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  • August 18, 2010
  • 03:24 PM

The ecosystems within us

by Aaron Berdanier in Biological Posteriors

In the guts of each of us there are trillions of microbes. They provide us with "enhanced metabolic capabilities, protection against pathogens, education of the immune system, and modulation of gastrointestinal development" (De Filippo et al. 2010). The diversity of these organisms can play a role in the future development of disease. But, what makes our guts so diverse? As De Filippo et al. (2010) report, one main factor appears to be diet.... Read more »

De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, & Lionetti P. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20679230  

  • August 18, 2010
  • 09:52 AM

Is the cancer research paradigm changing?

by Sally Church in Pharma Strategy Blog

Over the weekend, a reader (a scientist in translational medicine) kindly sent me the link to a paper on PARP inhibition and asked: "Is this a sign of the new wave of oncology drug development? Rather than basing treatment on...... Read more »

  • August 18, 2010
  • 09:47 AM

The many (scientific) uses of penguin poop (Part I)

by Sam W in From C to Carnivore

Tracking penguins in (& from) space Penguins are charismatic animals with a large role in popular culture. They are seen as cuddly (though personally, I think that penguins are from the dark side). Regardless of personal inclination regarding cuddliness, it is easy to see that penguins are unique animals. Something your average penguin fan will [...]... Read more »

  • August 18, 2010
  • 08:20 AM

GFP gets flashier yet

by Becky in It Takes 30

A recent report in Chemistry & Biology (Subach et al 2010 Red fluorescent protein with reversibly photoswitchable absorbance for photochromic FRET.  Chem Biol. 17 745-55. PMID: 20659687) describes the discovery of the first red fluorescent protein that has switchable absorbance spectra. The switch is thought to happen because the chromophore undergoes a cis-trans isomerization in [...]... Read more »

  • August 18, 2010
  • 08:00 AM

Dude looks like a lady? Male lizards courting males

by Zen Faulkes in NeuroDojo

Oh, mistaken gender identity. Are you ever not funny?

Sudden change creates uncertainty. This is as true in evolution as it is in financial crises. Evolutionarily speaking, the eastern fence lizard, Sceloporus undulatus is in a moment of sudden and fast chance – some of them, at least.

These lizards find themselves in a situation rather like some mice I’ve talked about before (here and here). A couple of thousand years ago, a new habitat opens up with very light coloured sand. Humans, in a fit of cleverness a few thousand years later, name it White Sands, New Mexico. The lizards see an opportunity and move in. For those that do, the darkest animals tend to have a hard time of it, because their high contrast make them easy pickings for predators. Lightly coloured animals get the advantage.

The rest of the population, though, in a more normal habitat, are being not picked on for having a darker hue. So the colour of the individual in the two habitats get more and more different over time.

What happens when you put members from these two divergent populations together in the same room? Will there be any behavioural differences, or will it just be as though one lizard thinks, “Oh, my brother, though we are long separated by the shifting sands, yet I still recognize you as a member of my kind, my tribe, my species!”

It didn’t quite work out that way. When they put together two males, a male from the White Sands habitat tended to react to a darkly coloured male from another habitat with:

“Whoa. Who’s the hottie?!”

The light coloured males gave courtship displays to those dark coloured males more than half the time. This is not usual behaviour: more typically, males who get introduced to another male will usually react aggressively, because these guys are territorial.

Although the colour of the lizards’s back is the most obvious cause to point to, the authors say it’s probably not the major difference between the populations that is driving this odd behaviour. When animals are displaying to each other, they do so in such a way as to show their undersides, not their backs.

The colouring of the lizards’ undersides also varies between the white sands and the dark soils. Lizards from the white sands tend to have bigger display patches on their undersides, and this is true for both males and females. Because the display patches of females from the white sands are larger, they tend to be fairly close in size to those of the males from the dark soil environments.

Extract from Figure 4. WS = white sands, DS = dark soil.
While this seems a plausible explanation, it is an untested hypothesis at this point. And it’s not clear right why larger patches might have had a selective advantage in a light sand environment.

But you could see how anyone could make that sort of mistake. Right?


Robertson JM, & Rosenblum EB. 2010. Male territoriality and ‘sex confusion’ in recently adapted lizards at White Sands Journal of Evolutionary Biology. DOI: 10.1111/j.1420-9101.2010.02063.x.

Photo by TrombaMarina on Flickr, used under a Creative Commons license.... Read more »

Robertson JM, & Rosenblum EB. (2010) Male territoriality and ‘sex confusion’ in recently adapted lizards at White Sands. Journal of Evolutionary Biology. info:/

  • August 18, 2010
  • 07:37 AM

Warming caves: A stop-gap prevention to thwart white-nose syndrome?

by DeLene Beeland in Wild Muse

I’ve been trying to tune into developments with white-nose syndrome because it’s one of the worst emerging pathogens to hit North American wildlife in recent history. Ever since the first breakout in a New York cave in February 2006, this white fungus has killed off well more than a million bats from six different species. [...]... Read more »

  • August 18, 2010
  • 06:15 AM

Environmental Constraints on Colour Term Evolution

by Sean Roberts in A Replicated Typo 2.0

Continuing my series on the Evolution of Colour terms, this post reviews evidence for environmental constraints on colour perception.... Read more »

Regan, B., Julliot, C., Simmen, B., Vienot, F., Charles-Dominique, P., & Mollon, J. (2001) Fruits, foliage and the evolution of primate colour vision. Philosophical Transactions of the Royal Society B: Biological Sciences, 356(1407), 229-283. DOI: 10.1098/rstb.2000.0773  

Clarke, B.C. (1979) The evolution of genetic diversity. Proceedings of the Royal Society of London B, 453-474. info:/

Webster, M., Webster, S., Bharadwaj, S., Verma, R., Jaikumar, J., Madan, G., & Vaithilingham, E. (2002) Variations in normal color vision. III. Unique hues in Indian and United States observers. Journal of the Optical Society of America A, 19(10), 1951. DOI: 10.1364/JOSAA.19.001951  

LAENG, B., BRENNEN, T., ELDEN, A., GAAREPAULSEN, H., BANERJEE, A., & LIPTON, R. (2007) Latitude-of-birth and season-of-birth effects on human color vision in the Arctic. Vision Research, 47(12), 1595-1607. DOI: 10.1016/j.visres.2007.03.011  

Dowman, M. (2007) Explaining Color Term Typology With an Evolutionary Model. Cognitive Science: A Multidisciplinary Journal, 30(1), 99-132. DOI: 10.1207/s15516709cog3101_4  

Griffin LD. (2006) Optimality of the basic colour categories for classification. Journal of the Royal Society, Interface / the Royal Society, 3(6), 71-85. PMID: 16849219  

  • August 17, 2010
  • 11:57 PM

Bruneau Sand Dune tiger beetles caught in the act!

by Ted MacRae in Beetles in the Bush

The newest issue of CICINDELA (“A quarterly journal devoted to Cicindelidae”) contains an interesting article by my good friend and fellow tiger beetle enthusiast Kent Fothergill, who presents a fascinating sequence of photos documenting a field encounter with a mating pair of the endangered Bruneau Sand Dune tiger beetle (Cicindela waynei) (Fothergill 2010).  This is one of [...]... Read more »

Fothergill, K. (2010) Observations on mating behavior of the Bruneau Dune tiger beetle, Cicindela waynei Leffler (Coleoptera: Carabidae: Cicindelinae). CICINDELA, 42(2), 33-45. info:/

  • August 17, 2010
  • 05:01 PM

Hitchhiking through the nervous system

by Lab Rat in Lab Rat

I while ago I wrote a post about how virus's get from the outside of the cell to the interior of the nucleus and found that virus particles are able to hitchhike on the cells internal transport systems. I was quite interested therefore to find a paper in Nature Reviews (reference below) that revealed that not only do virus's latch on to host proteins to travel around inside the cell, they also use host extracellular processes for travelling around the body. And outside the cell it's not just virus's either, bacterial toxins need transport systems too, unlike whole bacteria they can't move around under their own power.One place that the body wants to protect particularly well against infection is the central nervous system. It provides this protection by surrounding it with a wall of tightly sealed endothelial cells known as the blood-brain barrier. However despite this the body itself still need to get some things into the CNS; small molecules such as glucose and oxygen as well as larger cells of the immune system. These immune system cells provide the first sneaky point of entry; virus's such as HIV can hitch a ride inside these cells and get into the central nervous system that way. This is the equivalent of hiding in a truck to avoid border patrols.However some virus's and toxins use an even more sneaky method, dressing up as a border-patrol guard and simply walking in. Throughout the blood brain barrier there are long neuronal projections that connect the central nervous system to peripheral organs. A picture of one of these cells is shown below:Like all cells, this contains the transport molecules Kinesin and Dynein, which virus's can latch onto in order to transport themselves through the cell (see earlier post here). Once they get inside the cell, the cell's own proteins will carry the virus particles all the way through it, and into the central nervous system. However first it has to get inside the cell, through the little blue blob at the bottom (in the diagram above it's highlighted with a little dotted square).As well as receiving chemical signals for electrical impulses (that make the neuron function as a nerve) the blue blob also contains various different receptors capable of engulfing and uptaking small molecules, including those used to signal some neural impulses. This means that there are a range of chemical receptors on that blue blob which allow the uptake of molecules, and you can probably tell where this is headed...The diagram above is the intramolecular equivalent of Han Solo dressed as a Stormtrooper wandering into the Death Star. By changing its outer coat enough to mimic the proteins that are usually taken up by the cell the Herpesvirus can attach to the outer membrane and then be absorbed into the cell. Once inside, it can latch onto the dynein and get a free pass all the way into the nucleus (and neurons are pretty long so it is a bit of a journey). Poliovirus and rabies can also carry out this trick (at the neuromuscular junction for anyone interested) along with the bacterial botulinum toxin, which gets taken up by synaptic vesicles and essentially kills the end of the nerve, which can either lead to instant death or a scarily smooth robot-plastic forehead, depending what context you take it.I always find it quite spooky to think of my body in that way, as a huge maze of intracellular processes, being negotiated, infected and protected by tiny substances outside of my conscious control. I think that's another reason I find cellular biology so fascinating, by studying it we gain control (or if not control at least an understanding) of these detailed processes that we would not normally be able to influence.---Salinas S, Schiavo G, & Kremer EJ (2010). A hitchhiker's guide to the nervous system: the complex journey of viruses and toxins. Nature reviews. Microbiology, 8 (9), 645-55 PMID: 20706281... Read more »

  • August 17, 2010
  • 04:24 PM

So What Did the Turkeys Eat?

by teofilo in Gambler's House

As if on cue, given that I’ve been talking about turkey husbandry and stable isotope testing of human remains, a paper in the latest issue of the Journal of Archaeological Science combines the two, using similar stable isotope techniques on turkey remains from sites in southwestern Colorado to determine what the turkeys were eating.  The [...]... Read more »

  • August 17, 2010
  • 12:53 PM

Modern ecological research: what, where, how?

by Aaron Berdanier in Biological Posteriors

Just over ten years ago, Robert May published an article considering "the most important unanswered questions in ecology" (May 1999). This perspective piece offered some direction to a young field that was expanding rapidly. But, where is ecology going in the next thirty years (or so)?... Read more »

May, R. (1999) Unanswered questions in ecology. Philosophical Transactions of the Royal Society B: Biological Sciences, 354(1392), 1951-1959. DOI: 10.1098/rstb.1999.0534  

  • August 17, 2010
  • 10:14 AM

Whatever Happened to Seismosaurus?

by Brian Switek in Dinosaur Tracking

In 1991, paleontologist David Gillette announced that he had found the largest of the enormous sauropod dinosaurs. He called it Seismosaurus halli, and based on the parts of the skeleton that had been prepared at the time, Gillette believed Seismosaurus to be between 127 and 170 feet long! Even giants such as Diplodocus would have [...]... Read more »

David D. Gillette. (1991) Seismosaurus halli, gen. et sp. nov., A New Sauropod Dinosaur from the Morrison Formation (Upper Jurassic/Lower Cretaceuos) of New Mexico, USA. Journal of Verterbrate Paleontology, 11(4), 417-433. info:/

  • August 17, 2010
  • 10:00 AM

Learning mutation bias

by Kele in Kele's Science Blog

So. I have been reading about mutational bias primarily through the work of Arlin Stoltzfus and it’s been a bit difficult to decipher so far. For some reason I cannot find a source that provides a good explanation of how the different biases work and the relevant research. If anyone can recommend a source (a [...]... Read more »

  • August 17, 2010
  • 09:31 AM

Genetics is One: Mendelism and quantitative traits

by Razib Khan in Gene Expression

In the early 20th century there was a rather strange (in hindsight) debate between two groups of biological scientists attempting to understand the basis of inheritance and its relationship to evolutionary processes. The two factions were the biometricians and Mendelians. As indicated by their appellation the Mendelians were partisans of the model of inheritance formulated [...]... Read more »

Fisher, R. A. (1918) On the correlation between relatives on the supposition of Mendelian inheritance. Transactions of the Royal Society of Edinburgh. info:/

  • August 17, 2010
  • 09:05 AM

Turning up the alarms makes aphids careless

by Jeremy Yoder in Denim and Tweed

The oven in my apartment needs a serious deep-cleaning. A really serious deep-cleaning. To the point that, when I want to do some baking, smoke is more or less inevitable. As a result, I've developed the habit of responding to the apartment's smoke alarm by reaching up and un-mounting it from the ceiling, which completely disables it. If a fire were to start somewhere else in the apartment while I'm baking, I'd probably be in trouble.

That's more or less the idea behind an approach to agricultural pest control proposed in a paper just released online at PNAS: if you saturate insect pests with a predator warning signal, they become used to the signal, and more vulnerable to predators [$a]. Aphids are the target pest—they form huge, clonal swarms to literally suck the life out of plants, as described very nicely in this BBC Nature video.

As the video notes, those clonal swarms are vulnerable to all sorts of predators, most famously ladybird beetles. So when attacked, the aphids emit an alarm pheromone to warn the rest of the clone. But it's possible to habituate aphids to the alarm pheromone—if they're surrounded by it long enough, they won't respond to it by running away. The new study's authors proposed genetically engineering crop plants to produce the alarm pheromone, to automatically produce that habituation.

To see if this would work, they raised aphids on a line of Arabidopsis thaliana (the white lab mouse of the plant world) that had been engineered to produce the alarm pheromone. And, indeed, habituated aphids were much less likely to be repelled by the alarm pheromone—and were even in some cases attracted to it. Perhaps the most telling test involved leaving habituated and non-habituated aphids on an experimental plant with ladybird beetles introduced—habituated aphids were less likely to survive 24 hours with the beetles.

This is a pretty clever approach to pest control, but there's an obvious caveat. I don't see any reason why aphids couldn't evolve a way around this attempt to swamp out their own alarm signals—the paper notes that different aphid species have different responses to the particular alarm pheromone tested, so engineering one pheromone into crop plants doesn't leave the aphids without evolutionary options. Unless it's very cleverly designed, any pest-control strategy creates strong natural selection—and the better the strategy is, the stronger the selection is—to evolve resistance. Alarm-pheromone-producing crops might be another tool for pest control, but they won't be the last one we need.
.flickr-photo { }.flickr-framewide { float: right; text-align: left; margin-left: 15px; margin-bottom: 15px; width:100%;}.flickr-caption { font-size: 0.8em; margin-top: 0px; }
A ladybird beetle makes short work of some aphids. Photo by kenjonbro.
See also this press release from Cornell University, which discusses the paper's results.


de Vos, M., Cheng, W., Summers, H., Raguso, R., & Jander, G. (2010). Alarm pheromone habituation in Myzus persicae has fitness consequences and causes extensive gene expression changes. Proc. Nat. Acad. Sci. USA DOI: 10.1073/pnas.1001539107

... Read more »

  • August 17, 2010
  • 08:00 AM

Celebrate diversity: Old female salamanders

by Zen Faulkes in Marmorkrebs

Imagine, if you will, a line of ancient females, who trick males into having sex with them, so that the females can continue living indefinitely.

I know, you’ve seen it before in a dozens of movies, books, and television episodes. Who hasn’t seen a vain sorceress stealing youth, particularly from young men?

Something like this goes on in some salamanders, except that no one salamander is living unusually long. The evolutionary line of salamanders, though, is showing surprisingly longevity.

Some salamanders are all female... but they are not, strictly speaking, asexual or parthenogenetic. These unisexual female lineages engage in a little sperm “theft” from several sexual salamanders species (Ambystoma laterale is pictured), a process known as kleptogenesis. Genetically, these unisexual females are all over the map. Some unisexuals have a paired set of chromosomes like the more typical sexual species (i.e., they are diploid); others have three, four, or five sets of chromosomes.

This unusual mode of reproduction is interesting, because it might allow a unisexual species to avoid genetic stasis. In theory, sexual species have the edge in a changing environment because more genetic variations are possible through sexual reproduction. Having every individual be genetically identical is great as long as the environment never changes.

But environments do change, so it’s generally though that parthenogenetic species tend to go extinct at much higher rates than sexual ones.

This new paper by Bi and Bogart tries to settle how old this odd lineage of female salamanders is. One previous study suggested millions of years; another estimated tens of thousands of years. Bi and Bogart come down on the side of millions of years; a little over 5 million years, to be precise.

The reason for the discrepancy comes down to an issue concerning the wrong bit of DNA being amplified and analyzed. Most animal cells have DNA in two places: the cell nucleus (where most people think of it being), and in the mitochondria (the cell’s power plant). In normal sexual species, nuclear DNA comes equally from both parents, while mitochondrial come from mom.

Because these all-female salamanders get nuclear DNA from the sperm they “steal,” you can really only try to trace relationships using mitochondrial DNA in these animals.

The problem is that nuclear DNA sometimes has some bits in it that are extremely similar to mitochondrial DNA. These sequences, called numts, are probably derived from the mitochondria. Bi and Bogart argue that the previous research that suggested that these female salamanders split from the sexual salamanders about 25,00 years ago probably sequenced a numt instead of a mitochondrial gene.

That DNA. It’s tricky.

Parthenogenesis in Marmorkrebs is blessedly simple in comparison.


Bi, K., & Bogart, J. (2010). Time and time again: Unisexual salamanders (genus Ambystoma) are the oldest unisexual vertebrates BMC Evolutionary Biology, 10 (1) DOI: 10.1186/1471-2148-10-238

Photo by whiteoakart on Flickr, used under a Creative Commons license.... Read more »

  • August 17, 2010
  • 07:57 AM

Patterns of expression of DNA repair genes and relapse from melanoma

by Sally Church in Pharma Strategy Blog

Someone kindly sent me this pattern on how gene expression can be used to track insufficient DNA repair can lead to relapse in melanoma, making it potentially useful as both a prognostic and predictive biomarker for the disease. Regular readers...... Read more »

Jewell, R., Conway, C., Mitra, A., Randerson-Moor, J., Lobo, S., Nsengimana, J., Harland, M., Marples, M., Edward, S., Cook, M.... (2010) Patterns of Expression of DNA Repair Genes and Relapse from Melanoma. Clinical Cancer Research. DOI: 10.1158/1078-0432.CCR-10-1521  

  • August 17, 2010
  • 06:15 AM

Pigs (and their viruses) fly

by iayork in Mystery Rays from Outer Space

An emerging disease that I just missed directly seeing emerge is PRRS. PRRS is “porcine reproductive and respiratory syndrome”, which pretty much sums up the disease. It’s caused by — you’ll never guess — Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that emerged in 1987. That was the year I left large animal [...]... Read more »

  • August 17, 2010
  • 12:59 AM

Sex, Stress, and Neurogenesis

by Brian Mossop in The Decision Tree

There’s an article in the latest issue of Wired by Jonah Lehrer explaining just how dangerous stress can be to our health.  It’s a fascinating read — and instead of relying on my poor attempt to paraphrase — I suggest checking out the article in its entirety. The part of the story that struck a [...]... Read more »

  • August 16, 2010
  • 11:13 PM

An Anthropological Genetic View of Berkeley’s Personalized Medicine Project

by Kris in Ge·knit·ics

Recently, UC Berkeley announced their “Bring Your Genes to Cal” Project, offering personalized genetic testing for all incoming freshmen. The program allowed incoming students, on a voluntary and anonymous basis, to submit DNA samples, with the promise that they would receive their personal results of tests for three common genetic variants. The program had IRB [...]... Read more »

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