Posts tagged DNA
CU study: New public gut bacteria study expected to reach around world
0November 25, 2012
Ever wondered who is living in your gut, and what they’re doing? The trillions of microbial partners in and on our bodies outnumber our own cells by as many as 10 to 1 and do all sorts of important jobs, from helping digest the food we eat this Thanksgiving to building up our immune systems.
In association with the Human Food Project, researchers at the University of Colorado Boulder along with researchers at other institutions around the world are launching a new open-access project known as “American Gut” in which participants can get involved in finding out what microbes are in their own guts and what they are doing in there.
The project builds on previous efforts, including the five-year, $173-million NIH-funded Human Microbiome Project, to characterize the microbes living in and on our bodies, said Associate Professor Rob Knight of CU-Boulder’s BioFrontiers Institute. But unlike other projects that have focused on carefully chosen test subjects with a few hundred people, this project allows the public to get involved and is encouraging tens of thousands of people to do so, Knight said.
“Galileo saw outer space through his telescope, and we want to see the inner space of your gut through modern genetics,” said Rob Dunn, a scientist at North Carolina State University and a collaborator on the project. The new project will be “crowd-funded” by individuals interested in learning more about their own gut bacteria and by others who simply want to contribute to the project, said Dunn.
“By combining the crowd-funding model with the open-access data analysis model that we pioneered with the Earth Microbiome Project, we can finally give anyone with an interest in his or her microbiome an opportunity to participate, whether by contributing samples or by looking at the data,” said Knight, also a Howard Hughes Medical Institute Early Career Scientist.
Public interest is immense, says the research team. 18,000 people have already signed up to receive more information by email about the project when it launches. “The American Gut project builds on the Human Microbiome Project by allowing anyone to participate, and will let the public join in the excitement of this new field,” said Lita Proctor, program director for the Human Microbiome Project. “We can expect this to lay the groundwork for all sorts of fascinating studies in the future, that others will in turn build on.”
The American Gut project is an opportunity for the “citizen scientists” working with team of leading researchers and labs throughout the United States to help shape a new way of understanding how diet and lifestyle may contribute to human health through each person’s suite of trillions of tiny microbes, say the researchers. A key aspect of the project is to understand how diet and lifestyle, whether by choice — like athletes or vegetarians — or by necessity, including those suffering from particular autoimmune diseases or who have food allergies, affect peoples’ microbial makeup, said Knight.
“This will be the first project of its kind that might be able to address this question at such a large scale,” said Jeff Leach, founder of the Human Food Project and co-founder of American Gut. The gut microbiome has been linked to many diseases, including obesity, cancer, and inflammatory bowel disease — all of which are much more common in Western populations, he said.
“We should start thinking about diets not only from the perspective of what we should eat, but what we should be feeding our entire gut microbial systems,” said Leach. A key aspect of the project is to integrate studies of Americans of all shapes and sizes with studies of people living more traditional lifestyles in Africa, South America and elsewhere, he said.
The steep decline in the cost of DNA sequencing and recent advances in computational techniques allow for the analysis of microbial genomes orders of magnitude cheaper than was possible only a few years ago, said Knight. Sequencing is now getting cheap enough — participants who donate $99 or more can expect to get tens of thousands of sequences from microbes in their gut — that participants can include their families and even their pets, Knight said.
Doctoral student Daniel McDonald is one of several CU-Boulder students who will be involved in the effort. “I am excited to have the opportunity to develop new computational tools in order to further explore this frontier,” said McDonald, who is in the Interdisciplinary Quantitative Biology program at the BioFrontiers Institute.
“I am pleased to participate in this pioneering effort that marries the vast interest of the public in science with questions that are worth answering about human health and nutrition,” said Martin Blaser, chair of the Department of Medicine and professor of microbiology at New York University. “Through this consortium, the technical and intellectual resources are there to lead to important new knowledge.”
The project will seek to build on a growing canine and feline database as well. “The majority of data we currently have on the dog and cat microbiomes has come from a handful of small studies in research or clinically ill animals,” said Associate Professor Kelly Swanson of the Department of Animal Sciences and Division of Nutritional Sciences at the University of Illinois at Urbana-Champaign. “This study will apply the technology to free-living pets, where diet, genetics, and living environment are quite different from household to household.
“This research may identify important trends not possible with lab-based studies, and help guide us on how to feed our pets in the future,” said Swanson.
The backdrop to the project is the radical decline in the cost of DNA sequencing, which allows analysis of microbial genomes orders of magnitude cheaper than was possible only a few years ago, and recent advances in computational techniques. Participants in the project include many of the key players in the Human Microbiome Project and research facilities around the world.
To learn more about participating in or contributing to the project visit https://www.indiegogo.com/americangut. For a list of additional collaborators on the project visithttp://humanfoodproject.com/the-people/collaborators/.
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CU Boulder researchers uncover new target for cancer research
0October 25, 2012
In a new paper released today in Nature, BioFrontiers Institute scientists at the University of Colorado Boulder, Tom Cech and Leslie Leinwand, detailed a new target for anti-cancer drug development that is sitting at the ends of our DNA.
Researchers in the two scientists’ laboratories collaborated to find a patch of amino acids that, if blocked by a drug docked onto the chromosome end at this location, may prevent cancerous cells from reproducing. The amino acids at this site are called the “TEL patch” and once modified, the end of the chromosome is unable to recruit the telomerase enzyme, which is necessary for growth of many cancerous cells.
“This is an exciting scientific discovery that gives us a new way of looking at the problem of cancer,” Cech said. “What is amazing is that changing a single amino acid in the TEL patch stops the growth of telomeres. We are a long way from a drug solution for cancer, but this discovery gives us a different, and hopefully more effective, target.”
Nobel Prize winner Tom Cech
Cech is the director of the BioFrontiers Institute, a Howard Hughes Medical Investigator and winner of the 1989 Nobel Prize in chemistry.
Co-authors on the study include postdoctoral fellows Jayakrishnan Nandakumar and Ina Weidenfeld; University of Colorado undergraduate student Caitlin Bell; and Howard Hughes Medical Institute Senior Scientist Arthur Zaug.
Telomeres have been studied since the 1970s for their role in cancer. They are constructed of repetitive nucleotide sequences that sit at the ends of our chromosomes like the ribbon tails on a bow. This extra material protects the ends of the chromosomes from deteriorating, or fusing with neighboring chromosome ends. Telomeres are consumed during cell division and, over time, will become shorter and provide less cover for the chromosomes they are protecting. An enzyme called telomerase replenishes telomeres throughout their lifecycles.
Telomerase is the enzyme that keeps cells young. From stem cells to germ cells, telomerase helps cells continue to live and multiply. Too little telomerase produces diseases of bone marrow, lungs and skin. Too much telomerase results in cells that over proliferate and may become “immortal.” As these immortal cells continue to divide and replenish, they build cancerous tumors. Scientists estimate that telomerase activation is a contributor in up to 90 percent of human cancers.
To date, development of cancer therapies has focused on limiting the enzymatic action of telomerase to slow the growth of cancerous cells. With their latest discovery, Cech and Leinwand envision a cancer drug that would lock into the TEL patch at chromosome ends to keep telomerase from binding there. This approach of inhibiting the docking of telomerase may be the elegant solution to the complex problem of cancerous cells. Cech, a biochemist, and Leinwand, a biologist, joined forces to work on their latest solution.
“This work was really made possible by the fact that our labs are so close,” Leinwand said. “My lab was able to provide the cell biology and understanding of genetics, and Tom’s lab allowed us to explore the biochemistry. We have a unique situation at BioFrontiers where labs and people comingle to make discoveries just like this.”
Leinwand is the chief scientific officer of the BioFrontiers Institute and a professor of molecular, cellular and developmental biology.
Researchers at the University of Colorado have a significant history in developing marketable biotechnologies. Cech founded Ribozyme Pharmaceuticals Inc. Leinwand co-founded Myogen with CU professor Michael Bristow, Hiberna and recently launched MyoKardia (http://www.myokardia.com/about.php).
The BioFrontiers Institute is an interdisciplinary institute housed at the Jennie Smoly Caruthers Biotechnology Building at CU-Boulder. The institute is dedicated to training the next generation of interdisciplinary scientists through its IQ Biology Interdisciplinary Quantitative Biology Ph.D. program. For more information about BioFrontiers visithttp://biofrontiers.colorado.edu
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New CU-Boulder study clarifies diversity, distribution of cutthroat trout in Colorado
0September 24, 2012
Will the real greenback cutthroat trout please stand up?
A novel genetic study led by the University of Colorado Boulder has helped to clarify the native diversity and distribution of cutthroat trout in Colorado, including the past and present haunts of the federally endangered greenback cutthroat trout.
The study, led by CU-Boulder postdoctoral researcher Jessica Metcalf, was based largely on DNA samples taken from cutthroat trout specimens preserved in ethanol in several U.S. museums around the country that were collected from around the state as far back as 150 years ago. The new study, in which Metcalf and her colleagues extracted mitochondrial DNA from fish to sequence genes of the individual specimens and compared them with modern-day cutthroat trout strains, produced some startling results.
The biggest surprise, said Metcalf, was that the cutthroat trout native to the South Platte River drainage appears to survive today only in a single population outside of its native range — in a small stream known as Bear Creek that actually is in the nearby Arkansas River drainage. The strain from Bear Creek is thought to have been collected from the South Platte River drainage in the 1880s by an early hotelier who stocked the fish in a pond at the Bear Creek headwaters to help promote an early tourist route up Pikes Peak.
“We thought one way to get to the question of which cutthroat trout strains are native to particular drainages was to go back to historical samples and use their DNA as a baseline of information,” said Metcalf of the chemistry and biochemistry department and a former postdoctoral researcher at the Australian Centre for Ancient DNA. “Our study indicates the descendants of the fish that were stocked into Bear Creek in the late 1800s are the last remaining representatives of the federally protected greenback cutthroat trout.”
A second, key set of data was all of the Colorado cutthroat trout stocking records over the past 150 years, a task spearheaded by study co-author and fish biologist Chris Kennedy of the U.S. Fish and Wildlife Service. Between 1889 and 1925, for example, the study showed that more than 50 million cutthroat trout from the Gunnison and Yampa river basins were stocked in tributaries of all major drainages in the state, jumbling the picture of native cutthroat strains in Colorado through time and space.
Originating from the Pacific Ocean, cutthroat trout are considered one of the most diverse fish species in North America and evolved into 14 recognized subspecies in western U.S. drainages over thousands of years. In Colorado, four lineages of cutthroats were previously identified: the greenback cutthroat, the Colorado River cutthroat, the Rio Grande cutthroat and the extinct yellowfin cutthroat.
The museum specimens used in the study came from the California Academy of Sciences, the Smithsonian Museum of Natural History in Washington, D.C., the Academy of Natural Sciences in Philadelphia and the Harvard University Museum of Comparative Zoology. Colorado cutthroat trout specimens were collected by a number of early naturalists, including Swiss scientist and former Harvard Professor Louis Agassiz and internationally known fish expert and founding Stanford University President David Starr Jordan.
The new study, published online today in Molecular Ecology, follows up on a 2007 study by Metcalf and her team that indicated there were several places on the Front Range where cutthroat populations thought to be greenbacks by fish biologists were actually a strain of cutthroats transplanted from Colorado’s Western Slope in the early 1900s.
CU graduate researcher, Sierra Stowell (pictured here as a teenager) was a co-author of the study. She spends a lot of time in or near the water where cutthroat trout live.
Other co-authors on the new study included CU-Boulder Professor Andrew Martin and CU-Boulder graduate students Sierra Stowell, Daniel McDonald and Kyle Keepers; Colorado Parks and Wildlife biologist Kevin Rogers; University of Adelaide scientists Alan Cooper and Jeremy Austin; and Janet Epp of Pisces Molecular LLC of Boulder.
“With the insight afforded by the historical data, we now know with a great deal of certainty what cutthroat trout strains were here in Colorado before greenbacks declined in the early 20th century,” said Martin of CU’s ecology and evolutionary biology department. “And we finally know what a greenback cutthroat trout really is.”
Metcalf and her colleagues first collected multiple samples of tissue and bone from each of the ethanol-pickled trout specimens, obtaining fragments of DNA that were amplified and then pieced together like a high-tech jigsaw puzzle to reveal two genes of the individual specimens. The tests were conducted on two different continents under highly sterile conditions and each DNA sequencing effort was repeated several times for many specimens to ensure accuracy in the study, Metcalf said.
Roughly half of the study was conducted at CU-Boulder and half at the Australian Center for Ancient DNA at the University of Adelaide, where Metcalf had worked for two years. “By conducting repeatable research at two very different, state-of-the-art laboratories, we were able to show the Bear Creek trout was the same strain as the cutthroats originally occupying the South Platte River drainage.”
The Bear Creek trout strain is now being propagated in the Colorado Parks and Wildlife hatchery system and at the USFWS Leadville National Fish Hatchery.
In addition to identifying the Bear Creek cutthroat trout, Metcalf and her colleagues discovered a previously unknown cutthroat strain native to the San Juan Basin in southwestern Colorado that has since gone extinct. The study also confirmed that the yellowfin cutthroat, a subspecies from the Arkansas River headwaters that grew to prodigious size in Twin Lakes near Leadville, also had gone extinct.
Fortunately, most fish preserved by naturalists before 1900 were “fixed” in ethanol, which makes it easier for researchers to obtain reliable DNA than from fish preserved in a formaldehyde solution, a practice that later became popular. Prior to the new study — which included DNA from specimens up to about 150 years old — scientists working in ancient DNA labs had only performed similar research on ethanol-preserved museum vertebrate specimens less than 100 years old.
“One of the exciting things to come from this research project is that it opens up the potential for scientists to sequence the genes of other fish, reptiles and amphibian specimens preserved in ethanol further back in time than ever before to answer ecological questions about past diversity and distribution,” said Metcalf, who conducts her research at CU’s BioFrontiers Institute.
Funding for the study was provided by agencies of the Greenback Cutthroat Trout Recovery Team, including the USFWS, the U.S. Forest Service, the Bureau of Land Management, the National Park Service and Trout Unlimited.
“I think in many cases success depends less on the application of a new technology and more on the convergence of people with shared interest and complementary skills necessary for solving difficult problems,” said Martin. “Our greenback story is really one about what can be discovered when dedicated and talented people collaborate with a shared purpose.”
“We’ve known for some time that the trout in Bear Creek were unique,” said Doug Krieger, senior aquatic biologist for Colorado Parks and Wildlife and the Greenback Cutthroat Trout Recovery Team leader. “But we didn’t realize they were the only surviving greenback population.”
The decline of native cutthroats in Colorado occurred because of a combination of pollution, overfishing and stocking of native and non-native species of trout, said Metcalf. “It’s ironic that stocking nearly drove the greenback cutthroat trout to extinction, and a particularly early stocking event actually saved it from extinction,” she said.
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CU scientists find life forms in a lifeless land
0June 14, 2012
A team led by the University of Colorado Boulder looking for organisms that eke out a living in some of the most inhospitable soils on Earth has found a hardy few.
A new DNA analysis of rocky soils in the Martian-like landscape on some volcanoes in South America has revealed a handful of bacteria, fungi and other rudimentary organisms called archaea, which seem to have a different way of converting energy than their cousins elsewhere in the world.
“We haven’t formally identified or characterized the species,” said Ryan Lynch, a CU-Boulder doctoral student involved in the study. “But these are very different than anything else that has been cultured. Genetically, they’re at least 5 percent different than anything else in the DNA database of 2.5 million sequences.”
Life gets little encouragement on the incredibly dry slopes of the tallest volcanoes in the Atacama region, where CU-Boulder Professor Steve Schmidt and his team collected soil samples. Much of the sparse snow that falls on the terrain sublimates back to the atmosphere soon after it hits the ground, and the soil is so depleted of nutrients that nitrogen levels in the scientists’ samples were below detection limits.
One of the most hostile environments on the planet
Ultraviolet radiation in the high-altitude environment can be twice as intense as in a low-elevation desert, said Schmidt of CU-Boulder’s ecology and evolutionary biology department. While the researchers were on site, temperatures dropped to 14 degrees Fahrenheit one night and spiked to 133 F the next day.
How the newfound organisms survive under such circumstances remains a mystery. Although Ryan, Schmidt and their colleagues looked for genes known to be involved in photosynthesis and peered into the cells using fluorescent techniques to look for chlorophyll, they couldn’t find evidence that the microbes were photosynthetic.
Instead, they think the microbes might slowly generate energy by means of chemical reactions that extract energy and carbon from wisps of gases such as carbon monoxide and dimethylsulfide that blow into the desolate mountain area. The process wouldn’t give the bugs a high-energy yield, Lynch said, but it could be enough as it adds up over time. A paper on the findings has been accepted by the Journal of Geophysical Research-Biogeosciences, published by the American Geophysical Union.
While normal soil has thousands of microbial species in just a gram of soil, and garden soils even more, remarkably few species have made their home in the barren Atacama mountain soil, the new research suggests. “To find a community dominated by less than 20 species is pretty amazing for a soil microbiologist,” Schmidt said.
Nearly 20,000 feet in altitude, snowless for 48,000 years
He has studied sites in the Peruvian Andes where, four years after a glacier retreats, there are thriving, diverse microbe communities. But on these volcanoes on the Chile-Argentina border, which rise to altitudes of more than 19,685 feet and which have been ice-free for 48,000 years, the bacterial and fungal ecosystems have not undergone succession to more diverse communities. “It’s mostly due to the lack of water, we think,” he said. “Without water, you’re not going to develop a complex community.”
“Overall, there was a good bit lower diversity in the Atacama samples than you would find in most soils, including other mountainous mineral soils,” Lynch said. That makes the Atacama microbes very unusual, he added. They probably had to adapt to the extremely harsh environment, or may have evolved in different directions than similar organisms elsewhere due to long-term geographic isolation.
Growth on the mountain might be intermittent, Schmidt suggested, especially if soils only have water for a short time after snowfall. In those situations, there could be microbes that grow when it snows, then fall dormant, perhaps for years, before they grow again. High-elevation sites are great places to study simple microbial communities, ecosystems that haven’t evolved past the very basics of a few bacteria and fungi, Schmidt said.
“There are a lot of areas in the world that haven’t been studied from a microbial perspective, and this is one of the main ones,” he said. “We’re interested in discovering new forms of life, and describing what those organisms are doing, how they make a living.”
Schmidt’s lab, along with others, is studying how microorganisms travel from one site to another. One common method of microbe transport is through the air — they’re caught up in winds, sucked up into clouds, form rain droplets and then fall back to the ground somewhere else as precipitation.
But on mountains like Volcán Llullaillaco and Volcán Socompa, the high UV radiation and extreme temperatures make the landscape inhospitable to outside microbes. “This environment is so restrictive, most of those things that are raining down are killed immediately,” Schmidt said. “There’s a huge environmental filter here that’s keeping most of these things from growing.”
The next steps for the researchers are laboratory experiments using an incubator that can mimic the extreme temperature fluctuations to better understand how any organism can live in such an unfriendly environment. Studying the microbes and finding out how they can live at such an extreme can help set boundaries for life on Earth, Schmidt said, and tells scientists what life can stand. There’s a possibility that some of the extremophiles might utilize completely new forms of metabolism, converting energy in a novel way.
Schmidt also is working with astrobiologists to model what past conditions were like on Mars. With their rocky terrain, thin atmosphere and high radiation, the Atacama volcanoes are some of the most similar places on Earth to the Red Planet.
“If we know, on Earth, what the outer limits for life were, and they know what the paleoclimates on Mars were like, we may have a better idea of what could have lived there,” he said.
Other paper authors included Andrew King of Ecosystem Sciences, CSIRO Black Mountain in Acton, Australia; Mariá Farías of Laboratorio de Investigaciones Microbiologicas de Lagunas Andinas, Planto Piloto de Procesos Industriales Microbiologicas, CCT, CONICET in Tucuman, Argentina; Preston Sowell of Geomega, an environmental consulting firm in Boulder; and Christian Vitry of Museo de Arqueologia de Alta Montana in Salta, Argentina.
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Could JonBenet Ramsey’s Murder Be Solved? Boulder
0October 18, 2011
by Tommy Garrett on Oct 18, 2011 – Canyon News
BOULDER, Colo.—Nearly 15 years ago in 1996, a 6-year-old little girl, who the media constantly refers to as a pageant queen, JonBenet Ramsey was found dead in her parents’ Boulder, Colorado mansion the day after Christmas. Parents John and Patsy Ramsey, who worked hard to achieve the American dream, succeeded and became the quintessential beautiful affluent family in the Rocky Mountain region of the country were vilified by the Bolder authorities, including a former prosecutor and various police detectives, who were unable to solve the murder of their beautiful daughter. The media onslaught the Ramsey family endured would not only focus on John and Patsy but also journalists turned their ire on 9-year-old brother Burke, who was victimized all over again when he watched himself and his parents be accused of a horrific crime against a family member.
JonBenet in 1996
JonBenet Ramsey
John Ramsey’s adult children were also investigated, and it was well over a decade before the Boulder authorities, under new management would finally clear the parents of murder. Patsy Ramsey succumbed to ovarian cancer long before her good name was finally cleared. This case became an unsolved murder mainly because authorities decided the killer or killers were inside the family and living in the beautiful home, that many police officers on that cold December day felt envy of. John Ramsey had built up a technology business in the heart of Colorado and become one of the nation’s billionaires. Only to see his fortune disappear as he was forced to defend himself, his wife and children against an almost lynch-mob mentality in the media and in local law enforcement trying to pin the crimes against little JonBenet on the Ramseys themselves.
Now after the disgraced self-proclaimed pedophile John Mark Karr, who initially placed himself at the scene of the crime has been officially proved to be a liar. Many around the U.S. and the world are wondering if after almost a decade and a half has passed whether this is a case that can be solved by the Boulder Police, which lost a solid decade investigating an innocent couple, who barely had time to grieve because of the media spotlight placed on them.
Larry Schiller author of a book on the case, “Perfect Murder, Perfect Town” told ABC News last year, “This is a case that embarrassed an entire community,” he said, pointing to the inexperience of the Boulder Police Department in 1996. “They live under the shadow of this case.” Schiller is correct. The city still lives under the specter of this murder case, which over the past few years has yielded few clues, but all of which point away from John and Patsy Ramsey and all other Ramsey family members. JonBenet’s body was found beaten and strangled in a very dark corner of the Ramsey family’s home. At least two TV movies have been done on the case, countless hours of news programs and even the Ramseys themselves have appeared on CNN’s “Larry King Live” and all of the other major network news shows, and magazines.
John and Patsy Ramsey
Parents Patsy And John Ramsey
Ever since that morning after Christmas in 1996, when Patsy placed the frantic 911 call to Boulder authorities, Americans felt the loss of a little girl that was known to her family as the most beautiful child they’d ever seen, an American princess even though she became more famous after death than she ever was in her short six years on earth. However, recently I saw a documentary on the ID cable network about the kidnapping of Jaycee Dugard at the age of 11, by madman pedophile Phillip Garrido and his equally as evil wife Nancy Garrido. This couple kidnapped Jaycee at the tender age of 11-years-old and held her captive, even for months with her hands cuffed behind her back in the backyard of their Northern California home, where she was repeatedly rapped, tortured and forced to bear two children by her kidnapper, who now has been sentenced to well over 400 years for his crimes against Ms. Dugard. Wife Nancy Garrido has been sentence to at least 35 years.
When I watched the show, almost sickened to the stomach by the depravity of the two people, who masterminded the 18 year-long ordeal that Dugard faced, not to mention what she must be going through today, even away from the couple, I saw eerily similar aspects of the two crimes that gave me pause for consideration. Surely Phillip Garrido’s DNA is on file in California, and surely it’s been submitted to the authorities in Boulder, Colorado for examination, hasn’t it? I actually could not truthfully say yes to that question. The State of California very shamefully failed Jaycee and her two daughters for decades. Garrido, a paroled sex offender had his home inspected hundreds of times, even after a next-door neighbor reported seeing children playing in his backyard tent-city area. Yet the parole authorities in California never bothered to go 100 feet outside the back door to search or even inspect that location, even though Phillip Garrido’s ankle bracelet showed thousands of trips per month back to that part of his property.
Jaycee was kidnapped when Phillip Garrido used a stun-gun to disable her, so that Nancy Garrido, his wife could carry her and put her in the backseat of their car. They used binding on her to subdue her until they got her to their home less than one hundred miles away. So I wondered, could Phillip and Nancy Garrido have seen a photo of JonBenet in some pageant materials or literature, and could Phillip Garrido be so obsessed with her, that he and wife Nancy would break into the Ramsey home and wait for the family to return from a party they all attended on Christmsa night? The Ramsey family hired retired Boulder detective Lou Schmidt, who as stated repeatedly that he joined the Ramsey legal team, because of evidence that he felt pointed away from any Ramsey family member being involved in the murder of little JonBenet. Schmidt has said that he found on several of the autopsy photographs, markings on JonBenet that are consistent with a stun gun being used on her during the crime.
One of the things that stumped authorities for so long, was the ransom note left in the Ramsey home, written by what they believe to be by a woman. Nancy Garrido has proved over the years that she would protect her husband, and would commit unspeakable crimes on young girls, such as Jaycee, in order to offer her husband whatever sexual fantasies he had. Is it possible the couple drove to Boulder and are responsible for the murder of the young girl on that night? Perhaps Boulder, Colorado authorities should take it upon themselves not to assume that California has done the right thing by submitting Garrido’s DNA sample to the natoinal data bank, since they didn’t properly supervise his parole for close to two decades. Maybe the Boulder authorities should contact authorities in California to get a sample of Phillip and Nancy Garrido’s DNA for testing in the unsolved murder case of JonBenet Ramsey.
Perhaps one of America’s most celebrated unsolved mysteries could be solved by this testing procedure. Famed Attorney Robin Sax, who practices law in California and who is well versed in the Ramsey case, since she also was involved in the capture of John Mark Karr spoke to Canyon News from her beautiful new Century City offices. When asked about Garrido’s DNA being on file, Sax said, “Absolutely, yes and probably was on file from his previous prison conviction too!”
America and the Ramseys would like to solve this unsolved case. JonBenet deserves justice as well. The little girl would be a college student now, probably a pre-med major. Who knows what and where JonBenet Ramsey could have done with her life, which was snuffed out, brutally, by a deranged person, who should be in prison today.
Anyone with potential information regarding this case should contact the Boulder Police Department.
Also to learn more about JonBenet Ramse, go to: JonBenet-Ramsey.com
reprinted from Canyon News
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NEW CU-BOULDER STUDY REVEALS BACTERIA FROM DOG FECES IN OUTDOOR AIR OF URBANIZED AREAS
0August 18, 2011
NEW CU-BOULDER STUDY REVEALS BACTERIA FROM DOG FECES IN OUTDOOR AIR OF URBANIZED AREAS
Bacteria from fecal material — in particular, dog fecal material — may constitute the dominant source of airborne bacteria in Cleveland’s and Detroit’s wintertime air, says a new University of Colorado Boulder study.
The CU-Boulder study showed that of the four Midwestern cities in the experiment, two cities had significant quantities of fecal bacteria in the atmosphere — with dog feces being the most likely source.
“We found unexpectedly high bacterial diversity in all of our samples, but to our surprise the airborne bacterial communities of Detroit and Cleveland most closely resembled those communities found in dog poop,” said lead author Robert Bowers, a graduate student in CU-Boulder’s ecology and evolutionary biology department and the CU-headquartered Cooperative Institute for Research in Environmental Sciences, or CIRES. “This suggests that dog poop may be a potential source of bacteria to the atmosphere at these locations.”
The study was published July 29 in Applied and Environmental Microbiology. Co-authors on the study included Noah Fierer, an assistant professor in CU-Boulder’s ecology and evolutionary biology department and a CIRES fellow; Rob Knight, an associate professor in CU-Boulder’s chemistry and biochemistry department; Amy Sullivan and Jeff Collett Jr. of Colorado State University; and Elizabeth Costello of the Stanford University School of Medicine.
Scientists already knew that bacteria exist in the atmosphere and that these bacteria can have detrimental effects on human health, triggering allergic asthma and seasonal allergies, Fierer said. But it is only in recent years that researchers have realized that there is an incredible diversity of bacteriaresiding in the air, he said.
“There is a real knowledge gap,” said Fierer. “We are just starting to realize this uncharted microbial diversity in the air — a place where you wouldn’t exactly expect microbes to be living.”
To gain further understanding of just what microbes are circulating in urban environments, the team analyzed the local atmosphere in the summer and winter at four locations in the Great Lakes region of the U.S. Three of the locations — Chicago, Cleveland and Detroit — are major cities with populations of greater than 2 million, and one location, Mayville, Wis., is a small town with a population of less than 6,000.
The team used nearly 100 air samples collected as part of a previous study conducted by Colorado State University. The CSU experiment investigated the impact of biomass burning and involved studying the impacts of residential wood burning and prescribed fires on airborne fine particle concentrations in the midwestern United States.
“What we’ve been looking at are the numbers and the types of bacteria in the atmosphere,” Fierer said. “We breathe in bacteria every minute we are outside, and some of these bugs may have potential health implications.”
The researchers analyzed the bacteria’s DNA in the collected air samples and compared the bacteria they found against a database of bacteria from known sources such as leaf surfaces, soil, and human, cow and dog feces. They discovered that the bacterial communities in the air were surprisingly diverse and also that, in two of the four locations, dog feces were a greater than expected source of bacteria in the atmosphere in the winter.
In the summer, airborne bacteria come from many sources including soil, dust, leafsurfaces, lakes and oceans, Bowers said. But in the winter, as leaves drop and snow covers the ground, the influence that these environments have as sources also goes down. It is during this season that the airborne communities appeared to be more influenced by dog feces than the other sources tested in the experiment, he said.
“As best as we can tell, dog feces are the only explanation for these results,” Fierer said. “But we do need to do more research.”
The team plans to investigate the bacterial communities in other cities and to build a continental-scale atlas of airborne bacterial communities, Fierer said. “We don’t know if the patterns we observed in those sites are unique to those cities,” he said. “Does San Francisco have the same bacteria as New York? Nobody knows as yet.”
Fierer believes it is important to pin down the types of bacteria in the air, how these bacteria vary by location and season, and where they are coming from.With this information, scientists can then investigate the possible impacts on human health, he said.
“We need much better information on what sources of bacteria we are breathing in every time we go outside,” Fierer said.
The study was funded by the CIRES Innovative Research Program, the U.S.
Environmental Protection Agency, the National Science Foundation, the Howard Hughes Medical Institute and the National Institutes of Health. The aerosol sample collection for this project was supported by the Lake Michigan Air Directors Consortium.
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GUT MICROBES IN HUMANS AND OTHER MAMMALS HEAVILY INFLUENCED BY DIET, SAYS NEW STUDY C U Boulder
0May 20, 2011
by Boulder Channel 1
in News
You are what you eat whether you’re a lion, a giraffe or a human — at least in terms of the bacteria in your gut.
A new study led by the Washington University School of Medicine and involving the University of Colorado Boulder shows gut microbial communities in humans and in a wildly diverse collection of mammals carry out core physiological functions that are heavily influenced by whether they are carnivores, herbivores or omnivores.
The researchers sequenced intestinal microbes in stool samples from 33 mammalian species living in the wild or in zoos in St. Louis and San Diego. In addition to identifying the bacterial species living in the mammalian intestines, they characterized the pool of genes present in each microbial community and their related functions, said senior study author Dr. Jeffrey Gordon of the Washington University School of Medicine in St. Louis.
CU-Boulder professor and study co-author Rob Knight said despite the wide variation of mammals selected for the study, the different gut microbial communities share a set of standard metabolic functions common to all species that play a key role in digestion and immune health. Understanding the variation in human microbial intestine communities holds promise for future clinical research, said Knight, a faculty member in the chemistry and biochemistry department and the computer science department.
A paper on the subject was published in the May 20 issue of Science. Other co-authors on the study included CU-Boulder’s Justin Kuczynski, Dan Knights, Jose Clemente and Antonio Gonzalez, Washington University School of Medicine’s Brian Muegge and Luigi Fontana, and Bernard Henrissat of the Archictecture et Fonction des Macromolecules Biologiques in Marseille, France.
“This was the first time we were able to relate the microbial community members to the specific metabolic functions that were being performed,” said Knight, who also is a Howard Hughes Medical Institute Early Career Scientist. “This is surprising because even members of the same bacterial species can have genomes that are up to 40 percent different in terms of gene content.”
The team extracted DNA from the mammals and humans and used powerful computer methods to sort gene fragments and match them to the DNA of known organisms.
While there was considerable variation of bacterial gut communities between animals, the study showed many of the same microbial genes were found in all of the digestive tracts, with differences in their relative abundance dependent on whether they were meat-eaters, vegetarians or omnivores. Among the mammals whose fecal material was used to sequence gut bacteria microbes included giraffe, bighorn sheep, gazelle, kangaroo, hyena, lion, polar bear, elephant, gorilla, baboon, black bear and squirrel.
The team also showed how diet influences microbial communities in the human gut by sampling 18 lean people who purposely had cut their caloric intake by 25 percent or more using many different dietary strategies. The researchers found that the functions of gut microbes varied according to how much protein the individuals ate, and the bacterial species varied according to how much fiber was consumed.
In a related 2009 study led by CU-Boulder’s Knight, researchers developed the first atlas of microbial diversity across the human body, charting wide variations in microbe populations from the forehead and feet to noses and navels of individuals. One goal of human bacterial studies is to find out what is normal for healthy people, which should provide a baseline for studies looking at human disease states, said Knight, who also is a fellow at CU’s Colorado Initiative for Molecular Biotechnology.
“If we can better understand this microbial variation, we may be able to begin searching for genetic biomarkers for disease,” said Knight. It might someday be possible to identify sites on the human body, including the gut, that would be amenable to microbial community transplants with either natural or engineered microbial systems that would be beneficial to the health of the host, he said.
“Because the human microbiome is much more variable than the human genome, and because it also is much easier to modify, it provides a much more logical starting point for personalized medicine,” he said.
The latest findings emphasize the need to sample humans across the globe with a variety of extreme lifestyles and diets, including hunter-gatherer groups, said the researchers. Such studies could provide insight into the limits of gut bacteria variation and the possibility that human microbes co-evolved with human bodies and cultures, shaping our physiological differences and environmental adaptations.
Members of Knight’s lab and their many collaborators are studying how the human microbiome — all of a person’s hereditary information — is assembled in different people and how it varies in conditions such as obesity, malnutrition and Crohn’s disease. In addition to financial support from HHMI, Knight also has been supported by National Institutes of Health funds to develop new computational tools to better understand the composition and dynamics of microbial communities.
The Science magazine study was supported by the NIH and the Crohn’s and Colitis Foundation of America.
-CU-
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US issues WW travel alert; more security plans for possible reprisals Osama Bin Laden
0May 2, 2011
by Boulder Channel 1
in News
|
WIKILEAKS: Al Qaeda to unleash 'nuclear hellstorm' if Osama killed... |
SHOT IN HEAD; BIN LADEN IS DEAD.....
Mission was to kill, not capture...
Crowds gather at White House, Ground Zero to celebrate...
Obama: U.S. Carried Out Operation 'At My Direction'...
W: 'No Matter How Long It Takes, Justice Will Be Done'...
Killing brings anger, relief in Arab world...
Heat on Pakistan...
Hamas condemns killing of 'holy warrior'...
(Reuters) – The State Department on Sunday warned Americans worldwide of “enhanced potential for anti-American violence” following the killing of al Qaeda leader Osama bin Laden.
“Given the uncertainty and volatility of the current situation, U.S. citizens in areas where events could cause anti-American violence are strongly urged to limit their travel outside of their homes and hotels and avoid mass gatherings and demonstrations,” the State Department said in a statement.
(Reporting by Andrew Quinn, Editing by Will Dunham)
from US govt
Current Travel Warnings
Travel Warnings are issued when long-term, protracted conditions that make a country dangerous or unstable lead the State Department to recommend that Americans avoid or consider the risk of travel to that country. A Travel Warning is also issued when the U.S. Government’s ability to assist American citizens is constrained due to the closure of an embassy or consulate or because of a drawdown of its staff. The countries listed below meet those criteria.
Syria
Uzbekistan
Mexico
Burkina Faso
Nigeria
Cote d’Ivoire
Iraq
Bahrain
Lebanon
Algeria
Mauritania
Afghanistan
Yemen
Mali
Eritrea
Libya
Pakistan
Haiti
Central African Republic
Niger
Nepal
Sudan
Kenya
Somalia
Saudi Arabia
Chad
Guinea
Congo, Democratic Republic of the
Colombia
Burundi
Philippines
Iran
Korea, Democratic People’s Republic of
Israel, the West Bank and Gaza
| FEAR: Security Tightened at NY Airports, World Trade Center Site... U.S. issues worldwide travel alert... Chemical Biological Response Team Recalled from Japan... Islamists: Death will not mute Jihad call... USA 'Faces Broad Terror Threat'... REPORT: Pakistani intelligence agents on site during raid; unclear who fired fatal shot... WH OFFICIAL: Bin Laden 'did resist'; Was asked to surrender... 4 others killed, including son... Woman used as 'shield'... Obama spoke with Bush, Clinton before TV statement... Detainees captured after 9-11 gave crucial information... Bin Laden, Adolf Hitler both declared dead on May 1... |
| REPORT: Obama Canceled March Compound Bombing, Wanted Proof of Death... Flowers, Flags Left Outside Bush's Dallas Home... BIN LADEN ANNOUNCEMENT CAME IN MIDDLE OF TRUMP'S 'CELEBRITY APPRENTICE'... Egypt's al-Zawahri likely to succeed... Muslim bro'hood: USA should now leave Afghanistan, Iraq... |
| REPORT: Bin Laden already buried at sea...
OFFICIAL: U.S. didn't want to 'create shrine'... DNA tests won't be complete for days... WHITE HOUSE: BODY HANDLED IN 'ACCORDANCE WITH ISLAMIC PRACTICE'... Raid captured on TWITTER... |
