microbes and the immune system Flashcards
what is a symbiotic relationship?
a close, prolonged association between two or more different biological species.
symbiotic relationships involve the association of 2 or more partners.
what are some symbiotic relationships?
commensalism
mutualism
parasitism
commensals
opportunistic pathogens
primary pathogens
what are commensals?
those type of microbes that reside on either surface of the body or at mucosa without harming human health
what are pathogens?
Pathogens are the microscopic biological organisms capable of causing diseases. These mainly include bacteria, viruses, fungi, protozoa, helminths, and worms
define commensalism
a relationship between individuals of two species in which one species obtains food or other benefits from the other without either harming or benefiting the latter.
one organism benefits while the other remains unchanged.
define mutualism
a type of symbiotic relationship where all species involved benefit from their interactions.
may rely on each other for survival.
define parasitism
A parasitic relationship is one in which one organism, the parasite, lives off of another organism, the host, harming it and possibly causing death.
one species benefits at the expense of the other.
> parasitic microbe live or multiple within/on the host, causing damage in the process
opportunistic pathogens
infections occurring due to bacteria, fungi, viruses, or parasites that normally do not cause a disease, but become pathogenic when the body’s defence system is impaired
what is virulence?
an ability of an organism to infect the host and cause a disease.
what groups are involved in the human-microbe relationship?
viruses
bacteria
fungi
parasites
archaea
> microbial population exceeds us in terms of abundance and diversity
a lot remains unknown about these relationship specifically in relation to health and disease
in what form are microbes rarely found?
in isolation or pure culture
what is the microbiome?
the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment.
what are examples of a mutualist relationship?
> colonic bacteria provided with a niche in the host
organisms synthesise vitamin K and folate, metabolised by host
ruminococcis spp can be found in high numbers in the git and involved in cellulose breakdown.
> mycorrhizae
fungal mycelium associated with plant roots
fungi attach to the roots and allow root extension
in exchange, the plant provides sugars to the fungi
discuss mycorrhizae and its advantages to plants?
> fungal mycelium associated with plant roots
fungi attach to the roots and allow root extension
in exchange, the plant provides sugars to the fungi
over 80% of plants are associated with mycorrhizae highlighting how important they are, there are other advantages to plants;
- obtain immobilised nutrients e.g. phosphate, iron
- speed up decomposition of organic matter
- increased resistance to disease
- remove heavy metal toxicity
give examples of a commensalism relationship
> bateroides (and other anaerobes) benifit from escherichia coli
> staphylococcus epidermidis utilises dead skin cells without causing harm
> gut microbes e.g. bifidobacterium, bacteroides to breakdown/generate metabolites
what are the benefits of low gut inflammation and dietary fibre intake?
low gut inflammation; lower risk of some infections and increases antioxidant production
dietary fibre intake; increases SCFA production and improves lipid metabolism
what are SCFA?
Short-chain fatty acids, also known as SCFAs, are compounds produced by our good gut microbes.
what are examples of opportunistic pathogens?
(do not normally cause disease)
> candida albicans (candidiasis)
pseudomonas aeruginosa (burn-related infection)
toxoplasma gondii (toxoplasmosis)
herpes simplex virus (cold sores)
define zoonosis
an infectious disease transmitted to humans from animals
what is the germ theory?
specific microscopic organisms are the cause of specific diseases.
what are Koch’s 4 postulates?
- the suspected pathogen must be absent in all healthy individuals but present in all diseased hosts
- the pathogen must be isolated and grown in pure culture from all diseased patients
- the pathogen must cause the same disease if used to inoculate the healthy host
- the same organism must be re-isolated from the inoculated diseased host
what enables pathogen identification
isolation of genetic material enables pathogen identification
how do genes and knockouts correlate to disease?
specific genes correlate with disease
knockouts linked with disease reduction
*knockout= the use of genetic engineering to inactivate or remove one or more specific genes from an organism.
what is pathogenicity?
the ability to cause disease
pathogenicity vs virulence
pathogenicity; the ability to cause disease
virulence; the degree of pathogenicity of an organism e.g. infectivity/intensity
phenotypic switching
virulence factor; reflects a mechanism of adaptation to the changing environment by spontaneously generation of several phenotypes
-increased adherence
-biofilm development
-invasion
what are the difficulties with identifying microbes?
classical microbiology
restricts growth; does not cater for organisms found in all environments, lab environments is far removed from reality
time consuming
some organisms can take weeks to grow!
only 1% of microbial population is known
what percentage of the microbial population is known?
1%
how do we identify microbes?
- extract all DNA from the population and digested into smaller fragments
- cloned in to plasmid vectors before sequencing
- data analysis to identify organisms
what are the four ‘omics’?
genomic (DNA); what genes are present? organism identification.
transcriptomics (RNA); which parts of the DNA have been expressed to allow protein production?
proteomics (protein); what proteins are being produced and to what level?
metabolomics (metabolite); all metabolites produced by a population living together.
discuss microarray technology
> insert single stranded DNA in to each square of the grid; target gene
extract mRNA from samples and synthesise cDNA
combine the samples together and add to the microarray
measure fluorescence and determine what genes are expressed within each population
what is a microbiome?
large and mixed population of microorganisms coexisting together under many circumstances.
what are the molecular differences of DNA and RNA?
RNA;
uses uracil, typically single stranded, nuclear and cytoplasmic, OH at 2’ ribose position
DNA;
uses thymine, typically double stranded, mainly nuclear, H at 2’ ribose position
what are the molecular implications of RNA and DNA?
DNA is larger and more intrinsically stable
RNA is smaller and less intrinsically stable
discuss viral heterogenicity
> dependent on mutation rate
viral fitness will drive selection
most mutations are neutral with no selection pressure
negative mutations are typically lost
positive mutations are selected
positive selection can change
mutation rate and positive selection through viral fitness are drivers of antigenic variation
discuss the evolution of the SARS-CoV-2 spike
N439K> early mutation enhanced the binding affinity for the ACE2 receptor and reduces the neutralising activity of some mAbs
Y452F- associated with increased ACE2-binding affinity
Δ69-70 was predicted to alter the conformation of an exposed NTD loop and was reported to be associated with increased infectivity
Vaccination rises and ~90% of the plasma or serum neutralising antibody activity targets the spike receptor- binding domain (RBD)
E484K was identified as an escape mutation that emerges during exposure to mAbs C121 and C144. Multiple iterations: E484A, E484D, E484G and E484K.
S477G conferred resistance to two of the four sera tested. Multiple iterations: S477G, S477N and S477R
11-residue insertion in the NTD N5 loop between Y248 and L249, completely abolishing neutralization
Escape mutations emerging in viruses exposed to convalescent plasma were identified in both the NTD (ΔF140, N148S, K150R, K150E, K150T, K150Q and S151P) and the RBD (K444R, K444N, K444Q, V445E and E484K)
what are segmented viruses?
Segmented viruses have a genome whose encoded genes are divided across two or more molecules of RNA/DNA. All of them should be incorporated into the viral particle for a virus to be infective. E.g. Influenza virus has a genome with 8 segments; Rift Valley fever virus has 3 segments.
what is antigenic shift?
Antigenic shift: major alteration in antigen sequence by a process of genome reassortment (segmented virus) or inter strain recombination.
what is recombination?
Recombination allows major alterations acquisition of new or functionally altered proteins through exchange of genetic material between viruses or with the host. If can lead to antigenic shift.
discuss RNA vs DNA viruses
- RNA viruses have faster evolution capacity > rapid adaption
- RNA viruses have plastic genomes to increase coding capacity > segmentation, polyproteins splicing
- dsDNA viruses have greater storage capacity>broader protein arsenal
- dsDNA viruses are more stable and difficult to detect in the nucleus>persistent infections through latency
discuss the absence of antigens-latency
Long-lived nature of DNA allows long-lasting infections
Lack of immune response to infected cells in latent state
Impossibility to distinguish ectopic DNA from endogenous DNA in the nucleus
Important clinical consequences: recurrent infections
what drives bacterial genetic change?
mutation
horizontal gene transfer
genetic recombination
selective pressure
comment on bacterial organisms adapting to change?
organisms adapt rapidly to changing circumstances and pressures.
in nature, all DNA is subject to change. Single nucleotide polymorphisms (SNPs).
Majority of changes are lethal BUT if a mutation is advantageous, and the conditions offer a selection advantage the organism proliferates rapidly.
mutated clone is dominant
what are multiplication rates in bacteria?
logarithmic growth 20-25min, double population.
8h; single clone replicated 10^8 colonies.
evolution: RAPID
*humans; 10-12 years puberty, 9 months gestation, 1-2 offspring
discuss bacterial mutation.
> alter efficacy of antibiotic by alteration of target size
alter receptor recognition (of tissue)
alter recognition by the host (immunity)
what are specific virulence associated traits?
- toxins; damage the host at the site of bacterial infection or distanced from the site of infections
- adhesins; virulence factors that allow bacteria to attach to host cells
virulence= severity of harmfulness
bacterial toxins
(virulence factor) damage the host at the site of bacterial infection or distanced from the site of infections
bacterial adhesins
virulence factors that allow bacteria to attach to host cells
what does horizontal gene transfer facilitate for bacteria?
allows for bacteria to acquire new genetic traits. (rapid growth ensures spread within population)
what allows for a new genetic trait to be spread within a bacterial population?
rapid growth of bacteria ensures spread within population
three types of horizontal gene transfer
- natural transformation; uptake and incorporation of naked DNA
- conjugation; genetic exchange between bacteria
- transduction; exchange occurs as consequence of phage predation
what is natural transformation?
uptake and incorporation of naked DNA
what is conjugation?
genetic exchange between bacteria
what is transduction?
exchange occurs as consequence of phage predation
discuss transformation in terms of horizontal gene transfer in bacteria.
occurs in bacteria that are naturally ‘competent’
occurs when ssDNA is released when bacteria die and lyse; uptake of DNA and incorporation into genome of ‘competent’ bacteria through homologous recombination.
Only a few bacteria are naturally competent. Probably evolved as a mechanism of natural repair within the community.
Some become competent in response to quorum compounds released by bacteria- competency factors.
But if gene associated with antibiotic resistance- transformed bacteria will now be resistant.
in what type of bacteria does transformation occur (horizontal gene transfer)?
occurs in bacteria that are naturally ‘competent’
*Naturally competent bacteria actively pull DNA fragments from their environment into their cells.
what are naturally competent bacteria?
Naturally competent bacteria actively pull DNA fragments from their environment into their cells.
Only a few bacteria are naturally competent. Probably evolved as a mechanism of natural repair within the community.
Some become competent in response to quorum sensing compounds released by bacteria -competency factors.
what quorum sensing compounds (released by bacteria) do some bacteria respond to in order to become competent?
competency factors.
some bacteria become competent in response to quorum sensing compounds- released by bacteria (competency factors)
what is adaptive immunity?
which cells are part of the adaptive immune system?
how is the adaptive immune system activated?
what is immune memory?
what are adaptive immune cells? (examples)
cells that can respond specifically and in a tailored way
(e.g. viruses, bacteria, yeast and fungus, parasites)
- large diversity of pathogens which can infect hosts
what are the main cell types of the adaptive immune system? and what are the 2 classes?
- cellular adaptive immunity
- CD4 T cells
- Helper T cells
- CD8 T cells
- Killer T cells
- humoral adaptive immunity
- antibody producing cells
*these cells are grouped together as they have unique receptors that enables them to recognise antigens
B cells and T cells recognise different forms of antigen… true/false?
true
what do T cells recognise?
processed antigen presented on MHC molecules on the surface of antigen presenting cells
CD8 T cells see short peptides in MHC class I molecules
CD4 T cells see longer peptides in MHC class II molecules
what does the BCR bind to?
to native proteins/antigens
- antigens that cross-link surface BCR provide optimal B cell activation
- no accessory cells required
MHC
major histocompatibility complex (MHC), group of genes that code for proteins found on the surfaces of cells that help the immune system recognize foreign substances
B cells vs T cells
Your lymphocytes include T cells and B cells. Both types are part of your body’s defense.
B cells make proteins called antibodies to fight pathogens.
T cells protect you by destroying harmful pathogens and by sending signals that help control your immune system’s response to threats.
overview of T cell response
1.pathogens infect tissues
2. activates DCs move to lymphoid organs carrying the pathogen
3. DCs activate antigen specific T cells
4. T cells proliferate
5. T cells migrate out of the lymph node
6. T cells migrate to infected tissues to clear infection; some of these cells become memory T cells
*Dendritic cells (DCs) are a special type of leukocytes able to alert the immune system to the presence of infections. They play a central role in the initiation of both innate and adaptive immune responses
DCs
Dendritic cells (DCs) are a special type of leukocytes able to alert the immune system to the presence of infections. They play a central role in the initiation of both innate and adaptive immune responses
where does T and B cell activation take place?
In secondary lymphoid organs
*Paracortex or T cell zone: where DCs from the tissue meet naive CD4 and CD8 T cells.
Dendritic cells enter lymph nodes via afferent lymphatic vessels.
B cell follicles: where B cells are found and respond to antigen.
how to dendritic cells enter lymph nodes through?
via afferent lymphatic vessels
what happens at the paracortex/T cell zone (secondary lymphoid organs)?
where the DCs from the tissue meet naive CD4 and CD8 T cells
What happens at B cell follicles on secondary lymphoid organs?
B cells follicles: where B cells are found and respond to antigen.
what does T cell differentiation require?
requires continued activation and sustained differentiation signals
how many signals does T cell activation require?
3 signals.
- TCR - peptide MHC
- costimulation
- cytokine receptor; inflammatory cytokine
how do dendritic cells process antigen so that T cells can be activated?
- pattern recognition receptor (PRR) triggering enhances phagocytosis
- bacteria are digested inside endosomes
- MHC molecules inside endosomes meet pathogen containing endosomes
- MHC molecules containing peptides from pathogen are presented on the cell surface
- PRR triggering causes the DC to migrate from the tissue to the draining lymph node
- PRR triggering also causes the DC to express high levels of costimulatory molecules and make inflammatory cytokines
phagocytosis
phagocytosis, process by which certain living cells called phagocytes ingest or engulf other cells or particles. The phagocyte may be a free-living one-celled organism, such as an amoeba, or one of the body cells, such as a white blood cell.
what does triggering PRR cause?
pattern recognition receptor (PRR).
- triggering enhances phagocytosis
- causes the DC to migrate from the tissue to the draining lymph node
- Causes the DC to express high levels of costimulatory molecules and make inflammatory cytokines
what is clonal selection?
the selection of T cells with the right TCR (t-cell receptor). (can lead to clonal expansion).
*T cells with the right t-cell receptor are selected to respond
CD4 T helper subsets
T helper 1;
antiviral response, enhance function of innate immune cells, via cytokines (IFNy and TNF)
T helper 1;
enhance mucus response and wound healing via cytokines e.g. interleukin 4, IL-5
T helper 17;
activate neutrophils and production of antimicrobial molecules via cytokines (IL-17 and IL-22)
what does T helper 2 do? (CD4)
enhance mucus response and wound healing via cytokines.
e.g. Interleukin 4, IL-5
what does T helper 1 do? (CD4 helper cell)
anti-viral response.
enhance function of innate immune cells
via cytokines - IFNy and TNF
what does T helper 17 do? (CD4)
activate neutrophils and production of antimicrobial molecules via cytokines (IL-17 and IL-22)
what do CD8 ‘killer’ T cells do?
kill tumour cells
kill cells infected with viruses or intracellular bacteria
- release inflammatory cytokines; help other immune cells dispose of the infected cells
- release toxic granules that contain perforin to punch holes in the target cells and enzymes (granzymes) to trigger apoptosis in the target cell
B cell response
- pathogens infect tissues
- smaller antigen and pathogen products can drain into lymph nodes; dendritic cell can carry antigens and pathogens to the Lymph node and pass these onto B cells
- smaller antigens are often picked up by macrophages that then pass the antigen onto B cells
4a. some activated CD4 T cell move towards the B cell follicle
4b. activated B cells move towards the T cell zone; they present peptides from the pathogen on MHCII to the activated CD4 T cell; B cells undergo class switching
- the T and B cells move together to the B cell follicle that forms a Germinal centre; we call these CD4 T cells- T follicular helper cells
- B cells undergo rapid proliferation in the germinal centre
- B cells undergo somatic hypermutation- changing nucleotides in their B cell receptor
- B cells compete for antigen- those with the highest affinity win!
- these high affinity B cells present peptides from the antigen on MHCII to the follicular helper CD4 T cells leading to the formation of plasma cells and memory B cells
what is somatic hypermutation? what cells undergo this in the immune response?
B cells undergo somatic hypermutation; changing nucleotides in their B cell receptor
where to B cells undergo rapid proliferation during the B cell response?
germinal centre
what processes to BCR (B cells) undergo in the germinal centre?
- class switching
- somatic hypermutation
what does class switching lead to?
a range of differ types of antibody
what cells make antibodies?
plasma cells
give examples of different immunoglobulins (antibodies)
IgM: low affinity antibody, high avidity
IgG: most abundant in serum, activates the classical complement pathway
IgE: involved in allergy and anti-worm responses
IgA: found at mucosal sites
humoral immunity; give 3 ways in which antibodies protect the host
- neutralise pathogen;
antibody blocks the virus from binding to its receptor on cells, prevents infection - activate complement;
complement component C1q, is triggered- sets off the classical complement pathways. Including formation of C3a and C5a: increase inflammatory response and MAC formation. - enhance phagocytosis (opsonisation);
receptor for the Fc part of the Ab molecules helps macrophages and neutrophils phagocytose antigen
MAC
The complement membrane attack complex (MAC) is classically known as a cytolytic effector of innate and adaptive immunity that forms pores in the plasma membrane of pathogens or targeted cells, leading to osmolysis.
how does the immune response end?
Most T and B cells undergo apoptosis.
A few cell remain as memory cells.
These respond more quickly providing superior immune protection.
We take advantage of the functions of memory cells when we make vaccines.
T and B cells increase in number during the primary response. These cells then die during the contraction phase and some cells become memory T or B cells. Upon a secondary infection, these memory T or B cells respond quickly and reach a fast peak response that is higher than that in the primary response.
summarise adaptive immunity
> the adaptive immune cells are CD4 and CD8 T cells and B cells
they express specialised receptors that enable them to recognise specific antigens/proteins/peptides
T cells recognise processed antigens, B cells recognise native antigens
B and T cells are activated in secondary lymphoid organs (lymph nodes and spleen)
T cells protect the host by making cytokines and/or molecules that kill infected cells
B cell get help from CD4 T cells to differentiate into plasma cells that male antibodies that protect the host
memory B and T cells form following an infection and can provide enhanced protection to the same pathogen
what are the adaptive immune cells?
- CD4 T cells
- CD8 T cells
- B cells
what allows the adaptive immune cells to recognise specific antigens/proteins/peptides?
specialised receptors.
CD4 and CD8 T cells and B cells express specialised receptors that enable them to recognise specific antigens/proteins/peptides.
what type of antigens do T cells vs B cells recognise?
T cells; processed antigens
B cells; native antigens
where are B and T cells activated?
in secondary lymphoid organs
what are the secondary lymphoid organs?
lymph nodes and spleen
how do T cells protect the host?
by making cytokines and/or molecules that kill infected cells
how do B cells protect the host?
B cells get help from CD4 T cells to differentiate into plasma cells that make antibodies that protect the host
what provides enhanced protection to the same pathogen following an infection?
Memory B and T cells form following an infection and can provide enhanced protection to the same pathogen
what are the molecular differences of DNA and RNA?
RNA:
uses uracil; typically single stranded; nuclear and cytoplasmic; OH at 2’ ribose position
DNA:
uses thymine; typically double stranded; mainly nuclear; H at 2’ ribose position
what is antigenic drift?
a stochastic process in which antigens accumulate small mutations.
if any of these results advantageous, it will become predominant through selective pressure
RNA vs DNA viruses conclusions
RNA viruses have faster evolution capacity > rapid adaptation.
RNA viruses have plastic genomes to increase coding capacity>segmentation (polyproteins, splicing)
dsDNA viruses have greater storage capacity > broader protein arsenal.
dsDNA viruses are more stable and difficult to detect in the nucleus > persistent infections through latency.
summarise bacterial adaptation and survival
how natural mutation influences bacterial evolution
mechanisms associated with the acquisition of new genetic traits and described how this can influence virulence
discussed how bacteria sense and response to environmental change
all of which contribute to their amazing capacity to colonise out planet
what are 3 areas which microbes cover?
- microbes in the environment
- plastic degradation
- plankton in sea - microbes in technology
- polymerase chain reaction (PCR)
- restriction enzymes
- CRISPR-CAS
- vaccine - microbes in medicine
- cancer therapeutics
- antibiotics
what are the 4 life strategies and what they include?
photoautotroph:
- sunlight
- carbon dioxide
- plant, algae, cyanobacteria
phototheterotroph
- sunlight
- pre-formed organic compounds
- purple/green non-sulphur bacteria
chemoautotroph
- chemical oxidation
- carbon dioxide
- extremophiles
chemohetertoph
- chemical oxidsation
- pre-formed organic compounds
- humans, animals
temperatures of different types of microbes
psychrophile
- optimum growth <15 degrees celcius
- 90% ocean is <5 degrees celcius
- e.g. chlamydomonas nivalis, listeria monocytogenes
hyperthermophile
- survival at > 70 degrees celcius
- not only tolerate, but require for survival
- e.g. thermus aquaticus
Mesophile
- optimum growth at body temperature
- human pathogens
what are thermophiles?
spores used as a biological indicator, measuring sterilisation
temperature survival; how do organisms survive extreme temperatures?
CELL MEMBRANE
psychrophiles.
low temperature, membrane is too solid.
keep interactive and fluid
increase unsaturated fats.
hyperthermophiles.
high temperature membrane becoming too liquid.
to maintain integrity, solidity fats.
increase saturated fat content
good fat= liquid
bad fat= solid
what are cryoprotectants ?
cold/heat shock proteins.
- prevent proteins unfolding/denaturing
- maintain correct structure and activity
discuss the marine environment (neritic zone and oceanic zone)
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
ocean plankton
- oceanic planktons are responsible for the production of an estimated 50-80% of the oxygen on earth
- one specific bacterial species, known as Prochlorococcus, is responsible for producing one-fifth (20%) of the oxygen on our planet
- along with Synechococcus (another genus of cyanobacteria with Procholococcus) these cyanobacteria are responsible for approximately 50% of marine carbon fixation
- Prochlorococcus multiplies in a day
- adapts to changing environment
what is responsible for the production of 50-80% of the oxygen on Earth?
ocean plankton
what bacterial species is responsible for producing one-fifth (20%) of oxygen on our planet?
Prochlorococcus
what two cyanobacteria are responsible for approximately 50% of marine carbon fixation?
- synechococcus
- prochlorococcus
what is carbon fixation?
Carbon fixation is the process by which inorganic carbon from the atmosphere is assimilated into living organisms and converted into organic compounds. These compounds are used to store chemical energy. It is an essential process for the sustainability of life.
microbes in the environment
- plastic pollution increased since 1950
- plastic impact on the microbiome
(toxic effects, platforms for colonisation, provide carbon source)
what is biodegradation?
the physical or chemical change of a material by microorganisms (bacteria, fungi)
aerobic (plastic + oxygen -> CO2 + H2O + residual carbon)
anaerobic (plastic -> methane + CO2 + H2O + residual carbon)
microbes in technology (PCR)
application of DNA polymerase I from Thermus aquaticus (Taq polymerase) transformed the field of molecular biology.
(DNA template, forward primer, reverse primer, dNTP, buffer, polymerase)
denaturation (95 degrees)
annealing (55-60 degrees)
extending
elongation (72 degree)
microbes in technology (restriction enzyme)
restriction enzyme or restriction endonuclease
- proteins produced by bacteria that can cleave DNA specific sites
- bacteria uses restriction enzyme to defend from viral (bacteriophage) infection
*thousands of restriction enzymes have been identified from different bacteria.
identification of restriction enzymes has made the foundation for recombinant gene technology.
who received the nobel prize in physiology or medicine in 1978 for the discovery of restriction enzymes?
werner arber
hamilton smith
dan nathans
microbes in technology: CRISR-Cas9
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9).
Cas9 protein-nuclease
Pre-CRISPR RNA (pre-crRNA) needs to be converted to crRNA.
Trans encoded small RNA (tracrRNA)- coverts pre-crRNA to crRNA
Guide RNA (gRNA)- chimera of crRNA and tracrRNA
> feature of bacteria and archaea for acquired immunity
the first CRISPR sequence was discovered in E.coli K12 over 30 years ago
~36% of bacteria and ~75% of archaea are known to contain the CRISPR-Cas system
Prokaryotes containing CRISPRs are resistant to viruses or plasmids containing sequences matching the spacers
CRISPR-Cas9 can target any DNA sequence and generate cleavage
*emmanuelle charperntier and jennifer a. doudna receieved the nobel prize in chemistry 2020 for the discovery of the CRISPR-Cas9 system
microbes in technology (vaccine)
recombinant vaccine
- hepatitis B virus (HBV) infection causes chronic liver disease
- the current vaccines are produced by expressing the hepatitis B surface antigen (HBsAg) in yeast cells.
- recently, the recombinant vaccine for human papillomaviruses (HPVs) and SARS-Cov2 has also been produced
- ChAdO x 1 nCoV-19 vaccine (AZD1222)- used a replication-deficient chimpanzee adenoviral vector ChAdOx1 and introduced SARS-CoV-2 structural surface glycoprotein antigen (spike protein) gene
*if the patient later catches coronavirus, antibodies and T-cells are triggered to fight the virus
microbes in medicine
often associate microbes with disease; including their role in cancer
- cervical (and other) cancer - Human papillomavirus (HPV)
- gastric cancer - helicobacter pylori
- bladder cancer - schistosoma haematobium
organisms which produce antibiotics
actinomycetes
- filamentous gram +ve bacteria
- isolated from soil, marine water, insects, sand
- discovered by selman waksman and isolated streptomycin in 1943
- streptomyces griseus
- first curative agent of tuberculosis
describe methods that have revolutionised the microbiome field
describe how communities of micro-organisms colonise us
describe how microbial communities are important for out health
describe how the microbiota contribute to disease
microbiota
- tens of trillions of microbes (10^14)
- mostly in colon
- also in SI, lungs, skin, teeth, (everywhere)
- 80% non-culturable
what technology is used due to many bacteria still not being cultureable?
16S sequencing
whole genome sequencing + metagenomic
computation
what is 16S sequencing?
the 16S region of rRNA is conserved, with minor differences between groups of bacteria
16S vs WGS in terms of cost, computation, identity, functions
16S
cost= low
computation = OK
identity= OK
functions= inferred
WGS
cost= high
computation= intense
identity= better (where genome known)
functions= accurate
discuss bacterial communities
- colonise all body surfaces, especially mucosa
- communities differ at different sites
- bacteriodes is the most common genus in the colon
- communities are complex, stable and interdependent
- affected by many factors, especially diet
what is the most common bacterial genus in the colon?
bacteriodes
what three things describe bacterial communities?
- complex
- stable
- interdependent
what do does microbiota do for human health?
- metabolise complex carbs from plants -> short chain fatty acids
- synthesis of micronutrients- vit. B3, B5, B6, B12, biotin, tetrahydrofolate, vit. K
- limit pathogen colonisation
discuss short chain fatty acids
- include butyrate (most abundant), acetate and propionate
- produced by bacterial fermentation of dietary fibre, mostly in colon
- 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*
what are 3 short chain fatty acids and which is the most abundant?
- butyrate (most abundant)
- acetate
- propionate
what is the main energy source for epithelial cells?
short chain fatty acids
how are short chain fatty acids produced?
by bacterial fermentation of dietary fibre, mostly in colon
what effect does butyrate (short chain fatty acid) have on intestinal epithelial cells?
anti-inflammatory
inflammatory bowel disease
includes ulcerative colitis, crohn’s disease
interplay between
- host genetic factors
- innate and adaptive immune response
- the microbiota
-infiltration of bacteria drives inflammation
-lesions generated by immune response against microbes
-abnormal microbial colonisation might contribute to disease
*the intestinal immune system is specialised to deal with the food and bacteria in the gut
what can be said about the intestinal immune system which allows it to deal with food and bacteria in the gut?
the intestinal immune system is specialised to deal with the food and bacteria in the gut
In the adaptive immune response, activated B cells from germinal centres. What is the consequence of somatic hypermutation that takes place within the germinal centre?
B cell changes the affinity of the B cell receptor for its antigen??
Somatic hypermutation occurs in germinal centre B cells. This leads to changes in the gene sequence that codes for the B cell receptor (BCR). These mutations occur, in particular, in the complementary determining regions (CDRs) of the BCR that are the parts of the BCR that bind to the antigen. Somatic hypermutation alters the affinity of the BCR for the antigen. B cells with the highest affinity are most able to compete for the antigen found in the germinal centre. These high affinity B cells are most likely to get the help from CD4+T cells in the germinal centre that provides them with survival signals.
the intestinal microbiota can contribute to ill health. Changes in the microbiota are found in many disease, but there are few diseases for which microbial transplantation has been proven to be an effective therapy.
In which condition has faecal microbial transplantation been proven to be an effective therapy?
Clostridium difficile infection.
Faecal transplants are most likely to impact on disease that, like C. difficile infection, are restricted to the gut.
All organisms require an energy source and a carbon source for survival. What is a fungus called if it obtains energy from sunlight and uses carbon dioxide as its carbon source?
PHOTOAUTOTROPH
photo= light
autotroph= organism makes it own food (rather than having to consume other organisms as a food source)
what is the main immunoglobulin class that recognises helmonths?
IgE.
IgE is made by humans that are repeatedly infected by helminths. The increase in IgE is associated with reduced incidence in disease as individuals age.
what is the increase in IgE associated with?
with reduced incidence in disease as individuals age
what is a helminth?
parasitic worm
lymphocyte antigen specific receptors are best characterised by what?
(millions of different receptors are generated through gene rearrangement)
Lymphocyte antigen specific receptors are found on T and B cells that are located throughout the body.
These receptors are generated by gene rearrangement to provide a massive number of different B and T cell receptors that can recognise almost any possible antigen.
Tuberculosis, malaria and HIV are causes of massive global mortality, and we do not yet have effective vaccines against these infectious diseases. Why has developing vaccines against tuberculosis, malaria and HIV been difficult?
HIV has a high level of antigenic variation and the parasite that causes malaria also displays antigenic variation, but Myocobacterium tuberculosis has only limited antigenic variation. HIV does infect T cells but, the malaria parasite infects liver cells and red blood cells depending on its life stage, whilst M. tuberculosis infects macrophages. Cytotoxic T cells can provide some protection against HIV
e.g. in elite controllers and can provide some protection against the liver stage of malaria, but CTLs play little role in protection against M. tuberculosis.
All three pathogens do require a strong Th1 response to limit the growth of the pathogen and the diseases they cause.
*they are all intracellular infections that require Th1 responses for immunity??
what does antigenic drift refer to in the context of viruses?
Occurs through the build up of mutations in the virus’s genome when it replicates inside host cells. This happens more commonly in viruses, like influenza, that do not have proof reading protein to check the RNA.
Antigenic drift also occurs in viruses that can proof read their new RNA, as for SARS-CoV-2. Mutated viruses that have an advantage increase in the population. This advantage could allow the virus to bind to its host receptor more effectively to evade the host’s immune response.
*a mutation process that makes antigens change and evade immune responses??
give an example of something which can cause antibiotic resistance.
overuse of antibiotics in farming and fishing industries
- the extensive use of antibiotics in many areas of life leads to increased exposure of microbes to antibiotics, this provides more opportunities for bacteria to adapt to surviving in the presence of antibiotics
Extremophiles are organisms capable of surviving under the most extreme conditions. What environment would psychrophile grow best?
cold/low temperature.
Psycrophiles (or cryophiles), from the greek for ‘cold-loving’ are organisms that grow best at low temperatures.
Robert Koch is regarded the ‘father of microbiology’ and credited for many important scientific discoveries. What are Koch’s postulates used for in microbiology?
to demonstrate a relationship between a pathogen and disease.
Koch’s postulates state that a pathogen must be present in all infected hosts with a particular disease. The postulates help us to define that a particular pathogen causes a disease. The postulates state the pathogen cannot be found in healthy hosts- although in some cases
e.g. SARS-CoV-2 infection does not cause overt disease
The innate immune system is triggered following infection by a pathogen. What occurs during the initial immune response to a pathogen at the site of a primary infection?
increase in the permeability of local blood vessels.
One of the first responses to an infection at a barrier tissue is an increase in the permeability of blood vessels. This allows innate immune cells and molecules to quickly accumulate at the site of infection. These cells and molecules can then activate the adaptive immune response (T and B cells)
what is somatic hypermutation?
a physiologic process in which B-cell randomly mutates into immunoglobulin regions to produce a molecule with greater affinity for antigen
