Interesting Things

From a Cell press release:

Researchers have shown that they can create entirely new strains of infectious proteins known as prions in the laboratory by simply mixing infectious prions from one species with the normal prion proteins of another species. The findings are reported in the September 5th issue of the journal Cell, a Cell Press publication.

” The data demonstrate that PMCA is a valuable tool for the investigation of the strength of the barrier between diverse species, its molecular determinants, and the expected features of the new infectious material produced,” the researchers concluded. “Finally, our findings suggest that the universe of possible prions is not restricted to those currently known but that likely many unique infectious foldings of the prion protein may be produced and that one of the sources for this is cross-species transmission.”

This research makes it extremely clear that there is an inherent risk in feeding one species to another. As prions are believed to be able to cross the blood brain barrier, if you eat an animal that has infectious prions, even if those prions are not capable in and of themselves of infecting you, there is a risk that they will interact with your own prions to create a whole new variety of infectious prion protein that CAN harm us. Perhaps this is how Creutzfeldt-Jakob disease originated.

The sensible thing to do is to take great care in ensuring our food animals are free of prion disease, all the way down their food chain. Cattle feed is often surprisingly high in animal protein. Feeding animal protein to herbivores seems to me to be an entirely unnecessary risk factor in disease transmission. Equally, just because a prion disease is not known to be transferable in the traditional sense, does not mean that we should be eating infected deer or rabbits.

The North Carolina Department of Agriculture has a handy guide for removing all the parts of a deer that are especially high in prions.

Oh dear. There’s rather a lot of them.

Durham University is predicting that the UK, already famous for being a rather damp place, is likely to get moister still in the coming years.

Expert predicts ‘Monsoon Britain’

In terms of river flooding, the period since the early 1960s and until the late 1990s appears to be relatively flood free, especially when compared with some periods in the late 19th century and early 20th Century. As a result of analysing rainfall and river flow patterns, Prof. Lane believes that the UK is entering a flood rich period that we haven’t seen for a number of decades.

He said: “We entered a generally flood-poor period in the 1960s, earlier in some parts of the country, later in others. This does not mean there was no flooding, just that there was much less than before the 1960s and what we are seeing now. This has lowered our own awareness of flood risk in the UK. This has made it easier to go on building on floodplains. It has also helped us to believe that we can manage flooding without too much cost, simply because there was not that much flooding to manage.”

Flooding is one of the issues covered by the Institute of Hazard and Risk Research at Durham University where Prof. Lane is a resident expert. The IHRR, which launches this week, is a new and unique interdisciplinary research institute committed to delivering fundamental research on hazards and risks and to harness this knowledge to inform global policy. It aims to improve human responses to both age-old hazards such as volcanoes, earthquakes, landslides and floods as well as the new and uncertain risks of climate change, surveillance, terror and emerging technologies.

Cerro Paranal, home of ESO’s Very Large Telescope, is certainly one of the best astronomical sites on the planet. Stunning images, obtained by ESO staff at Paranal, of the green and blue flashes, as well as of the so-called ‘Gegenschein’, are real cases in point.

The Earth’s atmosphere is a gigantic prism that disperses sunlight. In the most ideal atmospheric conditions, such as those found regularly above Cerro Paranal, this will lead to the appearance of so-called green and blue flashes at sunset. The phenomenon is so popular on the site that it is now the tradition for the Paranal staff to gather daily on the telescope platform to observe the sunset and its possible green flash before starting their long night of observations.

The green and blue flashes are fleeting events that require an unobstructed view of the setting Sun, and a very stable atmosphere. These conditions are very often met at Paranal, a 2635m high mountain in the Chilean Atacama Desert, where the sky is cloudless more than 300 days a year. Paranal is home of ESO’s Very Large Telescope, an ensemble of four 8.2-m telescopes and four 1.8-m Auxiliary Telescopes that together form the world’s most advanced optical telescope.

ESO staff Stéphane Guisard has been chasing green flashes for many years and has been able to capture them on many occasions. The picture shown above is one of many examples from his collection. “The most challenging is to capture the green flash while still seeing the rest of the Sun with all its colours,” says Guisard.
His colleague Guillaume Blanchard was even luckier. On Christmas Eve, as he was one of the few to follow the tradition of looking at the sunset, he had the chance to immortalise a blue flash using his hobby telescope.

ESO astronomer Yuri Beletsky also likes to take photographs from Paranal, but he prefers the night views. This allows him to make use of the unique conditions above the site to make stunning images. On some of these, he has captured other extremely interesting effects related to the Sun: the so-called Zodiacal light and the ‘Gegenschein’.

Both the Zodiacal light and the Gegenschein (which is German for “counter shine”) are due to reflected sunlight by interplanetary dust. These are so faint that they are only visible in places free from light pollution.

Most of the interplanetary dust in the Solar System lies in the ecliptic, the plane close to which the planets are moving around the Sun, and the Zodiacal light and Gegenschein are thus seen in the region centred around the ecliptic. While the Zodiacal light is seen in the vicinity of the Sun, the Gegenschein is seen in the direction opposite to the Sun.

Each of the small particles of dust, left over from comets and asteroids, acts as a small Moon reflecting the light coming from our host star. “If you could see the individual dust particles then you would see the ones in the middle of the Gegenschein looking like very tiny full moons, while the ones hidden in the faint part of the dust band would look like tiny crescent moons,” explains ESO astronomer Colin Snodgrass. “But even the VLT cannot see such tiny individual dust particles out in space. Instead we see the combined effect, in photos like these, of millions of tiny dust particles reflecting light back to us from the Sun.”

You can see more of the discoveries being made at the ESO at www.eso.org.

GENEVA (AFP) - Forget retail therapy for some relief from that winter cold — a study by Swiss scientists revealed on Wednesday that the flu virus can nestle and survive on banknotes for more than two weeks.

Scientists from Geneva’s University Hospital were asked by a Swiss bank to carry out the study amid worries that a flu pandemic could be prolonged thanks to the millions of bank notes in circulation, Le Temps newspaper reported.

Between 20 and 100 million banknotes change hands in Switzerland alone each day, it said.

The researchers left small samples of the flu virus on used banknotes which were then left at room temperature. Although the virus only survived in most cases for a few hours, certain highly concentrated samples proved resistant for several days.

In the worst case, if the virus was mixed with human mucus on the banknote, it could survive for two and a half weeks, Le Temps said.

“This unexpected resilience of the virus suggests that this sort of inert, non-biological support should not be overlooked in pandemic planning,” chief researcher Yves Thomas told the paper.

The team will now do further research to see how much of a factor banknotes might be in flu transmission, though Thomas stressed that the main risks remain airborne transmission and direct human contact.

Turns out green really IS the colour of money!

Pretty nasty to think about. Influenza virus can survive outside of the body long enough to make any number of objects potential carriers. Door handles, keyboards, newspapers, ewww. All the more reason to wash hands regularly, especially before meals.

Just a couple of quickies today:

Stanford, CA — Carbon emissions from human activities are not just heating up the globe, they are changing the ocean’s chemistry. This could soon be fatal to coral reefs, which are havens for marine biodiversity and underpin the economies of many coastal communities. Scientists from the Carnegie Institution’s Department of Global Ecology have calculated that if current carbon dioxide emission trends continue, by mid-century 98% of present-day reef habitats will be bathed in water too acidic for reef growth. Among the first victims will be Australia’s Great Barrier Reef, the world’s largest organic structure.

Chemical oceanographers Ken Caldeira and Long Cao are presenting their results in a multi-author paper in the December 14 issue of Science* and at the annual meeting of American Geophysical Union in San Francisco on the same date. The work is based on computer simulations of ocean chemistry under levels of atmospheric CO2 ranging from 280 parts per million (pre-industrial levels) to 5000 ppm. Present levels are 380 ppm and rapidly rising due to accelerating emissions from human activities, primarily the burning of fossil fuels.

“About a third of the carbon dioxide put into the atmosphere is absorbed by the oceans,” says Caldeira, “which helps slow greenhouse warming, but is a major pollutant of the oceans.” The absorbed CO2 produces carbonic acid, the same acid that gives soft drinks their fizz, making certain minerals called carbonate minerals dissolve more readily in seawater. This is especially true for aragonite, the mineral used by corals and many other marine organisms to grow their skeletons.

“Before the industrial revolution, over 98% of warm water coral reefs were bathed with open ocean waters 3.5 times supersaturated with aragonite, meaning that corals could easily extract it to build reefs,” says Cao. “But if atmospheric CO2 stabilizes at 550 ppm — and even that would take concerted international effort to achieve — no existing coral reef will remain in such an environment.” The chemical changes will impact some regions sooner than others. At greatest risk are the Great Barrier Reef and the Caribbean Sea.

Carbon dioxide’s chemical effects on the ocean are largely independent of its effects on climate, so measures to mitigate warming short of reducing emissions will be of little help in slowing acidification, the researchers say. In fact, impending chemical changes may require emissions cuts even more drastic than those for climate alone.

“These changes come at a time when reefs are already stressed by climate change, overfishing, and other types of pollution,” says Caldeira, “so unless we take action soon there is a very real possibility that coral reefs — and everything that depends on them —will not survive this century.”

Coral reefs are vital to the ocean’s biodiversity. Their loss would be catastrophic for the entire oceanic ecosystem, as many open ocean species use their relative calm and safety to breed.

A Cardiff University archaeology team has recreated a 3,000-year-old glass furnace, showing that Ancient Egyptian glassmaking methods were much more sophisticated than thought previously.

Dr Paul Nicholson, of the University’s School of History and Archaeology, is leader of an Egypt Exploration Society team working on the earliest fully excavated glassmaking site in the world. The site, at Amarna, on the banks of the Nile, dates back to the reign of Akhanaten (1352 - 1336 B.C.), just a few years before the rule of Tutankhamun.

It was previously thought that the Ancient Egyptians may have imported their glass from the Near East at around this time. However, the excavation team believes the evidence from Amarna shows they were making it themselves, possibly in a single stage operation. Dr Nicholson and his colleague Dr Caroline Jackson of Sheffield University demonstrated this was possible, using local sand to produce a glass ingot from their own experimental reconstruction of a furnace near the site.

The team have also discovered that the glassworks was part of an industrial complex which involved a number of other high temperature manufacturing processes. The site also contained a potter’s workshop and facilities for making blue pigment and faience - a material used in amulets and architectural inlays. The site was near one of the main temples at Amarna and may have been used to produce materials in state buildings.

Dr Nicholson, who has been working at Amarna since 1983, said: “It has been argued that the Egyptians imported their glass and worked it into the artefacts that have been discovered from this time. I believe there is now enough evidence to show that skilled craftsmen could make their own glass and were probably involved in a range of other manufacturing industries as well.”

Brilliant Things for Akhenaten by Dr Paul Nicholson.

Once again, it turns out that the ancient civilisations were a fair bit more technologically advanced than we had previously given them credit for.

Record-breaking amounts of ice-free water have deprived the Arctic of more of its natural “sunscreen” than ever in recent summers. The effect is so pronounced that sea surface temperatures rose to 5 C above average in one place this year, a high never before observed, says the oceanographer who has compiled the first-ever look at average sea surface temperatures for the region.

Such superwarming of surface waters can affect how thick ice grows back in the winter, as well as its ability to withstand melting the next summer, according to Michael Steele, an oceanographer with the University of Washington’s Applied Physics Laboratory. Indeed, since September, the end of summer in the Arctic, winter freeze-up in some areas is two months later than usual.

The extra ocean warming also might be contributing to some changes on land, such as previously unseen plant growth in the coastal Arctic tundra, if heat coming off the ocean during freeze-up is making its way over land, says Steele, who is speaking Wednesday at the American Geophysical Union meeting in San Francisco.

He is lead author of “Arctic Ocean surface warming trends over the past 100 years,” accepted for publication in AGU’s Geophysical Research Letters. Co-authors are physicist Wendy Ermold and research scientist Jinlun Zhang, both of the UW Applied Physics Laboratory. The work is funded by the National Science Foundation.

“Warming is particularly pronounced since 1995, and especially since 2000,” the authors write. The spot where waters were 5 C above average was in the region just north of the Chakchi Sea. The historical average temperature there is -1 C – remember that the salt in ocean water keeps it liquid at temperatures that would cause fresh water to freeze. This year water in that area warmed to 4 C, for a 5-degree change from the average.

That general area, the part of the ocean north of Alaska and Eastern Siberia that includes the Bering Strait and Chukchi Sea, experienced the greatest summer warming. Temperatures for that region were generally 3.5 C warmer than historical averages and 1.5 C warmer than the historical maximum.

Such widespread warming in those areas and elsewhere in the Arctic is probably the result of having increasing amounts of open water in the summer that readily absorb the sun’s rays, Steele says. Hard, white ice, on the other hand, can work as a kind of sunscreen for the waters below, reflecting rather than absorbing sunlight. The warming also may be partly caused by increasing amounts of warmer water coming from the Pacific Ocean, something scientists have noted in recent years.

The Arctic was primed for more open water since the early 1990s as the sea-ice cover has thinned, due to a warming atmosphere and more frequent strong winds sweeping ice out of the Arctic Ocean via Fram Strait into the Atlantic Ocean where the ice melts. The wind effect was particularly strong in the summer of 2007.

Now the situation could be self-perpetuating, Steele says. For example, he calculates that having more heat in surface waters in recent years means 23 to 30 inches less ice will grow in the winter than formed in 1965. Since sea ice typically grows about 80 inches in a winter, that is a significant fraction of ice that’s going missing, he says.

Then too, higher sea surface temperatures can delay the start of freeze-up because the extra heat must be discharged from the upper ocean before ice can form. “The effect on net winter growth would probably be negligible for a delay of several weeks, but could be substantial for delays of several months,” the authors write.

As the report states, there is a serious risk of this being a vicious circle. Increased sea temperature causes less ice to be formed during winter than otherwise, causing an even great rise in sea temperature in the following summer. Makes you wonder how many more years til it’s effectively gone. At least the Northwest Passage will be clear, I guess.

While the biological basis for homosexuality remains a mystery, a team of neurobiologists reports they may have closed in on an answer — by a nose.

The team led by University of Illinois at Chicago researcher David Featherstone has discovered that sexual orientation in fruit flies is controlled by a previously unknown regulator of synapse strength. Armed with this knowledge, the researchers found they were able to use either genetic manipulation or drugs to turn the flies’ homosexual behaviour on and off within hours.

Featherstone, associate professor of biological sciences at UIC, and his co-workers discovered a gene in fruit flies they called “genderblind,” or GB. A mutation in GB turns flies bisexual.

Featherstone found the gene interesting initially because it has the unusual ability to transport the neurotransmitter glutamate out of glial cells — cells that support and nourish nerve cells but do not fire like neurons do. Previous work from his laboratory showed that changing the amount of glutamate outside cells can change the strength of nerve cell junctions, or synapses, which play a key role in human and animal behaviour.

But the GB gene became even more interesting when post-doctoral researcher Yael Grosjean noticed that all the GB mutant male flies were courting other males.

“It was very dramatic,” said Featherstone. “The GB mutant males treated other males exactly the same way normal male flies would treat a female. They even attempted copulation.”

Other genes that alter sexual orientation have been described, but most just control whether the brain develops as genetically male or female. It’s still unknown why a male brain chooses to do male things and a female brain does female things. The discovery of GB provided an opportunity to understand why males choose to mate with females.

“Based on our previous work, we reasoned that GB mutants might show homosexual behaviour because their glutamatergic synapses were altered in some way,” said Featherstone. Specifically, the GB mutant synapses might be stronger.

“Homosexual courtship might be sort of an ‘overreaction’ to sexual stimuli,” he explained.

To test this, he and his colleagues genetically altered synapse strength independent of GB, and also fed the flies drugs that can alter synapse strength. As predicted, they were able to turn fly homosexuality on and off — and within hours.

“It was amazing. I never thought we’d be able to do that sort of thing, because sexual orientation is supposed to be hard-wired,” he said. “This fundamentally changes how we think about this behavior.”

Featherstone and his colleagues reasoned that adult fly brains have dual-track sensory circuits, one that triggers heterosexual behavior, the other homosexual. When GB suppresses glutamatergic synapses, the homosexual circuit is blocked.

Further work showed precisely how this happens — without GB to suppress synapse strength, the flies no longer interpreted smells the same way.

“Pheromones are powerful sexual stimuli,” Featherstone said. “As it turns out, the GB mutant flies were perceiving pheromones differently. Specifically, the GB mutant males were no longer recognizing male pheromones as a repulsive stimulus.”

Featherstone says it may someday be possible to domesticate insects such as fruit flies and manipulate their sense of smell to turn them into useful pollinators rather than costly pests.-Press release from Nature Neuroscience

Fascinating research that has turned up an accidental discovery that could revolutionise pest control. Spraying sexuality-switching chemicals sounds to me an incredibly bad idea, even if it only affects insects, but I have no doubt that someone will try it. I’m more interested, however, in the aspect of this that proves that, in insects at least, homosexuality can be induced and repressed. With this being proved in insects, it is probably only a matter of time before similar discoveries are made for humans, though it is likely to be a far more complex combination of genes, and that will open up a whole can of ethical worms.

There are some people who view homosexuality to be a mental disorder rather than an aspect of diversity, and seek to provide a cure. Currently there are any number of therapies on offer, some more bizarre than others. They are especially popular amongst conservative christians and similar groups. Conversion therapy, as it is called, (or sometimes reparitive therapy), is not particularly effective, with frequent psychological side-effects, and only rarely results in a permanent conversion with no relapses. In spite of their ineffectiveness, and sometimes methods that in other circumstances might be described as torture, they are overwhelmingly endorsed by the evangelical movement. Should a reliable drug be found that changes sexual inclinations, it will find eager cheerleaders, and more importantly perhaps, extremely deep pockets where funding is concerned. It is likely that such research is already underway.

There are some homosexuals who, for religious and other reasons, really do desire to be “cured”. In such cases I suppose it would be right to provide such medication, just as sex-change operations are made available. But such a medication is also another tool in the arsenal of intolerance. No longer would people be able to claim that homosexuality is not a choice. One can imagine a state such as Iran, which already claims to contain no homosexuals, making such a drug mandatory for those with tendencies deemed deviant by the state. Of course, that could never possibly happen in our enlightened western world. (Insert laughter track here.)

Where homosexuality is now grudgingly tolerated, it is easy to imagine more and more pressure, from family, church, or employers, being heaped upon individuals to get themselves “fixed”. Consider that the US army, never shy about trying out interesting new drugs upon its troops, is utterly opposed to having homosexuals within its ranks. Currently they are fired upon discovery, but a conversion drug would allow someone to keep his or her job. It’s not hard to imagine that someone might make that choice in order to keep alive their career and their tight-knit support network. Someone in that position is incredibly vulnerable to coercion from their superior officers.

I wanted to keep this blog politics free, and just about science, but sometimes science and politics get intertwined. I apologise for the intrusion, but the ethics of science are always worthy of thought. We should always consider the darker possibilities of a discovery, as well as the hopeful ones.

What do you think? Should such a drug for humans even be researched in the first place, or is it too dangerous to our liberties? Myself, I find it a pretty scary thought.

A new species of bacteria discovered living in one of the most extreme environments on Earth could yield a tool in the fight against global warming.

In a paper published today in the prestigious science journal Nature, U of C biology professor Peter Dunfield and colleagues describe the methane-eating microorganism they found in the geothermal field known as Hell’s Gate, near the city of Rotorua in New Zealand. It is the hardiest “methanotrophic” bacterium yet discovered, which makes it a likely candidate for use in reducing methane gas emissions from landfills, mines, industrial wastes, geothermal power plants and other sources.

“This is a really tough methane-consuming organism that lives in a much more acidic environment than any we’ve seen before,” said Dunfield, who is the lead author of the paper. “It belongs to a rather mysterious family of bacteria (called Verrucomicrobia) that are found everywhere but are very difficult to grow in the laboratory.”

Methanotrophic bacteria consume methane as their only source of energy and convert it to carbon dioxide during their digestive process. Methane (commonly known as natural gas) is 20 times more potent a greenhouse gas than carbon dioxide and is largely produced by decaying organic matter. Scientists have long known that vast amounts of methane are produced in acidic environments, not only geothermal sites but also marshes and peat bogs. Much of it is consumed by methanotrophic bacteria, which serve an important role in regulating the methane content of the world’s atmosphere.

“Scientists are interested in understanding what conditions cause these bacteria to be more or less active in the environment” says Dunfield, “Unfortunately, few species have been closely studied. We now know that there are many more out there.”

Dunfield has tentatively named the new bacterium Methylokorus infernorum to reflect the ‘hellish’ location of its discovery where it lives in boiling waters filled with chemicals that are toxic to most life forms. The Maori caretakers of the site, the Tikitere trust, have supported scientific study of the area. The study was conducted while Dunfield was working for GNS Science, a geological research institute owned by the New Zealand government. He recently joined the U of C’s Department of Biological Sciences as a professor of environmental microbiology.

The bacterium’s genome has been completely sequenced by researchers at the University of Hawaii and Nankai University in China, which could help develop biotechnological applications for this organism.

Dunfield said he plans to pursue his work in Canada by hunting for new life forms in extreme environments such as northern peatlands, the oilsands of northern Alberta and the hot springs of Western Canada.

“Hot springs are exotic and extreme habitats, where you find a lot of bizarre organisms,” he said. “Bacteria are a fascinating group to work with because 95 per cent of them have never been studied in a lab and we have very little idea about what this huge amount of biodiversity is capable of.”

Could be a relatively cheap method to remove methane emisions from everything from cattle-houses to landfill sites. Currently, some folks use the methane as fuel, which isn’t a bad tactic, as carbon dioxide is far less powerful a greenhouse gas, and it saves burning fossil fuels. Given that these bacteria also turn the methane into carbon dioxide, but without providing energy for human consumption I’m not entirely sure that theres much practical benefit to using bacteria over burning, though it might be useful in situations where the amount of methane is too small to make a miniature powerplant impractical. Perhaps the bacteria can be turned into animal feed or somesuch. Still, it’s an avenue of research well worth investigating.

Interesting, if a bit grim!

From the Telegraph

It must be one of the most stomach-churning medical treatments ever devised.

“People will have a blood transplant or a kidney transplant – what’s the difference with this?”

I’m not sure whether the medicine wasn’t almost as bad as the affliction, but it seems to have worked! There are a lot of helpful bacteria in the human gut, performing a variety of useful tasks, including assisting with digestion. Some convert calcium into a form more easily absorbed by our bodies, while others help to break down fats, proteins, or carbohydrates. Some others are simply non-harmful, but help by outcompeting more dangerous bacteria.

I’m a bit surprised that there wasn’t a better way to boost the woman’s probiotic levels than the course they took though.