Wednesday, August 5, 2009

ECOLOGIST BRINGS CENTURY-OLD EGGS TO LIFE TO STUDY EVOLUTION

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Suspending a life in time is a theme that normally finds itself in the pages of science fiction, but now such ideas have become a reality in the annals of science.

Cornell ecologist Nelson Hairston Jr. is a pioneer in a field known loosely as "resurrection ecology," in which researchers study the eggs of such creatures as zooplankton -- tiny, free-floating water animals -- that get buried in lake sediments and can remain viable for decades or even centuries. By hatching these eggs, Hairston and others can compare time-suspended hatchlings with their more contemporary counterparts to better understand how a species may have evolved in the meantime.

The researchers take sediment cores from lake floors to extract the eggs; the deeper the egg lies in the core, the older it is. They then place the eggs in optimal hatching conditions, such as those found in spring in a temperate lake, and let nature take its course.

"We can resurrect them and discover what life was like in the past," said Hairston, who came to Cornell in 1985 and is a professor and chair of Cornell's Department of Ecology and Evolutionary Biology. "Paleo-ecologists study microfossils, but you can't understand much physiologically or behaviorally" with that approach, he said.

Hairston first became interested in the possibilities of studying dormant eggs in the late 1970s, when he was an assistant professor of zoology at the University of Rhode Island. There, he noticed that the little red crustaceans -- known as copepods -- in the pristine lake behind his Rhode Island home disappeared in the summer, only to return as larvae in the fall.

The observation prompted him to study why they disappear, research that revealed the copepods stay active under the ice in the winter, but they die out as their eggs lie dormant on the lake floor through the summer when the lake's fish are most active. When the fish become less active in the fall, larvae hatch from the eggs, and the copepods continue their life cycle.

This time suspension, where zooplankton pause their life cycles to avoid heavy predation or harsh seasonal and environmental conditions, also increases a species' local gene pool, with up to a century's worth of genetic material stored in a lake bed, Hairston said. When insects, nesting fish and boat anchors stir the mud, they can release old eggs that hatch and offer a wider variety of genetic material to the contemporary population.

In 1999 Hairston and colleagues published a paper in Nature that described how 40-year-old resurrected eggs could answer whether tiny crustaceans called Daphnia in central Europe's Lake Constance had evolved to survive rising levels of toxic cyanobacteria, known as blue-green algae. In the 1970s, phosphorus levels from pollution rose in the lake, increasing the numbers of cyanobacteria. The researchers hatched eggs from the 1960s and found they could not survive the toxic lake conditions, but Daphnia from the 1970s had adapted and survived.

(Photo: P. Spaak)

Cornell University

TRACKING TRASH

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What if we knew exactly where our trash was going and how much energy it took to make it disappear? Would it make us think twice about buying bottled water or "disposable" razors?

A team of MIT researchers today announced a major project called Trash Track, which aims to get people thinking about what they throw away. Trash Track relies on the development of special electronic tags that will track different types of waste on their journey through the disposal systems of New York and Seattle. The project will monitor the patterns and costs of urban disposal and create awareness of the impact of trash on our environment - revealing the last journey of our everyday objects.

"Trash is one of today's most pressing issues - both directly and as a reflection of our attitudes and behaviors," says Professor Carlo Ratti, head of the MIT SENSEable City lab. "Our project aims to reveal the disposal process of our everyday objects, as well as to highlight potential inefficiencies in today's recycling and sanitation systems. The project could be considered the urban equivalent of nuclear medicine - when a tracer is injected and followed through the human body.

"The study of what we could call the 'removal chain' is becoming as important as that of the supply chain," the lab's associate director, Assaf Biderman, explains. "Trash Track aims to make the removal chain more transparent. We hope that the project will promote behavioral change and encourage people to make more sustainable decisions about what they consume and how it affects the world around them."

Trash Track will enlist volunteers in two target cities - New York and Seattle - who will allow pieces of their trash to be electronically tagged with special wireless location markers, or "trash tags." Thousands of these markers, attached to a waste sample representative of the city's overall consumption, will calculate their location through triangulation and report it to a central server, where the data will be analyzed and processed in real time. The public will be able to view the migration patterns of the trash online, as well as in an exhibit at the Architectural League in New York City and in the Seattle Public Library, starting in September 2009.

Trash Track was initially inspired by the Green NYC Initiative, the goal of which is to increase the rate of waste recycling in New York to almost 100 percent by 2030. Currently, only about 30 percent of the city's waste is diverted from landfills for recycling. "We hope that Trash Track will also point the way to a possible urban future: that of a system where, thanks to the pervasive usage of smart tags, 100 percent recycling could become a reality," says project leader, Musstanser Tinauli.

"Carlo Ratti and his team have come up with a visionary project to help people take ownership of their pollution," says Roger Highfield, editor of New Scientist magazine, which will be helping to deploy a third batch of tags in London, U.K. "It's all too easy to throw something in the garbage and wash your hands of it if you don't know what effect you are directly having on the environment."

(Photo: E Roon Kang at SENSEable City Lab)

Massachusetts Institute of Technology

WHAT MAKES A ROLLING LANDSCAPE ROLL?

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Anyone who has flown over the western United States knows the patterns well: Seemingly endless repetitions of similar landforms, ridges and valleys and ridges and valleys arranged with nearly the regularity of the teeth on a comb. Now, an MIT geologist and co-workers say they have found the underlying mechanism that explains these widespread patterns - and how they vary from one place to another.

The fundamental understanding of the processes that lead to these parallel grooves is not just useful theoretically, but could ultimately allow geologists to predict how eroding landscapes will respond to a changing climate. It should also make it easier to determine the mechanical properties of the underlying rock from aerial surveys, without having to dig or drill. The research could even help reveal the processes that have shaped landscapes on other planets, including whether they bear the signature of life.

"Most landscapes are made up of ridges and valleys," says Taylor Perron, an assistant professor of geology in the Department of Earth, Atmospheric and Planetary Sciences. "The most fundamental question we can ask is 'What controls their size?'" The basic mechanism that forms ridges and valleys, explains Perron, is a balance between two competing processes: gradual incision of valleys by flowing water, and the tendency of the land to slump into more rounded forms as soil slowly creeps downslope. The first tends to create sharp relief in the landscape, while the second process tends to smooth it out.

While the process of valley incision is governed mainly by the amount of rainfall and the strength of the soil and rock, the smoothing in many landscapes is largely driven by biological processes - especially the activity of burrowing animals. "Biotic agents like burrowing rodents slowly stir the soil," Perron says. "On average, they displace it downslope. This smoothes out sharp corners in the landscape."

To sort out the relative roles of the different processes and how they interact, the team used a combination of aerial reconnaissance, airborne laser altimetry, and research on the ground in selected sites to determine exactly what forces were at work on the landscape. The researchers used their observations to formulate a mathematical model for the long-term evolution of the topography.

The new findings, which include computer simulations that show how evenly spaced ridges and valleys emerge over many thousands of years, are described in a paper appearing in the journal Nature on July 23, written by Perron along with James Kirchner and William Dietrich of the University of California, Berkeley.

While the patterns of evenly spaced ridges and valleys have long been noticed in landscapes with sparse vegetation, it took new technology to reveal just how ubiquitous these patterns are, and to measure them precisely. Laser altimeters mounted in aircraft can create detailed, high-resolution topographic maps of landscapes that are forested, revealing the contours that are obscured by the tree canopy. This technology produces digital maps that are "10 times better than anything we had before," he says.

Perron and his team used laser altimetry to study sites throughout the United States with valley spacing ranging from 30 meters to 300 meters. They found that the spacing correlates with the amount of rainfall and the strength of the underlying rock, with wetter conditions or harder rock giving rise to wider valley spacing. Perron suspects that the rainfall effect is largely a consequence of life: where water is more abundant, the biologically driven smoothing effect of soil creep is stronger, and tree roots and burrowing animals encourage water to travel through the ground rather than eroding the surface. "The ridge-valley wavelength is one way that Earth's landscapes bear the imprint of life," he says.

Perron hopes that such research will ultimately reveal distinctive effects that make it possible to infer the presence or absence of life on another planet, such as Mars, simply by studying the details of its topography. Just as importantly, he says, this analysis provides "a way of measuring the influence of life here on Earth."

(Photo: Ionut Iordache (UC Berkeley) / Taylor Perron (MIT))

Massachusetts Institute of Technology

PLANTS CAN'T DEFEND REMAINING CELIBATE

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In research published in Proceedings of the National Academy of Sciences, scientists from North Carolina State University and Duke University discovered that sexually produced evening primrose plants withstand attacks from plant-eaters like caterpillars better than plant relatives that reproduce by themselves.

The findings are important steps to learning more about how plants have evolved defenses against insect herbivores, says Dr. Marc Johnson, assistant professor of plant biology at NC State and the lead author of the research paper.

"The variation in sexual reproduction has a large impact on the ability of plants to evolve defenses against herbivores," Johnson says.

In the study, the researchers performed both lab and field experiments on evening primrose (Onagraceae) plants, a plant family that has 259 different species – 85 percent of which reproduce sexually with the remainder reproducing asexually – to gauge the effects of plant sex on defense mechanisms. The researchers found that so-called generalist herbivores – those that eat a variety of plants – preferred to feed on the asexual species and lived longer while doing so.

The results were a bit different for so-called "specialist" plant-eaters, however. Those insects that prefer just one kind of food were more apt to munch on sexually reproduced species of plant. This most likely occurs, Johnson says, because specialized plant-eaters evolve alongside their hosts and have found ways to co-opt plant defenses. Instead of being deterred by certain chemical compounds produced as defenses by the plant, the specialized plant-eaters are attracted to them.

Johnson says the nuanced results make sense.

"Sex shuffles up genes and allows individual plants to get rid of bad genes and keep good ones," he said. "That helps them evolve defenses against generalist herbivores. Though there are short-term benefits to asexual reproduction – populations can grow more rapidly and propagate even when pollination is not possible – losing sex puts plants at a long-term disadvantage.

"In the end, asexual reproduction appears to be an evolutionary dead-end."

North Carolina State University

A GLOBAL MODEL FOR THE ORIGIN OF SPECIES INDEPENDENT OF GEOGRAPHICAL ISOLATION

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Two views of the process of “speciation” -- the evolutionary process by which new biological species arise -- dominates evolutionary theory. The first requires a physical barrier such as a glacier, mountain or body of water to separate organisms enabling groups to diverge until they become separate species. In the second, an environment favors specific characteristics within a species, which encourages divergence as members fill different roles in an ecosystem.

In a new study, “Global patterns of speciation and diversity,” just published in Nature, Les Kaufman, Boston University professor of biology and associate director of the BU Marine Program along with a team of researchers from The New England Complex Systems Institute, have collaborated and found a way to settle the debate which deals with the origin of species independent of geographic isolation.

They demonstrated, using a computer model, how diverse species can arise from the arrangement of organisms across an area, without any influence from geographical barriers or even natural selection. Over generations, the genetic distance between organisms in different regions increases, the study noted. Organisms spontaneously form groups that can no longer mate resulting in a patchwork of species across the area. Thus the number of species increases rapidly until it reaches a relatively steady state.

“Our biodiversity results provide additional evidence that species diversity arises without specific physical barriers,” the study states.

The computer simulations, the authors, note showed the distribution of species formed patterns similar to those that have occurred with real organisms all around the world.

“The model we put forward in the paper lays the groundwork for more powerful tests of the role played by natural and sexual selection, as well as habitat complexity in shaping the patterns of biological diversity that we see around us today,” said Kaufman. Our insights can be applied to the immense challenge that we now face -- not only to prevent the extinction of a large chunk of life, but also to prevent ourselves from quenching the very forces that fuel the continuous creation of new life forms on earth.”

This study is also the fourth in a series from The New England Complex Systems Institute on the role of complexity in species coexistence and evolutionary diversification.

“One can think about the creation of species on the genetic level in the same way we think about the appearance of many patterns, including traffic jams,” said Yaneer Bar-Yam, president of The New England Complex Systems Institute and a senior author of the study. “While the spatial environment may vary, specific physical barriers aren’t necessary. Just as traffic jams can form from the flow of traffic itself without an accident, the formation of many species can occur as generations evolve across the organisms’ spatial habitat.”

Boston University

IOWA STATE UNIVERSITY RESEARCHERS DEVELOP PROCESS FOR SURGICAL GENETIC CHANGES

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Research led by scientists at Iowa State University's Plant Sciences Institute has resulted in a process that will make genetic changes in plant genes much more efficient, practical and safe.

The breakthrough was developed by David Wright, an associate scientist, and Jeffery Townsend, an assistant scientist, and allows targeted genetic manipulations in plant DNA, which could have a huge impact on plant genetic work in the future.

Until now, when scientists introduced DNA into plants, they would randomly inject that DNA into the plant cell. There was no way of knowing if it was in the right place or if it would work until many resulting plants were tested.

The new technique harnesses a natural process called homologous recombination to precisely introduce DNA at a predetermined location in the plant genome through targeted DNA breaks generated by zinc finger nucleases. This occurs about 1 in 50 attempts and is very efficient compared to unassisted methods that allow the same changes at a rate as low as 1 in 10 million.

"I've been working in this field for 29 years, just when we started learning how to modify genes," said Townsend. "From that day, this was the goal -- to actually get the research to the point where you can have homologous recombination. Now, we've done it."

Using this process, a specific gene is located in a living cell, then a break is made in the DNA of that gene. When the cell begins to heal itself, existing DNA can be deleted or modified, or new DNA can be added near the break site. Afterward, the cell carries the genetic change and passes the change on to its offspring.

"It's like surgery, only on the molecular level," said Wright.

"It's been known for a long time that if you make a break in a cell, you can get some DNA into that spot," said Wright. "It's just that you have three meters of DNA in a cell if you unwound it. Putting the break where you want it has always been the problem."

Zinc finger nucleases solve the problem and allows scientists to take greater advantage of homologous recombination, according to Wright and Townsend.

The research, published in the journal Nature, was performed in Dan Voytas' lab at Iowa State. Voytas recently left the university for a position at the University of Minnesota.

In addition to the difficulty introducing changes where researchers want them using current methods, government regulations often slow the movement of research from the lab to the field.

Wright and Townsend hope the precision of this technique will speed the regulatory process.

"In the random process, regulators would say, 'You really don't know what you're doing,'" said Townsend. "With this new technology, we can tell them, 'The genome looks like this, this is exactly the change we want to make.'

"That's the power of this technology. It makes it (genetic engineering) practical and much safer. It was impractical, and now it is practical."

There are many applications for this that could allow stunning advances for many crops, according to Wright and Townsend.

For instance, canola is a commodity grown for its oil, just as soybeans. However, after the oils are extracted, soybean meal is sold as feed. Once oils are extracted from canola, the meal has a much lower value as a livestock feed due to several factors, including the presence of the chemical sinapoylcholine, also called sinapine.

The new technique could allow scientists to remove the genes that make sinapine. The result would be a more versatile canola product. Farmers, especially in the upper Midwest and Canada, would benefit from this new market for canola meal.

Other plants could benefit as well.

Removing the genes that are responsible for peanut allergies, or removing genes that produce harmful chemicals or anti-nutritionals in other crops are just a few of the immediate crop improvements that Wright and Townsend envision for this technology.

Iowa State University

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