Gene duplications, paralogs etc, a phylogenetic phantom menace

Hurles, M., 2004. Gene Duplication: The Genomic Trade in Spare Parts. PLoS Biol 2(7): e206. DOI:10.1371/journal.pbio.0020206.

Here's a nice paper in PLOS about how gene duplications come about as a "major opportunities from which new genes evolve". Part of the research I do is based on paralogues of genes and how such phenomena can confound certain issues in IgE-binding capacity. The more I delve into this issue, I feel that gene duplication will be important in functional genomics. Gene duplications are really a fundamental toolkit in evolutionary genetics and the reductionists need to really take variation into consideration. Paralogs are a phylogeneticist's nightmare.

Orthologs are genes that divide via speciation so have counterparts in other species while paralogs are genes that arise through duplication.

See also this correspondence in Genome Biology - Orthologs and paralogs - we need to get it right. Jensen does a great job at teasing out the nitty gritty of the definitions, which when given enough thought can be really more profound than we'd normally imagine it to be.

Deep sea adaptations - whale bone-eating worms!

Excerpts:

'Announcing the discovery of two new species of worms, Osedax rubiplumus and Osedax frankpressi that feed on the bones of dead whales. No eyes, legs, mouths, or stomachs, but colorful feathery plumes and green "roots."

The roots infiltrate the bones of dead whales, digesting the fats and oils inside with the help of symbiotic bacteria, the first time that a lipid-degrading bacteria has been observed in a symbiotic relationship.

The plumes extend into the water and act as gills. Connected to a muscular trunk, the plumes are retractable.

At the other end of the trunk embedded inside the whale bone, the body widens to form a large egg sac. The greenish roots, branching off from the egg sac, are filled with bacteria that break down oil in the whale bones.

Most of the females worms have dozens of microscopic male worms living within their bodies. The male worms looked neotenous, with bodies still containing bits of yolk but also copious quantities of sperm. After a whale skeleton has been consumed, the worms die off, presumably after releasing enough eggs or larvae to colonize another whale carcass.

Key portions of the worms' DNA suggest the worms are closely related to the large tube worms found at deep-sea hydrothermal vents and cold seeps. Both types of worms obtain nutrition with the help of symbiotic bacteria.

The two new worm species' most recent common ancestor lived roughly 42 million years ago, about the same time whales themselves first evolved.'

Read the comnplete story at Monterey Bay Aquarium Reseach Institute.

Pete's featured in Nature!

Nature 430, 396 - 398 (22 July 2004)

"Biodiversity: A tragedy with many players"

"Peter Ng is a man with a mission: to catalogue the huge diversity of life dwelling in habitats long dismissed as uninteresting. It's a race against time, he tells Carina Dennis and Peter Aldhous.

A tropical peat swamp is not a welcoming place. Its acidic waters sting every tiny scratch on your body. Hold your hands just beneath the surface and you can't see them through the tannin-laden water. The only bonus is that leeches don't fancy the murk. But Peter Ng, a taxonomist and conservation biologist at the National University of Singapore, loves getting up to his armpits in the mire.

Ng has discovered that the peat swamps of southeast Asia are teeming with rare species of fish and crustaceans, many of which are new to science. "Peat swamps have been badly neglected," says Ng, who pulls out novel specimens on nearly every dip into these hostile waters. His team has found a treasure trove of biodiversity in other unlikely places too, including the broken rubble of dead coral found off tropical beaches.

Now Ng is engaged in a race to catalogue these neglected faunas before many of them are wiped out by Asia's relentless economic development. The peat swamps, in particular, are being drained as fast as he can sample them, sometimes for urban or agricultural development, at other times — in a bitter irony — under the guise of 'environmental improvement'...... "(read more at Nature 430, 396 - 398 (22 July 2004)

Also, see the editorial in the same issue, Ignorance is not bliss. If you the links are invalid later, see RMBRnews.

Hibernation in the tropics

Hibernation has been demonstrated in an animal with a relatively high body temperature.

The Fat-tailed dwarf lemur may do so for up to 7 months - without regulating its body temperature. It is the first primate and tropical animal to be detected doing this by scientists.

Body temperature varies widely - by almost 25°C (9-35°C) - depending on the ambient temperature of their tree hole. Apparently by "following the temperature of their nests closely, the lemurs can reduce their metabolism and their energy expenditure."

The team studying them suggests the lemurs hibernate during the dry season to save energy, as the fruit they like to eat are not available. "Everybody associates hibernation with low temperature. It's nothing to do with low temperature, it's an adaptation to do with periods of low food." See the report in New Scientist.

Reference: Dausmann et al., 2004. Physiology: Hibernation in a tropical primate. Nature, 429: 825-826, (24 June 2004).

What makes a good biology lesson?

Out of the blue I received notice that I will be 'volunteered' to attend a teaching workshop next Tuesday where lecturers and tutors gather to share their experience and exchange ideas. And to my horror, I cannot just slack away in the background; there is a chance I might have to speak.

So what can I share with the other tutors about my experience as a part time tutor teaching mainly undergraduate Biodiversity? A cursory attempt at thinking about it revealed nothing. All I can remember was preparing for the lesson before hand, arranging the specimens, sorting through what are the important points to deliver and finally roughing it out. At the end somehow you will feel if you had done a good job... or not.

What makes a good biology lesson? In my experience, making a subject interesting with stories and clear examples, infused with humour, should do the job. This was the formula I hold dear when I regard each lesson.

Does anyone have similar experiences to share? Or some pointers? Maybe this blog could be a crystallisation of various tactics of efficient teaching. Since the majority of us are biology educators in one way or another, this exchange should be useful.

Cheers all.

Rats as Proxy

No, this is not your internet proxy. This study involved using commensals to trace early human migration of the Pacific peoples - in this case it was the Pacific rat, Rattus exulans. The tool - Molecular Phylogenetics.

The researchers believe that the Pacific rat was introduced intentionally in the past possibly as a food item, based on the numerous bones in archaeological middens?

A wood carving depicts an ancestral Polynesian colonist of Oceania. Note the rats on top of the figure. Copyright Tim Mackrell/PNAS

Besides being an ideal commensal to proxy because they were canoed around with the early migrators as food, R. exulans also have several other properties that make them so ideal to "lab rats" to sequence. Like, the Pacific rats also do not swim hence cannot self-disperse. They also don't crossbreed with the European rat (Rattus rattus and Rattus norvegicus), so there are no problems with reticulate branching. Dogs, Pigs and Chickens interbreed readily with their european counterparts presenting the problem of admixture.

The phylogenies were based on the mere 250 base pairs in the D-loop of the mitochondrial DNA. (Where the heck is the equivalent for the plants!). The trees showed 3 highly supported groups with clear geographic patternings. The first group or interaction sphere consisted solely of Southeast Asian elements from the Philipines, Borneo and Sulawesi. The second had samples from both Southeast Asia and Near Oceania(e.g New Guinea, Australia and proximate islands) . The third group consisted of mainly Remote Oceanic (Vanuatu, Fiji and Samoa) rat populations. Their finding refutes the previous Express Train Theory of migrants that swept their way from Taiwan through Southeast Asia and Near Oceania and into Remote Oceania

Reference:
E. Matisoo-Smith, and J. H. Robins (2004) Origins and dispersals of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat. PNAS 101: 9167-9172

Our Final Hour

We seem to have an innate fascination for the morbid. Over time, there will be doomsday predictions and scenarios being predicted; rather zealously sometimes. Here's one from an astronomer.

Sir Martin Rees, Britain's Astronomer Royal, warns that civilization has only an even chance of making it to the end of this century. This is the result of advances in various fields, such as biotechnology and nanotechnology; which has the potential to breakaway if not monitored properly.

But what is more important are his comments on how science is supported and the actions of various governing bodies. To quote from the passage “It's possible to tip the balance to civilization's advantage, Rees concludes, believing that environmental and biomedical issues should be higher on the political agenda. To raise the debate above the level of rhetoric, however, the public must be better informed. He looks to the U.S. to take a leadership role. But so far he finds its handling of the controversies over stem cell research and global warming to be wanting: the U.S. "has been rather remiss in tackling issues that are taken more seriously elsewhere in the world, especially environmental problems."”

It will be good to have more of such books from prominent figures like Sir Martin.



Scientific American: Doom and Gloom by 2100
Unleashed viruses, environmental disaster, gray goo--astronomer Sir Martin Rees calculates that civilization has only a 50-50 chance of making it to the 22nd century

Mayr turns 100, comments on the development of ideas in evolutionary biology

Ernst Mayr pens a recent article and a republished interview from 2000 celebrates his 100th birthday. It provides some insight into the influences surrounding the directions of intellectual thought over the theory of evolution, and might have you reconsidering your fondness for a particular train of thought!

"As a student in Germany in the 1920s, I belonged to a German school of evolutionary taxonomists that was unrepresented in the United States. Our tradition placed great stress on geographic variation within species, and particularly on the importance of geographic isolation and its role in leading to the origin of new species. It accepted a Lamarckian inheritance of newly acquired characters but simultaneously accepted natural selection as facilitating gradual evolution. We decisively rejected any saltational origin of new species, as had been postulated by DeVries."

"Fortunately, there was one evolutionist who had the background to be able to resolve the conflict between the geneticists and the naturalists. It was Theodosius Dobzhansky.* He had grown up in Russia as a naturalist and beetle taxonomist, but, in 1927, he joined Morgan's laboratory in America where he became thoroughly familiar with population genetics. He was ideally suited to show that the findings of the population geneticists and those of the European naturalists were fully compatible and that a synthesis of the theories of the two groups would provide a modern Darwinian paradigm, subsequently referred to as the "Evolutionary Synthesis.""

Read the article at Science, 305(5680): 46-47 (2 July 2004).

See also Michael Shermer and Frank J. Sulloway article in 2000, "The Grand Old Man of Evolution - An Interview with Evolutionary Biologist Ernst Mayr." Skeptic Magazine, Vol. 8 No. 1, e-reprinted as "Happy 100th Birthday Ernst Mayr!" in E-Skeptic #26 for 5 July 2004.

The Evolution of Ernst: Interview with Ernst Mayr. The preeminent biologist, who just turned 100, reflects on his prolific career and the history, philosophy and future of his field. Scientific American, 6th July 2004. Thanks Cheng Puay!.

Mac users, copy and paste the printer-friendly version in Tofu!

Play for perfect vision

Myopia is not hereditary, as some would like to believe. A study by Australian scientists, which was quoted in this week's New Scientist argue there are no evidence to support genetic variations as reason for short-sightedness.

Children now spend more time indoors, reading or on the computer, so the eyeballs tend to grow longer to facilitate focusing on closer objects. Additionally, less than optimal lighting, compared to outdoor activities, places a strain on the eyeballs to focus close.

85% of 18-year olds in Singapore are myopic. More significantly, 70% of the 18-year old Indian Singaporeans are myopic compared to only 10% of their subcontinent counterparts, pointing to lifestyle as a highly probable factor for myopia.

So, perhaps, now that an internationally recognised journal has highlighted the obvious, our education administrators would be convinced to remove, or at least unlock the gates to the fences around the fields! They'll be doing National Service by letting the kids play!

King Penguin can supress acid production to store food in stomach

I have had a fascination for penguins since I worked with them between 1988-1990. So I enjoyed reading this:

From the New Scientist print edition e-zine, with some comments addded;

Original title - "How penguin dads keep fish for chicks".

"MALE king penguins have a unique way of putting the digestive process in their stomachs on hold. By producing less stomach acid and all but immobilising their guts, the birds can preserve fish in their bellies for up to three weeks to provide an emergency meal for hatching chicks." Smaller penguin species may be unable to do this - hours or days at most.

"Males take the last turn in incubating their eggs. Foraging females usually return to feed the chicks, but are often delayed (sometimes over 9 days), leaving the task to males who may have eaten their last meal weeks earlier. Yvon Le Mahon and his team at the National Centre for Scientific Research in Strasbourg, France, had previously shown that male penguin guts secrete antibacterial chemicals that preserve food. But that didn't explain why the food is not digested."

"To find out, the researchers inserted gastric probes into the bellies of 15 male penguins (Aptenodytes patagonica) on Possession
Island in the southern Indian Ocean. The stomach temperatures of all the birds remained constant They are incubating eggs after all. But pH levels in the gut were much higher than the optimum level at which digestive enzymes work.

That suggests that the birds suppress the amount of acid in their stomach to limit the digestion process. Most of the birds also significantly reduced their gut movements, helping keep their stomach contents intact."

Food protein quantity and quality is preserved since proteinases are inactivated. However, lipases may be active as some pancreatic enzymes from the duodenum may reflux into the stomach, apparently a feature of avian digestion. The researchers did detect a decrease in total lipid content.

For more, read their article at J. Exp. Biol., 207: 2715-2724. Access available for NUS accounts.