Inflammation & Immune Evasion

• • The innate immune system discriminates between 'self' and 'non-self' by pattern recognition receptors (PRR), expressed by cells or can be soluble factors (i.e. complement proteins), recognising pathogen associated molecular patterns (PAMPs) that are not found in host.
• • Non-specific defense systems consists of: lysozymes in tears & other secretions, which provide chemical barrier; skin surface, which provide physical barrier; rapid pH change, as many microorganisms don't survive in low pH; flushing of urinary tract, provides excretion of organisms; normal flora, protects against infection; stomach, provides low pH (pH 2); mucus lining trachea, provides wet surface for epithelia but also protection; & cilia in nasopharynx, provides particle removal functions.
• • An example of innate immune system receptor is toll-like receptors (TLR), which is a family of PRR that is membrane bound with extracellular, transmembrane & intracellular domain. It provides immune response by: extracellular domain binding to conserved pathogen molecules (i.e. PAMP) & causes conformational change for intracellular domain; activated intracellular domain begin a signalling cascade in host cells for transcription & translation of inflammation cytokines; & these cytokines then travel to & activates innate immune cells in lymphoid tissues, to bring them back to infection site.
• • Cells and components of innate immune system responds to microbes by cells rapidly producing acute phase proteins, that are: C-reactive proteins, bind to capsules of several bacteria to aid phagocytosis & trigger complement cascade; mannose binding lectin, bind to mannose residues on pathogens to trigger complement cascade; & complement proteins (i.e. pro-enzymes), activates from binding pathogen to produce a cascade of reactions that generate effector molecules against pathogen.
• • Complement proteins are constitutively produced plasma proteins that interact with pathogens to mark them for killing.
• • The three pathways to activate complement cascade are: classical pathway, where complement proteins bind to antibodies that are already bound to antigen on microbial surface; lectin pathway, where mannose-binding lectins bind to mannose-residues on microbial surface; & alternative pathway, where C3 complement proteins undergo spontaneous hydrolysis for activation cleavage into C3a + C3b fragments, while further hydrolysis inhibits C3 activation.
• • Complement proteins protect against infection by the three pathways converging for C3 activation/cleavage into C3a (smaller fragment) & C3b (larger fragment). Active C3b is deposited onto pathogen membranes as coating, which allows complement receptors on phagocytes to recognise & bind to microbes for killing (i.e. opsonisation). C3b further activates/cleaves C5 protein, so C5b recruits membrane-attack complex (MAC) that embeds in pathogen membrane for pathogen lysis via pores. Active C3a & C5a recruit neutrophils & monocytes, from blood, to induce inflammation at tissue's infection site.
• • The origin of cells in the innate immune system is from cells derived from pluripotent stem cells found in the bone marrow, with myeloid & lymphoid lineages.
• • The innate immune system cells are: macrophages, presents antigens, initiates phagocytosis & activates bactericidal mechanisms; neutrophils, initiates phagocytosis & bactericidal mechanisms; eosinophils, kills antibody-coated parasites; basophils, promotes allergic responses & augments anti-parasitic immunity; dendritic cells, presents antigens & uptakes antigens in peripheral sites; mast cells, releases granules containing histamine & active agents; & natural killer cells, releases cytotoxic molecules for killing after recognising infected cells.
• • Cells of the immune system communicate by producing cytokines & chemokines, which are considered messengers of the immune system. This is because cytokines are proteins secreted by cells that interact with & affect the behaviour of neighbouring cells with appropriate receptors. While chemokines are secreted cytokines that attract cells to infection site through inducing cell migrations.
• • Some different names for cytokines are: interleukins (IL-); interferons (IFN-); colony-stimulating factors (CSF's); & tumour necrosis factors (TNF's).
  • Some different names for chemokine receptors are: CCR, CXCR.
• • Neutrophil recruitment from blood to tissues occur by macrophage PRR recognising PAMP's & secreting cytokines (chemokines) to signal bone marrows to release more neutrophil in the blood. Macrophage released IL-8 get taken up & presented on endothelial cell surfaces for recognition/binding to chemokine CXCL8 receptor on neutrophils. Loosened neutrophils then stop rolling in bloodstream & bind tighter to endothelial surface via interactions with other integrins & selectins. It can then exit bloodstream through diapedesis into tissue space with high concentrations of cytokines being produced.
• • The different types of phagocytes are: polymorphonuclear neutrophils, which are numerous, short-lived cells found in circulation; & mononuclear phagocytes (with monocyte precursor), which are long-lived cells found in circulation & tissues.
• • The collective functions of phagocytes is to act as first line of defense against infections in blood & tissue by entering an infected site from circulation. This is done by phagocytes producing immunomodulatory substances (e.g. cytokines, chemokines) to initiate & regulate immune response. As well as it binding, engulfing & killing a wide variety of microbial agents.
• • The stages of phagocytosis occur by phagocytes binding to opsonised microbe, which are coated in complement protein (e.g. C3b) and/or antibody, via its receptors recognising the coatings & increasing its binding affinity to pathogen accordingly. This allows phagocyte pseudopods to form & take up the microbe, forming a phagosome. Lysosome is then recruited to/fuses with phagosome to form phagolysosome, containing enzymes/killing mechanisms that damage, digest & release degraded microbial products.
• • The phagocyte killing mechanisms involve: enzymes, such as lysozyme & acid hydrolases; acidification, such as low pH 3.5 - 4 which are unfavourable for many microbes; antimicrobial peptides, such as defensins & cationic proteins; competitors, such as lactoferrin; & toxic nitrogen and/or oxygen intermediates, such as nitric oxide & hydrogen peroxide obtained when lysosome is recruited.
• • Infectious agents are microbials that are within the range between electron microscopes & light microscopes. The types of infectious agents involve: prions, smallest 10nm infectious protein with no nucleic acid; virus, 20 - 80 nm & has protein coat, nucleic acid & sometimes lipid envelope; bacteria, 0.2 - 30 micrometre prokaryotic cells; fungi, 1 - 15 micrometre eukaryotic cells, yeast (single cell) or mould; & parasites, can be eukaryotic or protozoa (i.e. single celled, 2 - 30 micrometres) & metazoa (i.e. tissue differentiation, 3 mm - 5 m).
• • The global impact of infectious disease on human health is that infectious diseases are: becoming increasingly antibacterial resistant & harder to treat, which can result in death; old infectious disease coming back; contributing to other secondary diseases (i.e. heart diseases, peptic ulcers & cancer); evolving faster than humans, allowing new diseases (e.g. zoonotic diseases from zoonotic pathogens) to constantly emerge; & being caused by opportunistic pathogens, which are bodily bacteria that end up in wrong place (e.g. blood) in body.
• • Infectious agents are constantly evolving, through new variants emerging, to evade/escape the effects of antimicrobial drugs.
• • The drivers of new disease emergence include: increasing population densities; prevalent antibiotic usage; & changing agricultural practices. As these force microbes to undergo evolution for survival.
• • Infection control measures are ways to control & treat infectious diseases. These can occur by: improving housing, sanitation & education (on infection topics); surveillance, to monitor patterns & emergence of disease; drug therapy, involving antibiotics, anti-viral drugs & anti-parasitic drugs; & initiating vaccines.
• • Drug therapy of infectious control measures can fail because pathogens can develop resistance & some drugs have limited range & efficacy. Vaccines can fail because they have limited range & can be expensive to develop. The impact of these failures are that infectious diseases are becoming harder to prevent, which result in human death.
• • Strategies that are essential for disease prevention occur by gaining a better understanding of host-pathogen relationship. As this helps the development of: new, effective antimicrobials & vaccines; treatments for other diseases induced by infection; & blockade interactions between host cell & pathogen.
• • Common approaches to classify bacteria are based on: genetic composition, such as bacterial nucleoid, plasmids; physical properties, such as shape & specialised features visualised through staining; metabolic properties, such as bacteria's relationship with oxygen & biochemical activity; & pathogenicity, such as its surface antigens, susceptibility to be killed by specific viruses & capacity to cause disease.
• • Spores are essential features & physical properties of bacteria, as it is a specialised structure of a few bacterial genera. It is a dormant & non-replicative organism state that increases survival, because it is resistant to heat, desiccation, UV & chemicals.
• • Capsules are essential features & physical properties of bacteria, as it is a polysaccharide-based material (i.e. glycocalyx) that extends from cell surface, to: facilitate adherence to host cells; facilitate surface to create disease; protect against phagocytosis & immune system; & protect against dehydration for survival.
• • Flagella are essential features & physical properties of bacteria as they are thin, long, hollow & helical filaments that enable locomotion & bacterial motility. This occurs by: its basal body, locking flagella into membrane (i.e. between outer & inner membrane); its hook, forming a sharp bent with ring protein shaft which connects to basal body for motility (i.e. rotation, spinning); & its filament, forming a long extension from organism.
• • The composition of bacterial peptidoglycan involves two sugar derivatives (i.e. N-acetylglucosamine & N-acetylmuramic acid) that are alternatively linked in chains to form a lattice. Derivatives are also surrounded by small groups of amino acids, such as L-Ala, D-Ala, D-Glu & lysine/diaminopimelic acid.
  • This contributes to diversity of bacteria by linkage between sugar derivatives being different between Gram-positive & Gram-negative bacteria.
• • Genetic composition can be used to classify bacteria by surveillance of mutations & horizontal gene transfer (HGT) to help indicate bacterial type. Since bacterial genetic material can be contained in bacterial nucleoid (i.e. closed-circle, single chromosome that's looped & supercoiled) or independently-replicated plasmids (i.e. small, circular double-stranded, supercoiled DNA), that allows HGT through mechanisms of: plasmids, transposons, bacteriophages, pathogenicity islands & integrons. This gives 'beneficial' DNA insertions & integrations into genome for characterising bacterial types.
• • Bacterial physical characteristics allow for staining techniques by stains providing visualisation of bacterial cell shapes which are fixed due to cell wall & peptidoglycan. As bacteria cells can exist as single cells, pairs or clusters, with five basic shapes of cocci (i.e. spherical), bacilli (i.e. rod), spirilla (i.e. spiral), vibrios (i.e. comma) & spirochaetes (i.e. corkscrew).
• • The common staining techniques used to distinguish bacteria are: Gram-staining, which distinguishes cells by cell wall types/peptidoglycan; acid-fast staining, which distinguishes between acid-fast bacteria & non-acid-fast bacteria; endospore staining, distinguishes organism with endospore from those without; capsule (negative) staining, reveals bacterial capsule, if any; & flagella staining, reveals flagella, if any.
• • Gram staining occurs by exploiting the differences in fixed cell wall composition between bacteria, where: crystal violet is applied to heat-fixed bacteria sample; sample is treated with iodine to fix purple stain; sample is decolourised (via acetone); & sample is counter-stained with Safranin (i.e. pink).
  • This allows identification between Gram-positive bacteria, which have thick peptidoglycan cell wall & retain/appear purple even after decolourisation, & Gram-negative bacteria, which have thinner peptidoglycan cell wall & not retain purple/appear pink (from Safranin) after decolourisation.
• • Acid-fast staining occurs by exploiting the abundance of mycolic acid in cell walls (i.e. peptidoglycan) of certain bacteria, which may resist other staining methods. This allows acid-fast bacteria to be stained bright red & non-acid-fast bacteria to be counterstained blue, enabling primary application for identifying mycobacteria.
• • Endospore staining occurs by staining spores, formed when growth ceases due to lack of nutrients &/or moisture, for visual comparison. This allows the presence of spores to help bacteria classification, since sporulation & gemination (spores back to bacteria) are complex processes.
• • Capsule staining occurs by staining all areas/'background' around the capsule (i.e. negative staining), to highlight the presence of capsule as a 'halo' around the organism, since capsules cannot be stained. This allows subtyping of bacteria based on capsule antigen, since capsules contribute to virulence, so different serotypes within bacteria can be identified.
• • Flagella staining occurs by staining the flagella with special stain for visual comparison under light microscope. This allows the bacterial antigen on the surface of flagella to be used for serotyping bacteria/pathogen.
• • The different key physical characteristics between bacterial infectious agents, based on Gram-positive & negative, are that: Gram-negative has an outer membrane stablised by lipopolysaccharide (LPS) for more complex cell wall, while Gram-positive has only one membrane that functions similarly to Gram-negative inner membrane; & Gram-positive has large component of peptidoglycan in cell wall, along with teichoic acid & lipoteichoic acid, while Gram-negative's LPS can act as endotoxin, that is a type of PAMP.
• • Bacterial growth is the exponential growth of bacterial daughter cells, which are genetically identical to the original cell, if there are no mutations. It occurs by binary fission where constant growth remodels metabolism & gene expression, because: in lag phase, there is no division; in exponential (growth) phase, binary fission occurs; in stationary phase, growth is slowed down due to exhausted nutrients; & in death phase, cells face exhaustion & may no longer grow in medium.
• • Bacterial metabolism is the process of nutrient acquisition for growth. This occurs by: passive diffusion, for small, uncharged molecules (i.e. water); facilitated diffusion, using membrane proteins to provide pathways for essential nutrient & ions translocation, with permeation dependent on concentration gradient; & active transport, using cellular-energy requiring transporter to acquire molecules against concentration gradient.
• • Metabolism can be used for bacterial classification, because the energy generation from metabolic transports, for acquiring nutrients, & the enzymes used, can be used for classification based on the interaction of these with oxygen.