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Casey Finnerty

Discussion Ebola Research Needs | Video | C-SPAN.org - 2 views

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    This panel has the best overview of the research needs for Ebola virus that I have seen. It includes the presentation by CJ Peters that I discussed in class.
slgoogin8981

Virus-Mediated Compartmentalization of the Host Translational Machinery - 22 views

  • Similarly, the viral single-stranded RNA binding protein σNS localized to the factory margins and had a tubulovesicular staining pattern that extended a short distance from the margins of the factories and colocalized with endoplasmic reticulum (ER) markers.
    • nleonard11
       
      This reovirus has single-stranded RNA rather than double stranded. Research. σNS is a binding protein that has an affinitiy for single-stranded RNA. Why is it used for doulbe-stranded RNA.
  • We further show that the nonstructural protein σNS strongly colocalizes and immunoprecipitates with two proteins in the 43S preinitiation complex (PIC), eIF3A and pS6R, suggesting a role for σNS in the recruitment or maintenance of ribosomes within VF.
    • laceemarie
       
      If σNS is involved in ribosome recruitment and/or maintenance, this seems like a good target for an antiviral therapy. 
  • This model implies that newly synthesized viral proteins must, by some mechanism(s), be trafficked back into the factory to participate in replication and assembly. Data supporting this model are limited.
    • laceemarie
       
      "Limited," but still exists. So under what circumstances did/could this happen? Could it be a possible way to avoid an antiviral drug that inhibits σNS?
  • ...8 more annotations...
  • Within the VF, viral core particles transcribe and release viral mRNAs that possess a dimethylated cap 1 structure at the 5′ terminus but lack a poly(A) tail (19).
    • alexridesducati
       
      It seems that Reovirus recruits host proteins in order to replicate, and in this sentence we see that the viral mRNAs use a dimethlyated cap vs. the traditional host methylguanosine cap. Does this have any sort of impact on initiation factors associated with the ribosome? The viral mRNA also seems to be lacking in a poly-A tail. Is it because the mRNAs are created in a VF that they dont need to worry about having one?
    • abachman12
       
      I was also thinking the same thing. Does this have any effects on the initiation factors in whole? Does it change anything or do anything different than normal?
  • Consistent with our findings, the authors noted that the rough endoplasmic reticulum (RER) made numerous contacts with VF, which they suggested may indicate a role for RER in the transport of newly synthesized viral proteins to the VF, as is the case for rubella virus (64).
    • joeyevenson
       
      The rough endoplasmic reticulum may be involved in the transport of newly synthesizes viral proteins to the viral factory, could an antiviral that targets the endoplasmic reticulum prevent these newly synthesized proteins from ever getting that far? Does the host do this as a response to the virus? Or is it the virus controlling the cell to transport the viral proteins?
  • To address this, we monitored protein expression levels of eIF4E, eIF4A1, and eIF4G over the course of an infection. As others have found (39), we were unable to detect any difference in the levels of total protein in mock versus infected cells from 0 to 20 h p.i. (Fig. 3C and data not shown). Together, these data suggest that cellular translation proteins are redistributed to the VF.
    • becky214
       
      I am confused as to how the data is showing that these proteins are redistributed to the VF.
  • Most reovirus strains form filamentous VF through an association with stabilized microtubules. However, the T3D strain used in these experiments contains a temperature-sensitive mutation in the viral protein μ2 that prevents this association, resulting in the production of globular VF at 37°C (27, 28). Therefore, to evaluate if PMY labeling occurs within filamentous viral factories, we infected cells with the serotype 1 Lang (T1L) strain. As we found for T3D-infected cells, the PMY labeling localized to T1L VF at 18 h postinfection
    • rmeloche10
       
      Is this temperature sensitive mutation put in place by the authors? Or is the mutation a natural feature of the virus, if it is would there be any reason for inhibiting the micro tubule stabalization? 
  • It was unclear if this was a result of increased expression levels or as a consequence of redistribution of the proteins to the factories. To address this, we monitored protein expression levels of eIF4E, eIF4A1, and eIF4G over the course of an infection. As others have found (39), we were unable to detect any difference in the levels of total protein in mock versus infected cells from 0 to 20 h p.i. (Fig. 3C and data not shown). Together, these data suggest that cellular translation proteins are redistributed to the VF.
    • Sean Hogan
       
      I had a little trouble wrapping my brain around this part. If the IF proteins are expressed at similar levels then what is the cause of the redistribution? Does it have to do with the sigma NS interaction and then eventually the preinitiation complex is recruited?
  • Our finding that σNS interacts with eIF3A and pS6R suggests that translational machinery is recruited to the factory by viral proteins. This is consistent with the finding of others that σNS cosediments with 40S and 60S ribosomes (62) and suggests that σNS is directly involved in viral translation.
    • Sean Hogan
       
      I feel like a  loss of function experiment (sigma NS) would provide an answer for this.  
  • FIG 3  Cellular translation initiation factors colocalize to viral factories. (A, B) CV-1 cells were infected with T3D or T1L at an MOI of 1. At 18 h p.i., RPM-labeled cells were coimmunostained for μNS and eIF4E (A) or eIF3A (B). Scale bars, 10 µm. (C) CV-1 cells were infected with T3D, MOI of 3, for the times indicated. Protein levels were assessed by immunoblotting. M = mock.
    • apopp10
       
      I am having trouble interpreting both this figure and figure 4 immediately following it. How do these figures exactly support the claim that transcription initiation, elongation, termination and recycling factors are recruited to viral factories?
    • slgoogin8981
       
      Does the viral factor protect the dsRNA from RIG-1? Earlier the paper spoke of energy balances, does the viral factor require a lot of energy to be created?
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    Focus paper for friday
Casey Finnerty

Viruses as a Cure - NYTimes.com - 0 views

  • When they prevented germ-free mice from making a receptor on the surface of their cells, infection with norovirus didn’t lead to an improvement in their guts.That receptor only latches onto one type of molecule. It’s called Type 1 interferon, and it’s produced by cells when they’re invaded by viruses.
slgoogin8981

HSV carrying WT REST establishes latency but reactivates only if the synthesis of REST ... - 7 views

  • R111 recombinant is not reactivation-defective because it is able to reactivate in the presence of inhibitors of protein synthesis in the same manner as the WT parent virus, and (b) because the only significant difference in the WT and R111 viruses is the presence of the REST gene in the latter virus, the data suggest that expression of this gene blocks reactivation and that suppression of protein synthesis, including that of REST, enables reactivation.
    • becky214
       
      I am confused about when REST blocks reactivation and when it enables it. It says the gene blocks reactivation but continues to say it enables it. Does REST only enable reactivation if it plays a role in suppressing protein synthesis?
  • with dexamethasone or dexamethasone and cycloheximide
  • Specifically, a stress response generated by virus entry recruits or activates REST to enable the assembly of the HCLR complex. Stress responses have been postulated to activate REST
    • becky214
       
      I think this is interesting because REST is not usually found in neurons. I'm curious as to how the neuron recruits this gene. Does the virus actually recruit it? Or is it just a cellular response to the stress of viral entry? 
  • ...13 more annotations...
  • HSV takes advantage of the neuronal stress response to enter into a silent, latent state. To assist in the execution of this plan, HSV evolved a DNA sequence that allows itself to be suppressed in neurons and a mechanism to maintain an equilibrium between total suppression and potential to exit from the latent state.
  • translocated from satellite cells
  • The fundamental question is the identity of the mechanism by which a vigorously replicating virus, on entry into the body, is silenced in neurons harboring latent virus.
    • laceemarie
       
      Just to make sure that I understand this, once the virus enters the body, it quickly replicates and all the new virus particles find a nerve cell to infect and once there, the virus is able to sit in silence, so to speak?
  • Thus, VP16, a virion protein brought into the cells during infection, recruits several cellular proteins, including LSD1, to derepress α gene promoters
    • laceemarie
       
      VP16, a virion protein and a recruiter - this protein sounds pretty important to me. Is there a way or has there been work done with this protein to not allow the derepression at this checkpoint? Is it possible to keep a virus in latency because of alpha gene promoters not getting derepressed so as to not allow the virus to infect the host? I'm not sure if that's a reasonable antiviral therapy or not.
  • In some neurons, the virus establishes a latent, silent state. In other neurons, the virus replicates, and it is most likely that the virus in these neurons is transmitted and replicates in other ganglionic cells.
    • laceemarie
       
      Is this a random event or does this have something to do with the environment of the neuron? I would assume that specific, different environments would be ideal for each.
  • Finally, in contrast to the events following entry of virus after retrograde transport from the periphery, the data suggest that reactivation does not trigger a stress response that leads to activation of REST
    • alexridesducati
       
      Has anyone been able to pinpoint the exact step in infection that activates REST so that it can be studied? If so, perhaps it is possible to manipulate the effects of that step in order to induce an artificial response to the reactivation of HSV1 from its latency period in order to retrigger the stress response that leads to REST activation.
  • Thus, VP16, a virion protein brought into the cells during infection, recruits several cellular proteins, including LSD1, to derepress α gene promoters. One α gene product, infected cell protein 0 (ICP0), derepresses β and γ1 genes. Ultimately, the onset of viral DNA synthesis enables the expression of very late, or γ2, genes (4).
    • Sean Hogan
       
      Is this why the latent infection occurs in the ganglia of the PNS? The necessary proteins for gene derepression can't be recruited in the CNS or other cells?
  • In contrast, simultaneous expression of all viral genes during reactivation from latency is likely to minimize yield, but the mission of the virus is to assemble enough viruses to reach the portal of egress from the body (e.g., mouth, genitals) rather than to overwhelm the host with infectious virus.
    • Sean Hogan
       
      This might be the coolest statement in the whole paper. The discussion above kind of painted a picture of HSV infecting the PNS only but the reason for it's inability to reach the CNS didn't receive as much attention. I think this statement summed it all up though.HSV doesn't care about high virion yields or whether a productive or latent infection is necessary, it just wants to reach the body portals. The virus is "smart," enough to avoid the CNS and keep it's host alive.
  • Between 5 and 24 h after excision, mRNAs representative of all viral gene kinetic groups increase 100-fold in amount. Viral DNA also increases in amount, indicating that viral proteins are made. At the same time, viral LAT and miRNA concentrations decrease at least 10-fold (34). It is convenient to define the initial phase lasting no more than 5 h as the preactivation phase and the remaining time interval as the activation phase.
    • rmeloche10
       
      I'm having trouble grasping why the massive disparity between viral DNA and viral LAT. Obviously there would be some disparity when reactivation occurs, but wouldn't the production of more DNA contribute to even a small amount of LAT production and not a minimal 10 fold decrease?
  • The same concentration of HDAC inhibitor was ineffective in inducing the reactivation of R111 recombinant virus in ganglionic organ cultures maintained in medium containing anti-NGF antibody.
    • ameliaobert
       
      Interesting: That there is an inhibitor for chromatin remodelling (HDAC). Confusing: Is if HDAC can inhibit properly for WT virus, but not for R111 recombinant, that obtains REST. How does REST make the HDAC inhibitor ineffective ia stressed neuron? I understand that REST is what the DNA can be wrapped about and help with latency, so it that why the HDAC cannot inhibit, since REST is already aiding in latency.
    • nleonard11
       
      I thought this process of finding out that the HCLR complex activates from stress was very interesting. Using WT viral genomes appears to be a very effective way to test many virus functions.
    • nleonard11
       
      I was just wondering why the virus goes into a latent after 30 days? What exactly is it waiting to do and what conditions need to be present for it to become active again.
    • slgoogin8981
       
      It would be interesting to know the amount that REST is seen in non-neural cells and nerve cells in the absents of HSV-1. I was state earlier that REST is not normally found in never cells.
ameliaobert

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation - 2 views

  • The most significant residue, position 97 in the floor of the peptide binding groove of HLA-B, is associated with the extremes of viral load, depending on the expressed amino acid. This residue has been shown to have important conformational properties that affect epitope-contacting residues within the binding groove (26, 30) and has also been implicated in HLA protein folding and cell-surface expression
    • ameliaobert
       
      Most Interesting: That one specific residue can produce high results for a virus for comformational changes pertaining to the epitope binding groove. Most Confusing: If for HLA-B this residue position is important, than in HLA-A and HLA-C what residue would be important for the specific binding grove and conformational epitopes? Would 97 be most important or would if not what would be ther reaonsing behind different residues for different HLA?
Casey Finnerty

No Video. No Photos. No Names. Inside New York's Ebola Monitoring Operation. - NYTimes.com - 0 views

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    This article gives a very good description of the size of the Ebola monitoring effort underway in NYC and around the country.
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