Posts tagged CU
CU study; Death of microbes could determine time of death
Sep 27th
An intriguing study led by the University of Colorado Boulder may provide a powerful new tool in the quiver of forensic scientists attempting to determine the time of death in cases involving human corpses: a microbial clock.
The clock is essentially the lock-step succession of bacterial changes that occur postmortem as bodies move through the decay process. And while the researchers used mice for the new study, previous studies on the human microbiome – the estimated 100 trillion or so microbes that live on and in each of us – indicate there is good reason to believe similar microbial clocks are ticking away on human corpses, said Jessica Metcalf, a CU-Boulder postdoctoral researcher and first author on the study.
“While establishing time of death is a crucial piece of information for investigators in cases that involve bodies, existing techniques are not always reliable,” said Metcalf of CU-Boulder’s BioFrontiers Institute. “Our results provide a detailed understanding of the bacterial changes that occur as mouse corpses decompose, and we believe this method has the potential to be a complementary forensic tool for estimating time of death.”
Dead and dying microbes could determine time of death for forensics pathologists
Currently, investigators use tools ranging from the timing of last text messages and corpse temperatures to insect infestations on bodies and “grave soil” analyses, with varying results, she said. And the more days that elapse following a person’s demise, the more difficult it becomes to determine the time of death with any significant accuracy.
Using high-technology gene sequencing techniques on both bacteria and microbial eukaryotic organisms like fungi, nematodes and amoeba postmortem, the researchers were able to pinpoint time of mouse death after a 48-day period to within roughly four days. The results were even more accurate following an analysis at 34 days, correctly estimating the time of death within about three days, said Metcalf.
A paper on the subject was published Sept. 23 in the new online science and biomedical journal, eLIFE, a joint initiative of the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust Fund. The study was funded by the National Institutes of Justice.
The researchers tracked microbial changes on the heads, torsos, body cavities and associated grave soil of 40 mice at eight different time points over the 48-day study. The stages after death include the “fresh” stage before decomposition, followed by “active decay” that includes bloating and subsequent body cavity rupture, followed by “advanced decay,” said Chaminade University forensic scientist David Carter, a co-author on the study.
“At each time point that we sampled, we saw similar microbiome patterns on the individual mice and similar biochemical changes in the grave soil,” said Laura Parfrey, a former CU-Boulder postdoctoral fellow and now a faculty member at the University of British Columbia who is a microbial and eukaryotic expert. “And although there were dramatic changes in the abundance and distribution of bacteria over the course of the study, we saw a surprising amount of consistency between individual mice microbes between the time points — something we were hoping for.”
As part of the project, the researchers also charted “blooms” of a common soil-dwelling nematode well known for consuming bacterial biomass that occurred at roughly the same time on individual mice during the decay period. “The nematodes seem to be responding to increases in bacterial biomass during the early decomposition process, an interesting finding from a community ecology standpoint,” said Metcalf.
“This work shows that your microbiome is not just important while you’re alive,” said CU-Boulder Associate Professor Rob Knight, the corresponding study author who runs the lab where the experiments took place. “It might also be important after you’re dead.”
The research team is working closely with assistant professors Sibyl Bucheli and Aaron Linne of Sam Houston State University in Huntsville, Texas, home of the Southeast Texas Applied Forensic Science Facility, an outdoor human decomposition facility known popularly as a “body farm.” The researchers are testing bacterial signatures of human cadavers over time to learn more about the process of human decomposition and how it is influenced by weather, seasons, animal scavenging and insect infestations.
The new study is one of more than a dozen papers authored or co-authored by CU-Boulder researchers published in the past several years on human microbiomes. One of the studies, led by Professor Noah Fierer, a co-author on the new study, brought to light another potential forensic tool — microbial signatures left on computer keys and computer mice, an idea enthralling enough it was featured on a “CSI: Crime Scene Investigation” television episode.
“This study establishes that a body’s collection of microbial genomes provides a store of information about its history,” said Knight, also an associate professor of chemistry and biochemistry and a Howard Hughes Medical Institute Early Career Scientist. “Future studies will let us understand how much of this information, both about events before death — like diet, lifestyle and travel — and after death can be recovered.”
In addition to Metcalf, Fierer, Knight, Carter and Parfrey, other study authors included Antonio Gonzalez, Gail Ackerman, Greg Humphrey, Mathew Gebert, Will Van Treuren, Donna Berg Lyons and Kyle Keepers from CU-Boulder, former BioFrontiers doctoral student Dan Knights from the University of Minnesota, and Yan Go and James Bullard from Pacific Biosciences in Menlo Park, Calif. Keepers participated in the study as an undergraduate while Gonzalez, now a postdoctoral researcher, was a graduate student during the study.
“There is no single forensic tool that is useful in all scenarios, as all have some degree of uncertainty,” said Metcalf. “But given our results and our experience with microbiomes, there is reason to believe we can get past some of this uncertainty and look toward this technique as a complementary method to better estimate time of death in humans.”
Gene sequencing equipment for the study included machines from Illumina of San Diego and Pacific Biosciences of Menlo Park, Calif. The Illumina data were generated at CU-Boulder in the BioFrontiers Next Generation Sequencing Facility.
To access a copy of the paper visit http://dx.doi.org/10.7554/eLife.01104. For more information on the BioFrontiers Institute visit http://biofrontiers.colorado.edu.
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Professor grabs 8th MacArthur award for CU faculty
Sep 25th
Ana Maria Rey, a theoretical physicist and a fellow of JILA, a joint institute of the University of Colorado Boulder and the National Institute of Standards and Technology, today was named a winner of a 2013 MacArthur Fellowship, commonly known as the “genius grant.”
Rey also is an assistant research professor in the CU-Boulder Department of Physics. She teaches undergraduate and graduate classes.
Ana Maria Rey, a CU professor, won the prestigious MacArthur award.
Rey is the eighth CU-Boulder faculty member to win the prestigious award from the John D. and Catherine T. MacArthur Foundation of Chicago as well as the fourth physics faculty member and third JILA fellow. Rey, 36, was one of 24 recipients of the 2013 “no-strings attached” funding. She will receive $625,000 paid out over five years.
“It is a great honor for me to be a MacArthur fellow and to receive such great recognition of my work,” Rey said. “I want to thank JILA, NIST, CU-Boulder and the outstanding group of colleagues, collaborators and students who have allowed and helped me to accomplish the research I have done.”
The MacArthur Foundation selection committee cited Rey as an “atomic physicist advancing our ability to simulate, manipulate, and control novel states of matter through fundamental conceptual research on ultra-cold atoms.”
“We congratulate Professor Rey on this exciting award, and, we also congratulate our faculty, whose ranks now include five Nobel laureates and eight MacArthur Fellowship winners,” said CU-Boulder Chancellor Philip P. DiStefano. “I believe Professor Rey’s work is emblematic of the research, innovation, and discovery at CU-Boulder, a body of work and a collection of great minds that is unmatched anywhere in the Rocky Mountain region and few places around the nation.”
Tom O’Brian, chief of the NIST Quantum Physics Division and Rey’s supervisor, said, “Ana Maria has rapidly established herself as one of the world’s top young theoretical physicists. She has a special ability to make very practical applications of theory to key experiments. Ana Maria has been crucial to the success of such world-leading NIST/JILA programs as ultracold molecules, dramatic improvements in optical lattice clocks, and use of cold atom systems and trapped ion systems for quantum simulations.”
At JILA, Rey works with ultracold atoms and molecules that are trapped in an “optical lattice,” a series of shallow wells constructed of laser light. Atoms that are loaded into an optical lattice behave similarly to electrons in a solid crystal structure. But while it’s difficult to change the properties of a solid crystal, the properties of an optical lattice—which essentially acts as a “light crystal”—are highly controllable, allowing Rey to explore a whole range of phenomena that would be nearly impossible to study in a solid crystal system.
Ultimately, Rey hopes her research will lead to the ability to engineer materials with unique characteristics such as superfluids—liquids that appear to move without regard for gravity or surface tension—and quantum magnets—individual atoms that act like tiny bar magnets.
Rey began studying physics at the Universidad de los Andes in Bogota, Colombia, where she received a Bachelor of Science degree in 1999. She came to the United States to continue her studies, earning a doctorate in physics from the University of Maryland, College Park in 2004.
Before coming to JILA in 2008, Rey was a postdoctoral fellow at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass., and a postdoctoral researcher at NIST in Gaithersburg, Md.
Previous CU-Boulder faculty members who have won a MacArthur Fellowship include David Hawkins of philosophy in 1981, Charles Archambeau of physics in 1988, Patricia Limerick of history in 1995, Margaret Murnane of physics and JILA in 2000, Norman Pace of molecular, cellular and developmental biology in 2001, Daniel Jurafsky of linguistics and the Institute of Cognitive Science in 2002 and Deborah Jin of JILA, NIST and physics in 2003.
“Everyone at JILA is extremely proud of Ana Maria Rey’s accomplishments and wholeheartedly congratulate her for this prestigious MacArthur Fellowship,” said JILA Chair Murray Holland. “She has an incredibly quick mind for physics and is one of the truly creative and ingenious scientists of her time, while also being a wonderful teacher and mentor to both undergraduate and graduate students. This is a great honor for Ana Maria, and a tremendous recognition of the important research programs in JILA and NIST.”
Rey is a highly effective mentor for an unusually large group of graduate students and postdoctoral fellows given the early stage of her career, O’Brian said. One of her recent graduate students, Michael Foss-Feig, won the prestigious 2013 Best Thesis Award of the American Physical Society’s Division of Atomic, Molecular and Optical Physics. Rey herself won the same award in 2005 as a graduate student at the University of Maryland.
On Sept. 24, in another honor, the American Physical Society named Rey the winner of the 2014 Maria Goeppert Mayer Award, which recognizes outstanding achievements by a woman physicist in her early career:
Additional information on Rey is available on the Web at http://www.macfound.org/fellows/901 and http://jila-amo.colorado.edu/science/profiles/ana-maria-rey.
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Jerman dominates Rebels in Omni Hotels championship
Sep 24th
BOULDER – Behind two goals by junior Darcy Jerman, the University of Colorado soccer team defeated UNLV 3-1 in the final game of the Omni Hotels Colorado Women’s Soccer Classic.
In front of 1,211 fans, the Buffaloes shined for a full 90 minutes in another record-breaker. Colorado concludes non-conference play with a stellar 8-1 record, with their only loss coming to then-ranked No. 16 Denver.
Darcy Jarmen
After starting the season a program-best perfect 6-0, the Buffs continue one of their best starts. Colorado won a record eight conference games this season, topping the previous bests of seven in 1998, 2003, ’04 and ’08. This is also only the third time in program history the Buffs have won at least eight of their first nine games.
“It’s awesome just because we’re starting Pac-12 next weekend, and I feel like we really hit a lot of momentum,” Jerman said. “We’re making good strides and we’re really working hard this season, so it’s good to win this last one and be 8-1 going into the Pac-12.”
A tie on Friday and a loss to the Buffs moves UNLV to a 5-3-2 record.
Colorado held UNLV to just six shots, all coming in the second half. For the fifth time this season, the Buffs took at least 20 shots, this time striking the ball 23 times, ranking in the top 20 at CU for most shots in a single game. The win is the Buffs’ sixth multiple goal game of the season.
Once again, the Buffs scored early and in the closing minutes. Darcy Jerman put the Buffs up 1-0 in just the third minute of the game, scoring off an assist from Brie Hooks. Defender Heather Ward helped give the Buffs some insurance before the break, heading one in off an Anne Stuller corner kick. UNLV’s Brittney Gideon, who led the Rebels with three shots, got her team on the board in the 77th minute to remain in contention. Colorado put the game away in the 82nd minute when Tori Cooper got fouled in the box. Darcy Jerman booted the ball in from a penalty kick to give the Buffs the 3-1 victory.
“Well, the first goal was a great run from Brie,” CU head coach Danny Sanchez said. “She got to the end line and we’ve been talking a lot about when you get into dangerous spots, picking people out and she was able to pick out Darcy and it was good for Darcy to get that first goal. The second goal, and we had quite a few corner kicks in a row, we had some good service … So it was a very good finish on the corner. And the third goal was really just Tori Cooper’s work to get in the box and get pulled down and Darcy debarred the penalty kick. So, pretty good goals, maybe could have had a couple more. But at the end of the day three goals is a good performance.”
The Buffs were on an early attack all weekend. At 2:40, the Buffs not only took the first shot of the game, but netted the first goal. Hooks at the right found Jerman at the center of the net. From 18 yards out, Jerman had on open look and booted it in.
The goal was 12th fastest in program history. After scoring at the 2:15 mark against Stony Brook on Friday, the Buffs have now scored two goals in the first three minutes of the game twice this season. The only other times the Buffs have accomplished that feat was in 2007 and 2009. (Nikki Marshall scored at the 23 second and 2:36 marks against St. Mary’s College in the Buffs’ 8-1 blowout in ’09.)
“It felt really good just because I’ve been having chances earlier this season, it just hasn’t come together,” Jerman said. “Brie had a beautiful cross in there and I was just there and shot and it was awesome. It feels good to get one under my belt, well two now.”
The Buffs kept dominating the offense, taking four more consecutive shots in four minutes. Stuller was blocked in 11th minute, and Olivia Pappalardo got her head on the ball following a corner, but Kylie Wassell grabbed the save. Wassell had to work again just one minute later, when Madison Krauser had a great look in front of the net.
In the 25th minute, the Buffs had another chance, with Krauser closing in on the net and finding her ball saved at the left corner. Stuller was ready for the quick rebound, but Colorado was called offsides.
With less than 14 minutes left in the first half, Hayley Hughes rushed from deep to close to the net, up against two defenders, she shot the ball wide left. The Buffs kept the pressure, but the Rebels grabbed three consecutive saves.
Despite the defensive pressure, the Buffs kept the pace, with back-to-back corners. On the second, Stuller set up a great ball to Ward at the far post. Ward headed the ball in low to give the Buffs the 2-0 lead with six minutes remaining before halftime. Ward, who has shine as one of the starting four in the backline, has taken just four shots in two seasons with the Buffs, with three on goal.
“It was a great ball from Anne,” Ward said. “It was kind of outside the box and she just chipped it in to the back post and I was able to get up and get my head on it.”
The Rebels looked to even the score early in the second half. In the 48th minute, A UNLV corner kept the ball on the left side of the net. After some solid pressure by the Buffs, Susie Bernal took the Rebel’s first shot of the game from close range. Annie Brunner hopped on the ball for the save. Though the ball got loose, Hooks swooped by the left side of the net to clear the ball and keep the Buffs out of danger.
UNLV had another great opportunity in the in the 54th, but Brittney Gideon just missed the net with a hard shot at the crossbar. The Buffs quickly responded, with Tori Cooper taking her second straight shot. She got the ball from Krauser at the left, and with few defenders took a close range shot, but sent the ball high. Colorado was at it again in the 62nd. Stuller approached from the left, and edged the net at the right post. With the keeper out of the net, Stuller had an open look but knocked the crossbar.
Both teams kept up pressure, with the Rebels forcing Brunner to work for a save in the 65th minute. The Buffs then went on a 5-0 shooting run in a seven minute span, but couldn’t reach the back of the net. A Rebel line change helped give the squad some momentum. Less than a minute after the substitutions, UNLV got on the board. The Rebels created some space, and Gideon was able to get a look from 18 yards to score in the 77th minute. Gaby Vasquez and Jenn Wolfe were credited with the assists.
“We were winning 2-0, and that’s a dangerous lead in soccer,” Jerman said. “We might have relaxed for a minute and I think that their goal sparked us back up again, and we came back strong.”
Gideon went for it again at 80:39, but shot the ball just high. The Buffs got back on the attack, and with less than nine minutes remaining in regulation, Cooper drew a foul in the box to set up a penalty kick. Jerman took the shot in the 82nd minute, hitting the ball to the left corner and just past the keeper.
Jerman scored her first goals of the season and had her first multiple goal game of her career in the victory. She is the third player this season to have a multi-goal performance, joining Hooks and Stuller. This is just the fifth time in program history that at least three players have had a multi-goal game in a single season.
The Buffs are pleased with the win and hope to keep their momentum going, but know that a big challenge awaits them next weekend as Pac-12 Conference play begins against No. 2 Stanford.
“I feel like we’re ready,” Jerman said. “We’re at a way better spot than we were last year, and I’m just ready to prove a point in the Pac-12 because we have everything to prove and nothing to lose.”
Stand Shoulder to Shoulder with your CU soccer team as they play 2012 NCAA runner-up Stanford in the first Pac-12 match of the season! The first 500 fans to the match will receive a FREE pair of CU sunglasses. Make sure to sit in the Buff Brigade cheering section and help give CU soccer a real home field advantage!
UNC (4-3-2) took down Stony Brook (5-3-1) in Sunday’s opener. The 1-0 victory helped the Bears to a runner-up performance at the Classic.
