Friday, June 29, 2007

Craig Venter up to it again

Craig Venter et al. have apparently taken a big step towards creating synthetic life - they've managed to insert the whole genome of one species of bacteria into another species of bacteria. Some people are making a big deal about it and apparently there's a good editorial in the current Nature (though I wouldn't know since Roger Williams University apparently doesn't think it important to have a subscription)

There is however a NY Times piece on it. Without knowing the details of how this whole genome insertion is carried out, I must say that this technique doesn't seem particularly mind-blowing - we've been putting genes of one species into the cells of other species for decades (and microbes and viruses have probably been doing it billions of years). I would have thought that this sort of thing was inevitable and the next logical step in genetic engineering. In fact, now that I think about it, this isn't really different than cloning...

...I've just sat here for a few minutes thinking about how this new breakthrough is different from the cloning techniques currently being used. They seem fundamentally the same to me. If anyone out there knows otherwise, please tell me what I am missing (like I said, I haven't read up on Venter's method and the obstacles that had to be maneuvered along the way).

In any case, all we need to do now is to create a synthetic genome. How hard could that be?

Friday Science: How the kapok tree crossed the Atlantic

One of the long-standing hypotheses in biogeography is that sub-Sarahan and Neotropical rainforests have similar plant communities because Africa and South America were joined together previous to their separation some 120 million years ago. For most of their geographic history there was no oceanic barrier between these continents so organisms were free to disperse from one to the other as easily as you could walk from Rhode Island to Massachusetts (or from Rhode Island to California if you had the time and the legs). Therefore, the flora and fauna of these two land masses were remarkably similar to one another when plate tectonics began pulling the two apart. Over the past 100 million years or so species in both places continued to evolve independent of one another, but similarities remain because both continents started with a subset of the same organisms.

Within the angiosperms, Africa and South America share over 100 genera and nearly 100 species. The most common explanation for this pattern is vicariance - the geographic splitting of a population (in this case, the emergence of the Atlantic Ocean as Africa and South America "floated away" from each other) . However, a new study has tested this hypothesis and, for the Kapok tree at least, finds the vicariance model insufficient. Instead, it appears that this species is able to cross the Atlantic ocean.

[+/-] Show more/less

First some antural history. The Kapok, Ceiba pentandra, is a canopy-emergent, tropical tree that can grow up to 70m (230ft) with a trunk 3m (10ft) wide. The flowers atttract bat and moth pollinators with copious nectar production. The fruits contain large amounts of cotton-like fibers that are used to disperse the small seeds through the air (similar to milkweed or dandelion dispersal). So even though the distance between Africa and South America is great, C. pentandra at least has a plausible mechanism for cross-Atlantic dispersal. The question then is, is C. pentandra found both in the Amazon and in western Africa because it was already widely spread across both continents before they separated (the vicariance hypothesis) or because it was originally found in only one location and then dispersed across the Atlantic to the other?

Ceiba pentandra clockwise from left (1) emergent Amazon tree with a person beside the characteristic buttress trunk (photo credit R. Gribel); (2) dehiscing fruit with kapok (photo credit A. Gentry); (3) seed enveloped in kapok (photo credit C. Dick). (from Dick et al. 2007)

To answer that question, the authors used the molecular clock method. Briefly, the molecular clock method assumes that genetic mutations occur at a relatively constant rate. When two populations become separated, their genomes are free to mutate independently from one another. The longer two populations are separated, the more different we expect their genomes to be (each has acquired their own, different mutations). If the populations are not entirely separated, gene flow, the dispersal of genetic information, will homogenize the gene pool and the two sets of genomes will be relatively similar. If mutation rate is constant (and we know what it is) and we know how different two sets of DNA are, we can make a simple calculation of when the two groups became separated from one another. For example, if we know that one mutation arises every 1,000 years in a particular DNA sequence and two sets of this DNA sequence are different at 50 nucleotide locations, we know that these two groups separated from one another 25,000 years ago (we assume that each group has accrued 1/2 of the total differences - in this case each group has had enough time for 25 mutations to arise). Of course, it is much more complicated than this - sometimes the same mutation can occur independently in both lineages or a particular nucleotide may mutate and then "back-mutate" to its original (in both cases we wouldn't recognize any mutations when in fact there have been two), but the basic concept remains the same.

For this study, leaf tissue was collected from C. pentandra individuals from Western Africa, Central America, South America, and Puerto Rico. From these samples, stretches of nuclear and chloroplast non-coding DNA were sequenced. The nuclear sequences that were sequenced were for a subset of the internal transcribed spacers (ITS) found between the genes that encode ribosomal subunits. The sequenced chloroplast DNA was from intergenic spacers found between some photosynthesis genes. Basically, these areas are used for two main reasons:

1. They are highly variable
They do not encode any functional protein so the sequences are essentially freed from the pressures of natural selection. Since there are no selective pressures on them, mutations that arise in the sequence are not weeded out and over time the number of mutations build up. Thus, two groups of organisms that have been separated will build up different sets of mutations in these regions relatively quickly, making these regions useful, using the molecular clock method described above, when looking at phylogenetic relationships of closely related groups (usually at the species level or, as in this case, at the population level within a species).

2. They are easily located
The spacers are found flanking very important genes - those that are responsible for making ribosomes and for carrying out photosynthesis. These important genes are generally less variable as mutations in their sequences tend to be functionally disruptive and are thus naturally selected out. The sequences for these genes are therefore generally stable and are "easy" to locate in genomes. Biologists use these highly-conserved, known sequences as starting and ending points for locating the more variable, unknown sequences of the spacers between them.

Once the authors sequenced the spacers, they could examine how the sequences differed across the geographic range of the species. By using an amalgam of previously published values of mutation rates, and erring on the conservative side, the authors hypothesis was that if African and Neotropical populations of C. pentandra have been isolated since the breakup of Gondwana the ITS nucleotide sequences should be at least 7% different and the chloroplast spacers should be at least 19% different.

Those are the expected values under the vicariance hypothesis. When the authors tested this hypothesis, they observed that the ITS sequence divergence was less than 0.4% and that there was essentially no divergence in the chloroplast sequences (the only variation was found in one cluster in western Ecuador). The observed values were significantly lower than the expected values. This means that the African and Neotropical populations have not been isolated for 100 million years - kapok trees did not cross the Atlantic not as passengers on the drifting continents. The low level of genetic divergence between the geographic areas suggests that more recent (and thus long-range) dispersal is responsible for the kapok tree's geographic pattern. The authors suggest that cottony seed fibers could allow the seeds to be transported long distances via wind currents. Alternatively (or contemporaneously) floating kapok seeds may be dispersed via ocean currents.

But where did the great kapok tree originate? Africa or South America? Most cross-Atlantic dispersals are assumed to have been westerly - from Africa to the New World. However, the authors suggest that C. pentandra did it the other way - though, based solely on the suggestions in this paper, I am not convinced (whatever that is worth!). Regardless of which direction the kapok tree went, it is clear that it crossed the Atlantic relatively recently via seed dispersal, not through an ancient vicariance event.

Citation: CHRISTOPHER W. DICK, ELDREDGE BERMINGHAM, MARISTERRA R. LEMES, ROGERIO GRIBEL (2007) Extreme long-distance dispersal of the lowland tropical rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics. Molecular Ecology (OnlineEarly Articles). doi:10.1111/j.1365-294X.2007.03341.x

Tuesday, June 19, 2007

Worst Jobs in Science?

Popular Science has just released their annual bottom-10 "Worst Jobs in Science" report. While I agree that some of these jobs can't be good - like the Elephant Vasectomist - some are actually pretty cool if you ask me - like the Forensic Entomologist (certainly grisly, but a damn brilliant use of science). Still others I wouldn't give "job" status to - Gravity Test Subject? C'mon.

What I want to know most of all though is who the moron was who decided that Oceanographer should be on this list. As far as I can tell, most people, including non-scientists, would say that being an Oceanographer is on the list of coolest jobs in science. But maybe it's my own marine bias. Have the guys over at Deep Sea News seen this yet? Not sure how they're gonna like being lumped in with the "Garbologists"

(thanks Jeff for the link!)

Monday, June 11, 2007

Don't go a shellfishin' on George's Bank

My brother, who works for the federal fisheries observer program, sent me some info regarding a pretty impressive "red tide" event currently occurring on George's Bank. Both "Red tides" and George's Bank are rather interesting topics, so I thought I'd take the time to write something about them both. You probably won't find shellfish from George's Bank at your local fishmonger, but if you do, I wouldn't eat them at this point.

[+/-] Show more/less

George's Bank
George's Bank is a shallow shoal in the North Atlantic located approximately 100 km off the coast of Massachusetts. GB is a very productive area (or at least, used to be) and was one of the most important areas for New England and Canadian fishermen. Essentially, this area is so productive because it sits where the cold, nutrient-rich Labrador current meets the warmer Gulf stream. Combine this with its shallow waters and you end up with an ideal environment for phytoplankton, which in turns makes George's Bank an ideal breeding and feeding environment for cod, haddock, herring, flounder, lobster, scallops, and clams. Combine lots of fish and shellfish with proximity to land and you have an ideal environment for fishermen (not to mention a veritable cornucopia of seabirds and marine mammals). GB is so shallow and so close to the mainland that it was part of the mainland during the last glaciation event, then became "George's Island" as seas began to rise, before finally succumbing to the sea 6,000 yrs ago. Fishermen sometimes dreg up interesting fossils from GB.

(click image to enlarge)

In addition to the shallow waters and mixing of currents, GB has a rather complex and heterogeneous sea floor, including a number of small "canyons", which increases GB's appeal to an even greater range of biodiversity.

Verrazano discovered GB in the early 1500s (though Basque fishermen may have been fishing there since 1000 AD - there was a Basque fishing fleet stationed in Newfoundland) and the entire western North Atlantic become a hotbed of fishing, particularly for cod. You've probably heard the off-quoted aphorism that cod were so plentiful you could walk to shore on their backs.

GB and the western North Atlantic were so important (and profitable) that the U.S. and Canada had to appeal to the International Court in The Hague in 1984 to step in and set international boundaries where their EEZ's overlapped. Fishermen and officials from both countries still squabble over this "Hague Line", which cuts through GB (most of GB falls within the U.S. EEZ; only the eastern edge is in Canadian waters).

Over the years, increased fishing effort and increasingly efficient and technologically advanced fishing gear decimated the fisheries on GB, effectively causing their collapse in the late 80s and early 90s. in 1993 Canada placed a moratorium on cod fishing and placed strict regulations on other GB fisheries. In 1994 the U.S. closed most of GB to commercial fishing. In 1995, this ban was extended indefinitely.

Red Tides
First off, "red tides" are not tides, they're algal blooms. Second, not all "red tides" are harmful and not all harmful algae cause "red tides". So, the more appropriate and scientifically-acceptable term is not "red tide", but "harmful algal bloom", or HAB. HABs are defined as an event when toxic-producing algae populations increase to the point that they become hazardous. For some species of algae, this requires an enormous population explosion, but for other, more toxic species, even a few cells per liter would be considered an HAB.

In the western North Atlantic, most HABs are the result of the dinoflagellate Alexandrium fundyense - incidently, these HABs are also "red tides". These critters produce neurotoxins, such as saxitoxin. Saxitoxin selectively blocks cellular sodium channels, which are necessary for creating nerve impulses. Blocking sodium channels thus prevents nerve impulses. Since nerve impulses control our muscles, saxitoxin can, in severe cases, cause paralysis. Naturally then, HABs of Alexandrium fundyense are responsible for Paralytic Shellfish Poisoning (PSP).

PSP occurs because shellfish are natural filters. They take in seawater, pass it through their gills, trapping microscopic organisms that they then digest. During blooms of Alexandrium fundyense shellfish in the area eat the dinoflagellates, but end up storing the saxitoxins in their tissue. Luckily for shellfish, saxitoxins have no effect on them. Unluckily for us (and any other vertebrate that decides to dine on the "infected" shellfish), the toxins enter our bodies when we eat the shellfish, block our sodium channels, and cause PSP. Symptoms of PSP? How about "nausea, vomiting, diarrhea, abdominal pain, and tingling or burning lips, gums, tongue, face, neck, arms, legs, and toes. Shortness of breath, dry mouth, a choking feeling, confused or slurred speech, and lack of coordination are also possible."1 In the most severe cases paralysis sets in and respiratory failure and death may follow.

HABs on GB:
As if the fisheries on George's Bank haven't been hit hard enough by depleted stocks, it turn out that there is a rather severe Alexandrium bloom sitting right on top of the shoal. The R/V Endeavor has recently completed a survey of the Gulf of Maine and Georges Bank and has found an HAB only on GB.

(click image to enlarge)

Superimposing the survey data onto the North Atlantic chart, you can see how the HAB is right on top of GB (note thre lack of data from the eastern, Canadian end of GB):
(click image to enlarge)

The worst section of the HAB has over 13,000 Alexandrium cells per liter of seawater, more than enough to cause PSP.

So, ignore those "George's Bank Quahogs" on sale at your local neighborhood food mart. Unless of course you think your diet is lacking in saxitoxins. (Actually, if you do see "George's Bank Quahogs" for sale, you best notify your nearest employee of the National Marine Fisheries Service - shellfishing on GB has been closed for more than a decade).

Wednesday, June 06, 2007

Tangled Bank #81

Check out the newest installment of the Tangled Bank - some great posts as always.

Friday, June 01, 2007

Friday Science: from Parasite to Mutualist

This is the first in a, hopefully, weekly bi-weekly occasional series of posts in which I will summarize/discuss some new peer-reviewed research that I find interesting. My post on synthetic estrogen and extinction started me thinking that this would be a good addition here. In attempting this, I am in no way suggesting that I am an expert in any of the topics I will be posting, only that I find them interesting and that I hope to be able to present the material in a "chewable" form. I'll also try to restrict my summaries to articles available via open access. Wish me luck.

This week's article that caught my attention is from PLoS Biology and deals with the evolution of parasites into benign or even beneficial organisms. In particular, the researchers show that over approximately 20 years, a particular strain of Wolbachia has evolved in a manner such that it now causes infected female flies (Drosophila simulans) to lay more eggs. Here we have a parasite that used to cause reproductive harm evolving into a "parasite" that helps fly reproduction. Even better, this phenomenon is exactly what evolutionary theory predicts should have happened.

[+/-] Show more/less

Wolbachia is a bacterium that infects all sorts of invertebrates, particularly insects. Individuals that are infected with Wolbachia show decreased reproductive success - partly through a process called cytoplasmic incompatibility (CI). CI basically means that the gametes of an infected individual are incapable of (or less successful in) fusing with the gametes of uninfected individuals. Thus, infected females can only breed with infected males.

Another interesting thing about Wolbachia is that unlike most transmissible parasites, it is passed only from mother to offspring via infected eggs. Such "vertical transmission", combined with CI, can cause a rather rapid spread of the parasite within a population. And this is exactly what has been seen in the population of flies in this study. In the mid-1980s Wolbachia-induced CI was discovered in a population of D. simulans in southern California. Since that time, the Wolbachia infestation has spread north through California and is "now pervasive throughout most North American populations of D. simulans."

Notice though that there are two conflicting aspects of Wolbachia infection: 1) Wolbachia is only passed from mother to egg, yet 2) Wolbachia infections cause females to lay fewer eggs. Evolutionaryly speaking, this set-up is not in the bacteria's (nor the fly's) best interest. Under this type of vertically-transmitted infection scenario, evolutionary theory predicts that the parasite will become less virulent harmful over time. At worst, the parasite should evolve so as to have no affect on female fecundity (just hitching a ride on the eggs). At best, theory predicts that the parasite should come around 180° and become a mutualistic partner by actually increasing female reproduction.

Sure enough, 20 years after the initial "outbreak", Wolbachia infection in D. simulans now has a positive effect on female fecundity. Originally, infected females laid 20% fewer eggs compared to uninfected females. Now infected females lay 10% more eggs than uninfected females. The authors also point out that CI levels and transmission rates have stayed constant, so the fecundity effect is not a result of depressed CI or bacterial transmission.

So, is this change in fecundity an effect of an evolving bacterium or an evolving host (or both)? To test this, the authors essentially infected flies with the old strain of the Wolbachia (that had been kept in culture for the past 20 years?) and found that the fecundity advantage disappeared. Thus, the current fecundity effect appears to be mostly a result of the evolution of the bacteria.

Ah, but what if the current Wolbachia strain that is causing the fecundity advantage is actually a more recently introduced strain and not the direct evolutionary lineage of the old strain? To examine this possibility, the authors tested the CI levels between the current strain and the old strain. If they were two different strains, flies infected with one would be reproductively incompatible with flies infected with the other. This was not the case, supporting the idea that the new Wolbachia strain is an "evolved version" of the old strain.

I found this study fascinating for a number of reasons. First, the design and the thoroughness of the experiments seem flawless to me (given, of course, that I am neither a fly biologist nor a bacteriologist) - the authors seem to have covered all the appropriate ground, showing that indeed the effects they witnessed are the result of bacterial evolution. Secondly, the evolution of this strain of Wolbachia is a great example of how quickly natural selection can work given conducive conditions. Thirdly, this paper shows just how testable (and accurate) predictions from evolutionary theory are.

Based on what is known about evolution by natural selection, coupled with a firm understanding of the biology behind a given natural system, we are able to make hypotheses, design experiments (and/or make the necessary observations to test these hypothesis, and come to scientifically tenable conclusions.

What more could you ask for?

Citation: Weeks AR, Turelli M, Harcombe WR, Reynolds KT, Hoffmann AA (2007) From Parasite to Mutualist: Rapid Evolution of Wolbachia in Natural Populations of Drosophila. PLoS Biol 5(5): e114 doi:10.1371/journal.pbio.0050114

The perfect gift

How great is this? James Watson, co-discoverer of DNA the structure of DNA, was presented with the genetic sequence of his very own genome.

It only cost $1 million. Wonder if I should ask for mine for Father's Day...

(thanks for the link, Linda)