Monday, March 31, 2008

Flu Season

In the Northern hemisphere, December thru March is flu season. Every year 5% to 20% of us catch "the bug". This year, flu cases peaked around the end of February (see chart). Perhaps you've wondered "Why?".

Hypotheses for flu season are numerous and include:

  1. Because people are indoors more often during the winter, they are in close contact more often, and this promotes transmission from person to person.
  2. Cold temperatures lead to drier air, which may dehydrate mucus, preventing the body from effectively expelling virus particles.
  3. The virus may linger longer on exposed surfaces (doorknobs, countertops, etc.) in colder temperatures.
  4. Increased travel and visitation due to the holiday season.
  5. Less sunlight promotes virus survival.
  6. Our immune systems work poorly during the cold weather. (From Wikipedia).
Researchers from the National Institutes of Health have added another hypothesis to this list: influenza viruses get harder during cold temperatures. See, influenza viruses have a lipid coat. Most of us are familiar with lipids in the form of oils we use for cooking. Whether the lipid is solid or liquid depends on the temperature. Olive oil, for example, is liquid at room temperature, but will solidify if you place it in the freezer.

So too for the influenza virus. Its lipid coat helps protect it from the elements, but is only good when it is tough and rubbery. In a study reported in Nature Chemical Biology, NIH researchers used a sophisticated magnetic resonance technique, developed and previously tested in NIAAA's Laboratory of Membrane Biochemistry and Biophysics, to create a detailed fingerprint of how the virus’s outer membrane responded to variations in temperature. At low temperatures, the lipid coat was solidified as a gel. As the temperature approached 60 degrees Fahrenheit, the coat turned into a goopy mess.

We spread the flu from person to person when we cough and sneeze. In cold temperatures, the virus is better able to survive the elements and find a new host. Once the virus enters a host, the outer protective coat "melts like an M&M in your mouth", and enables the virus to enter the host's cells.

Dr. Joshua Zimmerberg, corresponding author of the study, suggested that people might better protect themselves against getting sick by remaining indoors at warmer temperatures than usual.

Progressive ordering with decreasing temperature of the phospholipids of influenza virus. Ivan V Polozov, Ludmila Bezrukov, Klaus Gawrisch, Joshua Zimmerberg. Nature Chemical Biology 4, 248 - 255 (01 Apr 2008), doi: 10.1038/nchembio.77, Article

Chart from the Centers for Disease Control.

Wednesday, March 19, 2008

Wellcome Image Awards 2008

From the website: Selected by a team of expert judges from recent acquisitions by Wellcome Images, the winning pictures show a wide variety of subjects, normally invisible to the naked eye, revealing new layers of complexity and making the ordinary extraordinary.

View the Award-winning images in the online gallery or in person, listen to interviews with their creators and find out how they were made. You may also like to vote online for your favourite image, or submit your images for a chance to win at next year's Awards.

Throughout history scientists have presented their findings in fascinating pictures - Hooke's 'Micrographia' for example. We present some of the latest of these offerings, astounding not only to the non-specialist, but also to those who produce these images as part of daily research and investigation.

These images have been captured using both traditional and cutting-edge imaging techniques, from the simple light microscope to the latest in computer-aided imaging. We can only look forward to the future when new advances will make possible even more astonishing pictures.

Photo: A fly on sugar crystals. Colour-enhanced image of a housefly (Musca domestica) on sugar crystals. To eat the sugar the fly releases its enzyme-containing saliva onto it, lets it digest, then sucks it all back up. Houseflies are well known for carrying gastrointestinal diseases such as Salmonella and dysentery, but they can also spread tuberculosis, anthrax and other major illnesses through their habit of visiting decaying organic matter and faeces, as well as humans and their food. Colour-enhanced scanning electron micrograph by Dave McCarthy and Annie Cavanagh.

This Week's Citation Classic

Robert H. MacArthur. Population Ecology of Some Warblers of Northeastern Coniferous Forests. Ecology, Vol. 39, No. 4. (Oct., 1958), pp. 599-619.

I really love the old-style
Ecology papers; they often stretched for dozens of pages and read like books. Robert MacArthur's paper on the population ecology of some warblers of northeastern coniferous forests is no exception, and is such a contrast to the terse, jargon-loaded style often found in the pages of Nature and Science.

The paper, MacArthur's first as an assistant professor after obtaining his PhD from G. Evelyn Hutchinson at Yale University, stemmed from his dissertation, and contained a marvelous exposition of the division of ecological niches among five closely related warbler species among the coniferous forests of upstate New York. As MacArthur writes, "these species are congeneric, have roughly similar sizes and shapes, and all are mainly insectivorous. They are so similar in general ecological preference, at least during years of abundant food supply, that ecologists studying them have concluded....these species might provide an interesting exception to the general rule that species either are limited by different factors or differ in habitat or range."

That is, the warblers seemed to violate the rule of one species per niche.

However, as MacArthur's research showed, the warblers subtly divided their living space, with different species focusing on slightly different habitats as the figure at the top of the blog shows. What's more is that warbler species were regulated in a density-dependent fashion; they increased when rare, and decreased when common. There were other differences too, differences only apparent to one that carefully observes the birds day in and day out over the seasons (MacArthur was a consummate birdwatcher): "there are differences of feeding position, behavior and nesting date, which reduce competition. These, combined with slight differences in habitat preference and perhaps a tendency for territoriality to have a stronger regulating effect on the same species than upon others, permits the coexistence of the species." The net effect was that several closely related species could share a common area without directly competing over the same resources.

MacArthur was a true artist of biology; "MacArthur would say that the best science comes, to a great extent, from the creation of de novo and heuristic classification of natural phenomena. 'Art,' he enjoyed quoting Picasso, 'is the lie that helps us to see the truth.'"

MacArthur was taken from us during his prime at 42 years of age by renal cancer. One wonders what contribution he may have made had he survived to the present.

MacArthur's impact on Ecology was so considerable that The Robert H. MacArthur Award is given biannually by the Ecological Society of America to an established ecologist in mid-career for meritorious contributions to ecology, in the expectation of continued outstanding ecological research. Talks by many recipients have been presented at the annual meeting of the society and subsequently published in Ecology.

Stephen Fretwell writes on "The Impact of Robert MacArthur on Ecology" in the Annual Review of Ecology and Systematics".

E.O. Wilson and E.G. Hutchinson. 1989. Robert Helmer MacArthur 1930-1972. National Academy of Sciences Biographical Memoirs 58: 319-327.

Tuesday, March 18, 2008

Goodbye Arthur C. Clarke

Sir Arthur C. Clarke passed away today at 90 years of age. Clarke has done much to popularize science, including for the author of this blog. His fiction, particularly 2001: A Space Oddessy, will always be among my favorite literature.

Photo: Clarke's tool-using apeman as seen in Kubrick's 2001: A Space Oddessy. Under the influence of the mysterious black monolith, an apeman discovers the club-like qualities of a bone, and later uses it to defend his tribe's waterhole from other apemen. In what may be one of the finest shots in film history, the victorious apeman flings the bone/weapon tumbling skyward, at which point the film jumps to the future, and the bone turns into an orbiting satellite. I believe this is the first instance where I considered the evolutionary history of man, and even at that young age (8-9?), I thought "That makes sense."

Saturday, March 15, 2008

Are bacteriophages picky eaters?

I don't often see bacteriophage ecology and evolution papers in the open source literature, but there is a nice one in next month's American Naturalist (occasionally Am Nat selects papers for open access).

The paper by Rick Heineman and colleagues addresses the question of optimal foraging, a body of theory that seeks to explain the food choices of organisms in terms of how they maximize energy intake over time. As a model organism, the authors use the bacteriophage T7, a parasite of Escherichia coli.

Naturally, phages don't "eat" per se, nor do the make conscious "choices", but for the purposes of the theory that's largely irrelevant. We can still model optimal foraging in terms of the evolution of phage host range (i.e. "dietary choices"), provided that phage are able to "discriminate" among possible host types. As the authors write, "Phages have no behavioral plasticity in the usual sense, yet they evolved to make host range choices that qualitatively match optimality predictions."

Heineman et al. found that T7 phage could evolve the ability to discriminate between several host strains. T7wild-type "was independently adapted in two mixes of Escherichia coli strains: C with either B or K12. In both adaptations, C was the permissive host, while the other (B or K12, depending on the adaptation) aborted T7 infections due to deletion of a host gene needed for viral replication. Both adapted phages evolved to largely avoid the nonpermissive host but maintained a high adsorption rate to C." Notably the phage evolved the ability to discriminate via single amino acid substitutions in the tail fiber gene (used to bind host receptors).
To see if discriminating phage could be favored over non-discriminating phage, Heineman et al. used E. coli strains that differed in their resistance to tetracycline with C being Tet resistant and K lacking Tet resistance. Adding tetracycline would alter K into poor quality hosts, but leave C unaffected.

The authors tested whether increasing tetracycline (at levels that disable, but not kill K cells) in the culture media would favor one phage strain over the other. The results showed that T7Choosy
out competed
T7wild-type when tetracycline levels were high, but not when they were low. The study has implications for other viruses. As the authors write, "the principles demonstrated here for phages may operate in other viral systems. The main requirement is that a virus that avoids infecting one host (or cell type) will have opportunities to infect a different type. This property may apply to many viruses infecting multicellular hosts with respect to tissue tropisms—differences in the ability to infect various tissues within the body. Viruses within a host are likely to be selected to use some tissues and not others, and the nature of selection on tissue tropism may parallel those found here for phages."

Overall this is a very nice study, with clever use of bacteriophages and bacteria, to test a body of theory that has not commonly been tested with microbes. The only main issue is that there is a lack of a quantitative aspect to the study (which is difficult with microbes), and as such, despite the cleverness of the approach, phages might not be the best arena to test optimal foraging theory. Nonetheless, it is an effective demonstration that organisms that cannot make conscious choices can evolve to prefer some resources over others.

Heineman, R., Springman, R., Bull, J. (2008). Optimal Foraging by Bacteriophages through Host Avoidance.. The American Naturalist, 171(4), E149-E157. DOI: 10.1086/528962

Photo: T7 phage from the The Microbial World.

Saturday, March 8, 2008

This Week's Citation Classic

Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H. 1986. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction.Cold Spring Harb Symp Quant Biol. 51 Pt 1:263-73.

Kary Mullis is an interesting guy. If I had to pick one invention that most impacted biology in the second half of the 20th century, I'd pick the PCR. The PCR allows one to amplify specific fragments of DNA using small, synthesized
oligonucleotides called primers. The basic technique involves three steps: denaturing a double-stranded DNA molecule via high temperatures, reducing the temperature to allow primers to "anneal", and then increasing the temperature to induce DNA polymerase obtained from thermophilic bacteria to synthesize new complementary DNA strands. The process is repeated many times to generate billions of new DNA fragments. The applications of the basic process are various, from sequencing DNA to introducing known mutations to DNA strands.

In the old days, the process was performed using water baths and a stopwatch (see photo). Now the process has been simplified using thermalcyclers. An animation describing the PCR is available here.

Mullis supposedly thought of PCR while driving. He describes the event here.

"I was working for Cetus, making oligonucleotides. They were heady times. Biotechnology was in flower and one spring night while the California buckeyes were also in flower I came across the polymerase chain reaction. I was driving with Jennifer Barnett to a cabin I had been building in northern California. She and I had worked and lived together for two years. She was an inspiration to me during that time as only a woman with brains, in the bloom of her womanhood, can be. That morning she had no idea what had just happened. I had an inkling. It was the first day of the rest of my life."

Outside of the PCR invention, Mullis has been quite controversial. He is a HIV skeptic, a global warming skeptic, and was supposedly aided in his discoveries by LSD. The HIV skepticism is largely moot since everyone now agrees that AIDS drug therapy works. Global warming skepticism is a bit more problematic, but Mullis appropriately cites the Scientific Method in defense of his claims:

"Very little experimental verification has been done to support important societal issues in the closing years of this century. Nor does it have to be done before public policy decisions are made. It only needs to be convincing to the misinformed voter. Some of the big truths voters have accepted have little or no scientific basis. And these include the belief that AIDS is caused by human immunodeficiency virus, the belief that fossil fuel emissions are causing global warming, and the belief that the release of chlorofluorocarbons into the atmosphere has created a hole in the ozone layer. The illusions go even deeper into our everyday lives when they follow us to the grocery store." [From Dancing Naked in the Mind Fields].

One man's kook is another man's iconoclast. I won't defend his views other than his right to have them.

Mullis received the 1993 Nobel Prize in Chemistry for his work.

Here are some of his thoughts on science:

"Science, like nothing else among the institutions of mankind, grows like a weed every year. Art is subject to arbitrary fashion, religion is inwardly focused and driven only to sustain itself, law shuttles between freeing us and enslaving us. Science consistently produces a new crop of miraculous truths and dazzling devices every year, truths and devices that enrich our lives and grow up out of the graciously willing puzzles of the unknown in an orderly but unpredictable way, out of a process of observation, hypothesis, experiment, conclusion; a process that as far as we know, was first proposed and adopted, only a few hundred years ago by a number of Europeans faced with a new world to explore and some worn out scholastic tools passed down from the ancient Greeks to explore it with.... Now we each of us have things and thoughts and descriptions of an amazing universe in our possession that kings in the Seventeenth Century would have gone to war to possess. We are the recipients of scientific method. We not only can luxuriate in its weed-like growth, but we can each of us be a creative and active part of it if we so desire. And we will. There is no stopping it, nor can there be any end to it."

Growing up, Mullis was given considerable latitude to explore his interests.

"I found a Gilbert Chemistry Set. Something about tubes filled with things with exotic names intrigued me. My objective with that set was to figure out what things I might put together to cause an explosion. I discovered that whatever chemicals might be missing from the set could be bought at the local drugstore. In the 1950s in Columbia, South Carolina, it was considered okay for kids to play with weird things. We could go down to the hardware store and buy 100 feet of dynamite fuse, and the clerk would just smile and say, 'What are you kids going to do? Blow up the bank?"

In today's hypersafety conscious world, I can't even imagine obtaining dynamite fuse as an adult.

Kary Mullis maintains a website here.

Photo: An "old-school" PCR machine from wikipedia.

Sunday, March 2, 2008

Blog Roll Updates

Thanks to all who responded with new blogs for me to check out! I will certainly enjoy reading them.

Here are some of the new additions...

James McGrath of Exploring Our Matrix recommends Scientific Blogging (I actually post there from time to time), PTET, Conspiracy Factory, Bad Idea Blog, The Austringer, and Northstate Science.

Ian Ramjohn of Further Thoughts gives shout outs to Seeds Aside and Hyphoid Logic.

Eric Johnson likes Mystery Rays from Outer Space which surprisingly "touches immunologically on viro, onco, autoimmunity, and evolution." I could have guessed that from the name, Eric :P

Marco Varella suggests his own blog, Marcoevolutivo.

Andrew recommends his blog the Naked Galaxy. I should have added this earlier... because I have chatted with Andrew a few times.

The Monkeyman points out that Chimpanzees are not Monkeys. They are apes!

Evolved has a blog called Evolved and Rational. Sigh... if only we all were.

Anonymous directed me to Bad Science.

Addy N. takes time out from doing what an untenured professor should be doing to suggest Science Woman.

I will add a few of my own, which I nominate for the E for Excellent blog award (Thanks Sam!):

Female Science Professor

Freelancing Science

Microbi0logy Bytes


This Week in Evolution

Thanks again for your suggestions!