Following the people and events that make up the research community at Duke

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Month: December 2014 Page 1 of 2

Passion, Modeling and Viruses are all Cool

Guest Post By Jaye Sudweeks, NC School of Science and Math

corona viruses

Corona viruses like SARS (CDC image)

Viruses are very cool.  Ashley Sobel taught me that.

Sobel is an MD/PHD student at Duke.  She currently works in the Koelle Research Group, a group that focuses on using mathematical models to understand the “ecological and evolutionary dynamics of infectious diseases.”

When I asked Ashley what in particular drew her to infectious diseases, she had a ready answer. “Infectious diseases are pretty awesome.  They have shaped more of human civilization than anything else. It’s very clear that the reason some wars came out the way they did isn’t because of good generals or good supply lines, but because of the viruses, pathogens and bacteria that people brought with them.”

Ashley Sobel is being groomed to be a physician-scientist.

Ashley Sobel is being groomed to be a physician-scientist.

Ashley’s interest in infectious diseases was piqued in high school, when the SARS virus hit. She recalls being intrigued that such a new phenomenon could have such a major impact.

It was this interest in SARS, along with participating in science Olympiad that drew Ashley to science. Ashley’s involvement in Science Olympiad began when the instructor found out that she was building her own cello out of a mannequin. “It’s name was Wilberta,” Ashley remembers fondly. “We gave it a coconut bra and a hula skirt.”

As a scientist, Ashley considers mathematics and modeling interesting tools to investigate infectious disease. “Modeling is basically taking key relationships that we know are true and putting them together in a mathematical context to see what we can learn about the underlying processes. You identify processes that you might not get by looking at the data.”

Ashley shared with me the process of building a model. The first thing to do when building a model, she explains, is to gain an understanding of the biology affecting the scenario. This should be followed by an examination of pre-existing models.

Next, it is important to make simplifications that allow your model to function, but don’t trivialize the subject matter. “There are a lot of standard assumptions,” she explains.

The time it takes to construct a model varies. Ashley has only recently completed a project that she started two years ago.  “It can take a long time to identify the mathematics that will give you the patterns that you see in nature.”

Jaye Sudweeks

Jaye Sudweeks

As a scientist, Ashley values the emphasis that the scientific community places on curiosity, a trait that she feels is looked down upon in other career fields. And, after just one conversation with Ashley, it is easy to see why she feels that way. Ashley is easily one of the most curious, passionate, and inspiring people I have ever had the privilege to meet.  In the span of our brief meeting, Ashley sat crossed legged in her spinning office chair and taught me a couple of very important things.

Passion is cool. Modeling is cool. Viruses are cool.

Is it Computer Science or Biology? A Bit of Both

Guest Post By Chichi Zhu, NC School of Science and Math

The National Evolutionary Synthesis Center (NESCent), is tucked away behind the supermarkets and youth-infested restaurants on Ninth Street in Durham. It’s a National Science Foundation brainchild with the purpose of consolidating data collected on small scales to help evolutionary biologists answer larger scale questions.

Allen Rodrigo

Allen Rodrigo directs NESCent and is a professor of biology at Duke

NESCent pursues a variety of missions, from answering these big ideas to connecting evolutionary science to linguistics and religious and cultural studies. Behind NESCent’s day-to-day function is evolutionary biologist Allen Rodrigo.

As a response to the question “so, what exactly is it that you do?” Rodrigo laughs. Here at NESCent, he oversees all of the programs, managing NSF grant money and keeping each part of the center on track with its mission. But NESCent is coming to the end of its funded run, and Dr. Rodrigo himself does far more than direct this innovative program.

Rodrigo is also a professor at Duke University and a computational evolutionary biologist. As a student, he was interested in three areas of study: mathematics, computer science, and biology. He continued pursuing all three tracks throughout his higher education, and allowed coincidence to launch him into his field today. The timing of his post-doc perfectly coincided with a late-1980s boom in technologic and scientific advances. With the invention of PCR and the subsequent increase in ability to study genetics, there came a demand for people with the skill and ability to conduct studies computationally, thus propelling Dr. Rodrigo into this growing field.

“There are many benefits to using computational methods,” Rodrigo said. “Suppose you want to compare two potential hypotheses on how a system might look, what patterns you might see. A computational biologist can help you with that.” He advocates for his area of study with a digestible list of its merits: “It helps experimentalists, it helps make inferences, and it helps make predictions about patterns.”

Today Rodrigo teaches classes at Duke, including courses on statistics for biologists and courses on computational science. He applies his passions for computational biology to his own research.

He is currently using computational study to track the evolution of traits of cancer related to their malignancy. “We start with a small set of cells and develop simulations that tell us how these cells change, grow, and divide,” Rodrigo said. “We can simulate how mutations accumulate, and can simulate, for a given collection of cells, what patterns of evolution you’d obtain.”

Chichi Zhu

Chichi Zhu

Working with oncologists from Duke, his job is to use these computational and mathematical methods to search for patterns that oncologists can then use to collect laboratory data. “To do this all in a lab would take quite a long time,” he said. “To apply computational biology is much more efficient.”

Engineer Wants to Get Antibiotics Right


A multi-chambered, micro-scale channel built in the Lingchong You lab is used to observe bacterial responses to different antibiotic treatments and to understand how mixed populations of bacteria swap genes. These chambers are empty for clearer viewing. A single microfluidic chip would typically hold 12 of these channels, each with 40 chambers, allowing for high-throughput experimentation. (Photo courtesy of Hannah Meredith)

Guest Post by Grace Xiong, NC School of Science and Math

For those who study antibiotic resistance, a future where people die from infected cuts or the measles is not some horrible alternative universe but something that could very well be a reality soon. In 1998, the House of Lords in London gave a stark report proclaiming, “Antibiotic resistance threatens mankind with the prospect of a return to the pre-antibiotic era.” They were especially concerned with findings that indicated an increase in resistance to antibiotics that treated common but deadly diseases such as typhoid, dysentery and various strains of meningitis.

As hospitals use antibiotics at an unprecedented rate to treat patients, there has been an increase in the number of infections that are antibiotic-resistant. This leads to more patient deaths from infections that could have been treated with antibiotics 20 or 30 years ago.

Hannah Meredith

Hannah Meredith is a PhD candidate in biomedical engineering

Hannah Meredith, a graduate student in Lingchong You’s lab at Duke, has been studying the phenomenon of altruistic cell death in bacteria, which is when a bacterial cell will self destruct, breaking down the antibiotics they’re faced with as well. This process not only protects its fellow bacteria, it creates bacteria selectively chosen to be more resistant to the antibacterial due to the fact that the only bacteria left will be the ones resistant to the antibacterial.

When I asked her why she believed why studying this was so critical, she immediately responded that, “Optimizing antibiotic regimens is imperative so that treatment outcomes are positive and negative side effects are minimized. Although doctors and researchers recognize the need to optimize treatments, no one has come up with a standard method to design the best antibiotic regimen, given a particular antibiotic and specific infecting bacteria.”

Given that most pharmaceutical companies have stopped researching new antibiotics, the solution Hannah Meredith wants to use is to change the antibiotic dosage and the time the dosage is administered so that the maximum amount of bacteria can be killed while not using an extraordinarily large amount of antibiotics.

Grace Xiong

Grace Xiong

Using computer modeling, she is able to predict when a strain is most susceptible to an antibacterial and what percentage of bacteria can be killed with a certain amount of antibacterial. Ultimately she hopes to model common strains of infections (she has started using samples from the VA hospital) and create a data base that hospitals can use to more effectively treat their patients and in turn, reduce the amount of antibiotic resistance present in hospitals by getting it right the first time.

Death with Dignity: the Brittany Maynard Story

By Nonie Arora

Is it acceptable for patients to choose to die on their own terms? Can physicians assist them with their wishes? Where do we draw the line for euthanasia and end-of-life decision making? Faculty and students discussed these thorny issues at a recent Science & Society Round Table event, co-hosted by the Duke Undergraduate Bioethics Society.

Brittany Maynard, "Death with Dignity" advocate. Credit: Wikipedia

Brittany Maynard, “Death with Dignity” advocate. Credit: Wikipedia

This event was sparked by the recent events regarding Brittany Maynard. On November 1st, Maynard, a 29-year-old terminally ill cancer patient, chose to take a pill that ended her life.

During the roundtable, professor Dr. Jennifer Hawkins and paramedic Anita Swiman discussed this case as a launching point to delve into ethical issues regarding decision-making and “Death with Dignity” laws. Dr. Hawkins is a philosopher in bioethics and has studies quality of life issues and the nature of suffering. Swiman, an emergency medical technician, has insight into what it’s really like to deal with families who are making decisions about end-of-life care.

Because of her brain tumor, Maynard would have to undergo a very difficult process of death. She chose to relocate from California to Oregon to take advantage of their “Death with Dignity” statute. Previously, about 750 people – mostly elderly – had used the statute, but Maynard changed the discussion by being a young, vibrant woman talking about a decision to end her life, according to round table moderator, Michael “Buz” Waitzkin.

Dr. Hawkins described three main worries that come along with physician-assisted suicide. She said the first struggle is whether it can be in someone’s best interests to die. “Death is the enemy for most of us most of the time because we are healthy and have things we want to do,” she said. However, some people are suffering deeply. She questioned how can we distinguish between those that could be helped in what remains of their lives from those who cannot.

“Even if we can agree that sometimes it’s in a person’s best interests to die,” Dr. Hawkins explained, “We can disagree about the roles of physicians or other health care workers in this process.” Physicians generally operate by the code of doing no harm. Some people believe including physician-assisted suicide violates sacred codes of physician conduct.

Editorial Cartoon by Dan Wasserman of the Boston Globe

Editorial Cartoon by Dan Wasserman of the Boston Globe

Finally, Hawkins said that even if we can agree that sometimes it is in some people’s best interests to die, and we don’t have a problems with physicians helping them, we may still worry about the effects on society of such a policy that permits physician-assisted suicide. She said that some people are concerned about how such a policy could impact end-of-life decision making if elders feel pressured to choose this option, against their own wishes, to not feel like a burden on their families.

 “Will we be able to keep the policy restricted to the terminally ill, those who request it, and those who are able to take the prescription on their own?” Dr. Hawkins asked the group. She questioned why we restrict the application of “Death with Dignity” laws to those who can ask for a prescription. Some people who are paralyzed or cannot take prescriptions for themselves are excluded.

Paramedic Anita Swiman provided a perspective based on practice. “As a health care provider in prehospital medicine, there are clear laws that we must follow. If a patient meets certain criteria, we know what we will do. We take our personal feelings out of the discussion. We (sometimes face) assault from family members who want something different from what their family member had written in their wishes.”

Swiman said that pre-hospital providers act as counselors as well. She described that while being receptive to what family members are saying, paramedics sometime have to explain, “This is what the person wanted. This is what the law states. I would like to fix the situation for you, but there is nothing that I will be able to do for you.”

Ultimately, scholarly work that addresses the nature of suffering or examines consequences of “Death with Dignity” laws in different states could further inform the difficult ethical issue of physician-assisted suicide.

Disease Modeler Does Commentary Too

Guest Post by Tingzhu Teresa Meng, NC School of Science and Math

How do scientific research and social commentary relate?

The answer became clear during my conversation with Rotem Ben-Shachar, a PhD candidate in the Computational Biology and Bioinformatics program at Duke, who is interested in understanding the infectious disease dynamics of dengue fever. But she’s also pondering the reasons why female scientists are leaving prestigious career paths.

Rotem Ben-Shachar

Rotem Ben-Shachar is a PhD candidate in computational biology and bioinformatics.

Ben-Shachar, advised by Katia Koelle, is utilizing mathematical and statistical methods to research dengue, the most prevalent vector-bourne viral disease in the world. Dengue can be caused by any of the four serotype (related strains of viruses) transmitted by mosquitos. Early recognition of infection and subsequent treatment of dengue infection can significantly lower the risk of severe clinical outcomes. The mechanism of progression to severe dengue, however, are poorly understood.

Ben-Shachar’s dissertation focuses on how dengue causes severe disease. Prior to her research, there was no model of this means. Ben-Shachar has recently finished creating the first “simple target cell limited model” of the immune response trigger when the dengue virus infects the host cell. Her model is consistent with current knowledge of virological indicators that predict the onset of severe dengue. Now she wants to determine the model’s accuracy by statistically fitting it to recent serotype-specific viral load data from infected patients. Finally, she plans to investigate how dengue control strategies influence the evolution of virulent dengue virus such as dengue serotype 2 virus. Her work will offer crucial information about a virus that causes 390 million infections and 12,000 deaths annually (Source: WHO).

Ben-Shachar also examines the phenomenon termed “the leaky pipeline,” which refers to the continuous loss of women in STEM fields as they climb the career ladder. Ben-Shachar’s first experience of gender bias was during college when a male student declined to be her partner for an advanced mathematics project. Since then, she has become increasingly aware of gender discrimination and the confidence gap between male and female scientists. She began her focus on women in science during a writing workshop at Duke University’s Center for Documentary Studies.

Tingzhu Teresa Meng

Tingzhu Teresa Meng

In her recently published article in New Republic, “Women Don’t Stick with the Sciences. Here’s Why,” she details her interviews with female researchers at Duke and supports her interpretations with conclusions from previous studies. For instance, she explains that “the leaky pipeline” results from “a combination of social, cultural, and psychological factors” that all contribute to the confidence gap that “plagues female scientists.”

She believes that eliminating gender stereotypes can solve this problem. Ben-Shachar agrees that current efforts to engage girls in STEM are empowering girls and allowing them to view themselves as future scientists.

Thanks to our discussion, I have realized that scientific research and social commentary both strive to understand and solve major issues facing the world and both require skills such as careful observation, analysis and inquiry. Therefore, these seemingly unrelated interests have much in common.

Touring Duke's Biggest Laboratory

Sari Palmroth

Sari Palmroth and the 130-foot research tower in the Blackwood Division of Duke Forest.

By Karl Leif Bates

You may think of Duke Forest as a nice place to run or walk your dog, but it’s actually the largest research laboratory on campus, and probably the oldest too.

Last week, Duke Forest director Sara Childs and operations manager Jenna Schreiber took about a dozen interested stakeholders on a whirlwind tour to see three active research installations tucked away in areas of Duke Forest the public often doesn’t see.


We had to hunt a little to find UNC Biology grad student Jes Coyle in the Korstian division off Whitfield Road, but at least she wasn’t 30 feet up in an oak tree like she usually is. Jes showed the group some of her cool climbing gear while explaining her work on figuring out which part of a lichen, the fungus or the algae, is more responsible for the lichen’s adaptation to microclimates.

She does this by climbing way the heck up into trees to affix little data loggers that track temperature and sunlight at various places on the trunk.

Coyle is looking at 67 lichen species in 54 sampling locations, which is a lot of climbing and a lot of little $50 loggers.

The whole time Jes was talking, we were eyeing her six-foot-tall slingshot and waiting for it to come into play.

Jes Coyle

UNC grad student Jes Coyle shows off her climbing gear.

Indeed it did, as she let three participants, including Sara Childs, have a go at shooting a ball on a fine string over a likely-looking branch to start a climbing rope. (None succeeded.)


Abundant data was the theme at our second stop too, where Sari Palmroth, an associate research professor in the Nicholas School of the Environment, explained how she measures how much water goes into and out of a tree.  Her installation is in the Blackwood Division off Eubanks Road, tucked behind the old FACE experiment.

Standing next to an imposing 130-foot scaffolding tower studded with active and abandoned instruments of all sorts, Palmroth said a square meter of Duke Forest exhales about 700 mm of rainfall a year, which is about half of what falls on it. “How do I know these numbers? Because it’s my job.”

In addition to being a lovely place to get away from the world and sway with the treetops, the tower measures CO2 levels at different heights throughout the canopy.

Sari Palmroth

Palmroth reveals where probes go into a tree trunk.

The tower also hosts a big white box stuffed with wires that capture data streaming in from sensors embedded in the tree trunks all around the tower.

Palmroth and her colleagues are seeing the trees breathe. During the day, when the tiny pores on the underside of their leaves – called stomata — are open and exhaling water and oxygen, roots in the top 40 centimeters of soil are pulling in more water. When the sun sets and the stomata close, then the tree’s deeper roots pull water up to the top level for tomorrow’s drinking.  Unless it doesn’t get cool at night and the stomata don’t completely close, which is the prediction for some climate change scenarios. What then?


Aaron Berdanier

Back in the vans and even deeper into the Blackwood division, we come upon an intrepid young man in a flannel shirt sitting in a sunny spot by the side of the two-track. He’s Aaron Berdanier, a doctoral candidate at Duke who is also looking at water use by taking  automated measurements of 75 trees every minute for four straight years.

His work is part of a larger research project established by Nicholas School professor Jim Clark 15 years ago. Every one of the 14,000 trees in this sloping 20-acre stand of the forest — from spindly saplings to giants —  is labeled and has its data regularly collected by a platoon of undergrads armed with computer tablets.

Other data flows automatically on webs of wiring leading to data loggers situated every few yards. Some of the trees wear a stainless steel collar with a spring that measures their circumference constantly and precisely. They change noticeably both seasonally and by the year, Berdanier says.

The forest is alive and its trees are breathing and pulsing. Berdanier likens his detailed measurement of water consumption to taking a human patient’s pulse. “We’re trying to determine winners and losers under future climate conditions.”

Duke Forest Q&A

Aaron handled a wide-ranging Q&A with the curious visitors as the sun set and the temperature fell.

Pain-Sensing Gene Named for Rocky

Guest Post By Sheena Faherty, graduate student in Biology

How do our neurons discriminate between a punch to the face or a kiss on the cheek? Between something potentially harmful, and something pleasant?

A new study published this week in Current Biology offers an answer by describing a previously uncharacterized gene required for pain sensing.

This work comes out of Dan Tracey’s lab at the Duke Institute for Brain Sciences. They named the gene balboa in honor of fictional prizefighter Rocky Balboa and his iconic immunity to pain.

Stallone as Rocky

Float like a drosophila, sting like a …oh, never mind.

The researchers found that the balboa gene is only active in pain-sensing neurons and is required for detection of painful touch responses. Without it, neurons can’t distinguish between something harmful and something pleasant.

Does the ultimate prize of naming of the gene inspire any boxing matches between lab mates?

“In the fly community, we are allowed to have these creative gene names, so discussions about the decision on naming are more fun than argumentative,” Tracey says.

Tracey’s lab is concerned with sensory neurobiology, the study of how neurons transform cues from the surrounding environment to signals that can be interpreted by the brain. Ultimately, the lab group hopes to identify the underlying molecular mechanisms that are involved in our sense of touch.

Pugilistic fly artwork designed by Jason Wu, a neurobiology graduate student in Jorg Grandl's lab

Pugilistic fly artwork designed by Jason Wu, a neurobiology graduate student in Jorg Grandl’s lab

“It’s unclear what happens during that moment of touch sensation when sensory neurons detect and convert a touch stimulus into a nerve impulse,” said graduate student Stephanie Mauthner, who is the lead author on the Rocky paper. “It’s also ambiguous how nerves are capable of discriminating the threshold of touch intensity.”

Although the fruit fly has a relatively simple central nervous system, Tracey’s group uses it as model because it has many of the same neural circuits that the human brain has.

“[Our goal was to figure out] what molecular components are required for pain neurons to detect harsh touch responses and what is the mechanism for performing this task,” Mauthner said.

Using fluorescent cells, their study also shows that balboa interacts with another protein of the same family named pickpocket. They’re hopeful that this gene duo can be a potential target for pain medications that could discriminate between different sites of pain throughout the body.

Pain relievers such as aspirin or ibuprofen work broadly throughout the whole body—with no discrimination to where the pain is actually occurring. But, by working towards the exact molecular mechanism of pain signaling, genes like balboa and pickpocket are potential candidates for more targeted therapeutics.

Grad student Stephanie Mauthner, hangs out with one of her many vials of flies (courtesy of Stephanie Mauthner)

Grad student Stephanie Mauthner hangs out with one of her many vials of flies (courtesy of Stephanie Mauthner)

CITATION: “Balboa Binds to Pickpocket In Vivo and Is Required for Mechanical Nociception in Drosophila Larvae,” Stephanie E. Mauthner, Richard Y. Hwang, Amanda H. Lewis, Qi Xiao, Asako Tsubouchi, Yu Wang, Ken Honjo, J.H. Pate Skene, Jörg Grandl, W. Daniel Tracey Jr. Current Biology, Dec. 15, 2014. DOI:

Pursuit Of Bird Brains Takes Researchers Back 66 Million Years

A handful of bird species survived the K-T extinction. Chicken genomes have changed the least since that terrible day.

A handful of bird species survived the K-T extinction. Chicken genomes have changed the least since that terrible day.

By Karl Leif Bates

In the beginning was the Chicken. Or something quite like it.

At that moment 66 million years ago when an asteroid impact caused the devastating Cretaceous–Tertiary (K-T) extinction, a handful of bird-like dinosaur species somehow managed to survive.

The cataclysm and its ensuing climate change wiped out much of Earth’s life and brought the dinosaurs’ 160-million-year reign to an end.

But this week, the genomes of modern birds are telling us that a few resourceful survivors somehow scratched out a living, reproduced (of course), and put forth heirs that evolved to adapt into all the ecological niches left vacant by the mass extinction. From that close call, birds blossomed into the more than 10,000 spectacularly diverse species we know today.

Erich Jarvis

Erich Jarvis

Not all birds are descended from chickens, but it’s true that chicken genes have diverged the least from the dinosaur ancestors, says Erich Jarvis, an associate professor of neurobiology in the Duke Medical School and Howard Hughes Medical Institute Investigator.

He’s one of the leaders on a gigantic release of scientific data and papers that tells the story of the plucky K-T survivors and their descendants, redrawing many parts of the bird family tree.

From giant, flightless ostriches to tiny, miraculous hummingbirds, the descendants of those proto-birds now rule over the skies, the forests, the cliff-faces and prairies and even under water. While other birds were learning to reproduce songs and sounds, hover to drink nectar, dive on prey at 230 miles per hour, run across the land at 40 miles per hour, migrate from pole to pole or spend months at sea out of sight of land, the chickens just abided, apparently.

terror birds

Sweet little chickadees had a very big, very scary cousin. “Parrots and songbirds and hawks and eagles had a common ancestor that was an apex predator,” Erich Jarvis says. “We think it was related to these giant ‘terror birds’ that lived in the South American continent millions of years ago.”

The new analyses released this week are based on complete-genome sequencing done mostly at BGI (formerly Beijing Genomics Institute). and DNA samples prepared mostly at Duke. The budgerigar, a parrot, was sequenced at Duke. There are 29 papers in this first release, but many more will tumble out for years to come.

“In the past, people have been using 1, 2, up to 20 genes, to try to infer species relationships over the last 100 million years or so,” Jarvis says. But whole-genome analysis drew a somewhat different tree and yielded important new insights.

More than 200 researchers at 80 institutions dove into this sea of big data like so many cormorants and pelicans, coming up with new insights about how flight developed and was lost several times, how penguins learned to be cold and wet and fly underwater and how color vision and bright plumage co-evolved.

The birds’ genomes were found to be pared down to eliminate repetitive sequences of DNA, but yet to still hold microchromosomal structures that link them to the dinosaurs and crocodiles.

The sequencing of still more birds continues apace as the Jarvis lab at Duke does most of the sample preparation to turn specimens of bird flesh into purified DNA for whole-genome sequencing at BGI. (More after the movie!)

As one of three ring-leaders for this massive effort, Erich Jarvis is on 20 papers in this first set of findings. Eight of those concern the development of song learning and speech, but the other ones are pretty cool too:

Evidence for a single loss of mineralized teeth in the common avian ancestor. Robert W. Meredith, et al. Science. Instead of teeth, modern birds have a horny beak to grab and a muscular gizzard to “chew” their food. This analysis shows birds lost the use of five genes related to making enamel and dentin just once about 116 million years ago.

Complex evolutionary trajectories of sex chromosomes across bird taxa. Qi Zhou, et al. Science. The chromosomes that determine sex in birds, the W and the Z, have a very complex history and more active genes than had been expected. They may hold the secret to why some birds have wildly different male and female forms.

Three crocodilians genomes reveal ancestral patterns of evolution among archosaurs. Richard E Green, et al Science. Three members of the crocodile lineage were sequenced revealing ‘an exceptionally slow rate of genome evolution’ and a reconstruction of a partial genome of the common ancestor to all crocs, birds, and dinosaurs.

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Claudia C. Weber, et al, Genome Biology. The substitution of the DNA basepairs G and C was found to be higher in the genomes of birds with large populations and shorter generations, confirming a theoretical prediction that GC content is affected by life history of a species.

Low frequency of paleoviral infiltration across the avian phylogeny. Jie Cui, et al. Genome Biology. Genomes maintain a partial record of the viruses an organism’s family has encountered through history. The researchers found that birds don’t hold as much of these leftover bits of viral genes as other animals. They conclude birds are either less susceptible to viral infection, or better at purging viral genes.

Genomic signatures of near-extinction and rebirth of the Crested Ibis and other endangered bird species. Shengbin Li, et al Genome Biology. Genomes of several bird species that are recovering from near-extinction show clues to the susceptibilities to climate change, agrochemicals and overhunting that put them in peril. This effort has created better information for improving conservation and breeding these species back to health.

Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. Matthew J. Greenwold, et al. BMC Evolutionary Biology.  Keratin, the structural protein that makes hair, fingernails and skin in mammals, also makes feathers. Beta-keratin genes have undergone widespread evolution to account for the many forms of feathers and claws among birds.

Comparative genomics reveals molecular features unique to the songbird lineage. Morgan Wirthlin, et al. BMC Genomics. Analysis of 48 complete bird genomes and 4 non-bird genomes identified 10 genes unique to the songbirds, which account for almost half of bird species today. Two of the genes are more active in the vocal learning centers of the songbird brain.

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. Michael N. Romanov, et al. BMC Biology. Of 21 bird species analyzed, the chicken lineage appears to have undergone the fewest changes compared to the dinosaur ancestor.

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the cold aquatic environment. Cai Li, et al. Gigascience. The first penguins appeared 60 million years ago during a period of global warming. Comparisons of two Antarctic species show differences and commonalities in gene adaptations for extreme cold and underwater swimming.

Evolutionary genomics and adaptive evolution of the hedgehog gene family (SHH, IHH, and DHH) in vertebrates. Joana Pereira, et al. PLoS ONE. Whole-genome sequences for 45 bird species and 3 non-bird species allow a more detailed tracing of the evolutionary history of three genes important to embryo development.

A Duke lab led the effort to isolate bird DNA for sequencing at BGI: (L-R) Erich Jarvis, associate professor of neurobiology and Howard Hughes Medical Institute investigator, lab research analyst Carole Parent, undergraduate research assistant Nisarg Dabhi, and research scientist Jason Howard. (Duke Photo, Les Todd)

A Duke lab led the effort to isolate bird DNA for sequencing at BGI: (L-R) Erich Jarvis, associate professor of neurobiology and Howard Hughes Medical Institute investigator, lab research analyst Carole Parent, undergraduate research assistant Nisarg Dabhi, and research scientist Jason Howard. (Duke Photo, Les Todd)

Not Sure What To Do This Summer?

200+ clamor for info about summer research opportunities

By: Thabit Pulak

Dr. Grunwald discussing research opportunities at the Summer Research Programs event

Dr. Grunwald discussing research opportunities at the Summer Research Programs event

“What are you doing this summer?”

Whether it is coming from a concerned parent, or just a friend, this is a question that makes most of us anxious. What can I do this summer? Well, you can kick off your sandals and relax by the seashore. Or you can take a road trip across the country with your friends. Or go backpacking in Europe. Or sleep for 10 hours a day, and watch some extra… Oh, did you have something else in mind? I suppose there’s always some exciting summer research opportunities 🙂

When an info session titled “Summer Research Opportunities” popped up in one of my emails. I thought it would be pretty interesting, so I decided to attend. As I made my way to Perkins 217, I saw a flood of people  trying to enter at the same time as myself. The room had capacity to seat at least 200 people, and not only was it filled, but some people had to sit on the floor. This must have some pretty exclusive stuff, I thought. It was like Black Friday, except it was for people trying to get to a stack of handouts near the entrance of the room, which had a list of the summer opportunities (if you weren’t there never fear, here is a link!)

The event was lead by Dr. Ron Grunwald, who directs the Undergraduate Research Support Office. He started by pointing out Duke’s undergraduate research website, highlighting a few of the countless opportunities available to Duke undergrads for research.

I have listed a handful of them below with a brief description:

These programs are just a few of the opportunities that are available. Good luck in your summer research hunt!



How To Get Your Foot In The Door At A Research Lab

By: Thabit Pulak

So now you are at Duke — one of the world’s best research universities — but now what? You might be taking cool classes, but how can you take advantage of the world-class research happening here? Roughly 50 percent of Duke undergrads do so at some point. Getting involved in research as a freshman might sound intimidating (I know it did to me!), but a little luck and perseverance can get you off to a strong start.

Alan working in Dr. Eroglu's laboratory.

Alan working in Dr. Eroglu’s laboratory.

I had the opportunity to talk with Duke freshman Alan Kong about his experiences trying to get into research labs, and how he successfully ended up finding one to join. Alan is considering majoring in biology whilst on the premed track.

He initially started to look into labs within a month of  starting classes at Duke. He spent about two months sending out emails to professors who were working on interesting projects.

“It was a very frustrating search, and initially difficult. I emailed five professors, and emailed each many times,” Alan said. “But perseverance ultimately paid off.”

Alan now works in the lab of Dr. Eroglu who is an assistant professor of cell biology, associated with the Duke School of Medicine. According to the Duke Institute of Brain Science website description, Eroglu’s laboratory “is interested in understanding how central nervous system (CNS) synapses are formed.”

Alan was also accepted into two others labs, but ultimately felt Dr. Eroglu was the best fit. “I picked Eroglu because her research was very interesting, and relevant to my interests,” Alan says. “I felt I could learn more interesting techniques in research, such as working with live animals.”

Now, Alan has been working in Dr. Eroglu’s lab for a month. When I asked him how it was going, with a smile he exclaimed, “It’s great!”

“Right now I am learning techniques such as genotyping, western blot. I even took out the retina of a rat!” Alan said. “I am learning the ropes of the lab, and my mentor said that down the road, if I learn properly, I can eventually work on my own independent project!”

When asked for any advice for other students thinking of getting into research, Alan said “Persistence is key — don’t give up! It’s a difficult process; don’t let small things get in the way. Keep trying until you find one.”


“Persistence is key – don’t give up!” Alan says

Learn more:

More information regarding Dr. Eroglu and her research:

List of all Duke Faculty affiliated with Cell Biology with contact details:

Summer research opportunities in math and statistics:

Research opportunities in biology:

For other research and summer opportunities visit

For a list of research opportunities across the sciences, arts, humanities and social sciences visit:



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