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IMMUNOLOGY AND
VIROLOGY REVISION

Virology
Host selective, non-metabolic, Viruses are typically 30 – 100 nm but some are 200-400nm (poxvirus)
and 1000nm (filovirus)
...
The will contain all the genetic information they need and nothing more in the form of
nucleic acids
...

Non Enveloped Viruses

Also includes the blue Tounge virus which infects cattle and sheep, An RNA virus spread by midges
...

HPV
Those with a susceptibility to types 5 and 8 can end up with an overdevelopment of keratin structure
on the skin leading to disfigurement called Epidermodysplasia verruciformis
...
Ebola, tobacco mosaic virus (filamentous Influenza is common in clinical isolates, lab
isolates are the spherical form that everyone knows)
...


Viral Classes

^ also inc
...

RdRp = RNA Dependant RNA Polymerase or RNA replicase is an enzyme which uses the –sense RNA
strand to create a + sense strand of which all future –ssRNA is made from
...
Disadvantages are that there
is no backup DNA copy of the Data
...

Classification also follow:
Order (virales)
Family (Viridae)
Subfamily (Virinae)
Genus (virus) – Name of the Virus
Species (related to the location of the origin)

The aims of the virus are to be infectious, be able to manipulate the host machinery in order to
produce more viral components and more viral particles, encode any additional requirements not
available in the host cell (enzymes) and to self assemble into a virion
...

The virus has to enter the host in some way (via sex, respiratory system, blood, gastrointestinal
system) The virus must be able to induce tropism (the binding to and the turning of a specific type of
cells function to a specific goal, in this case a viral nursery)
...

Several factors contribute to viral entry to the host cell
...

Availability of host cell receptor (Such as in the case of
those with the CCR5 Delta 32 , this is a mutation which
deletes a segment of the original gene (a C-C chemokine
receptor type 5 found on the surface of white blood cells
...

Number of viral ligands present to bind to the host cell (less the number the less chance of binding
...
H+ will bind to
negative charges
...

Transcription DNA and –ssRNA are transcribed in mRNA
...

Viral DNA is transcribed by the host using DNA dependent RNA polymerase II
...

Once replicated the new viral RNA can be used in three ways:
Translation and polyprotein processing: Producing new virion pieces
Function as a template for further viral copies
Synthesised for packaging into new virions to then become active
Translation (RNA -> Proteins) This uses the host cell machinery
...
This can happen in multiple ways some picornaviruses phosphorylate a cap of host
mRNA (this cap acts as a recruitment site for ribosomes) and can therefore inhibit their selection by
sequestration of the caps
...

Production of proteins begins
Viral enzymes cleave the sequences and allow the proteins to fold into the required shape
...
Non-structural such
as internal protein and viral enzymes
...

Virion Release
Viral particles can exit the cell via: The Golgi network sending them to secretory pathways, Budding
(exocytosis) through the membrane (enveloped viruses such as RSV, respiratory syncytial virus) and
cell bursting
...

The exact process is virus specific and unknown in many cases
...

Viruses are the most abundant biological entity on the planet and are essential for maintaining the
environment
...

Phage experiment by Bratbak in 1990
...
The bacteria need the nutrients released by lysed
bacteria
...
Believed to
be the most important mechanism of recycling bacterial carbon in the environment
...
96%
have dsDNA
...
T4
kills E
...


Attachment via receptors and the
penetration of the bacterial membrane
using the tail structure to inject its own
genome
...


Expression of the phage gene leads to
the production of the phage
components
...


Release of the new virus which go on to
infect the surrounding cells
...

There are obstacles such as the combination of the bacteria and phage can cause a mild fever to the
death of the patient
...

They will be attacked by the human immune system and immunity created
...


Hepatitis C virus
Previously known as Non A / B Hep
...
and through PCR and sequencing of
infectious samples
...

It is a silent epidemic effecting 170 million people worldwide with another 3 – 4 million infections
annually
...

Blood borne, highest prevalence’s in Africa, Asia and South America
...


ALT is found in some of the highest levels in the liver so is tested to tell about liver damage
...


The virion is enveloped and contains +ssRNA
...

Virus enters the body and
travels to the liver
...
Binding of CD81
forces the virion closer to the
hepatocyte tight junctions
...

Directing to tight junctions
Purpose is to separate neighbouring cells while maintaining diffusion, Two types of tight junctions
are present CLDN1 and Occludin
...
The exact mechanisms are unknown
...
This produces Endocytic vesicles which (Email J
...

Delivery of the nucleosome
The vesicle coat is shed away due to the change in pH inside the envelope and capsid caused by P7
protein (an ion channel), delivering the viral nucleocapsid into the cell cytoplasm
...
The viral mRNA contains an IRES
sequence which acts as the binding site for the hosts ribosome
...

3, Processing
This polypeptide needs to be processed by host peptidases which cleave off the structural proteins
...
Envelope proteins are released and
form non-covalent heterodimeric complexes
...

The viral genome contains two viral proteases NS2/3 a zinc metalloprotease and NS3/4A A serine
protease which requires the cofactor NS4A, this associated prevent protease degradation, this
enzyme also cleaves the junctions between the non-structural proteins except for NS2
...


4, Viral Replication
Replication is driven by the viral enzyme RdRp encoded via NS5B, an essential viral component
...

5, Viral Assembly and Release
Viral particles exit the cell via the Golgi apparatus system using the secretory pathway, This causes
viral budding which causes the viral particle to leave the cell with a segment of the phospholipid
bilayer of the host cell
...
Although the exact
process is unknown it is known that the virions become tightly bound with Very Low Density
Lipoproteins
...

The virus exists as a quasispecies (many genotypes and subtypes existing at the same time)
...
This hinders vaccine development
...

IFN has anti-viral properties – its inhibits viral replication and stimulated lymphocytes
...

Weekly subcutaneous injections of PEG-IFN combined with around 1000mg of ribavirin taken orally
every day
...

Type 1 is treated for 48 weeks with a 50% responsiveness
...

Symptoms of nausea, depression, headaches and skin inflammation
...

Protease blockers - Telaprevir and Boceprevir
Recently approved by the FDA in America, it’s the first approved direct acting anti-viral for HCV,
primarily against genotype 1
...

Oral drug
...
Highly dependent on the
extent of current liver damage and previous treatment
...
Resistant
strains are emerging
...
The
Cap of host mRNA is captured
by PA and cut and used as
primers for PB1 to transcribe
viral mRNA
...
These proteins
participate in the formation
of the permeability transition
pore complex (PTPC)
responsible of the release of
mitochondrial products that
triggers apoptosis
...

The viral tropism is for
Ciliated columnar epithelial
cells which contain sialic acid
residues present inside
glycoproteins
...

2, Host extracellular trypsin proteases will begin to cleave H0 into H1 and H2, an irriversable
conformational change
...
5
...

Replication occurs in the nucleus, Viral PB2 (a primer) binds to the 5’ end of host mRNA
...
Viral mRNA
move into the cytoplasm and is
translated
...

Viral assembly occurs at the host
cell membrane
...

H and N undergo binding and the
virus buds from the membrane
...
Viral
replication is fast and the infection period begins
...

Many people will attempt to go to work and spread the bug further
...


Pandemic Flu
These outbreaks can effect an entire country or the world
...
Category system is the PSI, Pandemic
Severity Index
0, Russian flu/Asiatic FLu (possibly H3N8) of 1889 – 1890 with reoccurrences until 1894 Not well
documented
...
1 million deaths
...

1, Spanish Influenza H1N1 – 1918 – 1919
...

Estimated 50 – 100 million deaths
...

An Avian virus that jumped
...
Cat 2 Pandemic 0
...
5%
Who estimates around 2 million deaths
...


3, Hong Kong Flu – H3N2 – 1968 -1969
...
1 Million people dead
...

In one month the virus has spread across the globe due to trade and returned Vietnam
troops
...
By February 2016 18 people
had died due to Swine
Flu
...
1%
...


RNA polymerase lacks any proof reading abilities which leads to the creation of a viral quasispecies
...

If an animal is infected which more than one species of flu then the genome can be interchangeable
(as long as 8 segments are in a virion then it will be viable)
...

Haemagglutinin and Neuraminidase are immunogenic
...

Three types of influenza:
A – Infects both Humans and Animals and is responsible for pandemics
...

C – Causes a mild respiratory infection to which there is no vaccine
...

Antibodies cannot identify the viral epitope due to a novel sequence
...

Multiple infections challenge the immune system and is the cause for a vaccine
...

Antigenic Shift
Affects Type A only
...

There is no previous immunity as it is a novel subtype every time
...

This requires more than one type of flu in one animal at the same time
...


Flu needs a living host in order to replicate, same is needed to therefore make a vaccine
...
Consists of three predicted dominant strains that yea, data
collected by WHO
...
It is given to those most at
risk such as children, the elderly, physicians, asthmatics and pregnant women
...

Ebola

Filovirus – Filoviridae
80nm wide and 9000 – 14000nm long
-ssRNA genome
19000 bases making up 7 proteins

GP – trimeric spikes
...

Transmission
Human to human via blood and secretions which are rich
with the virus
...

Injections and the person is infectious for 61 days post
disease
...
Chimp are infected
Recently identified the natural host as fruit bats which
are asymptomatic
...

Infection of the cells activated them and they move towards the lymph nodes, spleen and the liver
...

In general they will bind to epithelial and endothelial cells as well as to fibroblasts
Immune response
TRAIL – TNF-related-apoptosisinducing-ligand is a cytokine
produced by normal cells to induce
apoptosis in tumour cells
...

The results of an infections lead to
Leucopenia (Low Immune cell
levels), Lymphopenia (T-cells),
Neutrophilia (Low neutrophil
count), Thromobocytopenia (low
platelets) and Hyperproteinaemia
(low protein in the blood)
...


The Infection
Incubation between 2 – 21 days
...


Recovery
Patients typically have a fever and malaise, they produce IgM and IgG responces (in around 10 days)
to NP and VP40 proteins
...

The response in those with the fatal disease is generally unknown but there is no presence of
specific IgG responses or very weak IgM, this may show a genetic weakness to the disease
...

Survival has been linked with psychosis, hepatitis, myelitis and uveitis (Swelling of the middle layer of
the eye)
...

1976 – Southern Sudan – Ebola Sudan – 50% mortality
...

318 cases of acute viral haemorrhagic fever which lead to 280 deaths and 38 confirmed survivors
...

Neighbouring country of Sudan many have a link to the epidemic
...
90% mortality
...
GP/VP30 which
encodes for a surface glycoproteins and a transcriptase activator and VP24/L which encode for a
viral matrix protein which inhibits the immune system and L encodes for the RdRp
...

1989 Reston – Reston ebolavirus – isolated from cynamolgus macaques in the US – asymptomatic in
humans (reservoir) but harmful to macaques
...
Believed to be airborne, which effected the pathogenicity of the virus in human to a

degree that it almost completely could not infect human
...

2008 – Bundibugyo ebolavirus – originally a 25% mortality rate but the more recent outbreak in
Democratic republic of Congo in 2012 had a 51% mortality rate
...
Whole family became
infected
...
The village also relies on bush meat for
food
...

Almost 5000 official deaths from Ebola, unofficial number is much higher
...
It consists of
three monoclonal
antibodies
...

Theory is that the Ab will
find the virus and tag it
for the immune system
...


Rabies – Meaning to rage
One of the oldest recognised infectious diseases
...
Despite the production of a vaccine
by louis Pasteur in 1885 there are still 30,000 to 70,000 people dying every year globally
...
Highest case of fatality ratio of any infectious
disease
...


The Virus is a bullet shaped RNA rhabdovirus member of the lyssavirus genus (Lyssa was the Greek
god of rage and rabies)
...

The virus is transmitted through saliva, scratches and secretions from mucous membranes,
aerosolised virus has been shown to be possible and transmission through corneal transplants has
been shown to be possible
...


The viruses tropism is the nervous tissue from
which it will spread along peripheral nerves and
muscle fibres (retrograde tracing by binding to CD56 and nicotinic acetyl choline receptors on cell
surface) until it reaches the central nervous system and causes encephalomyelitis (Swelling of the
brain and spine), the virus will particularly infect highly innervated areas such as the salivary glands,
causing hyper salivation and frothing at the mouth
...
Swallowing would severely reduce the ability of the
virus to spread when biting
...

A clue for diagnosis is a tingling at the site of infection after infection
...
Incubation can be between 1 week to several years in some cases though the average
is one to two months
...

Encephalitic rabies (occurs in 80-85% of cases) has the classical presentation of hydrophobia,
pharyngeal spasms and hyperactivity leading to paralysis, coma and then death
...


Virus causes encephalomyelitis by activating inflammatory cell (microglia) which release
inflammatory mediator to attract monocytes, Nk cells and T-cells
...

RABV causes neuronal and critical cells to die via apoptosis rather than via immunopathoglogical
responses
...
CD4+ is
essential to the process
...
3 weeks later she had initial symptoms
...
Ketamine which has been shown to have an antiviral effect on rabies, was used to
supress brain activity
...

Theories on her survival include:
A genetic resistance to the virus which may have aided her recovery
...

Being infected with a weakened strain of virus
...

Only two of 25 patients treated in the first revision of the protocol have survived
...

In June 2011 a 8 year old girl survived via the use of the Milwaukee protocol becoming the 5th person
to have survived the disease which usually once it reaches the brain was 100% fatal
...

Administration of a combined therapy including Vaccine and Anti-rabies serum containing virus
specific immunoglobulins is the most effective course of treatment
...

25% of those effected will die of abnormal heart arrhythmia
...

Breathing, heartbeat, blood pressure, homeostasis
...
RIG usually contains 8 – 15%
monomeric IgG
...
There is a specific dose of 20 IU/Kg of body weight any more than
this and there will be a marked decrease in the efficiency of the vaccine
...
There is a strict vaccination schedule on days 1, 3, 7, 14 and 28 any
variation leads to a failure of vaccination in the majority of cases
...
Became the first post-exposure prophylactic vaccine
...

Each virus will have one point mutation due to the high error rates of the RdRp
...

Virus is likely to thrive inside the host if it does not kill the host
...

So the primary objective of the host system is to eliminate all virally infected cells
...

Innate response – Cell intrinsic
The infected cell needs to identify the virus
...

Detection of virus occurs via:
- PAMPs which include viral nucleic acids, 5’ triphosphates
...

- A decline in host protein synthesis, ion channel activity and an increase in ER Stress
...


Cell Extrinsic
Host cell needs to block virus
and this uses TLR’s (Toll like
receptors) which recognise
PAMPs
...

They are Transmembrane
proteins with ectodomains
(spans out into the
extracellular space that
mediate the recognition of
PAMPs
...

This is mediated via specialised

immune cells such as the DC and macrophage
...
Type 1
consists of Alpha (13 genes for 12 types
of IFN-a subtypes) and Beta (1 gene for a
single IFN-b subtype)
...

IFN utilises the JAK STAT pathway
...
This leads to the production of over
300 ISGs (Interferon Stimulated Genes)
...

TLR recognition by DC - the most potent Ag presenting cell – connects innate and the adaptive
response
...
The virus
can block antiviral effects via:
- Global inhibition of cellular gene expression
...

- Inhibition of molecules involved in IFN production
...

All viruses encode for factors which counteract the antiviral functions of Type 1 IFN
...

Evasion of neutralising antibodies
includes:
- Mutation of surface proteins by
the use of antigenic shift or drift
(Influenza, HIV and HCV)
...

- Glycan shielding – Ebola and HIV
– Where surface glycoproteins can
become heavily glycosylated and
form a steric shield over viral
proteins at the cell surface,
therefore preventing interactions
with the immune system
...

- Multiple surface viral proteins and altered viral forms (quasispecies)
...

These are essential to the elimination of viral infections
...

Every step of the MHC 1 presentation pathway can be blocked, preventing activation of CD8+ T-cells
...

Peyton Rous discovered solid tumour formation did not require the transfer of intact tumour cells
...
So a filterable agent
could cause cancer: Viruses
...
Epstein Barr virus can
cause Nasopharyngeal carcinoma
...

Can cause Sarcomas, Leukaemia’s and Carcinomas
...


HPV
Human Papillomavirus Virus – Over 120 strains which cause warts
...

Low = Benign and causes no problems – HPV 6 and 11
...

High = Cancer of the cervix, vagina, anus and penis – HPV 16 (accounts for 50% of cases) and HPV 18
(accounts for 15%)
...

As the basal
epithelial cell
begin to
differentiate
they become
incompatible for
HPV
...


E6 and E7 encode short nuclear proteins which are essential for HPV to be infectivity
...

E6 binds to cellular proteins and
induces ubiquitin mediated
degradation (below)
...
Low risk HPV will not induce p53
Degradation
...

Also blocks the intrinsic apoptosis
pathway by binding Bak, Blocking the
release apoptopic mediators from
mitochondria
...


E7 targets and binds to the Rb family
proteins, blocking the pathway =
essential for transformation
...

High risk HPV E7 bindds to two CDK
inhibitors (p21 and p27) and blocks
growth inhibition
...


Normal Cell cycle including the points which can be
blocked by viral products
...

The virus doesn’t enter the blood and so Ag isn’t
seen by Ab
...
These
provide Physical and chemical barriers
...
Low Specificity, no flexibility, Possesses no memory
...

2nd line are immune cells and soluble factors
...

2 - Recruitment of effector mechanisms to kill and eliminate pathogens: Effector cells and soluble
factors such as complement
...

DAMPs (danger associated molecular patterns) include: DNA, RNA and Heat Shock Proteins
...

- These are scavenger receptors which recognise microbial lipopeptides such as LPS and CpG rich
DNA (CGI = Cytosine-Guanine Islands)
...

Receptor are expressed on innate immune cells
...

- Vasodilation: local dilation of the blood capillaries (leading the redness, warmth due to the
increase blood flow)
...

- Pain: Swelling puts pressure on nerve endings
...
This means that
white blood cells can attach and move through from the blood into the affected tissues to secrete
move cytokines
...

Disadvantages are that prolonged heat at 39 and 41oC causes host proteins to denature causes a
disruption in essential metabolic processes
...


2 – The cellular components include: Phagocytes (macrophages, Kupffer cells and DC), Endothelial
cells, Mastocyte cells (granulocyte carrying histamines and heparin), Basophils (releases histamines)
and NK cells
- The soluble components include: Cytokines which are short lived and have a short range
...


Adaptive immune system
Reacts slowly
High specificity
Flexible
Possesses a memory
Involves the use of B-cell, T-cells, DC and soluble
factors
...

Secondary lymphoid organs include the Lymph
nodes, Tonsils, Spleen and are where the
immune response occurs
...


Antibodies bind to the epitope of in infectious agent (Ag)
...

All of the antibodies produced by
a singular B-cell will have the
same Ag specificity
...

1 X Fc (@80kDa) which couldn’t
bind to Ag but could be
crystallised
...

The light chain could be either
Kappa or Lambda
...
These consists of alpha proteins and beta pleated sheets
...
It is
these CDRs which
determine the
specificity and affinity
of the Ab-Ag binding
interaction
...

- Viral Coat proteins can be either discontinuous or continuous
...

CDR3 on the heavy chain is the most important in binding to an Ag
...


IgM = used in the innate immune system due to high valence
...

IgE = Only found in mammals and gives immunity to parasites such as Plasmodium falciparum and
helminth infections
...

IgA = produced at mucosal membranes
...
Used in several
mechanisms ranging from opsonisation to activation of the complement system
...


B – cell Maturation in the bone marrow
Immature B-cells with
membrane bound IgM are
tested for binding against
self-antigens in the bone
marrow, if they do they
will die (Negative selection
and clonal deletion)
...
Some B-cells
do escape this clonal
deletion by light chain
editing via receptor
editing, this may change
the specificity to self Ag to
the point they now do not
bind or bind very weakly
...

Black circle surrounds a
RSS (Recombination
Signal Sequence)
...

Orange are One turn
RSS’s and consist of 12
bp
...

These gene
rearrangements only
occur in b-cells and can
be non-productive due
to frame shifts or
introduction of stop
codons
...

The number of
variations made by
gene rearrangements
are 2
...


B-cell Activation
Requires Ag cross-linking
Thymus dependant Ag
- Ag’s processed by B-cells and
other APC (antigen processing
cells)
...

Changes in gene expression
...

This links the BCR to the BCCR together
...

This helps early in the immune reaction when there is
low Ab affinity and Ag quantity is small
...
B-cells a Pro APC’s can present
antigens to initiate an immune response against them
...

Small Ag fragments (peptides) are then displayed on
the cells MHCII with-in an hour of activation
...


Class Switching of B-Cells
DNA looping remove large segments of genes dependent on which cytokines the B-Cell has been
exposed to during activation via T-Cells
...
They also express a
unique membrane bound binding molecule called the TCR
...

-T-Helper Cells are CD3+ and CD4+ and recognise MHC 2
...

-T-Cytotoxic Cells are CD3+ and CD8+ and recognise MHC 1
...
Upon
binding to an infected cell it will produces Perofrins, IFN-gamma and lymphotoxins which stimulate
an antiviral response and disrupts cell metabolism
...


Progenitor cells (also known as Thymocytes or Lymphoid stem cells) migrate to the Thymus, they
enter the outer cortex and begin to proliferate
...

Thymocytes are lineage negative (CD4- and CD8-)
...

During the rearrangement of TCR genes the newly synthesised Beta-chain combines with the
glycoprotein T alpha chain
...


The matured T-cells must recognise foreign antigens
combined with self MHC
...

Negative selection – Thymocytes bearing high affinity
receptors for self-MHC or self-antigen presented by a
self-MHC
The actual TCR is membrane bound, specific for antigens
bound to the MHC complex
...

TCR is associated with CD3
...


Sources for variability in TCRs, Combinational diversity (VDJ rearrangement), TCR Beta Chain
D segments can often be read in 3 frames
...
There’s no somatic
hypermutations/affinity maturation or Class switching
...

CD4 and CD8 co-receptors
TCR-Ag interactions are weak so they need accessory molecules which stimulate certain
signal pathways
...
They do not add to specificity, only aid binding
...
Signal 1
CD28 on T-cells interact with B7 on the target cell (APC or B-cells)
...
This is a nonspecific co-stimulatory signal
...
This changes gene expression to produce
cytokines
...

Early genes
Expressed in 2 hours – IL-2, 3, 6
...

Late genes
Expressed up to 2 days later – adhesion molecules to infected site such as VLA4
...


Viruses can escape T-cell detection by down regulating or blocking the production of
cytokines such as IFN-Gamma by NK cells and T-cells
...

Altering the Th cell response-switching response from Th1 to Th2 thereby switching off the
CD8+ response (no cytotoxic abilities)
...

T-cell exhaustion – leads to chronic infections

MHC
MHC determine the adaptive immune response – Influences TH and TC cell responses
...

Class 1 MHC is composed of three domains; a1, 2 and 3
...
Found on most nucleated cells and present
Ag to CD8+ T-cells (cytotoxic)
...

Classical MHC 2 present epitopes to CD4+ lymphocytes, Non-classical are accessories which
work inside cell membranes such as lysosomes, normally loading the Ag peptides onto
classical MHC class 2
...
It
codes for secretory molecules such as Complement, Cytokines and heat shock proteins
...

Tc Cells are CD3+ and CD8+ and recognize epitopes bound to MHC 1 (expressed by cells
which are nucleated)
...

MHC 1 (Endogenous Processing)
MHC 2
TAP (Transporter associated with Antigen Processing) pumps peptide chains into the ER for
binding to MHC 1
...


Inside the ER there are numerous proteins which aid in loading the MHC with a protein
...


Peptides to be presented to class 2 MHC are produced in the acidified lysosome
...


The Invariant chain prevents the binding of peptides to the MHC 2 molecules inside the ER
and helps the folding of the Alpha and beta chains
...
Once in the MIIC, HLA-DM will swap
itself for CLIP, it will never be on the cell surface, this would lead to autoimmunity
...


HLA also includes E, F and G for MHC 1
...

They require cell to cell contact (whilst anchored to a cell membrane)
...
A peptide must associate with a given MHC of that individual,
otherwise to immune response can occur
...

Cytokines (especially IFN-Gamma) increase MHC expression
...

Peptides from within vesicles are associated with MHC 2 and are recognised by Th Cells
...

The MHC can bind with thousands of peptides with different aa sequences, this is called
promiscuous binding specificity
...

There can be Cross-Presentation This is where exogenous Ag on the MHC 1 are presented
(even though they usually present endogenous peptides)
...
Cross-presentation of self Ag helps maintain tolerance by
eliminating CD8+ T cells with a self-attacking TCR
...


Gamma and Delta receptors are found on a small subset of T-cells
...

Cancerous cells will do the opposite
...

MHC act as inhibitory receptors to NK cells
...
HLA-A, B and C are detected by
KIR on NK cells (KIR, Killer-cell Immunoglobulin-like Receptors)
...

NK will carry three types of receptors:
1, Inhibitory
2, Activating
-DNAM-1, NKG2D
3, Chemokine
-CXCL19 directs chemotaxis
...


The Lytic granule – Already formed inside the CD56dim NK cells contains Granzymes,
Perforin and Granulysin
...

Signal amplification
Cytotoxicity – Precise targeting and release of lytic granules and cytokines
...


Cancer cell evasion of NK
1, Cleaving off ligands from the tumour surface
- The NK activating NKG2D recognises the tumour ligands MICA, MICB and ULBP1 – 4
...

2, Secretion of Immunosuppressive Cytokines
- Secretion of TGF (transforming growth factor) -Beta by tumour cell
...

- In Vivo cultures of NK cells with TGF-Beta result in the down regulation in the expression of
NK activating receptors NKp30, NKG2D and DNAM-1
...

Immunoregulation is the balance between activation and suppression of effector cells to
achieve an efficient immune response without damage to the individual
...

T-B cell interactions
B cells signal T-cells with Ag on an MHC
...

Tolerance is a process in
which the immune
system differentiates
between self and nonself Ag
...

Inducing tolerance
experiment
This experiment shows
that the administration
of an Ag to a very
immature animal can
create a tolerance to the
Ag
...

Has been tested in
humans to a degree,
desensitising to peanuts
worked in the majority of
children trialled
...

Immunosuppression: The suppression of the immune system to Ag
...


Only Ag receptor bearing cells can be conditioned to being tolerant to an Ag (i
...

Central Tolerance: Occurs during lymphocyte development early in the cell life
...

A faulty central tolerance sows the seeds for autoimmune disease, and faulty peripheral
tolerance leads to its eruption
...

In the thymus they will express either Gamma/Sigma or a Alpha/Beta
...


Peripheral Tolerance
encompasses various
safeguards that
prevent the
activation of selfreactive lymphocytes
...

Anergy – where the immune system is unable to mount a response to a specific Ag, directly
causes tolerance, may lead to apoptosis
...

Homeostatic imbalance – Many diseases cause an imbalance of the homeostasis, changing
these internal systems will result in less available nutrients for the host and therefore a
weakened immune response
...

Regulation
...

Hypersensitivity and Autoimmunities
Once an individual has become immune to an Ag the immune system may hyper-react to
that specific Ag
...


Drug reactions – Drugs can bind to RBC surface and antibodies can in turn bind to the drugs
and cause lysis of the RBC
...

Type 3 or Immune Complex Hypersensitivity
Ab reacting with free Ag causes insoluble immune complexes to form in blood vessels
(vasculitis) or lodge into surrounding tissue (glomeruonlephritis)
...

The CD8+ cells secrete cytokines such as IFN-Gamma and TNF
...

Tissue damage results from products of activated macrophages
...

The DTH test is one which abuses this hypersensitivity as it only occurs after the first
exposure, requires memory T-cells of both CD8 and CD4 types
...

Autoimmunity
Severity ranges between minor to lethal
...

Everyone has it to an extent but it is usually harmless
...
This breaks the usual tolerance of self
...

Genetic and hormonal factors may be at play as well as the formation of new epitopes and
the exposure of hidden Ag’s, which would not normally be seen by the immune system
...

HLA-DR2 is associated with goodpastures syndrome, where the basement membrane of the
lungs and kidneys, causing bleeding and organ failure
...

HLA-DR4 – rheumatoid arthritis, IgA nephropathy (where IgA is deposited into regions of the
kidneys nephrons
...
In the animal kingdom this leads to mosaicism if the two
chromosomes carry different genes
...

Model 2 – Certain HLA alleles are less efficient at presenting self-peptides to developing Tcells
...

Goodpasture’s syndrome destroys basement membrane collagen type 4
...
Systemic
lupus IgG raised against DNA, Histones and ribosomes
...
Insulin-dependent diabetes mellitus
...
Celiac disorder, Ab raised against gluten modified by transglutaminase
causes malabsorption of nutrients and atrophy of the intestinal villi by the immune system
...


Initial observation
A singular infection may not be enough to produce sufficient protective immunity to a
pathogen
...
This
process was used in the hope it would cause a milder version of the Smallpox disease
...


Vaccination is the deliberate stimulation of the immune system to protect an individual
against a disease
...

Passive Immunity – Protection which can be transferred from one person to another person

or animal, this is temporary
...

For this reason it is important to follow the immunisation programmes until infection can be
considered eradicated
...


Extracellular bacteria: Pneumococcus, Haemophilus influenzae, Streptococcus pneumoniae
Intracellular bacteria: Mycobacterium tuberculosis/leprae
...

Viral Infections: Polio virus, Measles virus, HIV, Influenza virus
Vaccines to produce Ab to bacterial infections and toxins much stimulate the maturation of
B-cells which requires T-cells
...
Most of these
vaccines are very effective in healthy people
...

-Anti-flu vaccines are effective but requires a best guess approach to the genetic shift and
drift of the genome bringing rise to novel virus sub species
...

- The closest is the RTS,S/AS01 vaccine currently being tested for use against Plasmodium
falciparum before it begins infecting erythrocytes (Exo-erythrocytic Cycle)
...


Immunisation is a procedure designed to increase concentrations of AB and/or effect tor Tcells which are reactive against infection (or cancer)
...

If done before exposure to a wild Ag then it is called Immunoprophylaxis (this accounts for
the majority of jabs taken), this will tend to prevent the infection
...


Vaccine types
Traditional types are:
- Inactivated (Killed), polio, flu, tetanus toxoid
- Live
- Attenuated (live but non-infectious), measles, chicken pox
Live vaccines are more efficient but have a higher chance of reversion
...
They also act like a natural infection so elicit a much better immune
response than a inactivated vaccine
...

Disadvantages: Potential to revert, cannot be given to the immunosuppressed, poor stability
and there’s a potential for contamination of the vaccine
...

Advantages: Stable, ingredients are clearly defines, unable to cause infection
...

Subunit – contains purified components from bacteria and viruses
...

Booster shots are required for some vaccines, DPT is given every ten years to refresh the
memory cell population
...

Aluminium clumps together the Ag making a more concentration region
...

Limitations to Traditional Vaccines
Not all can be grown in culture, safety, expense, insufficient attenuation, reversion,
refrigeration, doesn’t work for all infectious agents, Infants/children receive them –
immature immunity
...

Advantages: readily delivery, molecularly defined reagents, neither infectious nor capable of
infection
...
There’s no
risk of using an actual
infectious agent
...
This can be by Injection in the skeletal muscle or
by Gene gun, Where the naked DNA is coated in gold particles
...
The
Chikungunya virus is a mosquito borne virus which causes severe illness and rarely death
and believed to be increasing in infectivity, but in mice models treated with the prophylactic
DNA Vaccines there was a 100% survival rate along with long term protection
...
Peak efficiency was only 2 days after vaccination
...

Advantages of genetic vaccines are that they are easy to produce, induce cellular and
humoral responses
...

Peptide vaccines
Work via the use of Exogenous Ag processing where the extracellular protein is endocytosed
by the cell and ends up being presented in a MHC 2 complex to a CD4+ t-cell
...

A peptide vaccine relies on the identification and chemical synthesis of B-cells and T-cell
epitopes
...

In their most simple form they are linear polymers of 8 – 24 aa
...

Limitations with using Peptide vaccines are:
- They have a low immunogenicity
- The extensive genetic variability of HIV – Quasispecies
...

- The difficulties in using result from animal models to test human vaccines – transgenic

mice could solve this problem
...
This means that some peptides may not be universally effective at producing a
protective immunity
...

The whole genome is read and possible regions that could be immunogenic and easy for Ab
to get to and inserted into a surrogate organism such as E
...
These are then tested in
animal models and if successful produced as a vaccine, this will cut the time from traditional
vaccinology from 5 – 15 years to 1 – 2 years
...

2, X-ray crystallography where Ag-Ab complexes are crystalized and the structure scanned
for the contact regions
...

3, Prediction methods which are based on the x-ray crystal data available for Ag-Ab
complexes, the propensity of an amino acid to lie in an epitope is calculated
...
B-cell epitopes, predict
secondary structure, hydrophobicity, mobility/flexibility
...


Viral Vectors
Include: Adenovirus, Retrovirus, Lentivirus, Adeno-associated virus (AAV), Herpes Simplex
Virus (HSV)
...

Liposomes containing genes
...

Presence of an existing immunity against the chosen vector
...

There’s a high transfection rate (near
100%)
...

- Gene therapy
Several gene therapy trail and a huge
number of laboratory successes are
taking place and curing genetic conditions such as: Haemophilia (introducing blood
coagulation factors Viii or iX)
SCID (severe combined immunodeficiency)
Muscular dystrophy caused by an issue in the DMD gene which encodes for dystrophin
which binds muscle cells together and to the extra-cellular framework, in sufferers this
protein (which is carried on the X chromosome and therefore affecting almost entirely
males) contains a missense mutation and therefore when in use the muscle cells can burst
under the pressure and torque of unnatural movement
...
Due to the size of the dystrophin gene (2
...
So gene editing techniques are
now under study such as CRISPR/cas9 of which studies in mice have been positive in
reducing the presence of creatine kinase (an enzyme release by the lysing of muscle cells)
...


Cystic Fibrosis is caused by a well known mutation in the CFTR gene which would normally
form a chloride channel in the epithelia in the lungs and the gut leading to recurrent
bacterial infections, chronic inflammation and possibly respiratory failure
...
This group are using
an optimised (working) CFTR expression plasmid called pGM169 which contains a low G-C
content to reduce inflammation, a promoter to create a persistent expression of the gene
...
4% increase in lung function compaired to the control
(which were decreasing in lung function due to the progression of the disorder)
...
The symptoms vary in severity between person to person
...
A current clinical trial still requiring volunteers aims at harvesting bone marrow which
will then be transfected by a lentivirus which has had an anti-sickling gene inserted
...

- Vaccines
Viruses expressing pathogen proteins of the viral surface
...

Adenoviruses are being actively developed as vaccines
...


Immunotherapy
A form of therapy which targets the immune system to fight an infection, allergy, autoimmunity and
cancer
...

The immunotherapy may be used to:
Inhibit the unwanted or excessive immune response – allergies to autoimmunities
...

These can be achieved through the use of:
Monoclonal Ab Therapy (includes Anti-TNF-alpha which can aid IBD and Rheumatoid arthritis and
inhibits the inflammatory actions of TNF-alpha
...


Immunosupressives
Corticosteroids block cellular infiltration, cytokine
release, T-cell maturation
...


Immunotherapeutic agents – Cytokines
Interferon-alpha
-An anti-viral used to treat viral hepatitis
-An anti-proliferative used to treat Hairy cell leukaemia
Interferon-beta
-Possibly an anti-proliferative in gliomas (tumour in the brain or spine)
-Anti-viral and an antagonist of interferon gamma in multiple sclerosis



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