CU News
News from the University of Colorado in Boulder.
CU study; Death of microbes could determine time of death
Sep 27th
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.”
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.
-CU-
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Professor grabs 8th MacArthur award for CU faculty
Sep 25th
Rey also is an assistant research professor in the CU-Boulder Department of Physics. She teaches undergraduate and graduate classes.
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.
-CU-
CU researchers: Our brain is like a computer
Sep 23rd
Now, researchers at the University of Colorado Boulder have demonstrated that our brains could process these new situations by relying on a method similar to the “pointer” system used by computers. “Pointers” are used to tell a computer where to look for information stored elsewhere in the system to replace a variable.
For the study, published today in the Proceedings of the National Academy of Sciences, the research team relied on sentences with words used in unique ways to test the brain’s ability to understand the role familiar words play in a sentence even when those words are used in unfamiliar, and even nonsensical, ways.
For example, in the sentence, “I want to desk you,” we understand the word “desk” is being used as a verb even though our past experience with the word “desk” is as a noun.
“The fact that you understand that the sentence is grammatically well formed means you can process these completely novel inputs,” said Randall O’Reilly, a professor in CU-Boulder’s Department of Psychology and Neuroscience and co-author of the study. “But in the past when we’ve tried to get computer models of a brain to do that, we haven’t been successful.”
This shows that human brains are able to understand the sentence as a structure with variables—a subject, a verb and often, an object—and that the brain can assign a wide variety of words to those variables and still understand the sentence structure. But the way the brain does this has not been understood.
Computers routinely complete similar tasks. In computer science, for example, a computer program could create an email form letter that has a pointer in the greeting line. The pointer would then draw the name information for each individual recipient into the greeting being sent to that person.
In the new study, led by Trenton Kriete, a postdoctoral researcher in O’Reilly’s lab, the scientists show that the connections in the brain between the prefrontal cortex and the basal ganglia could play a similar role to the pointers used in computer science. The researchers added new information about how the connections between those two regions of the brain could work into their model.
The result was that the model could be trained to understand simple sentences using a select group of words. After the training period, the researchers fed the model new sentences using familiar words in novel ways and found that the model could still comprehend the sentence structure.
While the results show that a pointer-like system could be at play in the brain, the function is not identical to the system used in computer science, the scientists said. It’s similar to comparing an airplane’s wing and a bird’s wing, O’Reilly said. They’re both used for flying but they work differently.
In the brain, for example, the pointer-like system must still be learned. The brain has to be trained, in this case, to understand sentences while a computer can be programmed to understand sentences immediately.
“As your brain learns, it gets better and better at processing these novel kinds of information,” O’Reilly said.
Other study co-authors include David Noelle of the University of California, Merced, and Jonathan Cohen of Princeton University. The research was supported by an Intelligence Advanced Research Projects Activity grant through the U.S. Department of the Interior.
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