Posts tagged Colorado Boulder
CU study: Spruce beetle infestation in N. Colo. tied to drought
Oct 10th
The new study is important because it shows that drought is a better predictor of spruce beetle outbreaks in northern Colorado than temperature alone, said lead study author Sarah Hart, a CU-Boulder doctoral student in geography. Drought conditions appear to decrease host tree defenses against spruce beetles, which attack the inner layers of bark, feeding and breeding in the phloem, a soft inner bark tissue, which impedes tree growth and eventually kills vast swaths of forest.
Spruce beetles, like their close relatives, mountain pine beetles, are attacking large areas of coniferous forests across the West. While the mountain pine beetle outbreak in the Southern Rocky Mountains is the best known and appears to be the worst in the historical record, the lesser known spruce beetle infestation has the potential to be equally or even more devastating in Colorado, said Hart, lead author on the new study.
“It was interesting that drought was a better predictor for spruce beetle outbreaks than temperature,” said Hart of the geography department. “The study suggests that spruce beetle outbreaks occur when warm and dry conditions cause stress in the host trees.”
A paper on the subject was published online in the journal Ecology. Co-authors include CU-Boulder geography Professor Thomas Veblen; former CU-Boulder graduate student Karen Eisenhart, now at Edinboro University of Pennsylvania; and former CU-Boulder students Daniel Jarvis and Dominik Kulakowski, now at Clark University in Worcester, Mass. The National Science Foundation and the National Geographic Society funded the study.
The new study also puts to rest false claims that fire suppression in the West is the trigger for spruce beetle outbreaks, said Veblen.
Spruce beetles range from Alaska to Arizona and live in forests of Engelmann spruce and subalpine fir trees in Colorado. The CU-Boulder study area included sites in the White River, Routt, Arapaho, Roosevelt and Grand Mesa national forests as well as in Rocky Mountain National Park.
The CU-Boulder team assembled a long-term record of spruce beetle outbreaks from the northern Front Range to the Grand Mesa in western Colorado using a combination of historical documents and tree ring data from 1650 to 2011. Broad-scale outbreaks were charted by the team from 1843-1860, 1882-1889, 1931-1957 and 2004 to 2010.
The researchers used a variety of statistical methods to tease out causes for variations in the dataset at 18 sites in Colorado. “The extent to which we could distinguish between the warming signals and the drought signals was surprising,” said Veblen. “These are two things that easily can get mixed together in most tree ring analyses.”
There are several lines of evidence that drought is the main driver of the spruce beetle outbreak. The new study showed when northwest Colorado was in a warm, wet climate period from 1976 to 1998, for example, both spruce beetle reproduction and tree defenses like “pitching” beetles out of tree interiors with resin were likely high. But during that period of warming, outbreak was minimal.
The strongest climate correlation to spruce beetle outbreaks was above average annual values for the Atlantic Multi-decadal Oscillation, or AMO, a long-term phenomenon that changes sea-surface temperatures in the North Atlantic. Believed to shift from cool to warm phases roughly every 60 years, positive AMO conditions are linked to warmer and drier conditions over much of North America, including the West.
Veblen said the AMO shifted from its cool to warm phase in the 1990s, meaning the climate phenomenon could be contributing to drought conditions in the West into the middle of this century. A 2006 tree-ring study involving Veblen, his former student, Thomas Kitzberger and researchers from several other institutions concluded that the warm phase of AMO also was correlated to increased wildfires in the West.
In addition to AMO, the researchers looked at two other ocean-atmosphere oscillations — the El Nino Southern Oscillation and the Pacific Decadal Oscillation — as well as past temperatures, precipitation and aridity to better understand the spruce beetle outbreaks. The team found that another effective predictor of drought conditions was summer “vapor pressure deficit,” a measurement of atmospheric dryness, said Veblen.
In the new study, the researchers were particularly interested in “radial growth” rates of tree rings from sub-canopy trees of various species in the study areas that thrived following outbreaks. One hallmark of spruce beetle outbreaks is that slow radial growth rates in such areas are followed by extremely rapid radial growth rates, an indication smaller trees flourish in the absence of the larger spruce trees because of decreased competition for water and increased opportunities for photosynthesis, said Hart.
The area of high-elevation forests affected by spruce beetles is growing in the West, Hart said. “In 2012, U.S. Forest Service surveys indicated that more area was under attack by spruce beetles than mountain pine beetles in the Southern Rocky Mountains, which includes southern Wyoming, Colorado and northern New Mexico,” she said. “The drought conditions that promote spruce beetle outbreak are expected to continue.”
One big concern about spruce beetle outbreaks is their effects on headwater streams that are important for water resources, said Veblen. “In the short term, trees killed by spruce beetles will lead to less water use by trees and more water discharge into streams. But in the long term, the absence of the trees killed by beetles may lead to less persistence of snow and earlier runoff.”
Veblen said it might seem counterintuitive to some that spruce-fir subalpine forests in Colorado are larger by area than lodgepole/ponderosa pine forests. “It is probably because spruce and subalpine forests are found in more remote areas not as visible to most people,” he said. “But potentially, the current spruce beetle outbreak could affect a larger area than the mountain pine beetle outbreak.”
The study had its beginnings in 1986, when Veblen and his students began compiling spruce and subalpine fir tree rings from various study sites in the Colorado mountains. Tree rings from individual trees — which carry information about weather, climate and even events like volcanic eruptions — can be matched up and read with rings from other trees, much like the pages of a book, from year to year and even from season to season.
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CU research: Microchips using light instead of wires boosts speed exponentially
Sep 30th
could allow for faster and faster electronics
A pair of breakthroughs in the field of silicon photonics by researchers at the University of Colorado Boulder, the Massachusetts Institute of Technology and Micron Technology Inc. could allow for the trajectory of exponential improvement in microprocessors that began nearly half a century ago—known as Moore’s Law—to continue well into the future, allowing for increasingly faster electronics, from supercomputers to laptops to smartphones.
The research team, led by CU-Boulder researcher Milos Popovic, an assistant professor of electrical, computer and energy engineering, developed a new technique that allows microprocessors to use light, instead of electrical wires, to communicate with transistors on a single chip, a system that could lead to extremely energy-efficient computing and a continued skyrocketing of computing speed into the future.
Popovic and his colleagues created two different optical modulators—structures that detect electrical signals and translate them into optical waves—that can be fabricated within the same processes already used in industry to create today’s state-of-the-art electronic microprocessors. The modulators are described in a recent issue of the journal Optics Letters.
First laid out in 1965, Moore’s Law predicted that the size of the transistors used in microprocessors could be shrunk by half about every two years for the same production cost, allowing twice as many transistors to be placed on the same-sized silicon chip. The net effect would be a doubling of computing speed every couple of years.
The projection has held true until relatively recently. While transistors continue to get smaller, halving their size today no longer leads to a doubling of computing speed. That’s because the limiting factor in microelectronics is now the power that’s needed to keep the microprocessors running. The vast amount of electricity required to flip on and off tiny, densely packed transistors causes excessive heat buildup.
“The transistors will keep shrinking and they’ll be able to continue giving you more and more computing performance,” Popovic said. “But in order to be able to actually take advantage of that you need to enable energy-efficient communication links.”
Microelectronics also are limited by the fact that placing electrical wires that carry data too closely together can result in “cross talk” between the wires.
In the last half-dozen years, microprocessor manufacturers, such as Intel, have been able to continue increasing computing speed by packing more than one microprocessor into a single chip to create multiple “cores.” But that technique is limited by the amount of communication that then becomes necessary between the microprocessors, which also requires hefty electricity consumption.
Using light waves instead of electrical wires for microprocessor communication functions could eliminate the limitations now faced by conventional microprocessors and extend Moore’s Law into the future, Popovic said.
Optical communication circuits, known as photonics, have two main advantages over communication that relies on conventional wires: Using light has the potential to be brutally energy efficient, and a single fiber-optic strand can carry a thousand different wavelengths of light at the same time, allowing for multiple communications to be carried simultaneously in a small space and eliminating cross talk.
Optical communication is already the foundation of the Internet and the majority of phone lines. But to make optical communication an economically viable option for microprocessors, the photonics technology has to be fabricated in the same foundries that are being used to create the microprocessors. Photonics have to be integrated side-by-side with the electronics in order to get buy-in from the microprocessor industry, Popovic said.
“In order to convince the semiconductor industry to incorporate photonics into microelectronics you need to make it so that the billions of dollars of existing infrastructure does not need to be wiped out and redone,” Popovic said.
Last year, Popovic collaborated with scientists at MIT to show, for the first time, that such integration is possible. “We are building photonics inside the exact same process that they build microelectronics in,” Popovic said. “We use this fabrication process and instead of making just electrical circuits, we make photonics next to the electrical circuits so they can talk to each other.”
In two papers published last month in Optics Letters with CU-Boulder postdoctoral researcher Jeffrey Shainline as lead author, the research team refined their original photonic-electronic chip further, detailing how the crucial optical modulator, which encodes data on streams of light, could be improved to become more energy efficient. That optical modulator is compatible with a manufacturing process—known as Silicon-on-Insulator Complementary Metal-Oxide-Semiconductor, or SOI CMOS—used to create state-of-the-art multicore microprocessors such as the IBM Power7 and Cell, which is used in the Sony PlayStation 3.
The researchers also detailed a second type of optical modulator that could be used in a different chip-manufacturing process, called bulk CMOS, which is used to make memory chips and the majority of the world’s high-end microprocessors.
Vladimir Stojanovic, who leads one of the MIT teams collaborating on the project and who is the lead principal investigator for the overall research program, said the group’s work on optical modulators is a significant step forward.
“On top of the energy-efficiency and bandwidth-density advantages of silicon-photonics over electrical wires, photonics integrated into CMOS processes with no process changes provides enormous cost-benefits and advantage over traditional photonic systems,” Stojanovic said.
The CU-led effort is a part of a larger project on building a complete photonic processor-memory system, which includes research teams from MIT led by Stojanovic, Rajeev Ram and Michael Watts, a team from Micron Technology led by Roy Meade and a team from the University of California, Berkeley, led by Krste Asanovic. The research was funded by the Defense Advanced Research Projects Agency and the National Science Foundation.
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CU study; Death of microbes could determine time of death
Sep 27th
The clock is essentially the lock-step succession of bacterial changes that occur postmortem as bodies move through the decay process. And while the researchers used mice for the new study, previous studies on the human microbiome – the estimated 100 trillion or so microbes that live on and in each of us – indicate there is good reason to believe similar microbial clocks are ticking away on human corpses, said Jessica Metcalf, a CU-Boulder postdoctoral researcher and first author on the study.
“While establishing time of death is a crucial piece of information for investigators in cases that involve bodies, existing techniques are not always reliable,” said Metcalf of CU-Boulder’s BioFrontiers Institute. “Our results provide a detailed understanding of the bacterial changes that occur as mouse corpses decompose, and we believe this method has the potential to be a complementary forensic tool for estimating time of death.”
Currently, investigators use tools ranging from the timing of last text messages and corpse temperatures to insect infestations on bodies and “grave soil” analyses, with varying results, she said. And the more days that elapse following a person’s demise, the more difficult it becomes to determine the time of death with any significant accuracy.
Using high-technology gene sequencing techniques on both bacteria and microbial eukaryotic organisms like fungi, nematodes and amoeba postmortem, the researchers were able to pinpoint time of mouse death after a 48-day period to within roughly four days. The results were even more accurate following an analysis at 34 days, correctly estimating the time of death within about three days, said Metcalf.
A paper on the subject was published Sept. 23 in the new online science and biomedical journal, eLIFE, a joint initiative of the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust Fund. The study was funded by the National Institutes of Justice.
The researchers tracked microbial changes on the heads, torsos, body cavities and associated grave soil of 40 mice at eight different time points over the 48-day study. The stages after death include the “fresh” stage before decomposition, followed by “active decay” that includes bloating and subsequent body cavity rupture, followed by “advanced decay,” said Chaminade University forensic scientist David Carter, a co-author on the study.
“At each time point that we sampled, we saw similar microbiome patterns on the individual mice and similar biochemical changes in the grave soil,” said Laura Parfrey, a former CU-Boulder postdoctoral fellow and now a faculty member at the University of British Columbia who is a microbial and eukaryotic expert. “And although there were dramatic changes in the abundance and distribution of bacteria over the course of the study, we saw a surprising amount of consistency between individual mice microbes between the time points — something we were hoping for.”
As part of the project, the researchers also charted “blooms” of a common soil-dwelling nematode well known for consuming bacterial biomass that occurred at roughly the same time on individual mice during the decay period. “The nematodes seem to be responding to increases in bacterial biomass during the early decomposition process, an interesting finding from a community ecology standpoint,” said Metcalf.
“This work shows that your microbiome is not just important while you’re alive,” said CU-Boulder Associate Professor Rob Knight, the corresponding study author who runs the lab where the experiments took place. “It might also be important after you’re dead.”
The research team is working closely with assistant professors Sibyl Bucheli and Aaron Linne of Sam Houston State University in Huntsville, Texas, home of the Southeast Texas Applied Forensic Science Facility, an outdoor human decomposition facility known popularly as a “body farm.” The researchers are testing bacterial signatures of human cadavers over time to learn more about the process of human decomposition and how it is influenced by weather, seasons, animal scavenging and insect infestations.
The new study is one of more than a dozen papers authored or co-authored by CU-Boulder researchers published in the past several years on human microbiomes. One of the studies, led by Professor Noah Fierer, a co-author on the new study, brought to light another potential forensic tool — microbial signatures left on computer keys and computer mice, an idea enthralling enough it was featured on a “CSI: Crime Scene Investigation” television episode.
“This study establishes that a body’s collection of microbial genomes provides a store of information about its history,” said Knight, also an associate professor of chemistry and biochemistry and a Howard Hughes Medical Institute Early Career Scientist. “Future studies will let us understand how much of this information, both about events before death — like diet, lifestyle and travel — and after death can be recovered.”
In addition to Metcalf, Fierer, Knight, Carter and Parfrey, other study authors included Antonio Gonzalez, Gail Ackerman, Greg Humphrey, Mathew Gebert, Will Van Treuren, Donna Berg Lyons and Kyle Keepers from CU-Boulder, former BioFrontiers doctoral student Dan Knights from the University of Minnesota, and Yan Go and James Bullard from Pacific Biosciences in Menlo Park, Calif. Keepers participated in the study as an undergraduate while Gonzalez, now a postdoctoral researcher, was a graduate student during the study.
“There is no single forensic tool that is useful in all scenarios, as all have some degree of uncertainty,” said Metcalf. “But given our results and our experience with microbiomes, there is reason to believe we can get past some of this uncertainty and look toward this technique as a complementary method to better estimate time of death in humans.”
Gene sequencing equipment for the study included machines from Illumina of San Diego and Pacific Biosciences of Menlo Park, Calif. The Illumina data were generated at CU-Boulder in the BioFrontiers Next Generation Sequencing Facility.
To access a copy of the paper visit http://dx.doi.org/10.7554/eLife.01104. For more information on the BioFrontiers Institute visit http://biofrontiers.colorado.edu.
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