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 platypus, classified as a mammal because it produces milk and is covered in a coat of fur, also possesses features of reptiles, birds and their common ancestors, along with some curious attributes of its own. One of only two mammals that lays eggs, the platypus also sports a duck-like bill that holds a sophisticated electrosensory system used to forage for food underwater. Males possess hind leg spurs that can deliver pain-inducing venom to its foes competing for a mate or territory during the breeding season.

“The fascinating mix of features in the platypus genome provides many clues to the function and evolution of all mammalian genomes,” says Richard K. Wilson, Ph.D., director of the The Genome Center at Washington University and the paper’s senior author. “By comparing the platypus genome to other mammalian genomes, we’ll be able to study genes that have been conserved throughout evolution.”

The platypus represents the earliest offshoot of the mammalian lineage some 166 million years ago from primitive ancestors that had features of both mammals and reptiles. “What is unique about the platypus is that it has retained a large overlap between two very different classifications, while later mammals lost the features of reptiles,” says Wes Warren, Ph.D., an assistant professor of genetics, who led the project.

Comparison of the platypus genome with the DNA of humans and other mammals, which diverged later, and the genomes of birds, whose ancestors branched off an estimated 315 million years ago, can help scientists fill gaps in their understanding of mammalian evolution. The comparison also will allow scientists to date the emergence of genes and traits specific to mammals.

The Nature paper analyzes the genome sequence of a female platypus named Glennie from New South Wales, Australia. The project was largely funded by the National Human Genome Research Institute, part of the National Institutes of Health, and includes scientists from the United States, Australia, England, Germany, Israel, Japan, New Zealand and Spain.

“At first glance, the platypus appears as if it was the result of an evolutionary accident,” says Francis S. Collins, M.D., Ph.D., director of NHGRI. “But as weird as this animal looks, its genome sequence is priceless for understanding how mammalian biological processes evolved.”

“While we’ve always been able to compare and consider all of these creatures on the basis of their physical characteristics, internal anatomy and behavior, it’s truly amazing to be able to compare their genetic blueprints and begin to get a close-up look at how evolution brings about change,” Wilson says.

As part of their analysis, the researchers compared the platypus genome with genomes of the human, mouse, dog, opossum and chicken. They found that the platypus shares 82 percent of its genes with these animals. The chicken genome was chosen because it represents a group of egg-laying animals, including extinct reptiles, which passed on much of their DNA to the platypus and other mammals over the course of evolution.

The researchers also found genes that support egg laying - a feature of reptiles - as well as lactation - a characteristic of all mammals. Interestingly, the platypus lack nipples, so its young nurse through the abdominal skin.

The researchers also attempted to determine which characteristics of the platypus were linked to reptiles at the DNA level. When they analyzed the genetic sequences responsible for venom production in the male platypus, they found it arose from duplications in a group of genes that evolved from ancestral reptile genomes. Amazingly, duplications in the same genes appear to have evolved independently in venomous reptiles.

The platypus swims with its eyes, ears and nostrils closed, relying on electrosensory receptors in its bill to detect faint electric fields emitted by underwater prey. Surprisingly, the researchers found the genome contains an expansion of genes that code for a particular type of odor receptor. “We were expecting very few of these odor receptor genes because the animals spend the majority of their life in the water,” Warren says.

Similar genes are found in animals that rely on a sense of smell, such as rodents and dogs, and the scientists suspect that their addition in the platypus allows the animals to detect odors while foraging underwater.

At roughly 2.2 billion base pairs, the platypus genome is about two-thirds the size of the human genome and contains about 18,500 genes, similar to other vertebrates. The animal has 52 chromosomes, including an unusual number of sex chromosomes: 10. The platypus X chromosome bears resemblance to the sex chromosome of a bird, known as Z.

Sequencing and assembling the platypus genome proved far more daunting than sequencing any other mammalian genome to date. About 50 percent of the genome is composed of repetitive elements of DNA, which makes it a challenge to assemble properly.

The platypus genome sequence, along with those for other organisms, such as the mouse, dog, cow, and many other animals can be accessed at GenBank (www.ncbi.nih.gov/Genbank) at NIH’s National Center for Biotechnology Information.

[Caroline Arbanas @ Washington University School of Medicine]

Motorola’s Z9 is a slider phone with a mahogany exterior, which is a nice color to differentiate the Z9 from the rest. The external controls continue to be standard with a volume rocker and music shortcut on the left spine, and a camera shutter and a microUSB port on the right spine. The front packs a gorgeous 2.4-inch display with 262k color support, a crispness that’s required to view today’s digital content, including videos, photos and text. We had a blast navigating through the menu just because the display was so vibrant and exciting to use. Of course similar to a lot of smartphones, you can adjust the brightness and backlighting time to conserve battery, and trust us, with the display this bright, you are almost certainly going to have to work on reducing the brightness.

Going back to the navigation menu, do note that Motorola hasn’t updated its menu at all. It’s the same old way of browsing through your phone. We’re not pleased; half of the fun of getting a new phone is to take advantage of new features, and the Z9 is lackluster in that category.

Underneath the display is your OK button with four corresponding keys for navigation. Additionally, there are two soft keys, Talk/End-Power keys, a Clear-Back key and a Web browser shortcut key to further occupy the rest of the device.

Once you slide open the phone, you are welcomed to its keypad with alphanumeric keys. All keys offer tactile feedback that are difficult to feel. The keys underneath the display, especially, didn’t offer the best tactile feedback that we have experienced. Motorola needs to work on getting the most basic necessities of the phone right.

On the back, you will find the integration camera with its lens and flash. It’s a 2.0-megapixel camera with support for four resolutions (1,600×200, 1,280×960, 640×480, 320×240), three quality settings and 8x digital zoom. Other options, such as lighting (five), color tones (six), and exposure metering are all present. You can also record video in three resolutions (320×240, 176×144 and 128×96) with three quality settings. You can record for up to 30 seconds for MMS clips, or for an unlimited amount of time depending on onboard storage. The phone is equipped with 45MB of onboard storage + a microSD expandable slot for additional memory. There’s a memory meter to alert of you of total available memory, a delightful option.

The Z9 lacks a mirror, so taking self-portraits would be an interesting task at best. The camera quality was decent. It took crisp pictures, but there was some blurriness in them due to dull lighting. Even in the brightest of times, the photo quality didn’t quite get the colors right. While sharp, there were some issues with color contrast in our testing. We would qualify the overall quality to be good with reservations, or decent.

Motorola’s Z9 feels good when you are holding it, as it’s a sturdy, solid unit.

In addition to the onboard camera, it packs an alarm clock, a calendar, text and multimedia messaging and a host of other default, expected features. Most notable is AT&T’s Navigator GPS application, AT&T’s Video Share service, AT&T Music (thanks to 3G support), and a music player with support for MP3, AAC and WMA formats; playlists, shuffle and repeat modes; it also packs a host of mobile multimedia (music, video and weather) services to round out its features set. We liked the feature set in general. Although it’s limited in its potential, Motorola did its best to include as many applications as the phone would hold.

On the performance side, in one word: “Excellent!” The Z9 is an amazing phone with its excellent audio quality. We had no problem understanding callers, or vice versa, thanks to Motorola’s CrystalTalk and auto background noise canceling technology. The phone automatically adjusted our volume depending on extraneous noise, which is something we are greatly fond of with Motorola handsets.

The speakerphone was good, but not quite there with standard output. The volume output was poor, and we really had to focus on what callers were saying to understand them. That defeats the point of turning on the speakerphone option.

Signal strength for 3G was superior and so were audio and video streaming. Though video quality was okay, it was expected. Our videos didn’t pause for buffer or any other technical issues. We loved interacting with our digital control through Z9 and its speedy connection. For some odd reason, however, loading time for music and video files was all over the graph. Some files took longer to load, while others were fairly rapid.

Volume output for audio on the phone was surprising good, especially with a headset.

The Z9 is rated for four hours of talk time and 13 days of standby time. We confirmed these numbers in our lab, and they were inline with the company’s estimates. Four hours is a little iffy for our taste considering it’s a multimedia phone with a handful of battery heavy options.

All in all, the Z9 is a very good phone with solid exterior and a host of features. It’s not the phone for consumers who are looking for mobile innovation, but if you just want a cell phone without a learning curve, but with a bit trendy design, the Z9 is a superb option.

[Gundeep Hora]

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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)]