Author: Ashley Yeager Page 4 of 7

CSI-House teams could make better medical diagnoses

On June 28, 2012

In Biology, Cardiology, Computers/Technology, Genetics/Genomics, Lecture, Medicine

By Ashley Yeager

Comparing a child's DNA to his parents' could help with identification of hard-to-diagnose genetic diseases. Credit: Henrik Jonsson/iStockphoto

Dr. Gregory House, star of House, M.D., and the lab techs on CSI never fail at their jobs. But that’s Hollywood. In real life, diagnosing illnesses and sequencing DNA isn’t so straightforward. It doesn’t always lead to a happy ending either, especially for children who are sick but can’t be diagnosed, even by gifted, real-life doctors.

That’s exactly why geneticist David Goldstein has teamed with pediatrician Vandana Shashi to combine a little House and CSI to identify apparent genetic diseases and quickly end some families’ diagnostic odysseys.

So far, the team has provided likely genetic diagnoses in six of 12 children it has worked with, said Goldstein at a Cardiovascular Research Center Seminar Series talk on June 27.

The children were referred to Shashi for a pilot study where she would record their symptoms, or phenotypic behavior, much like House. Then, Goldstein and his team at the Center for Human Genome Variation collected DNA samples from the children and both of their biological parents.

Using next-generation genetic sequencers, as well as traditional DNA scanners, Goldstein and his team looked for genetic variations between the children’s and parents’ complete genome. Like looking at DNA to identify a criminal, Goldstein and his genetics team are scouring the sequences for genetic fingerprints of the diseases disrupting the children’s lives.

Once variations were identified, the entire team looked for known diseases with similar gene mutations and symptoms. Goldstein explained that the study not only pinpointed the undiagnosed congenital diseases in some patients but also presented new genes that could also be linked to the illnesses. The study’s success has led to the creation of the Genome Sequencing Clinic.

The clinic will begin to help the families of the 50,000 children (out of the four million) born each year in the US with difficult-to-diagnose genetic diseases. These types of studies will likely be the “earliest drivers for large-scale genetic sequencing,” Goldstein said.

But, he cautioned, “there’s a whole lot of junk,” or variation, in DNA. Every genome has the narrative potential for devastating diseases, and that means that House-CSI teams, like Shashi and Goldstein’s, need to be extremely careful when making diagnoses, especially if the results will influence treatment, he said.

Citation: Clinical application of exome sequencing in undiagnosed genetic conditions. Need, A. et. al. 2012. J. Med Genet. 49:6 353-361. doi:10.1136/jmedgenet-2012-100819

Culture shapes bird communication, too

By Ashley Yeager

On June 19, 2012

In Animals, Behavior/Psychology, Biology, Climate/Global Change, Environment/Sustainability, Field Research

A male swamp sparrow switches branches as he sings.Credit: Robert Lachlan, Duke.

Guest post by: Eugene Morton, York University

Bird song is one of the most fascinating and complex examples of animal communication, and the quest to understand its evolution and function has fueled the careers of many behavioral ecologists, psychologists and neurophysiologists.

Recently, scientists in the Departments of Biology and Neurobiology at Duke University have made incredible advances in this field. In “Songbirds learn songs least degraded by environmental transmission,” Susan Peters, Elizabeth P. Derryberry, and Stephen Nowicki show how a youngster chooses which songs to learn from the huge number they may be exposed to during their learning period.

Their simple but elegant experiment offered the birds a choice to learn songs that contained echoes versus no echoes and the birds chose to learn only those with no echoes. The rejected songs had been transmitted and re-recorded through 25 meters of habitat, and picked up reverberations and a few other changes along the way, but they were equally loud to the learned versions.

This says a great deal about how birds put to use their extraordinary ability to hear small time differences. What’s so great about hearing echoes?

Compared to our ability, where we hear only echoes from distant large objects, birds can hear echoes from tree trunks and vegetation. They use this ability to learn songs that transmit with the least amount of echoes or, more generally, degradation.

In this way, the birds themselves reject songs less well suited to their environment; cultural selection. As the birds were housed together while learning the songs it is not surprising that they came up with two that were never presented to them; they must also have learned from each other.

A male swamp sparrows sings to his neighbors.Credit: Robert Lachlan, Duke.

Why is it important to understand the criteria birds use to choose songs to learn? I would answer because then we can understand how cultural and natural selection interact. Cultural selection favors birds that learn songs that will propagate for the greatest distance and remain undegraded.

These songs must function better than a random selection of songs would. The function must related to how the listeners of these songs are affected by them: are they more efficiently repelled if they are competitors and attracted if they are potential mates? Natural selection will favor the birds whose songs do this the best.

And it turns out that this interplay is helping birds cope with increasingly human-influenced environments. The traffic noise we generate can favor learning songs that are higher or lower in than the frequency of this noise. This ability is based upon the same cultural choice of songs described here for swamp sparrows.

It is hoped that this excellent study will stimulate others to assess the role of learning in adapting songs, not only to habitats, but to the social functions songs have. Songs function over distance and this study describes how song learning can strengthen this role and the importance of distance in song evolution.

Eugene S. Morton
Hemlock Hill Field Station, Pennsylvania
York University, Ontario, Canada
mortone@si.edu

Lab "cloud" goes global

By Ashley Yeager

On June 15, 2012

In Computers/Technology, Faculty, Genetics/Genomics, Mathematics, Physics

By Ashley Yeager

A network of individual computers are linked through a server. Credit: TAS Software

The National Science Foundation has awarded computer scientist Jeff Chase $300,000 to move a computer cloud he now has in his lab to the university’s campus network, and beyond.

Chase has been building the cloud to improve server networks. In his new model, servers, the computers that process requests and deliver data over a local network or the Internet, have become critical, public infrastructures with open, flexible, secure, robust and decentralized control.

The work, once reproduced outside of the lab, will let Duke scientists across campus and throughout the world to more easily connect to one another through existing networks and to share computational services and access data, according to Tracy Futhey, Duke’s vice president for information technology and chief information officer.

Based on software-defined networking and other technologies, the new, on-demand cloud services will be launched through a distinct network that connects science resources, such as the large datasets generated in physics and genomics experiments.

The project is part of the NSF-funded Global Environment for Networking Innovation, or GENI.

Chase’s work was also recognized on June 14 when the White House launched an initiative, US Ignite, to develop a publicly available system of advanced networks based on important contributions from GENI scientists. Duke is among more than 60 universities across the country that has participated in the project.

Forgotten Deserts

By Ashley Yeager

On June 13, 2012

In Animals, Biology, Climate/Global Change, Environment/Sustainability, Field Research, Science Communication & Education

By Ashley Yeager

A cheetah walks through the African desert. Credit: Martin Harvey, ARKive.org

Deserts get a bad rap. They seem dry and, well, deserted.

“With perceptions such as these, it’s not hard to see why deserts are neglected,” says Andrew Jacobson, coordinator of the Big Cats Initiative intern team at Duke University and the National Geographic Society.

In a June 15 Letter to the Editor in Science, Jacobson and an international list of authors point out the neglect of deserts and argue that the ecosystem has disproportionally little funding or research interest when compared with forests and other habitats that are similar in size and biodiversity.

“Deserts are not barren, empty wildernesses. Many interesting species live there. They are just sparsely distributed,” says Jacobson, who is a research associate in the Nicholas School of the Environment. He studies and works to protect cheetahs, which live and rely on the sandy, barren stretches of land. “If we care about cheetahs, then we should care about deserts,” he says.

In the letter, the authors call on the United Nations Conference on Sustainable Development, Rio+20, to support the UN Convention to Combat Desertification (UNCCD) and take steps to meet its minimum target of halting land degradation. A statement of support should also include steps to ensure the restoration of desert ecosystems, Jacobson says.

“We want Rio+20 to help ensure that deserts are considered in global priority-setting exercises and consequently receive the attention and funding they deserve,” he says.

In the run-up to the group’s next meeting June 20-22, however, Rio+20 has received heavy criticism for failing to fulfill its initial pledges — reducing poverty, advancing social equity and ensuring environmental protection as population grows. In a June 14 editorial, Nature cautions Rio+20 that if the meeting is to be “a platform for major new treaties and commitments — the world is awash with both, and to no avail.”

Jacobson says one of the main benefits of getting Rio+20 to support the anti-desertification goals would be to raise consciousness about the issue. Desertification was originally identified as one of three great challenges to sustainable development at the original Rio conference in 1992. “Achieving the UNCCD goal will not be easy and success will depend on many factors, but for momentum to continue, we need high-level support that can only be achieved here,” he says, adding that “you never quite know the power of a global agreement until you travel around a bit.”

Citation:
“Forgotten Biodiversity: The Empty Desert.” S. Durant, et. al. Science. June 15 2012. 336: 1379-1380.

Betting on Bayesball

By Ashley Yeager

On June 13, 2012

In Behavior/Psychology, Faculty, Lecture, Mathematics, Physics, Science Communication & Education

By Ashley Yeager

Derek Jeter, upper left, and Alex Rodriguez, lower right, anticipate a grounder in a 2007 game . Credit: Wikimedia.

New York Yankees shortstop Derek Jeter has five golden gloves. Alex Rodriquez, a Yankees shortstop and third baseman, has three.

It wasn’t a surprise then when Sayan Mukherjee asked a crowd at Broad Street Café who was a better mid-fielder and Jeter got a few more cheers.

The question, and response, prompted Mukherjee, a statistician who studies machine learning, to launch into a discussion about intuition and statistics in sports, specifically in baseball. Mukherjee spoke on June 12 as part of Periodic Tables: Durham’s Science Café.

He admitted he was a Yankees fan, which elicited some booing. Laughing it off, he then showed a complex statistical equation his colleague, Shane Jensen at the University of Pennsylvania, and others use to calculate a player’s success at fielding ground and fly balls.

On the next slide, Mukherjee showed the results. Rodriquez was clearly on top, and Jeter closer to the bottom. “Jeter doesn’t have as big a range as other players, that’s all I’m suggesting,” Mukherjee said.

Of course, these statistics, called sabermetrics, aren’t new to Jeter and other players. The numbers, based on Bayesian statistics, are exactly what the Oakland A’s baseball team used in 2002 to build a winning team. And, when new numbers came out in 2008, the stats ranked Jeter fairly low as a defensive player. He responded by saying there was a “bug” in the model.

“He has a point. The exact conditions for each play are not the same, so it’s hard to truly compare them,” Mukherjee said. The equation, however, is a way to measure factors of the game, rather than rely on intuition, and statisticians are trying to add more factors to make the model more realistic. The next factor they want to add will account for the different designs of ballparks, Mukherjee said.

He added, though, that these stats don’t really put players’ jobs at jeopardy. Judging by the crowd’s first response, people obviously still rely on intuition when it comes to picking their favorite players. The cold, hard numbers therefore affect how players approach their game – ie Jeter’s post-2007 season focus on a training program to combat the effects of age, Mukherjee said.

The data also affect people betting on the games. “Betting is huge, in any sport,” Mukherjee said, and the numbers, it seems, can affect how people choose to risk their money, but not their team loyalty.

Rethinking science on pandemic-potential viruses

By Ashley Yeager

On May 18, 2012

In Animals, Biology, Genetics/Genomics, Global Health, Medicine, Students

By Ashley Yeager

Debates over experiments subjecting ferrets to modified bird-flu strains had scientists and politicians seriously questioning how to approach and publish studies on pandemic-potential viruses. Credit: J. Smalley/NaturePL.com

Making mutant forms of bird flu and publishing the results caused a major squawk in the public and in the political and scientific communities over the last year.

The issue was whether the new mutants could ward off a major pandemic of bird flu or start one, explained Stephanie Holmer, a graduate student in Duke’s Department of Cell Biology.

She raised the issue during the May 18 meeting of the Science and Society Journal Club.

The row began when researchers at the University of Wisconsin-Madison and the Erasmus Medical Center in the Netherlands independently tweaked strains of the H5N1 virus, commonly named the bird flu. The strains, the teams report, are more easily transmitted between ferrets, the lab-double for humans.

“The fear was that if the mutant forms of the virus got out of the lab, bioterrorists could use them to make a super-virus and start a pandemic. But there was not any guarantee that what the scientists had was a weapon. The mutant strains weren’t even that efficient at killing a ferret,” Holmer said.

During the forum, about a dozen students and faculty from departments across campus debated whether this kind of research should have been done, if journal editors should publish the full results and what can be done to prevent future squawks about similar types of research.

Electron micrograph of influenza A virus. (Centers for Disease Control, Erskine Palmer)

Scientists want to study H5N1 to find out how fast the virus mutates and how virulent those strains are in mammals, including humans. So far, outbreaks of the non-mutant form of the bird flu in humans have been limited. The cases, about 100 to 200 from 2003-2012, have occurred most often in Indonesia, Egypt and Vietnam, according to statistics from the World Health Organization.

In two separate papers, the teams from Madison and the Netherlands reported the strains of H5N1 that seemed to be more virulent in ferrets. The Madison team submitted its paper to Nature; the Netherlands’ team submitted to Science. Both papers came under government scrutiny before they were published because the methods in each could potentially be misused to make a bioweapon.

But the researchers had already presented their data at conferences, and they had institutional approval to initiate the experiments, facts that led Subhashini Chandrasekharan, co-coordinator of the journal club, to wonder aloud why it took until the point of publication to prompt a government and scientific scuffle over the experiments and the results.

“I’m not a virologist, but I don’t find any reason that the study should not be done or that the results should not be published. The jump of this virus from birds to humans is going to happen. It’s only a matter of time. If we already understand the mutations, then we’ll be faster at finding treatments and vaccines,” Chandrasekharan said.

She added that if a bioterrorist is going to make a weapon from a virus, it didn’t seem likely that they’d need the papers, which were finally approved for publication on April 20, to make the mutations. They’d do it anyway, she said, explaining that preventing publication was probably not going to be “the wall” to stop a terrorist from plotting an attack.

That issue, of course, raises another whole set of squawks.

Molecule traps treasure like a kid with M&Ms

By Ashley Yeager

On April 16, 2012

In Chemistry, Lecture, Visualization

By Ashley Yeager

A new guest molecule knocks out the captive one in a cavitand just before it snaps shut. Credit: Lubomir Sebo.

Kids know when they’re going to get a tasty treat like M&Ms. They hold out their hands, palm up, and the snap their fingers around the chocolaty treats like a venus fly trap around a fly.

About a decade ago, Julius Rebek of the Scripps Research Institute in La Jolla, Calif., and his collaborators created a molecule that could do the exact same thing, trapping other molecules in much the same way.

Rebek’s goals was to understand how molecules behave when confined to small spaces. To do this, the chemists created a molecule called a cavitand, which self-assembles through bonds of hydrogen atoms into hand-like structures.

During an April 11 chemistry seminar, Rebek described how the walls or “fingers” of a cavitand use strong hydrogen bonds to curl around and snare another molecule. As a result, prying the cavitand open is a lot like trying to take candy from the closed grip of a child. It can be done but it takes energy and a bit of coaxing.

Rebek said that the cavitands’ finger-based hydrogen bonds can rupture. In response, the molecule then acts like a kid who opens his hand to show his M&Ms to a sibling, tempting her to take some. The captive molecule in the cavitand is exposed, and another can come in and knock it out of place, like a sister throwing something into her brother’s hand to knock out M&Ms for herself. Both the hand and the cavitand clasp shut quickly, taking a new type of treasure into their clutches.

By designing cavitands and other self-assembling molecular traps, chemists have begun to explore the way acids bind when trapped, how to control nano-sized spaces and how to switch molecules in and out of these nanospaces. The discoveries, Rebek said, will help scientists understand the binding and movement of molecules and the nanospaces where life’s most fundamental chemical reactions occur.

Neutrinos change their flavors, again

By Ashley Yeager

On March 8, 2012

In Lecture, Physics, Science Communication & Education

By Ashley Yeager

Two anti-neutrino detectors at Daya Bay, shown here prior to the pool being filled with ultrapure water. Courtesy of Roy Kaltschmidt, Lawrence Berkeley National Laboratory.

Elusive particles called neutrinos can change their flavors, just like the Wrigley Company trying out a new taste of Starburst candy.

Now, physicists say they have gotten the best glimpse yet of the most elusive change in neutrino flavors. The result is the “missing piece in the puzzle to understand the phenomenon of how the particles transform,” said University of Wisconsin-Madison physicist Karsten Heeger, a collaborator at the Daya Bay experiment.

He announced the new result at a symposium at Duke on March 8. The team has also submitted a paper on the result to Physical Review Letters.

Neutrinos are elementary particles that come in three flavors — muon, electron and tau. In past experiments, physicists have measured two of the ways that neutrinos can change flavors.

But no one had seen the third transformation yet. “It revealed itself in the disappearance of electron-flavored antineutrinos over a distance of only two kilometers at the Daya Bay experiment,” Heeger said. An anti-neutrino is the anti-matter counterpart of a neutrino.

By observing the change over short distances, the physicists have measured the “mixing angle,” called theta one-three. Measuring the angle will help them design new experiments to better understand why matter predominates over antimatter in the universe.

Last year, physicists at the T2K neutrino experiment in Japan said they had seen hints of neutrinos flipping flavors in a way to give them theta one-three. But the experiment was interrupted when Japan was hit by an earthquake and tsunami on March 11, 2011. Their results at that point did not have enough significance to constitute a discovery in particle physics.

In the new neutrino experiment, Heeger and his collaborators looked for anti-neutrinos coming from the six nuclear reactors at the Daya Bay Nuclear Power Plant in southern China. The team built and installed six anti-neutrino detectors in the mountains near the plant. Three of the detectors sit only about 500 meters from the plant, while the other three sit 1700 meters from it.

The nuclear reactors produced tens of thousands of electron antineutrinos. Recording the particles’ signals, the scientists found that the far detector registered six percent fewer electron-flavored particles. The deficit, according to Heeger and his collaborators, is the signal for the elusive neutrino flavor changes in neutrinos. He thinks there is less than a 1 in 3.5 million chance that the result happened by random chance.

Another hint of the Higgs, maybe

By Ashley Yeager

On March 8, 2012

In Faculty, Physics, Visualization

By Ashley Yeager

This cartoon shows a "line-up" of possible suspects for the Higgs boson. Click image for a larger view. Credit: Mark Kruse, Duke University.

Scientists may have spotted the Higgs boson again.

But, Duke physicist Mark Kruse says Fermilab has made its latest announcement prematurely.

Physicists have been searching for the Higgs for more than 40 years, hoping to find it and at last explain how mass in the universe is created.

Last year, the Fermilab team announced no significant hint of the particle when it had analyzed about 80 percent of the data from its two Higgs-hunting instruments, CDF and DZero.

Now, after adding the remaining 20 percent of the data, and some analytic improvements, the team is suggesting that Fermilab has seen the particle.

The signal, however, would be “almost fantastically high” if seen with other Higgs detection methods, Kruse says. He is on one of the committees reviewing the analyses from Fermilab’s CDF experiment and once led the instrument’s Higgs Discovery Group.

He also works at LHC, where teams made a similar announcement last December.

A “tremendous amount of work” has gone into the latest Fermilab results, Kruse says. But, the team could have waited for upcoming improvements in the CDF and DZero studies and also worked to better understand the discrepancy between the lab’s latest results and those from last year.

This might, of course, all be sorted out soon, he adds. But, “my feeling is that it was a little soon to make this announcement with the suggested claims we made, without the full results and proper understanding of the present analyses.”

This “rush to announce” mentality may also create a certain amount of distrust in the public eye, Kruse says.

Leading nuclear physicists to speak at Duke

By Ashley Yeager

On March 7, 2012

In Lecture, Physics, Science Communication & Education

By Ashley Yeager

Physics grad student Georgios Laskaris, left, and Haiyan Gao, the chair of Duke's physics department, right, work on an experiment to look for a new force of nature. Credit: Megan Morr, Duke Photography.

More than 20 years after Haiyan Gao began her work on the neutron, she is hosting the Symposium on Electroweak Nuclear Physics at Duke to celebrate Caltech physicist Robert McKeown’s influence on her and others in nuclear physics.

The event will also honor his achievements in the field and celebrate his sixtieth birthday. The conference will be held March 8-9 in the French Family Science Center. Click here for a full schedule of the talks. Physicist Steve Koonin will also give a public lecture on addressing the nation’s energy issues as part of the symposium.

Gao will present her latest research, describing how she and her collaborators are identifying the factors that cause a neutron to spin. Other leading scientists will present their research on protons, neutrinos, dark matter and more exotic particles, such as free quarks and dark photons.

You can read more about Gao’s work in Duke Today.