOCl |
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| Antimicrobial Serprocidins |
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| (1) Cathepsin G - gram positives - peptides are also antimicrobials - stimulates acute phase response (2) Elastase - gram negatives cuts OM proteins and secreted peptides |
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| Wegeners Granulomatosis |
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| Anti-neutrophil cytoplasmic antibodies (ANCA) loop |
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| BPI |
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| binds LPS since its positive Bacterocidal - binds LPS, disrupts membrane Immunosuppresion - mop up |
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| NET |
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| Neutrophil Extracellular Traps - DNA and granular proteins Elastase is kept active (despite being extracellular) = liver necrosis |
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| Contact Activation Pathway (coagulation) |
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| (1) Factor 12 -> Factor 11 (2) Kallikwein -> Factor 11 (3) HMW Kinninogen (4) Brandykinin |
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| MacI (Function and Inhibitor) |
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| Receptor on neutrophil activated by M protein inhibited by beta2-integrin |
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| hemmorhagic skin lesions |
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| Purpula fulminans |
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| LBP domains |
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| BPI-1: binds LPS - common amoung acute phase proteins BPI-2: transfer to Cd14 |
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| Mice for LPS Discovery |
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| C3H/HeJ |
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| TLR/IL-1 Receptor Pathway |
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| MyD88->IRAK->TRAK->TAK (1)NIK-> IKK -> NFKB (2)MIKK->JNK-> AP-1 |
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| HPA-axis |
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| Hypothalamus -> CRF Pituitary Gland -> ACTH Adrenal Cortex -> Glucocorticoid |
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| Mif |
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| Migration inhibitory factor - produced by adrenal gland |
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| Role of Protein C |
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| (1) Thrombin binds Thrombomodulin (2) Activates protein C (3) Protein C cleaves Factor 5 and 8 (4) Inhibits coagulation and starts breaking down clot |
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| APC drug |
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| Drotrecogin alfa (activated protein c) |
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| PIC |
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| Protease involed in colonization E. coli and shigella activate PMN but not migration break PSGL-1 sugar linkages kill T cells deleted from shigella - more inflammation |
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| Anti-microbial peptides |
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| alpha-defensins beta defensins hCAP18 -> IL37 All positive defensines have Cys |
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| Beta Defensins (location and organisms) |
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| hBD1 - negative (GI, reprodu, urine) hBD3 - positive (oral, skin, respir) |
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| Systems for recognizing LL-37 (3 organisms) |
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| CovS/R (Strep) ApsS/R (staph) PhoQ/P (enter) |
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| Upregulated genes in Strep after Cov system (6) |
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| 1. Hyaluronic acid capsule 2. SpyCep and PrtS - IL-8 proteases 3. Mac/IseL - IgG proteases 4. Streptokinase 5. SpeA 6. DNase |
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| Upregulated genes in Staph after Aps system (4) |
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| 1. ApsS - membrane integrety 2. VraFG - influx pump 3. dltABC - D-alanine make less negative - techonic lipids 4. mprF - Add positive Lys to phospholipids |
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| Upregulated genes in Enter bacteria after Pho system (4) |
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| PagP, PagL, LpxO, pmrAB - Lipid A modification |
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| mga |
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| Multipkle gene activator in strep emm - M protein C5a protease inhibitor of complement (sip) IgG binding protein |
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| Phage SA3 genes (5) |
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| extracellular adhesion protein SAgs CHIP Staphlyococcal inhibitor of complement Staphylokinase |
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| Scn |
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| Staphylococcal inhibitor of complement - binds C3Bb in an inactive binding state (both) |
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| CHIP |
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| Chemotaxis inhibitor protein - produced by staph - inhibits C5a and fmlp signaling by binding sulfanated Y residues on receptors |
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| SpyCep |
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| Cell enevlope protein on Strep degrades Il-8 and other CXC chemokines |
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| Pigments |
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| Staphyloxanthain Prodigiosin (serratia) |
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| Fat Transcription Factor |
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| Ppar-Gamma |
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| Antimicrobial produced by Fat Cells |
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| Cathelicidin |
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| Secreted Anti-microbial Lipids |
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| Sapienic Acid (Palmitoleic Acid) Cholesterol Esters: Linoleic Acid and Arachiclonic Acid |
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| Mass formed by TB |
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| Granuloma - caseous necrosis |
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| Drugs for TB |
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| Isoniazid, Pyrazinamide - Inhibit Fatty Acid Synthesis Rifampin - RNAP Ethambutol - Arabinogalactin synthesis |
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| TB - important cell wall components (3) |
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| 1. Mycolic Acid 2. Arabinan Layer 3.Lipoarabinomannon |
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| Mycolic Acid Structure |
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| Trehalose dimycolate |
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| TDM binding |
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| Macrophage Scavenger Protein Macrophage-Inducible C-type Lectin (MINCLE) - MAC1 expression |
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| TB dMINCLE Mice |
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| No immune cells in lung (H and E stain) |
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| PI Head Group |
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| D-myoinositol with P = 3, 4, 5 |
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| Phagocytosis |
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| Fc-IgG Fc-P PI3KI -> PI345P3 Rab5 (GTPase) -> PI3KIII PI3KIII-> PI3P EEA1 EEA1 delivers hydrolases and H+ ATPase |
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| Role of Lipoarabinomannon (LAM) |
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| MBL EEA1 |
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| PIM |
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| Precurser to LAM Promotes homotypic fusion - feeding from endosomes |
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| TB - Proteases |
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| SapM - deP PIP3 PtpA - no ATPase PtpB - Il-6, Caspase 1 |
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| TB - Esx-1 |
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| Type IV secretion EsxA (ESAT6) -> lysis, phagosome rearrangement EsxB (CFP10) -> phagosome rearrangement eDNA |
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| Listeria - entry |
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| Zipper E-Cadherin (Ca2) basolaterial face blocked by b2-integrin uses internalins |
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| Listeria - internalins (classes, structure) |
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| (1) LPXTG - InA (2) GW - InB (3) LXW Look like TLR |
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| Mouse E-Cadherin |
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| Has Glu-16 not P-16 |
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| Saprophytic |
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| Extracellular Listeria |
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| Listeria - riboswitch (name and genes -5) |
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| Ptg 1. hly - pore 2. plcA/B - break phagosome 3. mpl - help plcB 4. actA - movement 5. hpt - hexose phosphate transfer |
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| Listeria - movement |
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| ActA localizes pole 1. Actin 2. Arp2/3 3. WASP-homology domain |
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| Salmonella PI secretion type |
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| III |
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| Salmonella entry genes |
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| SipC -> actin nucleation, bundling SipA -> helps SopE/E2 -> GEF for Rac CDC42 (can recruit Arp2/3 for branches) |
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| Salmonella Il-8/inflammation factors |
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| SopE/E2 -> GEF also promotes MAPK signaling SipB -> Activates Caspase 1 SopB -> Inositol phosphatase - activates Rho and Cdc42, secretion of Cl-, disrupt tight junctions |
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| SaPI - 2: genes for microtubules |
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| SspH2, SpvB, SseI -> actin nest SifA, PipB2 -> Sif formation SseF, SseG -> promotes budding and collecting vesicles from golgi |
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| Salmonella - inhibition of death |
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| SseK glucosylatea FADD, TRADD, RIPK1 |
