Tasmanian devil genome holds secret to survival

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Scientists have sequenced the complete genomes of two Tasmanian devils in the hope of finding clues to preserving this highly endangered marsupial.

Devil populations have been decimated by a highly contagious facial cancer that is transferred when these aggressive animals bite each other.

The findings will help researchers select the best individuals to be kept in captivity for eventual re-release.

The research is outlined in Proceedings of the National Academy of Sciences.

The Tasmanian devil, Sarcophilus harrisii, gets its name from its high-pitch, blood-curdling squeal, and is renowned for fighting over access to animal carcases, which it grinds with the bone-crushing force of its jaws.

Candid cancer

In 1996, a wildlife photographer snapped an image of an animal in the far north-east of Tasmania with a peculiar growth on its face.

The growth, it turned out, was neither benign, nor isolated to this one individual, but was a highly contagious, fatal cancer that seemed to be spreading through the population at lightning speed.

By 2007, conservationists reported that Devil Facial Tumour Disease, DFTD, had wiped out more than 90% of devil populations in the north-east of Tasmania, and was spreading west.A strategy to save the devil from extinction was begun.

Now, an international team of genomicists is offering a helping hand.

The researchers took advantage of the latest technology to read the genetic sequence of two devils – an uninfected male called Cedric, and an infected female called Spirit – along with smaller segments of DNA from 175 other individuals.

The team hopes to use the genomes to pinpoint which individuals should be placed into “protective custody” to wait out the cancerous epidemic before being reintroduced.

From their analysis, the scientists predicted how best to capture as much genetic diversity among the individuals put aside for captive breeding, explained lead author Webb Miller, a genomicist from Pennsylvania State University, US.

He said that choosing individuals who were very genetically dissimilar should take priority over whether they were resistant to the cancer.

The devil you know

“It is a big step forward to actually get the genome sequence from this animal… the [world’s largest] remaining carnivorous marsupial,” said zoologist David Rollinson from the Natural History Museum, UK.

Getting two complete genomes was very valuable, said Dr Rollinson, but getting as many samples as they did, from as many different animals was “just the icing on the cake”.

Dr Rollinson thinks that a similar approach could be used to study and save other endangered animals.

The researchers also sequenced one of the five tumours from Spirit’s head for clues to why the Tasmanian devils fail to recognise the cancer as “non-self”, and destroy it before it takes hold.

Understanding what it is about the devil’s immune system that makes it so ineffectual at picking up the facial cancer will not only help treat those already infected, but will hold clues about whether the cancer can jump species.

“The greatest worry is that it will jump into another marsupial,” said cancer geneticist Elizabeth Murchison from the Welcome Trust Sanger Institute in Hinxton, UK.

The transmissible facial cancer

  • Devil Facial Tumour Disease (DFTD) is spread by biting during aggressive encounters
  • The living cancer cells exist as a contagious clone; highly unusual for a cancer. In fact, there is only one other transmissible cancer known, which infects dogs’ genitals
  • The devil’s immune system seems unable to detect the cancer
  • The disease forms tumours around the mouth interfering with feeding leading to death
  • The cancer originally arose in Schwann cells – cells which wrap themselves around nerve tissue
  • First seen in 1996, the cancer has since decimated devil populations

:: Read original here or listen to me talk about the results on the BBC’s Science in Action.

A rare he-she butterfly is born in London’s NHM

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A half-male, half-female butterfly has hatched at London’s Natural History Museum.

A line down the insect’s middle marks the division between its male side and its more colourful female side.

Failure of the butterfly’s sex chromosomes to separate during fertilisation is behind this rare sexual chimera.

Once it has lived out its month-long life, the butterfly will join the museum’s collection.

Only 0.01% of hatching butterflies are gynandromorphs; the technical term for these strange asymmetrical creatures.

“So you can understand why I was bouncing off of the walls when I learned that… [it] had emerged in the puparium,” said butterfly enthusiast Luke Brown from London’s Natural History Museum.

Mr Brown built his first butterfly house when he was seven, and has hatched out over 300 thousand butterflies; this is only his third gynandromorph.

Half and half

It is not only the wings that are affected, he explained. The butterfly’s body is split in two, its sexual organs are half and half, and even its antennae are different lengths.

“It is a complete split; part-male, part-female… welded together inside,” he told the BBC.

The dual-sex butterfly is an example of a Great Mormon, Papilio memnon –a species that is native to Asia.

With a shortage of butterfly-specific gender neutral pronouns, the butterfly is being referred to as “it”, and is already middle-aged at three and a half week’s old.

So the public has only a narrow window of opportunity to see it alive.

Though rare, gynandromorphy isn’t unique to butterflies; individual crabs, lobsters, spiders and chickens have all been found with a mix of two sexes.

There are likely many more cases in the natural world, but sexual chimeras are more difficult to spot in animals where females and males look alike.

:: Read original here ::

Over-fished tuna in ‘hot water’, study finds

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Two more species of tuna have been added to the Red List of Threatened Species.

They join the Southern bluefin tuna – listed as critically endangered.

The report, published in this week’s Science, is the first global assessment of this highly prized family of fish, which are at risk of being over-fished.

The World Conservation Union (IUCN) says there is a lack of resolve to protect against overexploitation driven by high prices.

Until this latest study, attempts to assess the health of scombrid and billfish populations, families of fish that include tuna and swordfish, have been carried out at a regional scale.

This study, which relies on the IUCN Red List criteria to judge the stocks’ health, took a more global approach.

Of the 61 species of fish assessed, seven were earmarked as either vulnerable, endangered or critically endangered. All suffer from over-fishing, habitat loss and pollution.

Along with the two species of tuna, two mackerel and two marlin joined the Red List.

The ‘sapphires of seafood’

Per kilo, bluefins are among the most expensive seafood in the world.

“All three bluefin tuna species are susceptible to collapse under continued excessive fishing pressure. The Southern bluefin has already essentially crashed, with little hope of recovery,” said one the the study’s authors Kent Carpenter the IUCN’s Marine Biodiversity manager.

Southern bluefin numbers have reached levels that are one twentieth of those recorded before industrial fishing began.

Atlantic bluefins have probably gone the same way, add the authors, while bigeye tuna is labelled “vulnerable”.

“Tunas are highly migratory fish, swimming across ocean basins and between the waters of various countries during their lifetimes. Conserving them requires regional and global co-operation,” commented Susan Lieberman, director of international policy with the Pew Environment Group in a statement.

What is more, tuna’s restricted spawning grounds make them exceptionally susceptible to collapse if over-fishing continues, reports the international team of scientists.

And tuna’s long lifespan means it would take their population several years to recover if fishing stopped altogether.

Pew’s Dr Lieberman adds: “The IUCN Red List assessment reinforces that it is time for governments to live up to their responsibilities.”

The report comes days before the tuna regional fisheries management organizations (RFMOs) assemble in in La Jolla, California for the Kobe III meeting.

Read original here

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Worms’ sex life yields advantage over parasites

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Sex gives worms the power to fight off parasites, report researchers this week in the journal Science.

Worms forced to reproduce asexually succumbed to a nasty bacterial infection and died.

The researchers say the results are the most convincing evidence to date for a key theory in evolutionary biology.

The theory holds that sex evolved because it lets organisms reshuffle their genes into new combinations to stay a step ahead of parasites.

Sex has long troubled evolutionary biologists.

Reproducing asexually – where organisms clone themselves – makes much more sense; there is no need for an organism to search and seduce a mate, fight off competitors, or risk contracting a sexually transmitted disease.

What is more, given that an organism has survived long enough to reproduce, it is likely to have a first-rate set of genes under its pelt.

Why run the risk of diluting these good genes with potentially poorer ones from another organism?

And yet sex exists; the vast majority of animals and plants reproduce this way.

Fluctuating futures

Parasites, many biologists believe, might be the answer.

Parasites create a situation where, in spite of the disadvantages of sex, it is good for an organism to reshuffle its genome with that of another.

This reshuffling creates offspring with new gene combinations that are potentially better than older combinations at resisting a parasite’s advances.

The genetic “arms race” between a parasite and its host is often refered to as an example of Red Queen-style interaction – a term coined by biologist Leigh Van Valen who summoned the image of the constantly running Red Queen from Lewis Caroll’s Through the Looking-Glass.

The analogy seemed to him fitting for describing how species must continually evolve to keep up with each other.

But despite the theory’s popularity, there has been little hard evidence for it.

Out in the field, biologists have noted that organisms are more likely to reproduce sexually when there are more parasites loping around in their vicinity.

What has been missing is a direct manipulation to organisms’ sex lives to test if it makes them more or less resistant to parasites.

Direct evidence

Now researchers working at Indiana University in the US have used the round worm Caenorhabditis elegans to do just this.

The team engineered two types of worms – some that could only reproduce by having sex, and some that could only clone themselves.

The researchers watched the worms gorge themselves on a lawn of a nasty bacterium, Serratia marcescens, which invades the worms’ guts and from there multiplies into every crevice of their body, killing the worms from the inside.

Across five different populations, worms that reproduced sexually fared well over the 20 generations, while all animals that cloned themselves died quickly.

Testing theory

“What is really beautiful about these lab systems is that you can manipulate the system and show that [the theory] can work,” said evolutionary biologist Aneil Agrawal from the University of Toronto in Canada.

Dr Agrawal described the experiment as “elegant” because it allowed the researchers to demonstrate that it was not simply the presence of the parasite that spelled the end for the cloners, but the presence of a parasite that had co-evolved alongside the worms.

To do this, the team created two treatments: one used bacteria from an original stock kept in the freezer, and the other used bacteria that had lived alongside the worms for many generations and so had adapted along with them.

Clonally doomed

In essence, “the bacteria got more and more infective, but the [clonal worms] did not get more and more resistant, and that is why they went extinct,” explained lead author Levi Morran, an evolutionary biologist from University of Indiana in the US.

“I am really excited about this; I think this is really cool,” Dr Agrawal told BBC News.

“Whether this is actually happening in nature is another thing; we can’t know that from a lab system,” he explained.

But he adds that as a first step it is important to demonstrate that under conditions where you expect sex to alleviate the effects of parasites, it does.

:: Read original here ::

Dinosaurs were animal world’s top bone heads

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Scientists have compared a dinosaur with several modern-day animals to settle who wins the heavy-weight head-butting title.

The new findings confirm that the ancient bipedal dinosaur Stegoceras could knock out any of today’s top head-butters.

Stegoceras probably used their domed skulls to ram each other over access to fertile females.

The hard-hitting research was published in the journal PLoS ONE.

Stegoceras was a member of the leaf-eating genus Pachycephalosauria that roamed the Earth around 70 million years ago.

The goat-sized dinosaur supported a 7.5cm (~3 inches) thick bony skull, which some palaeontologists believe acted as a shock-absorber when these animals ran at each other.

Big hitters

However, images of the insides of Stegoceras‘ fossilised skull, which reveal two layers of dense bone that encase a spongy sinus held apart by tiny struts, has led some scientists to doubt this interpretation.

Hoping to clear up the controversy, biomedical engineer Dr Eric Snively wandered down the corridor at the University of Calgary in Alberta, Canada to enlist the help of colleague Dr Jessica Theodor, a vertebrate palaeontologist.

The duo performed computer tomographic (CT) scans on the skulls of Stegoceras, along with a variety of modern animals, and used these bone density measurements to create 3D models of the animals’ heads.

The team was then able to exert virtual stresses to test how the different skulls held up.

Compared to some of today’s big hitters, such as the Northern American bighorn sheep, the Arctic musk ox and African duiker, Stegoceras ‘ head was able to withstand the most stress.

“The argument that they couldn’t withstand the forces of head-butting seems to have been refuted by this evidence,” said Dr Theodor.

Crushing collisions

Dr Snively explained that if two animals ran at each other with a combined speed of 6.7 metres (22 feet) per second, which he estimates to be a realistic speed, Stegoceras‘ dome-head would have had to withstand an impact of over 13,000 Newtons (2,918 pounds-force).

“In human terms, that’s like balancing a Ford Focus on your head,” Dr Snively told BBC News.

“Even at these forces, only a few struts of bone might break; these would heal easily,” he said.

Offering further protection from these crushing collisions, Stegoceras‘ head was covered by a layer of keratin, the material nails are made from, and articulations between the vertebrae would have let the “backbone scrunch up like an accordion”, explained Dr Snively.

:: Read original here ::

Researchers switch on genes with blue pulse

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Scientists have developed a technique that could be used to deliver precise doses of hormones to people who don’t make them naturally.

To do this, they rewired kidney cells with light-sensitive molecules from the eye, they reported in the journal Science.

When pulsed with blue light, these cells churned out proteins on demand.

Ultimately, this technique could avoid the need for people with diabetes to inject themselves regularly.

“When I speak to diabetes patients they say that if you could take away always having to inject themselves it would really increase their quality of life,” said lead author Martin Fussenegger, a bioengineer of the Swiss Federal Institute of Technology, Zurich.

Dr Fussenegger thought he saw a solution in his own field of optogenetics. Optogenetics, as the name suggests, uses light to control the behaviour cells.

To get a cell to respond to light you first have to rejigger it so it has a light-sensitive molecule on its surface. Dr Fussenegger coaxed kidney cells to express melanopsin, a molecule usually found in animals’ eyes.

Blue genes

He then placed these cells into diabetic mice. Along with the cells he placed an optic fibre, down which he could pulse blue light to expose the cells at his command.

In the dark, these cells behaved as usual; In the light, however, genes in the cell were switched on and the cell pumped out a protein required for the breakdown of sugars in the blood, helping the mice to control their glucose levels.

He hopes that cells like these could ultimately be implanted into people, and exposed to light – either through the skin or down a optic fibre – to release proteins that would help treat diabetes.

The new technique is a proof of principle. He told BBC News that it was not limited to treating diabetes; this technology could be usedto switch on genes to produce many different proteins in people who do not make them naturally, or are not making enough of them to be healthy.

Light switch

“I think this is a phenomenal research tool,” said James Collins, a synthetic biologist at Howard Hughes Medical Institute, Maryland, US, who was not involved in the work.

Dr Collins explained that as we move into an age of regenerative medicine, and begin to think of how we use stem cells to produce different tissues in the body, one of the challenges will be to work out which genes are needed to produce certain tissues and cells.

This new technique allows researchers to switch genes on and off to determine which are essential to make a specific tissues.

:: Read original here ::

Early human fossils unearthed in Ukraine

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Ancient remains uncovered in Ukraine represent some of the oldest evidence of modern people in Europe, experts have claimed.

Archaeologists found human bones and teeth, tools, ivory ornaments and animal remains at the Buran-Kaya cave site.

The 32,000-year-old fossils bear cut marks suggesting they were defleshed as part of a post-mortem ritual.

Details have been published in the journal PLoS One.

Archaeologist Dr Alexander Yanevich from the National Ukrainian Academy of Science in Kiev discovered the four Buran-Kaya caves in the Crimean mountains in 1991.

Since then, roughly two hundred human bone fragments have been unearthed at the site.

Among the shards of human bones and teeth, archaeologists have found ornaments fashioned from ivory, along with the abundant remains of animals.

The artefacts made by humans at the site allowed archaeologists to tie the ancient people to a cultural tradition known as the Gravettian.

This culture came to span the entire European continent and is named after the site of La Gravette in France, where this stone age culture was first studied.

Researchers were able to directly date the human fossils using radiocarbon techniques. The shape and form of the remains told the scientists they were dealing with modern humans (Homo sapiens sapiens).

Eastern promise

One thing that intrigued researchers was the scarcity of human long bones (bones from the limbs) in the caves.

The site yielded countless limb bones from antelope, foxes and hares.

But the human remains consisted of vertebrae, teeth and skull bones no larger than 12cm.

What is more, the positions of cut marks found on the human fragments were distinct from those found on the animal bones.

And while the bone marrow had been removed from butchered animals, it had been left alone in the case of the human remains at the site, explained co-author Sandrine Prat from the French National Centre for Scientific Research (CNRS) in Paris.

She suspects this demonstrates that human bones were processed differently from those of animals. Human flesh was removed as part of ritual “cleaning”, not to be eaten.

Defining culture

The finds offer anthropologists a glimpse into a very early and important human culture, said Professor Clive Finlayson, an evolutionary ecologist and director of the Gibraltar Museum.

“Gravettian culture is the culture that defines modern humans.

“These people had knives, lightweight tools, open air camps, they used mammoth bones to make tents,” he said, adding that this was the earliest example of the Gravettian cultural tradition.

Professor Finlayson said that uncovering evidence of this culture in Ukraine gave weight to the idea that early modern people spread into Europe from the Russian plains, not north through the Balkans from the Middle East.

“What has excited me is that we have found evidence of humans where I would expect them to be, exploiting foods that I would expect them to be exploiting,” Professor Finlayson told BBC News.

:: Read more here ::

Scientists to sequence thousands of insect genomes

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Thousands of insects are being lined up to have their genomes sequenced.

The five-year project will help researchers pinpoint vulnerable regions of insects’ genomes, which could be targeted with pesticides.

The project’s leaders hope the initiative will make a dent in the $50bn spent globally each year to control diseases transmitted by insects.

The final list of six-legged critters has yet to be finalised.

The project, called the 5000 Insect and Other Arthropod Genome Initiative, comes at a time when the costs of genome sequencing have fallen substantially and it is feasible to cheaply sequence large numbers of animals and plants.

Handfuls of bugs

Among the list of agriculturally important insects and other arthropods – animals with exoskeletons – to be sequenced are handfuls of bugs that act as disease vectors.

By comparing the genomes of these insects with those of their close relatives that don’t carry pathogens, researchers hope to pinpoint the genes that make one insect a disease-vector and another not.

What’s more, knowing the genes involved will help researchers better predict how insect immune systems will evolve in response to biopesticide control measures, such as Beauveria bassiana, a fungus used to control mosquitoes in malaria-ridden countries in Africa.

It is also hoped that the project will aid the search for suitable compounds for use as pesticides; ones that kill a targeted pest but leave the beneficial pollinating insects that also visit the crop plants unharmed.

:: Read original here ::

Powerful cosmic blast as black hole shreds star

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Astronomers have spied a star’s swan song as it is shredded by a black hole.

Researchers suspect that the star wandered too close to the black hole and got sucked in by the huge gravitational forces.

The star’s final moments sent a flash of radiation hurtling towards Earth.

The energy burst is still visible by telescope more than two-and-a-half months later, the researchers report in the journal Science.

The Swift spacecraft constantly scans the skies for bursts of radiation, notifying astronomers when it locates a potential flare.

These bursts usually indicate the implosion of an ageing star, which produces a single, quick blast of energy.

But this event, first spotted on 28 March 2011 and designated Sw 1644+57, does not have the marks of an imploding sun.

What intrigued the researchers about this gamma ray burst is that it flared up four times over a period of four hours.

Astrophysicist Dr Andrew Levan from the University of Warwick, and his colleagues suspected that they were looking at a very different sort of galactic event; one where a passing star got sucked into a black hole.

The energy bursts matched nicely with what you might expect when you “throw a star into a black hole”, Dr Levan told BBC News.

Gasless centres

Black holes are thought to reside at the centres of most major galaxies. Some black holes are surrounded by matter in the form of gas; light is emitted when the gas is dragged into the hole. However, the centres of most galaxies are devoid of gas and so are invisible from Earth.

These black holes only become visible when an object such as a star is pulled in. If this happens, the star becomes elongated, first spreading out to form a “banana shape” before its inner edge – orbiting faster than the outer edge – pulls the star into a disc-shape that wraps itself around the hole.

As material drops into the black hole it becomes compressed and releases radiation that is usually visible from Earth for a month or so.

Events like these, termed mini-quasars, are incredibly rare – researchers expect one every hundred million years in any one galaxy.

The researchers used some of most powerful ground-based and space-based observatories – the Hubble Space Telescope, the Chandra X-ray Observatory and the Gemini and Keck Telescopes.

:: Read original here ::