Acute Inflammation: protective response

• Inflammation serves as a protective response in living, vascularized tissue, aiming to neutralize harmful agents that cause cell or tissue damage.
• Acute inflammation arises from infections, tissue necrosis, hypoxia, foreign bodies, and hypersensitivity reactions.
• Hallmarks of acute inflammation include heat (calor), pain (dolor), redness (rubor), swelling (tumor), and altered function.

Acute Inflammation Components

• Vascular changes: Smooth muscle dilation and increased permeability of endothelium.
• Cellular events: Neutrophil emigration, their metabolic activation, chemotactic migration to the injury site, and phagocytosis of microbes or damaged tissue.

Fluid Dynamics in Inflammation

• Transudate: Increased intravascular hydrostatic pressure pushes fluid through the vessel wall, resulting in extravascular fluid accumulation (tumor).
• Exudate: Increased vascular permeability causes leakage of protein-rich fluid, large molecules, and cells into surrounding tissue.

Functions of Transudates and Exudates

• Dilution of toxins from dead cells.
• Pain: Limits use and prevents additional injury.
• Transportation of blood cells and proteins (antibodies and complement) to the site.
• Transportation of toxins and waste from the site, mainly through the lymphatic system.

Mechanisms of Increased Vascular Permeability

• Endothelial cell contraction: Mediated by histamine, bradykinin, and leukotrienes; the response is rapid.
• Endothelial retraction: Leads to widened intercellular gaps in post-capillary venules.
• Direct endothelial injury: Causes immediate and sustained leakage.
• Leukocyte-mediated injury: Activated leukocytes release toxic substances that damage the endothelium.

Cellular Events Sequence

• Selectins: facilitate the early rolling phase with weak adhesion
• Integrins: provide firm adhesion and prepare cells for migration
• Adhesion molecules (ICAMs): aid leukocytes in squeezing between endothelial cells to enter tissues and regulate transendothelial migration.
• Neutrophils: accumulate early at inflammation sites and are later replaced by macrophages.
• Leukocytes: move unidirectionally toward the injury site following a chemical gradient.
• Chemical factors: Induce leukocyte activation by binding to cell surface receptors and initiating metabolic changes.
• Leukocyte phagocytosis: Engulfs cell debris, microbes, and foreign material, primarily executed by neutrophils, monocytes, and macrophages.

Microbial Killing and Degradation

• Involves reactive oxygen species produced in phagolysosomes.
• Phagocytosis: Causes a burst in O2 consumption, as NADPH oxidase converts O2 to superoxide free radical, which is then dismutated to H2O2.
• Lysosomal myeloperoxidase: Uses Cl- + H2O2 to create HOCI free radical, leading to bacterial killing via halogenation or protein/lipid peroxidation.
• Dead bacteria: Bacteria are degraded by lysosomal acid hydrolases.
• Myeloperoxidase deficiency: Individuals can still kill microbes via superoxide, hydroxyl free radical, and OONO radical.
• NADPH oxidase deficiency: Results in chronic granulomatous disease and recurrent infections.

Microbial Killing Non-Oxygen Dependent Mechanisms

• Bacterial permeability increasing protein.
• Lysozyme: degrades bacterial coat oligosaccharides.
• Arginine-rich cationic peptides: kill microbes by creating holes in membranes.
• Major basic protein produced by eosinophils: Cytotoxic to parasites.
• Leukocytes: Secrete granule components to destroy extracellular microbes.
• Leukocyte function defects: Result in increased susceptibility to infection and defective inflammation.

Chemical Mediators of Inflammation

• Vasoactive amines: Histamine (vasodilation) and serotonin (vasoconstriction during clotting).
• Arachidonic acid metabolites: Prostaglandins and leukotrienes. Lipoxins inhibit inflammation and PMN chemotaxis/adhesion to the endothelium.
• Cytokines and chemokines: TNF, IL-1, IL06
• Reactive oxygen species: Help kill ingested microorganisms.
• Nitric oxide: Causes vasodilation and inhibits platelet aggregation.
• Lysosomal constituents: Enzymes and bactericidal factors contribute to inflammation and tissue destruction during phagocytosis.
• Plasma proteases: C3a and C5a anaphylatoxins, C3B opsonin enhance phagocytosis, and C5-9 membrane attack complex
• Neuropeptides: Substance P and neurokinin A initiate inflammatory response.

Chronic Inflammation

• Characterized by prolonged duration.
• Macrophages: The predominant cell type.
• Classical macrophage activation: Induced by bacterial LPS, foreign material and interferon-y secreted by T cells which increases inflammatory response.
• Alternative macrophage activation: Induced by other cytokines like IL-4 and IL-13 (Th2 cells, mast cells, and eosinophils), involved in tissue repair.
• Chronic inflammatory cells: Include B and T lymphocytes, and CD4+ cells, including Th1, Th2, and Th17.
• Eosinophils: Found in inflammatory sites caused by parasitic infections and immune reactions mediated by IgE.
• Mast cells: Widely distributed in connective tissue, they respond to various stimuli and are important in both acute and chronic inflammation.
• Neutrophils: More prominent in acute but present in chronic inflammation.

Granulomatous Inflammation

• A form of chronic inflammation with multinucleated giant cells.
• Could be caseating or noncaseating.
• Causes: bacterial, parasitic, fungal, inorganic, metal, dust, foreign body, or unknown agents.
• Granuloma formation: It does not always eradicate the offending agent but walls it off.

Tissue Repair

• Regeneration: Replacement of cells with the same type to restore function.
• Replacement by connective tissue (scarring): Occurs when there is no regeneration or the connective tissue matrix is extensively damaged.

Labile Tissues

• Composed of continuously dividing stem cell populations, which can readily regenerate after injury if the stem cell pool remains.
• Examples: Bone marrow and most surface epithelia, such as skin, the oral cavity, the gastrointestinal tract, and the urinary tract.

Stable Tissues

• Quiescent cells in G0 phase with low-level replication can be activated to proliferate rapidly by re-entering G1.
• Aside from the liver, these tissues possess limited regenerative capacity.

Permanent Tissues

• Composed of terminally differentiated cells that do not proliferate postnatally and have left the cell cycle
• Examples: Nerve cells, skeletal muscle, and cardiac muscle with minimal or no regenerative ability, wherein repair is dominated by scarring.

Repair by Scarring

• Occurs when damage to parenchyma and connective tissue is extensive, especially in chronic inflammation, or when permanent tissues are damaged.
• Involves four steps:
• Formation of new blood vessels.
• Migration and proliferation of fibroblasts.
• Deposition of new ECM by fibroblasts.
• Maturation and organization (remodeling) of the ECM to form a scar; results in granulation tissue.
• TGF-B: Important in increasing collagen deposition in scar formation. Myofibroblasts are involved in wound contraction.
• Wound strength: Skin wound achieves about 70-80% of its original strength.
• Wound healing factors: Include nutrition, circulatory status, hormones, and local infection.

Cellular Injury

• Cellular injury is fundamental to disease pathology.
• Understanding the mechanisms of injury helps in identifying disease causes and consequences.
• Injury severity: it depends on cell type, insult type, damage degree, and whether it is reversible or irreversible

Internal Causes of Cell Injury

• Water damage: DNA hydrolysis leading to mutations.
• Oxygen damage: Free radicals cause DNA modifications, strand breaks, and oxidative stress.
• Methylation changes: Impacts gene expression and promote mutation.
• Unrepaired DNA damage: Leads to mutations, cancer, or death.

External Causes of Cell Injury

• Free radicals: Induce reactive oxygen species and cause base damages and strand breaks in DNA leading to the production of protein crosslinks, and membrane peroxidation of lipids.
• Physical agents: Trauma, radiation, extreme temperatures, electric shock.
• Chemical agents: Mercury, lead and drugs cause direct or metabolically activated injury.
• Infectious agents: Bacteria, viruses, fungi, prions.
• Autoimmune diseases: Self-attack by the immune system, it may be mediated by T or B lymphocytes.
• Gaining: Telomere shortening, DNA errors, and cumulative damage.

Carbon Tetrachloride

• Induced by barbiturates.
• N-2-acetylaminofluorene: Potent hepatocarcinogen that is first oxidized and then sulfated, leading to carcinogenesis
• Hypoxia: Reduced oxygenation

Ischemia

• Hypoxia due to reduced blood flow, commonly from blockage of a blood vessel
• It can result in myocardial infarcts and strokes.
• Reduced oxygenation with normal blood flow: Pulmonary disease, anemia, CO poisoning Factors Affecting Cellular Responses Metabolic rate, Presence of specific viral receptors, Nutritional state of host, Metabolism of an inert compound to a toxic agent, Metabolic states of host, Idiosyncratic factors Cell Injury Mechanisms
• damage to cell membranes and subcellular organelles.
• ATP depletion causes decreased phospholipid synthesis
• Degradation of membranes by Ca2+ activated phospholipase A2 and proteases
• Lipid peroxidation by free radicals
• Detachment of membranes from protease-damaged cytoskeleton
• Cell injury: Programmed suicide which is also known as Apoptosis, release of cytochrome c.
• Cell injury and necrosis: Reversible, non-lethal injury.

Cell Injury Morphology

• Reversible injury: Fat accumulation in hepatocytes and cardiac myocytes, commonly caused by hypoxia and chemical exposure.
• Intracellular accumulations: Cholesterol, lipofuscin, iron (hemosiderin, hemosiderosis, hemochromatosis).
• Bilirubin accumulation: Seen in jaundice
• Carbon deposits: Anthracosis is carbon accumulation in lung macrophages caused by coal work which causes severe lung fibrosis.
• Calcium deposits: Dystrophic calcification occurs in damaged tissues. Metastatic calcification results from high calcium levels.
• Coronary artery calcifications: Atherosclerotic plaque buildup leads to cardiovascular disease.

Cellular Adaptation

• Understanding how cells respond to injuries is crucial for understanding disease mechanisms.
• Factors influencing cellular responses include type, degree, and duration of alteration as well as affected cell type.

Types of Adaptations

• Increases: Regeneration (replacement of losses by cellular multiplication), hyperplasia (increase in cell number), and hypertrophy (increase in cell size).
• Decreases: Hypoplasia (decreased cell number), atrophy (decreased cell size), and involution (loss of cellular content, often via apoptosis).
• Changes: Modulation (phenotypic modification), metaplasia (replacement with another cell type), neoplasia (cancerous transformation) and subcellular adaptations (adaptation of intracellular organelles).

Hypertrophy

• caused by increased functional demand, endocrine stimulation, hormones, local mitogens, increased nutrition, increased blood flow, mechanical factors, pharmacologic agents, imbalance between anabolism and catabolism.
• Hyperplasia: Results from stimulation of target tissues by hormones or growth factors, puberty, menstrual cycle, and pregnancy. If prolonged, it can be a precursor for cancer.
• Grave's disease: Affects the thyroid gland, causing enlargement leading to the condition called a goiter which causes asymmetrically enlarged glands.
• Atrophy: Means decreased cell size and diminished functional capability without cell death. Can decrease the size and capacity of affected organ.
• Atrophy can be due to hunger or pressure
• Involution: Decrease in cell number. Mechanism apoptosis which results in decreased size and function of affected organ and can occur in development/involution of thymus and common with hormone withdrawal.

Metaplasia

• Involves replacement of one type of differentiated cell by another derived from the same germ layer.
• Example: Squamous metaplasia of the respiratory tract in smokers, Leading to a deficiency loss of protection conferred by mucous secretions and ciliary removal of particulate matter.
• Tissue repair from injury involves regeneration dependent on proliferative capacity, and connective tissue formation leading to scar.
• Regeneration: Driven by cytokines, growth factors, and cellular interactions with the extracellular matrix
• Cell death: Necrosis is an uncontrolled cell death with inflammation that results in cell and cellular organelle swelling and Leakage of cellular contents. Necrosis has outside factors that kills cells and is always abnormal.
• Apoptosis: Programmed cell death without inflammation involving cell shrinkage, chromatin condensation, and the formation of cytoplasmic blebs.
• Induction of apoptosis: By p53 protein and Release of cytochrome C, it involves cell breakage into small fragments while Phagocytosis occurs without inflammation.
• The cell kills itself and is sometimes normal in development.

Necroptosis

• A hybrid of necrosis and apoptosis and is relevant in neurodegeneration
• Pyroptosis: Cell death with fever-inducing inflammation
• Anoikis: Programmed cell death occurring upon cell detachment from the correct extracellular matrix, thus disrupting integrin ligation.

Types of Necrosis

• Coagulative necrosis: Typical in cell death resulting from ischemia or hypoxia.
• Liquefactive necrosis: Typical of CNS infarctions and bacterial infections.
• Caseous necrosis: Cheesy macroscopic appearance of necrotic tissues.
• Fat necrosis: Gangrene infarction of extremities.
• Necrotic changes result in protein denaturation and enzymic digestion of dead cells.
• Diseases of dysregulated apoptosis: Inhibited apoptosis is linked to cancer and autoimmune diseases, while Excessive apoptosis is seen in neurodegeneration, viral infections, and ischemic injuries.
• Pharmacological applications: Focus on apoptosis regulation in cancer therapy, which target death receptor domains and other external pathway regulators.

Bacterial Structure

• 16S rRNA phylogeny is used to classify bacteria based on evolutionary relationships.
• Dendrograms: Show relatedness among bacterial species.
• Three domains: Bacteria, archaea (found in extreme environments), and eukaryote
• Bacterial classification includes: Kingdom, phylum, class, order, family, genus, species.
• The bacterial cell wall is made up of peptidoglycan, which is made of NAG-Nam chainsProvides shape and prevents lysis.
• Crosslinking adds strength to peptidoglycan
• Gram staining: Differentiates based on cell wall structure.
• Gram-positive: Have thick peptidoglycan layer and an inner cytoplasmic membrane.
• Gram-negative: Have an outer membrane, thin peptidoglycan layer, and an inner (cytoplasmic) membrane.
• Mycoplasma lack a cell wall and stain well
• Peptidoglycan: Prevents cell lysis and confers shape and arrangement.
• Some bacteria can form stable wall defective cells.
• Teichoic acids and cell wall-anchored proteins: Sattached to the wall confer a negative charge.

Peptidoglycan Biosynthesis

• NAM is synthesized from NAG
• Pentapeptide chain attaches
• Undecaprenyl carrier transfers NAG-NAM pentapeptide subunit to the outer membrane
• Crosslinking by penicillin-binding protein
• Antibiotics targeting peptidoglycan Vancomycin binds D-Ala D-Ala of subunit and is so large it blocks insertion of subunits by penicillin-binding proteins
• B-lactams Directly bind and inhibits penicillin-binding proteins, Phosphonomycin/ Fosfomycin blocks NAM synthesis, Bacitracin blocks carrier recycling, D-cycloserine – blocks addition of D-AIA.
• Bacterial Membranes are made up of phospholipids
• Negative Structure has Inner and outer membrane and Also LPs lipopolysaccharides so it can cause septic shock.
• Porins: Can bring in endotoxins or superantigens.
• Capsules: Discrete layer associated with individual cells that protect bacteria from phagocytosis, and drying.
• Matrix – Biofilms communities Embedded in matrix, protect bacteria.
• Pilli/fimbriae: composed of protein and are used for attachment, DNA transfer, and movement Gliding and twitching.
• Flagella composed of flagellin. Powered by proton motive force and is used for attachment
• Bacteria do not have a nucleus or organelles and DNA is compacted to fit bacterial cell
• Gyrase and topoisomerase V allow for DNA replication
• Quinolones and fluroquinolones drugs target DNA gyrase.
• Bacteria have extrachromosomal plasmids. Circular similar to chromosome. Important genes in virulence and antibiotic resistance.

Bacterial Metabolism

• Bacteria live in multispecies biofilms in microbiota. Diverse metabolism of bacteria supports microbiota ecology.
• Bacteria use Embden-Meyerhof-Parnas pathway to convert glucose to pyruvate. ATPs and high energy phosphate are consumed in this process. 4 ATPs are produced and must be oxidized by reduction of pyruvate (fermentation/oxidation) or by electron transport system (respiration).
• Sugars enter glycolysis at Fructose-1,6-diphosphate which is the rate-limiting step.
• Breakdown of complex polysaccharides for metabolizable sugars: Fermentation
• Fermentation of pyruvate: Occurs when bacteria reduces pyruvate to recycle NADH+ H+.
• End products are acids (short chain fatty acids), alcohols, diols, and gases. Types of substrates used, types of endproducts and regulation of pathways vary between species SCFA specifically acetate, proportionate, and butyrate have influences on human host. metabolism of dietary sugars causes drop in PH as they are metabolized. S. mutans use numerous dietary sugars, fermenting them to produce lactic acid. They can store excess sugars as intracellular polysaccharide and metabolize them after depletion of dietary sugars. Sucrose is used to make matrix material S. Mutans fund in the dental plaque which results in lactic acid produced by fermentation lowers PH and dissolves enamel (demineralization).
• Xylitol: Can be transported into S. mutans using fructose phosphotransferase system and is toxic to S. mutans and can cause cell death, thus it can be used to reduce dental caries.
• Krebs cycle: For bacteria that respire Electron transport chain: Is for the generation of proton motive force oxidative phosphorylation. Bacteria have no orangalles so ETC is of cellular membrane single bacteria can use multiple pathways depending on environmental conditions. Requirements for growth of bacteria are energy and carbon source with Micro biota organisms that Can't synthesize particular compound required for growth are auxotrophic.

Bacterial Genetics

• Bacteria genomic flexibility through SNP or genetic content due to mobile genetic elements.
• Bacteria are Haploid and genetic mutations are random being able to be due to error-prone polymerases.
• Horizontal Gene transfer allows bacteria to acquire new traits including antibiotic resistance and virulence factors transformation is the uptake of DNA with bacteria that must be competent and DNA is incorporated via homologous recombination so it relies on RecA dependent
• Conjugation is the transfer of plasmids between bacteria via pillus being a type of F-plasmid conjugation Transduction is bacteriophages viruses that infect bacteria and transfer bacterial genes
• Transposons- DNA sequences that can move within the genome causing genetic changes and Do not require homologous recombination so does not need RecA Processes that require RecA transformation single stranded DNA Hfr conjugation plasmid Generalized transduction
• Processes that use non-homologous recombination, Specialized transduction or ICE or integrative and conjugative elements
• transformation doesn't require cell to cell transfer to add dnses to interfere Pathogenicity large genomic regions containing Virulence genes Prevent in pathogens
• CRISPR-cas system: bacterial immune system that limits the acquisition of mobile genetic elements.
• Antimicrobial therapy Microbes can be good if in right place and at right time is like normal flora serves protecting as well, assist in digestion and promotes survival of ofittest. If microbes are in the wrong place wrong amount can cause infections of diseases.
• Microbes (pathogens) are infectious agents that cause illness or disease. Include bacteria, viruses, retroviruses, fungi, parasites, protozoa, helminths. Type of microbial infections community acquired Get through everyday life Nosocomial (hospital acquired) Through catheter or disease picked up at hospital that hospitals are very selective only strongest survived. Superinfection, this is the secondary infection that come with antimicrobial therapy. Selective Antibiotics can suppress or kills infecting microbe without harming the host that is safe and drug accumulates at microbe so cells have specific action
• Types of antimicrobial therapy Prophylactic- Prevent you taking something Empiricist that isn't sure, Definitive the goal Post Lower antimicrobial around

Classification of Antibiotics

• Chemical structure
• Mechanism of action Spectrum of activity b-lactams have similar chemical structure includes penicillin S and others
• Some drugs are super selective drugs like penicillin selective drugs
• Over time microbe can develop resistance to drug and the drug can't permeate the membrane anymore
• Combination antimicrobial therapy can be added so affects are synergistic or antagonistic drugs. Can combine to add affect of antibiotics Synergistic can have great affect than you want, potentiation and antagonist

Antimicrobials 1

• Successful antimicrobial resiles on factor and pharmacetics. Minimum is concentration that kill organism, bacteria Static or Dynamic death, Bacteriastic better than the other, Empiric when you don't have time, Resistance, drug with interaction, change, less broad
• B/lacatam antibiotics- Pencicilin cephalosporin carbapendems Antimicrobial 2
• Cell wall membrane integrity such as Vancomycin Disrupts of protein that is not a ribosome, Linasomide and so bacteria is not ribosome made