Tech & Science
Technology and Science news from Boulder, Colorado
New CU-Boulder study clarifies diversity, distribution of cutthroat trout in Colorado
Sep 24th
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 led mission to study past climate on Mars enters final phase before slated 2013 launch
Sep 11th
The mission, NASA’s Mars Atmosphere And Volatile EvolutioN, or MAVEN, passed the critical agency milestone known as Key Decision Point-D, or KDP-D on Monday, said NASA officials. The key decision meeting moving MAVEN forward was held at NASA Headquarters in Washington and was chaired by NASA’s Science Mission Directorate.
“The spacecraft and instruments are all coming together at this point,” said CU-Boulder Professor Bruce Jakosky, the MAVEN principal investigator and associate director for science at the university’s Laboratory for Atmospheric and Space Physics, or LASP. “Although we’re focused on getting everything ready for launch right now, we aren’t losing sight of our ultimate objective — getting to Mars and making the science measurements.”
NASA’s $670 million MAVEN mission will be the first devoted to understanding the Martian upper atmosphere. The goal of MAVEN is to determine the role that loss of atmospheric gas to space played in changing the Martian climate through time. Clues on the Martian surface, including features resembling dry lakes and riverbeds as well as minerals that form only in the presence of water, suggest that Mars once had a denser atmosphere that supported liquid water on the surface, Jakosky said.
“I’m incredibly proud of how this team continues to meet every major milestone on schedule on its journey to Mars,” said David Mitchell, MAVEN project manager at NASA’s Goddard Space Flight Center in Greenbelt, Md. “Being ready for the start of system level integration and test is critically important to ultimately being ready for launch on November 18, 2013.”
KDP-D occurs after the project has completed a series of independent reviews that cover not only technical health of the project but also programmatic health, including schedule and cost. KDP-D represents the official transition from the Phase C development stage to Phase D in the mission life cycle. During Phase D, the spacecraft bus is completed, the science instruments are integrated into the spacecraft, spacecraft testing occurs and the MAVEN mission launches late in 2013.

Signs of water on Mars
The huge amount of public interest in NASA’s Curiosity Rover, which landed on Mars Aug. 6 and is currently being driven remotely around the planet, is no surprise to Jakosky. “Mars has a lot of similarities to Earth,” he said. “It’s the closest planet, it has similar day lengths, and it has an atmosphere, weather and geologic processes similar to those on our own planet.
“But the real kicker is the potential for life,” said Jakosky, who also directs the Center for Astrobiology at the University of Colorado. “Because of that, I think Mars has always held a special place in the hearts and minds of the public.”
Jakosky, also a professor in CU-Boulder’s geological sciences department, cautioned that there is much more work to be done before launch. “This decision by NASA marks the start of integration of all of the instruments on the spacecraft. It’s cool to see the spacecraft coming together, but there is a lot of work still to go and a lot of challenges to solve between now and when the spacecraft is ready for launch.”
The next major review for the MAVEN team is the Mission Operations Review in November 2012. This review assesses the project’s operational readiness and its progress towards launch. The project will continue to work with partners to deliver all instruments in the next four months.
“CU-Boulder’s participation in Mars exploration missions goes back decades, beginning with NASA’s Mariner 6 and Mariner 7 missions launched in 1969,” said Vice Chancellor for Research Stein Sture. “LASP is a proven training ground for students seeking hands-on experience in building, testing and flying space hardware and is the only institute in the world to have designed and built instruments that have been launched to every planet in the solar system.”
The MAVEN spacecraft will carry three instrument suites. The Particles and Fields Package, built by the University of California at Berkeley with some instrument elements from CU’s LASP and NASA’s Goddard Space Flight Center in Greenbelt, Md., contains six instruments that will characterize the solar wind and the ionosphere of the planet.
The Remote Sensing Package built by LASP will determine global characteristics of the upper atmosphere and ionosphere, while The Neutral Gas and Ion Mass Spectrometer, provided by NASA Goddard, will measure the composition and isotopes of neutrals and ions.
MAVEN will launch during a 20-day period in November-December 2013. It will go into orbit around Mars in September 2014, and, after a one-month checkout period, will make measurements from orbit for one Earth year.
In addition to leading the mission and providing instrumentation, CU-Boulder will provide science operations and direct education and public outreach efforts. NASA’s Goddard manages the project. Lockheed Martin of Littleton, Colo., is building the spacecraft and will perform mission operations. NASA’s Jet Propulsion Laboratory in Pasadena provides program management via the Mars Program Office, as well as navigation support, the Deep Space Network and the Electra telecommunications relay hardware and operations.
The MAVEN science team includes three LASP scientists from CU-Boulder heading instrument teams — Nick Schneider, Frank Eparvier and Robert Ergun — as well as a large supporting team of scientists, engineers and mission operations specialists.
MAVEN will include participation by a number of CU-Boulder graduate and undergraduate students in the coming years. Currently there are more than 100 undergraduate and graduate students working on research projects at LASP, which provides hands-on training for future careers as engineers and scientists, said Jakosky.
For more information about MAVEN visit http://lasp.colorado.edu/home/maven/ and www.nasa.gov/maven. For more information on LASP visithttp://lasp.colorado.edu/home/.
CU Boulder sends high school students experiments into space
Sep 11th
The two winning experiments — one of which tests the ability of spiders to learn how to catch prey in the low-gravity of space, and the other which investigates how nutrients and compounds affect virulent bacteria growth in space — were announced in March. The contest is sponsored by YouTube, Lenova and Space Adventures with the involvement of NASA, the European Space Agency and the Japanese Space Agency.
“We took the ideas of the two winning experiments and transformed them into actual experiments that could be conducted in space,” said Stefanie Countryman, the business manager and outreach coordinator for BioServe Space Technologies, a NASA-sponsored center located in CU-Boulder’s aerospace engineering sciences department. The CU team also manifested the payload on an unmanned Japanese HTV rocket, conducted safety verifications and trained the astronaut flight crew on using BioServe hardware aboard the International Space Station, or ISS, for the project.
The global initiative sponsoring the contest is a new program known as YouTube Space Lab. YouTube Space Lab is one component of YouTube for Schools, a program that allows educators to access YouTube’s broad library of educational content from inside their school network. The contest generated more than 2,000 entries.
The student winners are Amr Mohamed, 18, of Alexandria, Egypt, who developed the idea for the spider experiment, and Dorothy Chen and Sara Ma, both 16, of Troy, Mich., who created the idea for the bacteria study. BioServe completed all of the mission integration and operations work for the two experiments and hand-delivered the loaded space flight hardware to the Tanegashima National Space Flight Center in Japan for launch to ISS on July 21.
The live, 45-minute YouTube Space Lab program stream from ISS, slated for 8:30 a.m. MDT on Sept. 13 will be hosted by Bill Nye “The Science Guy” and will include Mohamed, Chen and Ma. The winning experiments — selected by a panel that included British theoretical physicist Stephen Hawking, two NASA administrators, European Space Agency and Japanese Space Agency astronauts and Cirque de Soleil founder Guy Laliberte — will be performed by NASA astronaut Sunita Williams.
Countryman, who also will be part of the YouTube Space Lab live stream as she describes the role of BioServe in the project to Nye, said she was surprised by the sophistication of some of the experiments entered in the contest. “Seeing the level of intellect, not only from the top two winners but from six regional winners, makes us feel confident in the next generation of scientists and engineers,” she said.
Countryman said BioServe worked closely with Paula Cushing at the Denver Museum of Nature and Science and MaryAnn Hamilton of the Butterfly Pavilion in Westminster, Colo., to obtain the jumping spiders and analyze their behavior. BioServe designed, developed and built the flight habitat for the spiders. Once aboard ISS, the habitat will be placed inside a BioServe-built device known as a Commercial Generic Bioprocessing Apparatus, or CGBA.
In addition, BioServe worked with AgraQuest in Davis, Calif., a company that manufactures and sells the bacteria strain B. subtilis, which will be used in the experiment by Chen and Ma. BioServe researchers worked with the students to design the experiment, which included 48 fluid processing devices carried in six Group Activation Packs built by BioServe and which have flown on dozens of space missions.
BioServe also developed an HD camera system to record high-resolution still images and HD video of the spider habitat, which included both the arachnids and their food, fruit flies, Countryman said. One of BioServe’s CGBA devices on board ISS is providing power for the lighting system of the spider habitat and thermal control for both experiments, said Countryman.
As part of the contest, 14- to 18-year-olds, either alone or in groups of up to three, submitted videos describing their experiments to YouTube. All experiments submitted to the contest had to involve either biology or physics. People tuned into the YouTube Space Lab event can vote for their favorite experiments, Countryman said.
“For decades, one of our major thrusts at CU-Boulder’s BioServe Space Technologies has been to provide educational opportunities for hundreds of thousands of K-12 students around the world,” said Countryman. “This has been another opportunity for us to work with students on space payloads, a unique project that we hope will help steer many students from around the world into careers in the sciences.”
BioServe is a nonprofit, NASA-funded center founded in 1987 at CU-Boulder to develop new or improved products through space life science research in partnership with industry, academia and government, said BioServe Director Louis Stodieck. Since 1991 BioServe has flown payloads on 40 NASA space shuttle microgravity missions and additional payloads on several Russian and Japanese space vehicles.
YouTube, a video-sharing website, is a subsidiary of Google. Lenovo, a global company headquartered in Morrisville, N.C., is the world’s third-largest PC maker. Space Adventures, headquartered in Vienna, Va., provides flights for private citizens into space, including trips to the ISS.
To watch the winning experiments being performed on ISS go to http://www.youtube.com/spacelab. For more information on BioServe visithttp://www.colorado.edu/engineering/BioServe/.