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BERKELEY, Calif — In the middle of the South Pacific, about 12 miles west of Tahiti, is a tropical island that soon will emerge as a model ecosystem, thanks to the efforts of a U.S.-French research team led by University of California, Berkeley, biologists.

Moorea, home of the UC Berkeley Richard B. Gump South Pacific Research Station and France’s Centre de Recherches Insulaires et Observatoire de l’Environnement (CRIOBE), will be the site of an ambitious project to create a comprehensive inventory of all non-microbial life on the island. Supported by a new $5.2 million grant from the Gordon and Betty Moore Foundation, the Moorea Biocode Project over the next three years will send researchers climbing up jagged peaks, trekking through lush forests and diving down to coral reefs to sample the French Polynesian island’s animal and plant life.

“This is the first effort to catalog and barcode an entire tropical ecosystem, from the bottom of the ocean to the top of the mountains,” said George Roderick, UC Berkeley professor of environmental science, policy and management, curator of the campus’s Essig Museum of Entomology and co-principal investigator of the project.

“We’re constructing a library of genetic markers and physical identifiers for every species of plant, animal and fungi on the island, then making that database publicly available as a resource for ecologists and evolutionary biologists around the world,” he said. Roderick is a former director of the Gump Station, where the National Science Foundation has established one of its 26 Long Term Ecological Research sites (the Moorea Coral Reef LTER).

The work will expand upon a 2005 pilot biocode project at Moorea, also funded by the Moore Foundation, which tested the feasibility of such a large undertaking. That project was limited to genetic barcoding of the fishes, geckos and selected insects.

In the spirit of leaving no stone unturned, larvae and contents of animals’ guts will be fair game in the full project. “We’ll check the gut contents of a gecko, spider or fish to find out what it’s eating,” said Chris Meyer, who managed the pilot project while he was a researcher at UC Berkeley.

There are an estimated 5,000 plant, animal and fungal species on Moorea, although that number may change as cryptic communities and organisms are sampled and genetic markers reveal novel species. “I’d be disappointed if we don’t hit at least 10,000 species,” said Meyer.

The number of species on the 51-square-mile island of Moorea is small compared with that on larger islands and continents. In California, for example, the number of insect species alone tops 30,000. Yet, the researchers say Moorea provides the right balance of being small enough to be studied manageably while being sufficiently complex to reliably serve as a microcosm of the challenges faced in larger ecosystems.

At the end of the three-year project, the Moorea Biocode Project will have sequenced a whole tropical ecosystem. “Like the Human Genome Project, however, this unprecedented accomplishment is, in some ways, merely a necessary first step,” said Davies. “Its goal is to accelerate progress on the larger questions: how to maintain a healthy ecosystem and what to do when things go wrong.” More at UC Berkeley, Berkeley.edu/Biocode. Photo Credits: UC Berkeley.

Cataloging an ecosystem
UC Berkeley biologist George Roderick talks about working on the South Pacific island of Moorea and an ambitious project to create a genetic inventory of all non-microbial life in the island’s ecosystem. (2:06 min. Flash video)

Nanotubes may have high-tech applications, study involving UCR engineers reports.

RIVERSIDE, Calif — Dec 07, ‘07 — Two engineers at the University of California, Riverside are part of a binational team that has found semiconducting nanotubes produced by living bacteria – a discovery that could help in the creation of a new generation of nanoelectronic devices.

The research team believes this is the first time nanotubes have been shown to be produced by biological rather than chemical means. It opens the door to the possibility of cheaper and more environmentally friendly manufacture of electronic materials.

Study results appear in today’s issue of the early edition of the Proceedings of the National Academy of Sciences.

The team, including Nosang V. Myung, associate professor of chemical and environmental engineering in the Bourns College of Engineering, and his postdoctoral researcher Bongyoung Yoo, found the bacterium Shewanella facilitates the formation of arsenic-sulfide nanotubes that have unique physical and chemical properties not produced by chemical agents.

“We have shown that a jar with a bug in it can create potentially useful nanostructures,” Myung said. “Nanotubes are of particular interest in materials science because the useful properties of a substance can be finely tuned according to the diameter and the thickness of the tubes.”

The whole realm of electronic devices which power our world, from computers to solar cells, today depend on chemical manufacturing processes which use tremendous energy, and leave behind toxic metals and chemicals. Myung said a growing movement in science and engineering is looking for ways to produce semiconductors in more ecologically friendly ways.

Two members of the research team, Hor-Gil Hur and Ji-Hoon Lee from Gwangju Institute of Science and Technology (GIST), Korea, first discovered something unexpected happening when they attempted to remediate arsenic contamination using the metal-reducing bacterium Shewanella. Myung, who specializes in electro-chemical material synthesis and device fabrication, was able to characterize the resulting nano-material.

The photoactive arsenic-sulfide nanotubes produced by the bacteria behave as metals with electrical and photoconductive properties. The researchers report that these properties may also provide novel functionality for the next generation of semiconductors in nano- and opto-electronic devices.

In a process that is not yet fully understood, the Shewanella bacterium secretes polysacarides that seem to produce the template for the arsenic sulfide nanotubes, Myung explained. The practical significance of this technique would be much greater if a bacterial species were identified that could produce nanotubes of cadmium sulfide or other superior semiconductor materials, he added.

“This is just a first step that points the way to future investigation,” he said. “Each species of Shewanella might have individual implications for manufacturing properties.” More at University of California, Riverside.

IRVINE, Calif — Dec 05, ‘07 — The herbal extract of a yellow-flowered mountain plant indigenous to the Arctic regions of Europe and Asia increased the lifespan of fruit fly populations, according to a University of California, Irvine study.

Flies that ate a diet rich with Rhodiola rosea, an herbal supplement long used for its purported stress-relief effects, lived on an average of 10 percent longer than fly groups that didn’t eat the herb. Study results appear in the online version of Rejuvenation Research.

“Although this study does not present clinical evidence that Rhodiola can extend human life, the finding that it does extend the lifespan of a model organism, combined with its known health benefits in humans, make this herb a promising candidate for further anti-aging research,” said Mahtab Jafari, a professor of pharmaceutical sciences and study leader. “Our results reveal that Rhodiola is worthy of continued study, and we are now investigating why this herb works to increase lifespan.”

In their study, the UC Irvine researchers fed adult fruit fly populations diets supplemented at different dose levels with four herbs known for their anti-aging properties. The herbs were mixed into a yeast paste, which adult flies ate for the duration of their lives. Three of the herbs – known by their Chinese names as Lu Duo Wei, Bu Zhong Yi Qi Tang and San Zhi Pian – had no effect on fruit fly longevity, while Rhodiola was found to significantly reduce mortality. On average, Rhodiola increased survival 3.5 days in males and 3.2 days in females.

Rhodiola rosea, also known as the golden root, grows in cold climates at high altitudes and has been used by Scandinavians and Russians for centuries for its anti-stress qualities. The herb is thought to have anti-oxidative properties and has been widely studied.

Soviet researchers have been studying Rhodiola since the 1940s on athletes and cosmonauts, finding that the herb boosts the body’s response to stress. And earlier this year, a Nordic Journal of Psychiatry study on people with mild-to-moderate depression showed that patients taking a Rhodiola extract called SHR-5 reported fewer symptoms of depression than did those who took a placebo.

Jafari said she is evaluating the molecular mechanism of Rhodiola by measuring its impact on energy metabolism, oxidative stress and anti-oxidant defenses in fruit flies. She is also beginning studies in mice and in mouse and human cell cultures. These latter studies should help understand the benefits of Rhodiola seen in human trials. More at University of California, Irvine.

Amsterdam, The Netherlands — Dec 04, ‘07 — At the annual Nokia World conference today, Nokia Oyj announced it has agreed with the world’s largest music group Universal to offer free 12-month access to Universal artists’ music for buyers of Nokia’s music phones.

The world’s top cellphone maker said it has signed up Universal Music Group International, owned by French media giant Vivendi, for its new “Comes With Music” offering and is eyeing similar deals with other labels before the offer starts in the second half of 2008.

Nokia said the new offering would differ from other packages on the market as consumers can keep all the music they have downloaded for free during the 12 month period.

“We set out to create the music experience that people are telling us they are looking for - all the music they want in the form of unlimited downloads to their mobile device and PC,” said Anssi Vanjoki, Executive Vice President and General Manager, Multimedia, Nokia.

“Even if you listened to music 24 hours a day, seven days a week, you would still only scratch the surface of the music that we’re making available. Comes with Music fulfils our dream to give consumers all the music they want, wherever they want it, while rewarding the artists who create it.”

“The financial barrier to try new music is completely removed. It fundamentally changes a lot of business logic in the music industry,” said Nokia spokesman Damian Stathonikos. The free access to new music could hurt peer-to-peer networking while also raising pressure on Apple Inc.

Nokia outlines its vision of Internet evolution and commitment to environmental sustainability:

Ovi - your personal dashboard to life
Nokia also gave further details of the upcoming Ovi Internet services environment. Ovi, meaning ‘door’ in Finnish, enables consumers to easily access their existing social network and content, acting as a dashboard to a person’s life.

“Ovi combines the mobile, PC and web environments into an easy to use experience with common user interface elements that provide consistency and simplicity,” said Vanjoki. “We started the Ovi services rollout with the individual services in navigation, music and games, and the next step is to provide an integrated experience. The complete Ovi environment and new services will be rolled out continuously throughout 2008.”

Towards greater environmental sustainability
Nokia also outlined its long heritage in addressing environmental issues and commitment to driving new initiatives in the mobile industry in areas such as energy efficiency, materials used in products, take back, recycling, and packaging. This was against the background of the launch of the Nokia 3110 Evolve, a mobile device with bio-covers made from more than 50% renewable material. The device is presented in a small package made of 60% recycled content and it comes with Nokia’s most energy efficient charger yet, using 94% less energy than the Energy Star requirements. More at Nokia.

WASHINGTON –BUSINESS WIRE– Dec 02, ‘07 — Carl Zeiss SMT today introduced the new CENTRA 100 transmission electron microscope (TEM) at the 47th Annual Meeting of the American Society of Cell Biology in Washington D.C.

The CENTRA 100 is a TEM with up to 100 kV accelerating voltage. Specially designed as a sophisticated “imaging system”, the highly compact and robust instrument offers maximum resolution down to 0.2 nm. The ease-of-use and fast specimen exchange capability make this microscope particularly well-suited for biomedical or clinical laboratory environments.

A key technical feature of the system is the choice between two different imaging modes: high resolution and high contrast. This is particularly important for investigating low-contrast biological specimens. The specially developed mini-lens design leads to a very compact size where the electron-optical lens elements exhibit only minimum aberration.

The use of four lens elements in the projection system enables rotation-free imaging while the magnification is being changed. Furthermore, additional deflection systems support the image-fine-shift that enables the generation of panorama images.

Researchers at the National Institute of Standards and Technology (NIST) and George Mason University have demonstrated what is probably the world’s smallest microwave oven, a tiny mechanism that can heat a pinhead-sized drop of liquid inside a container slightly shorter than an ant and half as wide as a single hair. The micro microwave is intended for lab-on-a-chip devices that perform rapid, complex chemical analyses on tiny samples.

In a paper in the November 2007 Journal of Micromechanics and Microengineering, the research team led by NIST engineer Michael Gaitan describes for the first time how a tiny dielectric microwave heater can be successfully integrated with a microfluidic channel to control selectively and precisely the temperature of fluid volumes ranging from a few microliters (millionth of a liter) to sub-nanoliters (less than a billionth of a liter).

Sample heating is an essential step in a wide range of analytic techniques that could be built into microfluidic devices, including the high-efficiency polymerase chain reaction (PCR) process that rapidly amplifies tiny samples of DNA for forensic work, and methods to break cells open to release their contents for study.

The team embedded a thin-film microwave transmission line between a glass substrate and a polymer block to create its micro microwave oven. A trapezoidal-shaped cut in the polymer block only 7 micrometers across at its narrowest—the diameter of a red blood cell—and nearly 4 millimeters long (approximately the length of an ant) serves as the chamber for the fluid to be heated.

Based on classical theory of how microwave energy is absorbed by fluids, the research team developed a model to explain how their minature oven would work. They predicted that electromagnetic fields localized in the gap would directly heat the fluid in a selected portion of the micro channel while leaving the surrounding area unaffected.

Measurements of the microwaves produced by the system and their effect on the fluid temperature in the micro channel validated the model by showing that the increase in temperature of the fluid was predominantly due to the absorbed microwave power.

Once the new technology is more refined, the researchers hope to use it to design a microfluidic microwave heater that can cycle temperatures rapidly and efficiently for a host of applications.

The work is supported by the Office of Science and Technology at the Department of Justice’s National Institute of Justice. NIST.

Emily Singer at TechnologyReview writes an in-depth article on  The emerging field of connectomics could help researchers decode the brain’s approach to information processing.

“New technologies that allow scientists to trace the fine wiring of the brain more accurately than ever before could soon generate a complete wiring diagram–including every tiny fiber and miniscule connection–of a piece of brain. Dubbed connectomics, these maps could uncover how neural networks perform their precise functions in the brain, and they could shed light on disorders thought to originate from faulty wiring, such as autism and schizophrenia.

“The brain is essentially a computer that wires itself up during development and can rewire itself,” says Sebastian Seung, a computational neuroscientist at MIT. “If we have a wiring diagram of the brain, that could help us understand how it works.” For example, scientists previously identified the part of the songbird’s brain that is important in the birds’ ability to generate songs. Seung would ultimately like to develop a wiring diagram of this structure in order to elucidate the features underlying its unique capability.

Only one organism’s wiring diagram currently exists: that of the microscopic worm C. elegans. Despite containing a mere 302 neurons, the C. elegans mapping effort took more than a decade to complete, in the 1970s. It has been an invaluable research resource and earned its creators a Nobel Prize.

With an estimated 100 billion neurons and 100 trillion synapses in the human brain, creating an all-encompassing map of even a small chunk is a daunting task. Using standard methods, it would take roughly three billion person years to generate the wiring diagram of a single cortical column, a narrow functional unit of neurons in the cortex, estimates Winfried Denk, a neuroscientist at the Max Planck Institute for Medical Research in Heidelberg, Germany.

Denk, Seung, and their collaborators are now developing sensitive new imaging techniques and machine-learning algorithms to automate the construction process. They have already generated a partial wiring diagram of part of the rabbit retina. But they’ll need to make their technique a million times faster to finally bring larger maps–like that of a cortical column–into the realm of reality.

Previous efforts to map the wiring of the brain have focused on larger anatomical features, such as the thick wiring tracts that connect different parts of the brain, or on the paths of single neurons, stained a particular color to distinguish them from their tangled multitude of neighbors.

But to truly understand how a network of neurons can perform a particular function, scientists need a new kind of map. “A lot of properties of brain function are at the level of the circuit–information is being integrated, processed, extracted,” says Elly Nedivi, a neuroscientist at MIT who is not involved with the research. “To understand what that means, you need to be able to see who connects to who.”

Denk and his colleagues developed a new technique to make more fine-scaled wiring maps using electron microscopy. Starting with a small block of brain tissue, the researchers bounce electrons off the top of the block to generate a cross-sectional picture of the nerve fibers in that slice. They then take a very thin–30-nanometer–slice off the top of the block and repeat the process. Scientists go through the images slice by slice to trace the path of each nerve fiber. “Repeat this [process] thousands of times, and you can make your way through maybe the whole fly brain,” says Denk.

Seung and Denk aim to dramatically speed up the tracing process, which takes a single graduate student weeks to complete, with automated machine-learning algorithms. The researchers use data from a manually generated wiring diagram to train an artificial neural network to emulate the human tracing process. They can then use the resulting algorithm to analyze new chunks of brain tissue. To date, they’ve been able to speed the process about one hundred- to one thousand-fold.

The researchers presented their initial findings to an awed crowd at the Society for Neurosciences meeting in San Diego earlier this month. They showed the three-dimensional reconstruction of part of the rabbit retina called the inner plexiform layer, which is a piece of neural tissue at the back of the eye that senses light and sends visual information to the brain. (See a movie of the reconstruction here.) “But we need to improve 10⁶-fold or more,” says Denk, who estimates that this would shrink the three billion person years it would take to trace a cortical column down to about two years. “I’m confident in the end that we will be able to do it,” he says. “But I don’t know how long it will take us–if we’re lucky, maybe a year or so.”

Earlier this month, scientists at Harvard described a new method of tracing neurons in the living brain by labeling them with up to a hundred different colors. (See “The Technicolor Brain.”) “We’re starting to think about wiring diagrams as being fundamental,” says Jeff Lichtman, one of the researchers who developed the technique.

Researchers say that the two approaches will likely be complementary, allowing scientists to look at neural circuits of different dimensions. Eventually, Seung aims to generate maps of the complete fly connectome, as well as partial wiring diagrams of interesting locations in larger brains, such as the hippocampus, olfactory bulb, and retina.

Just exactly how much light these maps will shed on the brain is still somewhat controversial. “Just knowing the [wiring] data won’t take us far if we don’t put it in the framework of processing and transferring data in the brain,” says David van Essen, a neuroscientist at Washington University, in St. Louis, and president of the Society for Neurosciences. Seung and others eventually hope to generate maps that incorporate the biochemical and physiological properties of various cells into the wiring diagrams.” TechnologyReview.