

## Prokaryotes
<ul>
  <li>No membrane-bound nucleus or organelles</li>
  <li>Bacteria</li>
  <li>Rickettsia</li>
  <li>Chlamydia</li>
</ul>

## Eukaryotes
<ul>
  <li>Nucleus enclosed in membranes (eg. plants)</li>
  <li>Fungi</li>
  <li>Animal cells</li>
</ul>

## Bacterial structure
<ul>
  <li>Prokaryotic cells</li>
  <li>Most have cell walls which are inert</li>
  <li>The cell membrane however is an osmotic barrier</li>
  <li>Contain DNA and RNA</li>
  <li>Nuclear DNA lies free in the cytoplasm</li>
  <li>Plasmids contain DNA fragments</li>
  <li>No other organelles as such</li>
  <li>Mesosomes are sacs containing enzymes</li>
  <li>Flagella for motility</li>
  <li>Reproduction by binary fission</li>
</ul>

## Bacterial metabolism
<ul>
  <li>Bacteria need CO2 to grow</li>
  <li>Energy comes from</li>
  <ul>
    <li>Respiration (primarily used by aerobes): producing CO2 and H2O</li>
    <li>Fermentation (primarily used by anaerobes): producing lactic or pyruvic acid</li>
    <li>
      Note: aerobes and anaerobes MAY use the other method too (eg. aerobes that also use
      fermentation are termed facultative anaerobes. Strict anaerobes rely only on fermentation)
    </li>
  </ul>
</ul>
<HotTopic>
  <>
    <p>Culture mediums</p>
    <div>
      <table>
        <tbody>
          <tr>
            <td>
              <strong>Culture mediums</strong>
            </td>
          </tr>
          <tr>
            <td>Nutrient broth</td>
            <td>pH of 7.3</td>
            <td>Watery extract of meat sterilised by heat</td>
          </tr>
          <tr>
            <td>Blood agar</td>
            <td>Most common bacteria and fungi except haemophilus, neisseria and moraxella</td>
            <td>Horse or sheep blood added to nutrient broth</td>
          </tr>
          <tr>
            <td>Chocolate agar</td>
            <td>Fastidious bacteria, namely Haemophilus influenzae, Neisseria and Moraxella</td>
            <td>Same as blood agar but cells have been lysed through heating</td>
          </tr>
          <tr>
            <td>Sabouraud dextrose agar</td>
            <td>Fungi</td>
            <td>Low pH with chloramphenicol to prevent bacterial growth</td>
          </tr>
          <tr>
            <td>Non-nutrient agar with E.coli</td>
            <td>Acanthomoeba</td>
            <td>E.coli is a food source for acanthomoeba</td>
          </tr>
          <tr>
            <td>Desoxycholate citrate agar</td>
            <td>Salmonella</td>
            <td>&nbsp;</td>
          </tr>
          <tr>
            <td>MacConkey agar</td>
            <td>
              Distinguishes lactose from non-lactose fermenting organismsPrevents Gram positive
              growth and identifies Gram negatives
            </td>
            <td>&nbsp;</td>
          </tr>
          <tr>
            <td>Lowenstein-Jensen</td>
            <td>Isolated mycobacteria</td>
            <td>&nbsp;</td>
          </tr>
          <tr>
            <td>Thayer-Martin&rsquo;s media</td>
            <td>Gonococcus&nbsp;</td>
            <td>Contains vancomycin, colistin, nystatin</td>
          </tr>
          <tr>
            <td>Thioglycolate broth</td>
            <td>Aerobes grow on the surface, anaerobes beneath the surface</td>
            <td>&nbsp;</td>
          </tr>
          <tr>
            <td>McCoy media</td>
            <td>Chlamydia</td>
            <td>&nbsp;</td>
          </tr>
        </tbody>
      </table>
    </div>
  </>
</HotTopic>

## Gram staining
<ul>
  <li>Gentian/crystal violet stains the peptidoglycans in Gram positive cells walls</li>
  <li>Lugol&rsquo;s iodine is applied which fixes the crystal violet to the cells</li>
  <li>A black-purple complex is seen</li>
  <li>Treated with acetone or alcohol</li>
  <li>Some bacteria retain the complex: Gram positive</li>
  <li>Others lose it and become colourless: Gram negative</li>
  <ul>
    <li>These are stained pink with safranin for contrast (counterstain)</li>
  </ul>
</ul>
<p>
  <strong>Note</strong>: methylene blue is used as a counterstain when producing a Ziehl-Neelsen
  stain for acid-fast bacilli
</p>

## Fungal stains
<ul>
  <li>Haematoxylin and eosin (pink)</li>
  <li>Gomori methanamine/Grocott hexamine silver (black)</li>
  <li>Periodic acid-Schiff (purple)</li>
</ul>

## Antibody detection
<ul>
  <li>Complement fixation</li>
  <li>Haemagglutination inhibition</li>
  <li>Indirect immunofluorescence</li>
</ul>

## Bacterial virulence
<ul>
  <li>Invasiveness</li>
  <ul>
    <li>Adherence to target cells</li>
    <li>Local tissue damage</li>
    <li>
      Hyaluronidase (dissolves collagen), streptokinase and collagenase promote bacterial spread
    </li>
    <li>Haemolysins: kill host phagocytes</li>
    <li>Coagulases precipitate fibrin clots to wall the bacteria off from defences</li>
  </ul>
  <li>Toxigenicity&nbsp;</li>
  <li>Defence strategies</li>
  <ul>
    <li>Interference with complement activation</li>
    <ul>
      <li>
        Eg. Streptococci possess a surface M-factor which facilitates C3b breakdown and binds
        fibrinogen
      </li>
      <li>E. coli (and other Gram negatives) can divert complement activation</li>
      <li>Pseudomonas releases elastase which inactivates C3a and C5a</li>
      <li>Neisseria gonorrhoeae binds complement</li>
    </ul>
    <li>Some bacterial capsules are antiphagocytic</li>
    <li>Intracellular bacteria evade the immune system by living within macrophages</li>
    <ul>
      <li>Eg. mycobacterium tuberculosis</li>
      <li>Listeria monocytogenes</li>
    </ul>
  </ul>
</ul>
<HotTopic>
  <>
    <p>Exotoxins vs endotoxins</p>
    <ul>
      <li>Exotoxins: proteins</li>
      <ul>
        <li>Heat labile</li>
        <li>Antigenic</li>
        <li>More potent</li>
        <li>
          Predominantly produced by Gram positives but can be made by Gram negatives such as E. coli
          and Shigella
        </li>
        <li>
          Superantigens (eg. produced by staph aureus) activate large numbers of T cells leading to
          massive cytokine release and life-threatening immune reactions
        </li>
      </ul>
      <li>Endotoxins: made from lipopolysaccharide of the cell wall</li>
      <ul>
        <li>All Gram negative bacteria contain similar endotoxins</li>
        <li>Produce a non-specific acute inflammatory response (ie. non-antigenic)</li>
        <ul>
          <li>Release of IL-1</li>
          <li>Initial leucopenia</li>
          <li>Alternative complement pathway activation</li>
        </ul>
        <li>Detected by the Limulus test</li>
        <li>Heat stable</li>
        <li>Non-antigenic&nbsp;&nbsp;</li>
      </ul>
    </ul>
  </>
</HotTopic>

## Staphylococcus aureus
<ul>
  <li>Flora of many normal people therefore infection often endogenous</li>
  <li>Transmission: air, direct, indirect</li>
  <li>Virulence factors:</li>
  <ul>
    <li>Lysozymes</li>
    <li>Coagulase</li>
    <li>Hyaluronidase</li>
    <li>Adherence to cell surfaces</li>
    <li>Capsule resistant to opsonisation</li>
    <li>Protein A: decreases phagocytosis and inhibits complement</li>
    <li>Epidermolytic toxin (&ldquo;scalded skin&rdquo;)</li>
    <li>Enterotoxin (food poisoning)</li>
  </ul>
  <li>Produces coagulase (which staphylococcus epidermidis does not)</li>
  <li>MRSA:&nbsp;</li>
  <ul>
    <li>Coagulase positive</li>
    <li>May also be a normal commensal</li>
    <li>Actually NOT more virulent or resistant to sterilisation than normal staph aureus</li>
    <li>Resistant to conventional antimicrobials</li>
    <li>Found in the anterior nares</li>
  </ul>
</ul>

## Disinfection vs sterilisation
<ul>
  <li>Disinfectants (removal of most microorganisms)</li>
  <ul>
    <li>UV radiation</li>
    <li>
      Pasteurisation: steam generated at 80 degrees at half an atmosphere of pressure kills
      vegetative organisms but not spores
    </li>
    <li>Examples</li>
    <ul>
      <li>Chlorhexidine</li>
      <li>Ethyl alcohol with povidone-iodine</li>
    </ul>
  </ul>
  <li>Sterilisation (removal of all microorganisms)</li>
  <ul>
    <li>Gamma radiation</li>
    <li>Dry heat: requires temperatures of 160 degrees for several hours</li>
    <li>
      Moist heat: requires temperatures of 134 degrees for 3 minutes, or 121 degrees for 120 minutes
    </li>
    <li>Ethylene oxide</li>
  </ul>
</ul>

## Normal ocular flora
<ul>
  <li>No viruses exist as normal flora in the eye</li>
  <li>
    Staphylococcus epidermidis (40-45%) is the most common (coagulase negative, catalase positive)
  </li>
  <li>Staphylococcus aureus (25%), coagulase positive</li>
  <li>Diphtheroids (25-40%)</li>
  <li>Streptococcus viridans (2-3%)</li>
  <li>Propionibacterium acne (most common anaerobe)</li>
  <li>Demodex folliculorum (protozoa)</li>
  <li>Corynebacteria</li>
  <li>Micrococcus&nbsp;</li>
  <li>Up to 100 fungi/yeasts live on the lashes and lids</li>
</ul>

## Toll-like receptors
<ul>
  <li>Single transmembrane receptors</li>
  <li>Recognise intact microbial products</li>
  <li>
    Activation of TLRs results in proinflammatory and chemotactic cytokine release (recruiting
    neutrophils, macrophages and lymphocytes)
  </li>
  <li>TLR4/MD-2 recognises the lipid A moiety of lipopolysaccharide (LPS)</li>
</ul>

## NOD-like receptors
<ul>
  <li>Intracellular family of PRRs (pattern recognition receptors)</li>
  <li>
    Recognise components of degraded bacterial cell wall peptidoglycan therefore respond to invading
    Gram-negative and Gram-positive bacteria
  </li>
  <li>NLRC4 recognises the flagellin of Gram-negative bacteria including Pseudomonas</li>
  <li>
    Activated NLRs form a large multi-protein complex called an inflammasome which activates
    caspase-1 and cleaves multiple interleukins to their active forms with proinflammatory and
    chemotactic effects
  </li>
  <li>Prolonged inflammasome activation can lead to caspase-1 mediated cell death (pyroptosis)</li>
</ul>

## C-type lectins
<ul>
  <li>
    Fungal cell wall components are recognised via activation of C-type lectins on cell surfaces
  </li>
</ul>

## Neutrophils
<ul>
  <li>Most common leucocytes in blood (25% of total WBCs)</li>
  <li>Recruited from capillaries to infected tissues</li>
  <ul>
    <li>
      Pro-inflammatory cytokines at site of infection induce expression of adhesion molecules on
      vascular endothelium (selectins) which bind to integrins on neutrophils
    </li>
    <li>They then transmigrate across endothelium (mediated by chemokines)</li>
    <li>Chemokine (eg IL-8) gradient then dictates their migration to site of infection</li>
  </ul>
</ul>

## Contact lenses
<ul>
  <li>Most common risk factor for corneal infections</li>
  <li>
    Long-term wear inhibits epithelial proliferation, migration and suppresses limbal stem cell
    production of basal epithelial cells
  </li>
  <li>Reduce flow and effectiveness of tears: trap microbes on cell surfaces</li>
</ul>

## Prions
<ul>
  <li>Small proteinaceous infective elements</li>
  <li>No genome</li>
  <li>Not antigenic: do not produce an immune response</li>
  <li>Highly resistant: to formaldehyde, ionizing radiation and other methods</li>
  <ul>
    <li>Autoclaving at 15 psi for 1 hour destroys them</li>
  </ul>
</ul>
<p>
  Prion protein may be detected in a biopsy sample using <strong>Western blot</strong>
</p>


Microbiology

Intro

FRCOphth Part 1 Study Notes

Orbit and ocular adnexae

Orbit

Extraocular Muscles

Orbital Blood Vessels

Paranasal Sinuses

Lacrimal Glands

Tear Film

Eyelids

Blinking

Anterior segment - ocular surface

Conjunctiva

Conjunctivitis

Sclera

Cornea

Corneal Structure And Development

Corneal Physiology

AC to Lens

Angle

Ciliary Body

Aqueous Humour Dynamics

Iris

Pupil

Lens

Posterior segment

Choroid

Vitreous

Retinal Macrostructure

Neurosensory Retina

Retinal Pigment Epithelium

Neuroanatomy

Venous Sinuses

Cerebral Ventricles

Cerebral Blood Supply

Supranuclear Gaze Pathways

Head And Neck Autonomic Nervous Supply

Head And Neck Glands

Osteology

Nerves

Muscles And Pharyngeal Arches

Extraocular Nerves

Sensory Nerves

Physiology

Physics Of Blood Flow

Neuronal Control Of Blood Vessels

Oxygen-Haemoglobin Dissociation Curve

Cytochrome p450

Pituitary Gland

Thyroid Hormone Production

Insulin

Glucagon

Parathyroid Hormone

Corticosteroids

Catecholamines

Cardiac Cycle

Renal Physiology

Fluid Balance

Acid-Base Balance

Muscle Physiology

Sensory Fibres

Cutaneous Receptors

Endocytosis

Glycosaminoglycans

Condensed Ocular Biochemistry

Eye Movements

Accomodation

Vision

Visual Cycle And Phototransuction

Visual Pathway

Visual Acuity

Colour Vision

Binocular Vision

Pathology

Collagen

Tissue Damage

Inflammation

Disease Entities

Wound Healing

Thrombosis / Atherosclerosis

Cell Growth

Neoplasia

Histopathology

Nystagmus

Free Radicals And Antioxidants

Immunology

Ocular Immunology

Viral Infections

Bacterial Infections

Fungal Infections

Protozoa

Nematodes

Antimicrobials

Genetics

Chromosomes

Mitosis

Meiosis

Genes

Polypeptide Synthesis

Histones

MicroRNA

Hardy-Weinberg Equilibrium

Mutations

Chromosome Defects

Autosomal Inheritance

X-Linked Inheritance

Mitochondrial Inheritance

Multifactorial Inheritance