Final Flashcards
Restriction Endonuclease (6)
- Bacterial defense against viral infection
- Enzyme
- Targets dsDNA
- Makes sequence specific incisions
- Viral DNA is targeted because it is methylated (unlike host DNA)
- Useful in research because each RE has a different target sequence so they can be used to splice DNA in targeted regions.
Why is study of parasites important? (3)
- Kill million of children a year
- Parasitic infection is endemic/epidemic in third world countries
- Multicellular parsites weaking the immune response to other disease
Helminths (3)
Nematodes (roundworms)
Cestodes (tapeworms)
Trematodes (flukes)
- Immune modulation by helminths
- Its impact on kidney transplant and pregnancy
- Steer immune response from Type 1 to Type 2 effectors.
- Induce polyclonal B cell activation and proliferation
- Directly
Innate immune responses to viral infection (2)
Structural protection
IFN a and B
Structural protection against viruses
Skin is #1 protection
GI tracts, lungs, upper respiratory tract are major sites of infection and have special structure;
Muscous in intestine from goblet cells;
Epithelial cell packed tightly and bound by tight junctions to prevent virus entry into bloodstream;
IFN a and B response to viral infection
- Cell infected w virus is stressed; releases IFN a and B
- IFN a and B bind to IFN a/B receptor on neighbouring cell;
- Activation of Jak Stat pathway
- Stimulation of ISGF3 and AAF
- Neighbour
- inactivates protein translation
- induces RNAse activity
- Neighbour suicides - prevents spread of virus
Adaptive immune to virus involves (2)
antiobody
cytotoxic T cells (CD8+)
Role of antibody in fighting virus
Block attachment - beinds to vurs and prevents viral penetration. Neutralizing antibody.
Aggregate for phagocytosis - many viral particles removed by monocytes and myeloid liver cells (after made into immune complexes)
Activate complement and Mac Attack - some viruses are susceptible to complement activation by its classical pathway
Activation and killing by T cells in viral infection
- Infected cells are killed via IFNa/B and Jak Stat pathway
- DCs phagocytose viral antigens from cell lysis; some contents go to cytoplasm;
- Viral antigens in cytoplasm are broken down by proteosome, go through Tap and then bind to class 1 MHC
- Class 1 MHC takes viral antigen to cell surface - called cross presentation
- In the node, CD8+ cells interact with Class 1 MHC; Co-stimulation;
- CD8+ cells activated; Proliferate; exit via blood and go to site to produce granules and kill
- Recognize infected cells by presentation on class 1 MHC;
- Perforin perforates the cell so that granzyme can enter and activate caspases leading to apoptosis
- If this doesn’t work, Fas ligand on CTL binds to Fas receptor that activates another caspase pathway leading to death as well.
Cross presentation
Can only be done by DCs
taking something on the outside and popping it out onto cell surface
Virus fights back against immune response (2)
- Downregulate Class 1 MHC expression;
- allows virus infected cells to hide from CTLs
- but Natural Killer cells will see cells without MHC1 and kill them
- Produce immune regulatory proteins
- Steal IL-10 gene from cells and incorporate it into viral genome
- IL-10 downregulates CTS activity and NK cells activity
Major action of HTVL 1 and 2
Virus that wants to get into T cells and lymphocytes
What is the worst thing a virus can do to the immune system
kill CD4+ T cells.
These produce cytokines that help CD8+ cells function
What vaccine do you get often? Why
Tdap because it is a pure protein vaccine and needs to be boosted because it doesn’t have good persistence.
Locus of enterocyte effacement (LEE)
ex:
Pathogencity island associated with intestinal cell attachment and diarrheal disease
Infects effectors into hot cells that function to alter cellular activities
STEC e coli get insert long protrusions into microvilli and hold on tight
Listeria
Gram +ve bacterium that is common in food-borne illness
- Intracellular pathogen; taken up by phagocytes
- Gets into cell using Interlanin B; mediated endocytosis using clathrin;
- LLO is produced at the perfect time; Generates pores in phagosome so that bacterium can escape
- ActA (actin modulating protein); forms a Listerio-pod and pushes bacterium from cell to cell.
May lead to gastroenteritis, encephalitis
Mother to fetus transmission
Prions
Proteins that adopt novel conformations that inhibit normal protein function and cause degredation of neural tissue
Mad cow disease
HIV capsid maturation requires
Viral proteases
Pre proteins are cleaved into vital forms this way
Egress of naked icosahedral viruses typically requires
virus ex
apoptosis
poliovirus
Enveloped viruses can escape the cell by (2)
Budding into an internal membrane, followed by exocytosis
Budding directly from plasma membrane
Poliovirus preparation and egress
- 2 protease steps: when cleaving polyproteins and when scultping capsid
- genome replicates quickly in cytoplasm
- VP0, VP3 and VP1 capsid proteins; 60 copies each for icosahedron
- +ssRNA genome associates with capsid proteins when forming capsid
- VP0 undergoes autocatalytic cleavage to bcm VP2 and VP4 after assembly - no viral particle is infectious
- timing of apoptosis precisely timed to completion of the capsid
herpes virus egress
via exocytosis - 2 models
- Virus picks up envelopes from internal structures and uses them to get out by natural mechanisms
- herpes capsids are enveloped inside the cell and use the normal protein secretory pathway for egress
Egress via budding from plasma membrane
- virion proteins assemble at the plasma membrane
- virions bud out of cell, acquiring host plasma membrane (and some host cell surface proteins)
Ex: Influenza, HIV
HIV egress
Egree via budding from plasma membrane
- Virus proteins gather at PM and recruit 2 copies of HIV genome
- Once virus buds, proteases cleave components of gag proteins to complete maturation
Influenza:
route of transmission
target cells
cell receptor
person-to-person contact or aerosols
targets epithelial cells of respiratory tract/alveolar macrophages
sialic acid
Influenza entry into the cell
via endocytosis
- Initial attachment of HA envelope glycoprotein to cell curface sialic acid
- Receptor mediated endocytosis
- pH drops in endosomes inducing conformational chnage in HA; exposes hydrophobic fusion peptide
- Fusion; viral and cell membranes mix
- flu genome delivered to host cell
- -ssRNA viral genome migrates to nucleus
Influenza genome replication
-ssRNA genome is segmented
8 segments encode 11 proteins
virus encoded RNA-dependent-RNA-polymerase makes +ssRNA from -ssRNA template which is then exported to cytoplasm and translated and used as template for progeny -ssRNA genome.
cause of antigenic drift in influenza
RNA-dependent-RNA-polymerase is error prone. Used to transcribe the -ssRNA genome to +ssRNA.
Leads to mutations that lead to evasion of host immune recognition -> Antigenic Drift
Antigenic Shift
common influenza
target cells con-infected with 2 different strains of influenza.
Allows for reassortment of genome segments in viral progeny
A dramatic single step
Often the cause of pandemics
Influenza virus assembly and egress
- HA and NA proteins have hydrophobic signal sequences so they are translocated into the ER and proceed through golgi apparatus and then become embedded in PM
- The glycoproteins must be properly processed
- glycosylated in ER and golgi so they resemble host protein
- cleaved by proteases in golgi
- HA and NA proteins cluster on PM
- Viral proteins and genome ‘home in’ on this cluster and assembly takes place
- virions bud from PM, taking some host proteins with them
- NA has sialic acid cleaving ability; allows virus to leave cell
Some cells lack the enzyme required to cleave HA into its active form. Are virus particles produced by these cells infectious?
No protease = no HA modification = HA can no longer bind to allow membrane fusion bt progeny virus and next host cell
Influenza drugs
ANtivirals: tamiflu and relenza
NA inhibitors - influenza virus stays tethered to surface
HIV assembly and egress
- Reverse transcriptase makes dsDNA from +ssRNA in cytoplasm
- dsDNA is taken to nucleus to integrate into host genome
- Has to inegrate to replicate
- Once viral genome is in context of host DNA, transcription occurs using host machinery
-
ENV is the HIV envolope protein;
- N terminal signal sequence removed by signal peptidase
- Cleavage in golgi to gp160 to gp120 and gp41
- Transported to PM
- gp41 fusion peptide buried in viral membrane
- Gag recruits HIV +ssRNA to budding site
- HIV escapes host cell by budding from PM, acquiring some host PM as they do
Vpu
HIV-1 egress is inefficient in some cell types due to tetherin inhibiting the retrovirus release
Vpu is an accessory protein that antagonizes tetherin and allows these HIVs to escape host cell.
HIV protease
Cleaves viral proteins into their final products
allows for virus maturation
Cleaves Gag into functional products leading to huge morphological changes in escaped capsid
Host defenses against HIV (2)
Pattern recognition receptors recognize +ssRNA genome
Toll Like Receptors 7 and 8
Host protein, TRMalpha can recognize uncoming HIV capsids and
- cause their degredation
- trigger an innate immune response
emergent
diseases that suddenly become prevalent
zoonitc infections
Animal diseases that are trasnmissible to humans
wild animals that interact with humans/domestic animals are often the source
we can use sequencing technology to find out which viruses are present in which animals
zoonotic HIV
- HIV is from a large family of primate retroviruses that are natural in African nonhuman primates
- Our immune systems weren’t prepared for HIV bc it was a primate retrovirus
- Don’t cause severe issues in the primates they come from
- Closes virus to HIV-1 is SIVcpzPtt
- HIV-1 groups M, N and O each resulted from independed cross-infections of SIVcpzPtt
- Probably transmitted locally then south to congo river where the group M pandemic probably spawned
Co-evolution
- Explains why many pathogens aren’t harmful in their primary host organisms
- Innate and addaptive arms of our immune system evolve to defeat a virus and virus simultaneous evolves to beat our immune system
- Escalating warfare
- The Red Queen Hypothesis = for an evolutionary system, continuing development is needed just in order to maintain fitness relative to the system it is co-evolving with
genetic armed race
Viruses promote fitness by hijacking host genes
Strong natural selection for non-synonymous substitutions in coding regions for both viral and host genomes.
Substitutions can weaken or strengthen interactions
Poxvirus morphology
resevoir hosts
interaction with host
Enveloped, core capside ancases genome
many different resevoir hosts
Numerous poxvirus genes that target host defense and multiple nodes of interaction
Poxvirus
Antigenic drift experiment
-
PKR is a pattern recognition receptor that sees foreign viral structures and initiates immune response
- Recognizes dsRNA, a viral PAMP and phosphorylates to block host translation of the viral genome
- Poxvirus has proteins, E3L and K3L that are involved in antagonizing the action of PKR
-
Delete E3L
- Virus either does not persist, or persists very well
- When it persists very well, that is because poxvirus makes a second copy of K3L, which is amplified
- Mistakes are made and within amplification there is an advantageous variation of K3L
- Genome collapses to just the advantageous new copy of K3L
- Poxvirus can rapidly evolve under selective pressure even in the absense of an error-prone polymerase (influenza)
Influenza Antigenic Drift
Host antibodies can neutralize influenza viruses
RNA-dependent-RNA polymerase is error prone
Gradual viral evolution that leads to evasion of antibodies
Antigens that drift are mostly on HA (where blocking attachment would occur)
Mutated amino acids are clustered on receptor binding region
Model of antigenic shift in the lab
serial passage in mice
- Use reference strain called PR8 (non-pathogenic H1N1)
- generate 3 identicle virus stocks
- Innoculate each stock into a naive mouse and a vaccinated mouse
- Harvest/homogenize lungs, harvest virus and infect next mouse
- After serial passage HA and NA are sequenced
- HA protein mutated in vaccinated mice, not naive mice because it is under massive selective pressure from vaccine
What happens when HA mutant viruses infect a naive host?
There is no circulating antibody to provide selective pressure
New mutations lowered receptor binding avidity to optimal range
Illustrates important of binding avidity - strong enough to enter, but not so strong as to impede the release of progeny viruses
impact of serial passage/antigenic shift experiment?
Antigenic drift is accelerated by sequential passage of IAV between immune and non-immune individuals.
Non immune are mostly children
Decreaseing naive population by increasing vaccination will likely slow antigenic drift.
