CU News
News from the University of Colorado in Boulder.
“American Gut” sequencing project involving CU raises $340,000 online
Feb 7th
In hopes of better understanding nutrition and health, the University of Colorado Boulder is playing the leading science role in a “crowd funding” effort that has raised more than $340,000 for a project designed to sequence the gut bacteria of thousands of people around the world.
Known as the American Gut project, the effort raised the money through a crowdfunding effort online in which collective groups of people pool money to support various initiatives, said CU-Boulder Associate Professor Rob Knight of the BioFrontiers Institute. The $340,477 raised for the American Gut project is the largest amount of money ever raised through crowdfunding for a science project, said Knight, who is co-leading the effort with Jeff Leach, founder of the Human Food Project.
The money contributed by 2,005 funders will be used to sequence gut bacteria from about 3,500 people said Knight. Each human is believed to harbor roughly 10 trillion microorganisms — about 10 times more than the number of cells in the human body — that undertake a number of important functions ranging from digesting food to the strengthening of immune systems.
In 2009, a consortium of 200 researchers from 80 institutions organized by the National Institutes of Health, including Knight, mapped the normal microbial makeup of healthy humans as part of the $173 million Human Microbiome Project. Building on the massive NIH effort, the American Gut project will be an “open source” effort, meaning participants will have access to the data gathered to help understand how diet and lifestyle may contribute to human health through the interaction of our microbiomes, cells and genes, said Knight.
“The outpouring of public support for this research project demonstrates how public awareness of the role of our microbial systems in human health is growing,” said Knight, the project’s scientific lead who holds joint faculty appointments in CU-Boulder’s chemistry and biochemistry department and computer science department. “By looking at samples from the general public, we can get a far better sense of what a ‘normal’ microbiome is and what factors have the largest effects.”
The scientists are particularly interested in how diet and lifestyle, whether by choice or necessity, affect peoples’ microbial makeup, including those suffering from particular autoimmune diseases or who have food allergies, said Knight, also a Howard Hughes Medical Institute Early Career Scientist.
“The large number of participants in American Gut, coupled with our ongoing work in Africa and South America, will allow us to explore the impact of diet and lifestyle between western and more traditional societies,” said Leach. “We may find that our modern gut microbiome has shifted significantly away from our ancestral one, but reinstating some of that primal balance may be within our grasp.”
“I’m super excited about helping to build a system that not only integrates so much data but also presents it to the user in a useful way,” said Meg Pirrung, a graduate student in Knight’s lab. “This is an amazing opportunity for me and everyone involved.”
Daniel McDonald, a graduate student in the BioFrontiers Institute’s IQ Biology Program, said the American Gut project is allowing him to hone his interdisciplinary experience. IQ Biology students are involved in semester-long rotations that immerse them in disciplines ranging from mathematical and computational biology to biophysics and bio-imaging. “It’s an extraordinary opportunity for discovery,” he said.
The American Gut data also will also be used in the several IQ Biology Program courses taught by Knight with Manuel Lladser, an associate professor in the applied mathematics department. Last year the IQ Biology program at CU’s BioFrontiers Institute, which offers doctorates in eight disciplines, was awarded a $3 million grant from the National Science Foundation’s Integrative Graduate Education and Research Traineeship, or IGERT.
Second Genome, a biotech company headquartered in San Bruno, Calif., is working with the American Gut project to explore the connection between the human microbiome and type 2 diabetes, said company president and CEO Peter DiLaura.
“The American Gut project has succeeded in bringing together the largest citizen science network ever for human microbiome sample collection,” DiLaura said. “By building this extensive reference database, we now have the opportunity to explore the connections between the human microbiome and metabolic and inflammatory diseases.”
Although the first round of funding that enabled the project to commence has ended, a second phase also allows anyone in the world to join, said Leach. Once the scientific results are in from the initial group of participants, a third phase will allow new participants to obtain additional analyses crucial to understanding the microbiome.
“By integrating the tens of thousands of environmental samples that the scientific community has provided from around the world and applying powerful modeling approaches, we will be able to gain unprecedented insight into the links between our own microbes and those in our environment,” said Argonne National Laboratories microbial ecologist Jack Gilbert, a member of the Earth Microbiome Steering Committee.
“With advances in DNA sequencing, we are moving towards a world in which no infectious disease goes undiagnosed, and in which we have full knowledge of the microbes that inhabit us and our surroundings,” said Knight. “By participating in this project, thousands of people are helping us to make this future a reality.”
For more information on the American Gut project go to http://www.indiegogo.com/projects/american-gut. For more information on the BioFrontiers Institute go to http://biofrontiers.colorado.edu.
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Can plants be altruistic? You bet, says new CU-Boulder-led study
Feb 4th
![CSU_cornfield02[8]](http://c1n.tv/boulderchannel1/files/2013/02/CSU_cornfield028-300x225.jpg)
We’ve all heard examples of animal altruism: Dogs caring for orphaned kittens, chimps sharing food or dolphins nudging injured mates to the surface. Now, a study led by the University of Colorado Boulder suggests some plants are altruistic too.
The researchers looked at corn, in which each fertilized seed contained two “siblings” — an embryo and a corresponding bit of tissue known as endosperm that feeds the embryo as the seed grows, said CU-Boulder Professor Pamela Diggle. They compared the growth and behavior of the embryos and endosperm in seeds sharing the same mother and father with the growth and behavior of embryos and endosperm that had genetically different parents.
“The results indicated embryos with the same mother and father as the endosperm in their seed weighed significantly more than embryos with the same mother but a different father,” said Diggle, a faculty member in CU-Boulder’s ecology and evolutionary biology department. “We found that endosperm that does not share the same father as the embryo does not hand over as much food — it appears to be acting less cooperatively.”
A paper on the subject was published during the week of Jan. 21 in the Proceedings of the National Academy of Sciences. Co-authors on the study included Chi-Chih Wu, a CU-Boulder doctoral student in the ecology and evolutionary biology department and Professor William “Ned” Friedman, a professor at Harvard University who helped conduct research on the project while a faculty member at CU-Boulder.
Diggle said it is fairly clear from previous research that plants can preferentially withhold nutrients from inferior offspring when resources are limited. “Our study is the first to specifically test the idea of cooperation among siblings in plants.”
“One of the most fundamental laws of nature is that if you are going to be an altruist, give it up to your closest relatives,” said Friedman. “Altruism only evolves if the benefactor is a close relative of the beneficiary. When the endosperm gives all of its food to the embryo and then dies, it doesn’t get more altruistic than that.”
In corn reproduction, male flowers at the top of the plants distribute pollen grains two at a time through individual tubes to tiny cobs on the stalks covered by strands known as silks in a process known as double fertilization. When the two pollen grains come in contact with an individual silk, they produce a seed containing an embryo and endosperm. Each embryo results in just a single kernel of corn, said Diggle.
The team took advantage of an extremely rare phenomenon in plants called “hetero-fertilization,” in which two different fathers sire individual corn kernels, said Diggle, currently a visiting professor at Harvard. The manipulation of corn plant genes that has been going on for millennia — resulting in the production of multicolored “Indian corn” cobs of various colors like red, purple, blue and yellow — helped the researchers in assessing the parentage of the kernels, she said.
Wu, who cultivated the corn and harvested more than 100 ears over a three-year period, removed, mapped and weighed every individual kernel out of each cob from the harvests. While the majority of kernels had an endosperm and embryo of the same color — an indication they shared the same mother and father — some had different colors for each, such as a purple outer kernel with yellow embryo.
Wu was searching for such rare kernels — far less than one in 100 — that had two different fathers as a way to assess cooperation between the embryo and endosperm. “It was very challenging and time-consuming research,” said Friedman. “It was like looking for a needle in a haystack, or in this case, a kernel in a silo.”
Endosperm — in the form of corn, rice, wheat and other crops — is critical to humans, providing about 70 percent of calories we consume annually worldwide. “The tissue in the seeds of flowering plants is what feeds the world,” said Friedman, who also directs the Arnold Arboretum at Harvard. “If flowering plants weren’t here, humans wouldn’t be here.”
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CU researchers say deep ice cores show past Greenland warm period may be ‘road map’ for continued warming of planet
Jan 23rd
A new study by an international team of scientists analyzing ice cores from the Greenland ice sheet going back in time more than 100,000 years indicates the last interglacial period may be a good analog for where the planet is headed in terms of increasing greenhouse gases and rising temperatures.
The new results from the NEEM deep ice core drilling project led by the University of Copenhagen and involving the University of Colorado Boulder show that between 130,000 and 115,000 years ago during the Eemian interglacial period, the climate in north Greenland rose to about 14 degrees Fahrenheit warmer than today. Despite the strong warming signal during the Eemian — a period when the seas were roughly 15 to 25 feet higher than today — the surface of the north Greenland ice sheet near the NEEM facility was only a few hundred yards lower than it is today, an indication to scientists it contributed less than half of the total sea rise at the time.
Greenland ice burg
The NEEM project involves 300 scientists and students from 14 countries and is led by Professor Dorthe Dahl-Jensen, director of the University of Copenhagen’s Centre of Ice and Climate. CU-Boulder geological sciences professor and ice core expert Jim White is the lead U.S. investigator on the project. The National Science Foundation’s Division of Polar Programs funded the U.S. portion of the effort.
The new Nature findings showed that about 128,000 years ago, the surface elevation of ice near the NEEM site was more than 650 feet higher than present but the ice was starting to thin by about 2 inches per year. Between about 122,000 and 115,000 years ago, Greenland’s surface elevation remained stable at roughly 425 feet below the present level. Calculations indicate Greenland’s ice sheet volume was reduced by no more than 25 percent between 128,000 years ago and 122,000 years ago, said White.
A paper on the subject was published in the Jan. 24 issue of Nature.
“When we calculated how much ice melt from Greenland was contributing to global sea rise in the Eemian, we knew a large part of the sea rise back then must have come from Antarctica,” said White, director of CU-Boulder’s Institute of Arctic and Alpine Research. “A lot of us had been leaning in that direction for some time, but we now have evidence that confirms that the West Antarctic ice sheet was a dynamic and crucial player in global sea rise during the last interglacial period.”
Dahl-Jensen said the loss of ice mass on the Greenland ice sheet in the early part of the Eemian was likely similar to changes seen there by climate scientists in the past 10 years. Other studies have shown the temperatures above Greenland have been rising five times faster than the average global temperatures in recent years, and that Greenland has been losing more than 200 million tons of ice annually since 2003. The Greenland ice loss study was led by former CU-Boulder scientist Isabella Velicogna, who is currently a faculty member at the University of California, Irvine.
The intense melt in the vicinity of NEEM during the warm Eemian period was seen in the ice cores as layers of re-frozen meltwater. Such melt events during the last glacial period were rare by comparison, showing that the surface temperatures at the NEEM site were in a cold, nearly constant state back then. But on July 12, 2012, satellite images from NASA indicated 97 percent of Greenland’s ice sheet surface had thawed as a result of warming temperatures.
“We were quite shocked by the warm surface temperatures observed at the NEEM ice camp in July 2012,” said Dahl-Jensen. “It was raining at the top of the Greenland ice sheet, and just as during the Eemian period, meltwater formed subsurface ice layers. While this was an extreme event, the present warming over Greenland makes surface melt more likely, and the predicted warming over Greenland in the next 50-100 years will very likely be so strong that we will potentially have Eemian-like climate conditions.”
The Greenland ice core layers — formed over millennia by compressed snow — are being studied in detail using a suite of measurements, including stable water isotope analysis that reveals information about temperature and greenhouse gas levels and moisture changes back in time. Lasers are used to measure the water stable isotopes and atmospheric gas bubbles trapped in the ice cores to better understand past variations in climate on an annual basis — similar in some ways to a tree-ring record.
The results from the Nature study provide scientists with a “road map” of sorts to show where a warming Earth is headed in the future, said White. Of the nine hottest years on Earth on record, eight have come since the year 2000. In 2007 the Intergovernmental Panel on Climate Change concluded that temperatures on Earth could climb by as much as 11 degrees F by 2100.
Greenland glacier grooves
Increasing amounts of carbon dioxide in the atmosphere from sources like vehicle exhaust and industrial pollution — which have risen from about 280 parts per million at the onset of the Industrial Revolution to 391 parts per million today — are helping to raise temperatures on Earth, with no end in sight, said White.
“Unfortunately, we have reached a point where there is so much carbon dioxide in the atmosphere it’s going to be difficult for us to further limit our impact on the planet,” White said. “Our kids and grandkids are definitely going to look back and shake their heads at the inaction of this country’s generation. We are burning the lion’s share of oil and natural gas to benefit our lifestyle, and punting the responsibility for it.”
In the past, Earth’s journey into and out of glacial periods is thought to be due in large part to variations in its orbit, tilt and rotation that change the amount of solar energy delivered to the planet, he said. But the anthropogenic warming on Earth today could override such episodic changes, perhaps even staving off an ice age, White said.
While three previous ice cores drilled in Greenland in the last 20 years recovered ice from the Eemian, the deepest layers were compressed and folded, making the data difficult to interpret. Although there was some folding of the lowest ice layers in the NEEM core, sophisticated ice-penetrating radar helped scientists sort out and interpret the individual layers to paint an accurate picture of the warming of Earth’s Northern Hemisphere as it emerged from the previous ice age, White said.
In addition to White, other CU-Boulder co-authors on the NEEM paper include INSTAAR scientist Bruce Vaughn and graduate student Tyler Jones of INSTAAR and CU-Boulder’s Environmental Studies Program.
“It’s a challenge being on the ice sheet, because we are out of our comfort zones and are working long, physical hours in an environment that is extremely cold and where the sun never sets,” Jones said. “Being a member of the research team allowed me to understand the ice core recovery process and the science behind it in terms of learning more about past climates and the implications for future climate change.”
Other nations involved in NEEM include Belgium, Canada, France, Germany, Iceland, Japan, Korea, the Netherlands, Sweden, Switzerland and the United Kingdom. Other U.S. institutions involved in the effort include Oregon State University, Penn State, the University of California, San Diego and Dartmouth College.
For more information on INSTAAR go to http://instaar.colorado.edu/. Additional information, photos and videos on NEEM can be found at http://www.neem.ku.dk.
A video and a slide show on the project will be available on the CU-Boulder news site by clicking on the story headline at http://www.colorado.edu/news.
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