The Great Beyond

Hot on the heels of the pig genome comes news of another animal sequenced down on the farm. Writing in this week’s Science, researchers report the genome of Twilight, an adult female Equus caballus.

While this worthy feat of science has attracted much media interest, none of the coverage seems to mention that the horse genome was actually sequenced back in 2007 and widely reported at the time, although it was only published this week.

It is a useful genome to have though.

“Horses and humans suffer from similar illnesses, so identifying the genetic culprits in horses promises to deepen our knowledge of disease in both organisms,” says Kerstin Lindblad-Toh, of the Broad Institute of MIT and Harvard and Uppsala University in Sweden (press release). “The horse genome sequence is a key enabling resource toward this goal.”

The equine sequence is roughly 2.7 billion letters long and is not dissimilar to our own. “Indeed, 17 horse chromosomes (53%) comprise material from a single human chromosome (in the dog, it is 29%),” the authors write.

The horse genome joins not only the pig, but also the chicken and the cow, with the sheep on the way. All together now: “Old Macdonald had a genome…”

Image: Twilight / courtesy of Doug Antczak, Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University

Posted by Daniel Cressey on November 06, 2009
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The cost of sequencing a human genome has dropped to just below $5,000. Well, sort of. The Mountain View, Calif.-based company Complete Genomics published a paper today describing its efforts to sequence three genomes at a materials cost of $4,400. Included in the trio is the genome of George Church, personal genomics evangelist and an adviser to the company, who has already posted the analysis of his data here.

Continue reading "Complete Genomics publishes a genome" »

Posted by Erika Check Hayden on November 05, 2009
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A new analysis of a dinosaur skull recovered from an English reservoir in 1910 has concluded it is the oldest-known relative of Tyrannosaurus Rex.

Initially named Megalosaurus bradleyi, the skull was later relabelled as Proceratosaurus.

“Although this specimen is still one of the most complete and best preserved theropod skulls from, and one of very few theropod skulls from the Middle Jurassic globally, it has received surprisingly little attention in recent literature,” write Oliver Rauthhut, Angela Milner and Scott Moore-Fay in the Zoological Journal of the Linnean Society.

To deal with this lack of attention, the researchers cleaned away rock from the fossil and subjected it to CT scans. Their conclusion: the 3-metre long beast was probably a 165-million-year old ancestor of the most iconic of dinosaurs.

“It was quite a surprise when our analysis showed we had the oldest known relative of T. rex,” says Milner, of London’s Natural History Museum (press release).

Image: NHM

Posted by Daniel Cressey on November 04, 2009
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Many thanks to genome scientists for giving us tastier sausages, for according to the Telegraph’s food and drink section, the best thing about the recently unveiled pig genome is that it will lead us to better bangers.

The announcement was made from the Wellcome Trust Sanger Institute in Hinxton, UK, but the pig, a red-haired Duroc pig came from a farm at the University of Illinois, US.

"The pig is the ideal animal to look at lifestyle and health issues in the United States," the AP reports Larry Schook as saying. Schook, from the University of Illinois in Champaign, led the DNA sequencing project.

The 98% complete genome sequence will be valuable to agriculturalists looking to improve pig breeding practices, look at their immunity to certain diseases, and also help preserve species fo rare, endangered pigs. And it might also help create a swine flu vaccine – but only for pigs (Daily Mail).

The pig genome is particularly useful because our porcine friends are like us in many ways that may not be obvious to the naked eye; they have similar psychology, behaviour and nutritional needs to us says WA today. Except I bet pigs don’t eat sausages.

Image: Scott Bauer - USDA, ARS, IS Photo Unit

Posted by Katharine Sanderson on November 03, 2009
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Posted for Jane Qiu

Qian Xuesen, widely known as the father of China’s missile and space missile programme, died on 31 October at the age of 98.

A prominent rocket scientist who helped establish the Jet Propulsion Laboratory at the California Institute of Technology, Qian decided to return to China after being accused of being a communist and spy, but was detained for five years before being deported in 1955.

One year after his return, Qian established China's first ballistic missile programme, which led to the successful launch of the Dongfeng missile in 1964 and nuclear-weapon testing the following year. Qian's research has also led to the development of the Long March Rocket, which successfully launched Shenzhou V, China's manned spacecraft, in October 2003.

The Chinese Academy of Sciences has also reported the death of biophysicist Bei Shizhang, who died the age 107 on October 29. “As the founder, the first chief director and later honorary director of the Institute of Biophysics, CAS, he was considered ‘Father of Chinese Biophysics’,” the academy said in a statement.

Posted by Daniel Cressey on November 02, 2009
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Earlier this month it looked like the UK government had abandoned plans to keep the DNA of innocent people on its massive police database.

The European Court of Human Rights has already said that data on innocent people should not be retained. Now, however, leaked emails indicate that the government will try to keep hold of their DNA for six years, says the Daily Mail. The previously abandoned position of the government was to keep DNA of innocents for 12 years (see: UK won't be able to store DNA data – 20 October, 2009).

It was also reported today that the profiles of 5.5 million people – over 10% of the population of England and Wales – are now on the database (Daily Telegraph). In addition, over 90,000 innocent people have had their DNA added to the database since that European Court ruling that this shouldn’t be happening (Guardian).

The UK government’s approach seems to be catching on too: the University of Akron in the US is now apparently requiring job applicants to be willing to supply a DNA sample (Inside Higher Ed).

Image: Getty

Posted by Daniel Cressey on October 29, 2009
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A single dose of gene therapy greatly improved the vision of 12 patients with a rare, inherited visual disorder. The best results were achieved in the youngest patients, including a 9-year-old boy named Corey Haas, who was considered legally blind before the treatment began and now has the same level of light sensitivity as his normal-sighted schoolmates.

The study "holds great promise for the future" and "is appealing because of its simplicity", Frans Cremers and Rob Collin, of the Radboud University Nijmegen Medical Center in the Netherlands, wrote in a commentary accompanying the report, which was published online 24 October in the Lancet.

Leber's congenital amaurosis is an inherited eye disease characterized by severe degeneration of the retina and loss of vision in the first few months of life. The disease, which affects around 1 in 80,000 people, can be caused by mutations in 13 different genes. But all 12 of the patients in the Phase I study, led by researchers at researchers at the Children's Hospital of Philadelphia and the University of Pennsylvania School of Medicine, suffered from a defective gene called RPE65, which codes for a vitamin A derivative that is essential for detecting light.

The researchers injected each patient's worse eye with a functional copy of the RPE65 gene inserted into an adenovirus vector. The investigators last year reported success with three adult patients (see 'Gene therapy treats blindness'), and now they've added an additional nine patients, including four children under the age of 11. These youngsters displayed the greatest visual recovery, presumably because their defective retinal cells did not yet have time to completely die off.

Continue reading "Gene fix helps blind boy see" »

Posted by Elie Dolgin on October 26, 2009
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Butterflies did not mistakenly mate with worm-like animals to give rise to caterpillars, according to a new report that challenges previous claims to the contrary.

"It's a nutbar idea," says study author Michael Hart, an evolutionary biologist at Simon Fraser University in Burnaby, Canada. "There's just nothing to it."

In August, the Proceedings of the National Academy (PNAS) published a paper online by Donald Williamson, a retired zoologist at the University of Liverpool, UK, arguing that at some point in the distant past a larva-less insect hybridized with a velvet worm, and the resulting descendants now develop successively through stages that resemble both parents. The study — which was 'communicated' by academy member Lynn Margulis, of the University of Massachusetts, Amherst, via the soon-to-be-obsolete 'Track I' submission route, which allows academy members to handle the review of a colleague's manuscript — became embroiled in controversy after questions were raised about the peer review process (see 'Row at US journal widens').

The paper's print publication was suspended for more than a month, but it was ultimately given the green light in mid-October by the PNAS editorial board. The journal also plans to publish a short 'letter to the editor' by Gonzalo Giribet, an invertebrate zoologist at Harvard University in Cambridge, Massachusetts, and a response from Williamson. In addition, PNAS today published a full-length counter-argument to Williamson's hypothesis.

Williamson's paper offered little direct evidence for hybridization other than physical resemblances between caterpillars and velvet worms. But he predicted that insects with caterpillar larvae should show genetic similarities to the worm-like invertebrates, and he called on genomicists to test his ideas. Now, two non-academy members — Hart and fellow evolutionary biologist Richard Grosberg, of the University of California, Davis — have taken Williamson to task and turned to published data on genome sizes and contents to rubbish his proposals.

Continue reading "No species mixing to make caterpillars" »

Posted by Elie Dolgin on October 26, 2009
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The secret is out: Neanderthals and modern humans had sex, geneticist Svante Pääbo declared Sunday during a conference at Cold Spring Harbor Laboratory in New York. But the jury's still out on whether these relations resulted in offsrping and, if so, whether those offspring contributed to humans today. (The Times)

Pääbo led the three-year project to sequence the Neanderthal genome at the Max Planck Institute in Leipzig, Germany. The team completed the draft sequence in February, but the preliminary genetic analysis, announced at the American Association for the Advancement of Science annual meeting in Chicago, was little more than a tease.

It seems Pääbo is continuing to be rather tight-lipped about the findings, disclosing few details to The Times, besides announcing that he's "sure that they had sex". Pääbo will publish his analysis of the entire Neanderthal genome "shortly", The Times reports.

Continue reading "Did Neandermen Roam the Earth?" »

Posted by Lizzie Buchen on October 26, 2009
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Direct-to-consumer genetic testing can count one more consumer — the director of the US National Institutes of Health, Francis Collins.

Collins announced today at a personalized medicine colloquium in Washington DC that he spat into a set of tubes and sent off his genetic material under a pseudonym to three of the leading personal genetic testing companies. He said that all the companies provided highly accurate genotyping, but with substantial differences in the information that was revealed and the interpretations provided — similar to the conclusions reached by Collins's former human genome sequencing rival, Craig Venter, in a recent opinion article in Nature.

On a more personal level, Collins discovered that he carries two copies of the most common risk factor of type II diabetes. Collins, whose laboratory investigates the underlying genetic basis of adult-onset diabetes, said he was "surprised" by these findings since his family has no history of the disease. Upon learning the test results, Collins got off his Harley-Davidson and instigated a regular exercise regime. The svelter NIH director said he has now lost 20 pounds.

Official NIH photos from before and after Collins became director. Check out those gaunt cheeks!

Posted by Elie Dolgin on October 26, 2009
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A new understanding of one of nature’s most complicated eyes could lead improvements in a huge range of modern electronic devices, according to a paper published in Nature Photonics.

Nicholas Roberts, of the University of Bristol, and colleagues have worked out how the ‘quarter-wave plates’ in the eyes of mantis shrimp work.

As you may have guessed, a quarter-wave plate rotates the plane of polarization of a light wave by a quarter. Crucially, they can convert between linearly polarized light and circularly polarized light, something that makes them useful for DVD players, CD players, and camera filters.

“Our work reveals for the first time the unique design and mechanism of the quarter-wave plate in the mantis shrimp’s eye,” says Roberts (press release). “It really is exceptional, outperforming anything we humans have so far been able to create.”

Shrimp eyes use cleverly designed cell membranes rolled into collections of tubes to make their quarter wave plates and to help them see polarized light (as well as twelve colours as opposed to human eyes, which have a rather paltry three colour palette), the authors report.

Study author Justin Marshall of the University of Queensland says shrimp also reflect circular polarized light off their bodies.

“They have a cuticle on their skin that reflects it,” he told ABC. “They’re talking to each other with a secret light channel.”

Now we’re closer to understanding how shrimp eyes work, we may be able to use their advanced optics to make better electronics, using liquid crystals to mimic them, say the authors.

This is undoubtedly very cool science, but won’t we just be downloading our movies and games by the time they get this working for DVDs?

Image mantis shrimp (Odontodactylus scyllarus) / Roy Caldwell.

Posted by Daniel Cressey on October 26, 2009
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Tarantulas don’t make silk with their feet, according to a new paper which refutes previous research.

In 2006, Stanislav Gorb of the Max Planck Institute for Metals Research in Stuttgart, and his colleagues wrote in Nature that zebra tarantulas (Aphonopelma seemanni) could secrete silk from their feet. This, they argued, helps them climb smooth vertical surfaces and “avoid catastrophic falls”. The finding played well with the media.

Now Fernando Perez-Miles, of the Universidad de la República in Uruguay, and colleagues may have disproved this. They took four zebra tarantulas and used paraffin to seal their spinnerets – the abdominal structures spiders make silk with. After 72 hours they found no silk at all in the containers they were keeping the spiders in, they write in Nature.

They also say that the spinneret structures detailed by Gorb on spiders’ feet are actually sensory structures.

“Tarantulas entangle silk threads from the spinnerets with their tarsi. They often use hind legs to entangle silk, but we also observed A. seemanni entangling with their other legs. This behaviour might explain the presence of the thread footprints photographed by Gorb et al.” write the authors.

However Gorb and his team maintain that spiders may be producing foot-silk. Firstly they argue that the silk in question is laid down in parallel tracks, implying it is not a secondary deposition. Additionally they say that examination of this silk shows a broad area at the beginning of the fibre that could be where it was an initial fluid. If the silk had come from an abdominal organ fluid phases would be lost in transference to the feet, they argue.

“We remain satisfied that the most plausible explanation for our observations is the existence of tarsal-silk-producing structures scattered within the setae on tarantula tarsi,” says their response.

Image: tarantula entangling a silk thread with its hind leg, from Perez-Miles et al.

Posted by Daniel Cressey on October 22, 2009
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The question of why most animals have sex with other animals is answered today by a paper published in Nature (no snickering at the back).

This issue isn’t as simple as you might think. The real problem is that men are actually rubbish, note the paper’s authors Levi Morran, Michelle Parmenter and Patrick Phillips, who all work at the University of Oregon, Eugene.

Males “do not directly contribute offspring”, they say, so animals that self-fertilize should have numerical advantage over their sexually reproducing relatives. On the flip side reproducing sexually does mean you avoid inbreeding and you can adapt faster to environmental changes.

To get a better understanding of this, the researchers genetically tweaked C. elegans worms to be either sexually reproducing hermaphrodites (‘outcrossing’) or ‘selfing’ animals. They then exposed these animals to a chemical that upped their mutation rate. They also tested how well they adapted to a nasty bacterial pathogen.

Selfing animals showed a decline in fitness and were less good at adapting to the pathogen. The bottom line: animals that don’t do it on their own did better when forced to mutate or adapt to a new environment.

“Many scientists have argued that outcrossing has evolved to avoid the genetic consequences of inbreeding, while others have emphasized the role that outcrossing plays in generating the genetic variation necessary for evolutionary change,” says Morran (press release). “Our work shows that both of these factors are important.”

Image: hermaphrodite nematode C. elegans / Patrick Phillips, University of Oregon

Posted by Daniel Cressey on October 22, 2009
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The UK must grow GM crops to avoid food shortages in the future, a report from the Royal Society, the UK’s national academy of sciences, is expected to say (Telegraph).

The study was commission in July 2008 in response to a prediction from the United Nations that world food production would need to double by 2050 to sustain a global population expected to reach nine billion.

Previous plans to grow GM crops commercially in the UK were withdrawn at the beginning of the decade after protests from green groups and consumers’ rejection of the technology.

The Telegraph says that the report, which is due to be published this week, examines several options to increase crops yields in the UK and around the world, including growing GM crops.

A source told the Sunday Telegraph, “The report will say the right GM crops should be used in the future to alleviate food shortages. This study is going to move the debate forward. The government will have to take notice of this.”

But opponents of GM crops told the Telegraph, “There is no scientific evidence that GM produces huge yields.”

Posted by Natasha Gilbert on October 19, 2009
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Bird of paradise plant seed Credit: Annie Cavanaugh, Wellcome Images

From captivating cancer cells to stunning sensory nerve fibres, the winners reveal "the ability of the picture to communicate the wonder and fascination of science", according to the Wellcome Trust's press release.

To view all the selected images, head over to the Wellcome Collection in London before Spring 2010, or just click through the Image Awards Website, which details how the images were captured and why they were tapped by the judges.

Over at the BBC, there's also a video of Mark Walport, director of the Wellcome Trust, discussing his top three picks.

Summer plankton
Credit: Spike Walker, Wellcome Images

Mouse liver with blood cells
Credit: EM Unit, UCL Medical School, Royal Free Campus, Wellcome Images

Posted by Elie Dolgin on October 16, 2009
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Posted for Brendan Maher

Yesterday, Nature published a map of human DNA methylation at singe base pair resolution, basically the precise location of millions of methyl groups hanging on the cytosine bases in the genome.

For the ‘omics’ lovers, this is the methylome, a subset of the epigenome which presumably also includes the extent of different modifications made to histone proteins and the attachment of other molecules known to influence gene expression.

No doubt journalists around the world had a difficult time wrapping their nut grafs around this one.

Defining what makes something “epigenetic” has been a prickly practice (one briefly outlined in a Nature news feature last year).

Purists say that it has to do with modifications to gene expression that do not involve mutation but are inherited at least from cell to cell during division,if not through sexual reproduction as well. The NIH, which funded the current work, defines it a bit more loosely, not tying the modifications down to inheritance.

Metaphors are helpful in explaining the importance of the epigenome, but they can be equally sticky.

Continue reading "On methylome metaphors" »

Posted by Daniel Cressey on October 15, 2009
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A nearly totally vegetarian spider has been discovered in a remarkable ecological niche in Central America.

While most spiders dine on tasty insects and the like, the new species lives on acacia shrubs. These provide shelter and food for ants that in turn protect them from predators, in theory at least.

The new spider – named Bagheera kiplingi after the panther in the Jungle Book – lives on the plants, eating the nectar produced for the ants and the leaf tips that produce it.

It is not totally veggie, as it occasionally snacks on ant larvae and flies that try to dine on the nectar. However it is, say its discoverers, “the first report of a spider that feeds primarily and deliberately on plants”.

The spider was discovered independently by two research teams; Eric Olson, of Brandeis University in Massachusetts, found it in Costa Rica in 2001 and Christopher Meehan, of Villanova University, Pennsylvania, found it in Mexico in 2007.

“What surprised us most about discovering this spider's extraordinary ecology was to find it on the ant-acacias,” says Robert Curry, also of Villanova University. (press release).

“This well-known mutualism has been studied by tropical ecologists for nearly 50 years, yet the spider's role was not noticed until Olson's discovery in 2001. We were lucky to find in Mexico an area where the spider is both exceptionally abundant and even more herbivorous than in Costa Rica.”

This is, as the comment piece from Duncan Jackson, of the University of Ulster in the UK, running alongside the paper in Current Biology notes remarkable for a number of reasons:

This is wholly remarkable, because all other known spiders are carnivorous predators, and unlike most other nutritional mutualism exploiters, jumping spiders are specialized hunters rather than generalized foragers.
...
It is truly remarkable that a spider should thrive on a vegetarian diet, because all spiders are constrained by their narrow gut, specialized mandibles and a solids filtration system to consume a liquid diet.
...
It seems that the transition from hunter to gatherer in this uniquely vegetarian spider has facilitated a suite of additional behavioural changes which might suggest an alternative route to sociality. One wonders how many more surprises await us in this remarkable system.

Image: adult female Bagheera kiplingi eats Beltian body harvested from ant-acacia / R. L. Curry

Posted by Daniel Cressey on October 13, 2009
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Practicing a task like juggling that requires you to focus your vision and your movement actually increases the amount of white matter in your noggin.

This is the result of research from the Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, UK. They used a technique known as diffusion MRI to test for changes in the brain before and after a group of 24 young people learned to juggle over six weeks, and the paper is published in Nature Neuroscience.

Changes in grey matter of the brain had already been seen in similar studies, but the white matter is the stuff that matters – it passes the information between bits of grey matter. Increases in white matter are a previously unobserved phenomena, the authors claim. In their study, white matter increased by 5% after the juggling novices had mastered their task.

Juggling isn’t important other than to illustrate the point Heidi Johansen-Berg, who led the team, tells the BBC, the changes they see might apply to any other task that needs to be learned. The AFP suggest the work proves that juggling rewires the brain and the excitement has spread to the British tabloids, (Daily Mirror) which are advocating juggling to increase brain power, which isn’t necessarily the message to take from the study, rather that white matter changes were spotted.

Anyway, I'm off to join the circus.

Image: Photo by dpadua via Flickr under creative commons.

Posted by Katharine Sanderson on October 12, 2009
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Computer giant IBM is the latest company to say it will try to build a DNA sequencing machine. IBM appears to be years behind other companies that are taking similar approaches, but the company's announcement has caused quite a stir among tech journalists.

PC World says that IBM will "expand the life span of humans," while the New York Times' John Markoff predicts that the company will cut the cost of DNA sequencing to under $100, "making a personal genome cheaper than a ticket to a Broadway play."

Sequencing a whole human genome currently costs tens of thousands of dollars at a minimum.

Continue reading "IBM dips toe into DNA sequencing; tech press swoons" »

Posted by Erika Check Hayden on October 06, 2009
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Animal-human hybrid embryo research has been “driven out of Britain”, according to the front page of today’s Independent. However, one of the scientists involved has already cast doubt on the paper’s story.

The paper claims that “all research involving the controversial creation of animal-human ‘hybrid’ embryos has been refused funding in Britain”. It also says that “every one of the three projects to develop embryonic stem cells from cloned embryos created by fusing human cells with animal eggs has now been abandoned”.

Earlier this year the UK bodies responsible for funding (or not funding) such research were forced to deny that moral objections played a part in the rejection of funding applications (see: Moral objections to hybrid embryo research claims rejected).

The three holders of licences for animal-human hybrids in the UK were Stephen Minger, Lyle Armstrong, and Justin St John.

Minger recently departed King’s College London to work in industry (see: Top scientist’s industry move heralds stem-cell shift). When this issue reared its head earlier this year Minger claimed he was misinterpreted by the Independent, which claimed he suggested moral factors were an issue in funding rejections.

Armstrong, says the Independent, has departed Newcastle University for Spain (although no-one at the university’s Institute for Human Genetics was immediately available to confirm this).

Finally, and the apparent trigger for the story, Justin St John is leaving the UK for Australia. In a statement distributed by the Science Media Centre, St John says:

The MRC [Medical Research Council] funded me to make mouse-pig hybrids and I am grateful to them for their support for my work. Hybrid work will continue in the UK. However my hybrid work was a spin off from my main research interest which I will be pursuing at Monash [University in Australia].

Both the Medical Research Council and the Biotechnology and Biological Sciences Research Council also released statements defending their use of peer-review as the best way to approve or reject grant applications. “Having a HFEA licence and legislative approval to conduct certain research does not give an area special treatment,” said Colin Miles, BBSRC’s Head of Integrative and Systems Biology.

Posted by Daniel Cressey on October 05, 2009
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Nature's full news story on this prize is now live: Chromosome protection scoops Nobel

The prize committee notes:

The long, thread-like DNA molecules that carry our genes are packed into chromosomes, the telomeres being the caps on their ends. Elizabeth Blackburn and Jack Szostak discovered that a unique DNA sequence in the telomeres protects the chromosomes from degradation. Carol Greider and Elizabeth Blackburn identified telomerase, the enzyme that makes telomere DNA. These discoveries explained how the ends of the chromosomes are protected by the telomeres and that they are built by telomerase.

The work of these three, says the prize committee, has added a “new dimension” to our understanding of cells and disease and provided a new avenue for treatments (more here).

The committee references three papers for this newly-Nobel winning work: two in Cell and one in Nature.

Congratulations to all, and to the University of California, San Francisco, Johns Hopkins University in Baltimore and the Howard Hughes Medical Institute and Harvard Medical School [corrected 10/5] in Massachusetts which all now have one more laureate on their staff.

This year’s Physiology or Medicine prize is the 100th ever awarded. A full news story on this prize will appear shortly on Nature News. Tune in tomorrow for the physics prize.

The scores so far:

By country of residence
USA - 3

By country of birth
USA – 1
UK – 1
Australia – 1

By journal paper
Cell – 2
Nature – 1

See also
Elizabeth Blackburn - Nature Medicine 7, 520 (2001)

Image top: Alfred Nobel, via wikipedia
Image lower, left to right: Blackburn, Greider, Szostak all by Gerbil, Licensed by Attribution Share Alike 3.0

Posted by Daniel Cressey on October 05, 2009
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Last night Cambridge’s clown school gave the world’s best and brightest the awards they deserved. Harvard University hosted its 19th First Annual Ig Nobel Prize Ceremony, where its Annals of Improbable Research recognized the usual combination of mad scientists and asinine leaders.

Pulling in the biology prize was a Japanese team that discovered pandas are more than just cuddly tax dollar vacuums — their poop packs a potent punch. The group isolated bacteria in panda feces that can reduce kitchen waste by more than 90 percent in mass. Good news, given that pandas produce about 40 pounds of poop a day — and as one might expect, it doesn’t stink.

The Ig Nobel prizes also continued their fascination with skivvies. Back in 2001 the biology prize went to the inventor of panties that filter out flatulence with a replaceable charcoal filter, and this year the public health prize went to the inventors of a bra that can be “quickly converted into a pair of gas masks, one for the brassiere wearer and one to be given to some needy bystander” — in this case that needy bystander was Wolfgang Ketterle, 2001 winner of the Nobel Prize in Physics.

Continue reading "Panda poop, panties and more at the Ig Nobels" »

Posted by Lizzie Buchen on October 02, 2009
Categories: Biology & Biotechnology, Chemistry, Earth, environment & ecology, Financial Crisis, Health and medicine, Physics & Mathematics | Permalink | Comments (2) | TrackBacks (0)

Many Tyrannosaurus rex may have been laid low by a single celled parasite that is still taking down modern birds.

Many tyrannosaurid fossils have multiple smooth holes in their mandibles. These have generally been attributed to either bacterial bone infection or bite wounds.

Now a study published in PLOS One instead points the finger at the trichomonosis parasite. By comparing the lesions seen in fossil dinos to those caused by modern bird maladies and crocodile pox the research team concludes tyrannosaurs were commonly infected with a trichomonas type protozoa.

The population probably became infected through consumption of infected prey, or even through cannibalism, write Ewan Wolff, of the University of Wisconsin, Madison, and colleagues.

Perhaps the most famous victim may have been ‘Sue’, the huge T. rex now on display at the Field Museum in Chicago. “The lesions we observe on Sue suggest a very advanced stage of the disease and may even have been the cause of her demise,” says Wolff (press release).

“It is a distinct possibility as it would have made feeding incredibly difficult. You have to have a viable pharynx. Without that, you won't make it for very long, no matter how powerful you are.”

Field Museum palaeontologist Peter Makovicky told the Chicago Tribune. “It ... reinforces what I and many others thought, that [the jawbone holes] were the result of some kind of pathogen.

He adds, “The problem with ... making a diagnosis of an animal that old is that we know she had many things going wrong with her health. [Sue] was old and beat up, with a large lesion on her left leg that may have slowed her. She could have died simply of old age or had been so weakened by age or injury that some other disease took over.”

Image: artist’s impression of a T. rex suffering from a trichomonosis / Chris Glen, University of Queensland

Posted by Daniel Cressey on September 30, 2009
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The US Food and Drug Administration admitted yesterday that political influence led to the agency's decision last year to approve a device to repair damaged knees against the recommendation of its own scientists.

Since 2006, the FDA's scientific reviewers have twice turned down applications for the device, known as Menaflex and manufactured by ReGen Biologics of Hackensack, New Jersey, according to an FDA report. The company did not show "that patients who received the device experienced any benefit", one scientist wrote in a rejection letter. (AP)

But following persistent lobbying from four New Jersey Democratic congressmen — Senators Robert Menendez and Frank R. Lautenberg and Representatives Frank Pallone Jr and Steven R. Rothman — FDA officials overruled the scientists' advice and granted approval for the US$3,000 knee patch last December. All four legislators received significant campaign contributions from ReGen; for example, Rothman alone took in US$13,300 last year, according to OpenSecrets.org.

The director of the FDA's device division who gave the go-ahead, Daniel Schultz, resigned last month following numerous safety concerns and other scandals. (Reuters)

Continue reading "FDA's review process knee-deep in trouble" »

Posted by Elie Dolgin on September 25, 2009
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With less than two weeks to go until the Nobel Prize winners are announced, the soothsayers at Thomson Reuters have rubbed their crystal balls and come up with a shortlist of favourites.

The contenders, as predicted by Thomson Reuters' citation analyst David Pendlebury, are based on the number of citations and high-impact papers published in Nobel-worthy fields of study. Since 2002, 15 'citation' Laureates have gone on to win Nobel Prizes, seven of which were tapped in the same year as their triumph, including last year’s chemistry champ, Roger Tsien of the University of California, San Diego.

This year’s frontrunners for physiology or medicine include the codiscoverers of telomeres, the repetitive DNA add-ons at the ends of chromosomes that have been linked to ageing and cancer as they shrink, the researchers who worked out cellular membrane trafficking, and the Japanese researcher who showed that magnetic resonance imaging (MRI) could track oxygen flow, making real-time brain scans and functional MRI possible.

Continue reading "Nobel nod" »

Posted by Elie Dolgin on September 24, 2009
Categories: Biology & Biotechnology, Chemistry, Health and medicine, Physics & Mathematics | Permalink | Comments (1) | TrackBacks (0)

Hydrolagus melanophasma is a slippery customer. It is a new species, in that scientists identified it for the first time this month, but it is also an old species, probably branching off from modern sharks 400 million years ago, and collected in jars by museums since the 1960s, writes National Geographic News.

And it was not easy to classify. “They have some shark characteristics and they have some that are very non-shark,” Doug Long of the California Academy of Sciences and an author on the Zootaxa article classifying the species told Wired News. The creature flaps its fins like a ray, is shaped more like a modern shark, and the males feature what Wired News calls a "most intriguing" retractable sexual organ dangling from its head. In fact, the researchers classified it as a member of the chimera order, also known as ghost sharks.

Continue reading "Ghostly shark no longer dead to science" »

Posted by Lucas Laursen on September 23, 2009
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Cross-posted for Monya Baker from The Niche

The Maryland company NeuralStem has the U.S. Food and Drug Administration’s permission to test its spinal cord stem cells in twelve patients with amyotrophic lateral sclerosis. The approval comes a month after the FDA placed Geron’s planned clinical trial on hold for a second time. NeuralStem’s trial had also previously been placed on hold by the FDA in February before receiving the go-ahead in September.

Though both trials involve placing cells into the spinal cord, NeuralStem’s product is made of cultured neural stem cells derived from a single 8-week fetus; Geron’s product, intended to treat spinal cord injury, is derived from embryonic stem cells that have been differentiated into precursors of neuron-support cells.

“This is certainly the first stem-cell approach for ALS,” says Lucie Bruijn, a scientist at the ALS Association, a patient group that also funds relevant research. Most other approaches for treating ALS are small molecule drugs, she says, and she’s not aware of other cell therapy or other invasive approaches entering human testing in the near future.

Continue reading "FDA green lights stem-cell clinical trial for Lou Gehrig’s disease" »

Posted by Lucas Laursen on September 22, 2009
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This giant squid, found by National Oceanic and Atmospheric Administration and the Interior Department's Minerals Management Service scientists during a sperm whale diet study on 30 July, measured 5.9 metres and weighed in at 46.7 kg according to a Reuters report.

See the full post for another photo...

Continue reading "One that didn't get away: giant squid found in Gulf of Mexico" »

Posted by Lucas Laursen on September 22, 2009
Categories: Biology & Biotechnology, Earth, environment & ecology | Permalink | Comments (0) | TrackBacks (0)

The National Institutes of Health started accepting applications today to evaluate which human embryonic stem cells will be eligible for federal dollars.

A panel of nine scientists, lawyers and ethicists — led by Jeffrey Botkin of the University of Utah — will scrutinize submissions to ensure that they meet the new requirements for informed consent from embryo donors. The working group's "expertise and sound judgment will help NIH move forward in this important effort," NIH director Francis Collins, who will have the final say on the eligibility of particular lines, said in a statement.

The panel will review cell lines made before the guidelines went into effect on 7 July. Fundable lines must be derived from leftover embryos that were created solely for assisted reproduction and donated voluntarily with no financial incentives.

"We're open for business in a new era," Lana Skirboll, director of policy at NIH, told Nature. The working group has not yet appraised any cell lines — including the 21 lines approved under former President George W. Bush, which will need to be reassessed — and will start considering particular cells after scientists submit their petitions on the NIH website. "The speed at which this moves is really in the hands of the scientific community at this point," she said.

Having a mechanism in place to expand the number of eligible cell lines "is what we've been working toward for a very long time," said M. William Lensch, a stem cell researcher at Children's Hospital Boston and the Harvard Medical School, who expects to start submitting requests "sooner rather than later."

Image: James Thomson, University of Wisconsin-Madison

Posted by Elie Dolgin on September 21, 2009
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A Yale University animal technician was charged yesterday with murdering the 24-year-old pharmacology graduate student Annie Le, whose body was found behind a wall of an off-campus research facility on Sunday.

The suspect, Raymond Clark III, had been a full-time lab technician since he graduated from high school in 2004, first working in the washing centre and then caring for mice and other animals. In a statement, Yale president Richard Levin said that "nothing in the history of [Clark's] employment at the University gave an indication that his involvement in such a crime might be possible."

But a team leader in the Amistad Street building where Clark worked said otherwise. He told the New York Times that several researchers complained last year to Clark's supervisor that he was rude and overly critical of others. "Everyone enforces rules, but he enforced them in an officious manner," the anonymous man said. Other Yale workers called Clark a "control freak," according to the Associated Press.

Continue reading "Lab tech arrested for Yale murder" »

Posted by Elie Dolgin on September 18, 2009
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Posted on behalf of Kerri Smith

Well, not quite red herrings, but Atlantic salmon. Allow me to explain. Reported on the Neuroskeptic and Neurolaw blogs this week is a study that aimed to demonstrate the risks of finding false positives in brain scanning studies - correlations that aren't really there.

A group of scientists led by Craig Bennett at the University of California at Santa Barbara conducted their study with an unusual participant. From their Methods section:
"Subject: One mature Atlantic Salmon (Salmo salar) participated in the fMRI study. The salmon was approximately 18 inches long, weighed 3.8 lbs, and was not alive at the time of scanning." Warning: below the fold it gets a bit fishy.

Continue reading "Study warns of red herrings in brain scan data" »

Posted by Lucas Laursen on September 18, 2009
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T. Rex's notoriously massive head, sharp teeth and piddly diddly arms first evolved in a runty ancestor one hundredth its size, paleontologists reported in Science yesterday. The nine-foot-long Raptorex kriegsteini lived about 35 million years before its multi-ton descendant, but already bore many of its hallmark features.

The findings come as a surprise for paleontologists, who thought these features evolved as the tyrannosaurids grew to become the colossal beasts we see in the movies — the limbs withering as the head and body expanded. Raptorex throws this idea a pretty nasty curve ball, suggesting that the same body plan could have withstood two orders of magnitude of growth.

The Chicago Tribune give some juicy details of the fossil's shady legal history: The specimen was smuggled out of a fossil field in Inner Mongolia, an autonomous region in northern China, then carted off to an "illegal international black market for fossils." A Massachusetts eye surgeon and amateur paleontologist named Henry Kriegstein (hence the fossil's name) later purchased it (legally) for "tens of thousands of dollars, but well below $100,000", he told the Tribune.

Continue reading "Tiny T Rex ancestor still pretty scary" »

Posted by Lizzie Buchen on September 18, 2009
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The makers of Creation, a British film about the life of Charles Darwin, have attracted as much attention for saying it won't be shown in the US as they might have hoped to get from a creationist protest at a hypothetical US premiere. Today, Nature hosted a screening of the film at the Science Museum in London with members of the production team.

The film, which opened the Toronto Film Festival over the weekend, premiered in the UK Sunday. It was adapted from the book Annie's Box, a novel by Randal Keynes, Darwin's great-great-grandson, about Darwin's personal life. But rumors that it won't reach the US have set off a cascade of debate, ranging from blaming religious conservatism to simply guessing that the film wouldn't sell. The Daily Telegraph led Friday with a quote from the film's producer, Jeremy Thomas: "It has got a deal everywhere else in the world but in the US, and it's because of what the film is about."

Continue reading "Creating a controversy" »

Posted by Lucas Laursen on September 16, 2009
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Maori legends told of a giant predatory bird called the Te Hokioi, whose wingspan approached the length of a full-grown man and whose prey included human beings. Now Kiwi scientists are adding to the legend by claiming that a skeleton found in the 1870s shares some of the legendary bird's traits.

"We don't think it carried off men and women but it could well have carried off children," says Paul Scofield, who along with colleagues at the Canterbury Museum in Christchurch published a report in the Journal of Vertebrate Paleontology indicating that the extinct Harpagornis moorei swiftly evolved wings 3 metres across and weighed in at 18 kilograms, twice the size of today's largest living eagle, soon after its arrival on New Zealand's South Island.

Continue reading "Kiwi scientists add to Maori man-eating bird legend" »

Posted by Lucas Laursen on September 15, 2009
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A blind listening test at a forestry conference suggests that foresters, at least, prefer a modern violin made from fungus-treated wood to an original Stradivarius.

Last year Francis Schwarze of the Swiss Federal Laboratories for Materials Testing and Research in St Gallen published results suggesting that treating wood with fungus might help recreate the unusually low density that prevailed when Antonio Stradivari carved his legendary instruments.
(Nature News, 16 June 2008)

Schwarze teamed up with luthiers (violin-makers) to build violins with the treated wood, along with some control copies made from untreated wood. At a blind competition in the German city of Osnabrück on 1 September this year, 180 attendees of a German forestry conference (Osnabrücker Baumpflegetagen) rated the test violins and an original Stradivarius played by British violinist Matthew Trusler (World Radio Switzerland, 1 September 2009). One of the fungus-treated violins, called "Opus 58" garnered 90 votes for the best sound, with the Strad second at 39, according to a press release.

Blind violin identification is notoriously difficult: In a BBC test in 1974, experts were only able to correctly identify 2 of 4 instruments, and confused a modern instrument with a Stradivarius. Schwarze noted that the fungus treatment might make violins which sound like Strads, at least to foresters, for as little as 25,000 Swiss francs (World Radio Service, 10 September 2009).

Photo: The 5 violins in the competition. By Egmont Seiler.

Posted by Lucas Laursen on September 15, 2009
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One of the first researchers to clone animals and another who first reprogrammed skin into stem cells have been awarded the 2009 Albert Lasker Basic Medical Research Award — a $250,000 accolade that is often seen as a prelude to a Nobel Prize.

John Gurdon, a developmental biologist at the University of Cambridge, UK, was the first to show that the vast majority of the body's cells retain the ability to become any other cell type even after they have committed to a particular developmental fate. In 1962, Gurdon, then at Oxford University, transferred the nucleus of an adult intestinal cell into a hollowed out egg cell of the South African clawed frog, Xenopus laevis, to create the first cloned animal. This work paved the way for the cloning of other animals including Dolly the sheep by the technique known as somatic cell nuclear transfer.

More than four decades later, Shinya Yamanaka of Kyoto University in Japan and the Gladstone Institute in San Francisco, California, showed that the developmental clock could be turned back on cells even without the use of eggs. In 2006, Yamanaka introduced four genes — which have come to be known as the "Yamanaka factors" — into mouse skin cells to transform them into induced pluripotent stem cells, or iPS cells, which are almost indistinguishable from embryonic stem cells. A year later, Yamanaka achieved the same feat in human cells.

Continue reading "Stem cell pioneers take home Lasker" »

Posted by Elie Dolgin on September 14, 2009
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Darwin’s On the Origin of Species is the keystone text for evolutionary theory; now you can see how the book itself evolved, thanks to Ben Fry.

Fry is the director of information design company Seed Visualization and he has constructed a rather wonderful graphic that shows the changes in the book over its six editions.

“We often think of scientific ideas, such as Darwin's theory of evolution, as fixed notions that are accepted as finished,” writes Fry. “In fact, Darwin's On the Origin of Species evolved over the course of several editions he wrote, edited, and updated during his lifetime.”

Fry’s other scientific information design projects include a redesign of genetic code diagrams and illustrations of the relationships between different genomes. He was also behind the rather cool Nature HapMap cover.

His Traces graphic allows to you not just to watch the changes accumulate as time passes – and editions are published – but also to see where words and passages have been added into the text (image left).

“The idea that we can actually see change over time in a person’s thinking is fascinating,” says Fry. “Darwin scholars are of course familiar with this story, but here we can view it directly, both on a macro-level as it animates, or word-by-word as we examine pieces of the text more closely.”

Traces uses text from The Complete Work of Charles Darwin Online, run by John van Wyhe.

Hat tip: Flowing data

Posted by Daniel Cressey on September 07, 2009
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The Biogen Idec boardroom battle continues to rage on. Mere months after billionaire activist investor Carl Icahn succeeded in getting two of his endorsed directors elected to the board, two of the Cambridge, Massachusetts-based company's scientific directors have resigned. In July, Phillip Sharp, a Nobel Prize-winning geneticist at the Massachusetts Institute of Technology and the co-founder of Biogen, relinquished his spot on the board after serving for 27 years. And last month, Cecil Pickett, president of research and development, announced that he would retire from both his full-time day job and the board on 5 October. Both men were not due to step down until 2011.

Nature spoke with Pickett about his decision to resign prematurely. (Sharp declined to be interviewed.)

Did Carl Icahn's attempted takeover of the board influence your decision to retire early?

Not really, the plan all along was just a four-year tenure. That's how I went into it. I cut my job short because I just thought I had accomplished everything I could in the timeframe I had actually given it. We did a lot to build up the mid-stage pipeline and the small molecule discovery efforts, we did some licensing deals, and I did some significant recruiting where there were some weak spots. And given all the flux in the industry I thought it might be a good time to go out and recruit my successor.

Continue reading "Biogen Idec R&D head talks" »

Posted by Elie Dolgin on September 02, 2009
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Cross-posted from The Niche

Differentiated human cells have been reprogrammed to an embryonic-like state with the addition of only one gene, rather than the standard four. The research, published in Nature, should advance techniques for the efficient production of high-quality patient-specific stem cells.

The ability to make induced pluripotent stem (iPS) cells using cells from specific patients could enable unprecedented new ways to study disease and also ease the development of cell therapies. However, such applications have been stymied in part because making induced pluripotent stem cells efficiently requires the introduction of pluripotency genes, which are typically inserted at random sites throughout the genome. This unwanted source of variation stymies rigorous comparisons between cells, and could make them behave in unpredictable, dangerous ways if used for cell therapies. Several techniques to make cells without permanent insertion of the genes have been reported, including some that do not use genetic material at all.

See: Human iPS cells with no genetic integration; Virus free pluripotency for human cells; Integration-free iPS cells; Reprogramming to pluripotency without genetic engineering; Generation of human induced pluripotent stem cells by direct delivery of reprogramming proteins

However, researchers are eager for additional, ‘gentler’ ways to reprogram cells, and one possibility would be starting with cells that are more prone to reprogramming. Evidence in mice suggests that the tissue of origin affects how often and how well differentiated cells reprogram. See: Cell origin and variation in induced pluripotent stem cell lines; Stomach and liver cells reprogrammed

Scholer and colleagues reasoned that neural cells would be a good candidate, since these cells already express high levels of three of the four standard pluripotency factors (Sox2, Klf4 and c-myc). The team had previously shown that this strategy worked in mice. The researchers used viruses to insert copies of the fourth pluripotency factor, Oct4, into the cells. This produced reprogrammed cells that passed all standard tests of pluripotency.

The current study reprogrammed neural stem cells from human fetal tissue. While adult tissues tend to be more difficult to reprogram, and brain biopsies are difficult to obtain, Scholer and colleagues say they are already working out practical solutions. More-accessble cells, such as those found in dental pulp, might also be good candidates.

Posted on behalf of Monya Baker

Posted by Mark Peplow on August 28, 2009
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The culprit responsible for delaying the first-ever clinical trial involving human embryonic stem cells has been identified: microscopic spinal cysts.

Last week, the US Food and Drug Administration put the brakes on Geron Corp's clinical trial in spinal cord injury because of just-completed animal studies that raised red flags. The Menlo, California-based biotech company announced Thursday that the animals developed microscopic cysts in the injury site. These lumps, however, did not spread to other parts of the body and none of the animals developed tumours. A second concluded study showed no cysts in spinal cord injured rats, according to a Geron press release.

“I think it provides people with a reasonable explanation,” said Stephen Brozak, an analyst with WBB Securities LLC in Westfield, New Jersey. “Everybody was afraid of the T- word, teratomas, and it clearly wasn’t that.” (Bloomberg)

Analysts rejoiced at the news. Geron shares rose more than 3% yesterday, closing higher than any day since the clinical hold was announced.

Geron is now working with the FDA to relaunch the stalled trials, the company said. No date was set.

Posted by Elie Dolgin on August 28, 2009
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Women with high levels of testosterone are more likely to make risky financial decisions, according to research published this week. The finding, reported in Proceedings of the National Academy of Sciences, is another twist to the controversy over ‘traders’ testosterone’.

Women are generally more risk averse than men, says Dario Maestripieri, of the University of Chicago. Maestripieri’s team had 550 MBA students play financial computer games to determine how risky their behaviour was. They also measured the students’ levels of testosterone.

Higher levels of testosterone meant less aversion to risk in women, but not in men, they found. In addition, and perhaps unsurprisingly, testosterone levels and risk aversion appeared to predict career choice with those high in the former and low in the latter being more likely to choose risky careers in finance.

“This is the first study showing that gender differences in financial risk aversion have a biological basis, and that differences in testosterone levels between individuals can affect important aspects of economic behaviour and career decisions,” says Maestripieri (press release).

Previous research has linked testosterone levels to success in trading (see: The testosterone of trading). However, any female traders reading this should be dissuaded from artificially boosting their testosterone levels to compete in the markets; another study in women found that raising their levels of testosterone made no difference to how risky their behaviour was (see: Testosterone boost doesn't fuel risky behaviour in women).

Some papers have inevitably managed to make this research about sex, given testosterone's links to sex drive, and are suggesting that women who are risky may also be risqué.

When published, the PNAS article will be available here.

Image: punchstock

Posted by Daniel Cressey on August 25, 2009
Categories: Biology & Biotechnology, Financial Crisis | Permalink | Comments (0) | TrackBacks (0)

After almost three-and-a-half years, the trial of Korean stem-cell researcher Woo Suk Hwang may be drawing to a close.

In two seminal papers published in Science in 2004 and 2005, Hwang claimed to have created patient-specific embryonic stem cells using cloning techniques. In January 2006, a committee at Seoul National University, where Hwang held a post, found that the results were all fabricated.

On 24 August this year, in a final evidence hearing, prosecutors requested a four-year prison term for Hwang, who is charged with fraud, embezzlement of state funds and violation of the country’s bioethics law. Hwang has continually claimed he was duped.

Korean media report that the court is expected to hand down a decision in mid-October.

Posted by Daniel Cressey on August 24, 2009
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Posted for Mico Tatalovic

That you can extract ink from a 150 million old squid-like fossil and still use it to draw is pretty cool and so it caused a bit of a media frenzy this week.

Phil Wilby, a researcher at the British Geological Survey who is behind the discovery of the fossil and the subsequent drawing, ground the solidified, black ink from a fossil of an ancient squid like animal (Belemnotheutis antiquus) and then mixed it with ammonia to create a paint then used to draw a picture of the animal. This might suggest that the ancient ink has similar properties to modern ink, something that awaits confirmation from Yale University in America where it was sent for an in-depth chemical analysis, after which the results will be published.

Wilby told Nature that “fossil cephalopod ink has been found in even older specimens (more than 300 million years old) and, counter intuitively, appears to be amongst the most frequently fossilised soft tissues.”

Continue reading "Drawing with ancient ink" »

Posted by Daniel Cressey on August 19, 2009
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Cross posted for Monya Baker from The Niche, Nature's stem cell blog

Six months after giving it the green light, the US Food and Drug Administration has told Geron to put plans for a clinical trial in spinal cord injury on hold. The company has differentiated embryonic stem cells into precursors of cells known as oligodendrocytes, which help keep neurons alive. Geron hopes this cell product could promote healing in people who have recently severed their spinal cords.

In a press release, Geron said that the hold was placed after the company submitted data on animal studies done to support delivery of increased doses of its cell product and on animal studies applying the cell product to other neurodegenerative diseases. (See the story from the San Jose Mercury News; here’s the Nature story when trial won approval)

I asked Evan Snyder, who directs the stem cell program at the Burnham Institute and is not privy to the confidential information, to speculate what might have been in the preclinical data that prompted teh FDA's action. It’s possible that the FDA just wanted more time to review newly submitted data, he said. Or on the other end of the extreme perhaps some sort of tumour or adverse reaction had been observed in the animals. Most likely, he thought, given that the company is trying to make larger doses of the cells, is that undifferentiated or non-neural cells have been observed in the cell product.

Clinical holds are not unusual particularly for innovative therapies. The FDA issued a clinical hold for NeuralStem in February on a trial in Lou Gehrig’s disease (the company uses neural stem cells derived from fetal cells)

At a large FDA advisory committee meeting in April last year, experts discussed the risks and benefits of products derived from embryonic stem cells. They were particularly concerned about uncontrolled cell growth. Even if the cells are not cancerous, tumours in the contained spaces of the brain and spinal cord could be devastating. Committee members were particularly concerned for diseases that are debilitating but not immediately deadly, since adverse events caused by experimental procedures could mean that people with years to live die early or end up suffering more. Patient advocates protested that they should be allowed to decide whether to take that risk.

Previous posts
Overview of FDA meeting (includes links to transcripts)
Nitty-gritty questions for making safe products

Posted by Daniel Cressey on August 19, 2009
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Rub-a-dub-dub, three men in a hub -- of scientific commercialization. Cellular Dynamics International (CDI), a Madison, Wisconsin-based company founded by stem cell pioneer James Thomson, announced this week that it has recruited two of the world's most prominent biologists to its scientific advisory board: genomics guru George Church and systems biology trailblazer Leroy Hood. Church and Hood are not generally known for an interest in the fast-moving field of stem cell research, but they are jumping on-board the personalized medicine bandwagon.

“Stem cells have the potential to transform 21st century medicine -- perhaps in a manner similar to antibiotics in the 20th century,” said Hood, president of the Institute for Systems Biology in Seattle, in a statement.

“The commercial opportunity associated with human iPS cells is rapidly becoming complementary and/or competitive,” said Harvard University's Church in a statement.

Continue reading "A dynamic trio" »

Posted by Elie Dolgin on August 14, 2009
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The genomics blogosphere is abuzz over allegations that a purchasing decision of next-generation sequencing machines was politically motivated. In a November 2008 letter sent to a UK House of Lords select committee, Kevin McKernan, senior director of scientific operations at Applied Biosystems (ABI), cried foul at the Sanger Centre's decision to return five of ABI's SOLiD System machines in favour of the platform developed by Illumina/Solexa.

The letter accused Sanger researchers of bearing a grudge against ABI because of its Craig Venter-tinged connections in the race to sequence the human genome. McKernan also asserted that the institute leadership took "a more historical approach" in its decision to go with more Illumina Genome Analyzer sequencers, noting that many Sanger staff members have close ties with the rival company.

Nick Loman of the University of Birmingham ridiculed this claim. "Calling the approach historical is slightly ironic given that ABI used to be the only show in town and the Sanger had over a hundred ABI machines running during the [Human Genome Project]," he wrote on the blog Pathogens: Genes and Genomes. Moreover, Solexa, which Illumina acquired in January 2007, was headquartered in Cambridgeshire, and many of their former workers turned Hinxton, UK-based Sanger staff stayed close to home, Loman noted.

Continue reading "A rock SoLiD complaint?" »

Posted by Elie Dolgin on August 14, 2009
Categories: Biology & Biotechnology, Policy | Permalink | Comments (1) | TrackBacks (0)

Stanford University engineer Stephen Quake has added his name to the growing list of people who have had their individual genomes sequenced.

Quake did it using a machine made by a company he co-founded, Helicos Biosciences of Cambridge, Mass. J. Craig Venter was the first scientist to sequence his own genome; six other individual human genomes have been published and others have been sequenced by private companies.

Quake describes his achievement in a paper in Nature Biotechnology, in which he reports that he sequenced his genome with the help of two other scientists and read out 90 percent of his genome, or 2.5 billion base pairs. Quake estimated that it cost $48,000, not including the cost of the sequencing machine itself, which approaches nearly $1 million. Stanford University purchased a Helicos sequencing machine last year at an undisclosed price.

Continue reading "Live nude genes: another scientist bares his genome to the world" »

Posted by Erika Check Hayden on August 11, 2009
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Posted for Mico Tatalovic

Rooks can figure out how to use tools to get the food floating at the bottom of a long tube, just like their relative does in Aesop’s ancient fable The Crow and the Pitcher, according to a new study published in Current Biology. Zoologists report that rooks, which do not usually use tools in the wild, were able to size up the problem and solve it by using stones as tools.

The experiments echo Aesop’s fable, published more than 2,000 years ago, where a crow drops stones into a pitcher to raise the water level so it can quench its thirst. The experiment here involved a bird figuring out how to get to its favourite food item – the larvae of a wax moth, because the researchers couldn’t deprive the birds of water for ethical reasons.



Nathan Emery, co-author of the paper, from Queen Mary University of London, said: "The rooks have to put multiple stones in the tube until the worm floats to the top." And when they were presented with rocks of different sizes, they went for the larger ones that get the worm out quicker. "They are being as efficient as possible," Emery told the BBC.

Emery’s co-author is the appropriately named Christopher Bird, who has previously featured on the Great Beyond for his 2008 paper ‘Using video playback to investigate the social preferences of rooks’.

This study adds to the growing evidence that corvids, like great apes, have evolved a problem-solving intelligence requiring a general understanding of physical rules.

More videos below the fold.

Continue reading "Rooks with rocks prove Aesop right" »

Posted by Daniel Cressey on August 07, 2009
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Posted for Mico Tatalovic

Pterosaurs may have been able to fly just as well as birds, thanks to their complex wing fibres, according to a paper published this week in Proceedings of the Royal Society B.

An international team of scientists used a new technique involving shinning ultra-violet light on fossils of the pterosaur Jeholopterus ningchengensis to study in detail the fossilised tissue structure. They found that their wings contained several layers of fibres to control movement, and not just a single layer as previously thought.

“The configuration observed in Jeholopterus might have allowed subtle changes in the membrane tension during flight, resulting in more control of flight movements,” write the authors in their paper.

They also found that hair-like fibres covered pterosaurs’ body and wings. “They are different from other furs we find in mammals and they provide us another hint that these animals were able to control their body temperature, they were hot-blooded animals,” says Alexander Kellner, a palaeontologist at Brazil's National Museum in Rio (Reuters).

The finer aspects of pterosaur flight are still a mystery. Some of these animals weighted 250kg and scientists have previously suggested they had to run on all four legs to get off the ground. Others were tiny creatures (with wing span of just 25 cm), likely living in trees and hanging on with their claws.

But new fossils of pterosaurs are still being found (http://blogs.nature.com/cgi-bin/mt/mt-search.cgi) and although some have already inspired biomechanical flying robots it looks like we’ve still got a lot to learn about these extinct animals.

Image: Jeholopterus ningchengensis under natural and UV light / Xiaolin Wang

Posted by Daniel Cressey on August 06, 2009
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The complex shapes that the HIV genome twists itself into have been totally mapped by the first time by a team of US researchers.

RNA viruses such as HIV like to fold themselves up and a proper picture of the shapes they form has been lacking, with researchers generally confining themselves to looking at small sections. In this week’s Nature, Joseph Watts, of the University of North Carolina, and his colleagues set out to look at the bigger picture.

In a News and Views article accompanying the research paper, Hashim Al-Hashimi of the University of Michigan, Ann Arbor, notes that structural biologists usually “cut out” the motifs formed by RNA and then “zoom in to determine their three-dimensional structures in an attempt to further understand their function. … However, Watts et al. zoom out and provide an ‘aerial view’ of the secondary structure of the entire HIV-1 genome.”

What they produced is, in Wired’s words, “the cellular equivalent of a rough wiring diagram”.

“What this may reveal is some of the proteins operating at a level below the structures, which may have all sorts of functions within the virus,” says David Robertson, of the University of Manchester (BBC). “More generally, if we can unpick the structures then we can compare the systems of different viruses and gain new understanding of how they work.”

Study author Kevin Weeks says the technique used here with HIV could also be applied to other virus such as influenza and might open up new opportunities for drug treatments (press release).

Posted by Daniel Cressey on August 06, 2009
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Posted for Mico Tatalovic

Arachnophobes may want to think twice before checking out the new 3D models of “scary ancient spiders” released today.

Russell Garwood, of Imperial College London, and his colleagues, used a new technique called high-resolution X-ray micro-tomography to scan two fossilised specimens of 300 million old arachnids called Cryptomartus hindi and Eophrynus prestvicii to produce the 3D computer models of what these creatures would have looked like. The aim of their study, soon to be published in Biology Letters, was to use the physical traits of these extinct animals to reveal how they lived (press release).

For example, from seeing that C. hindi's first two legs were angled towards the front of the body, they deduced that it used these limbs to grab prey, suggesting it was an ambush predator. It may have been much like modern day crab spiders, which wait for insect prey at the edge of the flowers before grabbing them with similarly positioned legs.

The study also indicates that many of the morphological features seen in these ancient animals still exist in modern day relatives and some could even be used to provide evidence for evolutionary relatedness of some of these organisms. This new X-ray technique could be used to re-analyse already studied fossils to provide a clearer picture of how ancient extinct species lived and has “the potential … to revolutionise the study” of many fossils, Garwood’s team write.

Image: Cryptomartus hindi / Natural History Museum and Imperial College London

Posted by Daniel Cressey on August 05, 2009
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The US National Academies has launched its long-awaited review of the scientific evidence used to track down the alleged creator of the deadly anthrax attacks of 2001. A 15-member expert panel met in Washington DC on 30-31 July to determine whether the Federal Bureau of Investigation (FBI) relied on appropriate scientific techniques when it implicated government biodefence researcher Bruce Ivins, who committed suicide last July as prosecutors prepared to indict him as the person responsible for mailing the Bacillus anthracis spores that killed five people and sickened 17 others.

"It is important that we understand what happened," Representative Rush Holt (D-NJ) told the committee on Friday. "The illogic of the investigation that I witnessed leads me to question whether the scientific and technical steps were well undertaken."

Continue reading "Anthrax investigation probe underway" »

Posted by Elie Dolgin on July 31, 2009
Categories: Biology & Biotechnology, Policy | Permalink | Comments (2) | TrackBacks (0)

Posted for Mico Tatalovic

It seems counterintuitive, but a paper published in Nature raises the possibility of losing weight by injecting fat cells.

In the paper American researchers describe using a molecular switch – two proteins PRDM16-C/EBP-beta – to turn mouse and human skin cells into brown fat cells (paper, press release).

White fat cells store fat, while brown fat cells use those stores to produce heat. Heavier people seem to have more white fat but less brown fat than slim people, so one idea for treating obese people is to increase stores of the energy-burning fat. Until now this could not be done since making brown fat was a mystery.

“Brown fat is one of the body’s natural defenses against obesity,” said cell biologist Bruce Spiegelman of Harvard Medical School, who co-authored the paper. “We’re trying to tap into a natural pathway involved in this kind of biology.” (Wired.)

Continue reading "Fighting fat with fat " »

Posted by Daniel Cressey on July 30, 2009
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A former SLAC National Accelerator Laboratory researcher who allegedly destroyed $500,000 worth of protein crystals earlier this month was arrested and charged on Monday for willfully ruining government property.

The 4,000 to 5,000 now-useless protein crystals represented a “whole variety of different samples” involved in the Protein Structure Initiative, a federally-funded project to expedite the discovery of atomic-level protein structures, says Ian Wilson, director of the Joint Center for Structural Genomics (JCSG), which oversees the initiative. Some crystals were aimed at matching three-dimensional protein structures with their corresponding DNA sequences; others were part of targeted research projects including the Human Microbiome Project and efforts to map every protein made by the bacterium Thermotoga maritima.

Continue reading "Vandal destroys protein crystals in California" »

Posted by Elie Dolgin on July 29, 2009
Categories: Biology & Biotechnology, Chemistry, Policy | Permalink | Comments (5) | TrackBacks (0)

How do orangutans swing through the trees? Carefully.

That awful joke takes us smoothly into the first of two studies today on the science of swinging.

First up: in a paper published in PNAS three researchers describe their work on how Sumatran orangutans move on spindly branches that appear incapable of holding their hefty weight. It seems that the animals carefully avoid setting up resonance effects of the kind that causes bridges to wobble when people march in step across them.

“We found that certain locomotor behaviours clearly are associated with the most compliant supports; these behaviours appear to lack regular limb sequences, which serves to avoid the risk of resonance in branch sway caused by high-frequency, patterned gait,” write the authors.

“Balance and increased stability are achieved through long contact times between multiple limbs and supports and a combination of pronograde (horizontal) and orthograde (vertical) body postures, used both above branches and in suspension underneath them.”

While the fact that orangs move through trees by gripping multiple branches and not using regular movements may seem obvious, the animals do differ from other primates, which often suspend themselves below branches rather than carefully balancing their way through, say the authors. Smaller animals also have to worry less about those resonance effects.

Continue reading "Man vs Orang in swinging science" »

Posted by Daniel Cressey on July 29, 2009
Categories: Biology & Biotechnology, Earth, environment & ecology | Permalink | Comments (1) | TrackBacks (0)

Here’s one way in which candy might be good for you. A chemical dye similar to the compound that gives a blue hue to some types of Jell-O and M&Ms could protect injured spinal cords from further damage. Researchers at the University of Rochester Medical Center in upstate New York found that rats injected with a dye called Brilliant Blue G (BBG) recovered from spinal injury and regained the ability to walk, albeit with a limp, whereas control rats remained paralyzed. The only side effect: the rats turned blue.

The finding came five years after the research team first reported in Nature Medicine that adenosine triphosphate (ATP), a vital energy metabolite, surges at the site of spinal injury to overstimulate and stress nerve cells. The Rochester researchers targeted an ATP receptor, which mitigated the spinal damage, but the ATP blocker was too large to cross the blood-brain barrier and had to be injected directly into the site of the wound — a less-than-desirable treatment for spinal cord patients. So the researchers went on the hunt for compounds with a similar structure, and they happened upon BBG. Publishing online today in the Proceedings of the National Academy of Sciences, Maiken Nedergaard and her colleagues show that the blue dye can be given intravenously to reduce the size of spinal lesions and to improve motor skills.

This could be a boon for a new field of culinary neuroscience, hinted Nedergaard. “One of the reasons no one had done this before is that food science is very separate from neuroscience. Those two fields don’t interact at all.” (Wired) Nedergaard noted that the average American ingests about a teaspoon of blue dye each year, so the compound is likely safe for consumption. Even so, while humans might eat enough dye to turn their tongues blue, “the levels ingested in food stuffs don't make us go blue,” said Mark Bacon, head of research at the British charity Spinal Research. (BBC) “What is safe at one dose may not be safe at higher doses,” he cautioned. No need to run to the sweetshop quite yet, it seems.

Posted by Daniel Cressey on July 28, 2009
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A multi-million refurb on the site at the epicentre of the UK’s 2007 foot-and-mouth disease outbreak has done a Lazurus and come back to life.

Earlier this year plans to do up the Institute for Animal Health at Pirbright to the tune of £120 million appeared to have been scuppered when the Department for Environment, Food and Rural Affairs backed off (see: Britain hits a hurdle in replacing key animal-pathogen facility).

But yesterday the Government announced it would be funding a £100 million overhaul, with investment from a different sector, the newly formed Department of Business, Innovation and Skills. The money will allow the institute to implement the recommendations of reviews produced in the wake of the foot-and-mouth outbreak, including new labs (press release).

“What I hope is that it will give confidence to all our stakeholders that here at Pirbright we have the world’s leading experts. That it will be state-of-the-art and it will be as safe as it can possibly be,” says institute director, Martin Shirley (BBC).

The funding, says Shirley, is also a recognition of the “increasing threats” posed by animal diseases such as … err … foot and mouth.

Previous Pirbright
Britain hits a hurdle in replacing key animal-pathogen facility – Nature News, 10 February 2009
Setback for key UK animal lab – Nature News, 5 December 2008
British government tightens up lab biosecurity – The Great Beyond, 10 October 2008
Anybody know a good plumber? – The Great Beyond, 07 September 2007

Posted by Daniel Cressey on July 28, 2009
Categories: Biology & Biotechnology, Earth, environment & ecology, Policy | Permalink | Comments (0) | TrackBacks (0)

Posted for Lizzie Buchen

Researchers in the newly emerging field of synthetic biology need to explain their science to the public to avoid unwarranted fears over its potential, an international group of researchers warned this week.

Public education and engagement are two of most important challenges facing the field, which aims to build biological components with potentially useful functions, they told a symposium held at the US National Academy of Sciences. But the relatively new discipline also presents a unique opportunity for public outreach, according to keynote speaker Arden Bement, Jr, director of the National Science Foundation: “we have the chance to get it right at the outset”.

Continue reading "‘Shiny happy biology’" »

Posted by Daniel Cressey on July 10, 2009
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The UK government announced £150 million of investment for small technology firms by way of a venture capital initiative on 29 June, to general approval from venture capitalists, and particularly the biotech industry, who had been lobbying for support.

The newly-created UK Innovation Investment Fund will invest in a collection of other venture capital funds thereby ultimately boosting investment in start-ups and spin-outs - in life sciences, clean technology, digital sciences and advanced manufacturing, according to prime minister Gordon Brown. A private-sector fund manager will choose where the money goes, and first funds are due by the end of the year.

"We need the Google or Genentech of the future and they will only be created if there is the capital to back them," said science minister Paul Drayson (Wall Street Journal).

Continue reading "£150 million ventured, shot-in-the-arm for UK biotech gained?" »

Posted by Richard Van Noorden on June 30, 2009
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Roche has decided it is tired of having its name prefixed with the words ‘pharma giant’. In response, the company is bailing out of the pharmaceutical industry associations in both the UK and the US.

Instead, it will be signing up with the US Biotechnology Industry Association (BIO). The move follows the company’s merger with biotech firm Genentech earlier this year for around $46 billion.

“As part of the world's largest biotechnology company, Genentech and Roche believe that BIO’s purpose is closely aligned with the direction of the new company and, therefore, can represent the company’s interests in Washington, among policymakers, legislators and the general public,” said the company (AP).

Farewell big pharma, hello big biotech.

Continue reading "Roche: we’re not pharma anymore" »

Posted by Daniel Cressey on June 30, 2009
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deCODE Genetics, a biotechnology company based in Reykjavik, Iceland, has been relisted on the NASDAQ Global Market stock exchange, the company announced last Friday.

deCODE is famous for its aggressive pursuit of DNA sequence variations linked to human disease, and aims to use this information to develop diagnostic tools and uncover new drug targets. Last October, its steadily declining stock price combined with a crashing market to drive the company's market capitalization (a measure of a company's worth, based on share price) below the $50 million minimum required to be listed on the NASDAQ Global Market stock exchange. (See 'Icelandic biotech feels the pinch', subscription required.) At that time, CEO Kari Stefansson said management was restructuring the company. The stakes were high -- in November, one analyst told Nature (subscription required) that if deCODE didn't find a way to boost their financial position, the company had little chance of surviving to see 2009.

But the company has lived on (and continued to crank out high profile genome-wide association studies). The decision to relist deCODE reverses a February decision to bump the company to the NASDAQ Capital Market, which generally lists companies with smaller market capitalization. deCODE hasn't released information about what might have spurred the change of heart -- the company's market capitalization still hovers around $37 million, and that's including the ~33% bump in stock price following last week's announcement.

Posted by Heidi Ledford on June 30, 2009
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Biologic drugs should face the same generic competition as standard pharmaceuticals after seven years, aides of US president Barack Obama have stated.

Be they called bio-similars, bio-generics, follow-on biologics or something else, products derived from biotechnology have been a hot topic in the US recently. Obama has come down somewhere between the extremes currently proposed for these drugs.

Democratic House rep Henry Waxman proposed legislation that would give biotech drugs just five years of exclusivity before other companies could muscle in. Another rep, Republican Anna Eshoo, put forward a proposal offering 12 years.

Now Bloomberg has obtained a letter from Nancy-Ann DeParle, director of the White House Office of Health Reform, and Peter Orszag, director of the Office of Management and Budget, pushing for a “generous compromise” on seven years.

“Lengthy periods of exclusivity will harm patients by diminishing innovation and unnecessarily delaying access to affordable drugs,” they wrote.

Continue reading "Biosimilars: Obama’s seven year pitch" »

Posted by Daniel Cressey on June 29, 2009
Categories: Biology & Biotechnology, Chemistry, Policy | Permalink | Comments (0) | TrackBacks (0)

Last year Nature’s Phil Ball wrote about the amazing parrot Snowball, the first animal to be scientifically proven to dance. Earlier this year the research was published, to great media interest.

Now a video has surfaced of Snowball dancing with some of the world’s leading bird biologists at the recent World Science Festival (55 seconds in to the clip below).

The struttin’ scientists (as ID by The Scientist) are: Duke University's Erich Jarvis, University of Cambridge's Nicola Clayton, Brandeis University's Irene Pepperberg, and City College New York's Ofer Tchernichovski.

Personally, I think Snowball has the best moves.

Posted by Daniel Cressey on June 23, 2009
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This is a drill, actual inventory procedures may vary.

It's a fact of lab life that stuff gets lost in the shuffle. Digging up that old data spreadsheet or lab notebook is probably not too much more than an inconvenience for most researchers. But if you happen to work at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) at Fort Detrick in Fredrick, Maryland then it's a lot more serious than that.

At a press conference yesterday Col. Mark Kortepeter, USAMRIID's deputy commander told reporters that a recent inventory had turned up some 9,300 vials of previously uncatalogued pathogens, including serum samples from patients who had contracted hemorrhagic fever during the Korean War. The inventory also turned up Ebola, plague, anthrax, and botulism. Most of the samples were left by researchers who had since retired from the laboratory.

The report was bound to get tonnes of press, in part because USAMRIID is the former employer of Bruce Ivins, a researcher who the FBI named a "person of interest" in the 2001 anthrax attacks. Ivans died of a Tylenol overdose in July of 2008. This February, it emerged that Venezuelan equine encephalitis virus at the lab had gone unaccounted for, and all work was suspended until this inventory was completed.

Officials told reporters that numerous new security measures have been installed at the lab since 2001, and they've instituted an "aggressive" inventory system to ensure that future samples don't go unnoticed. It's clear that USAMRIID hopes to use this event to draw a line under its recently troubled past.

Image: US Army/ArraySarah

Posted by Geoff Brumfiel on June 18, 2009
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Woolly mammoths roamed the UK far later than is normally believed, according to a paper published today in the Geological Journal.

Adrian Lister, of the London Natural History Museum, says new carbon dating of bones first excavated in 1986 also shows climate change, rather than humans hungry for mammoth steak, may have been behind their eventual extinction.

“Mammoths are conventionally believed to have become extinct in North Western Europe about 21,000 years ago during the main ice advance, known as the 'Last Glacial Maximum',” says Lister (press release). “Our new radiocarbon dating of the Condover mammoths changes that, by showing that mammoths returned to Britain and survived until around 14,000 years ago.”

This new date ties in with the takeover of grassy plains by forests. Mammoths preferred plains and were not very good in forests, as their tusks would get tangled in the branches (possibly).

Continue reading "Mammoths around longer than thought" »

Posted by Daniel Cressey on June 18, 2009
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Eli Lilly, the Indiana-based pharmaceutical company perhaps best known for developing Prozac, has offered to conduct preliminary drug screening of compounds developed in academic labs. The company will screen the compounds using in vitro assays against Alzheimer’s disease, diabetes, cancer, and osteoporosis -- all for the low, low price of getting the first shot at subsequent licensing deals or collaborations.

Lilly’s latest move is another sign of big pharma’s increasing creativity as it prowls academic labs for new early drug leads. Although broad agreements between universities and industry make some uneasy, pharma’s hunger for pipeline-replenishing drug candidates comes as funding agencies pressure academics to translate their results into therapies that will provide a clinical benefit. (See, for example, ‘Chemical screening centers get funding boost’ and 'Flagship drug-development initiative picks projects'; subscription required). The result: more collaboration between the two sectors.

For Lilly’s latest endeavor, called the Phenotypic Drug Discovery programme (PD2), the company hammered out a universal material transfer agreement that would be signed by institutions, sparing researchers the hassle of negotiating individual agreements. The company also claims that the identity of submitted compounds will be kept secret, even from Lilly’s own researchers, by a special computer algorithm. According to The Scientist, about 65 institutions have already signed up.

Posted by Heidi Ledford on June 17, 2009
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Who can resist a study that shows stress really does make your hair turn grey? Sadly the latest paper from Emi Nishimura has not found a link between, say, your office environment and the number of your colleagues sporting salt and pepper hairstyles.

Rather, in the latest issue of Cell, Nishimura and colleagues report that ‘genotoxic stress’ from ionising radiation damages DNA in the melanocyte stem cells that give mouse hairs their colour.

“It is estimated that a single cell in mammals can encounter approximately 100,000 DNA damaging events per day,” says Nishimura, of Tokyo Medical and Dental University (press release). “Once stem cells are damaged irreversibly, the damaged stem cells need to be eliminated to maintain the quality of the stem cell pools.”

Rather than causing the death of these stem cells, the damage makes them differentiate to form mature melanocytes instead of more stem cells, meaning nothing is left to dye the next growth of hair. So, mice exposed to radiation in their study turned permanently grey.

This may even be a mechanism to prevent damaged stem cells becoming cancerous.

“Greying may actually be a safety mechanism, that’s a cool twist,” David Fisher, of the Massachusetts General Hospital told Bloomberg. “They’ve shown that this mechanism is actually removing damaged stem cells. The good news is if you do find yourself greying, you’re probably better off not having those cells persist.”

Stress watch
“When an aging mouse's lovely brown fur turns grey, she can now officially blame stress — at least, the kind of stress that damages DNA” – CBC
“If you’ve ever blamed your gray hair on stress, you weren’t far from the truth” – Science
“We've all heard that stress causes gray hairs. Now, new research suggests it’s true” – LiveScience

Image: Ken Inomata

Posted by Daniel Cressey on June 12, 2009
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Cross-posted for Monya Baker from The Niche

Transplants of a fetal neural stem cell product seem safe, according to a 12-month study on six children with a horrible neurodegenerative disease called neuronal ceroid lipofuscinosis or Batten disease. Furthermore, the company reported results from an autopsy of a treated patient who died from the disease. (See Girl dies in stem cell trial for Batten disease ). These indicate that the injected cells engraft and survive in the brain for close to a year.

Whether cells can survive after transplant is considered a crucial requirement for whether many cell therapies can work at all, and StemCells Inc, the company sponsoring the trial, explicitly thanked the child’s parents for allowing the autopsy to be performed.

Batten disease is a progressive neural degenerative disease in which brain cells poison themselves because they lack a crucial enzyme that clears away unnecessary fats and proteins. The hope is that transplanted cells can make enough of the enzyme to stall toxic build-up in the host cells as well.

As is typical in clinical trials, the small study, which lacked a control group, was not designed to assess whether the experimental procedure could help patients, only whether or not it would harm them. A summary of data and results can be found in this press release. Each patient received injections to 8 spots in the brain totaling approximately 500 million or a billion cells. Adverse events were reported, but none could be attributed to the stem cell injections.

Continue reading "StemCells clinical trial results: Cells survive, seem safe" »

Posted by Katharine Sanderson on June 10, 2009
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Posted on behalf of David Cyranoski

On Monday 8 June, the Jang Yeong-sil Memorial Foundation wanted to give cloning expert Woo Suk Hwang an award for scientific excellence. But according to The Korea Herald, Hwang had another appointment - with the Seoul district court that is still, after more than 3 years, trying to figure out if his scientific fraud is legally actionable.

An official from the foundation said, "Even though he is on trial, we have made our decision by considering his achievements in the embryonic stem-cell development and his success in cloning dogs." One might contest both those points. Investigation into Hwang’s embryonic stem-cell research left little to believe in after picking away the layers of fabrication.

And the successful dog cloning is largely credited to another scientist, Byeong Chun Lee, who was also at the hearing and, like Hwang, is under investigation for fraud related to their previous experiments.

Lee and Hwang have since ended up on opposite sides of another court case - over the patents related to dog cloning.

Posted by Mark Peplow on June 09, 2009
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Termites and other pests are challenged by microbial invaders like bacteria and fungi. So, why can’t our enemies’ enemies be our friends?

Ram Sasisekharan and his colleagues from the Massachusetts Institute of Technology looked to some termite immune molecules, particularly a gram negative bacteria binding protein tGNBP-2 that is used by the wood chewers to fend off infections, for a way to create new pesticides.

tGNBP-2 recognizes carbohydrates associated with infectious microbes, and also cleaves the structure, alerting the immune system to the pathogen. Termites have the protein in their cells, but also secrete it and infuse their nests with it. The researchers found a modified glucose molecule that can bind to an active pocket of tGNBP-2 and deactivated it. This molecule, D-δ-gluconolactone (GDL) made termites more susceptible to subsequent infection with the fungus Metarhizium anisopliae in lab tests. The insects were also more susceptible to opportunistic infections.

See all the gory coverage at The Scientist, The Telegraph and in National Geographic News.

Kudos to The Scientist (full disclosure: they are my former employers), for getting some needed words of caution from a pathologist/entomologist who has experience in pest control.

Image: Turning Termite from Anauxite under creative commons.

Posted by Brendan Maher on June 09, 2009
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It’s that time of year again – the annual battle for control of Biogen Idec, one of the grande dames of biotech. And today’s installment did not disappoint.

For those of you who haven’t been glued to the Biogen soap opera, here’s a quick catch-up: Biogen is one of the oldest biotechnology companies and arguably the founder of the Cambridge, Massachusetts biotech cluster. The company chugged along for nearly thirty years until 2007, when billionaire ‘corporate raider’/’shareholder activist’ (depending on whose side you’re on) Carl Icahn became one of Biogen’s largest shareholders. With an eye on the multi-billion dollar prices pharmaceutical companies were paying for biotech firms, Icahn immediately tried to force Biogen executives to sell the company. The execs put the company on the market for a few months, then shrugged and said they couldn’t find any takers. Icahn didn't buy that: he accused Biogen of lying to investors and interfering with the search for a suitor, and then sued the company for access to records pertaining to the failed sales attempt. (More details available here, subscription required.) After that, Icahn riled Biogen executives again when he lobbied for the company to be split into two. “Once again, Icahn and his associates have demonstrated that they fundamentally do not understand our business,” board chairman Bruce Ross and CEO James Mullen wrote in a letter to shareholders.

Which brings us to today. In what promises to become a yearly tradition, Icahn tried to forcefully take hold of Biogen’s board of directors by nominating four of his associates to the board. (He tried this approach last year as well, and failed.) Biogen was to tally voting results today at the annual shareholder’s meeting, which started at 9am, but then Ross unexpectedly announced a recess until 2pm. The delay prompted an outcry from Icahn’s posse, with one of his nominees reportedly protesting, “This isn’t North Korea.” When the meeting rejoined in the afternoon, Ross said votes were still being tallied and winners would not be announced until later this month. Before the afternoon was over, Icahn had called Biogen's behavior "sort of despicable" (Boston Globe), declared victory for two of his nominees (although no official vote tallies have been released) and, of course, filed another lawsuit against the company.

What did the shareholders decide? What will Icahn try next? How long will Biogen survive as an independent company? All of this and more, to be continued…

Posted by Heidi Ledford on June 03, 2009
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Posted for David Cyranoski

Researchers in China have made pluripotent stem cells from a pig. The cells could be useful for making humanized pig organs for transplant to humans, pig models of human disease useful testing drugs, and for improving pig farming productivity and nutritional value.

Lei Xiao, head of the research group at the Shanghai Institutes for Biological Sciences where the research was done, admits that none of these will happen for the next several years. But his creation in pigs of induced pluripotent stem (iPS)-cells which share with embryonic stem cells the ability to differentiate into any cell type in the body-is still a huge accomplishment. (Paper).

The isolation and culture of embryonic stem (ES) cells from mice in 1981 revolutionized the use of mice as a developmental and biomedical research model. But it is a difficult process. It took 17 years to culture human iPS
cells. Even now there are ES cells for only four mammals: mice, humans, monkeys, and rats. Pig ES cells, despite many attempts, still do not exist.

Continue reading "Forget swine flu-bring on the humanized pigs!" »

Posted by Katharine Sanderson on June 03, 2009
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Deuterium drugs have hit the big time. Concert Pharmaceuticals, a start-up company based in Lexington, Massachusetts, US, which specialises in swapping hydrogen atoms on known drugs for deuterium atoms, (Nature, subscription required) has signed a deal worth potentially $1 billion with pharma giant GlaxoSmithKline.

The company, which was founded in 2006, will develop 3 drugs with GSK: a protease inhibitor to treat HIV, a drug for chronic renal disease and a third mystery product. The company will also do their deuterium magic with 3 of GSKs pipeline products. They get $35 million upfront, with future payments being made for milestones reached and more upfront payments. (Press release).

The news has gone big, with pick up in major news outlets, (AP, Wall Street Journal, FierceBiotech) and GSK’s shares fell slightly after the deal was announced (Reuters).

In future the patent field around deuterating known drugs is likely to get murky, as Derek Lowe points out in The Atlantic but for now it looks like Concert is sitting pretty in its deuterium world.

Posted by Katharine Sanderson on June 02, 2009
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Yesterday Nature published a paper heralding the birth of the first transgenic non-human primates - in other words a genetically modified adult gave birth to offspring that inherited the modification.

Their birth offers to researchers the chance to use more human-like models for disease than the currently-favoured mice, or rhesus macaque (another monkey disease model, but one in which transgenic offspring have never been produced). The marmosets have been born expressing the gene for green fluorescent protein (GFP). The neat thing about GFP is that it’s easy to spot – the marmosets have green feet under UV light.

But also, and this might be why they received just quite so much coverage, these marmosets are unbelievably cute.

Favourite headline/standfirst of the day came from WA Today, with “The green Monkeys are coming / They’re monkeys but not as we know them”

Coverage was generally positive, although NPR ran a story about 50 years since monkeys were sent to space, with a disturbing picture.

The cuteness of the animals will undoubtedly give animal activists new ammunition, and this warning is covering in an editorial to accompany the paper.

Continue reading "Marvellous marmosets" »

Posted by Katharine Sanderson on May 28, 2009
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Rooks can't bend spoons with their minds just yet, but they did bend wires using their beaks to hook food in a recent study (video here, large file).

Led by the appropriately named Chris Bird, this experiment adds rooks, a member of the Corvid family, to the list of animals that create and use tools. Unlike most known tool-using species, such as chimpanzees or other types of crows, rooks do not appear to use tools in the wild. Previous studies have shown that capuchin monkeys are more likely to resort to tool use in labs than in the wild.

Rooks may simply be too lazy to bother making tools in the wild, write the study authors: "Rooks exploit a number of different, readily-available food sources, such as seeds, insects, carrion, and refuse and as such may lack the motivation to use tools in the wild."

The researchers also argue that the tool-making is an example of an original insight, since the birds in the study were hand-raised and had neither seen other birds attempt the task, nor practised the task themselves before solving it.

They add that the finding adds to evidence that birds may have independently evolved a kind of problem-solving intelligence comparable to primate intelligence.

The paper should be available on this link by the end of the week:
http://www.pnas.org/cgi/doi/10.1073/pnas.0901008106

Headline watch
Rook with a hook proves bird brains are the equal of monkeys' - Daily Mail
Clever rooks have plenty to crow about - Irish Times
Rooks are not so bird-brained - Daily Telegraph
Caw blimey! Rooks can make tools - Cambridge News

Image: PNAS

Posted by Lucas Laursen on May 26, 2009
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...and it's not a director's cut of David Attenborough

According to a Nature paper that's receiving some pickup (Reuters, CSM ) the history of life on earth may just have got roughly 15% longer. That may not sound a huge difference, but a 15% extension on life's lease adds up to 600 million years -- roughly equivalent to the time taken for animals to get from creepy little things that couldn’t even crawl to your pet cat.

There were no animals on earth, though, during the 600 million years in question. The paper by Oleg Abramov and Stephen Mojzsis [link fixed] at the University of Colorado is about the earliest life, not the latest. Previous research has suggested that the heavy rain of asteroids, comets and the like that characterised the early solar system would have made the earth too hazardous a place for life to persist until after what is known as the "Late Heavy Bombardment" some 3.9 billion years ago. Impacts by large objects, it was thought, would vapourise whole oceans and wrap the earth in an atmosphere of superheated steam which would sterilise the planet.

The model developed by Abramov and Mojzis tells a different story. Pretty much everywhere on the planet gets zapped by a big rock, often more than once – but there are never any occasions where the whole planet including all the subsurface is simultaneously uninhabitable. If life had got started during this time, they argue, it could have persisted ever since.

At present the first evidence for life comes right after the Late Heavy Bombardment, about 3.8 million billion years ago. The speed with which that life developed after the bombardment has been seen by some as evidence that life is implicit in the way the universe is set up, and will arise spontaneously PDQ wherever it gets the chance. If it took 600 million years, though, then one would have to start thinking that life is relatively unlikely, which obvioulsy has implications for astrobiology.

It may still be the case that life arose as soon as it could, right at the beginning of the earth's history – but it is going to be harder to prove it. While bacteria may have been able to survive the horrible early history of the earth, rocks were not so lucky – there are no major bits of crust left over from back then.

In a related happy accident, this week Nature also has a fine feature on Mike Russell and his research on the metabolism-first approach to the origins of life.

Image: simulation of the state of the Earth at the end of Late Heavy Bombardment. Circles are crater locations; colors show temperature / Oleg Abramov

Posted by Oliver Morton on May 21, 2009
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Yesterday's announcement of a 47-million-year-old primate fossil nicknamed "Ida" has provoked a large, if uneven, media response.

A press release entitled "WORLD RENOWNED SCIENTISTS REVEAL A REVOLUTIONARY SCIENTIFIC FIND THAT WILL CHANGE EVERYTHING" got reporters’ attention last week, after a pair of earlier scoops (which Nature blogged) revealed that the finding was an unusually intact primate fossil dating to 47 million years ago, a time when most primates looked more like squirrels than people.

The fossil’s official announcement yesterday came one week ahead of the US premiere of a television documentary unashamedly entitled “The Link”. A book by the same title appeared on US and UK bookshelves today, after waiting Harry Potter-style in sealed boxes, wrote the New York Times. The Times labeled the furore “science for the Mediacene age”.

Scientists and others have expressed admiration for the find and contempt for its reception in many media outlets.

Continue reading "Missing link, evidence thereof - media analysis" »

Posted by Lucas Laursen on May 20, 2009
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Posted for David Cyranoski

Korean newspapers are reporting that Woo Suk Hwang and his research group are trying to get back in the big leagues by doing in pigs what he had once claimed to do in humans.

The once-famed cloner and now famed fraudster has been running the Sooam Biotech Research Centre, funded with private money, outside of Seoul for a couple years now.

On 15 May, Hyun Sang-hwan, identified as "Hwang's key colleague" told the Korea Times that they had succeeded in creating a cloned pig embryo, extracting stem cells from it, and establishing lines of self-reproducing cloned cells from them.

Continue reading "New Hwang cloning claim" »

Posted by Daniel Cressey on May 18, 2009
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With the help of some carefully chosen words to the Daily Mail and a belated "Oops, I've said too much" to the Wall Street Journal, a team of researchers and public relations virtuosos have attracted extraordinary attention to a primate find.

Philip Gingerich, the Director of the University of Michigan's Museum of Paleontology and Jørn Hurum of the University of Oslo will reportedly publish a peer-reviewed article about a new primate skeleton found in Germany with the Public Library of Science tomorrow. The timing coincides with the opening of a related exhibition at the American Museum of Natural History in New York hosted by Mayor Michael Bloomberg and a BBC documentary hosted by Sir David Attenborough, according to the Wall Street Journal and Daily Mail articles.

Continue reading "Missing link, evidence thereof" »

Posted by Lucas Laursen on May 18, 2009
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The United States Department of Agriculture (USDA), which regulates animal research in the US, has found animal welfare lapses at the New Iberia Research Centre.

The Humane Society carried out an undercover investigation of the centre, which is run by the University of Louisiana in Lafayette, and filed a complaint to the USDA, according to a statement . The Humane Society investigator claimed to have recorded videos of animal handlers allowing sedated primates to fall to the ground, and video of animals with open wounds.

The USDA confirmed that a March inspection found "evidence of several issues with the facility’s compliance with Animal Welfare Act (AWA) standards" and problems with "review and approval of research protocols." This included a number of African Green Monkeys whose tails had been amputated due to trauma or frostbite, reports The Scientist, in part because their enclosure was inadequately heated.

Violators of the Animal Welfare Act can get warning letters, fines or lose their licenses. In this case, the USDA is working with the centre administrators to improve animal care standards. A follow-up visit in late April found that most of the issues identified on the USDA's March visit had been addressed.

Previous coverage on The Great Beyond: Primate mistreatment allegations at Louisiana research lab - March 05, 2009

Posted by Lucas Laursen on May 13, 2009
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Count Lennart Bernadotte of didn’t quite make it to 100. He died in 2004 at the age of 95, but not before ensuring that his life’s great project had a future. Great grandson of King Oscar II who presented the first Nobel awards in Stockholm in 1901, Count Lennart launched, exactly sixty years ago, the Nobel Laureates Meeting in Lindau, a pretty but very provincial town on Lake Constance. The original aim of the weeklong meetings was to encourage isolated and struggling scientists and doctors in post-war Germany by bringing them into social contact with great living scientists from around the world.

Over the next 55 years or so, not a lot changed, even though Germany was no longer isolated or struggling. The meetings – morning lectures, afternoon discussions, evening dances - were popular but remained anachronistically provincial. By the turn of the millennium that had become unsustainable. Laureates were becoming less interested in a long trip to speak with locals at meetings primarily conducted in German, however charming the location.

In 2005, the meetings were internationalised and thrust into the modern world (Nature 436, 170-1). Now 600 hand-picked students from all around the world mingle, discuss and dance with 20 or more Nobel laureates during summer.

To commemorate the centenary of Count Lennart’s birth on 8 May, the Meetings organisers set up a science-history project to digitalise selected lectures from their archives and make them openly available on their webpage (www.lindau-nobel.de). The first eleven selected lectures are now live, more will follow in phases throughout the summer.

The cleaned up voice recordings, accompanied by an introduction and charming black-and-white photos taken in Lindau, bring legendary scientists to life – be it Rita Levi Montalcini (Physiology or Medicine, 1986) pushing her human-rights agenda, Rosalyn Yalow (Physiology or Medicine, 1977) appealing to women to help solve social problems or simply the extraordinary plumminess of the British tones of Lawrence Bragg (Physics 1915) and Dorothy Crowfoot Hodgkin (Chemistry 1964). A particular treasure is the lecture on the gravitational constant by Paul Dirac (1933, Physics). Dirac was renowned for being almost pathologically socially withdrawn. Despite this, he showed up to the first ten meetings in Lindau, where, they say, he remained almost silent aside from his lectures.

Coming soon – Werner Heisenberg, Konrad Lorenz, James Watson and other stellar personalities.

Image: Nobel Laureate Dorothy Crowfoot-Hodgkin (Chemistry 1964) and young researchers at
the Lindau Nobel Laureate Meeting 1986.

Posted by Alison Abbott on May 11, 2009
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Last year the European Court of Human Rights told the UK government it couldn’t keep the DNA of innocent people on its police database. Today the UK government announced how it would deal with the ruling, in a response that basically amounts to two fingers to the court.

Home Secretary Jacqui Smith, who has already been beset by controversy this year, wants to keep DNA profiles of innocent people arrested but not convicted of serious violent or sexual crimes for 12 years. Innocent people arrested but not convicted of other crimes would be kept for six years.

Opposition party shadow Home Secretary Chris Grayling said, “The government just doesn’t get this. People in Britain should be innocent until proven guilty.” (Reuters.)

Civil liberties groups and opinion writers have also reacted with outrage to the proposals.

Continue reading "UK will retain DNA of innocent accused" »

Posted by Daniel Cressey on May 07, 2009
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The UK’s charming Royal Botanic Garden at Kew in London is 250 years old.

To celebrate this anniversary our hereditary ruler the Queen and her consort the Duke of Edinburgh are visiting, and the former will be presented with a new specially bred thornless rose called the Kew Gardens.

In an event the UK’s republican types will doubtless consider symbolic, the pair will also plant two living fossils at the gardens, according to the Daily Telegraph:

The Queen will plant a Ginkgo, an ancient tree known as a "living fossil" which is now native only to a small area of central China. Prince Philip will plant a Wollemi pine, also known from fossil records. It was thought to be extinct until it was rediscovered in Australia in 1994 and it is now part of an international conservation programme.

It is to be hoped that these planting go better than the royal couple’s last additions to the gardens, as the Times notes:

The royal couple’s last official visit to Kew Gardens was 50 years ago for its 200th anniversary when they both planted trees. The swamp cypress planted by the Duke in front of Kew Palace is doing extremely well, but it is understood that the Queen will learn only today that the walnut tree she planted was a victim of the 1989 storms.

Even Google is getting in on the celebrations, with a special graphic on its UK homepage.

Posted by Daniel Cressey on May 05, 2009
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Back in June last year Nature’s own Philip Ball reported on new research showing that a male sulphur-crested cockatoo named Snowball really can dance:

Aniruddh Patel of The Neurosciences Institute in La Jolla, California, and his colleagues say that Snowball’s ability to shake his stuff is much more than a cute curiosity. It could shed light on the biological bases of rhythm perception, and might even hold implications for the use of music in treating neurodegenerative disease.

Patel and colleagues videoed Snowball’s movement to music and slowly altered the tempo of his tunes. Statistical analysis showed that he was synching to the beat. Now Patel’s research has been published in Current Biology, and the world’s media has gone predictably crazy.

“People are not the only ones who've got rhythm – birds can also get into the groove claim scientists,” says the Daily Telegraph. “Parrots join humans on the dance floor,” says NPR. The Daily Mail says Snowball’s musical taste is “questionable” as he generally dances to the Backstreet Boys, a fact that has led the Sun to brand him “Beakstreet Boy”.

Here’s what you all want to see:

See: Birds that boogie, 25 June 2008, for more.

Posted by Daniel Cressey on May 01, 2009
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Posted for Rex Dalton

The plankton record doesn’t lie. And again it is showing that the meteor that created the Chicxulub impact crater in Mexico didn’t cause the Cretaceous/Tertiary [KT] mass extinction, says Gerta Keller – the Princeton University paleontologist whose group has been a primary questioner of the widely accepted theory that the asteroid wiped out the dinosaurs and most life 65 million years ago.

As researchers were wrapping up last week’s European Geosciences Union meeting in Vienna, Austria, the Keller group is publishing an article April 27 online in the Journal of the Geological Society, London, [JGSL 166, 393-411 2009 doi: 10.1144/0016-76492008-116] on its latest data in support of its view that the impact occurred 300,000 years before the KT mass extinction. Keller’s work also is among research discussed last weekend at a post-EGU workshop on Austrian geological sections of the KT.

The article focuses on stratigraphy in northeastern Mexico, in particular a site called El Penon outside Monterrey in the state of Nuevo Leon that is about 1,200 kilometres from the impact location on the Yucatan Peninsula. At El Penon, Keller and colleagues located a line of the spherules reflecting blast material from the Yucatan impact. Looking above and below this spherule-laced section, Keller checked the fossil record of foraminifera that are used to chart life around mass extinctions.

Below the spherule line, they found 52 foraminifera species – and above the line after the impact the same 52 species were abundant. “We found not a single species went extinct as a result of the Chicxulub impact,” says Keller. This means the Chicxulub impact couldn’t have been the sole event causing the extinction, she says.

Continue reading "Plankton undermine dino extinction theory" »

Posted by Daniel Cressey on April 27, 2009
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Researchers and students staged a rally on the UCLA campus yesterday in support of animal research.

The rally was organised by the new University of California, Los Angeles branch of Pro-Test, a UK group founded in Oxford which supports animal research. A group of about 40 animal rights protesters held a rally opposite the Pro-Test event, which attracted over 400 people, according to the Los Angeles Times.

UCLA neuroscientist David Jentsch, the victim of a car bombing last month, founded UCLA Pro-Test. The North American Animal Liberation Press Office posted a 'communiqué' from a group calling itself the Animal Liberation Brigade taking credit for the attack and threatening to harm Jentsch.

"I hope this rally lessens the sense of helplessness and fear that has pervaded our community," Jentsch said (UCLA newsroom). "We’re just not going to take the harassment anymore."

Nature also interviewed him last week.

A member of UCLA's Animal Law Society told a Science reporter that violence gave other animal rights activists "a bad name."

No arrests have been made in the car bombing case yet, though the FBI did report arrests in other animal rights-related cases this week and in February. The FBI is offering a reward of $75,000 for information leading to an arrest and conviction in the Jentsch case.

Video below the fold.

Continue reading "California animal researchers protest protesters" »

Posted by Lucas Laursen on April 23, 2009
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A potential ‘missing link’ in the evolution of seals has been discovered. A new fossil described in Nature shows features suggesting it was semi-aquatic, but had not yet fully accepted the sea as its home.

Named Puijila darwini, the animal has the long tail and limbs of a terrestrial carnivore but other features, such as indications of webbing on the feet, suggest an affinity for water. Previously the earliest pinniped – the group that includes seals, sea lions and the walrus – was an animal that already had flippers.

According to Natalia Rybczynski, of the Canadian Museum of Nature, interviewed on the Nature Podcast, the animal was “something like a river otter, but much more muscular” and was “almost a wolverine that could hunt on land and also in water” around 21 and 24 million years ago.

“The remarkably preserved skeleton of Puijila had heavy limbs, indicative of well developed muscles, and flattened phalanges which suggests that the feet were webbed, but not flippers,” says paper author Mary Dawson, of the Carnegie Museum of Natural History (press release). “This animal was likely adept at both swimming and walking on land.”

Continue reading "Flippin’ heck! Proto-seal discovered" »

Posted by Daniel Cressey on April 23, 2009
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Panayiotis Zavos does not shy away from media attention. The fertility specialist has told The Independent that he has been trying to implant human embryos using material cloned from living individuals. Everybody from the Indy's local competition to outraged scientists and sober wire services have weighed in.

Zavos has attempted to implant 11 human embryos in four women since 2003 according to The Independent, and a Discovery Channel film-maker who has witnessed the process and whose television programme premieres tonight at 9pm:

The cloning was recorded by an independent documentary film-maker who has testified to The Independent that the cloning had taken place and that the women were genuinely hoping to become pregnant with the first cloned embryos specifically created for the purposes of human reproduction.

Zavos has previously attempted controversial cloning-related treatments and attracted the ire of other fertility researchers in 2004, when he announced a result ahead of academic publication. Zavos, born on Cyprus but a naturalized US citizen, reportedly carries out his cloning attempts in the Middle East to avoid anti-human cloning laws in other countries.

He also claims to have spliced tissue from a dead child with an embryo from a cow as a learning exercise, though he has not attempted to implant the hybrid embryo. The child's mother reportedly wouldn't mind if he did. While none of these attempts with living cloned material have succeeded, his group plans to try again with 10 younger couples, according to the Indy.

Posted by Lucas Laursen on April 22, 2009
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An animal rights activist has been added to the FBI’s Most Wanted list, ranking him among terrorists such as Osama Bin Laden and Ayman Al-Zawahiri.

Daniel Andreas San Diego is wanted for allegedly bombing two biotechnology facilities near San Francisco, says the FBI. He is the first US ‘domestic terrorist’ to make the Most Wanted list.

Both of the buildings bombed were apparently targeted for doing business with Huntingdon Life Sciences, a company that has long been targeted by animal rights extremists.

“San Diego is a known San Francisco Bay-area animal rights extremist, involved with the Stop Huntingdon Animal Cruelty campaign, commonly referred to as SHAC,” says Michael Heimbach, assistant director of the FBI’s Counterterrorism Division (statement). “We continue to make great strides in dismantling animal rights and environmental extremists, like Daniel Andreas San Diego.”

According to Heimback, animal rights and environmental extremists have committed over 1,800 criminal acts and caused over $110 million in damages. A reward of up to $250,000 is on offer for information leading to the location and arrest of San Diego, who is considered armed and dangerous.

Coverage
Animal rights activist on FBI terror list – SF Chronicle
In defense of people – Chronicle editorial
Vegan Daniel Andreas San Diego who tried to close British animal lab is put on FBI list – (London) Times
Wanted: FBI Adds Environmental Terrorist to Most-Wanted List – WSJ Environmental Capital blog

Image: detail from FBI wanted poster

Posted by Daniel Cressey on April 22, 2009
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Rock ants refuse to live in any old hole in the ground, and researchers from the University of Bristol have been finding out how they choose between a des res and a hovel.

Temnothorax albipennis have been previously shown to pick the better of two potential nest sites even when it is nine times further away from their current abode than the less salubrious residence. If ants decide a nest site is a good place to settle down they often return to their soon-to-be former home and recruit friends.

A nest is chosen by the number of ants in a potential nest reaching a quorum, but most ants appear not to visit both sites, say Elva Robinson and her colleagues.

They fitted micro-transmitters to every worker ant in nine colonies housed in artificial nests. Each colony contained between 100 and 200 workers and larvae. The team destroyed the ants' homes and gave them a choice of a good, far-away site and a worse, closer site to move to. Chip readers on both potential nests recorded ant coming and goings.

“Each ant appears to have its own ‘threshold of acceptability’ against which to judge a nest individually,” says Robinson (press release). “Ants finding the poor nest were likely to switch and find the good nest, whereas ants finding the good nest were more likely to stay committed to that nest.”

This contrasts with previous assumptions that ants compare nests, the team write in Proceedings of the Royal Society B. Ant house hunting isn’t perfect though, in this study only four of the nine colonies chose the far-away, ‘good’ nest, with three putting up the 'home sweet home' signs in the poor site and two splitting in half and moving into both.

Coverage
Tracking bugs so tiny they fit an ant – Sun
Transmitters show house-hunting ants have gift for locating a des res – Times
Ants 'go further for better nest' – PA
Ants' home search habit uncovered – BBC

Photo: Elva Robinson

Posted by Daniel Cressey on April 22, 2009
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The Union of Concerned Scientists has released a report attacking big farma's claims that genetically modified crops produce a higher yield per cultivated acre than traditional crops.

The report [pdf] examines academic reports of crop yields over a 20-year period, including 13 years of real-world commercial results in the US. Author Doug Gurian-Sherman attributes most yield gains in most crops to technique, not genes:

Overall, corn and soybean yields have risen substantially over the last 15 years, but largely not as result of the GE traits. Most of the gains are due to traditional breeding or improvement of other agricultural practices.

Gurian-Sherman also distinguishes between intrinsic yield, which is an idealized measure, and operational, or real-world yield. Genetic engineering only improved operational yields for corn modified with genes from Bacillus thuringiensis, a bacteria which helps the corn resist certain pests, he writes.

An industry group has responded with its own release claiming that "marker-assisted breeding has nearly doubled the rate of yield gain when compared to traditional breeding alone" and pointing out that a growing number of farmers are adopting genetically modified strains of crops.

Gurian-Sherman concedes that farmers may find certain modified crops easier to work with, but that this does not directly translate into an improved yield or a wider benefit to society.

Related in Nature News: Germany banned a breed of genetically-modified corn yesterday, joining a handful of other European countries in contradiction of EU law.

Photo: Seabamirum on Flickr

Posted by Lucas Laursen on April 15, 2009
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In January, an in-press article criticizing the statistical methodology of social scientists using fMRI to back their hypotheses caused a major stir. The no-holds-barred paper claimed that many published papers are worthless because brain imaging data have been inappropriately analysed.

Those scientists personally attacked were not only upset by the content. They were also offended by the title which referred to ‘voodoo correlations’. Many argued that they were not only well aware of the importance of good statistical practice, but also used it.

The editor of the journal in question, Perspectives in Psychological Research, has now said the final version to be published in May will appear with a more circumspect title: ‘Puzzlingly High Correlations in fMRI Studies of Emotion, Personality and Social Cognition’. The authors, Edward Vul from MIT and Harold Pashler from the University of California, San Diego and their colleagues also answer the specific criticisms they received in response to the widely circulated original version in an accompanying paper.

Posted by Alison Abbott on April 14, 2009
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US scientists today report preliminary data on a brain imaging study they say may help lead to the identification of a ‘footprint’ of post-traumatic stress disorder (PTSD) in the brain. Rajendra Morey, director of the neuroimaging lab at Durham Veterans Administrative Medical Centre, and his colleagues are presenting results of their study on 42 US soldiers who had recently served in Iraq or Afganistan at the World Psychiatric Association International Congress on Treatments in Psychiatry in Florence. Journalistically speaking, the group of probands is attractive, and so the study has been press-released in advance.

One group of 22 suffered from PTSD while a second group of 20 did not. Using an experimental paradigm designed to indicate how easily distracted the soldiers were, the neuroscientists showed that there were differences between the two groups of soldiers in activation of a brain area called the dorsal lateral prefrontal cortex, a region they say is associated with the ability to maintain vigilance. The