By JOHN GEROME Sunday, May 11, 2008 Carrie Underwood is the newest member of the Grand Ole Opry. via WQXI-AM Atlanta

The greater dwarf cloud rat (Carpomys melanurus) has dense, soft reddish-brown fur, a black mask around large dark eyes, small rounded ears, a broad and blunt snout, and a long tail covered with dark hair. An adult weighs about 185 grams.

“This beautiful little animal was seen by biologists only once previously ??C by a British researcher in 1896 who was given several specimens by local people, so he knew almost nothing about the ecology of the species,” said Lawrence Heaney, Curator of Mammals at the Field Museum and Project Leader. “Since then, the species has been a mystery, in part because there is virtually no forest left on Mt. Data, where it was first found.”

On 24 April, the research team completed its field work, the first comprehensive survey of the small mammals of Mt. Pulag National Park, according to Samuel Penafiel, the Regional Executive Director for the Philippine Department of Environment and Natural Resources for the Cordillera Administrative Region. Among the results was the capture of the dwarf cloud rat, which is a smaller relative of the giant clouds rats, spectacular animals found only on Luzon Island, but widespread and comparatively well known.

The dwarf cloud rat was captured by Danilo Balete, Project Co-Leader and Research Associate of the Philippine National Museum, in a patch of mature mossy forest (also called cloud forest) high on Mt. Pulag, at about 2,350 meters above sea level. It was in the canopy of a large tree, on a large horizontal branch covered by a thick layer of moss, orchids, and ferns, about 5 meters above ground, Balete said. “We had suspected from its broad, hand-like hind feet that it lived up in big trees, but this is the first evidence to confirm that.”

Since this is the first time the dwarf cloud rat has been seen in its natural habitat, the data collected from this specimen “will significantly augment our understanding of how these rodents evolved, what makes them tick, and how we can keep them around,” said William Stanley, Collections Manager of Mammals at The Field Museum. “Also, finding this animal again gives us hope for the conservation of one of the most diverse and threatened mammal faunas of the world.”

The research team thinks that this species probably lives only high in the big canopy trees in mature mossy forest, at elevations from about 2,200 to 2,700 meters, high in the mountains of the Central Cordillera. “Now that we know where to look for them, it will be possible to learn more,” Heaney said.

Much of the mossy forest in Mt. Pulag National Park where the biologists found the dwarf cloud rat was logged during the 1960s, and few large trees remain. The mossy forest has been gradually regenerating, but many local people now have vegetable farms there, and some of the mossy forest has disappeared as a result, according to Park Superintendent Emerita Albas. “Other parts of the park have extensive areas of mossy forest,” she said. “But where there are roads into the park, the vegetable farms are expanding. The people deserve to have a place to live and to have their farms, but the mossy forest needs to be protected.”

The mossy forest is like a giant sponge when it rains, soaking up the water and releasing it gradually. This produces clean water for irrigation, household use, hydroelectric dams, and industry in the lowlands. The mossy forest gets up to 5 or 6 meters of rain per year, or more.

Most of the species that the team documented on Mt. Pulag live only in the Central Cordillera, and most live only in mossy forests. Other unusual species documented by this research team during this survey are the bushy-tailed cloud rat, a spectacular animal of 1.5 kg with long, flowing black fur that they found to be common in mossy forest at 2,600 to 2,800 meters elevation, as well as three species of small rodents that feed primarily on earthworms. One of these small rodents was originally discovered by the same Field Museum research team and formally described as a new species only in 2006. Mt. Pulag is the only place currently known that has four species of cloud rats known to be present.

The team found that the pest rodents that cause damage around buildings and in the vegetable gardens on Mt. Pulag are not native species. Instead they are species, such as the Norway rat, that were accidentally brought to the Philippines centuries ago. The native species avoid humans, live in the forest, and cause very little if any economic damage. Some, like the dwarf cloud rat, probably are not able to withstand much disturbance of their natural habitat.

Cloud rats are one of the most spectacular cases of adaptive radiation by mammals anywhere in the world, with at least 15 species ranging in size from 2.6 kg to 15 grams, all living only in the Philippines. Cloud rats are a prime example of why biologists refer to the Philippines as “the Galapagos times ten,” Heaney said. “The Philippines may have the greatest concentration of unique biological diversity, relative to its size, of any country in the world.”

[Greg Borzogborzo @ Field Museum]

In a paper published today in Nature Biotechnology, researchers led by Los Alamos National Laboratory and the U.S. Department of Energy Joint Genome Institute announced that the genetic sequence of the fungus Tricoderma reesei has uncovered important clues about how the organism breaks down plant fibers into simple sugars. The finding could unlock possibilities for industrial processes that can more efficiently and cost effectively convert corn, switchgrass and even cellulose-based municipal waste into ethanol. Ethanol from waste products is a more-carbon-neutral alternative to gasoline.

The fungus T. reesei rose to dubious fame during World War II when military leaders discovered it was responsible for rapid deterioration of clothing and tents in the South Pacific. Named after Dr. Elwyn T. Reese, who, with colleagues, originally isolated the hungry fungus, T. reesei was later identified as a source of industrial enzymes and a role model for the conversion of cellulose and hemicellulose — plant fibers — into simple sugars.

The organism uses enzymes it creates to break down human-indigestible fibers of plants into the simplest form of sugar, known as a monosaccharide. The fungus then digests the sugars as food.

Researchers decoded the genetic sequence of T. reesei in an attempt to discover why the deep green fungus was so darned good at digesting plant cells. The sequence results were somewhat surprising. Contrary to what one might predict about the gene content of a fungus that can eat holes in tents, T. reesei had fewer genes dedicated to the production of cellulose-eating enzymes than its counterparts.

“We were aware of T. reesei’s reputation as producer of massive quantities of degrading enzymes, however we were surprised by how few enzyme types it produces, which suggested to us that its protein secretion system is exceptionally efficient,” said Los Alamos bioscientist Diego Martinez (also at the University of New Mexico), the study’s lead author. The researchers believe that T. reesei’s genome includes “clusters” of enzyme-producing genes, a strategy that may account for the organism’s efficiency at breaking down cellulose.

On an industrial scale, T. reesei could be employed to secrete enzymes that can be purified and added into an aqueous mixture of cellulose pulp and other materials to produce sugar. The sugar can then be fermented by yeast to produce ethanol.

“The sequencing of the Trichoderma reesei genome is a major step towards using renewable feedstocks for the production of fuels and chemicals,” said Joel Cherry, director of research activities in second-generation biofuels for Novozymes, a collaborating institution in the study. “The information contained in its genome will allow us to better understand how this organism degrades cellulose so efficiently and to understand how it produces the required enzymes so prodigiously. Using this information, it may be possible to improve both of these properties, decreasing the cost of converting cellulosic biomass to fuels and chemicals.”

[James E. Rickman @ DOE/Los Alamos National Laboratory]

The dime-sized laser, to be described Thursday, May 8, at the Conference on Lasers and Electro-Optics, emits 10 billion pulses per second, each lasting about 40 femtoseconds (quadrillionths of a second), with an average power of 650 milliwatts. For comparison, the new laser produces pulses 10 times more often than a standard NIST frequency comb while producing much shorter pulses than other lasers operating at comparable speeds. The new laser is also 100 to 1000 times more powerful than typical high-speed lasers, producing clearer signals in experiments. The laser was built by Albrecht Bartels at the Center for Applied Photonics of the University of Konstanz.

Among its applications, the new laser can be used in searches for planets orbiting distant stars. Astronomers look for slight variations in the colors of starlight over time as clues to the presence of a planet orbiting the star. The variations are due to the small wobbles induced in the star’s motion as the orbiting planet tugs it back and forth, producing minute shifts in the apparent color (frequency) of the starlight. Currently, astronomers’ instruments are calibrated with frequency standards that are limited in spectral coverage and stability. Frequency combs could be more accurate calibration tools, helping to pinpoint even smaller variations in starlight caused by tiny Earthlike planets. Such small planets would cause color shifts equivalent to a star wobble of just a few centimeters per second. Current instruments can detect, at best, a wobble of about 1 meter per second.

Standard frequency combs have “teeth” that are too finely spaced for astronomical instruments to read. The faster laser is one approach to solving this problem. In a separate paper, the NIST group and astronomer Steve Osterman at the University of Colorado at Boulder describe how, by bouncing the light between sets of mirrors a particular distance apart, they can eliminate periodic blocks of teeth to create a gap-toothed comb. This leaves only every 10th or 20th tooth, making an ideal ruler for astronomy.

Both approaches have advantages for astronomical planet finding and related applications. The dime-sized laser is very simple in construction and produces powerful and extremely well-defined comb teeth. On the other hand, the filtering approach can cover a broader range of wavelengths. Four or five filtering cavities in parallel would provide a high-precision comb of about 25,000 evenly spaced teeth that spans the visible to near-infrared wavelengths (400 to 1100 nanometers), NIST physicist Scott Diddams says.

Osterman says he is pursuing the possibility of testing such a frequency comb at a ground-based telescope or launching a comb on a satellite or other space mission. Other possible applications of the new laser include remote sensing of gases for medical or atmospheric studies, and on-the-fly precision control of high-speed optical communications to provide greater versatility in data and time transmissions. The application of frequency combs to planet searches is of international interest and involves a number of major institutions such as the Max-Planck Institute for Quantum Optics and Harvard Smithsonian Center for Astrophysics.

[Laura Ost @ National Institute of Standards and Technology (NIST)]