TWiV 351: The dengue code

August 23, 2015

Genetic CodeHosts: Vincent Racaniello, Dickson DespommierAlan DoveRich Condit, and Kathy Spindler

The Masters of the ScienTWIVic Universe discuss a novel poxvirus isolate from an immunosuppressed patient, H1N1 and the gain-of-function debate, and attenuation of dengue virus by recoding the genome.

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Timestamps by Jennifer. Thanks!

Weekly Science Picks 1:29:35

Alan – Genetic roulette
Rich
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Kathy – Simulated vomiting machine (video)
DicksonLast Cassini Saturn flyby
Vincent – Decaying Still Life (YouTube)

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Ken – Cave meterology (Times, Nature)

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9 comments on “TWiV 351: The dengue code

  1. The ‘letters read’ link points to page for twiv 349 rather than 351

  2. Fiona Tulloch Sep 2, 2015

    Firstly, we would like to thank you for the segment on the current debate as to the mechanism of how viruses can become attenuated through wholescale genome modification. We really appreciated the comments made during the discussion – and enjoyed listening to the viewpoints of those on the panel.

    At one point during the discussion it was suggested RNA structure could play a
    role in the mechanism of attenuation. This had occurred to us, too, so we included a permuted control in our studies (Atkinson et al., 2014; http://www.ncbi.nlm.nih.gov/pubmed/24470146 and eLife paper). Here, the peptide sequence was maintained, but we randomised the order of codon usage – whilst preserving CpG/UpA dinucleotide frequencies. Permuting codon usage in this manner would destroy any undetected RNA structures within these regions of the viral sequence. The replication kinetics of this mutant virus were identical to wild-type, supporting the notion that in
    this case RNA secondary structure is not involved in virus attenuation.

    A key point was made about the use of cell-free translation systems to analyse protein synthesis in the absence of any cellular innate immunity-based translational control mechanisms. We, and Burns et al.,(2006; http://www.ncbi.nlm.nih.gov/pubmed/16537593), carried out such experiments and did not observe any differences in protein synthesis between wild-type and the different mutant viruses.

    Whilst the mechanism of attenuation remains unknown, data generated by Atkinson et al., (2014) demonstrated that high and low CpG/UpA mutated genomes were not sensitive to the cellular IFN response but were, however, sensitive to the addition of the kinase inhibitor C16 (thought to be PKR specific; Jammi et al., 2003): the replication phenotype reversed following inhibitor treatment. With regards to the Dengue paper under discussion, (i) the results in BHK cells and (ii) the effects of the Jak inhibitor 1 upon the attenuated phenotype of both the hmin and NS3hmin viruses (in accord with the C16 Atkinson data), suggest attenuation occurs through an unknown component of a cellular stress response pathway – and does not support the hypothesis of attenuation arising from a defect in translation.

    Again, thank you for highlighting and discussing this topic.
    We think you all agreed it is certainly very interesting and we hope your
    listeners enjoy the podcast as much as we did.

    Fiona Tulloch, Peter Simmonds, David Evans and Martin Ryan.

    • Thanks for your comments, Fiona. Do listen to TWiV #353, as there is a letter from a listener relevant to the mechanism of attenuation. I agree it’s not translation.

  3. 24:00 table 2 irrelevant to the argument. Even if it were true that some
    group used

    publication “tricks” (or bad newspaper headlines, Vincent’s favourite) to
    get more attention,

    that doesn’t tell us anything about the correct,reasonable judgement of the
    issue.

    24:50 Frankenstein does not apply. This is not a public (artificial fear)
    debate,

    but rather an experts discussion.

    25:55 lots of laughter (I didn’t understand, somehow about the origin of
    science-fear)

    27:00 Pittsburg center = origin of (evil) GOF-critics

    [ if they become right, TWiV will enter history as the center of
    GOF-dangers ignorism ?! ]

    [ attacking the arguers, not the argument ]

    27:30

    1977 is no longer an argument ?

    Why would a vaccine trial that went wrong be _any_ better

    than a lab escape wrt. that science-distrust – Frankenstein theme

    or the other examples that gave you so much laughter ?

    There was a danger that the scientists didn’t consider enough

    in their research. It can’t happen again, because now we know

    about that danger and such trials won’t be done ? (in humans)

    What’s the logic ?

    Besides that, I think the paper does bad science.

    When you consider all the segments, not just HA, then it’s clear

    that the common ancester is in summer or fall 1976.

    And the 4-places virus became extinct while the Hongkong virus

    did spread worldwide. They also don’t mention the earthquake

    and the political trouble in 1976. Looks agenda-driven to me.

  4. As for the codon-bias, I remember that Wimmer also used codon
    de-optimization for
    flu (PR8,1934), see TWiV236,10:00-26:20.
    I first saw
    it in a 2006-paper by Rabadan (Columbia,who was also in TWiV, afair) who
    showed
    that Avian and Human flu can be distinguished by their Nucleotide-bias
    :
    human ones have more A,T which was astonishing to me at that time.

    Wimmer et.al. use this for de-optimization and vaccine, but it is clear
    that the same could
    be used for optimization. TWiV didn’t mention this …

    It will probably be more difficult to optimize than to deoptimize, but
    eventually they might
    get the patterns and use computers to effectively
    optimize viruses.
    Similar to what was done with reassortment until it was
    “stopped”.

    23:00

    I couldn’t find the letter on TWiV 353 which led to discussion of the
    mechanism

    BTW., I get this error here:
    https://wordpress.org/support/topic/disqus-browser-legacy-error

    • searching google-scholar for citations of that Wimmer et.al.
      paper on influenza codon-de-optimization :
      —————————————————————————–

      http://www.nature.com/nrm/journal/v15/n2/abs/nrm3738.html
      [2014] Recent
      progress in DNA manipulation and gene circuit engineering has greatly

      improved our ability to programme and probe mammalian cell behaviour. These
      advances

      have led to a new generation of synthetic biology research tools and
      potential therapeutic

      applications. Programmable DNA-binding domains and RNA regulators are
      leading to

      unprecedented control of gene expression and elucidation of gene function.
      Rebuilding

      complex biological circuits such as T cell receptor signalling in isolation
      from their

      natural context has deepened our understanding of network motifs and
      signalling

      pathways. Synthetic biology is also leading to innovative therapeutic
      interventions

      based on cell-based therapies, protein drugs, vaccines and gene
      therapies.

      ——————————————————————————-

      http://www.sciencedirect.com/science/article/pii/S0167779911001636

      Genetic design automation: engineering fantasy or scientific renewal?

      ————————————————————————————

      Large-scale de novo DNA synthesis: technologies and
      applications
      ————————————————————————————-

      http://www.pnas.org/content/110/23/9481.short

      A long-held dogma posits that strong presentation to the immune system of
      the dominant

      influenza virus glycoprotein antigens neuraminidase (NA) and hemagglutinin
      (HA) is

      paramount for inducing protective immunity against influenza virus
      infection. We have

      deliberately violated this dogma … We conclude that the suppression of
      HA and NA

      is a unique strategy in live vaccine development.

      [cited by 21 at google scholar]

      ——————————————————————–

      Efficient manipulations of synonymous mutations for controlling translation
      rate:

      an analytical approach

      ————————————————————————

      Species-specific codon context rules unveil non-neutrality effects of
      synonymous
      mutations
      ————————————————————————–

      Many ways to make an influenza virus–review of influenza virus reverse
      genetics
      methods
      ———————————————————————–

      Slow fitness recovery in a codon-modified viral
      genome
      ——————————————————————–

      Pandemic influenza A virus codon usage revisited: biases, adaptation and
      implications

      for vaccine strain development

      ———————————————————————–

      Synthetic genomics and synthetic biology applications between hopes and
      concerns
      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580775/

      ——————————————————————-

      http://jvi.asm.org/content/88/18/10525.full.pdf

      [they have an algorithm to de-optimize, they detect variants that are
      likely less optimal.

      You can use the same for optimizing. If you know which variants are likely
      less

      optimal, then you also know which variants are likely more optimal]

      —————————————————————————-

      Codon usage in vertebrates is associated with a low risk of acquiring
      nonsense
      mutations
      —————————————————————

      Synthetic genomics: from synthesis of prokaryotic genomes to synthesis of a
      fully

      functional eukaryotic chromosome

      … It also raises concerns about the risks of its use in bioterrorism.

      ———————————————————–

      Event report: SynBio Workshop (Paris 2012)–Risk assessment challenges of
      Synthetic
      Biology
      ————————————————————-

      live attenuated influenza vaccine (LAIV)
      mimics natural virus
      infection, which consequently has risks and benefits [37]

      ——————————————————————————–

      http://jvi.asm.org/content/early/2015/08/07/JVI.01443-15.short

      [Aug.2015] converting its codon usage … to avian … gave a new H1N1
      attenuated

      in humans but not in eggs

      [as well you could start with an avian flu virus and convert its codon
      usuage to human.

      [[There you have your possible Frankenvirus]

      use reassortments and assaging to improve the process. Make a statistics,
      figure out

      which start-viruses lead to most virulent end-results. Find the
      patterns]]

      [[[ loss of function research can be abused for gain-of-function ]]]

      ——————————————————————————

      Large-Scale Nucleotide Optimization of Simian Immunodeficiency Virus
      Reduces Its

      Capacity To Stimulate Type I Interferon In Vitro

      ——————————————————————————

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