Island Biogeography and Evolution

ISLAND BIOGEOGRAPHY AND EVOLUTION: SOLVING A PHYLOGENETIC PUZZLE USING MOLECULAR GENETICS

R.P. Filson

DNA Song

This was quite funny. Had a good time in class today.

Swine flu update

Latest update in Swine Flu. Over 70 confirmed cases in US, Canada and Mexico. WHO alert level raised up to 4 – which means verified human-to-human transmission able to cause community-level outbreaks. Significant increase in risk of a pandemic.

This is certainly worrying and I have students who are now studying in the states. Hope they will be fine.

Thought this was a good biology lesson to discuss why certain diseases in animal hosts seem to have an easier time when crossing the species barrier to infect humans. We have bird flu, SARS, pigs.. the usual suspects.

Jared Diamond’s article on domestication of plants and animals in Nature Reviews (2002) [Diamond, J. 2002. Evolution, consequences and future of plant and animal domestication. Nature 418 pp700 - 707] offered a keen insight on this phenomena.

“The main killers of humans since the advent of agriculture have been acute, highly infectious, epidemic diseases that are confined to humans and that either kill the victim quickly or, if the victim recovers, immunize him/ her for life. Such diseases could not have existed before the origins of agriculture, because they can sustain themselves only in large populations that did not exist before agriculture… The mystery of the origins of many of these diseases has been solved by molecular biological studies of recent decades, demonstrating that they have evolved from similar epidemic diseases of our herd domestic animals with which we began to come into close contact 10, 000 years ago…. For instance, measles and tuberculosis arose from diseases of cattle, influenza from a disease of pigs and ducks..

How the concept of food miles hurt the planet

It used to be simple. The further the food is away from you, the more ecologically unsound it is as it would have emitted lots more carbon dioxide via transportation (trucks, planes, trucks etc).

Of course nothing is ever simple in ecology, where you get a myriad of inputs influencing the outcomes. So transportation is only one factor contributing to total emissions in food production.

This article from Guardian sums it up nicely.

How the myth of food miles hurts the planet

Greater Mousedeer back in Ubin

Greater Mousedeer Sighted in Ubin
. Also the report in Straits Times by Ang Yiying.

Could be from the 7 that was reintroduced in 1997 and never spotted since.

Such is the wonders of Web 2.0. A quick search in google revealed others were ahead before me.

The Biodiversity Crew@NUS – By Siva, who else.

Embryonic Stem Cell Therapy Causes Cancer in Teenage Boy

From Discover Blogs, 80 beats

A

new study shows that teenage boy developed cancerous tumors because of the stem cell therapy he received years ago for a rare genetic condition. The boy, now 17, suffered from ataxia telangiectasia, or AT, a neurodegenerative disease that interferes with the part of the brain that controls movement and speech. AT patients do not usually live past their teens or 20s, and the Israeli boy, whose identity was not publicly revealed, was taken to Russia for experimental treatment. The first neural stem cells, taken from fetuses, were first injected into his brain and spinal cord when he was nine, and he received further injections at ages 10 and 12.
His condition deteriorated and he was using a wheelchair by age 13, when he also began to complain of headaches. Tests showed two growths, one pushing on his brain stem and the other on his spinal cord. The tumors were removed in 2006 and his health has since remained stable. But scientists at Tel Aviv University who wanted to determine the origin of the cancer have been in the lab ever since, and their findings have just been published in PLoS Medicine. The team found that the tumor could not have arisen from the boy, because he [has two disease-causing versions of the gene] that causes AT, while the DNA from the tumor cells carried only the normal version [The Scientist].The tumor studied was the one removed from the spinal cord; they could not test the growth that appeared in the brain, but believe it was also caused by the injected tissue. Donor-derived cells might have been able to spark tumours in this patient because people with ataxia telangiectasia often have a weakened immune system, say the researchers. It is not clear whether the stem cell therapy helped his genetic condition [BBC].
The case raises a number of ethical questions. For all the promise, researchers have long warned that they must learn to control newly injected stem cells so they don’t grow where they shouldn’t, and small studies in people are only just beginning [AP]. And, because the patient’s immune system was impaired, it’s not yet clear whether the increased risk of cancer is specific to patients with suppressed immune systems, something particular to the procedure done in Moscow, or a danger with neural stem cell transplantation in general, said Uri Tabori, a pediatric hematologist and oncologist…. “It’s a cautionary tale for studies currently being done in the US and elsewhere,” said [Arnold] Kriegstein [The Scientist], a U.S. stem cell researcher.

PCR song

From a bunch of scientists…

The PCR Song

There was a time when to amplify DNA,
You had to grow tons and tons of tiny cells.

Then along came a guy named Dr. Kary Mullis,
Said you can amplify in vitro just as well.

Just mix your template with a buffer and some primers,
Nucleotides and polymerases, too.

Denaturing, annealing, and extending.
Well it’s amazing what heating and cooling and heating will do.

PCR, when you need to detect mutations.
PCR, when you need to recombine.
PCR, when you need to find out who the daddy is.
PCR, when you need to solve a crime.

(repeat chorus)

The future of food

An excellent summary of what the food situation will look like by WIRED magazine.

Darwin and Lamarck

Now epigenetic inheritance pertaining to DNA methylation influence phenotypic expression. That implies that traits can be inherited without changing the gene sequence at all.

Lamarck might be right in some sense.

After so many years of dismissing Lamarck’s theory, AND telling students that no, a giraffe’s neck does not grow long because of all the stretching its parents did, I never thought the day will come where one has to look at his theory closely again.

For more read this fascinating article by New Scientist

Some interesting excerpts:

but over the past decade it has become increasingly clear that environmental factors, such as diet or stress, can have biological consequences that are transmitted to offspring without a single change to gene sequences taking place.

Epigenetics deals with how gene activity is regulated within a cell – which genes are switched on or off, which are dimmed and how, and when all this happens. For instance, while the cells in the liver and skin of an individual contain exactly the same DNA, their specific epigenetic settings mean the tissues look very different and do a totally different job. Likewise, different genes may be expressed in the same tissue at different stages of development and throughout life. Researchers are a long way from knowing exactly what mechanisms control all this, but they have made some headway.

Inside the nucleus, DNA is packaged around bundles of proteins called histones, which have tails that stick out from the core. One factor that affects gene expression is the pattern of chemical modifications to these tails, such as the presence or absence of acetyl and methyl groups. Genes can also be silenced directly via enzymes that bind methyl groups onto the DNA. The so-called RNA interference (RNAi) system can direct this activity, via small RNA strands. As well as controlling DNA methylation and modifying histones, these RNAi molecules target messenger RNA – much longer strands that act as intermediaries between DNA sequences and the proteins they code for. By breaking mRNA down into small segments, the RNAi molecules ensure that a certain gene cannot be translated into its protein. In short, RNAi creates the epigenetic “marks” that control the activity of genes.

We know that genes – and possibly also non-coding DNA – control RNAi and so are involved in determining an individual’s epigenetic settings. It is becoming increasingly apparent, though, that environmental factors can have a direct impact too, with potentially life-changing implications.

Evidence that climate change has shifted plants northwards

Read this bbc article – Warming world sends plants uphill

Climate change has caused plants to seek cooler conditions at higher altitudes, scientists suggest.

A study of 171 forest species in mountain ranges of western Europe found that many plants had climbed an average of 29 metres each decade.

Smaller species such as ferns, which had shorter reproduction cycles, were the quickest to relocate, the researchers said.

The findings have been published in the Science journal.

“This is the first time that it has been shown that climate change has already had a significant effect on plant species over a wide range of temperatures during the past century,” explained Jonathan Lenoir, the paper’s lead author.

Climate ‘fingerprints’

Professor Lenoir, an ecologist at AgroParisTech, France, said the team wanted to establish whether “fingerprints of climate change were already apparent in ordinary ecosystems”.

In order to do this, the team of French and Chilean researchers compared the distribution of forest species between 1905 and 1985 with their distribution between 1986 and 2005.

“This work was possible because of two large-scale, long-term databases that have recorded the presence of forest species since 1905,” he explained.
“We used 171 species commonly found over French mountains, which are part of Mediterranean, temperature and mountainous forest ecosystems between 0m to 2,600m above sea level.

“We found a significant change in species’ altitudinal distribution towards higher elevation of about 29 metres per decade.

“Out of the 171 species, most are shifting upwards to recover temperature conditions that are optimal for their development and reproduction.”

Co-author Jean-Claude Gegout added that different types of plants displayed different responses to the temperature changes.

“Long-life plants, such as trees and shrubs, did not show significant shifts, whereas short-life species, such as herbs, showed a strong upward shift,” he said.

“Herbs, by having a short life cycle, have had several generations during a decade that allows for a faster dispersal of seeds.

“By contrast, trees have had just one or two generations during the same period of time, which may affect their ability to track the climate changes.”

Professor Gegout said that this suggested that long living woody plant species, such as trees, were likely to be more threatened by climate change than herb species like grasses.

“This may imply profound changes in the composition and structure of plant communities and animal species that depend upon them.”

The researchers concluded by saying that further studies were needed to understand the full magnitude of the changes, and to assess the impact on the ecosystems’ long-term future.