Comprehensive Study Notes: HSC Biology Module 7 – Infectious Disease

Module 7: Infectious Disease — Syllabus Outcomes and Overview

• BIO11/12-1: Develops and evaluates questions and hypotheses for scientific investigation.

• BIO11/12-2: Designs and evaluates investigations in order to obtain primary and secondary data and information.

• BIO11/12-3: Conducts investigations to collect valid and reliable primary and secondary data and information.

• BIO11/12-4: Selects and processes appropriate qualitative and quantitative data and information using a range of appropriate media.

• BIO12-14: Analyses infectious disease in terms of cause, transmission, management, and the organism’s response, including the human immune system.

Understanding Disease

• Definition: Diseases are defined as any process or conditions that disrupt the regular functioning of the organism, including both animals and plants.

• Example — Influenza: Causes the body to become weak, creates difficulty breathing, and can ultimately lead to death.

• Indications of Disease: Diseases are usually identified through symptoms, which are indications of a possible disease within the organism. Examples include fever, spots, and swelling.

• Disease Range: Disease severity ranges significantly:     * Deadly: Examples include major pathogens that cause high mortality.     * Hindrance: Examples include Athlete's Foot (Tinea).

• Infectious vs. Communicable: This module focuses exclusively on infectious diseases — those caused by a pathogen or spread by another person or vector (also known as communicable diseases).

• Common Infectious Diseases:     * Influenza: Known as the flu.     * Chlamydia: A common sexually transmitted infection (STI).     * Hepatitis: Often vaccine-preventable.

Cause: Pathogens

• Pathogens: These are agents of any kind that cause disease. They are categorized based on whether they are living or non-living.

• Living Categories:     * Bacteria: Single-celled prokaryotic organisms.     * Fungi: Eukaryotic organisms.     * Protozoa: Single-celled animal-like eukaryotes.     * Parasites: Multicellular organisms.

• Non-Living Categories:     * Viruses: Non-cellular genetic material in a protein coat.     * Prions: Abnormal proteins.

• Infection: Occurs when a microorganism enters another organism and causes harm.

• Pathogenicity: Refers to the ability of a pathogen to cause disease. This is affected by the host organism's defense system.

• Visibility: While some pathogens like ticks and mosquitoes are visible to the naked eye, the majority are microscopic.

Detailed Classification of Pathogens

Bacteria (Bacterium)

• Structure: Single-celled prokaryotic organisms (living). They possess a cell wall but lack a nucleus and most other organelles.

• Reproduction: They use binary fission (dividing into two). They can regenerate in as little as $10\,\text{min}$ to $24\,\text{hrs}$.

• Growth: Exhibit exponential growth, forming enormous groups quickly.

• Metabolism: Includes both anaerobic (no oxygen) and aerobic (oxygen needed) examples.

• Beneficial Uses: Used in vaccines, antibiotics, and digestion.

• Diseases: Whooping cough (pertussis), salmonellosis (food poisoning), tuberculosis, tetanus, and chlamydia.

• Treatment: Most are treated with antibiotics.

Fungi

• Structure: Eukaryotic, plant-based cells that are heterotrophic (do not generate their own food due to a lack of chlorophyll).

• Composition: Can be uni- or multi-cellular; microscopic or macroscopic.

• Habitat: Commonly live on dead plant and animal matter; act as decomposers.

• Infection Sites: Internal wounds, surface of skin, hair, or nails. Often target weakened immune systems.

• Diseases: Tinea (athlete's foot), ringworm, and yeast infections.

Parasites

• Description: Multicellular organisms that vary greatly in size. They can be macro (visible) or micro (microscopic).

• Endoparasites: Live within the organism. Examples include flat and round worms.     * Diseases: Taeniasis (tapeworm disease), hydatidosis (hydatid disease), and liver fluke disease.

• Ectoparasites: Live on the outside of the organism. Examples: mosquitoes, fleas, ticks, leeches, and lice.     * Actions: Inject toxins, suck blood, cause allergic reactions, or use the host for laying eggs.

Viruses

• Nature: Non-cellular; possess both living and non-living characteristics. They are not "free-living" like bacteria.

• Structure: Contain genetic material (DNA or RNA) within a protective protein coat called a capsid.

• Replication: Require a host cell to survive. They attach and inject DNA into host cells, hijacking internal organelles to create copies. The cell eventually bursts, which kills the cell.

• Diseases: Influenza, measles, HIV, herpes, glandular fever, and SARS.

• Treatment: Cannot be treated with antibiotics because they lack a cell wall.

Protozoa

• Structure: Unicellular eukaryotes that behave similarly to animals. They lack a cell wall.

• Behavior: Can move independently and obtain their own food.

• Diseases: Malaria, caused by the protozoan Plasmodium. This pathogen infects red blood cells and is carried by mosquitoes.

Prions

• Definition: Abnormal proteins that influence healthy proteins to misfold and spread.

• Effect: Incredibly simple but cause devastating diseases in the nervous system.

• Transmission: Usually via ingestion of infected tissue.

• Example: Creutz-Jakob disease ("Mad Cow" disease), originating from cows consuming infected tissue.

Relative Sizes of Microorganisms

On a logarithmic scale:

• $0.1\,\text{nm}$: Atom.

• $1\,\text{nm}$: $C_{60}$ (fullerene molecule).

• $10\,\text{nm}$: Lipids, protein.

• $100\,\text{nm}$: Polio virus, flu virus, smallpox virus.

• $1\,\mu\text{m}$: Mitochondria, bacteria.

• $10\,\mu\text{m}$: Animal cell, plant cell, red blood cell.

• $100\,\mu\text{m}$: Pollen, human egg.

• $1\,\text{mm}$: Frog egg.

Transmission of Disease

• Definition: The transfer of pathogens between organisms.

• Carriers:     * Passive Carriers: Carry the pathogen (on or within them) but are not infected (e.g., a hospital worker with staph on unwashed hands).     * Active Carriers: Are infected by the disease. They may be asymptomatic (e.g., HIV or SARS-CoV-2 carriers).

• Hosts: Can be affected or unaffected.

Case Study: Typhoid Mary (Mary Mallon)

• Role: A cook in New York City in the early $20$th century.

• Status: An asymptomatic carrier of Salmonella typhi (typhoid).

• Impact: Spread the disease to hundreds of people due to poor hygiene; $53$ individuals contracted the disease, and $5$ died.

Modes of Transmission

1. Direct Contact

• Definition: Physical contact between two organisms, usually involving the exchange of bodily fluids.

• Examples: Touching, sexual contact, kissing, biting (rabies), contact with nasal/oral secretions, and mother-to-offspring (pre- and post-natal).

• Specific Examples:     * HIV/AIDS via sexual contact or sharing needles.     * Herpes (cold sores) through physical contact.     * Rubella or HIV transmitted via pregnancy or breastfeeding.

2. Indirect Contact

• Definition: No physical contact between two organisms; infection occurs via a reservoir (where a pathogen exists away from a host).

• Fomite: Any object or substance that carries infection (e.g., surgical equipment, contaminated cutting boards).

• Examples:     * Airborne Transmission: Coughing or sneezing (e.g., measles, SARS).     * Vehicle-borne: Contaminated food, water, or equipment (e.g., gastroenteritis, E. coli).

3. Vectors

• Definition: A third-party organism is involved in the transfer.

• Biological Vector: The vector carries the pathogen while being infected.

• Mechanical Vector: The vector carries the pathogen without being infected.

• Examples: Mosquitoes (Malaria, Dengue), ticks (Lyme disease), fleas (Bubonic plague).

• Global Impact: Vectors account for approximately $17\%$ of infectious diseases.

4. Zoonotic Diseases

• Definition: Diseases transmitted from animals to humans.

• Factors: Mutations allow the disease to evolve and jump species, especially in close contact.

• Examples: Rabies, West Nile virus, Anthrax, bird flu (avian influenza).

Historical Foundations of Germ Theory

Spontaneous Generation and Miasma

• Spontaneous Generation: The old belief that life emerged spontaneously from non-living material.

• Miasma Theory: The belief that "bad air" caused disease.

Francesco Redi ($1668$)

• Experiment: Used sealed vs. unsealed flasks to demonstrate that maggots came from flies, not from rotting meat.

• Finding: Maggots only appeared on surfaces flies could access.

Louis Pasteur

• Discoveries: Found that beet juice fermented due to yeast. Realized wine and beer went sour due to microbes.

• Pasteurisation: A process of heating products to kill microbes.

• Swan Neck Flask Experiment:     * S-shaped Flask: Prevented microbes from reaching the broth while allowing air in.     * Results: The broth in the swan-neck flask remained clear; the broth in the open-neck flask became cloudy (bacterial growth).     * Independent Variable: Exposure or non-exposure of the broth to open air.     * Dependent Variable: Amount of growth/cloudiness of the broth.     * Controls: Heating of flasks, same broth, same flask shape, same exposure time, same location.

• Germ Theory of Disease: Stipulates that disease is caused by pathogens that come only from other microorganisms.

Robert Koch ($1843$ – $1910$)

• Contributions: Created agar plates; identified bacteria for anthrax, cholera, and tuberculosis.

• Koch’s Postulates (4 Criteria):     1. The microorganism must be found in all organisms suffering from the disease but not in healthy ones.     2. The pathogen must be isolated from the diseased host and grown in pure culture.     3. The cultured pathogen should cause the same disease when introduced into a healthy organism.     4. The pathogen must be re-isolated from the newly infected host.

• Limitations:     * Not all pathogens (like viruses) can be cultured on agar plates.     * Healthy organisms may be immune.     * Presence of pathogens does not always result in symptoms (asymptomatic carriers).

Plant Disease and Agriculture

• Pathogens: Fungi, bacteria, nematodes, viruses, and phytoplasmas.     * Fungi: Enter via stomata; cause black spot, mildew, and wilt.     * Insects/Mites: Act as vectors or cause direct damage by eating/laying eggs.     * Bacteria: Cause rot in bad conditions.     * Nematodes (Roundworms): Attack plants and lay eggs on roots; cause long-term crop damage.     * Phytoplasmas: Spread by insects to the phloem; destroy tomatoes and pumpkins.

• Agricultural Impact: Reduced yields, loss of trade opportunities, economic loss for farmers and nations, and increased risk of zoonotic disease.

• Case Study — Footrot:     * Species: Sheep.     * Pathogen: Dichelobacter nodus.     * Factors: Thrives in wet, warm, dense areas. Overgrown hooves and dermatitis facilitate infection.

• Three Factors of Disease in Agriculture:     1. The Pathogen: Transmission, virulence, and establishment.     2. The Host: Immune system, nutrition, and stress.     3. The Environment: Overcrowding and lack of hygiene.

Epidemics and Pandemics

• Epidemic: Increase in disease prevalence to a high level within a specific population/area.

• Pandemic: Disease spreads globally beyond boundaries.

• Case Study — The Black Death (Bubonic Plague):     * Pathogen: Yersinia pestis (bacteria).     * Vector: Fleas (carried by rats).     * Mortality: $30\%$ to $90\%$; approximately $200\,\text{million}$ deaths.     * Driving Factors: Trade routes, urban crowding, poor hygiene, and presence of rats.

Pathogen Adaptations

• Strategies:     1. Adhesion and Invasion (Entry > Multiply > Resist Defense > Damage Host).     2. Transmission between hosts (Survival in vectors/environment).

• Specific Adaptations:     * Endocytosis (Viruses): Receptor-mediated entry into host cells.     * Pili and Fimbria (Bacteria): Structural hair-like projections for adhesion to avoid flushing (e.g., mucus/vomiting).     * Biofilm: Assists bacteria in grouping and sticking to surfaces.     * Toxins: Release chemical inhibitors to destroy host cells (e.g., Tetanus).     * New Antigens (Viruses): Continually mutate to avoid immune detection (e.g., Influenza).     * Coughing/Sneezing: Induced in the host to spread droplets (Transmission).

Plant Defenses

• Passive Defenses (Barriers):     * Physical: Thick cuticle, cell wall structure, bark, and stomata (entry points).     * Chemical: Glucosides and saponins (toxic to fungi and bacteria).

• Active Defenses:     * Recognition: Receptors detect PAMPs (Pathogen Associated Molecular Patterns).     * Rapid Response: Closing stomata, releasing Hydrogen Peroxide to destroy cell walls, and cell wall apposition (sealing off the infection).     * Apoptosis: Hypersensitive response where the plant sacrifices a portion of itself (leaf/cells) to kill the pathogen.     * Delayed Response: Repairing wounds via cork production or gum secretion.     * Systemic Acquired Resistance (SAR): Using salicylic acid to develop a "memory" of pathogens for future infections.

Human Immune System: First Line of Defense (Innate)

• Nature: Barriers to prevent pathogen entry.

• Physical Barriers:     * Skin: Thick layer of cells; shedding removes pathogens. Contains keratin for waterproofing.     * Cilia: Small hairs in the airway to catch pathogens.     * Mucus: Thick liquid to trap pathogens.

• Chemical Barriers:     * pH/Acids: Stomach acid ($HCl$) and bile create an environment pathogens cannot survive. Skin oils (sebum) and sweat are also acidic.     * Lysozymes: Enzymes in tears, saliva, and mucus that destroy bacterial cell walls.

• Biological/Mechanical Responses:     * Sphincters: Muscles that control movement through passages.     * Flushing: Vomiting (emesis), diarrhea, and urination to expel pathogens.     * Granuloma: Dead cells surrounding a pathogen to wall off infection (e.g., Tuberculosis).

Human Immune System: Second Line of Defense (Innate)

• Nature: Non-specific response triggered when any antigen (foreign molecule) is detected.

• Recognition:     * Antigens: Chemical markers on pathogens.     * PRRs: Pattern Recognition Receptors on host cells.     * TLRs: Toll-Like Receptors used to detect PAMPs (e.g., flagellin in bacteria).     * DAMPs: Damage-Associated Molecular Patterns released by host cells to indicate they are under attack.

• Inflammation Response:     1. Mast Cells: Detect pathogens and release histamines. Histamines dilate capillaries and increase permeability, causing redness and swelling.     2. Macrophages: Release cytokines to recruit other cells like neutrophils.

• Phagocytosis: Engulfing and digesting pathogens.     * Neutrophils: First responders from bone marrow; thin and mobile.     * Monocytes: Differentiate into Macrophages and Dendritic cells. Dendritic cells link the innate and adaptive systems.     * Natural Killer (NK) Cells: Release cytotoxic chemicals (perforin) to induce apoptosis in infected or cancerous cells.

• Additional Components:     * Complement System: $30$ plasma proteins that assist in cell bursting and macrophage stimulation.     * Interferons: Interfere with viral replication.     * Pyrexia (Fever): The hypothalamus releases pyrogens to increase temperature, which limits pathogen replication and stimulates white blood cells.

Human Immune System: Third Line of Defense (Adaptive)

• Difference from Innate: Not genetically pre-programmed; diversity of response; forms memory and self-tolerance.

1. Humoral Immunity (Antibody-mediated)

• Cells: B Lymphocytes (B-cells), originating in the bone marrow.

• Process:     1. Antigen attaches to the B-cell (presented by dendritic cells).     2. B-cell activates and divides into Plasma cells and Memory B-cells.     3. Plasma Cells: Factories that produce Antibodies (Immunoglobulins - $Ig$).     4. Antibody Structure: Y-shaped. The top portions are variable regions (specific to the antigen). The binding site is the epitope.

• Antibody Actions:     * Neutralize toxins.     * Bind to viruses to prevent cell invasion.     * Agglutination: Clumping antigens together to activate phagocytes.     * Precipitation of soluble antigens.

• Memory B-cells: Persist for the life of the organism. Second exposure to an antigen leads to a faster and larger antibody response (e.g., $15\,\text{days}$ down to $5\,\text{days}$).

2. Cell-Mediated Immunity

• Cells: T Lymphocytes (T-cells), produced in primary lymph tissue and maturing in the thymus.

• Recognition: Use MHC (Major Histocompatibility Complex) molecules.     * MHC I: Found on all nucleated cells; presents fragments from inside the cell.     * MHC II: Found on antigen-presenting cells (macrophages, dendritic cells, B-cells).

• Types of T-cells:     * Helper T-cells (CD4): Activate both humoral and cell-mediated responses by releasing cytokines.     * Cytotoxic/Killer T-cells (CD8): Release perforin to form pores in the cell membrane and granzymes to initiate apoptosis.     * Suppressor T-cells: Deactivate B and T cells once the infection is over.     * Memory T-cells: Store information for quick responses to future infections.

Prevention, Treatment, and Control

1. Prevention (Pre-exposure)

• Hygiene: Hand washing, dental hygiene, PPE (masks, gloves), and safe food storage (cooking chicken to $750^{\circ}\text{C}$ as mentioned in the text context).

• Quarantine: Isolating individuals to contain outbreaks (e.g., $2\,\text{week}$ quarantine for COVID-19).

• Vaccination: The "golden bullet."     * mRNA: Instructions for making the spike protein.     * Viral Vector: Uses a harmless virus to deliver genetic code.     * Live Attenuated: Weakened version of the virus.     * Herd Immunity: Requires $90-95\%$ vaccination to protect the immunocompromised and reduce mutation chances.

• Public Health Campaigns: Use of information (ads/posters) to inform the public (e.g., $1987$ Grim Reaper AIDS ad).

2. Control (During exposure)

• Pesticides: Used for environmental control of vectors like mosquitoes (e.g., DDT, Pyrethrum).

• Genetic Engineering: Creating disease-resistant plants; engineering mosquitoes to not carry pathogens.

3. Treatment (Post-exposure)

• Antibiotics: Targets bacterial processes. Penicillin is a major example.

• Antivirals: Inhibit viral replication by blocking entry, transcription, or exit from cells.

• Disinfectants: Used on surfaces (e.g., ethanol, chlorine, $H_2O_2$).

• Antiseptics: Used on the body (e.g., ethanol, iodine).

Case Study: Ebola Virus ($2014$–$2016$)

• Origin: Western Africa/Southern Guinea.

• Transmission: Bodily fluids, mucous membranes, or sexual contact.

• Severity: $50\%$ fatality rate; approximately $10,000$ deaths.

• Management:     * Administrative Controls: Resources and funding allocation.     * Environmental Controls: Barrier nursing, waste management, PPE.     * Quarantine: Isolation and tracking.

Epidemiology and Data

• Incidence: The number of new cases occurring during a specific time. Also known as the risk of contracting the disease.

• Prevalence: The proportion of the population that has the disease at a particular point in time (includes both new and previous cases).

• Historical Case Study — John Snow ($1854$):     * Investigated a Cholera outbreak in London.     * Mapped clusters of cases in Soho.     * Identified a correlation with water pumps on Broad Street.     * The removal of the pump handle subsided the outbreak; the culprit was later identified as sewage leaking into the water supply.

Indigenous Bush Medicine

• Tradition: Aboriginal Australians used bioactive compounds to treat ailments for thousands of years.

• Examples:     * Emu Bush: Decoction for sores; infusions for colds.     * Kakadu Plums: Antiseptic and flu treatment.     * Witchetty Grubs: Paste for burns and wounds.     * Smokebush: Found in WA, NSW, and Tasmania; investigated for HIV/AIDS and cancer treatment.

• Intellectual Property: Laws protect traditional indigenous medicine to prevent unauthorized manufacturing and profit without permission.

Questions & Discussion

• Discussion on Pathogen Origin: The transcript explores the shift from spontaneous generation/miasma theory to germ theory through the work of Redi and Pasteur.

• Discussion on Snow's Investigation: How mapping clusters helped identify water as the medium of transmission for Cholera.

• Outbreak History: Discussion on how historical outbreaks were stopped and their long-term effects on societal health management.