Virology Quiz 3

Characteristics related with disease progression

-tropism- specificity to a certain cell type or ability to spread to all cells -transmission success- if easy transmitted to new hosts, the virus doesn't need to be around that long within the host.

HSV capsid assembly

-use scaffold proteins to prepare the empty capsid 1. All structural proteins have an NLS, so are imported into the nucleus. 2. Scaffold proteins assemble the capsid 3. Protease chews up the scaffold itself to leave behind an empty capsid 4. Genome is slurped up into the capsid using ATP

Which of the following would require the lowest protein concentration to assemble into subunits? a. SV40 b. poliovirus c. adenovirus

ANSWER: poliovirus

Changing receptivity, permissivity, and local immune response to change attenuation

INCREASE ATTENUATION (less virulent) -doesn't bind at all or binds weakly. EX: herpes has many receptors. maybe breaking some can prevent infection. EX: preventing deglycosylation in ebola -decreased ability to replicate in host. EX: knock out host transcription factors DECREASE ATTENUATION (more virulent) -sites of infection. places with lower host immune response -host age -Immune status -basically all the stuff that determines severity.

Viral Pathogenesis Cycle

SEE IMAGE -it is key that the virus sheds before recovery/death of host in order to spread to new host -primary replication and innate immune response and the dissemination are during the incubation period. -especially see this cycle and variation in seasonal viruses. Not all viruses go through seasonal patterns. -Season variation may have to do with weather (humidity, temperature)

Signal transduction pathways activated by cytokines: The IFN response

Say a neighboring cell has sent out interferons that then bind into the interferon receptor, sending signaling pathway down and starts to express proteins to lead to the antiviral state start making proteins that are not initially active in the antiviral state start producing proteins that will show what is inside you, and also set things up to stop viral replication if it turns out that a virus is truly there proteins that result from iterferon binding are 2' -5' Trinucleotide that activate RNaseL and PKR

adaptive responses

are specific (very specific to a part of the pathogen ie epitope of an antigen) and memorable can mount autoimmune responses because cells can present self proteins (HIV does this because of high variability) There is some antigen A that will result in a primary antibody response. After a couple weeks we get a response of antibodies against A. when you inject the same antigen A. The cells that went into memory are the ones that are activated and triggered and are able to mount a more robust immune response. This can be to the point that you dont show the disease. it you add antigen B, you have to start over with a primary anti-B response. ' viruses that undergo high mutagenesis make it hard for our immune response to catch up because it has to start over each time.

generation of receptor diversity

V and DJ recombination to make the area highly variable similar thing happens in B cells

Two Types of Virulence Factors

VIRULENCE FACTOR: -not required for normal growth but required for disease. associated with pathogenicity -find by making random mutations in bacteria and seeing what changes -for viruses, split into "flavors." some cause unintended death by replication, where others cause death purposefully. Technically only the ones that purposefully cause death and virulence factors EXPERIMENT WITH MICE -Grew virus on plate to see number of plaques and injected into mice brains to see death/attenuation -Wild type- lots of big plaque formation, replication in brain, neurovirulent -mutation leading to general defect in replication- few plaques, poor replication in brain, attenuated -mutation in a gene specifically required for virulence (TRUE VIRULENCE FACTORS)- lots of small plaque formation, poor replication in brain, attenuated. Since we know it replicates well on a plate, it means that the host must be mounting defenses against it when we inject it into the brain.

In terms of virion production, which of the below cell types is the most permissive for VZV? a. cell expressing M6P receptor b. cell not expressing the M6P receptor c. M6P receptor has no effect on permissivity

b. cell not expressing the M6P receptor because it doesn't traffic the virion to the lysosome. Once it is infected, it is more permissible. The thing is just that it is less likely to get infected.

What part of the envelope proteins would you expect to have signals required for trafficking? a. exoplasmic side b. cytosolic side c. transmembrane domain

b. cytosolic side because coats are responsible for moving things and these are in the cytosol.

Which of the below determinants would best represent the tissue tropism of influenza? a. susceptibility b. permissivity c. accessibility d. local intrinsic and innate immune response

b. permissivity because this is an enzyme produced by those tissues that is required to make an infectious progeny virion. doesn't matter what exactly it is, just that it is required to make in infectious virion

facing the host immune defense: getting over the walls

basic concepts: host systems against viral infection are multistep, sequential, and intercommunicating. -innate- always present in the uninfected cell. EX: apoptosis, autophagy, RNA silencing, antiviral proteins -intrinsic- induced by infection but still general. EX: natural killer cells -adaptive- tailored to the pathogen first: physical and chemical defenses -The skin, surface coatings of tissues such as mucous secretions, tears, acid pH, and surface-cleaning mechanisms second: frontline defense cell-autonomous, intrinsic defense systems (doesn't need input from neighbors) -detection of altered cell metabolism -detection of unusual macromolecules -production of cytokines, induction of apoptosis, interference with early steps of viral replication third: attack and clean up innate and adaptive immune response -direct, amplified response by coordinated action of cytokines and lymphocytes -infection cleared by pathogen-specific antibodies, helper T cells, and cytotoxic T cells -production and maintenance of B-cell and T-cell memory cells -immune host ready to respond instantly to the same infection that induced the memory response.

counseling apoptotic cells

boxes are ways that viruses counsel the cell into not going apoptotic (dont need to know all of them) large DNA viruses will have a number of ways of keeping the cell from going through apoptosis

caspases are apoptotic effectors

caspases will degrade the cytoskeleton, or activating DNases caspase comes in and activates other caspases leading to a cascade event this can lead to cleavage of cytosolic proteins or cleavage of nuclear lamin

mechanism of antibody mediated neutralization

different steps that you could block, like the attachment, endocytosis, uncoating, etc. antibodies can interfere with the attachment phase, but also can have attachment but no longer can go through the conformational change that will allow for uncoating (etc).

autophagy

eating self to survive wrap around areas of high concentration of virus proteins and gobble them up and send them to the lysosome and clear the cell up if cell can clear infection by autophagy then it can survive normal pathway is to get rid of aging cells etc.

cellular induction of adaptive immunity

first is the innate immune response (0-4 hours) -interferons are about -natural killer cells help destroy the virus, activating the macrophage once we get the antigen presenting cells, like the dendritic cells, to pick up and present some of the antigens. As we go into the lymphnodes we get some of the T helper cells (CD4), this information as well as some of the other information that the dendritic cell received (cytokines/receptor activated as such) will push it to a TH1 (CD8 activated) or a TH2 response (which activates B cells so that the cell gets a humoral response) rarely a virus infection will only do one of these responses but can have a larger number of cells pushing it to a TH1 or a TH2

apoptisic intrinsic response seen through dying cells

green is marking cytochrome c, which can be seen in the mitochondria in the beginning cytochrome c is dispersed start to see turning red because there is a dye that is binding to phosphotidle serine only when it is present on the outside blue is representing the DNA, and can see it fragmented and dispersed into blebs if this happens while the virus is in eclipse then the virus is skrewed

IFN also activates expression of tetherin

also agaisnt retrovirus protein that is a huge transmembrane protein that when viruses start to bud away, they can get glued together because of this large protein HIV got around this by another accessory protein called Vpu which binds and sequesters tetherin in the internal vesicles and prevents them from going outside and as a result HIV is able to bud out from the surface and not get tethered together

antigen specific amplification of lymphocytes

antigen binds B cells and causes the receptor to cluster together. The clustering causes a signal transduction inside the cell, causing cell to ingest and present the antigen as the cell start to replicate getting an initial increase of this guy, but it is not fully activated yet (ie not secreting antibodies just increasing in number) need T helper cell to tell it it is good to go before it can turn on

Activation of PKR by dsRNA

in addition to the oligo product you start making protein kinase R (PKR) in its inactive state and it is not activated until double stranded RNA is present (changing the conformation to more open) it goes in a phosphorylates the eukaryotic initiation factor 2 (eIF2)subunit involved in translation inhibits translation and as a result both of the proteins made by interferon response halt translation (which all virus share the use of host translational machinery)

Cytosine Deamination:

inactivating future generations allows the HIV genome to heavily mutate NORMAL HIV: They bud out from one cell, they go into another cell, drop off their positive stranded RNA -> -DNA -> dsDNA, then they express their genome and bud out DELETION IN Vif: Vif is a Protein product from an alternative spliced mRNA. When the virus has the mutation, then the protein APOBEC3G (host protein) gets included into the virion in the capsid, and goes with it to the subsequent infection. As the RNA is converted to DNA and the DNA is made double stranded, the APOBAC3G functions as a cytosine Deaminase which changes cytosines into uracils. This means the virions are inducing mutation because the double stranded product will cause bonding with A's. This happens anytime there is a C, generating a lot of changes and heavily mutating the DNA or will fragment the DNA when trying to fix the U's prior to integration. This means that the viruses defense is preventing Vif from allowing APOBEC3G from being included intrinsic

Timing of immune responses: Innate and acquired?

when looking that the innate immune response we are seeing early on that there is an increase in the expression of interferon alpha and interferon beta which generate the antiviral state also an influx in natural killer cells and later on as the adaptive immune response comes up we have virus-specific CTLs

what are all the intrinsic responses

-apoptosis -autophogy -STING -cytosine deamination -RNAi

lysogen

-bacterium carrying a prophage -immune to further infection by similar phage because the phage functions are repressed (C1 from lab)

Entering the Respiratory Tract

-because the respiratory tract is easy to penetrate (because we are always breathing) we have strong innate immune responses. -goblet cells- secrete mucus -cilliated cells- move mucus around towards the gut, where the viruses are killed by the pH or enzymes don't need to know all of the names of the clinical manifestations. generally, get worse as they are deeper

Role of Mice in Clinical Medicine

-can alter host genes or viral genes or both to see the interplay

Tissue Tropism

-certain viruses infect certain sites. some sites are prone to more diversity than others. -different types of virus/different strains of virus that can go through bottlenecks leading to tissue tropism were certain viruses only attack certain sites.

HBV infection

-chronic -the younger someone is at the age of infection, the more likely it is for the infection to go chronic

Prohead/procapsid

-empty capsid that doesn't contain the genome. -there are major conformational changes between proheads and mature capsids because of nucleic acid interactions with proteins

Bunyavirus La Crosse

-enveloped virus buds in golgi -cap snatches like influenza -replicates in cytoplasm

Entering the Intestinal Tract

-have M cells along the gut lumen that take in samples and present them to immune cells. -Sometimes, the M cells accidentally pick up the wrong guys (bacteria or viruses) and get infected themselves.

Helical Capsid Assembly

-have a couple different conformations that the proteins can make (discs or washers). washers are the offset ones that stack STEPS: "Traveling loop model" 1. high presence of discs found in the cytosol due to the pH and concentration of monomers 2. loop of initiation region of gRNA binds to the jaws section of a disc 3. This bonding causes conformational change from disc to washer 4. As more discs/washers are added on, the 5' end of the gRNA gets pulled through

λ capsid assembly

-head/tail -go through multiple levels of procapsids before making the final mature capsid head 1. Procapsid 1 is made of the capsid proteins and contains the scaffold proteins and the portal proteins. 2. scaffold proteins leave to create procapsid II. This contains only the capsid proteins and the portal proteins. 3. concatemeric genome DNA has a specific sequence (cos) that is recognized by the portal protein and allows the DNA to go through. Mature capsid head now formed.

Adenovirus capsid assembly

-icosahedral 1. 3 main monomers are fiber, penton bases, and hexons. 2. Fiber monomers form trimers 3. Single fiber trimer combines with 5 penton bases to make "penton capsomere" 4. hexons form hexon trimers 5. penton capsomere and hexon trimers combine to make an empty particle. 6. Genome is imported once the entire capsid is made 7. Internal protease action can then be done, resulting in the final mature particle

SV40 capsid assembly

-icosahedral -VP1 and VP2/VP3 spontaneously assemble. Equilibrium shifted to have higher concentration of the pentamer than of the monomers

Polio capsid assembly

-icosahedral -one single polyprotein that keeps getting cleaved (end result is VP1, VP2, VP3, VP4) -one benefit to this is that the subunits are already in close proximity. Don't have to wait for diffusion or travel of the subunits

Horizontal and Vertical Transmission of Retroviruses

-if a mom mouse with the virus only in mammary cells nurses babies, the babies will only have the virus in their epithelial cells -is a mom with the virus in all cells (including gametes) breeds, the babies will have have the virus in all cells.

What virus is most likely to spread by germline?

-retroviruses because they integrate the provirus into the host genome

General Intracellular Trafficking Requirements

-togavirus is also at the plasma membrane

Arbovirus enter blood

-no direct human to human transfer -through an insect of some sort (sandfly, mosquito) and have a reservoir -Using an intermediate specimen is the norm in plant viruses because you don't really have plant-plant contact

which of the below viruses would be most likely to activate the STING pathway? (a) Rhino (b) pox (c) dengue (d) herpes

(b) pox it is a dsDNA virus that replicates in the cytoplasm has acquired a gene product that inhibits STING

Which of the below activities occurs only in the intrinsic pathway of apoptosis? (a) activation of executioner caspases (b) cleavage of genomic DNA (c) permeabilization of mitochondria (d) clustering of receptors at plasma membrane

(c) permeabilization of mitochondria

REVIEW: which of the below could be used to activate the innate immune response? (a) presence of apoptotic cells (b) presence of pathogens (c) presence of cytokines (d) all of the above

(d) all of the above

Budding sites are defined by envelope proteins

-HSV- env proteins localized to nuclear membrane. Made in ER, brought into nuclear envelope because they are contiguous. Also see some env proteins on the golgi. 2 budding sites -Corona- env proteins on ER. bud into ER, cross it, bud out, and get transported eventually to be secreted. -Bunya- env proteins in golgi. bud into golgi, packaged into virion as it leaves the golgi -vaccinia (pox)- env protein on late and post golgi. Have multiple membranes.

Picorna (VZV) controls its transmission

-M6P receptor is usually on the cell surface or on the golgi. it identifies things that are tagged with M6P and brings them from the endosome to the lysosome. This is how we get lysosome enzymes to the lysosome in the first place -VSV (specific type of picorna) attaches to M6P. Allows them to get into the cell, but then they would be trafficked to the lysosome and destroyed. The only way for progeny to spread is by the cells fusing, because they don't survive long enough to burst. -lower amount of M6P receptors means a lower likelihood of infection, but a higher likelihood to make progeny if they get infected somehow -because of this, we control the amount of M6P receptors on certain cells. Have a lower amount of M6P receptors as you go outward in the body (IE more on the surface than basal layer). Allows for much less systemic spread because major sites of infection have less M6P receptors.

Picornavirus Assembly

-Picornaviruses are often lytic but sometimes lysogenic GENERAL STEPS: 1. kiss and spit entry 2. Some of the genome gets associated with membrane vesicles, where genome replication occurs 3. Some of the genome is translated into a polyprotein and then cleaved. The proteins can create an empty capsid, but it isn't very stable. It may do this to keep the local concentration of monomers high so that they stay together when they are needed to form with the DNA. 4. Genome and the empty capsid can come together to make a provirion that is more stable. 5. Proteolysis occurs on the provirion to make the mature virion 6. virion leaves through the cell membrane. nobody totally knows how

Hepadnavirus Assembly

-after the genome is made, the concentration of envelope proteins determines what happens -is there aren't enough, it goes back to the nucleus for another round of replication. -if there is enough envelope proteins present, it forms internal membrane budding sites and is secreted.

prophage

-also called provirus -phage genome incorporates into the host bacterial genome

T4 Genome loading into capsid

-T4 builds concatemers via recombination -the head can hold slightly more DNA than the genome length -Therefore, more than a single genome length is packaged into the head. -When we map the genome, it initially appears circular

Extrinsic pathway of inducing apoptosis

-There are Fas death receptors on the cell, and a killer CD8 lymphocyte containing the Fas ligand (only when it is activated) -Fas ligand binds the Fas death receptor -this forms the DISC complex (death induced signaling complex) made of FADD adaptor proteins (containing a death domain and a death effector domain) and a procaspase-8 or 10 containing a death effector domain also -When Fas binds its receptor, it activates the inside portion to build up this complex, where these free FADD adaptor proteins bind and then once this is assembled procaspase-8/10 will bind -This DISC formation activates the protease activity which then clips the procapsase-8/10 to activated caspase-8/10. -cleavage makes the active protease that will go through and activate executioner caspases -this leads to an apoptotic target cell multiple levels to ensure that the cell needs to become apoptotic if actually necessary -for example if the DISC complex forms, it doesnt mean the cell will become apoptotic, it will just activate the caspases which go on and activate other things. Executioner caspases activated is when theres no turning back

Influenza infection

-acute -has antigenic drift that allows for variation in the binding sites. We see a ton of changes in the structure, but not in the receptor binding site. -Influenza is evolving to not be targeted by the immune system by changing the areas that antibodies might recognize

Dengue infection

-acute -type of flaviviridae -resistance to one strain actually makes you more susceptible to others. -In the primary infection, monocytes are not infected. Certain antibodies are made after this primary infection as a result of memory. -If you have a secondary infection with a different strain, the antibodies are able to bind, but instead of neutralizing, they basically just bring the virus to the monocyte. -The virus has basically hijacked the system and uses antibody binding to target it to the monocyte. Once it gets inside, it uses the monocyte to make more progeny.

Types of Infections

-acute- rapid onset, short duration. leave so quickly that no host memory is made. adaptive response is enough to clear the infection fully -subclinical- nearly or completely asymptomatic -persistent- mostly subclinical, prolonged -chronic- type of persistent that is eventually cleared -latent- never completely eliminated; microbe exists in host tissues without causing symptoms. Have on and off states -slowly progressive -tumorigenic WAYS TO DISTINGUISH BETWEEN THESE -production of infectious virions -ability to kill host cell -observable symptoms -duration of infection

Epstein-Barr Virus (herpes)

-latent -Epstein-Barr is the cause of mono 1. After primary infection, lies latent in B cells 2. Latent virus has cell express certain viral proteins that maintain the genome. Also expressed proteins that mimic signal proteins to induce cell replication, which also replicated the virus. This replication also often activates the virus, causing hosts to exhibit symptoms.

HSV-1 infection

-latent -in the HSV-1 infection, there is either VP16 or there isn't. Reason for this difference is that as host cells replicate, the concentration of VP16 lowers. Can eventually make progeny without VP16, which is when we see latency. VP16 PRESENT: (ACUTE) 1. alpha genes expressed 2. beta and gamma genes expressed 3. acute infection NO VP16 PRESENT: (LATENT) 1. alpha genes not expressed 2. latency- expression of LATs (latency associated transcripts) and miRNAs. These inhibit the expression of alpha gene ICP0. 3. External stimuli can lead to expression of alpha gene ICP0, which then up-regulates itself. 4. high enough amount of alpha ICP0 can reactivate acute infection AFTER REACTIVATION 1. neurons express ICP47 protein, which shuts down the protein that triggers the alert response in the host. 2. This gives the virus a short window to replicate without an immune response 3. Eventually natural killer cells recover and start producing interferon gamma that allows host to overpower ICP47. 4. Normal host response happens, and the virus is forces back into latency

Examples of vertical transmission

-vertical transmission refers transfer from mother to baby. Can happen at a couple different times: transplacental, during birth, or after birth (includes breast milk). NOTE: there is some debate about whether breast milk transfer is vertical or horizontal -Horizontal transmission refers to transfer in the same generation, so like between siblings -C sections can help avoid the spread during birth -exposure at such early points in fetuses can cause abortion, congenital abnormalities, and lesions. Also leads to persistent infections in the life of the child because their immune system is formed around the mothers. It is basically taught that the virus is self, so they don't mount a response against it. EXAMPLES: -Rubella (toga)- Transfer: transplacental. adverse outcomes: death of fetus, congenital abnormality, persistent infection -CMV primary (herpes)- means mom got initially infected during pregnancy. Transfer: transplacental. Adverse outcomes: possible death of fetus, congenital abnormality, persistent infection -CMV reactivated (herpes)- mom got infected before pregnancy, reactivates during pregnancy. Transfer: during birth and after birth (breastmilk). Adverse outcomes: persistent infection. -HIV1- Transfer: probably transplacental, during birth, and after birth (breast milk). Adverse outcomes: babies often develop AIDS early, persistent infection -HBV (hepadna)- transfer: transplacental, during birth, after birth. Adverse outcomes: persistent infection -HSV genital (herpes)- transfer: transplacental, during birth, after birth. Adverse outcomes: death of fetus, herpes lesions, persistent infection -HPV (papilloma)- transfer: during birth. Adverse outcomes: persistent infection

Entering the blood

-viremia-virus in the blood STEPS: 1. passive viremia- no replication in the organism 2. Primary viremia- initial amplification. some replication before entering the blood. Generally infect organs with lots of blood 3. secondary viremia- when transmission occurs. more systemic spread. more transmission occurs usually, but not often from the brain

Lambda Decision between Lysis and Lysogeny

-we learned about the lytic before a little bit. Q must be expressed to make late mRNA. THINGS TO BE ABLE TO IDENTIFY: -promoters- Pint, PL, PRM, PR, PRE, PR' -operators- OL1, OL2, OL3, OR3, OR2, OR1 -terminators- TL1, TR1, TR2/3, TR4 -proteins- N, Q, cro, CI, CII, CIII, int, xis IMMEDIATE EARLY -PL-> TL1 to make N -PR -> TR1 to make Cro -PR1 -> TR4 to make short RNA -all other promoters are off (DELAYED) EARLY -N antiterminating the PL-> TL1 to make CIII (Recombination proteins) -Cro antiterminating the PR-> TR1 to make CII and Q (replication proteins) LATE (LYTIC) -Q starts binding to TR4 -Cro starts to accumulate and bind to operators (OL3 and OR3 first). These are the farthest away from PL and PR. At this point, the operator is still not inhibiting. -by the time Cro accumulated to binding to all Operators, this completely shuts down PL and PR so that the only thing running is PR'. Can go through TR4 because of leftover Q LATE (LYSOGENIC) -CII activates Pint and PRE. The promoters are not functional without CII binding to it. -CII activating Pint produces integrase that integrates the virus genome into the host genome at site att. -CII activating PRE (repressor establishment) starts to make repressor (CI). PR and PRE go in opposite directions so they have a conflict. Interfering with PR means you are less likely to make Q which means you aren't ever going to make the lytic genes. -CII is very sensitive to proteolytic activity. CIII binds to CII and protects it. Expression of both (CII and CIII) are required for stable CII binding to promoter. -As C1 accumulates, it will also bind to operators (binds at OL1/2 and OR1/2 which is opposite of Cro). This immediately shuts down PR and PL. -Shutting down PR and PL means you no longer make CII or CIII. while you would think this would be CI essentially shutting itself down, it actually is able to activates its own expression from PRM. Constant expression of CI. -As CI increases, it will eventually bind to OR3 and OL3. When it does so, it shuts down the expression of CI. Ci levels drop, it lets go of the promoter. CI levels increase, it binds again. Does this to maintain a certain level of CI. -Don't want too much CI because it might make it hard to sense the SOS RecA response from bacteria. REMEMBER: RecA eats up CI to push lytic. -It is so sensitive to this level that sometimes in replication, one cell wont have enough CI to keep everything shut down. The cell can go lytic. This is why we saw some spontaneous plaques in lab. GENERAL SUMMARY: -both lysis and lysogeny- PR, PL, PR' active to synthesize N, Cro. Antitermination by N to synthesize CIII, CII, and Q -Lysis only- Low Cro levels binds to OR3 to shut off PRM. High Cro levels shut of PR and PL. antitermination by Q -Lysogeny- CII stimulates expression from PRE (CI repressor) and Pint (integrase). CIII stabilizes CII. CI repressor shuts of PR, PL, PR' (no lytic functions), stimulates PRM.

Herpesvirus (HSV) assembly and trafficking

1. Buds out of nucleoplasm and into ER. 1 end 2. Fuses with other side of ER and loses envelope. 0 env 3. Buds into Golgi where it picks up a different envelope with different proteins. 1 env 4. Vesicle is packaged (with the membrane) into secretory vesicles. 2 env 5. That fuses with the plasma membrane. 1 env Issue is that you need to move the virions pretty far along axons. Don't want to go back to the CNS because that is deadly. Want to go latent and spread without ever killing the host SOLUTION: -leaving cell: virion in vesicle, use kinesin -coming in: virion not in vesicle, use dynein

Poxvirus assembly

1. Crescent almost planar membrane (maybe from ER?) wraps around DNA and other proteins. 2. Come together into an immature virion. Sometimes this will accidentally close without the DNA and then the DNA gets slurped in, sometimes it wraps around the DNA immediately. 3. Some kind of processing event to make a "intracellular mature virion" that has a viroplasm. 4. host Golgi or early endosome vesicles wrap around the host mature virion and fuse, adding on 2 extra membranes. Called IEC (intracellular enveloped virion). 5. This can fuse to plasma membrane. membrane from the outer layer stays associated with the virion. virion is kind of stuck 6. A36R protein attached to IEV. This associates with kinesin and moves along microtubule 7. Fuses with plasma membrane, associating virion with membrane. Called CEV (cell associated virus) 8. B5R on other side of CEV activates Src when it comes into contact with some receptor 8. Src kinase phosphorylates A36R 9. this phosphorylation triggers the actin polymerization, pushing away the cell associated virus.

Transport Along Neurons

1. Enter the neuron at the axon, sensory terminal, or cell body, depending on site of infection. 2. Transport the virus particle or sub-viral particle toward the cell body of the neuron where replication occurs 3. Replicate the genome 4. Assemble virus particles that egress from the infected neuron in a directional matter -Retrograde- toward CNS -Anterograde- Toward PNS

Role of environmental glucose in choosing between lytic and lysogenic

1. GLUCOSE LEVELS AND ADENYLATE CYCLASE -high CAMP levels indicate low levels of glucose. -CRP-cAMP activated expression from PRE (forces lysogenic) 2. CAMP AND HFLA PROTEASE OPERON -HflA- high frequency lysogeny. inhibits lysogeny by chewing up CII. -as cAMP levels increase due to low glucose, expression of HflA protease decreases. CRP+cAMP serves as repressor to push lysogenic 3. HFLA PROTEASE COMPLEX AND CII CLEAVAGE -HflA protease cleaves and inactivates CII transcriptase activator (activates PRE and Pint).

General steps to build a virus

1. formation of individual structural units of the protein shell from one or several viral proteins 2. assembly of the protein shell by appropriate, and sometimes variable, interactions among structural units 3. Selective packaging of the nucleic acid genome and other essential virion components OPTIONAL: acquisition of an envelope 4. release from host cell OPTIONAL: virion maturation -naked viruses sometimes need a membrane while replicating, just don't have one in the mature virion

Propose 3 hypotheses to explain how virus replication if often limited to certain tissues

1. receptor presence on surface 2. certain host transcription factors 3. local environment (like pH) 4. Host factors required for maturing progeny (like proteolysis) not a complete list

Phenotypic effects of lysogeny

1. superinfection immunity to either the same type of virus or to other viruses. EX: lambda by lambda or T4RII by lambda 2. DNA methylation patterns. EX: dam methylase of P1 virus 3. Insertional mutagenesis. EX: inactivation of lipase and beta-hemolysin genes in S. aureus 4. specialized transduction- gal and bio by lambda virus 5. changes in cell wall- changes in O antigen carbs of salmonella by epsilon virus 6. production of exotoxins- Shiga toxin, diptheria toxin, enterotoxin, choleratoxin, etc

structure of antibodies

2 heavy and 2 light chains protein made up of 4 polypeptides help together by disulfide bonds between the cysteines Heavy chain doesn't vary very much blue regions are the highly variable regions containing the epitope binding site. the yellow C regions are constant regions FC receptors stick to the constant region to note its an antibody (dengue) some viruses/bacteria bind this constant region and use it to disguise itself arms rotate freely paratope binds the epitope region in the light chain

Which of the below viruses is least likely to have a packaging signal required at one end of the genome? A. HSV B. Polio C. T4 D. lambda

Answer: T4 because there isnt really a set end of the genome since it is always cut at different spots.

response to antigens

Antigens come in through cut or something this leads to: a humoral response -B cells activated to generate antibodies against virus particles T helper cell also helps by sending out different specific cytokines that activate specific B cells. cell mediated response: (better for getting rid of virus to kill the cell) where naive T cells that differentiate in T helper or Ctl. If T helper cells are directed in a particular way to activate CD8's and get them geared up to look for infected cells. infect cell is presenting using MHC proteins whats inside, and if it is recognized as foreign by the T cell receptor then signals will be sent (fast ligand and fast receptor building the death domain complexes, and other secreted components to induces apoptosis)

Stopping infection via suicide: apoptosis

As apoptosis begins the cell begins to change shape (cytoskeleton is cleaved, and lamins that support the nuclear envelope are degraded) Nuclear envelope is then fragmented leading to fragments on DNA that begin to form apoptotic bodies then macrophages come and clean up the apoptotic bodies (coating on outside to make them irresistible to macrophages- coating is phosphotidle serine) on the cytosolic leaflet of the PM, but when the cell is undergoing apoptosis, the phosphotidle serine gets flipped to the outside by flipases

Antigen Presentation

Dendritic cells serve as Narcs immature dendritic cell is like a street cop walking around. say it walks around and finds a criminal -ie it detects a virus or virus protein through its pattern recognition receptors (ie the Toll-like receptors ) or say that the cop hears screams -ie inflammatory cytokines or say that the cop stumbles over a dead body -ie dead or dying apoptotic bodies then as soon as the naive/immature cell is alerted, maturation occurs, Nf-kb (TF) is activated, and migration to the lymph node spreads out and presents everything out on its surface so that other cops can go by and test what is on its surface it may alert a different naive T cell and becomes an activated and directing against the pathogen (if it is a virus it is an intracellular pathogen, and if it is a bacteria it is an extracellular pathogen) HIV binds CD4 (ie targeting naive T cells) crippling the connection between the innate and adaptive immune response

Influenza Assembly

GENERAL STEPS 1. segments travel to the nucleus. steals caps to make mRNA that get exported and translated. 2. some of the products are M1 (matrix protein) and NEP (nuclear export protein). 3. M1 and NEP imported into nucleus where they interact with RNA. This is the nucleocapsid.NEP has a NES (nuclear export signal) that interacts with exportin to get out of nuclear pore. 3. At the same time, some translation occurs at ER membrane where the protein gets imbedded in the ER membrane (like cell bio). Specifically hemagglutinin, neuraminidase, and M2 are made. Pass through Golgi and get imbedded in plasma membrane. 4. AS they accumulate on the membrane, neuraminidase cleaves off the Sialic acid so that as soon as the virus buds away, they wont come right back. 5. Once in the cytoplasm, all 8 RNA segments form an organized complex. The complex interacts with M1 on membrane and the envelope proteins. HOW DOES INFLUENZA TRANSPORT AROUND CELL? -PROTEINS: normally, cargo proteins go from ER to Golgi to plasma membrane. proteins use this system -SEGMENTS: hitch a ride with another normal cellular process. Interact with recycling endosomes by interacting with resident protein on the endosome. These travel from MTOCs to PM.

Intrinsic pathway for inducing apoptosis

Intrinsic pathway: uses mitochondria that lose cytochrome c (in the intermembrane space) signal comes from within that it needs to undergo apoptosis (adaptive response is extrinsic when another cell tells the cell to die) 1. The mitochondria receives a apoptotic stimulus that causes release of cytochrome c (through a pore -stop preventing the pore from forming) that is normally within the inter-membrane space of the mitochondria. (a lot needs to be released) 2. cytochrome c then binds Apaf1, activating it, and causing hydrolysis of bound dATP to dADP 3. There are conformational changes that cause the CARD domain to be available. 3. assembly of apoptosome triggered by release of dATP in exchange for dATP (or ATP) 4. recruitment and activation of procaspase-9 5. caspase-9 cleaves and thereby activates executioner procaspases, which leads to a caspase cascade leading to apoptosis

Influenza Tropism

LEFT PICTURE -used to call the cells clara cells and the enzyme tryptase clara. Clara was a Nazi so we changed the name to Club cells -Club cells secrete tryptase club that cleaves Hemagglutinin on virions to make functional influenza virions. -cleavage allows for fusigenic peptide to mobilize upon acidification once inside the host cell. -club cells can be infected with influenza and will produce virions, but without tryptase club, they wont be infectious because they cant fuse If you were to expose cervical carcinoma cells to influenza in culture, would the virus replicate? -the virus would infect HeLa cells and they would produce virions. However, there wouldn't be a plaque because the virions that were produced were not activated. -get an initial infection, but does not produce infectious progeny virions RIGHT PICTURE What is tryptase were present throughout the body? -the virus could go systemic because it could infect virtually all of your cells. -Saw this in a H1N1 mouse adapted WSN strain -saw that it always went systemic -plasminogen is found all over the body. plasminogen is converted to plasmin (protease) that can cleave HA. Normally, (bottom picture) neuraminidase is heavily glycosylated so that plasmin cant get in close contact to cleave HA. The mice had a mutation (top picture) that was a loss of glycosylation that allowed NA binding onto plasmin and then plasmin would cleave HA.

Viral Epidemiology

MECHANISMS OF TRANSMISSION -aerosol -food and water -fomites -body secretions -sexual activity -birth -transfusion or transplant -zoonoses (animals, insects) FACTORS THAT PROMOTE TRANSMISSION -virus stability (enveloped tend to be less stable than naked) -virus in aerosols and secretions -asymptomatic shedding -ineffective immune response GEOGRAPHY AND SEASON -vector ecology (habitat and season) -school year -home heating season RISK FACTORS -age -health -immunity -occupation -travel -lifestyle -children -sexual activity MEANS OF CONTROL -quarantine -vector elimination -immunization -antivirals CRITICAL POPULATION SIZE -number of seronegative susceptible individuals. seronegative means you don't possess antibodies against infection.

Factors that determine viral tropism

Many of the receptors used by viruses are on all types of cells, but there is still tropism. WHY? 1. Permissivity- selective expression of host products by transcription factors 2. accessibility- can they be functional in that environment. ex: blood brain barrier 3. Local intrinsic and innate defenses- some barriers are easier to cross than others. how likely are you to undergo apoptosis

Determinant of nature and severity of viral diseases

NATURE OF THE DISEASE -Target tissue- site of entry, ability of virus to gain access to target tissue, viral tropism, permissivity of cells -strain of virus SEVERITY OF THE DISEASE -ability to kill cells (cytopathic effect) -immunity to virus -intact immune response (previous exposure) -immunopathology (do you have a good immune system) -quantity of virions inoculated -duration of infection -general health of the host -host nutritional status -other infections which might affect immune response (like HIV) -host genotype -age of the host (babies and old people have worse immune system)

Virus Budding

PROCESS: -Virions bud away from the cytosol (backwards compared to the main way in cells). -The cell mainly normally uses coat proteins for budding, but these are all in the cytoplasm so it cant go away from the cytoplasm using coat proteins. -the virus budding process resembles normal cell multivesicular bodies. In normal cells in late endosome, see a lot of uniform vesicular bodies (multivesicular bodies). The pathway is associated with recycling membrane proteins where they are pinched into late endosome and then send to lysosome to get destroyed. This normal pathway is called ESCRT complex. -Viruses use ESCRT complex, but don't only do it at the endosome. do it at a bunch of different sites specific to the virus type. BENEFIT OF BUDDING IN INTERNAL MEMBRANES RATHER THAN PLASMA MEMBRANE: -if virus buds from plasma membrane, it would be putting a lot of proteins on the surface that could easily bind to antibodies and get detected -Budding on the inside, there isn't as much exposure to antibodies.

Viruses open squeaky doors: activation of cell signal pathways

The virus binds to the receptor which can lead to... 1. Translation, and viral proteins released into the cell bind with cellular proteins 2. uncoating, exposure of genome, mRNA synthesis, replication, accumulation of viral RNA, binding to cellular proteins 3. various stress responses, ie protein overload in the endoplasmic reticulum

Activation of RNaseL

activated by 2' -5' Trinucleotide by bindin g of interferons to their receptors to stimulate the synthesis of : makes long oligio between 2' and 5' connections -inactive 2', 5'-A synthetase which becomes active when viral dsRNA is present (common with viruses) As a result of oligonucleotide being made, it binds and activates RNaseL which cuts up mRNA in the antiviral state this oligo product is made, but it is not active yet until it is sure that there is a virus (through dsRNA) knocks out virus and host RNA to halt translation

Which route of transmission from neurons most frequently occurs from HSV infections? a. anterograde b. retrograde c. neither

a. anterograde. anterograde direction is where we see cold sores. Retrograde infections are deadly

Cytokines - the short list of effector molecules released by innate defenses

interferon gamma (IFN-y): -Herpes virus -source: T cell/NK cell -target: activates macrophages; promotes adhesion of the Th cells to vascular endothelium; inhibits IL-6 effects; INDUCES ANTIVIRAL STATE interferon alpha/beta (IFN-a/B): -source: immature dendritic cells; many types -Target: INDUCES ANTIVIRAL STATE; inhibits cell proliferation; stimulates growth and cytolytic function of NK cells; increases expression of MHC class I and decreases expression of MHC class II Tumor necrosis factor (Tnf-a): cytokine -source: Tcells/ macrophages -target: Activates neutrophiles; induces inflammatory response, fever, and initiates catabolism of muscle and fat; induces adhesion molecules on vascular endothelial cells; potentiates lysis of some virus infected cells -Helps induce inflammatory response part of the antiviral state is the increase in proteins that present material

STING

intrinsic response detecting DNA in the cytoplasm 1. DNA virus enters via endocytosis 2. uncoats 3. DNA in the cytosol get recognized by an enzyme called cGAS that then makes cyclic GAMP (2'-5') (ATP and GTP made cyclic) 4. Unusual product cGAMP will bind to a receptor on the ER, that is maintained on the ER membrane called Sting 5. Binding results in recruitment into transport vesicles that will send it to the Golgi (normally the receptor is maintained in the ER) 6. In the Golgi it bumps into other proteins that can then lead to a signal transduction event of transcription factors that will cause changes in gene expression (Nf-kb is a TF used in this pathway that is also used in HIV, and Irf3 is an interferon in the innate response)

Routes of Transmission/Entry in Humans

know one example for each SKIN -arthropod bite- bunyavirus -Needle puncture, sexual contact, abrasion- Hep C, HIV -Animal bite- rhabdovirus RESPIRATORY TRACT -localized upper- rhinovirus -localized lower- influenza A and B -Respiratory tract to systemic- Measles ALIMENTARY TRACT (GI) -systemic- enterovirus (polio) -localized- coronavirus UROGENITAL TRACT -systemic- HIV -localized- papillomavirus EYES -systemic- herpes simplex -localized- adenovirus (pink eye)

innate response- interpreting molecular signals

lots of TLR (toll-like receptor) that are pattern recognition receptors recognize a variety of things (parts of the virus like double stranded RNA, or particular proteins, types of lipids atypical in host) this leads to signaling pathways to give info to the nucleus to make certain types of genes like interferon (all factors that are involved in activating the expression of the gene) interferon is then secreted and can bind to a receptor on the same cell to activate itself, but also can activate neighboring cells interferons generate anti-viral states in the cells

components of the adaptive immune system

lymphatic system (green) -movement of fluids leaving circulatory system into the lymphatic system then goes back into circulatory system. -lots of lymph nodes that dendritic cells run to (ie the police station) -bone marrow origin for T and B and white blood cell, and where B cell education takes place -thymus is where T cell education takes place -spleen and lymph nodes help in activating lymphocytes -lymphatic ducts -blood vessels

Innate immune response - interpreting molecular signatures

more coordinative effort there is generic patterns that are used to generate an immune response 1. pathogen comes in and is recognized by a pattern recognition receptor (looking for pathogen specific patterns ie anything that is not self/ foreign) 2. If the pathogen is not recognized then we are done and there is no innate or adaptive immune response. (however most viruses are recognized) 3. pattern recognition receptors activate the innate immune response through the use of cytokines 4. dendritic cells are surveying what is out in the environment and if it gets something pathogenic its alerted and elicit and innate response. 5. activation of dendritic cells and natural killer cells (NK cells) pushes towards the adaptive immune response (identify more specifically/adapts/fine tunes what virus to get effective B and T cells)

PKR inhibits translation via eIF-2

once translation is initiated, it goes from a GTP bound state to a GDP bound state (inactive form) uses eIF2B as a Gef to kick out the GDP and let GTP bind thus reactivating it for the second round eIF2 kinases when ER stress occurs and protein unfolding happens activates PERK pathway that activates a kinase that will phosphorylate and halt translation when eIF2 gets phosphorylated, this can no longer have the exchange take place and so it is unavailable to take place in the pathway and is maintained inGDP bound state and halts protein synthesis eIF2 when phosphorylated also activates autophagy, which directs autophagy to the area with lots of dsRNA

key players in adaptive immune response

players in primary immune response B cells: educated in bone marrow -antibodies start as transmembrane bound receptors on B cells (have the transmembrane domain through different poly adenylation). -antibodies then bind to antigens and those particular antibodies are activated. -they then make a whole bunch more of those antibodies that were activated and then change the poly adenylation site so that the antibodies are secreted (without transmembrane domain) T cells: educated in thymus two flavors -CD4 T cells. Called T helper cells. Have a receptor (kind of like the B cell receptor) called a T cell receptor (Tcr) with the highly variable region that can bind to a bunch of different things, but it doesnt act as an antibody. It acts as a way of detecting foreign substances, often times peptides. They also kinda play with dendritic cells by spitting cytokines at one another. They get together because the Tcr recognized one of the antigens being presented on the dendritic cell. It only recognizes and forms a strong interaction when it recognizes something foreign. -CD8+ T cell referred to as cytotoxic T cells. Help to mount an immune response. Tend to be cytotoxic and can kill. When it recognizes something on the dendritic cell it is able to mount a strong immune response (kill indirectly- extrinsic response). need to focus on how these key players only function when something really is foreign, and how this works (ie why do autoimmune response happen and cause allergies) something kills or stops these cells if they try to mount a response against our own cells each has highly variable regions that can bind to virtually anything but have been selected for so that they only bind to things that are foreign. `

suggestion to why some viruses have seasonal variation patterns

respiratory transmission requires aerosols of a particular quality virus particles are stable; droplet nuclei form at relatively low humidity. The dryer environment tends to happen at colder temperatures (maybe why winter seasons lead to more colds that are spread through aerosols). as the humidity increase, virus particles are also more stable when its cooler (around 5 degrees C) and particles are unstable at warmer temperatures (20 C) then as the humidity becomes warmer, the virus particles become more stable; droplet nuclei form then more and more humid makes them less likely to transmit but where does the virus go after this season (ie influenza can transmit to the southern hemisphere)

RNAi

sensing and shutting down expression of "bad" genes activated by dsRNA (occurs with class III if released from core, class IV, V, also some class I that can generate dsRNA (ie adenovirus because both strands expressed and generates strands that are complementary to each other)) 1. dsRNA gets recognized by DICER which will fragment those into smaller (20 nucleotides in length) 2. The fragments gets loaded into a complex with Argonaut. This complex is refered to as an RNA silencing complex or RISC) 3. denature the RNA into single strands and then us the single strand to find complementary strands of RNA and cut them at that site (RNA form of CRISPR) exposes 3' and 5' end so that the RNA can be degraded