Tuesday, July 7, 2009

NICKEL ISOTOPE MAY BE METHANE PRODUCING MICROBE BIOMARKER

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Nickel, an important trace nutrient for the single cell organisms that produce methane, may be a useful isotopic marker to pinpoint the past origins of these methanogenic microbes, according to Penn State and University of Bristol, UK, researchers.

"Our data suggest significant potential in nickel stable isotopes for identifying and quantifying methanogenesis on the early Earth," said Vyllinniskii Cameron, recent Penn State Ph.D. recipient in geosciences and astrobiology and currently a post-doctoral fellow at the University of Bristol. "Little is known about the actual timing of the evolution of methane producing organisms or their metabolism. Nickel stable isotope fractionation may well prove to be the fundamental unambiguous trace metal biomarker for these methanogens."

Fractionation of an element into its component stable isotopes occurs because each isotope is slightly different in mass. Biological organisms tend to favor one isotope over another and preferentially create stores of heavy or light isotopes that researchers can measure. The presence of a specific isotopic fraction can indicate that a biological process took place. Previous researchers have looked at transition metals other than nickel as potential biomarkers.

"There is a lot of interest in iron and copper isotopes and other metals that microbes use in trace amounts," said Christopher H. House, associate professor of geosciences and director of the Penn State Astrobiology Research Center, part of the NASA Astrobiology Institute. "However, iron goes through oxidation reduction processes with or without a biological component, so there is significant complexity when it is used as a biosignature."

In nature nickel does not seem to be as adversely affected by oxidation reduction changes so isotope fractionation might be more easily attributed to biological processes, such as during microbial assimilation or uptake of metals.

For this work the researchers did not look at ancient fossil cells, but grew modern day archaea in the laboratory, controlling their habitat and recording their rate of methane production. Archaea are single cell microorganisms similar to bacteria but with different evolutionary histories and biochemical pathways. The researchers report their results in the online edition of the Proceedings of the National Academy of Sciences.

Through a grant from the Worldwide Universities Network and a NASA research scholarship, Cameron performed the research, including setting up the protocols for the nickel isotopic system, at the University of Bristol with Derek Vance and Corey Archer, Bristol Isotope Group, department of Earth Sciences.

Cameron first investigated samples representative of the Earth's mantle and crust that were without any biological activity. These samples showed very little variation in nickel isotopic composition. She also analyzed samples from a group of meteorites, which exhibited even less variation. These studies showed that non-biological processes do not significantly fractionate nickel isotopes.

However, isotopic analyses of pure cultures of three archaea -- Methanosarcina barkeri, Methanosarcina acetivorans and Methanococcus jannaschii -- showed that all the archaea fractionated nickel so that the nickel component in the microbe was lighter relative to the starting isotopic value of the growth medium. To test whether non-methanogenic cells would also fractionate nickel, Cameron incubated an archaea that does not produce methane, Pyrobaculum calidifontis, under the same conditions. These cells did not fractionate nickel isotopes.

"While we only tested one non-methanogen and a more diverse suite of microorganisms should be investigated, at this time, it appears that nickel isotopic fractionation produced by microorganisms in general will not be as significant as the fractionation produced by methanogenic archaea," said Cameron.

"It may be possible in the future to test organic rich sedimentary layers from 2.7 billion years ago to see if nickel isotopic fractionation occurred," said House. "Because there are no known bacteria that are methanogenic and because archaea seem to fractionate nickel isotopes, perhaps such work can help pinpoint when these methane producing organisms came into being."

Penn State University

BACKING UP YOUR BRAIN: MCGILL RESEARCHERS DISCOVER HOW OLD MEMORIES ARE RE-SAVED AND CHANGED

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The McGill team led by Prof. Karim Nader discovered that extremely strong fear memories do not initially undergo reconsolidation, but over time (on the order of a month or so) even these memories can undergo reconsolidation. Furthermore, the authors identified some of the brain mechanisms that determine whether a memory will or will not undergo reconsolidation. Their results were published in the journal Nature Neuroscience on June 21.

“The old theory is that once a memory is wired in your brain, it stays that way,” explained Nader, William Dawson Scholar and EWR Steacie Fellow in the Department of Psychology. “But our discovery shows that once you remember something, it doesn’t stay wired in your brain, it becomes unwired and needs to be restored again - reconsolidation.”

This latest finding builds on Nader’s previous research which showed that it was possible to chemically erase fearful memories in rats. That research shed light on the neurobiology of memory and showed that long-term memories can be unlocked and even modified. Nader’s discoveries challenged traditional views about the neural basis for memory.

The new findings deepen our understanding of the molecular basis by which the brain controls which memories do and do not undergo reconsolidation. Reconsolidation blockade has been suggested as a possible new treatment for sufferers of psychological disorders, including those involving uncontrollable, intrusive memories, such as Post-Traumatic Stress Disorder (PTSD). The results of this research indicate that reconsolidation based therapies of PTSD should not attempt to treat patients shortly after the trauma. This is because these extremely strong memories may not undergo reconsolidation for a long period of time, up to a few months after experiencing the trauma. Nader has previously collaborated with a team led by Roger Pitman of Harvard University and McGill University Psychiatrist and the Douglas Mental Health University Institute researcher Dr. Alain Brunet; that collaboration demonstrated that interrupted reconsolidation can be used to relieve the suffering of patients with chronic PTSD. The therapy involves administering a common blood pressure drug, propranolol, as a traumatic event is recounted. The propranolol partially blocks the reconsolidation of the fear associated with the memory. Amazingly, the trend of these findings indicates that those with the oldest trauma responded best to the treatment, exactly the same effect as found by Nader’s group.

“These findings are very exciting because we have always known that not every memory undergoes reconsolidation. But there was nothing known about the mechanisms that determine when a memory does or does not undergo reconsolidation. These findings suggest a neurobiological principle that controls this process. Understanding these mechanisms is crucial because they tell us what has to happen on a neurobiological level in order to turn reconsolidation on and off. This is clinically important because in the clinic we want to be able to turn reconsolidation on and off if possible.” said Nader.

(Photo: McGill U.)

Mc Gill University

COLD CASE TECHNIQUES BRING MUMMYS FACE TO LIFE

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Thanks to the skills of artists who work on cold case investigations, people have a chance to see what the Oriental Institute’s mummy Meresamun may have looked like in real life.

A Chicago forensic artist and a police artist in Maryland prepared the images, which depict an engaging woman in her late 20s as she would have looked in 800 B.C. Both artists, though working independently, produced strikingly similar images. The drawings are on display at the Oriental Institute Museum, and have been placed on the institute’s Web site (http://oi.uchicago.edu/museum/special/meresamun/), on Meresamun’s Facebook page, her Wikipedia listing and on YouTube.

Dr. Michael Vannier, Professor of Radiology, began the process of restoring the mummy’s facial features with two exhaustive CT examinations of Meresamun in 2008 at the University of Chicago Medical Center.

“A huge number of CT scans of the skull were used to create a 3-D digital model of Meresamun’s skull,” said Emily Teeter, Research Associate at the Oriental Institute an curator of a museum exhibition about the mummy. “Those files were given to forensic artists who use methods employed in cold case investigations where skeletal remains need to be identified.”

The Oriental Institute wanted to compare multiple reconstructions, in order to obtain a trustworthy image of Meresamun’s face. Both a digital version of the traditional forensic reconstruction and a missing person-type sketch were submitted.

In the traditional forensic method, layers of fat, muscle and flesh are built up upon the skull. Starting with a three-dimensional image of the skull created from multiple CT scans, Chicago artist Joshua Harker used a technique known as the Gatliff-Snow American Tissue Depth Marker Method to calculate the contours of the face to digitally recreate Meresamun’s appearance.

“The skull is the driving architecture of the face—all the proportions and placements are there, you know how to read it,” Harker explained. “Even the shapes of the lips, nose and eyebrows can be determined if you know what to look for.”

The American Tissue Depth Marker method has been shown to be effective in accurately reconstructing a face, both in identifying victims and as admissible evidence in court.

“I try not to make any assumptions without expert direction, whether that be from an anthropologist regarding the race, gender or age, or from and expert like Emily Teeter who can give me an accurate description about details based on historical evidence,” Harker said. “I am ecstatic that my reconstruction of Meresamun has been so well received by the community who knows the most about her.”

Michael Brassell, who works with the Department of Justice/Maryland State Police Missing Persons Unit, used his skills as a trained sketch artist to produce a second, more traditional reconstruction.

“The project was no different than any of the postmortem drawings I have worked on for cold case homicides. The CT scans were very clear, making my job easy,” he said. “If this was a homicide case, I would almost go as far to guarantee a hit on the profile drawing.”

Meresamun lived in Thebes (ancient Luxor) about 800 B.C. and died of undetermined causes about age 29-30. An exhibit, “The Life of Meresamun: A Temple Singer in Ancient Egypt,” features her mummy and coffin and will be featured through Dec. 6 at the Oriental Institute Museum. A video display allows visitors to view features of Meresamun’s physical state and perform a “virtual unwrapping” of the mummy, enabling them to see how it was prepared. Advanced digital techniques have made it possible to recreate Meresamun’s appearance.

She was tall by ancient standards—5-and-a-half feet—her features were regular with wide-spaced eyes and she had an overbite. “Meresamun was, until the time of her death at about 30, a very healthy woman,” Vannier said. “The lack of arrest lines on her bones indicates good nutrition through her lifetime and her well-mineralized bones suggest that she lived an active lifestyle.”

(Photo: Michael Brassel)

University of Chicago

ICE SHEETS CAN RETREAT "IN A GEOLOGIC INSTANT," STUDY OF PREHISTORIC GLACIER SHOWS

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Modern glaciers, such as those making up the Greenland and Antarctic ice sheets, are capable of undergoing periods of rapid shrinkage or retreat, according to new findings by paleoclimatologists at the University at Buffalo.

The paper, published on June 21 in Nature Geoscience, describes fieldwork demonstrating that a prehistoric glacier in the Canadian Arctic rapidly retreated in just a few hundred years.

The proof of such rapid retreat of ice sheets provides one of the few explicit confirmations that this phenomenon occurs.

Should the same conditions recur today, which the UB scientists say is very possible, they would result in sharply rising global sea levels, which would threaten coastal populations.

"A lot of glaciers in Antarctica and Greenland are characteristic of the one we studied in the Canadian Arctic," said Jason Briner, Ph.D., assistant professor of geology in the UB College of Arts and Sciences and lead author on the paper. "Based on our findings, they, too, could retreat in a geologic instant."

The new findings will allow scientists to more accurately predict how global warming will affect ice sheets and the potential for rising sea levels in the future, by developing more robust climate and ice sheet models.

Briner said the findings are especially relevant to the Jakobshavn Isbrae, Greenland's largest and fastest moving tidewater glacier, which is retreating under conditions similar to those he studied in the Canadian Arctic.

Acting like glacial conveyor belts, tidewater glaciers are the primary mechanism for draining ice sheet interiors by delivering icebergs to the ocean.

"These 'iceberg factories' exhibit rapid fluctuations in speed and position, but predicting how quickly they will retreat as a result of global warming is very challenging," said Briner.

That uncertainty prompted the UB team to study the rates of retreat of a prehistoric tidewater glacier, of similar size and geometry to contemporary ones, as way to get a longer-term view of how fast these glaciers can literally disappear.

The researchers used a special dating tool at UB to study rock samples they extracted from a large fjord that drained the ice sheet that covered the North American Arctic during the past Ice Age.

The samples provided the researchers with climate data over a period from 20,000 years ago to about 5,000 years ago, a period when significant warming occurred.

"Even though the ice sheet retreat was ongoing throughout that whole period, the lion's share of the retreat occurred in a geologic instant -- probably within as little as a few hundred years," said Briner.

The UB research reveals that the period of rapid retreat was triggered once the glacier entered deep ocean waters, nearly a kilometer deep, Briner said.

"The deeper water makes the glacier more buoyant," he explained.

"Because the rates of retreat were so much higher in the deep fjord, versus earlier when it terminated in more shallow waters or on land, the findings suggest that contemporary tidewater glaciers in Greenland and Antarctica that are retreating into deep waters may begin to experience even faster rates of retreat than are currently being observed," said Briner.

Right now, Jakobshavn Isbrae is draining into waters that are nearly a kilometer deep, he said, which means that its current rates of retreat -- as fast as 10 kilometers in the past decade -- could continue for the next hundred years.

"If modern glaciers do this for several decades, this would rapidly raise global sea level, intercepting coastal populations and requiring vast re-engineering of levees and other mitigation systems," said Briner.



(Photo: U. Buffalo)

University at Buffalo

A PENNY FOR YOUR PRIONS

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North Carolina State University researchers have discovered a link between copper and the normal functioning of prion proteins, which are associated with transmissible spongiform encephalopathy diseases such as Cruetzfeldt-Jakob in humans or "mad cow" disease in cattle. Their work could have implications for patients suffering from these diseases, as well as from other prion-related diseases such as Alzheimers or Parkinson's.

Prion proteins, or PrPs, are commonly found in brain tissue and throughout the central nervous system. In humans or animals with prion diseases, these proteins deform and aggregate, creating clumps of PrPs that interfere with the nervous system's ability to function normally. A team of NC State physicists, led by Miroslav Hodak and Jerry Bernholc, has found that when PrPs bind with copper in the human body, their structure becomes more stable and less likely to misfold or aggregate.

"We believe that a prion protein's normal function is to serve as a copper buffer in the human body, binding with copper ions and keeping those ions from damaging human tissue," Hodak says. "We wanted to determine whether this was the normal function of the prion, and then look at how that binding affected the prion's structure."

The researchers created a 3-D model of the PrP using supercomputers at Oak Ridge National Laboratories. With the model, they determined that PrPs can bind up to four copper ions apiece, depending on the concentration of copper present. They also found that when the PrPs bind to the copper ions, the structure of the protein changes, becoming more stable.

Their results are published online in Proceedings of the National Academy of Sciences.

"Prion proteins are unusual in that half of the protein has a well-defined structure, but the other half of it - where the binding occurs - is a flexible, random tangle," Hodak says. "When we looked at the so-called 'random' portion of the PrP where that binding occurs, we found that the copper ions lend stability to the overall protein. This stability may play a role in preventing PrPs from misfolding or aggregating - which indicates that with prion diseases, copper binding may be beneficial."

North Carolina State University

ANCIENT DROUGHT AND RAPID COOLING DRASTICALLY ALTERED CLIMATE

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Two abrupt and drastic climate events, 700 years apart and more than 45 centuries ago, are teasing scientists who are now trying to use ancient records to predict future world climate.

The events – one, a massive, long-lived drought believed to have dried large portions of Africa and Asia, and the other, a rapid cooling that accelerated the growth of tropical glaciers – left signals in ice cores and other geologic records from around the world.

Lonnie Thompson, University Distinguished Professor of Earth Sciences at Ohio State University, and researcher with the Byrd Polar Research Center there, outlined the puzzle today to colleagues at the Chapman Conference on Abrupt Climate Change. The meeting was sponsored by the American Geophysical Union and the National Science Foundation.

Thompson, who has led more than 50 expeditions to drill cores through ice caps on some the highest and most remote regions of the planet, believes that the records from the tropical zones on Earth are the most revealing and that the last 1,000 years provides the best clues.

“I would argue that the last 1,000 years are most critical from the perspective of looking at the future,” he said

The first of the two tantalizing events is apparent in an ice core drilled in 1993 from an ice field in the Peruvian Andes called Huascaran. Within that core, they found a thick band of dust particles, most smaller than a micron in diameter, the concentration of which was perhaps 150 times greater than anywhere else in the core. That band dated back to 4,500 years ago.

“Dust that small can be transported great distance – the question is where did it come from?” Thompson said. “I believe that record accurately reflects drought conditions in Africa and the Middle East and that the dust was carried out across the Atlantic Ocean by the northeast trade winds, across the Amazon Basin and deposited on the Huascaran ice cap.

Thompson said that other records, including an ice core taken from glaciers atop Tanzania’s Mount Kilimanjaro, also show a dust event dating to a time when there was substantive drying up of lakes in Africa. He said that it is the only such huge event that the ice core records show for the past 17,000 years.

The other mystery surrounds a major cooling event that Thompson believes happened about 700 years earlier. During a 2002 expedition to the Quelccaya ice cap in Peru, the largest tropical ice field in the world, Thompson and colleagues discovered patches of ancient wetland plants that had been exposed as the edge of the ice cap retreated. When carbon-dated, the plants were shown to be 5,200 years old, meaning that they had been covered, and preserved, by the ice for the last 52 centuries.

Since then, recent expeditions have located similar patches of plants revealed by the ice’s retreat. All date back to at least 5,200 years ago and some as much as 7,000 years ago.

“This means that sometime around 5,200 years ago, there was a rapid cooling event in this region and the ice expanded shielding the plants from damage and decay,” Thompson said.

Other records from around the world seem to support the idea of a cooling event at this time. Divers in Lake Tahoe, Nevada, found nearly two dozen ancient tree trunks preserved at the lake’s bottom. Wood samples from the trunks date back 5,200 years and geologic records show the current lake levels have remained steady since that point in time.

Thompson also pointed to the timing of past climate changes in South America and the rise and fall of early cultures in the region.

Evidence from the ice cores from Quelccaya suggest that cultures might have grown during wet periods in the Peruvian Highlands and waned when the climate became drier. Conversely, cultures appeared to grow in the country’s coastal regions when the climate became wetter and were lost as drying increased.

“This suggests that there could have been persistent climate periods that allowed these cultures to flourish under certain conditions and fail under others,” he said.

Thompson leads a new expedition next week to two new sites in the Andes in hopes of drilling cores that will show more detailed records of both events.

The evidence that researchers have, both from ice cores and from the rapid retreat of glaciers, show that high-altitude ice fields reflect similar changes that are currently visible all across the temperate portions of the globe.

“The ice caps are sentinels of the earth’s overall climate,” he said. “And the data shows that at all of these sites, the rate at which the ice is vanishing is accelerating.

“To me, these are indicators that these areas are already being adversely impacted by changes in our current climate.”

(Photo: Thomas Nash)

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