Module 4

what is pathogen

a disease-causing microorganism

types of pathogens

• bacteria

• virus

• fungi

• protists

what is a communicable disease

diseases caused by pathogens- can spread

bacteria

• prokaryote

• produce toxins and damage cells

• in plants, they live in vascular tissue

• not all bacteria are pathogens

virus

• non-living→ genetic material surrounded by a protein

• infect cells by incorporating its own genetic material into DNA of a cell

• viruses multiply and burst out of the cell→ goes on to infect other cells

fungi

• eukaryotic

• produce spores that can infect other organisms

• bodies consists of filaments called hyphae

• form network a spread thru host/soil

protists

• eukaryotic

• uni or multicellular

• enter host, feed on host contents as they grow

• often require vector to transfer

bacterial diseases

• tuberculosis:

  • infects lungs→ causes chronic cough and bloody mucus

  • kills cells and tissues

  • M. bovine in cows can transmit to humans to cause TB

  • spread: airborne droplets

• Bacterial Meningitis:

  • infection of the meninges→ membranes surrounding brain and spinal cord

  • causes fever, headache, rash, neck stiffness→ can cause brain and nerve damage

  • spread: airborne droplets

• Ring rot:

  • infect vascular tissue→ prevents transport of water so plant wilts and dies

  • spreads into potato tubers→ produces black ring of rot

  • spread: contact with infected plants

viral infections

• influenza:

  • infect cells that line airways

  • cause high temp, body aches, fatigue

  • spread: airborne droplets

• HIV/AIDS:

  • retrovirus→ have ability to make DNA from its RNA

  • DNA inserted into host→ can remain inactive for many years

  • compromises immune system→ AIDS

  • spread: transfer of body fluids (STI)

• Tobacco Mosaic Virus:

  • Causes mottling and discolouration of leaves

  • spread: contact with contaminated plants

Protist Infections

• Blight:

  • transmitted via spores

  • causes brown marks on leaves which increase in size and number

  • protist destroys potato and tomato crops

• malaria:

  • spread by mosquitos

  • causes fever, chills, fatigue→ fatal

Fungal infections

• Ringworm:

  • affect cattle

  • growth of fungus in skin with spore cases erupting through skin to cause rash

• athletes foot:

  • growth of fungus under skin of feet- usually between toes

• Black Sigatoka:

  • affects bananas

  • reduces ability of plant to photosynthesise

  • causes parts of the leaf to die→ black streaks

  • eventually causes death

types of transmission of disease (with e.gs)

• direct contact→ from one host to another:

  • spores

  • airborne transmission

  • exchange of bodily fluids

  • direct contact

• indirect contact→ second organism transfers it to new host:

  • vectors

factors affecting disease transmission

• poor ventilation

• contact with people who have migrated from areas where disease is common

• socio-economic factors

• poor nutrition

• damp warm conditions→ ideal living conditions for pathogens

• compromised immune sytem

• poor waste disposal

• poor hygiene

types of defences in plants

• passive defences:

  • present before infection

  • prevent entry and spread of pathogen

  • physical and chemical defences

• active defences:

  • when pathogens attack

  • plants will fortify existing defences when attacked

physical defences in plants (7)

• cellulose cell walls:

  • physical barrier

  • contains variety of chemical defences→ activated with pathogen detected

• lignin:

  • thickening of cell walls→ waterproofing of cell walls

• waxy cuticle:

  • prevents water collecting on surface

  • no water= pathogen can’t survive

• bark:

  • prevents entry of pathogens

  • contains chemicals that work against pathogens

• stomatal closure:

  • when pathogens detected, guard cells close stomata in that part of the plant

• callose:

  • large polysaccharide deposited in sieve tubes

  • blocks flow of sieve tubes

  • pathogen prevented from travelling through plant via phloem

• tylose:

  • balloon-like swelling which fills xylem vessel→ plugs xylem so cannot carry water so stops spread of pathogens

  • contains high conc. of chemicals which are toxic to pathogens

chemical defences in plants

• produce chemicals with anti pathogenic properties

• terpenes in tyloses

• tannins in bark

active defences in plants

• cell walls thickened→ additional cellulose added to strengthen them

• deposition of callose between cell wall and cell membrane near invading pathogen→ impedes cellular penetration, blocks plasmodesmata

• oxidative bursts→ reactive oxygen molecules that can damage pathogenic cells

• necrosis→ deliberate cell suicide to limit pathogens access to water

primary defences

prevent pathogen entry

primary defences in humans

• skin:

  • acts as physical barrier

  • has antimicrobial substances

• blood clotting:

  • uses calcium and 12 clotting factors→ released from platelets

  • factors activate enzyme cascade

• mucus membrane:

  • line exchange surfaces

  • ciliated epithelial cells waft pathogens into mucus to be swallowed and destroyed

• wax:

  • e.g. in ears→ trap pathogens

• lysozyme:

  • enzyme that destroys pathogen by disrupting cell wall

• acid:

  • e.g. in stomach and vagina to kill pathogens

• inflammation:

  • mast cells (detect pathogens) release histamines

  • causes vasodilation and causes capillary walls to be more permeable to WBCs

• fevers:

  • body temp raised to kill/destroy pathogen

  • helps activate immune system

what is an antigen

glycolipids or glycoproteins that initiate an immune response

opsonins

proteins that bind to antigens on a pathogen to enhance a phagocyte’s ability to bind to and engulf the pathogen

types of phagocytes

• neutrophils

• macrophages

neutrophils

• multi-lobed nucleus

• travel in blood and move out of blood into tissue fluid

• die soon after digested pathogen (pus)

• made in large numbers when infection present

macrophages

• kidney shapes nucleus

• larger cells

• travel in blood as monocytes and settle in lymph nodes, where they mature into macrophages

• have a role in specific response

what is phagocytosis

neutrophils and macrophages engulf and digest pathogens

the process of phagocytosis

1. phagocyte receptors recognise opsonin’s antibody/antigen on surface as foreign

2. cytoplasm of phagocyte engulfs pathogen

3. pathogen is contained within phagocytic vacuole in cytoplasm

4. lysosome fuses with phagocytic vacuole→ releases lysozyme, which breaks down pathogen

Antigen presentation

• Macrophages only partially digest pathogen

• Antigen of pathogen is brought to cell surface membrane to trigger full immune response from T and B cells

The specific immune response

1. Antigen is presented on cell by macrophage

2. Specific B and T lymphocytes are recruited and are complementary to the antigen→ bind to the antigens

3. T cells divide by mitosis and differentiate to make variants of T cells→ clonal expansion

4. T helper cells release cytokines, which activate B cells

5. B cells divide by mitosis (clonal expansion) and differentiate to make plasma cells and B memory cells

6. T and B memory cells made and stored.

Result of the specific immune response

• Produces antibodies→ neutralise foreign antigens

• Provides immunological memory

T-cell mediated immunity

• When T cells have been recruited the bind to the antigen on the APC

• Divide by mitosis into clones

• Differentiate into:

  • T-killer cells: directly kills other cells by putting holes in the membranes

  • T- helper cells→ stimulates more phagocytosis by releasing cytokines and activate B cells by releasing cytokines to produce antibodies

  • T-memory cells→ develop into memory cells providing long term immunity

  • T-regulator cells→ shut down immune response once pathogen has been removed

B cell/ Humoral Immunity

• involves soluble antibodies in body fluid

• By lymphocytes develop into either:

  • B plasma cells→ circulate in blood, make and release antibodies

  • B memory cells→ remain in body to provide immunological memory

difference between primary and secondary immune responses

secondary is much quicker and stronger due memory cells

autoimmune diseases

• immune system stops recognising self antigens→ attacks health body tissues

• often requires use of immunosuppressant drugs to prevent immune system from working

examples of autoimmune diseases

• arthritis:

  • inflammation of joints

  • antibodies attack membranes around the joint

• lupus:

  • antibodies attack proteins in nucleus of cells and affect tissue

what is an antibody

• a molecule which is produced by lymphocytes in response to infection

• have quaternary structure

• bind to antigens on the surface of the pathogen to form antigen-antibody complexes

structure of anitbodies

• quaternary structure of 4 polypeptides

• specificity of antibody depends on its variable regions→ form antigen binding sites

• variable regions have unique tertiary structure→ complimentary to specific antigen

• all antibodies have the same constant region

types of antibodies

• opsonins

• agglutinins

• anti-toxins

opsonins

• bind to antigens on pathogens

• act as binding site for phagocytes→ can more easily bind and destroy the pathogen

• may bind to antigen molecules that would otherwise bind to host cells→ antigen is useless and pathogen cannot enter cell→ neutralisation

agglutinins

• two binding sites of antibody bind to antigens on different pathogens- crosslinks pathogens

• clumps pathogens together→ makes it easier to engulf and digest them

antitoxins

bind to molecules released by pathogenic cells and render them harmless

what is immunity

the ability to resist infection

types of immunity

• passive:

  • caused by introduction of antibodies from an outside source

  • short lasting→ not being replaced when they are broken down

  • natural→ breast milk

  • artificial→ injection with antibodies

• active immunity:

  • caused by the production of antibodies by the individual’s own immune system

  • loner lasting

  • natural→ immune response

  • artificial→ forms the basis of vaccination

vaccination

• provides immunity against a specific pathogen

• injection or orally administered antigenic material

• immune system makes antibodies and memory cells to antigens

antigenic material used in vaccines

• whole organisms

• weakened version of pathogen

• preparation of antigens from pathogen

• toxin from the pathogen

why are new drugs needed

• new diseases

• some diseases have no treatment

• some antibiotics are no longer effective

traditional remedies

• morphine:

  • comes from sap of unripe poppy seed heads

  • opium used as anaesthetic in 12th century

  • acts on nervous system→ no pain felt

• aspirin:

  • willow bark extract→ relieve pain and fever

  • modifies to stop stomach bleeding

  • led to development of aspirin and ibuprofen

• Observation of wildlife:

  • monkeys/ bears rub citrus oils into coats as insecticide

  • birds line nests with medicinal leaves to protect from mites

research into disease causing mechanisms

research carried out to find out how pathogens cause disease e.g. HIV binds to CD4 receptors of T helper→ if this is prevented, HIV can be stopped from infecting cells

personalised medicine

• genome of plants/microorganisms screened to identify medicinal compounds from DNA sequence

• potential to sequence human DNA with specific conditions and develop specific drugs for them

synthetic biology

development of new molecules→ particularly enzymes

antibiotic resistance

• antibiotics create selection pressures on population of bacteria

• variation exists in the population due to random mutation

• most bacteria killed by antibiotic→ some resistant species survive

• resistant species survive and reproduce→ more of resistant species

What is biodiversity

The range and variety of alleles, species and habitats in an ecosystem

Importance of biodiversity

• Maintains equilibrium of an ecosystem

• All ecosystems are interdependent→ if biodiversity was reduced, there wouldn't be links between interdependent organisms

Components of biodiversity

• Species diversity

• Genetic diversity

• Ecosystem diversity

What is species diversity

Number of different species and number of individuals of each species within any one community

What is ecosystem diversity

• The range of different habitats within a particular area

• Lots of habitats= high ecosystem diversity

What is genetic diversity

The number of different alleles within a population

Components of species diversity

• Species richness

• Species evenness

Species richness

• Number of different species living in a ecosystem

Species evenness

• The number of individuals of each species living in a community

Purpose of sampling

• Difficult/ inefficient to count all organisms in one area

• Sampling allows for representative estimate

Distribution

• Presence or absence of each species

• Where they all are

Abundance

• Frequency:

  • the likelihood of an organism occurring in a quadrat

  • Does not tell us density of

• Percentage cover:

  • Estimates area in quadrant covered by particular species→ useful when difficult to count

  • Difficult when there is species overlap

Random sampling

Individual organisms selected by chance→ every organism has equal chance of being selected

Non-random sampling

Sample not chosen at random→ involves element of choice

Random sampling+ pros and cons

• Sample sites randomly selected i.e. number generator

• Advantages:

  • Data is not biased

• Disadvantages:

  • Not cover all areas of habitat equally→ species with lower presence may be missed, underestimated

Opportunistic sampling+ pros and cons

• Researcher makes decisions based on prior knowledge→ may deliberately sample an area that they know contains certain species

• Advantages:

  • Easier and quicker than random sampling

• disadvantages:

  • May be biased→ overestimate of biodiversity

stratified sampling+ pros and cons

• dividing habitat into areas which appear different

• Advantages:

  • ensure all habitats are sampled and nothing is missed

• disadvantages:

  • over-representation→ if some of the areas are smaller than others, there may be a disproportionate number of samples taken

systematic/ transect sampling+ Pros and Cons

• samples take at fixed intervals across a habitat

• Advantages:

  • useful when showing change from one area to another

• Disadvantages:

  • only species on line or within the belt will be counted

  • species can be missed→ underestimate

Types of transects

• line transects:

  • record which species are touching the tape measure at regular intervals

  • quicker→ useful for determining distribution

• belt transects:

  • place a quadrat next to the tape

  • continuous→ quadrats placed along full length of tape

  • interrupted→ quadrats placed at regular intervals along tape

  • provides more detailed data on abundance

reducing effects of sampling bias

• create a grid and use random number generator to generate coordinates

• use larger sample size→ identify and eliminate anomalous results

methods of sampling animals (6)

• pooter

• pitfall trap

• sweep nets

• tree beating

• kick sample

• tullgren funnel

pooter

• device used to sample small insects

• sucking on a mouthpiece that draws the insect into a chamber through inlet tube

pitfall traps

• hole dug into the ground→ insects fall into hole

• covered by roof structure to stop rainwater entering

• can be left overnight to sample nocturnal species

• used to trap small crawling invertebrates e.g. spiders, beetles

sweep nets

• hand held nets that are swept across an area

• used to capture insects in areas of long grass

tree beating

• takes samples of invertebrates in a tree or bush

• sheet spread underneath and tree/ bush is shaken/ hit to dislodge species that fall into sheet

kick sampling

• done in stream/ river to measure invertebrates

• stream/ river bank kicked to disturb substrate

• net held downstream to capture any dislodged invertebrates

tullgren funnel

• litter spread on mesh screen within a large funnel with light bulb suspended above the litter

• combination of heat, light and drying of litter drives insects through the mesh→ drop into container at bottom of funnel

sampling plants

• sampled using quadrats:

  • point quadrat→ frame with pins placed through at regular intervals. Each species the pin touches is counted

  • frame quadrat→ square frame divided into equal grid. Type and number of each species are recorded

mark, release, recapture method

• used for larger animals

  1. set of animals caught and marked

  2. released back into community

  3. after specified length of time, community is revisited and same number of individuals are caught again

  4. number of marked individuals are counted.

calculating population size from MRR

Assumptions made when using MRR

• no migration into or out of the population

• mix randomly

• marks not lost

• marks do not cause harm or increase chance of being caught by predator

• marks do not increase chance of recapture

reliability

how consistently a method measures something

reducing effects of sampling bias

• use random number generation

• larger sample size

why is biodiversity measured

• conservation and environmental management→ impact of a factor on abundance of species

• indicates stability of an ecosystem

simpson’s index of biodiversity

• 0= no diversity

• 1= infinite diversity

what do levels of biodiversity tell us?

• Low biodiversity:

  • few species

  • stressful/extreme environment

  • very specific adaptations

  • simple food webs

  • change=major effect on ecosystem

• high biodiversity:

  • large number of species

  • not stressful environment

  • many species live in habitat→ few specific adaptations

  • complex food webs

  • change= small effect on ecosystem

what does genetic diversity depend on

• the number of different alleles in a species:

  • greater number of alleles= greater genetic diversity

  • fewer alleles= reduced genetic diversity

why is genetic diversity important

more genetic diversity= more alleles= more variation= greater chance of individuals surviving environmental change

factors affecting genetic diversity

• increasing:

  • mutations

  • interbreeding and gene flow

• decrease:

  • selective breeding

  • captive breeding programs

  • cloning

  • natural selection

  • genetic bottlenecks

  • founder effect

  • genetic drift

mutations

• bring about new alleles for a gene

• alleles can be passed onto offspring

interbreeding and gene flow

• gene flow→ when animal migrates from one pop. to another

• increases allele frequency of the new population

selective breeding and captive breeding

• reduces number of alleles in a population as favoured alleles are consistently being bred until individuals with other alleles become reduced

• in captive breeding, fewer individuals available to be bred together so reduced gene pool

cloning

identical genes to the parent sample= no genetic diversity

natural selection

as advantageous characteristics are favoured, other alleles from the population will be lost

genetic bottlenecks

sudden large reduction in pop. size= fewer alleles present

founder effect

when a few individuals from the original population start a new colony→ few alleles in the new gene pool

genetic drift

• when chance dictates which organisms survive and reproduces→ occurs randomly

• larger impact seen on small populations

polymorphism

when a gene has more than one allele e.g. hair colour

monomorphism

when a gene has only one allele- ensures that basic structure of species is similar

calculating genetic diversity

number of polymorphic gene loci/total number of loci