Microbes and Immune System Flashcards

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1
Q

What are 4 life strategies?

A

Photoautotrophism

  • Sunlight
  • Carbon Dioxide
    • Organisms that use this strategy are plants, algae and cyanobaccteria

Photoheterotroph

  • Sunlight
  • Pre-formed organic compounds
  • Purple/green non-sulphur bacteria

Chemoautotroph

  • Chemical oxidation
  • Carbon dioxide
  • Extremophiles

Chemoheterotroph

  • Chemical oxidation
  • Pre-formed organic compounds
  • Humans, animals
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2
Q

Give a brief overview of the Marine environmnet

A

It’s dominant!

  • Covers 2/3 of the surface
  • Several km deep

Highly diverse

  • Various environments within marine environment
    • Habitat to bacteria, fungi and algae

Physical parameters

  • Salinity
  • temperature
  • Pressure
  • Nutrients
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3
Q

Describe the different zones within the marine environement

A

Neritic zone

  • Mild temp, low pressure, nutrient rich
  • Diverse marine life
  • Photosynthetic organisms

Oceanic zone

  • Pressure increases with depth
  • Chemotrophs
  • Not as unstable as once thought
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4
Q

What organisms do the dead sea house due to its salinity?

A

The Dead Sea

  • Microscopic life only
  • Photoheterotrophs
  • Halophiles
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5
Q

How do halophiles stop the flow of water from low internal salinity?

A
  • Halophiles need to stop flow of water from low internal salinity
  • Production of compatible solutes increase internal salinity, preventing outflow of water
  • Maintenance of the water-salt balance in halophiles
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6
Q

What are compatible solutes?

A

Osmoprotectants or compatible solutes are small molecules that act as osmolytes and help organisms survive extreme osmotic stress. Examples include betaines, amino acids, and the sugar trehalose. These molecules accumulate in cells and balance the osmotic difference between the cell’s surroundings and the cytosol.

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7
Q

What are Piezophiles and the different types?

A

Piezophiles (barophiles) are organisms whose survival and reproduction is optimized to high pressures, such as those in deep sea environments.

Piezotolerant

  • Grow at atmospheric pressure but can also tolerate increased pressure.

Piezophile

  • Optimal growth above atmospheric pressure.

Extreme piezophile

  • Need high pressure for survival. Unable to survive at sea level.
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8
Q

What is the difference between extreme piezophile and piezotolerant membranes?

A

The membrane of the extreme piezophilic organism is highly unsaturated making it extremely fluid.

As opposed to the membrane of the piezotolerant organisms which have highly saturated membranes making them as rigid as possible.

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9
Q

Why are humans anomolous when it comes to withsatnding high oressures compared to other eukaryotes?

A

Humans are anomolous because we are not able to withstand high pressures like most other eukaryotes.

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10
Q

Why would extremophiles be found in caves despite them being a relativley stable enviornment?

A

Extremophiles also inhabit caves and mines which is associated with high level of salts, mineral-rich, extreme temperatures and no light.

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11
Q

How do organisms play a role in shaping mines and caves?

A

Organisms often play a role in the formation of these structures through:

  • Acidification of water, resulting in sculpture of caves
  • Changing the composition of rock and precipitate out chemicals:
    • Iron/sulphur oxidising minerals
    • Produces sulphuric acid
  • Removes sulphur from minerals
  • Negative pH values!
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12
Q

Different tyoes of thermophiles

A

Psychrophile

  • Optimum growth <15ºC
  • 90% ocean is <5ºC
  • Chlamydomonas nivalis, Listeria monocytogenes

Thermophile

  • Spores used as a biological indicator, measuring sterilisation

Hyperthermophile

  • Survival at >70ºC
  • Not only tolerate, but require for survival
  • Thermus aquaticus

Mesophile

  • Optimum growth at body temperature
  • Human pathogens
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13
Q

How do Psychrophiles and Hyperthermophiles survive their respective environments?

A

Psychrophiles

  • Low temperature, membrane is too solid
  • Keep interactive and fluid
  • Increase unsaturated fats

Good fat = liquid

Hyperthermophiles

  • High temperature, membrane becoming too liquid
  • To maintain integrity, solidify fats
  • Increase saturated fat content

Bad fat = solid

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14
Q

What are the Oxygen requirements of different organisms?

A

Aerobes

  • Growth in oxygen
  • Rhizobium spp - soil
  • Neisseria spp
    • Meningitis, gonorrhoea

Anaerobes

  • Death in oxygen
  • Clostridium spp - HAI
  • Actinomyces spp – soil

Facultative Anaerobes

  • Survive +/- oxygen
  • Staphylococcus spp.
    • E. coli

Aerotolerant

  • Can survive in oxygen but metabolise anaerobically
  • Rhizobium spp.
  • Streptococcus spp.

Microaerophile

  • Prefer reduced oxygen, can’t respire anaerobically
  • Lactobacillus spp.
  • Campylobacter spp.
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15
Q

What is the Rhizosphere?

A

Rhizosphere is an area of soil containing a diverse population of microorganisms that utilise plant secretions e.g. proteins and sugars. Microbes consume the minerals and feed them back to the plant, promoting growth

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16
Q

Give a brief overview of P. syringae

A
  • P. syringae allows ice formation at higher temperatures
  • Plants normally survive at -2°C to -8°C through internal proteins, changing freezing temp of water
  • Bacteria produce ice nucleation active (INA) proteins, increasing freezing temp
  • Punctures plants cells, allowing bacteria to penetrate
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17
Q

Define symbiosis, parasitism, mutualism and commensalism.

A
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18
Q

Hawaiian Bobtail Squid and the Aliivibrio fischeri have a mutualist relationship, describe how this is the case.

A

The Hawaiian Bobtail Squid provides a selective environment exclusively for A. fischeri. The A. fischeri produce fluorescent light which casts a light shadow from the squid. This is beneficial to the squid because it is nocturnal and the moon above the squid would cause a night shadow to be cast by the squid which would alert predators below of its presence and subsequently kill them. The light from the A. fischeri cancels out the moon shadow and shields the squid from predators.

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19
Q

How does the Hawaiian Bobtail Squid utilise the A. fischeri?

A
  • Light is omitted specifically from the light organ within the mantle of the squid.
  • The light organ has epithelial cells which form a ciliated surface on its structure, beating water into the light organ.
  • Water passes over tiny, microscopic pores in the light organ.
  • A. fischeri accumulates in the deep crypts on the squid.
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20
Q

How does the Hawaiian Bobtail Squid specifically accumalate A. fischeri?

A
  1. Water passes through the anterior appendage (ciliated cells) and over the pores.
  2. Bacteria travel down the light organs and colonise the deep crypts.
  3. This is where we see specific colonisation of A. fischeri.
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21
Q

How does the the Hawaiian Bobtail Squid specifically allow A. fischeri to colonise?

A
  • Peptidoglycan is a structure specific to bacteria and acts as a signal to epithelial cells.
  • Ciliated cells secrete mucus, trapping bacteria from passing freely.
  • Squid produces compounds which have an antibiotic effect against Gram +ve
    • A. fischeri is Gram –ve
  • A. fischeri outcompete other microbes and becomes dominant by activating chitinolytic enzyme within the squid, digesting chitin in the environment.
  • Broken down chitin (chitobiose) acts as an attracted for A. fischeri, specifically.
  • Acts as an attractant for more A. fischeri to more over the pores.
  • Only A. fischeri left, colonising the deep crypts of the squid. A. fischeri becomes non-motile, induces host-epithelial cell swelling and eventually releases light.
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22
Q

Diagram showing the stages of colonisation of a newborn Hawaiian bobtail squid’s deep cysts

A
  1. Sterille - The crypts of a newborn squid are sterile within the first 30 min.
  2. Permissive - Initial mixed bacterial population in the crypt. Mucus is shed to attract bacteria.
  3. Restrictive - Antibiotic production to inhibit certain types of bacteria. A. fischeri has immunity to these mechanisms.
  4. Specific - Specific A. fischeri colonisation due to chitobiose secretion
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23
Q

Diagram detailing squid and A. fischeri stages of colonisation

A
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24
Q

What is the Diel Cycle?

A

Cycle of colonisation of A. fischeri every day and night in the squid.

DAY

  • Nocturnal squid buries in the sand, doesn’t need to omit light.
  • Removal of most A. fischeri from the light organ into the environment.
  • Remaining bacteria begin to replicate throughout the day, to reach peak density.

NIGHT

  • Light organ is full of fresh A. fischeri.
  • Bioluminescence enables hunting.
  • Removal of bacteria from squid.

Fresh population of A. fischeri generated.

Seeding of the environment with A. fischeri for the next generation of squid.

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25
Q

What is Quorum sensing? And how is it useful to the Hawaiian Bobtail Squid and the A. fischeri?

A

Quorum – specific/minimum number

Quorum sensing

  • Bacteria sensing their population size and coordinating their behaviour (biofilms formation, virulence, antibiotics)
  • Behaviour changes depending on low or high cell density

In the A. fischeri emitting light is an energy expensive process and only emit it when the bacteria use qurorum sensing to decide whether there’s enough of them for the light to impact the host (Hawaiian Bobtail Squid).

The Individual behaviour is different from group of organisms - multicellular

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26
Q

What does Quorum sensing rely on?

A

Quorum sensing relies on autoinducers (AI) to sense the environment population.

Once a threshold has been reached, AI’s activate cellular process to respond to the environment – luminescence within the A. fischeri

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27
Q

What controls the ptoduction of light in A. fischeri?

A

The lux operon controls the production of light in A. fischeri.

  1. LuxI – synthesises AHL. At low A. fischeri densities, the AHL diffuses out of the cell and no light is produced.
  2. However, at high A.fischeri concentrations, there are also higher concentrations of AHL which can then re-enter the bacterial cell and bind to luxR.
  3. The binding of AHL to LuxR activated transcription of luxC, luxD, luxA, luxB and luxE.
  4. LuxA and luxB genes produce proteins which form luciferase. Luciferase then catalyses a redox reaction which produces light.
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28
Q

Which gene is the regulatory gene in the lux operon?

A

LuxR is the regulatory gene which produces transcription activator

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29
Q

What is a Biofilm?

A

A biofilm is a growth of organisms within a mucous bound film either in a substrate or on a surface.

Majority of microbes to be in a sessile state.

  1. They usually begin by colonising a surface. Here they can be easily detached.
  2. At this point an Extracellular matrix has been produced (like sugars and peptides).
    1. When the biofilm is fully formed. Quorum sensing detects growth slowing and aids biofilm dispersal and the cycle starts again,
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30
Q

What is Biofouling?

A

Biofouling – fouling of underwater structures with micro/macroorganisms

Can cause loss pf functionality in pipes, chains and bottoms of ships etc.

The biofilming of microbes onto these surfaces allow for other higher lifeforms to latch on like barnacles etc.

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31
Q

What are the stages of biofouling?

A
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32
Q

What is different in the disperesed cells from a biofilm than the original microorganisms?

A

They are usually more toxic to their environment.

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33
Q

How do Biofilms cause issues in Medicine?

A
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34
Q

What are the issues with culturing microbes in a lab?

A

Restricts growth

  • Does not cater for organisms found in all environments
  • Laboratory environment is far removed from reality

Time consuming

  • Some organisms can take weeks to grow (Mycobacterium spp.)

Therefore, it is approximated that we only know of 1% of all microbes that exist.

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35
Q

How do we idenitfy different species of microbes within an interspecies biofilm?

A
  1. Extract all DNA from the population and digested into smaller fragments.
  2. Cloned in to plasmid vectors before sequencing.
  3. Data analysis to identify organisms.
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36
Q

What are 4 omic studies?

A
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37
Q

How is Transcriptome tech used?

A
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38
Q

What is a Microbiome?

A

Large and mixed population of microorganisms coexisting together under many circumstances.

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39
Q

How are microbes found in the wild?

A

Although we tend to consider study these organisms in pure culture, in nature they are infrequently found in isolation, but rather as dynamic communities, which compete for resources but frequently depend on each other for survival.

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40
Q

What is a commensal relationship within communities?

A

Commensal: on or in host without injuring or benefiting the host

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41
Q

What is commensalism?

A
  • Commensalism: when a product produced by one organism can be used beneficially by another
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42
Q

What is the definition of a pathogen?

A
  • Definition: an organism that causes damage and disease to the host
  • Much smaller group of organisms
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43
Q

What does Koch postulate a pathogen to be?

A
  1. He said that to be a pathogen, the microbe must be absent in all healthy individuals but present in all diseased hosts.
  2. It should be possible to isolate and grow the microbe in pure culture from all diseased patients and that if this microbe was then used to inoculate a healthy host, it should cause the same disease in that host.
  3. And that finally it should be possible to reisolate the pathogen from the inoculated host.
  • These postulates are still valid today although recovery of the genetic material rather than the organism is now sufficient and resulted in renaming these as Kochs molecular postulates
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44
Q

What is the definition of pathogenicity?

A

The capacity of a microbe to cause damage in a host

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45
Q

What is the definiton of virulence?

A
  • Virulence refers to the degree of damage caused by the microbe
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46
Q

What are Virulence Factors?

A
  • A product made by the organism that contributes to overall virulence (eg toxin)
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47
Q

Describe the Virulence factor:

Tetanus toxin

A

Tetanus toxin

Released by C. tetani, following its growth within the anaerobic environment of a deep puncture wound. On release from the organism, the toxin binds to the peripheral neuronal axons and undergoes retrograde transport to the inhibitory interneuron, where it prevents the release of inhibitory neurotransmittors such as glycine and g-aminobuytric acid (GABA).

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48
Q

How does the tetanus toxins’ actions impact animals?

A

This prevents the deactivation of the neurone resulting in contraction in both agonist and antagonist muscles.

This causes tetanic muscle spasm, an extreme example of which is shown here.

The vaccine that is given to prevent disease results in antibody production that binds to the toxin, preventing its interaction with nerve endings. However, in the absence of such antibodies, mortality is high.

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49
Q

What are oppurtunistic pathogens?

A

The capacity of these organisms to cause disease depends upon the opportunity they are given to cause disease hence the term ‘opportunistic pathogens.

This may include the age the patient (with the very young and very old often being immunocompromised, antibiotic treatment that may reduce the presence of protective organisms, the prevalence of exposure, how much and in what form you are exposed to that pathogen, your host genetics and factors that influence your immune system including nutrition and stress

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50
Q

What are many of the oppurtunistic infections also classed as?

A

Many of the opportunistic infections on man are also zoonotic organisms in that these are diseases transmitted to man from animals

Interestingly many of these microbes are commensals in the animals – only causing disease when they cross the species barrier.

These include Campylobacter jejuni which is a common cause of diarrhoea in man, enterohemmorhagic E.coli or EHEC which causes kidney failure in children and rabies in bats, which is always lethal in man but can be carried without symptoms in bats.

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51
Q

Why is the rate of evolution much more rapid in microbes compared to humans?

A

Evolution in microbes is much more rapid than humans due to their high rate of multiplication. Under optimal growth conditions in a lab, there growth is rapid, with doubling times as short as 25 min under optimal conditions. This means that 1 organism can replicate to 100 million within 8h

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52
Q

How do bacteria mutate?

A
  • Alter sensitivity to particular drugs
  • Alter receptor recognition (of tissue)
  • Alter recognition by the host (immunity)

However, this type of mutation does not explain how much larger pieces of DNA that encode specific virulence traits such as toxins are acquired.

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53
Q

What are the three types of horizontal gene transfer in bacteria?

A
  1. In natural transformation, bacteria take up DNA from the environment, which depending on regions of homology between the DNA and the bacterial DNA may recombine and replace exitsing regions of the chromosome.
  2. In conjugation, DNA is exchanged between bacteria through the formation of a conjugative pilus
  3. And in transduction, genetic exchange is the result of predation by bacteriophage, small viruses of bacteria, which inject DNA into the cells as part of the infection process.
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54
Q

When does transformation occur?

And what is the probable reason for it?

A

Occurs in bacteria that are naturally ‘Competent’. Occurs when ssDNA is released when bacteria die and lyse. The uptake of DNA and incorporation into genome of ‘competent’ bacteria is done through homologous recombination.

Some become competent in response to quorum sensing compounds – released by bacteria – competency factors

But if gene associated with antibiotic resistance – transformed bacteria will now be resistant

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55
Q

How do competency factors change incompetent bacteria and how has thi sled to issues regarding antibiotic treatment?

A

These competency factors modify the membrane to enhance uptake of single strand pieces of DNA, which due to the homology found in closely related species, allows rapid recombination into the bacterial chromosome.

If the piece of acquired DNA encodes something like an antibiotic resistance gene, the clone with the acquired DNA will outgrow those bacteria that are not naturally competent.

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56
Q

What is conjugation?

A
  • Conjugation in contrast to transformation is an active process that requires the generation of a conjugative link between two bacteria that allows the direct transfer of Dna from one bacteria to another. Conjugative plasmids found in bacteria, are self replicating pieces of DNA that encode tra genes, which are essential for the transfer of DNA.
  • Once of the best described systems of conjugation if the transfer of the F pilus in E.coli.
  • Exchange of DNA occurs when an F +ve organism carrying the plasmid meets an F- organism that does not have this plasmid. The F pilus encoded on the plasmid and expressed on the surface of the F+ bacteria, is used to initiate contact with the F- cell. On contact, a structure is formed between the two cells, through which the plasmid DNA is able to pass.
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57
Q

What are the tra genes?

A

The tra genes found on the conjugative plasmid encode all the proteins necessary to make the the relaxasome, which is the structure through which the DNA passes.

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58
Q

In conjugation what is the process used to transfer DNA?

A

DNA is transferred in a process known as rolling circle, with the DNA cut at a site close to the original of replication of the plasmid. The DNA is then drawn through the relaxasome, with DNA polymerase activity required in both cells to generate a second strand of plasmid DNA. Both cells now contain the plasmid and are capable of producing an F pilus and transferring their plasmids to other strains.

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59
Q

What is Hfr transfer in the rolling circle process?

A

In some cases the plasmid may have regions that are homologous with the bacterial chromosome allowing direct integration of the plasmid through recombination. In this situation the integrated DNA can remain in the chromosome or can excise. Sometimes when they do excise, they do so imprecisely taking some adjacent bacterial chromosome DNA with them. The presence of this DNA means they are more likely to integrate at Higher frequency than normal conjugation. This is known as High frequency or Hfr transfer.

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60
Q

What is transduction?

A

Transduction, a process of genetic recombination in bacteria in which genes from a host cell (a bacterium) are incorporated into the genome of a bacterial virus (bacteriophage) and then carried to another host cell when the bacteriophage initiates another cycle of infection.

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61
Q

What are the two life cycles of bacteriophages?

A

They have 2 life cycles

  1. The lytic cycle in which the virus binds to a receptor on the surface of the bacteria and injects in its genome. Like mammalian viruses, It then hijacks the cellular machinery of the bacteria to produce multiple copies of its genome that are packaging inside structural proteins also made by the bacteria. It then escapes from its host by lysis of its bacteria membrane
  2. Bacteriophage are also also to undergo lysogeny, which occurs when the injected phage genome integrates into the host chromosome. In this form, it is replicated as part of the natural lifeccyle of the bacteria and is transferred from mother to daughter.

However, if the bacteria becomes stressed or under threat, the intact phage can excise from the chromosome and reinitiate the lytic cycle that results in the production of intact and infectious phage.

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62
Q

How does generalised transduction accidentally occur in bacteriaphages sometimes?

A

Although the infection process, including the packing of the viral DNA into the structural heads of the phage is largely efficient, occasionally a piece of bacterial chromosomal is packaged into a phage head by mistake. These defective phage will be released from the bacteria during lysis.

However, as the structure of the virus is unchanged, the defective phages are able to bind to any susceptible bacteria and the DNA inside the head injected into the bacteria by this molecular syringe. Once inside the cell, the DNA may or may not integrate into the bacterial chromosome. This type of transduction is known as generalised transduction

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63
Q

What is specialised transduction?

A

In contrast specialised transduction is linked to the lysogenic lifestyle that follows the integration of phage DNA into the bacterial chromosome and follows imprecise excision form the bacterial chromosome, that means that some of the DNA adjucaent to the site of integration is also excised and packaged, These chimeric phage that carry both viral and host DNA can transfer these genes to a new host.

As a phage head can package up to 40kb of DNA, this offers a significant opportunity for DNA exchange

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64
Q

How can microbes acquire virulence?

A

The best example of how acquiring DNA using these mechanisms can enhance virulence can be demonstrated using E.coli.

E.Coli is considered as a commensal organism that lives in the gut.

However, some strans of E.coli have acquired a plasmid that encodes 2 toxins, that cause toxin mediated diarrhoeal disease in humans

Other strains have acquired a plasmid that encodes an adhesin that allows successful adhesion and mediates invasion into the epithelial tissues

Enterohemmorahgic E.coli has acquired both the capacity to intimately adhere to the gut surface through gene found on an integrative plasmid and produce a toxin that was acquired through phage transduction.

Similarly enteropathogenic strains cause damage and diarrhoeal disease through acquisition on mechanisms that allow increased adhesion by this organism

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65
Q

What is a pathogenicity island?

A

When large pieces if DNA are integrated they are known as pathogenicity islands and frequently encode structures such as the very elegant type 3 secretion injector that is important in the attachment of several medically important gut bacteria including Salmonella and Shidella.

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66
Q

What can be problematic for the implementation of DNA into bacteria?

A
  • DNA introduced may not persist
  • Restriction systems, such as phage encoded CrispR/Cas recognise foreign DNA
  • Endonuclease activity
  • If persist may integrate and multiply within the chromosome
  • Many toxins – cholera toxin, diphtheria toxin (phage encoded)
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67
Q

What are the targets of antibiotics?

A
  1. Inhibition of bacterial cell wall synthesis or activation of enzymes that disrupt bacterial cell walls
  2. Inhibition of protein synthesis by bacteria or production of abnormal bacterial proteins. These drugs bind irreversibly to bacterial ribosomes, intracellular structures that synthesize proteins. When antimicrobial drugs are bound to the ribosomes, bacteria cannot synthesize the proteins necessary for cell walls and other structures.
  3. Disruption of microbial cell membranes
  4. Inhibition of organism reproduction by interfering with nucleic acid synthesis
  5. Inhibition of cell metabolism and growth
68
Q

What are the clinical uses of antibiotics?

A

Clinical usage:

  • Treatment of infections: wounds, burns, abcesses
  • Vital for recovery post surgery
  • Required for chemotherapy patients
  • Chronic diseases, diabetes, end stage renal disease
  • Changed life expectancy
69
Q

Who discovered Streptomycin?

A

Selman Waksman discovered streptomycin - effective against M. tuberculosis. They won a Noble prize in 1952.

70
Q

What are causes of antibiotic resistance?

A
71
Q

Intrinsic resistance Vs. Acquired resistance

A

Intrinsic Resistance

Intrinsic resistance is when a bacterial species is naturally resistant to a certain antibiotic or family of antibiotics, without the need for mutation or gain of further genes. This means that these antibiotics can never be used to treat infections caused by that species of bacteria.

Acquired Resistance

Acquired resistance is said to occur when a particular microorganism obtains the ability to resist the activity of a particular antimicrobial agent to which it was previously susceptible.

72
Q

What are pseudomonas?

A

Pseudomonas infections are diseases caused by a bacterium from the genus Pseudomonas. The bacteria are found widely in the environment, such as in soil, water, and plants. They usually do not cause infections in healthy people. If an infection does occur in a healthy person, it is generally mild.

73
Q

What is Triclosan and what is it effective against?

A

Triclosan is a chlorinated organic compound with antibacterial and antifungal properties, widely used in household and medical products. Triclosan is broadly effective against Gram +ve and many Gram –ves but does not inhibit Pseudomonas.

74
Q

What is the difference between gram posistive and gram negative bacteria?

A

Gram positive bacteria have a thick peptidoglycan layer and no outer lipid membrane whilst Gram negative bacteria have a thin peptidoglycan layer and have an outer lipid membrane.

75
Q

Why are pseudomonas bacteria insensitive to triclosan?

A

Pseudomonas carry a gene that makes a protein which is insensitive to the antibiotic.

76
Q

Why are gram negative bacteria more likely to be resistant to antibiotics?

A

More generally many Gram negatives are resistant to antibiotics because the antibiotics cannot cross the bacterial membrane.

77
Q

What are problems associated with triclosan?

A
78
Q

What are some of the mechanisms bacteria can use to acquire resistance?

A

Microbes can also acquire resistance by using one of several mechanisms:

  • Minimise entry of the antibiotic
  • Modify the target of the antibiotic (mutate)
  • Inactivate the antibiotic itself by hydrolysis.
79
Q

Why do pharma companies focus more time into chronic conditions treatments as opposed to antibiotics?

A
  • Pharma companies are profit making organisations
  • Antibiotics have always been very cheap, effective (single course) and therefore not good at generating revenues
  • Contrast to chronic conditions: arthritis, blood pressure or long terms conditions like HIV
80
Q

How does antibiotic resistance happen?

A
  • Bacteria susceptible to an antibiotic
  • Mutation of the target gives a target with reduced affinity
  • Modification of the target by addition of a chemical group can prevent the antibiotic binding

Natural selection occurs when an antibiotic is introduced onto a large population. The bacterial genomes are subject to variation (mutation) for example when they acquire additional genes from other species via plasmids, phages, recombination.

81
Q

Where are the sites for degradation of penicillins and cephaloporins?

A

Sites of b-lactam antibiotics

  1. b-lactamase
  2. Acylase
  3. Esterase
82
Q

What are potential solutions for the issue of antibiotic resistance?

A

According to the O’Neill report:

  1. Reduce demand- several steps to this.
  2. Increase the number of effective antimicrobial drugs to defeat infections that have become resistant to existing medicines.
  3. A global coalition for action on antimicrobial resistance (AMR)
83
Q

What are the steps to reducing the demand for antibiotics?

A
  1. A massive global public awareness campaign
  2. Improve hygiene and prevent the spread of infection
  3. Reduce unnecessary use of antimicrobials in agriculture
  4. Improve global surveillance of drug resistance
  5. Promote new, rapid diagnostics to cut unnecessary use of antibiotics
  6. Promote development and use of vaccines and alternatives
  7. Improve the numbers, pay and recognition of people working in infectious disease
84
Q

What is a Microbiota?

A

The microbiota is a collective term for the micro-organisms that live in or on the human body. Specific clusters of microbiota are found on the skin or in the gastrointestinal tract, mouth, vagina and eyes.

  • There are tens of trillions of microbes 1014
  • They mostly live in the colon.
  • However there are some in the lungs, skin, teeth and everywhere else

80% of the bacteria are unculturable. We know there are a huge number, however we cannot grow them in the lab environment.

85
Q

How is technology allowing us to culture more bacteria in the microbiota?

A

many bacteria are sgtill not culturable, so we analyse them using new tech such as:

  • 16S sequencing
  • Whole Genome Sequencing + Metagenetics
  • And computation
86
Q

What are the steps to 16S sequencing of bacteria?

A
87
Q

What are the steps to Whole Genome Sequencing

A
88
Q

16S vs WGS

A

16S rRNA Gene Sequencing. The 16S ribosomal RNA gene codes for the RNA component of the 30S subunit of the bacterial ribosome. It is widely present in all bacterial species. Different bacterial species have one to multiple copies of the 16S rRNA gene.

Whole-genome sequencing (WGS) is a comprehensive method for analyzing entire genomes. Genomic information has been instrumental in identifying inherited disorders, characterizing the mutations that drive cancer progression, and tracking disease outbreaks.

Diagram shows further differences

89
Q

Diagram displaying the type of bacteria in your microbiota?

A
90
Q

How do bacterial communities differ?

A

Bacterial communities differ at different sites

91
Q

What is the most common genus in the colon?

A

Bacteriodes is the most common genus in the colon.

92
Q

How does the Microbiota aid human health?

A
93
Q

Give a brief overview of the short chain fatty acids.

A
  • Include butyrate (most abundant), acetate and propinate
  • Produced by bacterial fermentation of dietary fibre, mostly in the colon.
  • The main energy source for epithelial cells
  • Butyrate has anti-inflammatory effect on intestinal epithelial cells
  • Involved in differentiation of colonic Tregs and ameliorates colitis in mice.
94
Q

What are the roles of Short Chain fatty Acids?

A

They are produced by micribiota in the colon however they do not just act locally, they can also be found in the blood and influence immune cells in the bone marrow and prevent them from being so activatory. They also prevent allergic reactions in the lungs.

95
Q

Give a brief overview of Inflammatory Bowel Disease

A

There are two types:

  1. Ulcerative Colitis
  2. Crohn’s disease

Essentially they inflame the bowels and is caused by three things:

  1. Host genetic factors has a weak causal explanatory factor as some people have genes which do not dictate the development of this disease but end up getting it.
  2. Innate and adaptive immune response - The immue system responds to the intestinal microbiota and ends up damaging our own tissues as a result.
    3.
96
Q

What drives the inflammation of the bowels in IBD?

A

The infiltration of bacteria out of the intestinal wall creates the immune response of inflammation

Lesions of white blood cells are generated by immune system against the microbes.

Abnormal microbial colonisation might contribute to disease.

97
Q

Give an overview of initial response to infection

A
  • Activation of local innate immune cells
  • Increased permeability of local blood vessel
  • Migration into tissues of more immune cells and plasma proteins
98
Q

What makes microbes look different from host cells?

A

PAMPs: Pathogen Associated Molecular Patterns

Key point is that the forms of these molecules expressed by pathogens are distinct from those expressed by mammalian host cells.

99
Q

What is the Danger Model of the immune system?

A

The immune responses triggered by damage or danger rather than “non-self” antigens.

The danger model is a theory of how the immune system works. It is based on the idea that the immune system does not distinguish between self and non-self, but rather between things that might cause damage and things that will not.

100
Q

What are Damage Associated Molecular Patterns (DAMPS)?

A
  • The molecules in the diagram are normally tightly sequestered in intracellular compartments of the cell.
  • When they are released from cells as a consequence of death or trauma, they act as signals of tissue damage.
101
Q

How are pathogens sensed in the immune system?

A
102
Q

What are the roles of the leukocytes and tissue cells?

A

Leukocytes and tissue cells detect and control pathogens at infection sites.

103
Q

Numerous host soluble and cell surface molecules help sense pathogens…

A

Numerous host soluble and cell surface molecules help sense pathogens. Pathogens that can evade these molecules are better at causing damage.

104
Q

What is complement?

A

Complement: series of plasma proteins that act in an enzymatic cascade

105
Q

What are the multiple ways complement controls pathogens?

A
106
Q

How do Host cells and some pathogens evade complement?

A

Key for acronyms in diagram:

  • Smallpox inhibitor of complement enzymes (SPICE)
  • CRIT: Complement C2 receptor inhibitor trispanning
107
Q

What recognisge Pathogen associated molecular proteins?

A

Pattern Recognition Receptors

108
Q

What are the various Pattern Recognition receptors?

A
109
Q

Why are there so many different pattern recognition receptors?

A

There are so many due to the rapid evolution of pathogens which would give redundancy in detection. The various PRRs make it harder for the pathogens to escape througj mutation.

110
Q

Diagram of the different places PRRs are found in the cell

A

The location of different PRR reflects their role in responding to different types of infection/threat.

111
Q

What cells have PRRs?

A

PRR can be found on leukocytes and tissue cells.

112
Q

What are the consequences of when PRR senses a microbe?

A
113
Q

What links pathogen activation of PRR to altered immune responses?

A
  1. TLR activation drives an intracellular pathway that activates NF-κB
  2. NF-κB translocates into the nucleus and drives altered gene transcription
  3. This allows the cell to warn the immune system about the infection
114
Q

How can bacteria fight against immune system?

A

Bacteria can reduce NF-κB activation and inhibit the immune response.

E.coli virulence factors degrade NF-κB

Shigella enzyme cause degradation of an activator of NF-κB

Thus the warning signal to the immune system is reduced.

115
Q

How does Influenza inhibit intracellular activation of PRRs?

A
116
Q

What is innate and Adaptive Immunity?

A
  • Innate immunity: always present; ready to attack
  • Adaptive immunity: stimulated by exposure to microbe; more potent
117
Q

What are the two types of adaptive immunity?

A

Humoral

  • Antibody mediated ‘extracellular attack’
  • Antibody from B cells
  • B cells mature in the bone marrow
    • In chickens the B cells mature in the Bursa of Fabricius

Cell Mediated

  • Intracellular attack
  • Due to T cells
  • T cells mature in the thymus
118
Q

How does the adaptive immune system respond to different microbes?

A

Different types of immune responses are mediated by different classes of lymphocytes and defend against different types of microbes

119
Q

Give a brief overview of Clonal Selection Theory

A
  1. Generation of clonal diversity in primary lymphoid organ - bone marrow.
  2. ‘Education’ to remove self reactivity in primary lymphoid organs - bone marrow and thymus
  3. Recirculation to peripheral secondary lymphoid organs – spleen and lymph nodes
  4. Clonal selection by antigen in secondary lymphoid organs
120
Q

What are the postulates of the clonal selection hypothesis?

A
121
Q

What are the phases of adaptive immune response?

A
  • Need for proliferation and differentiation results in delay
    • (typically 4-7 days) in effective adaptive immunity
122
Q

Give a brief overview of Cell Mediated Immunity

A
  • Mediated by T cells
  • Several components
  • Helper T cells – the managers of the immunological football team
    • Help B cells
    • Help cytotoxic T cells
    • Direct innate responses
  • Cytotoxic T cells
123
Q

Give a brief overview of the T cells

A
  • T lymphocytes mature in the thymus
  • T cell receptor complex on surface, part of which (CD3) identifies these cells
  • Further subdivided by expression of one of two surface molecules, CD4 or CD8
124
Q

What are the two types of T cells?

A
  • CD4 - Th –T helper
    • Recognise antigen presented in MHC II on the surface of antigen presenting cells and ‘help’ them
  • CD8 - Tc – Cytotoxic T cells CTL
    • Recognise antigen presented in MHC I on many cell types and can be induced to kill
125
Q

What are the links between differing aspects of immunity?

A
  • The link between innate and adaptive immunity is antigen-presenting cells (APCs) such as macrophages and dendritic cells
  • The link between humoral and cell mediated immunity is antigen presentation by B cells
  • Antigen is presented in the context of MHC (major histocompatibility complex)
126
Q

What do T cells need to activate?

A

T cell activation requires both T cell receptor (TCR) and CD3 binding to major histocompatibility complex (MHC) and co-stimulatory molecules, as with CD28 binding to CD80 (B7-1) or CD86 (B7-2).

  • Antigen presented in the context of MHC
  • Surface molecule ‘costimulation’
  • Soluble molecules - cytokines
127
Q

What are the two types of MHC Antigens (HLA)?

A
128
Q

How do the Helper T lymphocytes actually help?

A
  • “Help” the antigen-driven maturation of B and T cells
  • Facilitate and magnify the interaction between APCs and immunocompetent lymphocytes

Steps

  1. Th interacts through antigen-specific and antigen-independent mechanisms
  2. Undergoes differentiation
  3. Mature Th interacts with plasma or T-effector cells
  • There are different types of Th cell
    • Th cell subsets!
129
Q

Why do we need Th cell subsets?

A
130
Q

What are the three distinct sognals the Th cell needs to activate?

A
131
Q

Diagram of Dendritic Cell recieving cues from invading microbes

A
132
Q

What do Th1 cells protect against?

A
133
Q

What chronic inflammatory conditions are Th1 cells involved in and how do they contribute to the problem?

A

Coeliac Disease

  • Immune response to gluten proteins; T cells activate macrophages in the gut leading to inflammation.

Rheumatoid Arthritis

  • T cells in joints activate macrophages sustaining inflammation.

Inflammatory Bowel Disease

  • Immune system attacks components of the gut; T cell activation of macrophages plays central role in tissue damage.

Multiple Sclerosis/Experimental Autoimmune Encephalomyelitis (EAE)

  • Immune response against central nervous system
134
Q

What are Th2 cells essential to controlling?

A

Th2 cells are essential to control helminth infections

  • Collagen Production for wound repair and encapsulation of parasite egg
    • Note: Failure to wall of egg and its toxins leads to excess Th1 inflammation that causes death.
  • IL-5 induced eosinophilia: release of cytotoxic cationic proteins that damage parasite
  • IL-4 and IL-13 act on macrophages: involved in tissue repair and angiogenesis
  • IL-13 promotes mucus production – response to injury and promotes egg/worm expulsion
  • Mast cell degranulation: release of many mediators to enhance parasite expulsion
  • Parasite specific IgE
135
Q

How do Th2 cells cause allergy and asthma?

A
  • Collagen/Fibrosis driven by IL-13 e.g. in airways in asthma
  • IL-5 induced eosinophilia: release of cytotoxic cationic proteins that cause tissue damage
  • IL-4 and IL-13 act on macrophages: These cells are found in asthma/allergy models but role is unclear
  • Mast cell degranulation: release many mediators that cause smooth muscle constriction, vascular permeability e.g. in asthma and allergic dermatitis
    • Mast cell mediators: of cytokines, chemokines, histamine, heparin, serotonin, proteases
      *
136
Q

What are the 5 types of antibody?

A

IgM is usually seen first in the immune response.

It has a pentameric shape because it has a low affinity so putting 5 chains together would increase the affinity and also makes it better at glutanating pathogen.

With help from t cells, the b cells are able to make the other isotypes.

137
Q

How do T cells help B cells?

A

B cells are helped by helper T cells.

B cell presents antigen in context of MHC II

B cell presents peptide of antigen and is put in groove of MHC II

Now the T cell can recognise the peptide from the antigen and can respond in the appropriate way.

138
Q

How do t cells and b cells interact?

A
  • Activated T cells migrate towards follicles where the B cells are found.
  • Activated B cells migrate to the paracortex where the T cells are generally found.
  • These two sites are largely where these two immunoglobins interact.
  • They meet at the edge of the follicle. Their interaction gives rise to B cells returning to the follicle and undergo rapid proliferation and form a germinal centre.
  • Here, the affinity maturation of memory B cells is developed. Assisted by T cells.
  • Leads to long lived high affinity memory cells.
    *
139
Q

What is a follicle?

A

Lymphoid follicles are small masses of tissues that contain aggregations of inflammatory cells, mainly B cells with some T cells and dendritic cells. It is also a marker of germinal center origin of T cells.

140
Q

What are T follicular helper cells?

A

Follicular helper T (Tfh) cells are specialized providers of T cell help to B cells, and are essential for germinal center formation, affinity maturation, and the development of most high affinity antibodies and memory B cells.

On their surface they have a unique collection of effector molecules. Some are costimulatory molecules: ICOS, CD40L and some are associated with stabalising the interaction between the t cell and the b cell like the SLAM family (signalling lymphocyte activation) e.g. CD84

These T cells are very good at moving towards B cells in the follicle and the germinal centre.

141
Q

What are the important molecules in T-B cell interactions?

A

Soluble cytokines mediate a range of effects including:

  • Preventing death
    • IL-4
  • Promoting proliferation
    • IL-2, IL-4
  • Aiding maturation and differentiation
    • IL-5, IL-6, IL-21, TGFβ
  • Enhancing processing and presentation
    • IL-4 can increase MHC class II expression
  • Promoting isotype switching
    • IL-4 - IgG1, IgE, IFNγ - IgG2a, TGFβ - IgA
142
Q

What is the Germinal Centre?

A
  • First described in 1884 (Walther Flemming).
  • Saw sites of large lymphocytes undergoing division in follicles of secondary lymphoid tissue.
  • Now known that this site (GC) is associated with T-dependent antibody responses.
  • Main site where high-affinity antibody-secreting plasma and memory B cells are generated.
143
Q

Diagram of Germinal Centre

A
144
Q

What does the Germinal Centre allow the immune response to do?

A
  • Allows fot the average affintiy of serum antibody to increase over time.
    • This is termed affinity maturation
    • This is due to somatic hypermaturation (SHM) of the antibody variable region
  • SHM occurs in Germinal Centre B cells
  • Mutations cluster in regions of antibody that bind to antigen.
  • B cells in an individual GC are usually clonally related.
  • GC are specialised site supporting events required for affinity maturation
145
Q

What is the role of a Follicular Dendritic Cell and explain how there is Darwinian selection pressure in the Germinal Centre?

A

Follicular dendritic cells (FDCs) are non-haematopoietic cells that are present in the B cell follicles of secondary lymphoid tissues. They carry intact antigens that are held on their surface for long periods in antigen–antibody complexes and are crucial for the selection of B cells that produce high-affinity antibodies.

146
Q

Germinal Centre supports affinity maturation through the processes of…

A
  • Clonal proliferation
  • Somatic hypermutation (SHM)
  • Affinity maturation
  • Newly mutated receptors are…
    • Selected (‘checked for best fit’) against antigen held on follicular dendritic cells (FDC)
    • Require continued T cell help to survive the selection process
147
Q

Give a summary of Germinal Centre Responses

A
  • proliferating GC B cells accumulate in the dark zone (centroblasts)
    • SHM preferentially occurs here
  • now migrate to light zone (centrocytes)
    • moves among FDC network
    • higher affinity BCRs able to bind Ag on FDC
    • now process and present Ag on MHCII
    • presentation of pMHCII to cognate GC Tfh elicits help
    • higher affinity BCR - better Ag capture - more Ag presentation - better able to compete for limiting T cell help - Darwinian selection!
    • Tfh signals also important for memory
148
Q

Why is the interaction between t and b cells so important?

A
  • T-B cell interaction critical for generation of effective, long-lived Ab response.
  • Dysregulation of this interaction manifests as various immune diseases and disorders.
    • HIGM - hyper IgM syndrome - CD40/L
    • Over abundance of Tfh in murine models (e.g. sanroque mice) and patients with autoimmune disorders, SLE, rheumatoid arthritis, Sjogren’s syndrome etc
    • CD40L, ICOS mutations producing reduced Tfh in humans and mice result in severe defects in protective humoral immunity.
  • Take advantage of the interaction for rational vaccine design
    • conjugate vaccine (poor antigen conjugated to carrier protein) e.g. Haemophilus influenzae type b (Hib): polysaccharide
149
Q

What is a Vaccination?

A

A means of producing immunity agaisnt pathogens, such as viruses and bacteria, by the introduction of live, killed or altered antigens that stimulate the body to produce antibodies against more dangerous forms.

150
Q

Memory vs Naive B Lymphocytes

A
  • Long Lived
  • Increased frequency
  • Rapid proliferation
  • Produce more Ab
  • Produce higher affinity Ab
  • IgG & IgA have better effector function
151
Q

What is characteristic of the secondary Ab responses?

A

The secondary Ab response is faster

they have a different isotype (IGM to IGG)

The secondarry Ab response have a higher affinity.

152
Q

Why are secondary responses better?

A
  • The Germinal Centre reaction drives affinity maturation and class switching of Memory B cells and Long Lived Plasma Class
153
Q

How do most vaccines work?

A

Most vaccines work by inducing long lived plasma cells and plasma antibody responses.

154
Q

What is Virus Attenuation?

A
155
Q

What are Killed and subunit vaccines?

A

Killed vaccines

  • Usually use chemicals or heat
  • These kill the organism and render it completely uninfective
  • Killed organism can still induce immunity
    • e.g. whole cell pertussis vaccine

Subunit vaccines

  • Toxins are the pathogenic fragments of bacteria
  • Antibodies to toxins can protect from infection
  • Chemically inactivated toxins are called toxoids
  • e.g. acellular pertussis vaccine
156
Q

What are Recombinant subunit vaccines?

A

Certain viruses/bacteria/parasites are very hard to grow

  • e.g. they grow in host cells that are not readily cultivated.
157
Q

GIve a brief overview of Live Attenuated Influenza Viruses.

A
  • Effective in children over 2 years
  • Well-tolerated in children and adults
  • Ease of administration
  • Known limitations:
    • ineffective in over 50s
    • issues with safety in children with asthma/wheezing
    • not for immunocompromised
158
Q

What are some clinical vaccines?

A
  1. Attenuated - find or make an attenuated pathogen using culture methods
  2. Killed - Kill the pathogen
  3. Subunit - kill the pathogen and isolate its protective antigens (toxoids)
  4. Recombinant Subunit - clone genes for protective antigen, express in (e.g. yeast). Isolate the antigen
  5. Live Recombinant - clone genes for protective antigen, express in vaccine vector
159
Q

What are some experimental vaccine methods?

A
  1. Genetically attenuated - knock out virulence genes with recombinant tech.
  2. DNA vaccine - clone genes into expression vector. Inject construct.
160
Q

Diagram of the Drug Development Process

A
161
Q

What are NSAIDs?

A

Non-steroidal anti-inflammatory drugs (NSAIDs) are medicines that are widely used to relieve pain, reduce inflammation, and bring down a high temperature.

They’re often used to relieve symptoms of headaches, painful periods, sprains and strains, colds and flu, arthritis, and other causes of long-term pain.

162
Q

What are 5 signs of inflammation?

A
  1. Increased blood flow to the site fo inflammation
  2. Increased temperature
  3. Redness
  4. Swelling
  5. Pain
163
Q

What are the three properties of NSAIDs?

A

They are:

  • Analgesic
  • Antipyretic
  • Anti-inflammatory at high doses.
164
Q

Lipid Mediator Mechanism Pathway

A
165
Q

What causes a fever and how does Aspirin work to counteract it?

A

The release of endogenous pyrogens such as interleukin-1, released from leucocytes which act directly on the thermoregulatory centers in the hypothalamus thus increasing body temperature.

This is associated with an increase in brain prostaglandin (PG)-induced gonadotropin release.

Aspirin prevents the temperature rising effects of interleukin-1 by preventing the increase in brain PGs.

166
Q

What are some common adverse effects of NSAIDs?

A
  • platelet dysfunction
  • Gastritis and peptic ulceration with bleeding
  • Acute renal failure in susceptible
  • sodium + water retention and edema
  • prolongation of gestation and inhibition of labour
  • hypersensitivity