August 30, 2011

We've Moved ... Again!

Please stay and enjoy the posts about Duke University's research community below, but if you want to see the newer stuff, you should go here: http://sites.duke.edu/dukeresearch

The packaging has changed, but the blog is the same. We’ll be covering the people and events that capture the excitement and energy of Duke’s research environment; interesting findings, fascinating seminars, super-luminary guest speakers, amazing students. The blog is written by a team of professional journalists and curious students -- an ideal mix, we think! 

Way-Back Issues: 

We began this blog on the Google Blogger service in 2007, where it ran until May 2010. You can see that amazing collection of posts here: http://dukeresearch.blogspot.com/

August 26, 2011

Rushing to shore

By Ashley Yeager

Seeing the satellite images of Hurricane Irene reminded me of a piece of art I'd seen a few weeks ago. It was a stunning wax-fabric batik of Hurricane Katrina by Mary Edna Fraser.

Flipping to a print of it in Global Climate Change: A Primer, I read about a few cities that were swallowed by the sea.

Edingsville, S.C., in 1893. Broadwater, Va. in 1941.

But Diamond City, N.C., may have the best story.

After being pummeled by three successive hurricanes in the late 1800s, citizens tore down their houses, packed them on sailboats and navigated them across Back Sound to Harkers Island, where they rebuilt them.

Today, in the U.S., 53 percent of the population lives on the 19 percent of land area near the coast, according to the Primer's authors, geologist Orrin Pilkey and his son, Keith.

Imagine 165 million people tearing down their homes and moving them inland.

August 24, 2011

Z-prime search may hurdle Higgs hunt

By Ashley Yeager

If you're bummed about humanity's biggest accelerator not producing a Higgs particle yet, maybe the latest effort to find a Z-prime will make you feel better.

The new results can't claim a discovery of this sub-atomic particle, a gauge boson. But Duke physicist Ashutosh Kotwal says his team is narrowing in on this less press-frenzied particle, which, if discovered, means our understanding of particle physics would need a few revisions.

Physicists have been looking for Z-prime just as they have the Higgs, by slamming fast-moving particles into each other at the Large Hadron Collider, or LHC, in Europe.

Scientists are interested in predicted particles like Z-prime because they could fix holes in the current model, the Standard Model, that explains particle physics.

One of the biggest holes of the model is its inability to explain the origin of mass. The Higgs boson is supposed to correct this, but there are other problems, such as why neutrinos oscillate, why there is more matter than antimatter in the universe or where dark matter and dark energy originate.

Discovering new particles, like the Z-prime, could answer these questions, Kotwal says.

In April, scientists using Fermi Lab's Tevatron accelerator in Illinois reported possible signs of a Z-prime particle and with it, new forces of nature, but the physics community was cautious to claim discovery.

A few months later, Kotwal's team published data from LHC that did not find a Z-prime, despite working in similar energy levels as the U.S.-based accelerator.

Now, LHC is "far and away" more sensitive than the Tevatron, and by Christmas, the European collider will have produced four times more data in a range of energies and masses where Z-prime could be, Kotwal says. His team's latest LHC data has been submitted to the journal Physical Review Letters.

Kotwal adds that Z-prime particles also appear to behave similarly to gravitons, the hypothetical particles that could provide a quantum explanation for gravity. Any progress made in narrowing the mass and energy range where Z-primes sit will bring physicists closer to finding gravitons and possibly unifying the four fundamental forces of nature.

Of course, LHC has much more data to collect, and while hopes for a Higgs have been pushed back to the end of 2012, a Z-prime particle could pop into the data early next year, Kotwal says.

August 10, 2011

Managing On the Shoulders of Giants

Biologist Mohamed Noor recently shared some of his scientific wisdom and management philosophy with Duke's "Faith and Leadership" online magazine.

The magazine, a production of our Divinity School's leadership education program, thought it might be interesting to get a glimpse of teamwork and exploring difficult problems from the scientific perspective. Indeed it was.

Noor was only too happy to share. In addition to offering a seminar series called "Graduate School 101", he's currently working on a book aimed at helping graduate students figure out how to establish themselves as leaders and managers when they become faculty. He spends a lot of time thinking deeply about how and why we train scholars the way that we do and often blogs about it. 

Noor's thoughts on exploration. Noor's management philosophy.

August 9, 2011

Baby sea urchins aren’t all the same

Guest post by Viviane Callier, Duke biology

Sea urchin embryos have a lot more variation in the genes that regulate their early development than scientists thought, a new study shows.

Because getting early development “right” is fundamental, researchers believed that organisms that deviate from the typical pattern could not survive into adulthood. They also thought there was a strong constraint on the amount of genetic variation that could exist in the genes that regulate early development.

But David Garfield, a recent graduate from biologist Greg Wray’s lab, has shown that sea urchin embryos show variable patterns of gene expression even in the earliest stages of life.  Given that this early genetic variation should be harmful to a developing sea urchin, it was a mystery why the variation was not eliminated by natural selection.

The answer, Garfield says, may lie in the nature of interactions between early developmental genes. These genes do not act in isolation. They interact, forming a network of genes that regulate each other.

Garfield’s study is the first to link a gene’s place in a developmental gene network to the consequences of variation in that gene.

To study the networks, Garfield examined the correlations between the expression of genes and that of their downstream targets.  He also studied how genetic variation was related to variation in the shapes of larval sea urchin skeletons.  

He found that in early sea urchin development, gene interactions are typically switch-like. Genes are either turned on or off.  This switch-like behavior might prevent a lot of the variation from being expressed, unless it crossed a very specific on/off genomic threshold.

These interactions, however, are in direct contrast to the interactions of genes in the mid- to late-developmental stages. In these later stages, genes respond linearly to the amount of variation, so the differences will appear in the sea urchins’ skeletons, and affect their ability to survive in the wild. 

August 1, 2011

Running from math

By Ashley Yeager

. . . 158 . . . 159 . . . 160.

In the first minute of my morning run, my feet strike the ground 160 times, 80 times each foot.

Yes, I count. But not for the whole run. I cheat and do the math.

It's pretty astounding to calculate that in a short, 30-minute jog through Duke Forest, each foot hits the dirt 2,400 times.

While that's not much that compared to the pounding American marathoner Ryan Hall or former Duke runner Bo Waggoner give their feet (and shoes), thinking about the thousands of impacts made me curious about the science that could reduce the stress on my soles.

Unfortunately, "there's a lot we don't know about how our feet strike the ground when we run," Waggoner says.

He researched the topic for his senior thesis and found that while many scientists had done experiments to test the impacts of running, few had tried to model them.

The experiments show that, even on hard surfaces, runners without shoes who hit the ground with their forefoot made smaller collision forces with the ground than shoe-clad runners landing on their heels.

But, the tests can't measure the internal impacts between bones at the ankle or knee.

"And, there are a lot of simple, unanswered questions about what physics goes on when our foot hits the ground and pushes back off, like where the force is going and coming from and why," Waggoner says.

In other words, scientists don’t really know how, mechanically, a foot strike in running actually occurs.

Drawing of the tendons and muscles of the foot. Image courtesy of Runner's World.

To take strides in that direction, Waggoner turned human feet, ankles and legs into rods and springs. He simulated impacts between the rods and springs and a network of dots representing the ground.

Surprisingly, the "very basic" model began to show that impact forces were higher when hitting the ground with the heel. Hitting with the front of the foot created less stress.

With better models, which are "still an if at this point," scientists may learn where the stress and forces are going during different foot strike patterns and how and why runners get overuse injuries, Waggoner says.

The simulations could also alter shoe design. When Waggoner put mock shoes on his simulated feet, the sneakers with more padding at the front made less impact with the ground during a forefoot strike. Most real running shoes have more padding in the heel.

I know my shoes do, or they did, so I think the models are telling me to stay on my toes.

July 25, 2011

Drawing a Line on Preservation

Conservation programs that perform captive breeding for endangered animals  – like the Duke Lemur Center – face a difficult choice when choosing pairs to breed.

DNA analysis suggests that some populations of rare animals which have been isolated from one another by fragmented habitat may in fact be distinct sub-species. If they've been separated long enough without mating opportunities, their genomes have evolved subtle differences.

On the one hand, some conservationists argue that breeding programs ought to preserve those differences by avoiding mixing animals from different areas.

But on the other hand, there may not be enough captive animals in any one of these substrains to maintain that kind of purity without in-breeding the captive animals.  And soon, there may not be enough of them in the wild either.

What to do?

Ingrid Porton, curator of primates at the St. Louis Zoo,  talked her colleagues through the issue on Monday during the annual meeting of the Madagascar Fauna Group on the Duke campus. 

Some of the difficulty comes from the way different branches of biology think about species, Porton  said.  "Little did I know, there are actually 26 definitions for species!"  But this isn't just an academic exercise;  the crisis in lemur habitat is real and growing worse every day.  "We don't have a lot of time to deal with this. Every animal is drastically important."

The drive for keeping subspecies distinct "comes from a good place," said Duke Lemur Center Director Anne Yoder. But it may not be in the best interest of the bigger picture of species preservation.

Participants in the two-day meeting of the MFG being held at Duke this week agreed that they'll probably need at least a political consensus in the absence of a scientific one.

July 21, 2011

Flying high on stolen wings

Guest post by Viviane Callier, Duke biology

The wing color patterns on some butterfly species have evolved to copy wings on other butterfly species. In Heliconius butterflies, which are toxic to birds, the convergence of several species on the same wing color pattern gives them all mutual benefit – birds recognize one pattern saying “I’m poisonous; don’t eat me!"

On these butterflies, wing color pattern is primarily driven by differences in red coloring. Now, a team of researchers has discovered that a single gene, known as optix, controls where on the wing this red coloring appears. The results appear in the July 21 Science Express.

The researchers, including a Duke team led by biologist Fred Nijhout, studied species of Heliconius butterflies from five distinct regions in South America. Their color patterns differ depending on the region, but species co-existing in the same region have evolved wing color patterns that mimic each other.

This raised the question of how a single species has the ability to develop different color patterns in different regions, and also how different species have evolved convergent wing patterns in the same region, says Nijhout, who co-authored the new study.

He worked with the study's lead author, Robert Reed, a biologist at UC-Irvine and former postdoctoral researcher in the Nijhout lab, and also Mississippi State biologist Brian Counterman (a former graduate student of Duke evolutionary geneticist Mohamed Noor) to do gene mapping and expression, as well as population studies, to find that this optix gene controls the red color patterns on multiple Heliconius species.

This is the first study to identify a gene that controls mimicry, one of the most spectacular examples of convergent evolution by natural selection. And, according to the research, the observed convergence and divergence in the expression of optix does not come from changes in the protein coded from the gene. Instead, the expression comes from changes in the regulatory regions of optix, which ultimately change the new color patterns on the butterflies' wings.

July 13, 2011

Cooperating E. coli eat better

Guest post by Viviane Callier, Duke biology

In such a competitive world, it's surprising to find examples of animals working together rather than trying to outdo one another. But, under certain conditions, even lowly bacteria like E. coli cooperate to survive and thrive.

Figuring out how they do it could help doctors fight the human infections bacteria cause.

As they eat, bacteria make juices, or enzymes, that break down their environment, the plants and rotting wood they digest. The juices fill a bacterium's surroundings, so the producer not only gets the benefit of its digestive effort, but its neighboring bacteria do too.

Alone, one bacterium can't make enough juice to break down its food, and scientists thought that the cost to bacteria to make their digestive juice independently was too high so they won't get enough benefit back in terms of nutrition and growth.

Working in groups, however, all individuals share both the metabolic cost as well as the benefit of getting nutrition. Bacteria, therefore, have to have a method, called quorum sensing, to detect if they had enough neighbors to make juice and eat, says Duke graduate student Anand Pai.

Although it made sense for bacteria to produce their juice only when there are a lot of them in a small environment, the direct relationship between quorum sensing with bacterial growth success wasn't clear, Pai says.

At least it wasn't, until he worked in the lab of biomedical engineer Lingchong You to change the genetic material of bacteria and test the idea of quorum sensing. To do this, Pai engineered three types of bacteria: one type was unable to sense its neighbors and secreted digestive juice all the time. The second never produced juice. The third produced juice only when it sensed it had a lot of neighbors.

Measuring bacteria's growth rates, Pai saw that the bacteria that couldn't sense their neighbors grew more slowly than the bacteria that never produced juice or those that produced juice only when they had a lot of neighbors.

In other words, bacteria do seem to pay a metabolic cost for producing their digestive juices. Their ability to sense their neighboring bacteria and secrete enzymes together improves their ability to grow. But, keeping bacteria from sensing each other could lead to better defenses against bacterial infections and an alternative to antibiotics.

June 28, 2011

Health Care to Rebuild Rwanda

Guest Post by NCCU Summer Intern Chanel Laguna

More than a decade after a genocidal war devastated Rwanda, the Government of Rwanda and the Ministry of Health have a vision for rebuilding the country's health care system. They are looking for academic medical center partners to assist in the effort.

On June 20, the Dean of the National University of Rwanda, Dr. Patrick Kyamanywa, met with faculty and staff from the Hubert Yeargen Center for Global Health, Duke Global Health Institute, department chairs and the Chancellor for Health Affairs to share his country’s vision and to appeal for Duke's help.

“We are calling upon partners with different capacities and different strengths to help solve the challenge of health sector strengthening through improved medical and health sciences,” Kyamanywa told an audience of 30 students, residents, faculty and researchers at DGHI.

The lack of proper medical facilities throughout the country is hindering the rebuilding of Rwandan society, Kyamanywa said.  

The priorities for rebuilding health care in Rwanda involve building new infrastructure and human resource capacity. Called the Human Resources for Health Scale-up Plan,  the Ministry of Health wants to increase the university's number of physicians from approximately 480 generalists and specialists to over 1,200 and increase the skill level and number of nurses from 6,500 to more than 9,500 in the next seven years.

The goal of the scale up plan is to create a high-quality national health care system that can be sustained without requiring substantial foreign aid. But to get started, the Government of Rwanda, with the help of the Clinton Health Acceses Initiative and Partners in Health, is submitting a proposal to the US government for funding. At the same time, the ministry hopes to partner with academic medical centers to provide the needed expertise in internal medicine, pediatrics, obstetrics and gynecology, surgery, anesthesia, and family medicine.

 “This is an innovative and ambitious plan," Dr. Kyamanywa said. "But Rwanda has a strong track record of successful partnerships with medical institutions abroad.”