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Module 7 – Infectious diseases Causes of Infectious Disease Inquiry question: How are diseases transmitted? Disease: any process or condition that adversely affects the normal functioning of a living thing or parts of a living thing.

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describe a variety of infectious diseases caused by pathogens, including microorganisms, macro-organisms and non-cellular pathogens, and collect primary and secondary-sourced data and information relating to disease transmission, including: o classifying different pathogens that cause disease in plants and animals Pathogens are organisms or biogenic molecules that cause diseases. *A parasitic relationship is where there is a benefit to thing (bacteria) and a harm to the host Pathogens by size: - Prions – non-living protein infectious agents that cause disease -> non-cellular o It is an abnormal protein that is capable of causing degenerative diseases of the nervous system o Cause disease by inducing abnormal folding patterns in the normal proteins that they come in contact with. o The diseases caused by prions are known as transmissible spongiform encephalopathies (TSE’s) because they cause holes to form in brain tissue  Mad cow and kuru are examples o Transmission is by ingesting tissue that contains the prions (nervous and brain tissue), organ transplants that have it, inheriting the mutated gene that codes for prions. -

Virus – non-cellular agents genetic material protected by cellular coating -> noncellular o They are not free living, can only reproduce and metabolise in a host cell. o So small that they can only be seen under an electron microscope o They have a protective coat (capsid) that encloses their genetic material o Viruses that contain RNA are known as retroviruses o Examples are: HIV, HPV, influenza, measles, COVID-19

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Bacteria and Archea – prokaryotic microbes o Can be aerob (survive in oxygenated environments) or anaerob (survive in oxygen-free environments) o Can be gram positive (thick cell walls stain purple) or gram negative (thin cell walls stain pink). o In animals an example is tetanus o In plants an example is rot diseases – black leg (stem rot disease in potatoes). o They are susceptible to antibiotics o Transmission is directly through close contact with another infected organism or a contaminated object o Some bacteria can form an endospore and lay dormant for years (tetanus)

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Protists (Protozoa) – eukaryotic single cellular organisms -> cellular o Single-celled, eukaryotic organism with membrane bound nucleus, no cell wall o Live in the intestinal tract o Infection causes stomach problems o Occurs from contact with faecal contaminants (swallowing swimming pool water) o Example in humans is Malaria which is caused by insect bites and Amoebic dysentery

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Fungi – eukaryotic moulds and yeasts -> cellular o Eukaryotic organism o Some are unicellular and some are multicellular o Reproduce sexually or asexually o Ca be saprophytic (living or dead matter, decomposers) or parasitic (living in a host) o Can be cutaneous (outer skin layer), subcutaneous (beneath the skin surface, from wounds) or systematic (affecting internal organs) o Transmission is directly through close contact with another infected host organism or indirectly through contact with a contaminated organism. o An example in humans is ringworm o An example in plants is moulds

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Macroparasites – multicellular eukaryote o can affect its host from the exterior (ectoparasites e.g. tics) or interior (endoparasites e.g. flatworms) o Ectoparasites can inject a toxin or they can be a vector for the transmission of other pathogens o Example in Animals is helminths (heartworm that occurs in dogs)

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Parasitic arthropods – arthropods are invertebrates that have an exoskeleton o Fleas – can transmit tapeworms o Ticks – common ectoparasites. Injects a neurotoxin during feeding which causes progressive paralysis. o Lice – bite or suckle which causes itchiness o Mites – cause irritation, itchiness and redness of skin o Flies – can transmit pathogens between hosts, particularly E. coli. o Mosquitos – Transfer pathogens between hosts

o investigating the transmission of a disease during an epidemic Pathogenicity: The ability of a pathogen to cause a disease depends on its ability to 1) invade the host 2) reproduce in the host 3) avoid being affected by the host immune system.

Endemic – the disease occurs to some degree in the population Epidemic – the disease is occurring in higher than normal rates in a population Outbreak – the disease is out of control in the population Pandemic – the disease has travelled to other countries / gone global

Case study (Equine influenza virus) Symptoms: - Fever (38.5 degrees or higher), watery nasal discharge, hacking cough, muscle pain, horse has laboured breathing. Transmission: - Highly contagious, directly between horses through nasal secretions and other bodily fluids. Indirectly through humans who carry the virus from an infected horse via clothes, shoes… Management of the outbreak - State-wide, nation-wide lockdown on movement of all horse to prevent further spread

Horse properties were quarantined throughout NSW The spread of the disease was mapped (Sydney to Central Coast and Hunter valley in 2007; outbreak was controlled within 6 months, Australia was declared free of the virus in 2008) Control of future outbreaks - Decision not to mass vaccinate (virus mutates quickly, and vaccine is useless to new strains) - Strict biosecurity measures – horses quarantined for 14 days in their own country prior to export and then 14 days once in Australia

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design and conduct a practical investigation relating to the microbial testing of water or food samples

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investigate modes of transmission of infectious diseases, including direct contact, indirect contact and vector transmission There are three forms of transmission: - Direct contact - Transfer of the pathogen via exposure to infected skin of body secretions o Touching, kissing, sexual contact, biting, contact with blood and other bodily fluid, direct contact with wounds, contact with nasal or oral secretions o Examples of these are: ring worm, impetigo, HIV, herpes - Indirect contact - Transfer of the pathogen to a new host via a non-living object (a fomite and an object or substance that carries the disease) o Airborne transmission, contaminated food or water, touching infected surfaces o Examples are measles, gastroenteritis, toxoplasmosis (caused by protozoan toxoplasma gondii from cat droppings), influenza, Legionnaires’ disease (from contaminated water) - Vector transmission - Transfer of the pathogen via another organism o Bit from an organism (tics, flies, mosquitos), Infected plants o Examples are Changas disease, malaria

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investigate the work of Robert Koch and Louis Pasteur, to explain the causes and transmission of infectious diseases, including: o Koch’s postulates Disproved the theory of spontaneous generation of micro-organisms. - He developed the agar plate technique for growing micro-organisms and used it to culture the isolated anthrax bacillus which he carried out an extensive study on. - He examined the blood from sheep that had died from anthrax and discovered the bacillus. - He then injected these cultured bacteria into healthy sheep. These sheep ended up getting anthrax

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The principle is used to identify the specific micro-organism that is responsible for causing a particular disease.

The criteria that must be met to determine whether a particular micro-organism is responsible for causing a disease are known as Koch’s Postulates: 1. The same micro-organism must be present in every diseased host 2. The micro-organism must be isolated and cultured in the laboratory and accurately described and recorded 3. When a sample of the pure culture is inoculated into a healthy host, the host must develop symptoms of the original host 4. The micro-organism must be able to be isolated from the second host and cultured and identified as the same as the original species. o Pasteur’s experiments on microbial contamination Prior to Pasteur’s experiment, the theory of ‘spontaneous generation’ existed. The aim of his experiment was to prove that microbes were air-borne. 1. He set up a swan neck flask with broth inside it and boiled it to ensure there was not microbe contamination. 2. A second control flask was set up without the swan neck with broth in it. 3. They were left sitting still for a certain period of time. It was found that the flask wit the swan neck had no bacterial growth because the microbes could fall into the neck but could not make it to the broth, however the open flask had microbial growth. Pasteur’s contributions: - Disproved the theory of spontaneous generation - Helped to find vaccines for chicken cholera, anthrax and rabies - Proved that fermentation was caused by a living organism - Developed pasteurisation, which is used to ensure that products are safe to consume 

assess the causes and effects of diseases on agricultural production, including but not limited to: Diseases in agriculture can be the result of endemic or exotic causes. There are three factors that may contribute to the development of infectious diseases in organisms in agriculture: 1. host factors – susceptibility to disease, access to pathogen concurrent disease or poor nutrition leading to weakened immune response, drought and heatwave stress on the host. 2. Pathogen factors – the pathogens availability, its ability to transfer between hosts, as well as virulence factors including adhesion and invasion of host tissues and successful establishment inside the host tissues. 3. Environmental factors - overcrowding and lack of hygiene leading to a build-up of wastes, pathogen can flourish and cause disease. ** Diseases arise from an imbalance between the pathogenicity of the agent and the defences of the host. Factors contributing to the risk of infectious disease:

- Increased mobility of humans Travellers can import infectious diseases into Australia which can in turn affect the agriculture industry. - Rise in intensive and industrial-type agriculture This has led to feeding lots and a higher density of animals means that disease can spread more easily. - Changing patterns of land use Deforestation and irrigation can bring insects closer to the agriculture areas. Bats loss of habitat bring them into a closer proximity to animal populations (including humans, covid19) - Climate change Changes in rainfall can affect the number of pathogens in soil, plants and insects. Drought causes animals to be weaker and more susceptible to diseases - Antimicrobial resistance Antimicrobials are used to treat infections in livestock, the overuse of these has caused resistance to form against it. - Pesticide resistance Insecticides, acaricides and herbicides are chemicals used to manage Macroparasites and weeds on farms, their overuse has caused resistance. - Loss of genetic diversity Genetic variation is necessary or a population to evolve in response to a disease threat. The use of inbreeding in animals and plants can lead to reduced resilience in a population to a pathogenic threat.

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o plant diseases Abiotic roles assist in weakening the plants defences, such as; temperature variation, light availability, chemical agents, water quantity and quality and nutrients available in the soil.

Cause Fungi

Insects and mites

Bacteria

Nematodes Viruses Phytoplasmas

Effect Most common cause of plant disease. Enter the plant through stomata or other openings. They cause damage by destroying tissue or absorbing nutrients from the plant. They cause direct damage to the plant but can also carry pathogens. E.g. citrus leaf miner (lays larvae under leaf and it makes tunnels in the leaves). Pathogenic bacteria occur in soil, weeds and seeds. Bacteria only spreads if; it is humid, warm weather, overcrowding of plants, bad soil conditions. Thousands of nematodes live in soil, some can attack plant roots creating lumps. Plant viruses are intracellular parasites and are less understood. They cause disease to the plant and can be spread. They are related to bacteria but do not have a cell wall, transmitted from cell to cell through insect vectors.

Case study (panama disease of bananas): Most bananas come from plantations in north Queensland which produce 95% of all Australian bananas. In March 2015, the pathogen that causes pathogen disease was detected. It causes yellowing and wilting of the leaves and splitting of the stems. The disease is spread through root to root contact and soil contamination. The affected farming ground was ceased, and bananas could no longer be grown there because the fungi infects the soil permanently. -

Caused by the fungus – Fusarium oxysporum

o animal diseases Case study (footrot in sheep): An infectious disease of the hooves of sheep, goats and cattle caused by bacteria. It causes painful abscesses between the toes, lameness weight loss and grazing is decreased. The bacterium will only survive in soil outside the host for a maximum of 4 days, Warm weather also favours the growth of bacteria. Overgrown hooves increase the animals chance of getting dermatitis which can then be infected by the pathogen. -

Caused by the bacteria – Dichelobacter nodosus

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compare the adaptations of different pathogens that facilitate their entry into and transmission between hosts For an organism to cause disease it must, 1. enter the host 2. multiply in host tissues 3. resist or not stimulate host defence mechanisms 4. damage the host Pathogen Prions Viruses

Bacteria

Protozoan Fungus

Adaptions to facilitate adhesion and invasion Adhesion: Must enter the nucleus of the host cell to facilitate replication of the viral genome. Invasion: They can enter the cell by endocytosis for enveloped viruses (influenza). If they are unenveloped (polio) they create a pore in the host cell and deliver the viral genome through it. Adhesion: Pili and fimbria. They form a biofilm which helps to prevent washing action of secretion such as mucus, urine and cilia. Invasion: Capsules resist phagocytosis by host cells. They breakdown cell contents with enzymes. Toxins are secreted to damage host cells. Adhesion: assisted by host cell wall or capsule molecules that permit adhesion to host cells. Invasion: Heat shock proteins are synthesised to cope with body

temps. Cell wall protects from host attacks. Macroparasites Transmission between hosts Airborne on dust and respiratory secretions Waterborne

Vector-borne Faeco-oral

Soil-borne

Adaptions to facilitate transmission Can stay in the air for a long time, resistant to drying out. Pathogen causes sneezing and coughing which transmits it to the next host. Able to colonise in water. Pathogens have fimbria, flagella to allow movement in water. Many are not destroyed by boiling water. The vector is not affected by the pathogen. Usually stable in many environments, induction of diarrhoea and vomiting increases likelihood of transmission. Stable in environment under a range of conditions

Sexual Blood-borne

Take advantage of altered features of red cells to facilitate growth and development.

Vertical (mother to child)

Examples of pathogens Influenza

Giardia

Malaria, zika virus E. coli

Fungi, nematodes Chlamydia, HIV, gonorrhoea malaria Rubella virus, chickenpox virus

Case study (Malaria): 4 protozoan parasitic species can cause malaria. They are single celled organisms that cannot survive outside the host. - The plasmodium parasites have a complex life cycle in both the human and the mosquito. The life cycle: - Parasite enters the blood stream and infects liver cells. Then moves on to infect red blood cells, and form gametocytes which can then be ingested by mosquitos. Fertilisation of two gametes results in the formations of a zygote inside the mosquito. The zygote transforms into a ookinete that turns into an oocyst and sporogenesis. The spores are released from the oocyst and can then be transmitted from the mosquito. Adaptions: - The parasite changes several times, so at each stage different antigen molecules are produced, preventing the host from launching an effective immune system (our third line of defence). - While in the liver cells, the plasmodium parasite kills the cell, causing them to separate from the surrounding cells, creating gaps and enabling them to move around. - It has adapted to contain an anticoagulant which prevents clotting as it exits the mosquito mouth. Responses to Pathogens

Inquiry question: How does a plant or animal respond to infection? Students: investigate the response of a named Australian plant to a named pathogen through practical and/or secondary-sourced investigation, for example: Plants have a passive and active defence. Passive defence: - Physical barriers: Thick cuticles of the plant, small stomate and bark are all examples that help plants to inhibit pathogen access. Vertical hanging leaves make it less likely for a pathogen reservoir to build up. - Chemical: glucosides and saponins can prevent bacterial and fungal growth on the surface of plants. Chemical receptors can detect pathogens (Pathogen associated molecular patterns (PAMPs)) and activate the next stage of response. 

Active defence (when the passive defence is breached and has a more targeted response to the pathogen): - Pathogen response: can recognise pathogens from chemical and physical detection. - Rapid active response (minutes/hours): permeability of cell membrane is decreased so that cations (Ca2+) can trigger the expression of certain genes that will act as a defence. An oxidative burst can occur where the cells release hydrogen peroxide as an attempt to kill the microbe. Apoptosis can occur as an attempt to isolate the disease to a certain area. - Delayed active response (days): Repair wounds in the bark by cork cell production and gum secretion. Lysozyme enzymes are released to destroy invading microbes. Salicylic acid acts as part of the cell’s ‘memory’, this is called systemic acquired resistance.

**Biotroph: a pathogen that does not kill the host **Necrotroph: a pathogen that does kill the host o fungal pathogens Symptoms: - Chlorosis (yellowing as a result of less chlorophyll) - Mosaic - Growth stunting - Crunkling of leaves Phytophthora cinnamomic is a fungal pathogen that affects eucalyptus and acacia. It causes damage to all parts of the plant with wilting, yellow foliage, stunted growth and coloured

cankers (dead section of bark). In the 1970’s it caused the destruction of over 282,000 hectares of eucalyptus marginate in Western Australia. The eucalyptus produce and store oil in sub-dermal secretory glands that have anti-microbial properties. Barrier zones can form in new tissue, and prevents pathogen spread to adjacent tissue. o Symptoms: -

viral pathogens

Chlorosis Leaf and stem wilting Leaf blotching Leaf mildew Leaf rusting

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analyse responses to the presence of pathogens by assessing the physical and chemical changes that occur in the host animals cells and tissues First line of defence is barrier to prevent pathogens from entering the body. The second line of defence is chemical and is also non-specific, attempting to kill invading microbes (usually associated with inflammation). These defences are both non-specific and called innate immunity. The third line of defence is a specific defence mechanism.

Immunity Inquiry question: How does the human immune system respond to exposure to a pathogen?  investigate and model the innate and adaptive immune systems in the human body **Active immunity and passive immunity are both different types of ...