Thursday, May 13, 2010


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A rose by any other name may smell as sweet, but it would no longer be a rose. If a grass is booted out of the grass family, where does it go?

Leah Morris and Dr. Melvin Duvall from Northern Illinois University recently investigated the evolution of grasses, one of the most economic and ecologically important plant families, by sequencing the chloroplast DNA of an early diverging grass genus, Anomochloa, and comparing it to the chloroplasts of other grasses. Their results are published in the April issue of the American Journal of Botany ( There is only one known species of Anomochloa, and it is native to the coastal forests of Brazil in an increasingly fragmented habitat.

By comparing chloroplast genomes of grasses and related families, scientists have observed distinctive evolutionary characters of particular groups of plants, such as the presence or absence of certain genes, introns (non-coding sequences inside genes), and pseudogenes (sequences that resemble closely known genes, but are non-functional). Characters associated specifically with grasses have been based on the chloroplast genome of some of the most commonly studied species, among them the economically important rice, maize, wheat, barley, and bamboo.

However, none of these grasses are part of the small group of species—Anomochlooideae—that is thought to have been among the first to diverge in the evolutionary history of the grass family. The genus Anomochloa, one of two genera in Anomochlooideae, has presented challenges to investigators attempting to understand exactly how it relates to other grasses due to its striking morphogical differences—it has four anthers, where other grasses commonly have three (or occasionally one or six). In addition, the inflorescence of Anomochloa resembles the spikelet inflorescence seen in other grasses, but yet is not a true spikelet, making it difficult to compare "apples to apples."

Morris and Duvall's examination of the chloroplast sequence uncovered features the Anomochloa chloroplast shares with other grasses, features unique to Anomochloa, and features that call into question our definition of grasses or the classification of Anomochloa as a grass.

Among the unique features of the Anomochloa chloroplast are two that are found in the same operon—a cluster of related genes—called the RNA polymerase operon. An intron is present in the rpoC1 genes of all monocots other than the grasses previously studied, and the otherwise rare loss of this intron has long been thought to be a defining feature of grasses. However, the intron is present in Anomochloa. Anomochloa is also unusual in that it contains a uniquely short insert in the rpoC2 locus. Taxa closely related to grasses do not have this extra sequence at all; other grasses that have been studied have an insert that is nearly twice as long (about 400 nucleotides) as that found in Anomochloa.

Also notable is the fact that Anomochloa is missing the rpl23 pseudogene, another diagnostic marker in all other grasses. These features of Anomochloa require scientists to either revise their criteria of what characters are essential to a plant's identification as a grass or remove Anomochloa from the grass family.

Anomochloa may appear the same today as it did 100 years ago, but our understanding has changed, and Anomochloa may have to find a new family.

American Journal of Botany


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X-ray studies and fundamental calculations are helping physicists gain molecular level insight into the workings of some magnetic shape-memory materials, which change shape under the influence magnetic fields. Shape-memory materials could potentially serve as light weight, compact alternatives to conventional motors and actuators.

But developing practical devices will require creating materials that exhibit much larger changes in shape than most of the known shape-memory materials. A paper appearing in the April 25 issue of Physical Review Letters reports on the efforts of a team of Japanese physicists who probed the changes in a magnetic shape-memory material at the molecular scale. The work is highlighted with a Viewpoint article by Antoni Planes (Universitat de Barcelona) in the April 25 edition of APS Physics (

The new research focused on a shape-memory alloy made up of nickel, manganese and tin. In its ideal form, the alloy is a crystal with each element occupying specific crystal locations relative to one another. In some versions, however, excess manganese atoms replace some of the tin atoms. Although the compositional change is slight, it can have significant effects on the alloy's behavior. X-ray spectroscopy allowed the researchers to observe the microscopic characteristics of the alloy to see precisely how the excess manganese atoms affect the alloy's behavior.

By studying the way that composition affects a shape-memory material, and comparing measurements to theoretical calculations, it will be possible to understand what makes the materials work, and allow physicists to develop new and improved varieties shape-changing metals.

American Physical Society


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The physiology of microbes living underground could determine the amount of carbon dioxide emitted from soil on a warmer Earth, according to a study published online this week in Nature Geoscience.

Researchers at Colorado State University, UC Irvine and the Yale School of Forestry & Environmental Studies found that as global temperatures increase, microbes in soil become less efficient over time at converting carbon in soil into carbon dioxide, a key contributor to climate warming.

Microbes, in the form of bacteria and fungi, use carbon for energy to breathe, or respire, and to grow in size and in number. A model developed by the researchers shows microbes exhaling carbon dioxide furiously for a short period of time in a warmer environment, leaving less carbon to grow on. As warmer temperatures are maintained, the less efficient use of carbon by the microbes causes them to decrease in number, eventually resulting in less carbon dioxide being emitted into the atmosphere.

“Microbes aren’t the destructive agents of global warming that scientists had previously believed,” said Steven Allison, assistant professor of ecology and evolutionary biology at UCI and lead author on the study. “Microbes function like humans: They take in carbon-based fuel and breathe out carbon dioxide. They are the engines that drive carbon cycling in soil. In a balanced environment, plants store carbon in the soil and microbes use that carbon to grow. The microbes then produce enzymes that convert soil carbon into atmospheric carbon dioxide.”

The study, “Soil-Carbon Response to Warming Dependent on Microbial Physiology,” contradicts the results of older models that assume microbes will continue to spew ever-increasing amounts of carbon dioxide into the atmosphere as the climate continues to warm. The new simulations suggest that if microbial efficiency declines in a warmer world, carbon dioxide emissions will fall back to pre-warming levels, a pattern seen in field experiments. But if microbes manage to adapt to the warmth – for instance, through increased enzyme activity – emissions could intensify.

“When we developed a model based on the actual biology of soil microbes, we found that soil carbon may not be lost to the atmosphere as the climate warms,” said Matthew Wallenstein of the Natural Resource Ecology Laboratory at Colorado State University. “Conventional ecosystem models that didn’t include enzymes did not make the same predictions.”

Mark Bradford, assistant professor of terrestrial ecosystem ecology at Yale, said there is intense debate in the scientific community over whether the loss of soil carbon will contribute to global warming. “The challenge we have in predicting this is that the microbial processes causing this loss are poorly understood,” he said. “More research in this area will help reduce uncertainties in climate prediction.”

Colorado State University


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Studying comets can be quite dangerous - especially from close up. Because the tiny particles of dust emitted into space from the so-called active regions on a comet’s surface can damage space probes. Scientists from the Max Planck Institute for Solar System Research in Germany have now developed a computer model that can locate these regions using only the information available from Earth. The new method could help calculate a safe flight route for ESA’s space probe Rosetta, which is scheduled to arrive at the comet Churyumov-Gerasimenko in 2014.

A comet’s nucleus is much more than an unvarying chunk of ice and dust. Under the Sun’s influence, volatile substances such as water, carbon dioxide, and carbon monoxide are emitted from certain regions on its surface - the so-called active regions - carrying dust particles with a diameter of up to a few centimetres into space. Seen from Earth, these fountains of dust can be discerned as jets or spiral arms that surround the comet. These structures are embedded in a sheath of gas and dust called the coma that is produced by the more uniform activity of the overall surface.

"Pictures taken from Earth show the comet and its jets as a two-dimensional projection", explains Hermann Böhnhardt from the Max Planck Institute for Solar System Research (MPS). Where exactly the dust particles and gases originate from can not therefore be well identified.

In order to localize the active regions despite this problem, the MPS-researchers chose an indirect approach that for the first time also accounts for the three dimensional shape of the comet. "Until now, computer programs trying to find the active regions assumed the comet as a sphere or ellipsoid", explains Jean-Baptiste Vincent from MPS. Since in reality comets often have quite bizarre shapes, for many applications this approach is not good enough. The researchers therefore decided to take a standard approach: While watching a comet for an entire rotation period, changes in its luminance allow its true form to be calculated.

In a next step, the researchers fed their program with an initial assumption where the active regions might be located. Additionally they made an "educated guess" concerning the physical properties of the dust particles like size and initial velocity upon emission from the nucleus. As a result, the computer simulation delivers an image as it would be seen through a telescope on Earth. By comparing this with the actual image through a telescope the model can be refined step by step until simulation and actual image agree.

Already, the new method has passed its first test: The scientists could successfully apply it to the comet Tempel 1 that was the destination of NASA’s Deep Impact Mission in 2005. "Even though ever since this mission we know where Tempel1’s active regions are, we pretended not to", explains Vincent. For their computer program the scientists only used information that was available from Earth-base observations - apart from the nucleus shape model that was adopted from the mission results.

Next, the researchers intend to calculate the active regions of the comet Churyumov-Gerasimenko, the rendezvous target for ESA's Rosetta mission on which the Rosetta lander Philae will touch down in late 2014. The mission, to which MPS contributed many scientific instruments, has been on route to its destination beyond the orbit of Mars and the asteroid belt since 2004. In the crucial phase of the mission, the new method could help to determine a safe route for Rosetta through the cometary coma and maybe even find a suitable landing site.

(Photo: Instituto de Astrofisica de Andalucia (Luisa Maria Lara)/MPS)

Max Planck Institute


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Three new studies from researchers at Rensselaer Polytechnic Institute illustrate why graphene should be the nanomaterial of choice to strengthen composite materials used in everything from wind turbines to aircraft wings.

Composites infused with graphene are stronger, stiffer, and less prone to failure than composites infused with carbon nanotubes or other nanoparticles, according to the studies. This means graphene, an atom-thick sheet of carbon atoms arranged like a nanoscale chain-link fence, could be a key enabler in the development of next-generation nanocomposite materials.

“I’ve been working in nanocomposites for 10 years, and graphene is the best one I’ve ever seen in terms of mechanical properties,” said Nikhil Koratkar, professor in the Department of Mechanical, Aerospace, and Nuclear Engineering at Rensselaer, who led the studies. “Graphene is far superior to carbon nanotubes or any other known nanofiller in transferring its exceptional strength and mechanical properties to a host material.”

Results of Koratkar’s studies are detailed in three recently published papers: “Fracture and Fatigue in Graphene Nanocomposites,” published in Small; “Enhanced Mechanical Properties of Nanocomposites at Low Graphene Content,” published in ACS Nano; and “Buckling Resistant Graphene Nanocomposites,” published in the journal Applied Physics Letters.

Advanced composites are increasingly a key component in the design of new windmill blades, aircraft, and other applications requiring ultra-light, high-strength materials. Epoxy composite materials are extremely lightweight, but can be brittle and prone to fracture. Koratkar’s team has infused the advanced composites with stacks, or platelets, of graphene. Each stack is only a few nanometers thick. The research team also infused epoxy composites with carbon nanotubes.

Epoxy materials infused with graphene exhibited far superior performance. In fact, adding graphene equal to 0.1 percent of the weight of the composite boosted the strength and the stiffness of the material to the same degree as adding carbon nanotubes equal to 1 percent of the weight of the composite. This gain, on the measure of one order of magnitude, highlights the promise of graphene, Koratkar said. The graphene fillers also boosted the composite’s resistance to fatigue crack propagation by nearly two orders of magnitude, compared to the baseline epoxy material.

Though graphene and carbon nanotubes are nearly identical in their chemical makeup and mechanical properties, graphene is far better than carbon nanotubes at lending its attributes to a material with which it’s mixed.

“Nanotubes are incredibly strong, but they’re of little use mechanically if they don’t transfer their properties to the composite,” Koratkar said. “A chain is only as strong as its weakest link, and if that link is between the nanotube and the polymer, then that is what determines the overall mechanical properties. It doesn’t matter if the nanotubes are super strong or super stiff, if the interface with the polymer is weak, that interface is going to fail.”

Koratkar said graphene has three distinct advantages over carbon nanotubes. The first advantage is the rough and wrinkled surface texture of graphene, caused by a very high density of surface defects. These defects are a result of the thermal exfoliation process that the Rensselaer research team used to manufacture bulk quantities of graphene from graphite. These “wrinkly” surfaces interlock extremely well with the surrounding polymer material, helping to boost the interfacial load transfer between graphene and the host material.

The second advantage is surface area. As a planer sheet, graphene benefits from considerably more contact with the polymer material than the tube-shaped carbon nanotubes. This is because the polymer chains are unable to enter the interior of the nanotubes, but both the top and bottom surfaces of the graphene sheet can be in close contact with the polymer matrix.

The third benefit is geometry. When microcracks in the composite structure encounter a two-dimensional graphene sheet, they are deflected, or forced to tilt and twist around the sheet. This process helps to absorb the energy that is responsible for propagating the crack. Crack deflection processes are far more effective for two-dimensional sheets with a high aspect ratio such as graphene, as compared to one-dimensional nanotubes.

Koratkar said the aerospace and wind power industries are seeking new materials with which to design stronger, longer-lived rotor and wind turbine blades. His research group plans to further investigate how graphene can benefit this goal. Graphene shows great promise for this because it can be produced from graphite, which is available in bulk quantities and at relatively low cost, he said, which means mass production of graphene is likely to be far more cost effective than nanotubes.

(Photo: RPI)

Rensselaer Polytechnic Institute


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A newly discovered species of monitor lizard, a close relative of the Komodo dragon, was reported in the journal Zootaxa by a professor at UC Santa Barbara and a researcher from Finland.

Sam Sweet, a professor in the department of Ecology, Evolution and Marine Biology at UCSB, and Valter Weijola, a graduate student at Abo Akademi University in Turku, Finland, are the first to describe the distinctive lizard, which lives in the Moluccan islands of east Indonesia. Sweet is an authority on monitor lizard biology.

The scientific name of this lizard is Varanus obor; its popular names are Torch monitor and Sago monitor. It's called Torch monitor because of its bright orange head with a glossy black body. Obor means torch in Indonesian. It is a close relative of the fruit-eating monitor lizard recently reported from the Philippines. The Torch monitor can grow to nearly four feet in length, and thrives on a diet of small animals and carrion.

The Torch monitor exists only on the small island of Sanana in the western Moluccan islands. A unique aspect of this geographical region is the lack of mammalian predators, which may have given reptiles the space to evolve as the top terrestrial predators and scavengers. Several million years ago, this island was situated near New Guinea, and it is possible that the lizard lives on as a relic from that period. It is the only black monitor in its lineage, and the only monitor species anywhere that has evolved red pigmentation.

Sweet describes an important biological context: "East of Wallace's Line –– the boundary between Asian and Australian domains –– there are no native carnivorous mammals, and monitor lizards fill that role. There are more species there, doing more different things ecologically than in Africa or South and Southeast Asia, where competition and predation by mammals tend to keep monitor lizards down. East of Wallace's Line in Indonesia, New Guinea, and Australia, monitor lizards are on the top of the heap. It emphasizes again how little we know about some tropical regions, to find an animal so strikingly colored and so large only last year."

Weijola discovered the lizard last spring, and returned with Sweet in late 2009 for five weeks to do studies and take photographs of the animal. The Torch monitor is most common in the coastal sago palm swamps and belongs to the mangrove monitor, V. indicus group.

(Photo: Valter Weijola)





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