Monday, August 22, 2005

632: The Tubercular Hominid

The Tubercular Hominid: Corante > The Loom >:

French researchers have found that people in Djibouti carry strains of TB that are significantly different than anything seen before. They have many more genetic differences than have been found in human TB strains from anywhere else in the world. Yet they are more closely related to other human TB than to the Mycobacterium species that infect cattle and other animals. The scientists then turned the mutations of the Djibouti strains into a molecular clock. They estimate that the ancestor of today's human TB existed some three million years. The results have just been published in the new open access journal PLOS Pathogens.

If tuberculosis was infecting our ancestors three million years ago, it was infecting early, small-brained hominids. All of the hominids known from that time lived in Africa, and hominids would not be found outside the continent for over a million years. Our own species is believed to have evolved much later in Africa, and to have spread to Asia and Europe roughly 50,000 years ago. So it's telling that all these ancient strains are found in Africa, not far from some of the richest lodes of hominid fossils in Ethiopia. The genetic diversity of these bacteria reflects the genetic diversity of living Africans.
The evolution of TB.

Thursday, August 18, 2005

631: Worm ideal model for studying viruses in humans | Science Blog

Worm ideal model for studying viruses in humans | Science Blog:

For years researchers throughout the world have studied C. elegans because many aspects of its biology, such as genetics, development and the workings of neurons, mirror the biology of humans. However, no viruses were known to infect the millimeter-long roundworm so it was not used as a model for studying viral infections.

The Nature paper now shows that UC Riverside researchers have developed a strain of the worm, C. elegans, in which an animal virus could replicate, allowing them to map the delicate dance of action and reaction between virus and host.

The UCR team has shown that virus replication in the worm triggers an antiviral response known as RNA silencing or RNA interference (RNAi). RNAi specifically breaks down the virus’ RNA. Virus RNA creates proteins that allow the virus to function. The virus responds by producing a protein acting as a suppressor of RNAi to shut down the host’s antiviral response. Virus infection did not occur when the viral RNAi suppressor was made inactive by genetic mutations in the host system.

C. elegans’ RNAi system is considered a “blanket system,” meaning that it has parallels in humans, making the worm model discovered by Ding and his colleagues a valuable tool in studying the way viruses interact with hosts. This tool may speed the discovery of treatments for virus-caused diseases that plague humans.

“The RNAi machinery is very similar between humans and C. elegans, and human viruses such as Influenza A virus and HIV are known to produce RNAi suppressors,” Ding said. “So now, the question is can we treat human viral diseases using chemical inhibitors of viral RNAi suppressors?”
Common descent and the evolutionary arms race between viruses and their hosts.

Wednesday, August 17, 2005

Ohio science

At Thoughts from Kansas.

630: Scientists Crack 40-year-old DNA Puzzle And Point To 'Hot Soup' At The Origin Of Life

Scientists Crack 40-year-old DNA Puzzle And Point To 'Hot Soup' At The Origin Of Life:

In a paper published in the Journal of Molecular Evolution this week, researchers from the University of Bath describe a new theory which they believe could solve a puzzle that has baffled scientists since they first deciphered the language of DNA almost 40 years ago.

why there should be 64 words in the DNA dictionary which translate into just 20 amino acids, and why a process that is more complex than it needs to be should have evolved in the first place, has puzzled scientists for the last 40 years.

Dozens of scientists have suggested theories to solve the puzzle, but these have been quickly discounted or failed to explain some of the other quirks in protein synthesis.

One of quirks of the genetic code is that there are groups of codons which all translate to the same amino acid. For example, the amino acid leucine can be translated from six different codons whilst some amino acids, which have equally important functions and are translated in the same amount, have just one.

The new theory builds on an original idea suggested by Francis Crick - one of the discoverers of the structure of DNA - that the three-letter code evolved from a simpler two-letter code, although Crick thought the difference in number was simply an accident “frozen in time”.

The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes - but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.

By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids - explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons.

“When you evolve our theory for a doublet system into a triplet system, you get an exact match up with the number and range of amino acids we see today,” said Dr van den Elsen, who has worked with Dr Stefan Babgy and Huan-Lin Wu on the theory.

“This simple theory explains many unresolved features of the current genetic code. No one has ever been able to do this before, so we are very excited.”

The theory also explains how the structure of the genetic code maximises error tolerance. For instance, ‘slippage’ in the translation process tends to produce another amino acid with the same characteristics, and explains why the DNA code is so good at maintaining its integrity.

“This is important because these kinds of mistakes can be fatal for an organism,” said Dr van den Elsen. “None of the older theories can explain how this error tolerant structure might have arisen.”

The new theory also highlights two amino acids that can be excluded from the doublet system and are likely to be relatively recent ‘acquisitions’ by the genetic code. As these amino acids - glutamine and asparagine - are unable to hold their shape in high temperatures, this suggests that heat prevented them from being acquired by the code at some point in the past.
Research into the evolution of DNA, and evolutionary hypotheses to be tested.

629: The Questionable Authority: Applications of Evolution 1 - The Erythrina Gall Wasp

The Questionable Authority: Applications of Evolution 1 - The Erythrina Gall Wasp:

At the moment, there is a new invasive species that is making the news here in Hawai'i: a species of "gall wasp" that has been wrecking havoc on trees of the genus Erythrina in Singapore, Taiwan, and a number of other places was found in a valley on Oahu in April. Since then, it has been found in a large number of other places on Oahu, and has started to turn up on other islands, including Maui, and a number of scientists believe that it poses a serious threat to a culturally-significant endemic plant - the Wiliwili (Erythrina sandwichensis). The threat is being taken so seriously that scientists have reportedly begun to bank Wiliwlil seeds as a precaution in case the extant population is completely lost.

So what does this have to do with evolution?

Individual species do not evolve in a vacuum. They evolve in an environment, and natural selection favors the preservation of variations that increase the chances for an organism to survive within that environment. This is common knowedge. What people sometimes forget, however, is that when we discuss the "environment" that an organism evolves in, we are talking about much, much more than just the climate. The evolutionary environment also includes every other species of organism that has any sort of effect on it. Species evolve within the ecosystem or ecosystems that they inhabit, and they evolve as a part of those ecosystems.

So what happens when people - either intentionally or inadvertantly - introduce a species to a new habitat? That's a broad question, and one where the answer is obviously going to depend on a lot of things - not least, what the new species is, and where it is being introduced. (Biology can be really annoying that way, with the answers to so many questions depending on specific circumstances.)

Since the broad question isn't really answerable, let's narrow it in a way that is tailored to these specific circumstances: what happens if you introduce a pest species (either parasite or predator) into a new, hospitable environment that contains a species that is closely related to the pest's usual target? That is a very complexly worded question, but it has a simple answer. Nothing good is going to happen.

In the case of the Erythrina gall wasp, this is exactly what happened. The gall wasp is not native to Hawai'i, and it did not evolve here. This means that up until now, it has not been a part of the evolutionary environment for any of the native species. As a result, it should come as no surprise that the native species has no natural defences against the gall wasp. At the same time, the gall wasp has now found itself in an environment where it has lots of access to a number of species that it can use, and which completely lacks any of it's normal predators. In short, it's gall wasp heaven out here - at least until the Erythrina are all gone.
For more on how evolution helps us understand invasive species and vice versa, check out TQA, a new kid on the evolution blogging block.

628: Pleistocene Horses

Horse Evo Phylo Tree
Pharyngula::Pleistocene Horses:

Prior hypotheses of the relationship of these three North American groups suggested that, because of their morphology similarity to Asian stock, the stilt-legged horses were related the Asian asses, and had migrated into the Americas by way of the Bering land bridge. Hippidion was so distinctly different from other horses that it was considered to have diverged from the equid lineage about 10 million years ago. These species were thought to have spread into South America during the Great American Biotic Interchange about 2.5 million years ago, when the Isthmus of Panama formed and allowed animals to move north and south between the continents. Two competing models of these relationships, based on morphological analyses, are shown below.

The molecular data revealed a surprise, though. The tree below was constructed by analysis of mtDNA, and it groups the animals very differently. The caballines of America and Europe form a single clade, as expected. The stilt-legged horses and Hippodion, though, cluster together; Hippodion diverged only recently, and the stilt-legged horses are more closely related to the caballines than to the Asian asses. The authors also suggest that many species within the caballines ought to be lumped together, are more likely to represent regional variants than true species.
The figure is a maximum likelihood phylogeny based on mitochondrial DNA. Black numbers above/beside nodes are posterior probabilities and bootstrap values, respectively (only values > 50% are shown). White numbers on black background are divergence times as calculated from the molecular data. Numbers/letters in bold at the beginning of each specimen's name are sample numbers or GenBank accession numbers. Labels of prehistoric specimens are followed by their age, if available, in thousands of years. The outgroup (Rhinoceros and Ceratotherium) is not shown.

Tests of evolutionary hypotheses.

627: The Genetic Origins of Corn on the Cob | Science Blog

The Genetic Origins of Corn on the Cob | Science Blog:

In 1909, while harvesting a typical corn crop (Zea mays) in Illinois, a field worker noticed a plant so unusual that it was initially believed to be a new species. Its "peculiarly shaped ear" was "laid aside as a curiosity" and the specimen was designated Zea ramosa (from the Latin ramosus, "having many branches"). Due to the alteration of a single gene, later named ramosa1, both the ear and the tassel of the plant were more highly branched than usual, leading to loose, crooked kernel rows and to a tassel that was far bushier than the tops of normal corn plants.

Now, researchers at Cold Spring Harbor Laboratory in New York have isolated the ramosa1 gene and shown how it controls the arrangement and length of flower-bearing branches in corn, related cereal crops, and ornamental grasses. The study indicates that during the domestication of corn from its wild ancestor (teosinte), early farmers selected plants with special versions of the ramosa1 gene that suppressed branching in the ear, leading to the straight rows of kernels and the compact ears of modern-day corn on the cob (see photo). The findings are described in the July 24 advance online edition of the journal Nature.

" We've shown that corn and related grasses have either none, some, or a lot of ramosa1 gene activity, and that these different levels of activity have a big impact on the architecture of the plants," says Dr. Robert Martienssen of Cold Spring Harbor Laboratory, who led the study. "The ramosa1 gene appears to be a key player in the domestication of corn, and we've shown that it acts by signaling cells to form short rather than long branches," says Martienssen, who was joined in the study by lead author Dr. Erik Vollbrecht, now at Iowa State University.

Says Vollbrecht, "We solved this enduring puzzle by combining classical and modern molecular genetics. The former included our use of transposable elements or 'jumping genes'--discovered at Cold Spring Harbor by [Nobel laureate] Barbara McClintock--to 'tag' the ramosa1 gene. That enabled us to isolate the gene and determine its DNA sequence for a variety of other experiments."

" As corn was being domesticated, farmers selected a larger and larger ear with more and more rows of kernels, based on the activity of genes other than ramosa1. But we suspect that as the ear got larger, it needed special alleles of ramosa1 to prevent the extra rows from forming branches instead of kernels," says Martienssen. "There may have been other reasons for selecting an unbranched ear, including the interaction with other genes that were subsequently lost during domestication, but we don't yet know if this is the case."
The evolution of grasses, selection, and good biology.
" We also looked at a popular ornamental grass that grows outside my office and found the same result. It has a spiky top like corn, so we were delighted to find that they have similar profiles of ramosa1 activity," says Martienssen.
That's common descent.

626: Genetics links whale to two different ocean basins | Science Blog

Genetics links whale to two different ocean basins | Science Blog:

For the first time ever, a genetic study has followed a single humpback whale from one ocean basin to another, adding to traditional notions of the migratory patterns of these majestic marine mammals in the process, according to researchers from the Wildlife Conservation Society (WCS), the American Museum of Natural History (AMNH), and New York University. In the most recent Royal Society's Biology Letters, a male humpback whale that was first sighted in Madagascar's Antongil Bay in 2000 was found in 2002 swimming off the coast of Loango National Park in Gabon--on the other side of the African continent.
This is gene flow, one of the 4 evolutionary mechanisms, along with genetic drift, mutation, and natural selection. Understanding gene flow in whales improves conservation, and helps us understand how whales have evolved. It's known that there are a number of distinct genetic populations of humpbacks, and how often and by what means they exchange genetic information is crucial to conservation.

625: Generating right-left asymmetries

Pharyngula::Generating right-left asymmetries:

We're only sorta bilaterally symmetric: superficially, our left and right halves are very similar, but dig down a little deeper, and all kinds of interesting differences appear. Our hearts are larger on the left than the right, our appendix is on the right side, even our brains have significant differences, with the speech centers typically on the left side. That there is asymmetry isn't entirely surprising—if you've got this long coil of guts with a little appendix near one end, it's got to flop to one side or the other—but what has puzzled scientists for a long time is how things so consistently flop over in the same direction in individual after individual. There has to be some deep-seated mechanism that biases developmental events to favor one direction over the other. We know many of the genes involved in asymmetry, but what is the first step that skews development to make consistent asymmetrical choices?

In mammals, we're getting close to the answer. And it looks to be beautifully elegant—it's a simple trick to convert an anterior-posterior difference into a left-right one.

Nonaka et al. have examined the node of the mouse embryo. At the time of gastrulation, the mouse embryo (and the human embryo as well) is essentially a flat, two-layered sheet, with a groove in the middle called the primitive streak, and a dimple at the anterior end called Henson's node.

Zooming in on that area of the node in C, you can see the tops of the epithelial cells looking vaguely like cobblestones, with white strings scattered around. These are ciliated cells, and the strings the whip-like cilia that would be swinging around in a clockwise rotation if the cells were alive. You can watch a QuickTime movie of node cilia to see it in action.

When you watch those cilia spin around, here's the subtle but important thing to look for: their paths don't form perfect circles, which would indicate that they are pointing straight up at you, but are instead deformed to varying degrees, showing that they are tilted at an angle…and they are all tilted in the same direction, towards the posterior end of the embryo.
That tilt is what generates the left-right asymmetry. The tilt isn't asymmetric—all of the cilia are aimed just a little bit posteriorly, rather than straight up—but because the cilia are also rotating in a clockwise direction, it generates unequal lateral forces.
Why does the same mechanism operate in all mammals? Common descent.

Monday, August 15, 2005

624: Mutant mice helping cure diseases - Aug 10, 2005 - Mutant mice helping cure diseases - Aug 10, 2005:

Researchers first genetically engineered a mouse in 1980. But until recently, such creations were mostly scientific novelties.

That changed drastically after President Clinton announced the mapping of the human genome in 2000. That's because mice and men are nearly genetically identical, each possessing just a few hundred different genes out of a possible 25,000 or so. Cancer in mice is a lot like human cancer, for instance. Mice have become powerful, living research tools.

The number of mutant research mice has grown so dramatically in recent years that companies are now profiting by housing and breeding scientists' creations.
Common descent explains that similarity, and evolutionary biology is bringing us closer and closer to cures for cancer, Parkinson's and diabetes, among other things.

623: The rise of the hominids as an adaptive shift in fallback foods: Plant underground storage organs (USOs) and australopith origins

ScienceDirect - Journal of Human Evolution : The rise of the hominids as an adaptive shift in fallback foods: Plant underground storage organs (USOs) and australopith origins:

We propose that a key change in the evolution of hominids from the last common ancestor shared with chimpanzees was the substitution of plant underground storage organs (USOs) for herbaceous vegetation as fallback foods. Four kinds of evidence support this hypothesis: (1) dental and masticatory adaptations of hominids in comparison with the African apes; (2) changes in australopith dentition in the fossil record; (3) paleoecological evidence for the expansion of USO-rich habitats in the late Miocene; and (4) the co-occurrence of hominid fossils with root-eating rodents. We suggest that some of the patterning in the early hominid fossil record, such as the existence of gracile and robust australopiths, may be understood in reference to this adaptive shift in the use of fallback foods. Our hypothesis implicates fallback foods as a critical limiting factor with far-reaching evolutionary effects. This complements the more common focus on adaptations to preferred foods, such as fruit and meat, in hominid evolution.
Carl Zimmer discusses some of the implications and background of the research.

Sunday, August 14, 2005

622: Model Gives Clearer Idea Of How Oxygen Came To Dominate Earth's Atmosphere

Thanks to afarensis, Model Gives Clearer Idea Of How Oxygen Came To Dominate Earth's Atmosphere:

A number of hypotheses have been used to explain how free oxygen first accumulated in Earth's atmosphere some 2.4 billion years ago, but a full understanding has proven elusive. Now a new model offers plausible scenarios for how oxygen came to dominate the atmosphere, and why it took at least 300 million years after bacterial photosynthesis started producing oxygen in large quantities.

The big reason for the long delay was that processes such as volcanic gas production acted as sinks to consume free oxygen before it reached levels high enough to take over the atmosphere, said Mark Claire, a University of Washington doctoral student in astronomy and astrobiology. Free oxygen would combine with gases in a volcanic plume to form new compounds, and that process proved to be a significant oxygen sink, he said.

Another sink was iron delivered to the Earth's outer crust by bombardment from space. Free oxygen was consumed as it oxidized, or rusted, the metal.

But Claire said that just changing the model to reflect different iron content in the outer crust makes a huge difference in when the model shows free oxygen filling the atmosphere. Increasing the actual iron content fivefold would have delayed oxygenation by more than 1 billion years, while cutting iron to one-fifth the actual level would have allowed oxygenation to happen more than 1 billion years earlier.

The work is funded by NASA's Astrobiology Institute and the National Science Foundation's Integrative Graduate Education and Research Traineeship program, both of which foster research to understand life in the universe by examining the limits of life on Earth.

"There is interest in this work not just to know how an oxygen atmosphere came about on Earth but to look for oxygen signatures for other Earth-like planets," Claire said.
Research inspired by evolutionary biology.

Friday, August 12, 2005

621: Structural Basis for the Activation of Cholera Toxin by Human ARF6-GTP -- O'Neal et al. 309 (5737): 1093 -- Science

Structural Basis for the Activation of Cholera Toxin by Human ARF6-GTP -- O'Neal et al. 309 (5737): 1093 -- Science:

The Vibrio cholerae bacterium causes cholera, a serious diarrheal disease that claims thousands of victims in third-world, war-torn, and disaster-stricken nations each year (1). V. cholerae secretes its major virulence factor, cholera toxin (CT), when colonizing the mucosa of the human small intestine. CT is composed of a globular A subunit and a pentamer of B subunits (2, 3). Heat-labile enterotoxin (LT) produced by enterotoxigenic Escherichia coli, which is responsible for hundreds of thousands of children's deaths from diarrheal diseases annually (4), shares more than 80% sequence identity with CT. In both toxins, proteolytic cleavage of the A subunit and reduction of the Cys187-Cys199 disulfide bond covalently separate the A1 and A2 domains, formed by residues 1 to 192 and 193 to 240, respectively (5). A1 is solely responsible for the toxin's enzymatic activity; however, in vivo delivery of the A1 enzyme to its target requires the nonenzymatic B pentamer and A2 peptide, which testifies to an extensive coevolution of the diarrheal pathogens with their human hosts (6, 7).
Co-evolution and common descent explain why we get sick.

618-620: PLANT SCIENCE: Enhanced: The Right Time and Place for Making Flowers -- Blázquez 309 (5737): 1024 -- Science

PLANT SCIENCE: Enhanced: The Right Time and Place for Making Flowers -- Blázquez 309 (5737): 1024 -- Science:

Reproductive success in plants depends on the synchronization of flowering within a given species. Many plants have developed a highly complex signaling network that monitors environmental conditions, such as day length, temperature, or nutrient availability, and determines the appropriate timing for flowering (1, 2). This is the case for the model plant Arabidopsis thaliana and the pea that both flower in spring when day length and ambient temperature increase, or certain rice varieties and soybean that flower early in the fall when days get shorter. The initiation of flowering requires an additional developmental program to specify the floral identity of the new structures that continuously arise at the shoot apex (3). For instance, during the long vegetative phase in Arabidopsis, every primordium, the groups of cells poised to differentiate, forms a leaf. However, once the decision to flower has been made, all newly emerging primordia follow a developmental program that culminates in the formation of flowers rather than leaves. Thus, constructing a flower requires both temporal and spatial information that restricts the initiation of flowering to specific locations. But how this information is integrated has not been clear. Three studies now reveal the molecular mechanism by which this integration is achieved. In this issue, Abe et al. on page 1052 (4) and Wigge et al. on page 1056 (5) report that interaction between Flowering Locus T (FT), a protein encoded by a gene that is expressed in leaves, and FD, a bZIP transcription factor that is present only in the shoot apex, triggers the expression of floral identity genes in the new primordia. The third paper by Huang et al. in this week's Science Express (6) reports how the two factors meet--FT transcript travels from leaf to shoot via the plant vascular tissue.
Common descent reveals the way flowers form.

617: Plant pollen records ozone holes - Fossil measurements might reveals causes of mass extinction.

news @ - Plant pollen records ozone holes - Fossil measurements might reveals causes of mass extinction.:

There are many ideas about the Permian extinction, when almost 90% of all species died. "So far, no-one's come up with a definitive mechanism," says Andrew Saunders, a geochemist from the University of Leicester who has researched the event.

Some scientists think a comet or meteorite struck the Earth. Others link the event to an enormous volcanic eruption that left a large mass of lava in Siberia.

This eruption would have released dust, sulphur and halogen compounds, disrupting the chemistry of the atmosphere and possibly eating a hole in the ozone layer.

Spores from the time show severe mutations, which may have been caused by ultraviolet radiation let through by a thinner ozone layer1. But at the moment there's no conclusive evidence of an ozone loss at that time, says Barry Lomax, part of the Sheffield team, who presented the team's results on 10 August at the Earth System Processes conference in Calgary, Canada.

"We hope this method will be the first independent test of ozone levels from that period," says Wellman. There is an excellent fossil record of pollen spores, and although the para-coumaric acids break down over time, they leave signature chemicals that should remain in fossils that have not been heated, he says.

"If it works, we should see a massive increase in pigments during the Permian," says Wellman. With a thinner ozone layer, more ultraviolet radiation would hit plants, forcing them to slather on more sunscreen.
The evolutionary response to an ozone hole tells us about the climate 252 million years ago, and about the causes of the extinction of 90% of the species alive at the time.

616: A cure for HIV?

Hitting HIV Where It Hides -- Cohen 2005 (811): 1 -- sciencenow:

One of the most effective defensive tools used by the AIDS virus is its ability to hide out in some of the body's cells. This has prevented even the most powerful drug regimens from completely eradicating HIV in patients. Now, scientists report a strategy that flushes the virus from its hideout, and they claim that it paves the way for a cure.

In 1996, early enthusiasm about the power of new anti-HIV drug cocktails led to a proposition that totally eradicating the virus from the body might take only 2 to 3 years of treatment. But the concept lost currency when it became clear that HIV hides out in reservoirs of "resting" CD4+ white blood cells from which it is very hard to dislodge.

The new study takes an unusually precise approach to dislodging the latent pool. Using evidence that an enzyme called histone deacetylase 1 (HDAC1) plays a crucial role in keeping CD4+ cells in a latent state, virologist David Margolis of the University of North Carolina in Chapel Hill and colleagues gave AIDS patients valproic acid, an HDAC1 inhibitor that's licensed to treat epileptic seizures. Active CD4+ cells evict HIV from its hiding place, and the team administered a new drug, T-20, to help mop up bursts of the virus after the cells spat it out. After 4 months, the amount of infectious HIV in each patient's pool of latent cells declined an average of 75% in three of the four patients studied, the investigators report 13 August in The Lancet.
The resistance of HIV to treatment is a result of selection throughout its history, selection strengthened by treatment with the cocktails. This research is based on those evolutionary insights.

615: Guppy See, Guppy Do -- Mason 2005 (811): 4 -- sciencenow

Guppy See, Guppy Do -- Mason 2005 (811): 4 -- sciencenow:

in some species, generation after generation, animals still seem to copy each other's behaviors, leaving scientists to wonder if the copying habit itself can be inherited.

To test the idea, biologist Lee Dugatkin of the University of Louisville in Kentucky examined female guppies, which mimic the mate choices of their peers. After a group of female fish gave birth, Dugatkin watched the moms to see how likely they were to copy another female's mate choice. Each mom was put in a tank alone with two males in adjacent tanks on either side. Another female was placed in a tank next to one of the males, and the mom was able to watch the courtship unfold. The courting female was then removed, leaving the mom alone to make a selection. If she spent more of her time near the male "chosen" by the other female, she was a considered a copier. About 85% of the females proved to be copiers, Dugatkin found.

Once the offspring of the copiers were ready to mate, Dugatkin put them through the same tests and found that they also were more likely to be copiers than were the offspring of the 15% of moms with an independent streak. This suggests that the tendency to copy another's mate choice preference is a heritable trait, says Dugatkin, who presented his results here 9 August at a meeting of the Animal Behavior Society.
The evolution of imitation. Very cool.

Thursday, August 11, 2005

614: Canada the cradle of life, eh?

Via Majikthise, Canada the cradle of life, eh?:

A study of the Haughton Impact Crater on Devon Island in the Canadian Arctic by the Canadian Space Agency has revealed the presence of a number of features associated with the emergence of microscopic life forms. These include hydrothermal systems and fissures and cracks in rocks created by the blast.

While further study will be necessary, the findings could prod scientists to begin to examine the search for life on this planet or Mars slightly differently.
Evolutionary hypotheses.

613: Molecular mechanism of feather formation found | Science Blog

Molecular mechanism of feather formation found | Science Blog:

The results suggested that a simple interaction between Shh and Bmp2 is sufficient to model the creation and patterning of barbs in feather development. The team then tested whether such interactions truly exist in the developing feather. In the first steps of feather development, cells exposed to essentially the same levels of Bmp2 and Shh grow from a small bud to form a uniform ring. Shh then is expressed in specific spots along the ring, giving rise to bumps, seen microscopically as longitudinal stripes demarcating the edges of ridges in the developing barb.

"Each barb ridge grows in length by recruiting new cells, which proliferate at the growing base of the feather germ, to join the base of that barb ridge," Harris says. "The variations in the initial number of barb ridges will directly affect the shape, and consequent function, of the feather."

To test the activator-inhibitor model, Harris injected retroviruses to force the expression of either Shh or Bmp2 into the skin of six-day-old chick embryos. The virus infected only small patches of cells and allowed Harris to locally examine the effects of the treatment on barb patterning during feather development.

To assess the specific role of Bmp2 in regulating Shh expression, Harris tricked the cells into believing that Bmp2 was signaling them continuously by altering receptors in the cells. The over-expression of Bmp2 signaling via the altered receptors led to ongoing down-regulation of normal Shh expression needed to form the barbs.

Harris and colleagues used a similar experiment to test whether Shh could up-regulate its own expression during barb formation, and found that it could. Similarly, they found that regional expression of Shh led to detectable up-regulation of Bmp2 in feather buds as they first grew.

The underlying assumptions of the model were found to be true in developing feathers. These findings suggest that simple relationships between developmental genes can provide the basis for the formation of complex forms.

The researchers predict that a more complicated version of the model can be applied to the formation of more complex feathers. Termed pennaceous, these feathers occur in the duck and other birds, including adult chickens, and are not characterized as downy. The more primitive young chicken feathers, which are downy, are called plumalaceous.

"We don't have empirical evidence for this yet, but mathematical analyses lead us to believe that the addition of a third signaling factor leads to the development of the more complex pennaceous feather," Fallon says. " Our model supports paleontologic evidence that pennaceous feathers are more advanced than plumalaceous feathers."
Evolutionary hypotheses generated from a combination of fossils and molecular biology.

612: Drunken flies and fish

Drunken flies and fish:

Scholz et al. screened mutagenized flies, looking for mutants that never learned to hold their liquor. They found one, called hangover (hang). Flies mutant for hangover have significantly reduced tolerance, and similar doses of alcohol knock them out over and over again. They have some capacity for tolerance, but it's greatly reduced. There is also a second molecular pathway, the octopaminergic pathway (octopamine is a neurotransmitter used in the fly's brain), and mutating that in addition reduces the animal's tolerance still further.

Why would animals have a gene to help them cope with alcohol? Alcohol exposure is ubiquitous in the environment, especially if you have to share your diet with yeast, which spew the stuff all over. The interesting thing, though, is that alcohol tolerance is coupled to an animal's general ability to handle stress, such as heat and oxidants. Flies with the hangover mutation are also more sensitive to heat shock and reactive oxygen species, and tend to have a shorter life span. It's more than just an alcohol tolerance gene—it's a general stressor response gene.

What makes this relevant to us in a utilitarian way is that our response to alcohol is a generic property of many animals: flies, fish, mice, and people can all get drunk and exhibit similar symptoms and cope with similar molecular mechanisms. It's universal!

In summary, the development of ethanol tolerance in Drosophila engages two systems that function in parallel, one involving a cellular stress pathway defined by the hang gene and the other involving octopaminergic systems. Octopamine has recently been implicated in the formation of appetitive (sugar-reinforced) memories in Drosophila. The contribution of learned behaviours and stress, at both the cellular and systemic levels, to drug- and addiction-related behaviours in mammals is being increasingly recognized. Our studies in Drosophila suggest that these pathways are conserved, allowing further analysis in this genetically tractable model organism.

And that's why I'm thinking of trying a few pilot experiments to get my fish drunk. There are tools and techniques out there that will allow us to probe the details of these processes in our experimental animal, and they are applicable to lots of other beasties as well…this evolution idea is the glue that brings many ideas together.
Ah, common descent.

Tuesday, August 09, 2005

611: Chirality in Snails

Pharyngula::Chirality in Euhadra:

There are 22 species in the group, and 5 of them are sinistral, with the rest dextral. The question is whether speciation events can reasonably be traced back to changes in a single gene, whether this diverse assemblage can be explained by occasional mutations in chirality that split off new reproductively isolated groups.

To make a long and somewhat mathematical story short, the answer is no. There have to be other isolating mechanisms present to help out.

One observation is that if you are a newborn dextral snail in a population of sinistrals, you're going to have a much harder time finding a mate than your sinistral cousins. The more common your morphology, the more likely you are to find a compatible mate. This competitive advantage for the most common form will typically drive the population towards a single chirality.

There are, however, conditions under which it is good to be a weirdo. When two species of the same chirality overlap, it will be common for individuals of those two species to mate—which may be fun, but it's fruitless. If one species has a subpopulation with a different chirality, though, they may have an advantage. While they are only able to mate with conspecifics of the same handedness, they won't be wasting time and gametes on members of the other species. This is a phenomenon called character displacement, and could be an additional force for speciation.

In the simpler case where a single population has two chiral variants, though, chirality is insufficient in itself to isolate the two forms. With mathematical modeling, the authors showed that the separation will be incomplete because of gene flow, so the two types will reach an equilibrium, but outside of chance variations, one will not replace the other. The catch is the way maternal effects are delayed in the expression of their phenotype by a generation. That means that a sinistral snail can mate with a sinistral snail, and their progeny may be dextral, and able to breed with the dextral population. Similarly, some of those dextral snails will mate with other dextral snails, and produce progeny which are sinistral. Gene flow is slowed between the two subgroups, but it would require other phenomena, such as geographic separation, to complete the process.
Chirality is how the snail shell twists. Sinistral is to the left, dextral to the right. This is a speciation being studied, evolutionary hypotheses tested, and new ones being generated.

610: Convergent Evolution in Poison Frogs - Yahoo! News

Convergent Evolution in Poison Frogs - Yahoo! News:

Scientists have discovered one of the most intricate examples of convergent evolution with the help of South American "poison" frogs and ants and their cousins in Madagascar.

Poison frogs can't make their own poison--they steal it from ants. Poison frogs secrete a variety of chemicals called alkaloids to create a poisonous defense against predators. Since they can't produce alkaloids on their own, these frogs maintain a steady diet of specific alkaloid-rich ants to keep up their defense.

Now, Valerie Clark of Cornell University and her colleagues have detailed two instances of convergent evolution--the process in which organisms not closely related independently acquire similar characteristics while evolving in separate ecosystems--between frogs and ants on two continents.
Convergent evolution and a test of evolutionary hypotheses.

609: Big game hunters, not climate change, killed off sloths | Science Blog

Big game hunters, not climate change, killed off sloths | Science Blog:

“If climate were the major factor driving the extinction of ground sloths, you would expect the extinctions to occur at about the same time on both the islands and the continent since climate change is a global event,” Steadman said.

Gary Haynes, anthropology professor at the University of Nevada, Reno, said Steadman’s study “clearly shows that ground sloth extinctions in the New World didn’t happen after serious changes in climate or vegetation – and that the first appearance of humans must have been the decisive factor.”

The fossil record shows the people who arrived in North America were making sophisticated tools out of stone, bone and ivory, Steadman said. These “big-game hunters” had a traumatic effect on the animals living there, he said.

More than three-fourths of the large species of mammals that roamed the North American landscape became extinct within a few thousand years, which, besides ground sloths, included mammoths, mastodons, saber-toothed tigers and giant bears, Steadman said.

While the largest of the prehistoric ground sloths grew to the size of a modern elephant and fed on bushes and the leaves of lower branches of trees, today’s only surviving descendants are several small tree sloths whose range extends from southern Mexico to southern Brazil, he said.

The only reason the living species of sloths survive is that they live high up in trees, where their green-algae-colored fur camouflages them, Steadman said. “God save the sloth that comes down to the ground because usually somebody is there to kill it,” he said.
Interfacing human evolution and the evolution of the sloths. An evolutionary hypothesis tested.

608: Manipulative Malaria Parasite Makes You More Attractive (to Mosquitoes) - New York Times

Manipulative Malaria Parasite Makes You More Attractive (to Mosquitoes) - New York Times:

Malaria is a staggeringly devastating disease, striking an estimated 300 million to 500 million people a year and killing more than a million of them. Scientists have long wondered how the parasite that causes malaria - a single-cell creature, plasmodium, carried by mosquitoes - manages to be so successful.

New research has shown an unexpected source of its success. The parasite makes infected humans smell more attractive to mosquitoes.

The research, published on Monday in the journal Public Library of Science Biology, was carried out by a team of French and Kenyan scientists led by Jacob Koella, an evolutionary biologist at Pierre and Marie Curie University in Paris. Dr. Koella is a leading expert on the ways in which parasites manipulate their hosts.

Many parasites that need to live inside two different hosts during their life cycles also manipulate their hosts. A single-celled parasite called toxoplasma lives inside cats and then inside their prey, like rats. Research shows that infection with toxoplasma makes rats lose their fear of the odor of cats. Tapeworms that live in fish can turn them white and make them jump around near the surface of the water, where the fish are more likely to be eaten by birds, which the tapeworms make their new host. "It's amazing how much manipulation is going on in parasites," Dr. Koella said. "It would be hard to find a case where there wasn't some manipulation."

Scientists consider most of these examples as products of natural selection. A parasite's reproductive success depends on its ability to be transmitted toa new host. "And manipulation appears to be an obvious way to do it," Dr. Koella said.
The evolution of malaria. Hypotheses tested.

607: The Riddle of the Appendix - New York Times

The Riddle of the Appendix - New York Times:

Still, I wondered how such a dangerous and disposable organ could survive over evolutionary time. "We consider it maladaptive because we want to live to a very old age," Dr. Fisher said. "But from a strictly Darwinian view, it might not be."

Imagine a trait that helps an animal survive to adulthood, but that also has side effects that can cause trouble later in life. If, on balance, animals produce more offspring with the trait than without it, natural selection will favor it.

Perhaps the appendix lifted the odds that our ancestors could resist childhood diseases and live to childbearing years. Even if it also caused deaths by appendicitis, the appendix might have been a net plus. (It's also possible that appendicitis wasn't such a big problem in the past. Some scientists have argued that modern Western life has made appendicitis more common, either as a result of a change in hygiene or in the foods we eat.)

Dr. Fisher's "net-plus" hypothesis is one of several possible explanations. But they all remain speculation, she said, until scientists learn a lot more about the appendix. "It seems basic, but it's also very hard," she said.
Evolutionary hypotheses guide the search for an explanation of appendicitis, summarized in Carl Zimmer's explanation.

Sunday, August 07, 2005

606: Very Old Eggs Reveal A Fast, Changing Path Through Evolution

Philosophy of Biology: Very Old Eggs Reveal A Fast, Changing Path Through Evolution:

BIOLOGISTS STUDYING how species change over the eons have always been hampered by the little problem of previous generations of a species being, well, dead. Sure, you can infer something about what a creature was like from fossils, but fossils generally fail to preserve much except bone. As a result, some of an animal's most interesting features vanish into the dust of time.

But these days, not even death is forever. A few years ago, biologist W. Charles Kerfoot was examining "cores" -- basically, muck deposited decades earlier -- in a Michigan lake. Lo and behold, he and his colleagues discovered eggs, and not just any eggs. They had been laid long ago by tiny creatures (mostly insects and crustaceans) that no longer lived in the lake. Even better, there was still life in the eggs. Under the right conditions, they would hatch.
Testing evolutionary hypotheses.

Thursday, August 04, 2005

605: EVOLUTION: Sumptuous Survey of Hexapod History -- Jarzembowski 309 (5736): 880 -- Science

EVOLUTION: Sumptuous Survey of Hexapod History -- Jarzembowski 309 (5736): 880 -- Science:

If the number of described species is a measure of success, then insects (with nearly 1 million) are the most successful group of all time. And if the number of families known from the fossil record is a proxy for past biodiversity, then insects (with more than 1200) are also the most diverse paleo group. Insects have only existed for 11% of the duration of life on Earth. Yet in that time, they have pervaded all terrestrial ecosystems and evolved social organization several times. They conquered the air long before any flying vertebrate and have outlasted trilobites and dinosaurs. They pollinate our crops and arguably gave us our greatest laboratory animal, Drosophila. Love them or hate them, we have evolved alongside them.

There are a number of good entomology books on the market. Few, however, have integrated the living and fossil record as seamlessly as David Grimaldi and Michael Engel's Evolution of the Insects. None, moreover, has combined this integration with so much student-friendly text and such a wealth of illustrations (more than 900). The book shows that lavish photography and lucidity need not be the prerogative of popular entomology and that segregation of entomology and paleoentomology is tantamount to intellectual apartheid. While looking good, Evolution is no coffee-table adornment. Weighing in at 2.92 kg, it is the western challenger to History of Insects (1), a multiauthored, English-language account by Russian paleoentomologists. That work, which highlighted the fossil insect riches of Asia, is unashamedly phylistic; its approach to evolutionary relationships combines cladogenesis and evolutionary divergence. Evolution offers a cladistic treatment rooted in the Hennigian tradition--as one would expect from the previous contributions of Grimaldi (a curator of invertebrate zoology at the American Museum of Natural History) and Engel (a paleoentomologist at the University of Kansas). This methodological difference influences the interpretation of the evolutionary history of insects (e.g., the longevity of groups like caddisflies and cockroaches).

Evolution of the Insects by David Grimaldi, Michael S. Engel

Sounds like a good book.

604: Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel -- Long et al. 309 (5736): 897 -- Science

Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel -- Long et al. 309 (5736): 897 -- Science:

Most of our knowledge of Kv channel function comes from studies of the Shaker K+ channel from Drosophila melanogaster and its family members from mammalian cells (2). Shaker family channels have been extensively studied with electrophysiology, because they can easily be expressed in Xenopus laevis oocytes and in other cells. In contrast, nearly all of our knowledge of K+ channel structure is based on studies of prokaryotic K+ channels, because they are more easily expressed at high levels in Escherichia coli. Such studies have taught us much about their pores, selectivity filters, and gates (3).

Eukaryotic Kv channels in many respects are very similar to their prokaryotic counterparts. The selectivity filter sequence is so conserved that we expect its structure to be essentially the same in all K+ channels. The pore's "inverted teepee" arrangement of inner helices, which holds the selectivity filter in its wider half near the extracellular surface, is also expected to be a conserved feature (4). However, beyond their conserved pore and certain domains that regulate the opening of the pore's gate, eukaryotic Kv channels have certain unique features.
Evolutionarily conserved structures with various derived changes? Evolution at work.

603: Antagonistic Control of Disease Resistance Protein Stability in the Plant Immune System -- Holt et al. 309 (5736): 929 -- Science

Antagonistic Control of Disease Resistance Protein Stability in the Plant Immune System -- Holt et al. 309 (5736): 929 -- Science:

Pathogen recognition by the plant immune system is governed by structurally related, polymorphic products of disease resistance (R) genes. RAR1 and/or SGT1b mediate the function of many R proteins. RAR1 controls preactivation R protein accumulation by an unknown mechanism. We demonstrate that Arabidopsis SGT1b has two distinct, genetically separable functions in the plant immune system: SGT1b antagonizes RAR1 to negatively regulate R protein accumulation before infection, and SGT1b has a RAR1-independent function that regulates programmed cell death during infection. The balanced activities of RAR1 and SGT1, in concert with cytosolic HSP90, modulate preactivation R protein accumulation and signaling competence.
Understanding the Arabidopsis immune system reveals information about other plants because of common descent.

602: Stem Cell Depletion Through Epidermal Deletion of Rac1 -- Benitah et al. 309 (5736): 933 -- Science

Stem Cell Depletion Through Epidermal Deletion of Rac1 -- Benitah et al. 309 (5736): 933 -- Science:

Mammalian epidermis is maintained by self-renewal of stem cells, but the underlying mechanisms are unknown. Deletion of Rac1, a Rho guanosine triphosphatase, in adult mouse epidermis stimulated stem cells to divide and undergo terminal differentiation, leading to failure to maintain the interfollicular epidermis, hair follicles, and sebaceous glands. Rac1 exerts its effects in the epidermis by negatively regulating c-Myc through p21-activated kinase 2 (PAK2) phosphorylation. We conclude that a pleiotropic regulator of cell adhesion and the cytoskeleton plays a critical role in controlling exit from the stem cell niche and propose that Rac and Myc represent a global stem cell regulatory axis.
Research in mice teaches us about the regulation of stem cells in humans. Common descent!

601: Regulation of Blood Glucose by Hypothalamic Pyruvate Metabolism -- Lam et al. 309 (5736): 943 -- Science

Regulation of Blood Glucose by Hypothalamic Pyruvate Metabolism -- Lam et al. 309 (5736): 943 -- Science:

The brain keenly depends on glucose for energy, and mammalians have redundant systems to control glucose production. An increase in circulating glucose inhibits glucose production in the liver, but this negative feedback is impaired in type 2 diabetes. Here we report that a primary increase in hypothalamic glucose levels lowers blood glucose through inhibition of glucose production in rats. The effect of glucose requires its conversion to lactate followed by stimulation of pyruvate metabolism, which leads to activation of adenosine triphosphate (ATP)–sensitive potassium channels. Thus, interventions designed to enhance the hypothalamic sensing of glucose may improve glucose homeostasis in diabetes.
Understanding an evolutionarily conserved pathway (common descent) may help treat diabetes.

600: Export-Mediated Assembly of Mycobacterial Glycoproteins Parallels Eukaryotic Pathways -- VanderVen et al. 309 (5736): 941 -- Science

Export-Mediated Assembly of Mycobacterial Glycoproteins Parallels Eukaryotic Pathways -- VanderVen et al. 309 (5736): 941 -- Science:

Protein O-mannosylation is an essential and evolutionarily conserved post-translational modification among eukaryotes. This form of protein modification is also described in Mycobacterium tuberculosis; however, the mechanism of mannoprotein assembly remains unclear. Evaluation of differentially translocated chimeric proteins and mass spectrometry to monitor glycosylation demonstrated that specific translocation processes were required for protein O-mannosylation in M. tuberculosis. Additionally, Rv1002c, a M. tuberculosis membrane protein homolog of eukaryotic protein mannosyltransferases, was shown to catalyze the initial step of protein mannosylation. Thus, the process of protein mannosylation is conserved between M. tuberculosis and eukaryotic organisms.
A widely evolutionarily conserved biochemical pathway discovered thanks to an evolutionary hypothesis.

599: No oceans on Titan from the absence of a near-infrared specular reflection : Nature

No oceans on Titan from the absence of a near-infrared specular reflection : Nature:

With its substantial atmosphere of nitrogen, hydrocarbons and nitriles, Saturn's moon Titan is a unique planetary satellite. Photochemical processing of the gaseous constituents produces an extended haze that obscures the surface. Soon after the Voyager fly-bys in 1980 and 1981 photochemical models1, 2, 3 led to the conclusion that there should be enough liquid methane/ethane/nitrogen to cover the surface to a depth of several hundred metres. Recent Earth-based radar echoes imply that surface liquid may be present at a significant fraction of the locations sampled4. Here we present ground-based observations (at near-infrared wavelengths) and calculations showing that there is no evidence thus far for surface liquid5. Combined with the specular signatures from radar observations, we infer mechanisms that produce very flat solid surfaces, involving a substance that was liquid in the past but is not in liquid form at the locations we studied.
The presence of liquid hydrocarbon oceans was an idea that had exobiologists salivating. This doesn't necessarily eliminate speculation about life on Titan, but it changes the possible dynamics.

598: Dental microwear texture analysis shows within-species diet variability in fossil hominins : Nature

Dental microwear texture analysis shows within-species diet variability in fossil hominins : Nature:

Reconstructing the diets of extinct hominins is essential to understanding the paleobiology and evolutionary history of our lineage. Dental microwear, the study of microscopic tooth-wear resulting from use1, 2, 3, 4, provides direct evidence of what an individual ate in the past. Unfortunately, established methods5, 6, 7, 8, 9, 10 of studying microwear are plagued with low repeatability and high observer error11. Here we apply an objective, repeatable approach for studying three-dimensional microwear surface texture to extinct South African hominins. Scanning confocal microscopy12, 13 together with scale-sensitive fractal analysis14, 15, 16, 17, 18, 19 are used to characterize the complexity and anisotropy of microwear. Results for living primates show that this approach can distinguish among diets characterized by different fracture properties. When applied to hominins20, microwear texture analysis indicates that Australopithecus africanus microwear is more anisotropic, but also more variable in anisotropy than Paranthropus robustus. This latter species has more complex microwear textures, but is also more variable in complexity than A. africanus. This suggests that A. africanus ate more tough foods and P. robustus consumed more hard and brittle items, but that both had variable and overlapping diets.
Understanding the teeth of our ancestors tells us about our evolution.

597: Refractory periods and climate forcing in cholera dynamics : Nature

Refractory periods and climate forcing in cholera dynamics : Nature:

Outbreaks of many infectious diseases, including cholera, malaria and dengue, vary over characteristic periods longer than 1 year1, 2. Evidence that climate variability drives these interannual cycles has been highly controversial, chiefly because it is difficult to isolate the contribution of environmental forcing while taking into account nonlinear epidemiological dynamics generated by mechanisms such as host immunity2, 3, 4. Here we show that a critical interplay of environmental forcing, specifically climate variability, and temporary immunity explains the interannual disease cycles present in a four-decade cholera time series from Matlab, Bangladesh. We reconstruct the transmission rate, the key epidemiological parameter affected by extrinsic forcing, over time for the predominant strain (El Tor) with a nonlinear population model that permits a contributing effect of intrinsic immunity. Transmission shows clear interannual variability with a strong correspondence to climate patterns at long periods (over 7 years, for monsoon rains and Brahmaputra river discharge) and at shorter periods (under 7 years, for flood extent in Bangladesh, sea surface temperatures in the Bay of Bengal and the El Niño−Southern Oscillation). The importance of the interplay between extrinsic and intrinsic factors in determining disease dynamics is illustrated during refractory periods, when population susceptibility levels are low as the result of immunity and the size of cholera outbreaks only weakly reflects climate forcing.
Understanding the dynamics of disease means understanding the evolution of the infectious agent.

596: Licensing of natural killer cells by host major histocompatibility complex class I molecules : Nature

Licensing of natural killer cells by host major histocompatibility complex class I molecules : Nature:

Self versus non-self discrimination is a central theme in biology from plants1 to vertebrates, and is particularly relevant for lymphocytes that express receptors capable of recognizing self-tissues and foreign invaders. Comprising the third largest lymphocyte population, natural killer (NK) cells recognize and kill cellular targets and produce pro-inflammatory cytokines. These potentially self-destructive effector functions can be controlled by inhibitory receptors for the polymorphic major histocompatibility complex (MHC) class I molecules that are ubiquitously expressed on target cells2, 3, 4. However, inhibitory receptors are not uniformly expressed on NK cells, and are germline-encoded by a set of polymorphic genes that segregate independently from MHC genes5, 6. Therefore, how NK-cell self-tolerance arises in vivo is poorly understood. Here we demonstrate that NK cells acquire functional competence through 'licensing' by self-MHC molecules. Licensing involves a positive role for MHC-specific inhibitory receptors and requires the cytoplasmic inhibitory motif originally identified in effector responses. This process results in two types of self-tolerant NK cells—licensed or unlicensed—and may provide new insights for exploiting NK cells in immunotherapy. This self-tolerance mechanism may be more broadly applicable within the vertebrate immune system because related germline-encoded inhibitory receptors are widely expressed on other immune cells.
Common descent.

595: Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin : Nature

Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin : Nature:

Transcription of eukaryotic genes is performed by three nuclear RNA polymerases, of which RNA polymerase II is thought to be solely responsible for the synthesis of messenger RNAs1. Here we show that transcription of some mRNAs in humans and rodents is mediated by a previously unknown single-polypeptide nuclear RNA polymerase (spRNAP-IV). spRNAP-IV is expressed from an alternative transcript of the mitochondrial RNA polymerase gene (POLRMT). The spRNAP-IV lacks 262 amino-terminal amino acids of mitochondrial RNA polymerase, including the mitochondrial-targeting signal, and localizes to the nucleus. Transcription by spRNAP-IV is resistant to the RNA polymease II inhibitor alpha-amanitin but is sensitive to short interfering RNA specific for the POLRMT gene. The promoters for spRNAP-IV differ substantially from those used by RNA polymerase II, do not respond to transcriptional enhancers and contain a common functional sequence motif.
"Humans and rodents" says common descent.

594: A cytokinesis furrow is positioned by two consecutive signals : Nature

A cytokinesis furrow is positioned by two consecutive signals : Nature:

The position of the cytokinesis furrow in a cell determines the relative sizes of its two daughter cells as well as the distribution of their contents. In animal cells, the position of the cytokinesis furrow is specified by the position of the mitotic spindle1. The cytokinesis furrow bisects the spindle midway between the microtubule asters, at the site of the microtubule-based midzone, producing two daughter cells. Experiments in some cell types have suggested that the midzone positions the furrow2, 3, but experiments in other cells have suggested that the asters position the furrow4, 5. One possibility is that different organisms and cell types use different mechanisms to position the cytokinesis furrow. An alternative possibility is that both asters and the midzone contribute to furrow positioning6, 7. Recent work in C. elegans has suggested that centrosome separation and the midzone are implicated in cytokinesis8. Here we examine the relative contributions of different parts of the mitotic spindle to positioning of the cytokinesis furrow in the C. elegans zygote. By spatially separating the spindle midzone from one of the asters using an ultraviolet laser, we show that the cytokinesis furrow is first positioned by a signal determined by microtubule asters, and then by a second signal that is derived from the spindle midzone. Thus, the position of the cytokinesis furrow is specified by two consecutive furrowing activities.
Common descent at work.

593: Common mechanisms of nerve and blood vessel wiring : Nature

Common mechanisms of nerve and blood vessel wiring : Nature:

Blood vessels and nerve fibres course throughout the body in an orderly pattern, often alongside one another. Although superficially distinct, the mechanisms involved in wiring neural and vascular networks seem to share some deep similarities. The discovery of key axon guidance molecules over the past decade has shown that axons are guided to their targets by finely tuned codes of attractive and repulsive cues, and recent studies reveal that these cues also help blood vessels to navigate to their targets. Parallels have also emerged between the actions of growth factors that direct angiogenic sprouting and those that regulate axon terminal arborization.

During evolution, organisms have come to perform more specialized tasks, requiring an increased degree of information processing by neurons and supply of nutrients by blood vessels. Wiring of neuronal axons and blood vessels into functional circuits is therefore of utmost importance. The complexity of this task is underscored by the high degree of orderly patterning of the neural and vascular networks. The choreographed morphogenesis of both networks suggests that they are directed by genetically programmed mechanisms. Five centuries ago, Andreas Vesalius illustrated the parallels in the stereotyped branching patterns of vessels and nerves (Fig. 1a, b). Today, evidence is emerging that blood vessels, which arose later in evolution than nerves, co-opted several of the organizational principles and molecular mechanisms that evolved to wire up the nervous system. In this review, we highlight these common morphogenetic signals and mechanisms, and illustrate how intricately the navigational mechanisms for both systems are intertwined.
Co-opting of existing pathways is a common occurrence in evolution. This is all about testing evolutionary hypotheses.

592: Gli3 and Plzf cooperate in proximal limb patterning at early stages of limb development : Nature

Gli3 and Plzf cooperate in proximal limb patterning at early stages of limb development : Nature:

The vertebrate limb initially develops as a bud of mesenchymal cells that subsequently aggregate in a proximal to distal (P−D) sequence to give rise to cartilage condensations that prefigure all limb skeletal components1. Of the three cardinal limb axes, the mechanisms that lead to establishment and patterning of skeletal elements along the P−D axis are the least understood. Here we identify a genetic interaction between Gli3 (GLI-Kruppel family member 3) and Plzf (promyelocytic leukaemia zinc finger, also known as Zbtb16 and Zfp145), which is required specifically at very early stages of limb development for all proximal cartilage condensations in the hindlimb (femur, tibia, fibula). Notably, distal condensations comprising the foot are relatively unperturbed in Gli3-/-;Plzf-/- mouse embryos. We demonstrate that the cooperative activity of Gli3 and Plzf establishes the correct temporal and spatial distribution of chondrocyte progenitors in the proximal limb-bud independently of known P−D patterning markers and overall limb-bud size. Moreover, the limb defects in Gli3-/-;Plzf-/- embryos correlate with the transient death of a specific subset of proximal mesenchymal cells that express bone morphogenetic protein receptor, type 1B (Bmpr1b) at the onset of limb development. These findings suggest that the development of proximal and distal skeletal elements is distinctly regulated early during limb-bud formation. The initial division of the vertebrate limb into two distinct molecular domains is consistent with fossil evidence indicating that the upper and lower extremities of the limb have different evolutionary origins2.
A developmental pathway common to the vertebrates. Evolutionary hypotheses tested, new hypotheses generated.

591: Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs : Nature

Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs : Nature:

Birds are unique among living vertebrates in possessing pneumaticity of the postcranial skeleton, with invasion of bone by the pulmonary air-sac system1, 2, 3, 4. The avian respiratory system includes high-compliance air sacs that ventilate a dorsally fixed, non-expanding parabronchial lung2, 3, 5, 6. Caudally positioned abdominal and thoracic air sacs are critical components of the avian aspiration pump, facilitating flow-through ventilation of the lung and near-constant airflow during both inspiration and expiration, highlighting a design optimized for efficient gas exchange2, 5, 6, 7, 8. Postcranial skeletal pneumaticity has also been reported in numerous extinct archosaurs including non-avian theropod dinosaurs and Archaeopteryx9, 10, 11, 12. However, the relationship between osseous pneumaticity and the evolution of the avian respiratory apparatus has long remained ambiguous. Here we report, on the basis of a comparative analysis of region-specific pneumaticity with extant birds, evidence for cervical and abdominal air-sac systems in non-avian theropods, along with thoracic skeletal prerequisites of an avian-style aspiration pump. The early acquisition of this system among theropods is demonstrated by examination of an exceptional new specimen of Majungatholus atopus, documenting these features in a taxon only distantly related to birds. Taken together, these specializations imply the existence of the basic avian pulmonary Bauplan in basal neotheropods, indicating that flow-through ventilation of the lung is not restricted to birds but is probably a general theropod characteristic.
Fossilized evidence that birds' lungs are structured like dinosaur lungs, further strengthening the hypothesis that birds descended from dinosaurs.

590: An Arabidopsis hAT-like transposase is essential for plant development : Nature

An Arabidopsis hAT-like transposase is essential for plant development : Nature:

A significant proportion of the genomes of higher plants and vertebrates consists of transposable elements and their derivatives. Autonomous DNA type transposons encode a transposase that enables them to mobilize to a new chromosomal position in the host genome by a cut-and-paste mechanism. As this is potentially mutagenic, the host limits transposition through epigenetic gene silencing and heterochromatin formation. Here we show that a transposase from Arabidopsis thaliana that we named DAYSLEEPER is essential for normal plant growth; it shares several characteristics with the hAT (hobo, Activator, Tam3) family of transposases1. DAYSLEEPER was isolated as a factor binding to a motif (Kubox1) present in the upstream region of the Arabidopsis DNA repair gene Ku70 (refs 2, 3). This motif is also present in the upstream regions of many other plant genes. Plants lacking DAYSLEEPER or strongly overexpressing this gene do not develop in a normal manner. Furthermore, DAYSLEEPER overexpression results in the altered expression of many genes. Our data indicate that transposase-like genes can be essential for plant development and can also regulate global gene expression. Thus, transposases can become domesticated by the host to fulfil important cellular functions.
Yeast and plants reveal a developmental regulator shared across the plant kingdom. Understanding this regulatory gene reveals a path to phenotypic variation in plants.

589: A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response : Nature

A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response : Nature:

DNA breaks are extremely harmful lesions that need to be repaired efficiently throughout the genome. However, the packaging of DNA into nucleosomes is a significant barrier to DNA repair, and the mechanisms of repair in the context of chromatin are poorly understood1. Here we show that lysine 56 (K56) acetylation is an abundant modification of newly synthesized histone H3 molecules that are incorporated into chromosomes during S phase. Defects in the acetylation of K56 in histone H3 result in sensitivity to genotoxic agents that cause DNA strand breaks during replication. In the absence of DNA damage, the acetylation of histone H3 K56 largely disappears in G2. In contrast, cells with DNA breaks maintain high levels of acetylation, and the persistence of the modification is dependent on DNA damage checkpoint proteins. We suggest that the acetylation of histone H3 K56 creates a favourable chromatin environment for DNA repair and that a key component of the DNA damage response is to preserve this acetylation.
A potentially important evolutionary mechanism investigated in yeast.

588: The Lyme disease agent exploits a tick protein to infect the mammalian host : Nature

The Lyme disease agent exploits a tick protein to infect the mammalian host : Nature:

The Lyme disease agent, Borrelia burgdorferi, is maintained in a tick−mouse cycle1, 2. Here we show that B. burgdorferi usurps a tick salivary protein, Salp15 (ref. 3), to facilitate the infection of mice. The level of salp15 expression was selectively enhanced by the presence of B. burgdorferi in Ixodes scapularis, first indicating that spirochaetes might use Salp15 during transmission. Salp15 was then shown to adhere to the spirochaete, both in vitro and in vivo, and specifically interacted with B. burgdorferi outer surface protein C. The binding of Salp15 protected B. burgdorferi from antibody-mediated killing in vitro and provided spirochaetes with a marked advantage when they were inoculated into naive mice or animals previously infected with B. burgdorferi. Moreover, RNA interference-mediated repression of salp15 in I. scapularis drastically reduced the capacity of tick-borne spirochaetes to infect mice. These results show the capacity of a pathogen to use a secreted arthropod protein to help it colonize the mammalian host.
Co-evolution of the Lyme disease parasite and one of its hosts. Very cool.

587: Regulation of Mycobacterium tuberculosis cell envelope composition and virulence by intramembrane proteolysis : Nature

Regulation of Mycobacterium tuberculosis cell envelope composition and virulence by intramembrane proteolysis : Nature:

Mycobacterium tuberculosis infection is a continuing global health crisis that kills 2 million people each year1. Although the structurally diverse lipids of the M. tuberculosis cell envelope each have non-redundant roles in virulence or persistence2, 3, 4, 5, 6, 7, the molecular mechanisms regulating cell envelope composition in M. tuberculosis are undefined. In higher eukaryotes, membrane composition is controlled by site two protease (S2P)-mediated cleavage of sterol regulatory element binding proteins8, 9, membrane-bound transcription factors that control lipid biosynthesis. S2P is the founding member of a widely distributed family of membrane metalloproteases10, 11 that cleave substrate proteins within transmembrane segments12. Here we show that a previously uncharacterized M. tuberculosis S2P homologue (Rv2869c) regulates M. tuberculosis cell envelope composition, growth in vivo and persistence in vivo. These results establish that regulated intramembrane proteolysis is a conserved mechanism controlling membrane composition in prokaryotes and show that this proteolysis is a proximal regulator of cell envelope virulence determinants in M. tuberculosis.
A protein which occurs homologously in prokaryotes and eukaryotes has been co-opted into various processes in the cell. Understanding its operation in an infectious agent may lead to a better treatment for TB, and a better understanding of lipid metabolism in eukaryotes (like you and me).

586: Parasitology Triple genome triumph : Nature

Parasitology Triple genome triumph : Nature:

There is welcome news for scientists working on sleeping sickness, Chagas' disease and visceral leishmaniasis: the genomes of the three trypanosome parasites responsible for these devastating illnesses have now been cracked. The sequences from Trypanosoma brucei, Trypanosoma cruzi and Leishmania major were published in last week's Science by an array of international research teams (Science 309, 416−422, 409−415, 436−442; 2005).

In the terminology of global public health, these diseases don't even fall into the category of 'neglected diseases' such as malaria and tuberculosis. Rather, they are classed as 'most neglected diseases' — which nonetheless kill millions. But those affected have little means of paying for treatment, making drug development unprofitable. Consequently, there are no vaccines, and medicines are few, expensive and usually toxic.

The three parasites share around 6,200 'core' genes, so the proteins these encode might provide targets for drugs that are effective against all three. The parasites make a large and diverse set of kinase and phosphatase enzymes. This means that there could well be regulatory and other processes used by the organisms that could be vulnerable to disruption by drugs.

Many species-specific genes were also identified in the genome sequences, providing potential species- and stage-specific targets. Although the three parasites share many subcellular structures, such as kinetoplasts and glycosomes, the organisms are very different. They are spread by different insects, attack different tissues and cause different pathologies. The specimens of L. major pictured are in the form that is transmitted to humans by sand flies.

Each parasite also has its own mechanism for evading the human immune system: T. brucei does not enter its victim's cells, and evades the immune system by constantly changing its main surface proteins; T. cruzi holes up inside cells, but uses a similar strategy to hide from the immune system; and L. major infects certain immune cells and interferes with their function.
Understanding the evolution of these parasites reveals new paths to immunization and treatment.

585: Neural crest origins of the neck and shoulder : Nature

Neural crest origins of the neck and shoulder : Nature:

The neck and shoulder region of vertebrates has undergone a complex evolutionary history. To identify its underlying mechanisms we map the destinations of embryonic neural crest and mesodermal stem cells using Cre-recombinase-mediated transgenesis. The single-cell resolution of this genetic labelling reveals cryptic cell boundaries traversing the seemingly homogeneous skeleton of the neck and shoulders. Within this assembly of bones and muscles we discern a precise code of connectivity that mesenchymal stem cells of both neural crest and mesodermal origin obey as they form muscle scaffolds. The neural crest anchors the head onto the anterior lining of the shoulder girdle, while a Hox-gene-controlled mesoderm links trunk muscles to the posterior neck and shoulder skeleton. The skeleton that we identify as neural crest-derived is specifically affected in human Klippel−Feil syndrome, Sprengel's deformity and Arnold−Chiari I/II malformation, providing insights into their likely aetiology. We identify genes involved in the cellular modularity of the neck and shoulder skeleton and propose a new method for determining skeletal homologies that is based on muscle attachments. This has allowed us to trace the whereabouts of the cleithrum, the major shoulder bone of extinct land vertebrate ancestors, which seems to survive as the scapular spine in living mammals.
Evolutionary hypotheses lead to this research, which reveals new information on the evolution of the vertebrates, and yields new hypotheses, and new insight into genetic disorders.

584: Male-specific fruitless specifies the neural substrates of Drosophila courtship behaviour : Nature

Male-specific fruitless specifies the neural substrates of Drosophila courtship behaviour : Nature:

Robust innate behaviours are attractive systems for genetically dissecting how environmental cues are perceived and integrated to generate complex behaviours. During courtship, Drosophila males engage in a series of innate, stereotyped behaviours that are coordinated by specific sensory cues. However, little is known about the specific neural substrates mediating this complex behavioural programme1. Genetic, developmental and behavioural studies have shown that the fruitless (fru) gene encodes a set of male-specific transcription factors (FruM) that act to establish the potential for courtship in Drosophila2. FruM proteins are expressed in approx2% of central nervous system neurons, at least one subset of which coordinates the component behaviours of courtship3, 4. Here we have inserted the yeast GAL4 gene into the fru locus by homologous recombination and show that (1) FruM is expressed in subsets of all peripheral sensory systems previously implicated in courtship, (2) inhibition of FruM function in olfactory system components reduces olfactory-dependent changes in courtship behaviour, (3) transient inactivation of all FruM-expressing neurons abolishes courtship behaviour, with no other gross changes in general behaviour, and (4) 'masculinization' of FruM-expressing neurons in females is largely sufficient to confer male courtship behaviour. Together, these data demonstrate that FruM proteins specify the neural substrates of male courtship.
Understanding the operation of this protein in other insects and animals will give insight into the evolution of gender and mating behavior.

583: Deep sub-seafloor prokaryotes stimulated at interfaces over geological time : Nature

Deep sub-seafloor prokaryotes stimulated at interfaces over geological time : Nature:

The sub-seafloor biosphere is the largest prokaryotic habitat on Earth1 but also a habitat with the lowest metabolic rates2. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism2. Here we present results from two Pacific Ocean sites, margin and open ocean, both of which have deep, subsurface stimulation of prokaryotic processes associated with geochemical and/or sedimentary interfaces. At 90 m depth in the margin site, stimulation was such that prokaryote numbers were higher (about 13-fold) and activity rates higher than or similar to near-surface values. Analysis of high-molecular-mass DNA confirmed the presence of viable prokaryotes and showed changes in biodiversity with depth that were coupled to geochemistry, including a marked community change at the 90-m interface. At the open ocean site, increases in numbers of prokaryotes at depth were more restricted but also corresponded to increased activity; however, this time they were associated with repeating layers of diatom-rich sediments (about 9 Myr old). These results show that deep sedimentary prokaryotes can have high activity, have changing diversity associated with interfaces and are active over geological timescales.
Life keeps turning up in unexpected places, evolving and adapting to unusual conditions.

582: Genomic Sequencing of Pleistocene Cave Bears -- Noonan et al. 309 (5734): 597 -- Science

Genomic Sequencing of Pleistocene Cave Bears -- Noonan et al. 309 (5734): 597 -- Science:

Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of ~1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.
Direct comparison of modern bear DNA and DNA from bears roughly 42-45,000 years old reveals that Brown bear (grizzly) and polar bear both split off from a common ancestor more recent than the cave bear lineage. The cave bears are not necessarily that common ancestor, and the common ancestor may be older than 45,000 years old.

581: Genome-Scale Identification of Nucleosome Positions in S. cerevisiae -- Yuan et al. 309 (5734): 626 -- Science

Genome-Scale Identification of Nucleosome Positions in S. cerevisiae -- Yuan et al. 309 (5734): 626 -- Science:

The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. We developed a tiled microarray approach to identify at high resolution the translational positions of 2278 nucleosomes over 482 kilobases of Saccharomyces cerevisiae DNA, including almost all of chromosome III and 223 additional regulatory regions. The majority of the nucleosomes identified were well-positioned. We found a stereotyped chromatin organization at Pol II promoters consisting of a nucleosome-free region ~200 base pairs upstream of the start codon flanked on both sides by positioned nucleosomes. The nucleosome-free sequences were evolutionarily conserved and were enriched in poly-deoxyadenosine or poly-deoxythymidine sequences. Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access.
Testing evolutionary hypotheses.

580: Extreme Reversed Sexual Dichromatism in a Bird Without Sex Role Reversal -- Heinsohn et al. 309 (5734): 617 -- Science

Extreme Reversed Sexual Dichromatism in a Bird Without Sex Role Reversal -- Heinsohn et al. 309 (5734): 617 -- Science:

Brilliant plumage is typical of male birds, reflecting differential enhancement of male traits when females are the limiting sex. Brighter females are thought to evolve exclusively in response to sex role reversal. The striking reversed plumage dichromatism of Eclectus roratus parrots does not fit this pattern. We quantify plumage color in this species and show that very different selection pressures are acting on males and females. Male plumage reflects a compromise between the conflicting requirements for camouflage from predators while foraging and conspicuousness during display. Females are liberated from the need for camouflage but compete for rare nest hollows.
Evolutionary hypotheses tested.

579: Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps -- Murphy et al. 309 (5734): 613 -- Science

Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps -- Murphy et al. 309 (5734): 613 -- Science:

The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating to mammalian chromosomal evolution. Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres. Analysis of gene content in and around evolutionary breakpoint regions revealed increased gene density relative to the genome-wide average. We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement.
Evolutionary hypothesis testing, macroevolution, and common descent.

578: Web-Spinning Caterpillar Stalks Snails -- Rubinoff and Haines 309 (5734): 575 -- Science

Web-Spinning Caterpillar Stalks Snails -- Rubinoff and Haines 309 (5734): 575 -- Science:

Moths and butterflies compose one of the most diverse insect orders, but they are overwhelmingly herbivorous. Less than 0.2% are specialized predators, indicating that lepidopteran feeding habits are highly constrained. We report a Hawaiian caterpillar that specializes on snails, a unique food source requiring an unusual feeding strategy. The caterpillar uses silk to restrain live prey. All caterpillars have silk glands, but none are known to use silk in this spiderlike fashion. Considering the canalization of caterpillar diets, evolution to attack and feed on snails is an anomaly. Hawaii's isolation and consequently disharmonic biota likely promote evolutionary experiments that occur nowhere else.
An important principle of evolution is that you work with what you've got. In a low diversity area, normal traits get co-opted to unexpected uses.

577: EVOLUTION: Of Whale Knuckles and Placental Trees -- de Muizon 309 (5734): 559 -- Science

EVOLUTION: Of Whale Knuckles and Placental Trees -- de Muizon 309 (5734): 559 -- Science:

Cetaceans are probably the most extraordinary mammals. They are highly adapted to life in water and strictly dependent on their aquatic environment. As a consequence, their anatomy and physiology have been strongly modified and do not resemble those of other mammals. Because cetaceans are so drastically transformed from their terrestrial ancestors, their affinities with other mammals have long been debated. Although researchers agreed that cetaceans had their origin in some group of land mammals that lived during the early Tertiary, there was no consensus on the identity of the group that subsequently evolved into whales and dolphins. Whales have been seen as closely related to seals, creodonts (hyaenodonts), ungulates, and mesonychid condylarths (large carnivorous to omnivorous archaic ungulates). In the absence of a better candidate, the mesonychids were on the verge of becoming accepted when molecular biologists claimed that cetaceans were most closely related to artiodactyls (even-toed ungulates)--specifically to hippos. A few years later, paleontologists discovered postcranial remains of early Eocene cetaceans that demonstrated the presence of a double-pulleyed astragalus (like the sheep ankle bones that the Romans used to play at knucklebones), a characteristic of all artiodactyls and exclusively found in that order. This discovery, among the most important paleontological finds of the past hundred years, led to an immediate consensus on cetacean ancestry. It also demonstrated a remarkable complementarity of two different approaches to the study of the evolution and phylogeny of mammals.
This from a review of

The Rise of Placental Mammals : Origins and Relationships of the Major Extant Clades by Kenneth D. Rose, J. David Archibald

Sounds like a good book.

576: Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system : Nature

Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system : Nature:

Transposons have provided important genetic tools for functional genomic screens in lower eukaryotes but have proven less useful in higher eukaryotes because of their low transposition frequency. Here we show that Sleeping Beauty (SB), a member of the Tc1/mariner class of transposons, can be mobilized in mouse somatic cells at frequencies high enough to induce embryonic death and cancer in wild-type mice. Tumours are aggressive, with some animals developing two or even three different types of cancer within a few months of birth. The tumours result from SB insertional mutagenesis of cancer genes, thus facilitating the identification of genes and pathways that induce disease. SB transposition can easily be controlled to mutagenize any target tissue and can therefore, in principle, be used to induce many of the cancers affecting humans, including those for which little is known about the aetiology. The uses of SB are also not restricted to the mouse and could potentially be used for forward genetic screens in any higher eukaryote in which transgenesis is possible.
Common descent and an evolutionary hypothesis to test. Excellent.

575: Evolutionary biologyRelativity for molecular clocks : Nature

Evolutionary biologyRelativity for molecular clocks : Nature:

The relative constancy of the rate at which DNA sequences evolve has been a treasured icon of molecular evolution for nearly 40 years. The occurrence of such a stochastic 'molecular clock' was initially quite unexpected, and was explained by Motoo Kimura1 by assuming that most changes to amino-acid and nucleotide sequences were neutral — "neither beneficial nor injurious", in Charles Darwin's prescient phrase.

However, there have been several inklings2, 3, 4 that the rate of molecular evolution accelerates when measured over evolutionarily short timescales. As they report in Molecular Biology and Evolution, Ho and colleagues5 have now put the evidence together. Their analyses of primate and bird data sets reveal that there is indeed a decided acceleration of molecular evolution on short timescales. This is an effect that demands explanation; moreover, estimates for the timing of recent events in population biology will need to be reconsidered.

Much more remains to be done. There is the challenge of formulating a single theory that operates smoothly over disparate timescales, from current heterozygosity to the long-term rate of evolution. In addition, a single mutation rate (mu) does not really exist. Even for nucleotides there are many 'mutation rates', at least one between each pair of nucleotides, and these can be estimated separately using three-dimensional matrices12. The J-shaped curve cannot rest until a single theory holds for it: we live in interesting times.
An unsolved problem in molecular biology identified through phylogenetic analyses. What implications this has for evolution is unclear until a mechanism is developed. Is this variation an effect of evolution and natural selection on long time scales? Or a strange statistical artifact? We don't yet know, and that's what makes science fascinating.