Tuesday, 11 January 2011

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

Synthetic Genes Sub for Natural Ones in Microbe Experiment

Posted: 10 Jan 2011 03:47 PM PST

A handful of bacterial genes crucial to survival were successfully replaced by artificial ones in a new synthetic-biology experiment.

It's not clear how the synthetic genes rescued the doomed E. coli bacteria, which had several important sequences of DNA knocked out of its genome. But scientists think synthetic proteins produced by the new genes replaced the missing natural versions.

"To enable life you need genes and proteins, which are information and machines," said molecular biologist Michael Hecht of Princeton University, co-author of the study published online in PLoS ONE. "These evolved over a very long period of time, but we wanted to ask, 'Are they really special, or can we make stuff like them from scratch?' It seems we can."


One of synthetic biology's primary goals is to create customizable organisms able to produce food, fuel or pharmaceuticals; clean toxins from the environment; or even function as computers.

Most synthetic-biology experiments, including the J. Craig Venter Institute's recent creation of a synthetic life form, rely on existing genes in nature. In the new experiment, however, Hecht and his team engineered a semi-random library of 1.5 million made-from-scratch genes.

Genes contain instructions for building proteins, which are made of units called amino acids. There are 20 different amino acids a protein can be made of, and some sequencesmake a protein fold into three dimensions.

Each gene in Hecht's synthetic library calls for proteins made of 102 amino acids. Yet, instead of randomly filling each spot, the genes included sequences prompting them fold into four-helix structures (right).

"Folding in three dimensions [is required for functionality] when it comes to proteins, so the library isn't completely randomized," Hecht said. "You might think of it as a targeted shotgun of randomness instead of a bomb of it."

Twenty-seven strains of E. coli, each missing one gene critical for survival, individually mingled with the synthetic-gene library. Four strains of bacteria incorporated a synthetic gene into their DNA and grew on Petri dishes that contained only the bare nutrients for survival. Without the new genes, the four strains didn't grow at all.

Taking the rescue of doomed microbes further, Hecht's team made a strain of E. coli missing all four genes from the previous experiments. When the synthetic replacement genes from the library were added, the microbe was rescued.

"I think this is a very interesting start to some more research," said biotechnologist Andrew Ellington of the University of Texas at Austin, who was not involved with the experiments. "I'd like to see more proof that these proteins are doing what [Hecht] says they're doing…. There may be some weird things going on."

Hecht said "it would be nice" to untangle the biochemistry of his genetic rescues, adding that the synthetic genes weren't exactly optimum replacements for nature's versions that were chiseled over billions of years of evolution. But he said that's not the biggest takeaway from the experiment.

"We know which specific genetic sequences rescue the strains, even if we don't yet know how they work," Hecht said.

In addition to following up on the biochemistry of the genes that revived the bacteria, Hecht's laboratory plans to engineer more-complex libraries and knock out even-more-crucial genes.

"'How far can you go with this?' is what we want to know. Could you knock out 100 genes and rescue all of them? Eventually a whole genome?" Hecht said.

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Baby Galaxy Hosts Monster Black Hole

Posted: 10 Jan 2011 03:33 PM PST

SEATTLE — A tiny galaxy has been caught with a monstrously huge black hole at its center. The galactic oddity could be a transition case between young, small galaxies and stately spirals like our Milky Way, and suggests that galaxies grow around central black holes, not the other way around.

Most large galaxies, including the Milky Way, spiral around a central supermassive black hole millions of times more massive than the sun. In general, bigger galaxies host bigger black holes, suggesting a link between the two. But the nature of the link — whether black holes form first and gather galaxies around them, whether preformed galaxies crush the material in their centers into black holes, or whether the two grow in tandem — is unclear.

A newly discovered black hole in a nearby dwarf galaxy may hint at an answer.

"We might be witnessing an early stage of black-hole and galaxy evolution," said astronomer Amy Reines, a graduate student at the University of Virginia, in a press conference here at the meeting of the American Astronomical Society.


The galaxy, called Henize 2-10, is a blob-shaped dwarf galaxy 30 million light-years away. It's about 3,000 light-years across, one-thirtieth the width of the Milky Way, and is famous among galactic astronomers for its rapid bursts of star formation. Some astronomers think that with its small, blobby and starbursting form, Henize 2-10 could be a nearby analogue of some of the first galaxies ever formed in the universe.

Reines and her colleagues observed the galaxy with the Hubble Space Telescope and the Very Large Array of radio telescopes in New Mexico. They found a region near the center of the galaxy, between two bright regions of gas, that was spitting out more radio waves than would be expected from a dwarf-sized black hole.

The team searched images from the Chandra X-Ray Observatory and found that same region glowed brightly in energetic X-rays.

The combination of radio waves and X-rays "is a signpost for a supermassive black hole feeding on its surroundings," Reines said. The results were published in the Jan. 9 Nature.

Based on the amount of radiation, the black hole is about 2 million times the mass of the sun, Reines estimated. That's comparable to the size of the black hole at the center of the Milky Way, even though Henize 2-10 is only about the size of a satellite galaxy of the Milky Way called the Magellanic Clouds.

The object is too bright in radio to be a smaller black hole, and too bright in X-rays to be a supernova remnant, Reines said. "It's really this ratio of X-ray–to–radio emission that rules out other objects."

Because Henize 2-10 doesn't have a big bulge of stars at its center like other supermassive-black-hole–hosting galaxies, these big, bulging galaxies may form around their black holes.

"It's possible that the black hole formed before the galaxy," Reines said.

"If it really exists, it's very significant," said astronomer Hans Zinnecker of the SOFIA airborne observatory, who studied Henize 2-10 in the 1980s. "It surely was a surprise."

Zinnecker wondered why this dwarf galaxy hosts such a large black hole while others of similar size do not. Maybe two clouds of gas colliding at Henize 2-10's center collapsed into the large black hole after the galaxy had already formed.

"I find it hard to imagine that a black hole of a million solar masses could have been built from a merger of little black holes," he said. "There must be something specific about that galaxy that could explain it."

Composite image of Henize 2-10 dwarf galaxy. X-ray: NASA/CXC/Virginia/A.Reines et al. Radio: NRAO/AUI/NSF/Virginia/A.Reines et al. Optical: NASA/STScI/Virginia/A.Reines et al.

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Hubble Snaps Sharpest-Ever Photo of Dead Green Quasar

Posted: 10 Jan 2011 12:45 PM PST

The Hubble Space Telescope has photographed the eerie, green-glowing gas highlighted by a recently deceased quasar.

The Milky-Way-sized object, located about 730 million light-years away, surrounds a supermassive black hole that was once the heart of a galaxy.

The black hole gobbled up its last available meal of gas and dust as a quasar between 45,000 and 70,000 years ago, ionizing oxygen in distant gas clouds into a bright green glow before fading back into darkness. The glowing gas cloud, known as Hanny's Voorwerp, is now 100 to 10,000 times dimmer than the quasar was when it was still devouring matter.


The green object is named after Hanny van Arkel, the Dutch schoolteacher who discovered it in 2007 while helping classify more than 60 million galaxies for the Galaxy Zoo project.

In the new Hubble image (above) of Hanny's Voorwerp, taken with Hubble's Wide Field Camera 3 and Advanced Camera for Surveys, the nearby spiral galaxy IC 2497 is helping to spark star formation in the yellow-orange fringes of the Voorwerp. The new stars are a few million years old.

Images: 1) The Hubble Space Telescope's recent image of Hanny's Voorwerp. NASA, ESA, William Keel (University of Alabama, Tuscaloosa), and the Galaxy Zoo team (high-res). 2) The best image of Hanny's Voorwerp prior to Hubble's shot. WIYN Observatory/William Keel/Anna Manning

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Mice Kept on Unnatural Schedule Go Haywire

Posted: 10 Jan 2011 12:13 PM PST

Artificially separated from a natural cycle of light and dark, the bodies and brains of mice go haywire in ways that may mimic the human effects of circadian disruption.

The mice are not an analogue for humans who work a night shift or regularly travel across multiple time zones, but they could provide a model for deeper investigations of what happens when circadian rhythms are bumped.

After all, it's only been a century since mechanized timekeeping and artificial lighting made it possible to override a biological system calibrated for the last several billion years, with circadian systems found in even the most primitive algae.

"Modern society has resulted in a round-the-clock lifestyle, in which natural connections between rest-activity cycles and environmental light-dark cycles have been degraded or even broken," wrote researchers led by neuroscientist Bruce McEwen of Rockefeller University in a Dec. 11 Proceedings of the National Academy of Sciences study. "However, the ramifications of chronic disruption of the circadian clock for mental and physical health are not understood."


Yet if the effects are not understood in exact detail, a growing body of evidence points to problems. Circadian "clock genes," centrally controlled in mammals by a brain region that gets signals straight from the retina, have central regulatory roles in gene networks. Hormone-balance signals are tied to circadian cycles, and night-shift work has been correlated with increases in diabetes, heart disease and cancer.

Such correlations can flag a problem but don't say much about how it works, sending researchers to work on animals. To create chronic circadian disturbance, McEwen's team turned lab lights on and off to create 20-hour days for mice, while a control group was kept on a regular 24 hour schedule. Within six weeks, the disrupted group started to gain weight, despite eating the same diet as controls. They grew obese, and had altered levels of insulin and leptin, two key metabolic hormones.

Effects extended to their brains. In the prelimbic prefrontal cortex, a region important to emotional control and cognitive flexibility, neurons shrank and were arranged in less complex ways. The mice had trouble learning to navigate mazes, and were spooked by new environments.

The researchers hope their model of disruption will be used by other scientists to conduct further investigations of circadian disruption.

The findings demonstrate "the central role circadian rhythms play in both mental and physical health," they wrote. "How these findings translate to humans is an important area of research, because such effects could put chronically disrupted individuals at risk for developing metabolic and cardiovascular problems."

Images: 1) Richard Winchell/Flickr. 2) Weight gain and metabolic hormone levels in circadian-normal and circadian-disrupted mice./PNAS.

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Citation: "Disruption of circadian clocks has ramifications for metabolism, brain, and behavior." By Ilia N. Karatsoreos, Sarah Bhagat, Erik B. Bloss, John H. Morrison, and Bruce S. McEwen. Proceedings of the National Academy of Sciences, Vol. 108 No. 2, Jan. 5, 2011.

Kepler Finds First Definitively Rocky Exoplanet

Posted: 10 Jan 2011 12:02 PM PST

SEATTLE — The planet-hunting Kepler Space Telescope has spotted its first rocky exoplanet, astronomers announced today at the meeting of the American Astronomical Society.

"This is the first unquestionably rocky planet orbiting a star outside our solar system," said astronomer Natalie Batalha of San Jose State University, a member of the Kepler team. "It's an important milestone for our team, and I think it's an important milestone for humanity."

The new planet, called Kepler 10-b, orbits a sun-like star 560 light-years away. It was first spotted in July 2009 as it crossed, or transited, in front of its parent star.

The amount of starlight the planet blocked told astronomers that the planet is just 1.4 times the radius of Earth, making it the smallest exoplanet yet discovered. The planet blocked about a ten-thousandth of its star's light, "like if you had 10,000 light bulbs and take one away," Batalha said.

But the light dimming wasn't enough to tell astronomers how massive the planet is, a key clue to its composition. To figure out its mass, the team took 40 follow-up measurements with the Keck Telescope in Hawaii. As the planet orbits, its gravity gently pulls its parent star back and forth. Precise measurements of these tiny gravitational nudges let astronomers calculate the planet's mass.


These measurements revealed that the planet is just 4.6 times the Earth's mass. Combining the mass with the radius gives the planet's density, which, Batalha says, can only be explained by a rocky composition.

"No theoretical model is consistent with that mass, radius and density except a rocky world," Batalha told Wired.com.

Just to make sure, Batalha and colleagues turned back to Kepler. To find planets, Kepler stares unblinkingly at a field of 150,000 stars near the constellation Cygnus and watches for the periodic dimming of a star's light that indicates a transiting planet.

This strategy also lets the telescope take precise measurements of starquakes, subtle vibrations in the stars' outer layers that reveal their inner lives. Because astronomers only know a planet as well as they know its star, the starquake measurements let the Kepler team pin down Kepler-10b's properties to unprecedented accuracy.

"In the same way that we use a sonogram to probe the unborn fetus, and the same way we use earthquakes to probe interior of the earth, we use starquakes to probe the interior of the star itself," Batalha said.

Kepler-10b is not the first planet to be hailed as a truly rocky world. That honor went to COROT-7b, spotted in February 2009 with the COROT satellite (stands for COnvection, ROtation and planetary Transits).

But the starquake measurements make astronomers even more certain that Kepler-10b is a ball of rock. COROT-7b's host star is magnetically active, Batalha says, making it difficult to tease the planet's gravitational pull from the star's own magnetic jitters. Some measurements of the planet's mass leave room for other interpretations of the planet's composition, like a planet that is more than half water.

Kepler-10b, on the other hand, is denser than the Earth, meaning it is probably made up of rock and iron.

Unfortunately, the new rocky world is hot enough to melt iron. It orbits its star once every 0.84 days, meaning the planet is 23 times closer to its star than Mercury is to the sun. At such a close orbiting distance, the planet shows the same face to the star at all times, the same way the moon always shows the same face to the Earth. Temperatures on the daytime side of the planet would reach 2780 degrees Fahrenheit, as hot as some red dwarf stars.

"Natalie Batalha's report from NASA Kepler, I believe, will be marked as among the most profound scientific discoveries in human history," said planet hunter Geoff Marcy of the University of California, Berkeley. "This new planet is some transitional type of planet between what we've been finding and what we've been hoping to find…. Kepler-10b will go into every textbook in astronomy worldwide."

The Kepler team will release a new catalog of planets next month, Batalha added. She wouldn't say whether any of those worlds are smaller or rockier than Kepler-10b, but hinted that the odds are good.

Image and Video: NASA/Kepler

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East Coast Fish Die-Offs Linked to Extreme Cold Snap

Posted: 10 Jan 2011 10:48 AM PST

The death of 2 million fish in Chesapeake Bay isn't a sign of apocalypse, historical or otherwise, but it does offer a chance to consider what could happen if colder winters become routine in the eastern United States.

Some climatologists have proposed that, paradoxically, a warming Arctic will actually push cold air south, producing patterns like the one believed to have caused the Chesapeake fish kill.

If cold snaps grow deeper even as year-round temperatures rise, Chesapeake Bay's ecosystems would adapt — but perhaps not, as is usually forecast, through the northward migration of warm-loving species, but by favoring species that can handle extremes.

"The long-term makeup of ecological communities is more driven by extremes than average conditions," said Boris Worm, a marine biologist at Nova Scotia's Dalhousie University. "Whatever can survive the extreme makes it in the long-term."

The Chesapeake Bay fish kill was the latest in a series of animal die-offs to gain attention — and more than a little hysteria — after the dramatic New Year's Eve death of 5,000 red-winged blackbirds over Beebe, Arkansas, and the subsequent report of 100,000 drum fish dying in the Arkansas River.

Those die-offs were not exceptional in the history of single-event die-offs, and paled in comparison to what's ongoing among North American bats and bees, and in amphibians around the world. But the timing, proximity and general eeriness of the deaths captured the public's imagination, and suddenly people started paying attention to die-offs that would normally have gone unremarked.

Bird deaths were reported in Sweden, Kentucky and Louisiana, and dead crabs off the English coast. The "aflockalypse" went viral, and the internet filled with (mostly) tongue-in-cheek chatter about the End Times. When the Maryland Department of the Environment released a statement Jan. 5 about 2 million spot and croakers dying in Chesapeake Bay, the public was primed to perceive catastrophe.


Unlike the other die-offs, though, the Chesapeake fish kill occurred in a region where ecological monitoring is intensive, thanks to the importance of the estuary's historic fisheries, and ongoing efforts to fix the damages of pollution and overfishing. Oxygen, temperature and toxin readings are taken constantly throughout the estuary. History is also a guide: 20 million fish died in similar circumstances in 1976 and again in 1980. Researchers quickly identified unusually cold water as the prime suspect.

Chesapeake Bay waters were colder on average in December than they'd been in 25 years. In terms of temperature anomaly, they were actually the most unusually cold waters in the world. Extreme cold can alter the function of gill membranes, resulting in salt dysregulation and ultimately dehydration. And while fish can often swim away from environmental stress, they can be vulnerable to sudden temperature drops, or end up trapped by currents or other ocean conditions. That's what appears to have happened this time.

Biologists say that, from a long-term ecological perspective, the deaths will cause barely a ripple. They are interesting, though, in that the Chesapeake Bay has gradually warmed over the last several decades, particularly in the spring and summer, and even in winter. If, mid-Atlantic winters become severe or highly variable, "that's a very interesting dynamic," said David Secor, a population ecologist at the University of Maryland's Chesapeake Biological Laboratory. "We're shifting the range of warm-adapted fish like spot and croaker — but then we lure them into an ecological trap."

Whether Atlantic winters will remain cold, or even become colder or more prone to cold snaps, is a matter of ongoing speculation. In general, climate change is expected to produce warming.

Most extreme-weather predictions involve not temperature but precipitation: either rain and snow — as warmer air is able to load up with moisture — or droughts. But extreme cold has received more attention in the past several years, especially after last year's exceptionally cold mid-Atlantic winter. Some research suggests that global warming could paradoxically result in colder middle-latitude winters.

According to one hypothesis, as summer sea ice dwindles, exposed dark waters absorb sunlight and store heat, causing regional warming and changes in air pressure that push cold air south. This is called the "Warm Arctic–Cold Continents" pattern.

"Rather than a general warming everywhere, the loss of sea ice and a warmer Arctic can increase the impact of the Arctic on lower latitudes, bringing colder weather to southern locations," explained an October report from the National Oceanic and Atmospheric Administration (.pdf). The effect has been analogized to leaving a refrigerator door open.

One month is, of course, nothing more than a single data point among many, but it does show that average temperatures in much of the North American Arctic were 11 degrees Fahrenheit warmer than usual in December, and up to 18 degrees warmer in certain parts. In the eastern United States and western Europe, it was exceptionally cold.

Another possible mechanism was highlighted in a recent New York Times op-ed by Judah Cohen, a former NASA climatologist who now directs seasonal forecasting at Atmospheric and Environmental Research, a private forecasting company. Under this hypothesis, warmer temperatures can lead to increased autumn snowfall across the Eurasian arctic, producing snow cover that reflects sunlight back into space and creates a dome of cold air over Siberia. That dome could disrupt the east-to-west jet stream, pushing it north and south instead, flowing subtropical air into Alaska and Greenland and Arctic air down the eastern side of the Rocky Mountains and southwest into Europe.

The Siberian connection has been the subject of a scientific back-and-forth on Andrew Revkin's Dot Earth blog, and — like the Warm Arctic–Cold Continents pattern — it will ultimately stand or fall with further tested predictions. Another possible factor is natural changes in the North Atlantic Oscillation, a system of high and low pressure that produces mild winters in its positive phases and colder winters when negative. It seems to be going negative at the moment, though "at this point, this is highly speculative," said Kevin Trenberth, head of climate analysis at the National Center for Atmospheric Research.

If the speculation bears out, the question is then what it would mean for mid-Atlantic ecosystems like Chesapeake Bay.

"If there was a simple shift in climate (e.g. colder winters), then you might predict that the populations would gradually shift their use of habitat over time," said University of Maryland ecologist Lora Harris. "The challenge comes in the possibility that colder winters may actually be coincident with greater variability in temperatures."

According to Harris, changes in ecosystem composition would likely result, reducing the role of menhaden and other species ill-suited for sudden stresses. People would see an ecosystem with "lower diversity and centered on species that are more tolerant to large seasonal ranges in temperature," said Secor.

Nutrient cycling, hydrodynamics and plankton communities would also shift. These wouldn't spell disaster, though regular fish kills could be problematic, but would add a new wrinkle to understanding the environment, and perhaps to Chesapeake Bay fisheries.

Just as hardy generalists are favored in terrestrial ecosystems stressed by climate change and human disruption, the same could hold for aquatic systems in newly variable temperature regimes.

"An unstable climate not only causes a discomfort for us, but may also cause ecological disruption," said Worm.

Images: 1) Jan. 3 photo shows dead fish, mostly spot, along with a few small croaker, at Northwest Creek on Kent Island in Stevensville, Maryland./Charles Poukish/Maryland Department of the Environment/ AP 2) Climate simulations of unusually high temperatures (red) over Arctic regions without sea ice and subsequent, unusually cold weather (blue) over the eastern United States./Geophysical Research Letters 3) Map of temperature anomalies, December 2009/NOAA.

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