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Science

New Imaging Sheds Light On Basic Building Blocks of Life 49

Posted by samzenpus
from the look-at-that dept.
An anonymous reader writes "Scientists at the UK's national synchrotron facility are studying the structure of Containment Level 3 pathogens such as Aids, Flu and Hepatitis. They use high intensity X-Rays to study the atomic and molecular structure of pathogens too small to be examined under a microscope. This leads to a greater understanding of how they work. They have already produced results on the hand, foot and mouth virus. This is the first time Level 3 pathogens have been imaged in this way."
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New Imaging Sheds Light On Basic Building Blocks of Life

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  • So Polio and Foot and Mouth Disease, done decades ago, don't count?

    http://www.rcsb.org/pdb/101/motm.do?momID=20 [rcsb.org]

    • This is the first time Level 3 pathogens have been imaged in this way.

      What, on the page you linked to, contradicts this? It doesn't even seem to be about imaging.

      • by DrCJM (827451)
        The page is the summary, at the public repository for all biomolecular structures, of the viral capsid structures (determined by X-ray diffraction, just as in the OP linked story) for picornaviruses including polio and foot-and-mouth as well as less pathogenic virus such as rhinovrius. EV71 is just another picornavirus. If you'd taken the time to actually read anything on the page I linked you'd have noticed hyperlinks to the detailed structures for each virus, such as the PDB entry 2PLV for poliovirus whos
        • Rather than feet, you're plucking the words from my mouth. Well said. I'm not sure the OP, as well as other commenters, understands what's novel about this; there's absolutely nothing new about using X-ray crystallography in the study of pathogens, regardless of classification.
          • Re:First time? (Score:4, Informative)

            by the gnat (153162) on Monday February 18, 2013 @08:54PM (#42940735)

            there's absolutely nothing new about using X-ray crystallography in the study of pathogens

            The press release is horribly written. What they're doing that is genuinely novel, AFAIK, is crystallizing actual infectious virus in a biosafety level 3 facility. Usually crystallographers work with just the capsid or some other subset of viral proteins, which requires fewer (if any) special precautions. The native virus particles are typically studied by EM, which typically doesn't yield as high resolution as crystallography, but has the advantage of requiring much more portable and less expensive equipment than crystallography.

            They didn't bother to link to the actual paper, but it is (remarkably) free online [nih.gov].

            • Re:First time? (Score:4, Informative)

              by DrCJM (827451) on Monday February 18, 2013 @09:08PM (#42940829)

              The press release is horribly written.

              On this we agree...

              What they're doing that is genuinely novel, AFAIK, is crystallizing actual infectious virus in a biosafety level 3 facility. Usually crystallographers work with just the capsid or some other subset of viral proteins, which requires fewer (if any) special precautions.

              No, we don't. Intact viral particles are the norm.

              The native virus particles are typically studied by EM, which typically doesn't yield as high resolution as crystallography, but has the advantage of requiring much more portable and less expensive equipment than crystallography.

              While there are lots of EM studies of viral particles, X-ray studies are much more common - 33 full EM models versus 317 diffraction structures. The page I linked in the first response to this article shows just a few of the picornavirus structures that have been determined by X-ray diffraction studies over the past several decades. There are other virus structures out there as well, with an excellent website for anyone interested being Viper [scripps.edu].

              • by the gnat (153162)

                My mistake. Are these studies always done on less pathogenic viruses, then? I would imagine that taking a bunch of crystals of BSL 3 viruses to the synchrotron would present certain problems.

                • by DrCJM (827451)

                  The rules are changing - for the early structures I'm sure care was taken, but the current strict containment rules didn't exist. I can't imagine rocking up to the beamline with poliovirus in your cryostat would be regarded as appropriate behaviour any more... I know that in the past I have been prevented taking crystals of human rhinovirus to some facilities even though as a pathogen it's hardly BSL 3!

                  The only thing that the OP noted that was of interest was the Diamond now has an on-site BSL3 facility so

        • you'd have noticed hyperlinks to the detailed structures for each virus, such as the PDB entry 2PLV for poliovirus whose structure was determined in 1989...

          Again though:

          This is the first time Level 3 pathogens have been imaged in this way.

          The Slashdot story isn't "we've determined the structure of a virus" - it's "we've got a new way of taking its picture."

          • by DrCJM (827451)

            This is the first time Level 3 pathogens have been imaged in this way.

            The Slashdot story isn't "we've determined the structure of a virus" - it's "we've got a new way of taking its picture."

            If you'd like to interpret "we've got a new way of taking its picture" to mean "we're taking its picture in a new lab with slightly different equipment from all the other facilities around the world where X-ray diffraction studies of virus are done" then I would agree with you.

            They have an automated BSL3-level end-station on a beam at Diamond, so that viral crystals of pathogens can be studied. Apart from it being new at Diamond, there is nothing "first time" about this arrangement.

  • by ChrisMaple (607946) on Monday February 18, 2013 @05:46PM (#42939537)
    The causes of foot in mouth disease are too complex.
  • Strange that this reads like a PR puff piece..

    • The synchrotron is a publicly funded project, they should churn out more info like this and more often to show this is useful.
      • by the gnat (153162)

        The synchrotron is a publicly funded project, they should churn out more info like this and more often to show this is useful.

        Synchrotrons churn out stories like this all the time! Pretty much whenever someone scores a paper in a high-impact journal using their facilities, in fact. Most of the time the research involved is genuinely excellent work, but the actual impact is usually much less than the press releases suggest. They'd like everyone who's paying for the facilities to think they're on the verge

  • Wait a second... (Score:5, Interesting)

    by fuzzyfuzzyfungus (1223518) on Monday February 18, 2013 @06:21PM (#42939757) Journal

    AIDS(which, while nasty, is pretty stubbornly fluid-borne) shares a containment level with the flu(which, while merely annoying, cuts a broad and temporary swath through the population pretty much every time somebody gets the winter sniffles)? Are 'containment levels' based much less on ease of transmission than the name would suggest?

    • Re:Wait a second... (Score:5, Informative)

      by scheme (19778) on Monday February 18, 2013 @06:36PM (#42939873)

      The contaimination levels are explained in this article [wikipedia.org]. I believe aids and influenza are both BSL-2. I think the levels are based on ease of infection, potential severity, and treatments. AIDS is pretty hard to get outside of fluid transmission but it's pretty severe once you get it . OTOH, influenza A is fairly easily transmitted but most people recover (~30,000 die each year from it in the US).

    • Re:Wait a second... (Score:5, Informative)

      by ColdWetDog (752185) on Monday February 18, 2013 @06:45PM (#42939943) Homepage

      Just in the quick reading I've done, there appears to be at least a couple of different definitions involved here.

      There are Biosafety Levels [lbl.gov] that discuss the level of sterilization and staff protection appropriate for the vector. Organisms with airborne infectivity (ie, Influenza) are BL 3. Interestingly, the reference that I pulled doesn't describe HIV.

      For BL 3

      BL3 is applicable to facilities in which work is conducted with indigenous or exotic agents that may cause serious or potentially lethal disease as a result of exposure by the inhalation route.3

      Then there is Physical Containment (PC) [amr.org.au] levels:

      Risk Group 2 (moderate individual risk, limited community risk) - a pathogen that can cause human, plant or animal disease, but is unlikely to be a serious hazard to laboratory workers, the community, livestock, or the environment; laboratory exposure may cause infection, but effective treatment and preventive measures are available, and the risk of spread is limited. Generally work with Risk Group 2 microorganisms shall be carried out in Physical Containment level 2 (PC2).

      Risk Group 3 (high individual risk, limited community risk) - a pathogen that usually causes serious human, plant or animal disease and may present a serious hazard to laboratory workers. It could present a risk if spread in the community or environment, but there are usually effective preventative measures or treatment available. Work with Risk Group 3 microorganisms shall be carried out in Physical Containment level 3 (PC3).

      Seems confusing which doesn't surprise me.

      • by cusco (717999)
        We have a customer which creates HIV test kits, which require culturing the stuff. They said that they're required to maintain all live virus in a Bio-Hazard Level 4 lab. Not a location that you want to make a mistake setting up the security on . . .
    • I'm not sure about influenza (BSL-3 requires a respirator, and since influenza is very easy to catch through aerosol, makes sense to protect against breathing it in), but HIV at the University I work at is considered BSL-2* (that's BSL-2 star). Basically BSL-3 minus the breathing apparatus, as you cannot contract HIV by breathing it in. So you double glove, no sharps, and bleach everything down, and make sure everything in there stays in there unless you are absolutely sure the virus is dead.
  • It seems that this summary is suggesting that AIDS, Flu and Hepatitis are the basic building blocks of life. What biology class did samzenpus take?
    • Furthermore, AIDS (not "Aids"), flu, and hepatitis are diseases and not pathogens. The pathogens are the HIV, flu, and hepatitis viruses.
  • This article is about viruses, last time I checked they make you sick. How does this relate to the building blocks of life?

    • by Anonymous Coward
      Viruses are made of mostly the same building blocks of life as humans: proteins and nucleic acid.

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