Thursday, April 30, 2009

Laurie Garrett on Flu pandemics, past and future

Courtesy of TED, we have some useful media bringing typically well-informed perspectives on the flu now unfolding. Let's start of with a Q&A with Laurie Garrett, author of "The Coming Plague: Newly Emerging Diseases in a World Out of Balance":



TED took 20 minutes with Laurie Garrett this afternoon to follow up on her TEDTalk from 2007, posted today, about pandemic flu. Garrett is the author of The Coming Plague, and a fellow on the Council for Foreign Relations who studied global health and emerging diseases. (As you can imagine, she is very busy this week.) We asked Garrett: What has changed since the last pandemic panic, 2007's avian flu? What does she worry about now? And really, should we not wash our hands?


Read her responses on the TED website.


TED has also posted video of a lecture Garrett gave in 2007:


In 2007, as the world worried about a possible avian flu epidemic, Laurie Garrett, author of "The Coming Plague," gave this powerful talk to a small TED University audience. Her insights from past pandemics are suddenly more relevant than ever.




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How the influenza virus can drift and shape-shift to keep us on our toes

As you may have read by now, the new swine flu virus, this new strain H1N1 which is threatening to turn into a pandemic according to the WHO (even though there is much confusion about the actual number of infected/dead victims confirmed to have this strain), is actually an interesting genetic mixture, a chimera if you will with a potpourri of genes from different influenza strains: these may be from multiple host taxa — birds (thought to be the original source of all influenza viruses), humans, and, of course, pigs (from North America and Asia!) — or perhaps all from pigs (the picture is still cloudy). In any case, if you are wondering how such reassorted viruses form, the following video paints a cartoon picture to help you understand. The key thing to remember is that viruses, like many other microbes, are rather promiscuous when it comes to swapping bits of DNA - even across "species" - and such lateral transfer can allow new strains to evolve, even drug-resistant ones, much more rapidly. Here's how influenza may be able to shift the shape of its antigens, and potentially jump between host species:






But, that is not the only trick up this virus' sleeve. Ever wonder why, unlike with other vaccinations which are often a once-in-a-lifetime deal, you've got to take that flu shot over every single year? Because, even in the absence of opportunities to hook-up and swap genes with other viruses, i.e., even when a host is infected by just a single strain of the flu, the virus is constantly changing shape. Mutations arise all the time, and those that change the shape of the antigen such that it is no longer recognized by host antibodies will be naturally selected. Antigen shape therefore drifts around constantly, making it a much more fun game for the host immune system - and our vaccines - to keep up with the flu! It's evolution in action, right within our own bodies and those of animals we cohabit with! You didn't think we had quite liberated ourselves from the clutches of evolutionary processes now, did you? As you ponder that, here's another cartoon depicting antigenic drift:






[Hat-tip: GrrlScientist for finding the videos]


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Tuesday, April 28, 2009

Applying phylogenetics: Did the California H1N1 swine flu come from Ohio?

Just as we (in Biol 105) finish up studying how phylogenetic trees are estimated, and how they might be used to answer interesting questions, comes this highly topical example - microbiologist and science blogger Sandra Porter spent a happy afternoon applying phylogenetic analyses to try and answer the health scare du jour:


This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. Here's the data.



Once I realized that the genome sequences from the H1N1 swine flu were in the NCBI's virus genome resources database, I had to take a look.



And, like eating potato chips, making phylogenetic trees is a little bit addictive. Or maybe it was just the adrenaline rush that hit when I realized that every tree was telling me the same thing.



What did those trees say?


Read the full blog post to study the results yourself, and see what you think of the remarkable concordance between the trees, providing a plausible answer to the question of where this virus may have originated.



In the process, Dr. Porter has also given us all a glimpse at the working product of a fresh analysis - raw results hot off the computer before they are published in a peer-reviewed journal! Is this a first for the blogosphere? I don't know, but given the high level of public interest, I can see why one might want to get the results out quickly. Surely some top science journal would be interested in publishing this quickly as well?



Thanks to Porter's blog, we all get to see how genomic data available in the public domain can be used to help address problems that might affect us in real time! How cool is that?! As I try to impress upon my students every time we discuss the subject: Phylogenies are not just static graphic depictions of inferred relationships between organisms long gone - trees of dead wood, so to speak: they also serve as working models of ongoing evolutionary processes! And often enough, they help us pinpoint the origins of new diseases, in turn helping us develop treatment strategies before the outbreak gets too far out of hand. And how is that for putting those phylogenetic trees to work?



Meanwhile, Tara Smith, of Aetiology (also on ScienceBlogs) following up on Porter's big discovery, notes that the peer-reviewed paper describing the Ohio swine flu strain came out only recently. And here's the bit that really raises the eyebrow, if not the hair on your head:


I also assume this is where the human-avian-swine reassortant claim came from. The authors note that:


The H1N1 viruses contain the HA and NA from the classical swine virus and the internal genes from the triple reassortant H3N2 viruses (rH1N1); the H1N2 viruses contain the HA from the classical swine virus and the NA and internal genes from the triple reassortant H3N2 viruses (Karasin et al., 2002; Webby et al., 2004). Contemporary triple reassortant viruses were demonstrated to have acquired a PB1 gene of human virus origin; PA and PB2 genes of avian virus origin; and the remaining internal genes, M, NS, and NP, of swine virus origin, thus giving rise to the triple reassortant designation (Zhou et al., 1999).



So what it looks like to me is that this isn't a *new* reassortant virus, but is closely related to one that had already been identified in swine--and that had already caused an outbreak in humans right here in the US.


So why is the virus getting so much more media attention this time around? Is the strain in Mexico really the same or different? And if it is the same (or close) how did it get from Ohio to Mexico City and back to Texas and California? Gotta love that globalization, eh!


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Friday, April 17, 2009

This might be depressing to watch...

... but probably worth watching as we head towards another Earth Day next week!






This episode of Nature airs this sunday, April 19, 2009 at 8 PM. on PBS (check local listings).


In the meantime, if you want to get a head start on your depression, here's an extended clip:






There's even a web exclusive about Gibbon matchmaking!


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Tuesday, April 7, 2009

When fishes started to walk on land and breath air

As an impressionable youth, I first saw "Life on Earth" in 1983 during my first year as an undergrad at the Institute of Science in Bombay,, pursuing a degree in zoology. And did it ever leave an impression on my mind! Of course, this was back in the days before video players, let alone DVDs. And we didn't yet have a television at home - nor do I remember the show actually being telecast in India anyway. So how did I see it? I was actually lucky enough to get to watch it projected on a big screen, with a 16mm projector whirring away quietly at the back of the big classroom. Someone at the Institute had borrowed the films for the entire series from the wonderful British Council Library! Of course, that same library which (along with the American and the Soviet ones) had already helped change the course of my life away from medical school towards zoology! Thank you Messrs. Darwin, Gould, Commoner, PGW, Steinbeck, Tolstoy... and David Attenborough. Ahh... the formative memories from those formative years. Nostalgia aside, I find it astonishing that 3 decades on, when we know so much more about the evolution of life on earth, when video technology has advanced so much, and when we have 24/7 cable channels dedicated to coverage of the living world, we still haven't seen but the one, and only, David Attenborough! Enjoy:









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Monday, April 6, 2009

Islands in the Sky - at tonights Valley Cafe Sci!

Its time for another Café Scientifique tonight here in Fresno. And this time we have Robin Vijayan, a Fulbright scholar visiting my lab for his graduate research (he actually roped me in as a coadviser for his Ph.D. for some odd reason!) telling us about "Islands in the Sky: Science and conservation in the montane forests of India" - well, southern India, to be exact.


We meet, as usual, at the wonderful Lucy's Lair Ethiopian restaurant in north Fresno, from 6:30 - 8:30 PM. Perhaps I'll see you there!



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The Bad Astronomer insists: Science IS imagination

Here's an excellent read this spring break week, when you may take a step back from all those little details from science you've been studying all semester, and take a look at the big picture! What is Science, really? How does it enrich human existence? Here's what the Bad Astronomer has to say, in response to yet another article equating science with religion and ideology:



People don’t understand science.



And I don’t mean that your average person doesn’t understand how relativity works, or quantum mechanics, or biochemistry. Like any advanced study, it’s hard to understand them, and it takes a lifetime of work to become familiar with them.



No, what I mean is that people don’t understand the process of science. How a scientist goes from a list of observations and perhaps a handful of equations to understanding. To knowing.



And that’s a shame, because it’s a beautiful thing. It’s not mechanical, not wholly logical, and not plodding down a narrow path of rules and laws.

[via Science IS imagination | Bad Astronomy | Discover Magazine]

I often wonder how many of our students get this? Are we doing a decent job of conveying this beauty of science and the scientific process? Would any of you students care to chime in?



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