Friday, August 14, 2009

Forced Fungus Sex Could Unlock Key Energy Sources

By Charles Q. Choi

Helping a fungus have sex could lead to better ways of making biofuels, scientists now suggest.

To make renewable biofuels instead of manufacturing them from the sugars in food crops, researchers want to employ organisms that can make use of the hundreds of millions of tons of cellulose in sawdust, weeds and other plant scrap that would otherwise go to waste.

One especially promising organism when it comes to breaking down cellulose is the soil fungus Trichoderma reesei. It was originally discovered in the Solomon Islands during World War II eating away at the canvas and garments of the U.S. Army.

Improving this fungus was difficult because scientists thought it was asexual, which meant they couldn't breed different useful strains of it together for offspring better tailored to degrade cellulose.

Now researchers in Austria find this fungus isn't asexual after all. For the first time after its discovery more than 50 years ago, researchers have made it have sex.

The group this fungus belongs to, Trichoderma, includes several hundred species, including both sexual and asexual ones. By probing their DNA, investigators uncovered the genes responsible for mating and found them in Trichoderma reesei, proving it was theoretically capable of sex. However, it could not assume the female role.

Past studies had revealed that Trichoderma reesei was in fact genetically identical to another fungus, Hypocrea jecorina, which could assume both the male and female roles. The scientists managed to successfully mate Hypocrea jecorina with two mutant Trichoderma reesei strains known to be especially good at breaking down cellulose with existing wild strains.

Although researchers could in the past dose the fungus with radiation or chemicals to randomly create potentially useful mutations, "it was not possible to combine beneficial mutations of efficient production strains," said researcher Monika Schmoll, a microbiologist at the Vienna University of Technology. " Now it has become possible to cross these strains and mix their genetic material. Of course there is no guarantee that the combination of properties really results in even better strains, but in many cases it will work."

Sex can also lead to more fit strains. The methods used to create mutants could lead to strains of Trichoderma reesei that are good at making enzymes that break down cellulose, but otherwise "sometimes look quite poor and helpless," Schmoll explained. By crossing such a mutant with an ordinary 'wild-type' strain of the fungus, "there is the chance to preserve the high enzyme production, but to get rid of mutations that reduce growth and fitness by replacement with wild-type genes."

These findings might lead to better and more cost-effective ways of making biofuel. "I would be happy to see gas stations selling affordable bioethanol made from waste and plant material one day," Schmoll said. The researchers also noted that Trichoderma includes species that help plants by killing harmful fungi, and discovering ways of breeding strains of them together could help out farmers.

In the future, Schmoll and her colleagues want to find out what leads to this absence of females in Trichoderma reesei in the first place. If they do, they could reverse the situation, she explained.

The researchers detailed their findings online August 10 in the Proceedings of the National Academy of Sciences.

Copyright © 2009 Imaginova Corp.

Physicists hold breath as Large Hadron Collider prepares to rise from ashes

If all goes to plan, the LHC will come back to life in November. Sam Wong explains the measures being taken to prevent another catastrophic failure, and gauges the mood of physicists at Cern. Can they bag the Higgs before the Americans?

Magnets damaged in an explosion in the LHC tunnelView larger picture

A region between two magnets in the LHC that was crushed in the incident on 19 September 2008. Photograph: Public Domain

It's been nearly a year since the world's biggest science experiment, the Large Hadron Collider (LHC), was fired up for the first time in a flurry of excitement at Cern, the European Centre for Nuclear Research in Switzerland. But ever since a catastrophic explosion in the particle accelerator's tunnel just nine days after startup, the gargantuan machine has sat idling, to the acute frustration and no little embarrassment of all involved.

The incident on 19 September, variously described as an "electrical failure", "engineering breakdown" and "technical malfunction", was a major setback to physicists hoping to discover the Higgs boson (or "champagne bottle boson", as we rechristened it). It was caused when a short-circuit in a connection between superconductors in the tunnel burned a hole in a vessel containing liquid helium – resulting in an explosion.

Engineers have been working hard to get the $9bn supermachine up and running. They have now finished testing the 10,000 high-current, superconducting connections and repairing those in which the resistance was found to be abnormally high.

They've also installed highly sensitive warning systems in an attempt to avoid a repeat of the liquid helium leak.

There's more work to be done, though, including calibrating the detectors, installing 160km of new cabling around the tunnel, and cooling down the sectors that had to be warmed up to allow repairs (when it's colliding particles, the accelerator tunnel is cooled close to absolute zero).

All in all, the atom smasher's refit will rack up a bill in the region of 40m Swiss francs (£23m).

Last week, Cern announced that the LHC will finally begin firing protons around its 27km circular tunnel again in November. Initially, it will run at an energy of 3.5 tera-electronvolts (TeV) per beam – just half of what it's meant to achieve at full blast, but still several times more than the LHC's American competitor, the Tevatron at Fermilab, can manage. After operating at this lower level for a period, the energy will be increased to 5TeV per beam.

According to Cern spokesman James Gillies, the mood at Cern is optimistic.

"We're looking forward to getting going," he said. "There's consensus that the choices that have been taken to run the machine safely at 3.5TeV per beam are good choices. They allow the machine operators to learn how to drive the machine, if you like, under what should be very easy conditions for them, and they don't compromise the physics."

Gillies is confident that there won't be another serious mishap this time around.

"There will be small things, and that's part of life, but I don't think we're going to see another major setback like the one we had last year."

Once a good amount of data has been collected at lower energy levels, the LHC will have to be shut down again while it is geared up to reach 7TeV per beam. This will require dozens of superconducting magnets to be "retrained" – conditioned by gradual exposure to higher and higher currents.

The energy of a collision between two particles in the tunnel is converted into the mass of any new particles that are created, in keeping with Einsteins's celebrated equation E=mc2. The more energetic the collision, the more massive the particles that might be created, as physicist Adam Yurkewicz explains on the LHC's US blog.

"For example, to discover a dark matter particle, the energy of the collision is converted into the mass of the new particle. Right now, we don't know exactly what mass the dark matter particle has, so the higher the collision energy, the more massive particle we could potentially make. Our potential to discover something new depends on the energy of the collisions."

For this reason, physicists are eager to get the collider running at full energy as soon as possible. But according to Peter Kalmus, emeritus professor of physics at Queen Mary, University of London, there are other considerations.

"We're looking for something that is almost bound to be rare," he said. "One has to have a very well understood apparatus, not just the accelerator but also the detectors that would be looking for it. It seems to me that people probably need, I would think, certainly much more than a year of operating the machine just to make sure that they understand all the nitty-gritty of quirks in the equipment."

Kalmus believes Cern are still the favourites to get their hands on the elusive Higgs before their American rivals.

"I think Cern ought to have the edge, but there is still a chance that Fermilab could come up with it," he said.

The Higgs boson would certainly be the prize in any hunt, but it is by no means the only target in the LHC's sights. Physicists also hope to verify the existence of supersymmetry – the idea that the known particles have heavier partners that have yet to be discovered.

"If they exist, and if the masses are not very much higher, then they could be discovered with the lower energy machine," says Kalmus.

There will be an anxious wait for the physics community between now and November. For researchers desperate to get their hands on some data, the resurrection of the LHC can't come a minute too soon.

"Collisions this year will bring joy, but first probably relief," Yurkewicz writes. "Relief at not having to answer questions about the LHC not working, and relief for graduate students who would have data they could analyse in order to graduate.

"Many of us will be holding our breath for the next few months. After we see some collisions we can experience that joy, and then start down the long path towards answering some of the fundamental questions we have about the universe."

Original here

Storms of Saturn's Moon Titan - A Model of the Early Earth?

Titan2_h NASA's Cassini spacecraft buzzed Titan last year, coming close enough to taste the Saturnian moon's atmosphere. The data acquired has implications for our understanding of life throughout the galaxy, as well as Earth's own past.

Meanwhile, just this month astronomers used the NSF-supported Gemini Observatory to capture the first images of clouds over Titan's tropics. The images clarify a long-standing mystery linking Titan's weather and surface features, viewed by some scientists as an analog to Earth when our planet was young.

The effort also served as the latest demonstration of adaptive optics, which use deformable mirrors to enable NSF's suite of ground-based telescopes to capture images that in some cases exceed the resolution of images captured by space-based counterparts.

On Titan, clouds of light hydrocarbons, not water, occasionally emerge in the frigid, dense atmosphere, mainly clustering near the poles, where they feed scattered methane lakes below. Closer to the moon's equator, clouds are rare, and the surface is more similar to an arid, wind-swept terrain on Earth. Observations by space probes suggest evidence for liquid-carved terrain in the tropics, but the cause has been a mystery.

Titan1_f Emily Schaller from the University of Hawaii and her colleagues used NASA's Infrared Telescope Facility, situated on Hawaii's Mauna Kea, to monitor Titan on 138 nights over a period of two years, and on April 13, 2008, the team saw a tell-tale brightening. The researchers then turned to the NSF-supported Gemini North telescope, an 8-meter telescope also located on Mauna Kea, to capture the extremely high-resolution infrared snapshots of Titan's cloud cover, including the first storms ever observed in the moon's tropics.

The team suggests that the storms may yield precipitation capable of feeding the apparently liquid-carved channels on the planet's surface, and also influenced weather patterns throughout the moon's atmosphere for several weeks.

The second largest moon in the solar system, Titan has long been of interest for hopeful exobiologists. As the only other body we know of with surface bodies of liquid, complete with nitrogen, methane and complete seasonal weather weather patterns (similar to Earth's). It even has beaches, though you'll need a little more than a swimsuit to visit. Vast bodies of chemicals constantly stirred by wind and wave, heated over a gentle sunlight heat with the occasional dash of articles from Saturn's magnetosphere for spice - a perfect recipe for life. Just like a certain planet you might be familiar with (look down if you forget).

Of course there a few minor differences from our own blue-green globe. There's no oxygen for one thing, but if you think that's a problem then you're guilty of "aerobic respiration prejudice" (don't worry, most multicellular organisms are). It's also really quite amazingly cold - so cold that it has awesomely-named "cryovolcanoes", where boiled (or even just melted) water is enough to set off seismic-level explosions. Again, that's a barrier that's been overcome by homegrown Earth bacteria, so there's no reason it couldn't be managed elsewhere.

Cassini's onboard instruments have detected hydrocarbons containing up to seven carbon atoms. How important is that for life? Here's a hint: molecules with carbon in them are called organic, and those without are inorganic. Carbon is kind of a big deal, and the more (and more complicated) carbon compounds present the further towards the great cosmic chemical cocktail that is "life" you are. Some scientists believe that the Titanian interior, with its greater temperature, could already host microbial life - but it'll be a while before we can check that (unless we get real lucky, and some alien cells get real unlucky, with a cryovolcano eruption). One thing's for sure - the craft is only on the sixth of forty-five planned flybys so we can expect to hear a lot more about this real soon.

PS: Yes, it is ironic that we're expecting Titanic lifeforms to be single celled.

Posted by Luke McKinney. Photo Credit: James Estrin/New York Times.

Original here

New hope for intelligent life on other planets

By Clara Moskowitz

Image: Artist's concept of the Milky Way galaxy
An artist's concept of the Milky Way galaxy, with the location of the Sun marked in yellow. Scientists think interactions between our planet and its galactic environment played a role in shaping the evolution of life on Earth.

Intelligent life beyond Earth might not be as dim a hope as many scientists think, according to a new study challenging a widely held anti-ET argument.

Many skeptics tout an idea called the anthropic argument that claims extraterrestrial intelligence must be very rare because the time it takes for intelligent life to evolve is, on the average, much longer than the portion of a star's existence that is conducive to such life.

But now astrobiologist Milan M. Cirkovic and colleagues say they've found a flaw in that reasoning.

The anthropic argument, proposed by astrophysicist Brandon Carter in 1983, following on his pioneering work on anthropic principles in 1970s, is built on the assumption that the two timescales - the lifecycle of a star and the time required for evolution of living and intelligent creatures - are completely independent. If this is true, Carter argued, it's extremely unlikely that these two windows of possibility would last roughly the same amount of time, and would occur at the same time.

But that mode of thinking is outdated, Cirkovic claims. In fact, he says the relevant timescales are not independent; they are deeply entwined. "There are many different ways in which planets in our solar system are not isolated," Cirkovic said. "We must not regard habitable planets as closed boxes. If you abandon that assumption of independence, then you have a whole new background in which you can set up various models of astrobiological development."

Cirkovic points to gamma ray bursts, nearby supernovae, and perturbations of comet clouds as possible events in the astrophysical environment of the star that can influence the biological environment on a planet. For example, when a star travels through one of the dense spiral arms of the Milky Way, both its own development and that of its planets could be disrupted by higher levels of interstellar electromagnetic radiation and cosmic rays, due to the higher frequency of star-forming regions and supernova explosions.

All these connections conspire to rule out the independence suggested by Carter and connect the life of a star and the evolution of life on a planet, Cirkovic argues.

In the case of the Earth, the two timescales have lined up fortuitously to enable life. Our Sun is about 4.6 billion years old, and Earth is just slightly younger, at 4.5 billion years old. The first, most basic cells are thought to have formed on our planet about 3.8 billion years ago, although the homo genus, to which humans belong, did not appear until about 2.5 million years ago. And modern humans are only about 200,000 years old.

For more than 80 percent of the Sun's existence, life has existed in some form on Earth. It seems the timescales of biology and astrophysics have favorably aligned in our case. According to the anthropic argument, this coincidence means that Earth, and its life, are unique. But Cirkovic thinks the two timescales may not have overlapped by chance. Instead, they may be part of a complex history, involving interdependence of the Earth system with the rest of the Milky Way.

Clocking Catastrophes
Cosmic events like gamma ray bursts or nearby supernovae could reset the astrobiological clock to give a planet and star a second chance to sync up and try again to produce life. Gamma ray bursts are mysterious explosions that release huge amounts of energy, occurring either as the dying explosions of super-massive stars (like Eta Carinae) or collisions of neutron stars in close binary systems. If a gamma ray burst occurred in a large region near a planetary system, it might cause a flash of radiation and possibly cosmic-ray jets that could disrupt life on planets. Supernova explosions, though not quite as energetic as gamma ray bursts (but much more frequent overall), pack quite a wallop as well, and could send a shock of energy to any nearby planets.

"A gamma ray burst won't affect whether life will begin at some particular point in time, but it would affect how quickly life develops or takes hold by causing changes in atmospheric chemistry on the planet," Cirkovic said. "This can be interpreted as resetting astrobiological clocks which tick on each habitable planet in the Milky Way."

This idea leads to a new way of thinking about the origin of life. Instead of a long, gradual evolution, a catastrophic event could spur development of a complex biosphere and intelligent beings, much like the evolutionary theory of punctuated equilibrium predicts that species will undergo long periods of slow evolution punctuated by brief bouts of drastic change.

For instance, paleontologists say that human beings evolved to our present state only thanks to an asteroid impact 65 million years ago that wiped out the planet's primary predator – the dinosaur. Earth has over the course of its history experienced many mass extinctions that had various causes. While extinctions wipe out life, they are also a "reset" button that alters the environment and allows other types of life to emerge. Overall, this is part of a complex set of astrobiological histories that Cirkovic and colleagues dub the "astrobiological landscape" of our Galaxy.

"The speed of evolution is very variable," Cirkovic said. "There is no reason to think that life on Earth has only one single origin. It is quite possible that there were several beginnings of life on Earth."

Cirkovic also notes that the evolution of intelligent life could occur slower or faster in different settings, and need not follow the astrobiological history of the Milky Way.

"Large-scale correlations might cause more such SETI targets to be contemporary with us than would be expected on the basis of planetary age distribution only," Cirkovic said.

Cirkovic and team outline their argument in the June 2009 issue of the journal Astrobiology.

© 2009