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New Imaging Sheds Light On Basic Building Blocks of Life

samzenpus posted about a year ago | from the look-at-that dept.

Science 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."

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49 comments

First time? (1)

DrCJM (827451) | about a year ago | (#42939489)

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]

Re:First time? (1)

wonkey_monkey (2592601) | about a year ago | (#42939547)

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.

Re:First time? (1)

DrCJM (827451) | about a year ago | (#42939797)

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 whose structure was determined in 1989... http://www.rcsb.org/pdb/explore/explore.do?structureId=2plv [rcsb.org]

Re:First time? (1)

skitknapp (2844819) | about a year ago | (#42940463)

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? (3, Informative)

the gnat (153162) | about a year ago | (#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? (4, Informative)

DrCJM (827451) | about a year ago | (#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] .

Re:First time? (1)

the gnat (153162) | about a year ago | (#42941057)

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.

Re:First time? (2)

DrCJM (827451) | about a year ago | (#42941163)

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 that you can handle such pathogens within the current regulations.

Re:First time? (1)

wonkey_monkey (2592601) | about a year ago | (#42942487)

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."

Re:First time? (1)

DrCJM (827451) | about a year ago | (#42949963)

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.

Re:First time? (0)

Anonymous Coward | about a year ago | (#42939819)

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.

Reading comprehension is on the decline. That's all.

Re:First time? (0)

Anonymous Coward | about a year ago | (#42940315)

... is now the first and only place in Europe...

Try BioCARS at the Advanced Photon Source in 2004 in the US.

A little late? (0)

Anonymous Coward | about a year ago | (#42939513)

Shouldn't they have started this, say, 15 years ago?

Re:A little late? (1)

fuzzyfuzzyfungus (1223518) | about a year ago | (#42939771)

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 (5, Insightful)

ChrisMaple (607946) | about a year ago | (#42939537)

The causes of foot in mouth disease are too complex.

Re:Never done, never will be (0)

Anonymous Coward | about a year ago | (#42940341)

Virus?

Re:Never done, never will be (2)

slick7 (1703596) | about a year ago | (#42940703)

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.

this is AWESOME (0, Interesting)

Anonymous Coward | about a year ago | (#42939605)

Scientific progress like this is moving along at a rate completely unprecedented in all of history.

These are very exciting times to be alive and conscious.

There is something that you learn, if you are scientifically literate, that goes something like this:

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.

Reading research like this makes me wonder, "What else can we build out of this stuff?"

Understanding how things like viruses are put together and how they work is a step to answering that question.

What do you guys think?

Re:this is AWESOME (3, Interesting)

Sulphur (1548251) | about a year ago | (#42939713)

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.

Re:this is AWESOME (1)

Errol backfiring (1280012) | about a year ago | (#42943505)

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.

Re:this is AWESOME (1)

paiute (550198) | about a year ago | (#42939749)

We have a reasonably good idea of how the basic building blocks work. We could build nucleotide sequences which would lead to proteins of our choice. What we don't know shite about really is the secondary, tertiary, etciary environment in which these things interact. It's like the difference between knowing how to print a dollar bill and understanding the US economy.

Re:this is AWESOME (3, Interesting)

Empiric (675968) | about a year ago | (#42939763)

I think the term you are looking for (for the "philosophy-literate") is Supervenience [wikipedia.org] .

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.

Re:this is AWESOME (1)

skitknapp (2844819) | about a year ago | (#42940595)

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/pdb/statistics/contentGrowthChart.do?content=total&seqid=100 [rcsb.org]

Re:this is AWESOME (1)

Empiric (675968) | about a year ago | (#42940903)

Really. Okay, show me the form of the function of "freedom" (the specific atoms will do, and note that "freedom" here does -not- mean "assumed atoms broadly inferred by EEG readings correlating with a particular selected individual contemplating 'freedom'"--I don't mean that, I mean freedom) as it applies to its presence in biological entities, or deny that "freedom" has functional effect on biology.

This is a much older, much less tractable problem than your aphorism would suggest. [wikipedia.org]

That is not to say biological structures do not have effects and are not scientifically useful to know, it was specifically the assumption of the universality of supervenience I was commenting on.

To put it another way, which of these statements is true?

1. The behavior and nature of all systems are exhaustively determined by their constituent parts.
2. Molecules are purely physical entities, interacting only with other physical entities by physical means.
3. People are constituted of molecules.
4. People have mental states constituted of mental concepts, such as "happiness".
5. No mental concept can be logically derived from any purely physical description.

Re:this is AWESOME (0)

Anonymous Coward | about a year ago | (#42941349)

1 to 4 are true. 5 is false. "Mental concepts" are the result of electrochemical interactions between the molecules in the brain, as clearly shown by the mountains of evidence from patients with brain disorders as well as by those taking mood-altering drugs.

"Freedom" is simply the brain's rationalization of the actions it takes, which is evidenced by the results of split brain experiments (among others).

Re:this is AWESOME (1)

Empiric (675968) | about a year ago | (#42941451)

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.

"The mountains of evidence" simply say the the brain in involved in the process of cognition around the concept, and nothing else.

And no, "freedom" is what it means, which you can refer to the dictionary to determine. It is not defined by your dubious redefinition, and again that the brain is necessary in utilizing it does not address the issue.

Re:this is AWESOME (1)

Empiric (675968) | about a year ago | (#42941503)

To correct my wording for precision, that should read "5 is also plausible". Which are -true- is the dilemma at the core of the Mind-Body Problem.

Re:this is AWESOME (0)

Anonymous Coward | about a year ago | (#42942559)

Has anyone ever told you that you should eschew obfuscation?

Re:this is AWESOME (1)

newcastlejon (1483695) | about a year ago | (#42939799)

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.

Re:this is AWESOME (1)

ColdWetDog (752185) | about a year ago | (#42939827)

What do you guys think?

We think you should spend less time doing drugs and more time paying attention in class.

PR? (2)

Stuy 2 MIT (317723) | about a year ago | (#42939639)

Strange that this reads like a PR puff piece..

Re:PR? (2)

muon-catalyzed (2483394) | about a year ago | (#42939765)

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

Re:PR? (0)

Anonymous Coward | about a year ago | (#42939925)

It's incredibly hard to get crystals of proteins (or whole viruses) that actually diffract and give you information that you can use to obtain a molecular structure with. There's dozens of structures being solved every month, you just have to know where to look. Take a look at the RCSB PDB (http://www.rcsb.org/pdb/home/home.do), scroll down to latest structures, and click the link. There you'll see all the latest protein, RNA, and DNA structures that have recently been solved.

Re:PR? (1)

the gnat (153162) | about a year ago | (#42940787)

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 of curing cancer, but it's usually really basic research - vital stuff, but just one step in a long process. In fact some of us worry about the effect of these stories; it really sets the public up for disappointment when scientists still haven't cured cancer (etc.) ten years later. (The Human Genome Project had similar issues.)

(The big exception to this that I can remember off the top of my head was the recently approved melanoma drug, Zelboraf, which was the result of structure-based drug design based on data collected at the Advanced Light Source in Berkeley. But we never hear about most structures like this, because the pharma companies pay a substantial amount of money to the synchrotrons for the right to keep their results private - it helps offset operation costs.)

Wait a second... (4, Interesting)

fuzzyfuzzyfungus (1223518) | about a year ago | (#42939757)

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... (5, Informative)

scheme (19778) | about a year ago | (#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... (5, Informative)

ColdWetDog (752185) | about a year ago | (#42939943)

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.

Re:Wait a second... (1)

cusco (717999) | about a year ago | (#42940245)

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 . . .

Re:Wait a second... (0)

Anonymous Coward | about a year ago | (#42939945)

I can't help but notice something very wrong here. AIDS itself is not a virus. The Human Immunodeficiency Virus (HIV) is the cause. AIDS is the eventual effect.

Re:Wait a second... (1)

kwyjibo87 (2792329) | about a year ago | (#42941289)

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.

Somewhat misleading title (1)

Algae_94 (2017070) | about a year ago | (#42940223)

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?

Re:Somewhat misleading title (1)

conrad_halling (1335699) | about a year ago | (#42940469)

Furthermore, AIDS (not "Aids"), flu, and hepatitis are diseases and not pathogens. The pathogens are the HIV, flu, and hepatitis viruses.

HIV != AIDS (0)

Anonymous Coward | about a year ago | (#42940397)

AIDS is a syndrome which can be caused by various factors, including but NOT limited to, the virus HIV. Just because you have HIV doesn't mean that you have TEH AIDZ, and just because you have developed AIDS doesn't mean you're HIV+.

I do wish the media (especially a source which is theoretically supposed to be oriented toward technically-minded folks) would get this straight. Maybe it seems to be picking at nits for those who want to just gloss over it all and say "yeah same thing whatever", but HIV+ people have to deal with enough stigma as it is without having to constantly educate a public which still labors under the horrors of the early '90s.

Let's face it, the last time you really heard about HIV or AIDS in the mainstream world was back when it was "the gay disease" or "everyone was dying from AIDS AIDS AIDS AIDS AIDS!" like a sick parody of Team America. Since then, the world (of medicine) has changed radically, and the Slashdot crowd in particular should know this, what with a new story about research on HIV hitting the front page here every week.

TL;DR: HIV = the virus, arguably a lifeform. AIDS = acquired immuno-deficiency syndrome, a condition cancer and lupus patients and organ-recipients, among others, can develop during or because of treatment.

Re:HIV != AIDS (1)

Anonymous Coward | about a year ago | (#42941429)

AIDS is specific to the immune system deficiency caused by HIV. While lupus and many other things cause immune system deficiencies, they are not referred to as AIDS.

Uhhh... Building blocks of life? (1)

wakeboarder (2695839) | about a year ago | (#42941679)

This article is about viruses, last time I checked they make you sick. How does this relate to the building blocks of life?

Re:Uhhh... Building blocks of life? (1)

Anonymous Coward | about a year ago | (#42942109)

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