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CU study: New public gut bacteria study expected to reach around world
Nov 25th
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 invites public to Nov. 26 workshop on oil and gas development on groundwater
Nov 19th
Following the recent Colorado Oil and Gas Conservation Commission hearing on creation of statewide regulations for groundwater sampling and monitoring near new oil and gas wells, the University of Colorado Boulder will host an informational workshop on Monday, Nov. 26, from 1 to 5 p.m. at the Wolf Law Building.
The workshop, titled “Monitoring and Protecting Groundwater during Oil and Gas Development,” will focus on oil and gas development procedures that can impact groundwater, the current state regulations that protect groundwater, the changes proposed by the commission, and other recommendations. The commission will hold a second hearing and plans to finalize new regulations on Dec. 10, 2012.
The workshop is free and open to the public and is co-sponsored by the CU-Boulder Natural Resources Law Center’s Intermountain Oil and Gas Best Management Practices Project and the Colorado Water and Energy Research Center.
The Oil and Gas Conservation Commission of the state of Colorado has required water well sampling and monitoring for many years through numerous state orders, rules and conditions of approval. The proposed water-sampling rule would establish sampling and monitoring requirements on a statewide basis and would eventually supersede other commission water sampling rules and orders, with the exception of rules concerning sampling in coal-bed methane areas.
The sampling rule is intended to provide the commission with a mechanism to obtain data consistently across the state. These data are intended to help verify that water wells, ground and surface waters, and residents of producing basins are adequately protected and that impacts, should they occur, are quickly identified and mitigated.
“Energy, jobs and a clean environment, including clean and sufficient groundwater, are extremely important to Colorado today and for our future,” said Kathryn Mutz, Natural Resources Law Center senior research associate and Intermountain Oil and Gas Best Management Practices Project manager. “Ensuring groundwater protection during oil and gas development is one important part of the puzzle. This workshop is providing a venue outside of the formal commission rulemaking process to discuss and educate ourselves and the stakeholders about the alternatives so that we get this rule right for Colorado.”
For more information about the Nov. 26 workshop and the proposed amendments, visit http://www.oilandgasbmps.org/workshops/COGCCgroundwater/index.php. To RSVP, email your name and contact information to nrlc@colorado.edu. Continuing Legal Education credits are available to attendees for a fee.
The Intermountain Oil and Gas Best Management Practices Project website and database are maintained as part of the Natural Resources Law Center within the CU-Boulder Law School. Best Management Practices are mitigation measures applied to areas being developed for oil and gas to promote energy development in an environmentally sensitive manner. The project is supported, in part, by the Environmentally Friendly Drilling Project and a CU-Boulder Outreach Award.
The Colorado Water and Energy Research Center, led by Mark Williams, CU-Boulder professor of geography, provides a neutral clearinghouse for information on the potential hydrologic impacts of natural gas development.
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CU project: Degraded military lands to get ecological boost
Nov 15th
Some arid lands in the American West degraded by military exercises that date back to General George Patton’s Word War II maneuvers in the Mojave Desert should get a boost from an innovative research project led by the University of Colorado Boulder.
Headed up by CU-Boulder Assistant Professor Nichole Barger, the research team is focused on developing methods to restore biological soil crusts — microbial communities primarily concentrated on soil surfaces critical to decreasing erosion and increasing water retention and soil fertility. Such biological soil crusts, known as “biocrusts,” can cover up to 70 percent of the ground in some arid ecosystems and are dominated by cyanobacteria, lichens, mosses, fungi and bacteria, she said.
The project is aimed at restoring fragile habitats in desert areas that have been affected by the movement of U.S. military vehicles, including tanks, as well as high foot traffic, said Barger, a faculty member in CU-Boulder’s ecology and environmental biology department. The team has two U.S. Department of Defense study sites — Fort Bliss, which straddles southern Texas and New Mexico and is located in a hot desert environment, and the Dugway Proving Ground in northwest Utah, seated in a cool desert environment.
“Biocrusts often are associated with increased soil nutrients and water retention, but their most important task is to stabilize soil surfaces against wind and water erosion,” Barger said. “While most biocrusts are relatively resilient to wind and water erosion, they are highly susceptible to compressional forces like those generated by foot and vehicle traffic associated with ground-based military activities.”
At military installations like Fort Bliss, the Dugway Proving Ground and in the California/Arizona Maneuver Area in the Mojave Desert used by Patton’s troops, scars of past military activity still are evident, said Barger. “You can go to these places and see that the biocrusts in the old tank tracks, for example, are completely different than nearby biocrusts undisturbed by military activity.”
The project is being funded by a five-year, $2.3 million grant from the Strategic Environmental Research and Development Program, the U.S. Department of Defense environmental science and technology program that partners with the U.S. Department of Energy and the Environmental Protection Agency. The research team also includes Jayne Belnap, Michael Duniway and Sasha Reed from the U.S. Geological Survey’s Biological Resources Division in Moab, Utah and Ferran Garcia-Pichel of Arizona State University in Tempe.
The first step of the program will be to grow biocrusts in laboratories at ASU, said Barger. “Our approach will be to expose laboratory biocrusts over time to a physiological ‘boot camp’ that includes increasing stressors like heat, light and dryness,” she said. “By doing that, we believe the biocrusts we eventually transplant into the study areas will have a higher probability of survival.”
The lab-grown biocrust products will be dried, bagged and transported to field test sites at each respective military installation and sprinkled on soil surfaces, said Barger.
Once in the field, the stress-adapted biocrusts developed in the lab nurseries for both hot desert and cool desert environments will be combined with other soil stabilization strategies, she said. The team, for example, will also experiment with adding polyacrylamide — a soil-stabilizing compound shown to increase soil porosity and reduce erosion, compaction, dustiness and water run-off — to the mix.
The researchers will evaluate the effectiveness of such soil “inoculations” and determine the optimum dosage for the test sites. Following the assisted recovery of the local biocrusts at Fort Bliss and the Dugway Proving Ground, the team will begin a series of seeding trials to develop strategies for native plant re-establishment, Barger said.
The last step of the project will involve a series of rainfall simulations and wind tunnel experiments combined with broad-scale soil erosion modeling to evaluate the influence of biocrust and native plant restoration in terms of precipitation and soil erosion.
While DOD military installations cover nearly 30 million acres — 70 percent of which are located in arid regions of the West — Barger said the research also could aid in the effective management of other federal lands. “We think our work on biocrusts also will be of interest to land managers at agencies like the Bureau of Land Management and the U.S. Forest Service,” Barger said.
The adaptation of biocrusts to extreme environments likely will come into play even more as climate change continues to heat and dry the West, she said. “We expect the drought in the Southwest to intensify as a result of climate change, and this project should tell us more about how adaptive these biocrusts are under shifting environmental conditions.”
The research project also has health implications, said Barger, since the disturbance of biocrusts can trigger the release of significant amounts of atmospheric dust, a dominant pollutant in some desert metropolitan areas. “There is a broad societal interest in stabilizing dryland soils in order to protect not only the functioning of local ecosystems but also human populations that reside in surrounding communities.”
“In terms of tackling an important environmental issue, this is by far the most exciting research project that I have been involved in,” said Barger, who has worked in Hawaii, Central America, South America, China and South Africa.
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