New Imaging Sheds Light On Basic Building Blocks of Life 49
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."
First time? (Score:1)
http://www.rcsb.org/pdb/101/motm.do?momID=20 [rcsb.org]
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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.
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Re:First time? (Score:4, Informative)
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)
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].
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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.
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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
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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."
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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.
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At a facility whose first stage was opened in 2007? They were going to start on the timetable you suggested; but they couldn't find enough researchers with 10 or more years experience working at the UK national synchrontron facility...
Never done, never will be (Score:5, Insightful)
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The causes of foot in mouth disease are too complex.
Foot and mouth disease? Mostly generated by greedy CONgressMEN. I believe you mean "hoof" and mouth disease.
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Re:this is AWESOME (Score:4, Interesting)
Quantum Mechanics explains Physics (but nobody really knows why).
Physics explains Chemistry
Chemistry explains Biology
All of biology (indeed, all of life) is created from an infinite number of configurations of the same small number of building blocks.
Like Mexican cooking.
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And Theology explains Economics.
Economics is a belief system far beyond the capability of ordinary religious people, and even beyond the capability of quantum physicists.
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Re:this is AWESOME (Score:4, Interesting)
One thing you'll discover investigating that is that your hierarchical arrangement does not necessarily apply, so thinking it universally does can be more of an indicator of scientific illiteracy, rather than literacy.
For example, the constituent atoms of paper money do not determine, and one cannot infer from that, the higher-order property of the money's value (as this is dependent on extrinsic factors, such as the economy). Assuming a universal to reality automatically because it is a premise useful to science, is an epistemological error.
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I may very well be missing the point you're trying to make here, but there seems to be a disconnect between the example you use, and what the post is about.
Money today, seems to me like an abstraction layer between people and the economy at large.
There are no abstraction layers in nature. Form *IS* function, if you want to be pithy about it.
This is the reason there are >88'000 macromolecular structures deposited in data banks; it's been shown over and over again to be very useful information. http://www [rcsb.org]
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This is a much older, much less tractable problem than your aphorism would suggest. [wikipedia.org]
That is not to say
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No, 5 is also true. Your description of "caused by" is irrelevant to "logically derived", which is to say, being able to say -therefore- (mental concept) -given- (specific physical description). The state, however, is simply not the concept, as I thought I had made even clearer than is manifestly obvious. "The next prime in the series 2, 3, 5, 7..." does not have as its correct answer an EEG of someone contemplating the problem. The answer is a number. The biochemical activity is not a number. Simple.
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What do you guys think?
Rambling and somewhat trite, but your heart appears to be in the right place so do keep it up.
Give some thought to looking more closely at a particular branch of science; you might find it much more rewarding to get answers to smaller questions than to philosophise endlessly on the big ones.
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What do you guys think?
We think you should spend less time doing drugs and more time paying attention in class.
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PR? (Score:2)
Strange that this reads like a PR puff piece..
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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)
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)
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)
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.
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Somewhat misleading title (Score:2)
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Uhhh... Building blocks of life? (Score:1)
This article is about viruses, last time I checked they make you sick. How does this relate to the building blocks of life?
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