Category: Genetics/Genomics Page 6 of 11

Nature vs. Nurture: Predicting Our Futures

On November 4, 2016

In Behavior/Psychology, Faculty, Genetics/Genomics, Neuroscience

Sitting in The Connection at the Social Science Research Institute in Gross Hall was intimidating. I was surrounded by distinguished people: professors, visiting professors from distinguished universities, researchers, and postdocs, all of whom had gathered together to view a showing of the documentary, Predict My Future: The Science of Us.

Dr. Terrie Moffitt, a Duke professor. Image courtesy of Moffitt and Caspi.

Dr. Avshalom Caspi, a Duke professor. Image Courtesy of Moffitt and Caspi.

Predict My Future documents the work of Terrie Moffitt and Avshalom Caspi, two Duke professors who study people in Dunedin, New Zealand. They have followed the lives of all the children born within a year in Dunedin for the last 40 years to measure genetics, personal habits, environment, jobs, physical attributes, and etc. The Dunedin Longitudinal Study is the largest study of its kind and offers deep insights into how children become adults.

The episode, “The Early Years,” first posed the questions, “Why do some people become successful and others become outcasts? Why are we the way that we are?” By tracking all of these personal factors and some behaviors, including risky sexual activities, criminal activities, and drinking and smoking habits, the Dunedin Longitudinal Study can answer these questions. The researchers can tell which children are likely to become “problem children,” “geniuses,” and so on, based on the child’s personality type.

Q&A Session After the Viewing of the Documentary. Image Courtesy of Duke SSRI and Taken By Shelbi Fanning.

The study first identified five different personality types in young children, and researchers discovered that the children’s’ personality types did not change in adulthood. The three personality types that are typically associated with doing well in life, having better health, having friends, and being more successful are: “well-adjusted,” “reserved,” and “confident.” The two personality types associated with having poorer quality of life in adulthood are “inhibited” and “undercontrolled.”

Then, the study identified other factors that lead to serious consequences later in life or simply predict futures. Children who experienced delays in walking and in talking were likely to have issues with brain development. Boys with these traits typically disliked school, did poorly in school, and were more likely to be involved in criminal activity.

The full house watching the documentary. Image Courtesy of Duke SSRI and Taken by Shelbi Fanning.

The amount of sleep children received between the ages of five and eleven would determine obesity in adulthood. Adults who received the least amount of sleep as children tended to be obese by age 32.

Schizophrenia, researchers discovered, starts developing in young children, not just adults as had previously been thought. About half of the 11-year-olds in the study who said they had seen or heard things that weren’t there had developed schizophrenia two decades later.

Watching more TV was associated with a higher likelihood of smoking and having anxiety. Regardless of IQ or environment, children who watched more TV were more likely to leave school without qualifications.

The important lesson the documentary emphasized was that having a good childhood is important. Warm, sensitive, stimulating, family-feeling invoking environments are great protective factors to risk factors.

Overall, this was a brilliant, stimulating, easy-to-understand documentary.

meg_shieh_100hed Post by Meg Shieh

Meet the New Blogger: Shanen Ganapathee

By Shanen Ganapathee

On October 5, 2016

In Art, Genetics/Genomics, Neuroscience, Science Communication & Education, Students

Hi y’all! My name is Shanen and I am from the deep, deep South… of the globe. I was born and raised in Mauritius, a small island off the coast of Madagascar, once home to the now-extinct Dodo bird.

Shanen Ganapathee is a senior who wishes to be ‘a historian of the brain’

The reason I’m at Duke has to do with a desire to do what I love most — exploring art, science and their intersection. You will often find me writing prose; inspired by lessons in neuroanatomy and casting a DNA strand as the main character in my short story.

I’m excited about Africa, and the future of higher education and research on the continent. I believe in ideas, especially when they are big and bold. I’m a dreamer, an idealist but some might call me naive. I am deeply passionate about research but above all how it is made accessible to a wide audience.

I am currently a senior pursuing a Program II in Human Cognitive Evolution, a major I designed in my sophomore year with the help of my advisor, Dr. Leonard White, whom I had to luck to meet through the Neurohumanities Program in Paris.

This semester, I am working on a thesis project under the guidance of Dr. Greg Wray, inspired by an independent study I did under Dr. Steven Churchill, where we examined the difference in early human and Neandertal cognition and behavior. I am interested in using ancient DNA genomics to answer the age-old question: what makes us human? My claim is that the advent of artistic ventures truly shaped the beginning of behavioral modernity. In a sense, I want to be a historian of the brain.

My first exposure to the world of genomics was through the FOCUS program — Genome in our Lives — my freshman fall. Ever since, I have been fascinated by what the human genome can teach us. It is a window into our collective pasts as much as it informs us about our present and future. I am particularly intrigued by how the forces of evolution have shaped us to become the species we are.

I am excited about joining the Duke Research blog and sharing some great science with you all.

Lemur Poop Could Pinpoint Poaching Hotspots

By Robin Smith

On September 22, 2016

In Animals, Biology, Field Research, Genetics/Genomics

DNA detective work aims to map the illegal pet lemur trade in Madagascar

Local business owners in Madagascar sometimes use ring-tailed lemurs to sell photo ops to tourists. Tourists visiting the country can easily support the illegal pet lemur trade unknowingly by paying to touch or have their picture taken with a lemur. Photo courtesy of the Pet Lemur Survey project (www.petlemur.com)

Businesses in Madagascar sometimes use ring-tailed lemurs to sell photo ops to tourists. Tourists visiting the country can easily support the illegal pet lemur trade unknowingly by paying to touch or have their picture taken with a lemur. Photo courtesy of the Pet Lemur Survey project (www.petlemur.com)

When Tara Clarke went to Madagascar this summer, she packed what you might expect for a trip to the tropics: sunscreen, bug spray. But when she returned seven weeks later, her carry-on luggage contained an unusual item: ten pounds of lemur droppings.

“That’s a lot of poop,” Clarke said.

A visiting assistant professor of evolutionary anthropology at Duke, Clarke and colleagues are analyzing DNA from lemur feces to pinpoint poaching hotspots in Madagascar’s pet lemur trade.

Pet lemurs are illegal in Madagascar, the only place on Earth where lemurs — the world’s most endangered primates — live in the wild.

More than 28,000 lemurs were taken from the wild and kept as pets on the island between 2010 and 2013 alone, surveys suggest.

Many pet lemurs are captured as babies, separated from their mothers and sold for less than two dollars apiece to hotels and restaurants to lure tourists, who pay to touch the animals and have their photo taken with them.

Anyone caught removing lemurs from the forest, selling them, or keeping them without a government permit can be fined and sentenced to up to two years in jail. But the laws are difficult to enforce, especially in remote villages, where rural poverty is common and law enforcement personnel may be few.

Clarke (left) and LaFleur (right) co-direct a nonprofit called Lemur Love that aims to protect ring-tailed lemurs and their habitat in southern Madagascar. Follow them at https://www.facebook.com/lemurloveinc/.

Primatologists Tara Clarke (left) and Marni LaFleur (right) co-direct a nonprofit called Lemur Love that aims to protect ring-tailed lemurs and their habitat in southern Madagascar. Follow them at https://www.facebook.com/lemurloveinc/.

In 2011, Malagasy officials began confiscating pet ring-tailed lemurs, the most popular species in the pet lemur trade, and handing them over to a non-governmental organization in southwestern Madagascar called Renalia, home of the Lemur Rescue Center.

About two dozen ring-tailed lemurs are currently being rehabilitated there in the hopes that many of them will one day be reintroduced to the wild.

But rounding up all the lemurs held illegally in private hands and taking them in would be nearly impossible, Clarke said. “There just isn’t a facility big enough, or the funding or the manpower.”

If we can figure out where the animals are being taken from the forest, Clarke said, we might be able to target those poaching hotspots and try to prevent them from becoming pets in the first place through education and outreach initiatives.

Ring-tailed lemurs live in southern Madagascar, an island nation off the coast of Africa. Map by Alex Dunkel.

This summer, Clarke and biological anthropologist Marni LaFleur of the University of California, San Diego began collecting baseline samples of ring-tailed lemur poop from national parks and protected areas around southern and southwestern Madagascar, where ring-tailed lemurs live in the wild. They also collected samples from 19 ex-pets at the Lemur Rescue Center.

The samples are being shipped to the Primate Molecular Ecology Laboratory at Hunter College in New York for analysis.

There, with help from lab director Andrea Baden, the team will use DNA extracted from the wild samples to build a map of variation in ring-tailed lemur genes across their range.

By analyzing the DNA of the ex-pets housed at the Lemur Rescue Center and comparing it with their map, the researchers hope to pinpoint or rule out where the animals were first taken from the wild.

In addition to collecting feces, Clarke and LaFleur also worked with local guides to count ring-tailed lemurs in their natural habitat and estimate how many are left.

The pet trade isn’t the only threat to lemur survival. Over the past 40 years, logging, slash-and-burn agriculture, and charcoal production have reduced forest cover in southwestern Madagascar by nearly half.

“Their habitat is disappearing,” said Clarke, who has conducted field research in Madagascar since 2004.

Their 2016 census suggests that fewer than 2000 ring-tailed lemurs remain in the wild — a significant decline compared with the last census in 2000, when ring-tailed lemurs were estimated based on satellite images to number more than 750,000.

In every town the researchers visited they also passed out hundreds of posters about the illegal pet lemur trade as part of a nationwide education campaign called “Madagascar’s Treasure: Keeping Lemurs Wild,” which aims to raise interest in protecting the few wild populations that remain.

Lemur protection programs such as theirs can also benefit other threatened wildlife that share the lemurs’ forest habitat, such as the giant-striped mongoose and the radiated tortoise.

Keeping lemurs as pets isn’t unique to Madagascar. “There are thousands of lemurs in private hands in the U.S. too,” said Andrea Katz, curator at the Duke Lemur Center. Every year, the Duke Lemur Center gets phone calls from people in the U.S. looking for answers to questions about their pet lemurs’ health or behavioral problems.

“In some states it’s legal to have a pet lemur,” Clarke said. “You can find them online. You can find them in pet stores. A lot of times what happens is they reach sexual maturity and they get aggressive, and that’s when people call a zoo or a sanctuary.”

“Because you can see ring-tailed lemurs in zoos and movies people don’t think that they need our help. They don’t believe that they’re endangered. We’re trying to change that view,” Clarke said.

This research was supported by grants from the Margot Marsh Biodiversity Foundation and Conservation International’s Primate Action Fund.

These crowned lemurs are among more than 30 of the roughly 100 known lemur species in Madagascar that are affected by the pet lemur trade. Explore interactive data visualizations of pet lemur sightings in Madagascar by species, date and location at http://www.petlemur.com/data-visualization.html. Photo courtesy of the Pet Lemur Survey project (www.petlemur.com)

Robin Smith

Post by Robin A. Smith

A Link Between Stress and Aging in African-Americans

By Karl Bates

On March 14, 2016

In Cancer, Cardiology, Genetics/Genomics, Guest Post

A recent study finds that lifetime stress in a population of African Americans causes chemical changes to their DNA that may be associated with an increased risk of aging related diseases.

(Image: Rhonda Baer, National Cancer Institute)

Using a previously established DNA-based predictor of age known as the “epigenetic clock,” researchers found that a cohort of highly-traumatized African Americans were more likely to show aging-associated biochemical signatures in their DNA’s epigenetic clock regions at an earlier age than what would otherwise be predicted by their chronological age.

These chemical alterations to DNA’s epigenetic clock were found to be a result of hormonal changes that occur during the body’s stress response and corresponded to genetic profiles associated with aging-related diseases.

The study was performed by researchers at the Max Planck Institute of Psychiatry in Germany, including Duke University adjunct faculty and psychiatrist Dr. Anthony S. Zannas. The findings were published in a recent issue of Genome Biology.

“Our genomes have likely not evolved to tolerate the constant pressure that comes with today’s fast-paced society,” says lead author Zannas.

Though it may come as no surprise that chronic stress is detrimental to human health, these findings provide a novel biological mechanism for the negative effects of cumulative lifetime stressors, such as those that can come with being a discriminated minority.

Epigenetics is the study of how environmental factors switch our genes on or off. The epigenetic clock is comprised of over 300 sites in our DNA that are subject to a certain chemical modification known as methylation, which physically prevents those sites from being expressed (i.e., turns them off). Conversely, areas within the epigenetic clock can also be de-methylated to turn genes on. Each methylation event can be thought of as a tick of the epigenetic clock’s metaphorical second-hand, corresponding to the passing of physiological time.

During times of stress, a family of hormones known as glucocorticoids becomes elevated throughout the body. These glucocorticoids cause the chemical addition or removal of methyl groups to areas of DNA that the authors found to be located in the same regions that comprise the epigenetic clock. What’s more, the specific changes in methylation were found to correspond with gene expression profiles associated with coronary artery disease, arteriosclerosis, and leukemias.

This link between stress, glucocorticoids, and the epigenetic clock provides evidence that lifetime stress experienced by highly traumatized African Americans promotes physiological changes that affect their overall health and longevity.

The authors make an important distinction between cumulative lifetime stress and current stress. A small number of instances of acute stress may result in a correspondingly small number of methylation changes in the epigenetic clock, but it is the cumulative methylation events from chronic stress that give rise to lasting physiological detriments.

Though the authors make no direct claims regarding the physiological effects of racial inequities prevalent in today’s society, the findings perhaps shed light on the health disparities observed between disadvantaged African American populations and more privileged demographics, including increased mortality rates for cancer, heart disease, and stroke.

Glucocorticoids become elevated during the body’s stress response and lead to changes in DNA methylation that promote the expression of genes associated with aging.
Illustration by Katy Riccione

Interestingly, the epigenetic effects of lifetime stress were blunted in individuals who underwent significant childhood trauma, suggesting that early trauma may trigger mechanisms of physiological resilience to chronic stress later in life. In other words, if racial minorities are more likely to face hardships during their upbringing, perhaps they are also better prepared to cope with the chronic stress that comes with, for instance, losing a job or ending a marriage.

Though the study relies on data from an African American cohort, Dr. Zannas believes that the same conclusions are likely applicable to other highly stressed populations: chronic stress leads to lasting changes in our epigenome that may increase our likelihood of aging-related diseases, while acute stress was not found to have any long-term epigenetic effects.

So a single tough calculus exam won’t shave years off of your life, but consistent 80-hour work weeks just may.

In a world where everyday stress is unavoidable, whether it be from the hardships faced as a minority or the demands of being a full-time student, what lifestyle choices can we make to limit the detriments to our health? Dr. Zannas emphasizes that the “solution is not to avoid all stressors, but to prevent excessive stressors when possible and to learn to live with unavoidable stress constructively.”

The study underscores the importance of stress management on our general well-being. Future research may highlight the direct chemical benefits to our epigenome that are afforded by mindfulness, psychotherapy, diet/exercise, and other modes of stress relief. “Learning to better cope with stress is the best way to reduce our physiological response to it and the resultant harmful effects.”

Guest Post by Katy Riccione, Ph.D. Candidate in Biomedical Engineering

One Small Worm, One Duke Senior, and One Big Conference

By Kara Manke

On February 18, 2016

In Animals, Biology, Genetics/Genomics, Students

Duke senior Grace Lim isn’t grossed out by the innards of the tiny worm C. elegans. In fact, she finds them beautiful.

As a researcher in the David Sherwood Lab, she peers inside the transparent 1-millimeter creature under a microscope, watching for “cell invasion” — a process that occurs when one type of cell literally bursts into an area occupied by another type of cell.

Grace Lim presenting the results of her research at the AAAS Annual Meeting on Saturday.

Last weekend, the aspiring developmental biologist had the opportunity to take her work to the national stage when she presented at the Student Poster Competition as part of the annual AAAS meeting in Washington, D.C.

“It’s been really exciting,” said Lim. “The researchers here are experts and it is great to learn about their projects. At the same time, I’ve met scientists from all different fields who have asked questions and provided insights that I didn’t expect.”

Cell invasion plays a key role in organism growth and development, Lim said. For example, a fertilized egg will use cell invasion to implant itself into the uterine wall. However, cell invasion can also occur in less desirable processes, like cancer and other diseases.

In her work, Lim created C. elegans mutants that lacked specific genes related to cell invasion. She then observed whether uterine cells in the growing mutants could still invade tissue in the vulva — a key milestone in the growth of the developing larva.

“C. elegans is a good system to study because it is transparent, so you can watch these biological processes happening under a microscope,” she said.

The tiny transparent C. elegans. Photo courtesy of the National Human Genome Research Institute

Her experiments uncovered four new genes that appear to regulate cell invasion in C. elegans. In addition to presenting at the conference, Lim will also be writing up these results as an honors thesis.

Lim, who wants to pursue a graduate degree in biology after finishing up at Duke, says her favorite part of working in the Sherwood lab has been interacting with the graduate students. “We work together to come up with creative ways to solve problems, which is something you don’t always get to do in class,” she said.

And her favorite part of working with C. elegans?

“They have this amazing ability to control their metabolism,” she said. “We grow these worms in petri dishes, and when the plate fills up and they run of out food, they just stop growing. But if you take a few and put them on a new plate they grow again, as if nothing had happened.”

Post by Kara Manke

Kara J. Manke, PhD

A Dead Parrot? Not Yet. But It Could Sure Use Your Help

By Karl Bates

On February 15, 2016

In Animals, Biology, Genetics/Genomics

An international team of gene sequencing scientists, including some at Duke, want to sequence the genomes of all living kakapo — a critically endangered flightless parrot of New Zealand – while there are still 125 of them left in the world.

A one-year-old Kakapo named Pura on Codfish Island in 2005, by Mnolf, via Wikimedia Commons.

This is the first project aiming to sequence every member of a given species. The scientists and their collaborators are hoping the public can help through a crowd-funding effort. They hope to raise $45,000 US and are a little more than halfway there. With just 2 and a half months left, you can help write the end to this story.

Four years ago, Duke research specialist Jason Howard picked up a children’s book from the library to read to his 6-year-old daughter. It was about the kakapo (Strigops habroptilus), a flightless, nocturnal parrot that smells like honey.

Howard works in the Duke lab of neurobiologist Erich Jarvis, a Howard Hughes Medical Investigator who is co-leading a massive, ongoing effort to sequence the genomes of all 10,000 bird species. So, Howard’s library book pick was not exactly random. (In fact, he was sequencing the parakeet genome at the time.)

This sweet face belongs to Felix the Kakapo, photographed in 2006 by Brent Barrett (originally posted to Flikr – via Wikimedia Commons)

But as Howard read about efforts to save this beloved — and rapidly aging — bird population, he asked his daughter whether she thought he should make the kakapo’s genome a priority. (To which she said, “Yes, daddy, do it!”)

Howard was able to obtain a DNA sample from the kakapo, a feat in itself, and get a rough draft of the sequence. “But the sequencing technology [three years ago] wasn’t as good then and it was a lot more expensive,” he said.

He wanted to get a higher quality genome and study genomes of individuals, in part because there are so few kakapo left. Because this bird is among the most ancient species of parrot, it would also give Jarvis’s lab a better understanding of the evolution of vocal learning and speech imitation, where many of their studies focus.

Advances in genome sequencing even in the past year have already answered the group’s wish for a more-detailed kakapo genome. Jarvis’s lab completed the genome of a kakapo named Jane; their so-called ‘reference’ genome will allow them to more simply and inexpensively piece together the sequences of other individual kakapo. They just needed the funds to do more.

As luck would have it, molecular ecologist Bruce Robertson, an associate professor at the University of Otago, Andrew Digby of the New Zealand Department of Conservation and David Iorns of the Genetic Rescue Foundation approached Howard, while he was working on Jane’s genome, about funding and crowdsourcing a project to sequence all of the remaining kakapo. “I had never dreamed of doing all 125,” Howard said.

Jason Howard

Conservation efforts that started in the 1980s have already employed breeding strategies to boost dwindling population, but with individual genomes in hand, the group will be able to understand which kakapo harbor genetic susceptibility to specific diseases and to more effectively breed them to produce offspring with more robust immune systems. (One day, scientists might even be able to modify disease-vulnerable genes using gene-editing technology.) The genomes will also allow them to investigate any genetic causes of low fertility in these birds, which mate only intermittently.

Kakapo currently reside in the wild on just two of New Zealand’s small islands, because human-introduced predators, including cats and dogs, ran them off the mainland.

Kakapo Recovery has access to museum samples of deceased birds from areas where they are now extinct, including some from nearly 200 years ago. If the project is well-funded, they can tap into these museum specimens to get a better understanding of the various island populations and possible clues about their demise.

As of February 15, the team’s crowdfunding effort has reached more than 150 backers, but they would like to see more make a donation. To learn more about kakapo, check out Kakapo Recovery and Genetic Rescue Foundation.

Please stick around and watch a male Kakapo named Scirocco acting inappropriately as Stephen Fry narrates. (BBC-TV)

[youtube https://www.youtube.com/watch?v=9T1vfsHYiKY]

KellyRae_Chi_100 Post by Kelly Rae Chi

Pace of Aging Story Makes Top Ten

By Karl Bates

On January 11, 2016

In Behavior/Psychology, Biology, Field Research, Genetics/Genomics, Guest Post

A study led by Center for Child and Family faculty fellows Daniel Belsky and Terrie Moffitt which found that some people grow old significantly faster than others, was named the No. 4 news story of 2015 by Science News.

The paper, published the week of July 6 in the Proceedings of the National Academy of Sciences, compared a panel of 18 biological measures that may be combined to determine whether people are aging faster or slower than their peers.

Dan Belsky

The data comes from the Dunedin Study, a landmark longitudinal study that has tracked more than a thousand people born in the same town between 1972-73. Health measures like blood pressure and liver function have been taken regularly, along with interviews and other assessments.

“We set out to measure aging in these relatively young people,” said first author Belsky, an assistant professor in the Department of Medicine. “Most studies of aging look at seniors, but if we want to be able to prevent age-related disease, we’re going to have to start studying aging in young people.”

Belsky said the progress of aging shows in human organs just as it does in eyes, joints and hair, but sooner. So, as part of their regular reassessment of the study population at age 38 in 2011, the team measured the functions of kidneys, liver, lungs, metabolic and immune systems. They also measured HDL cholesterol, cardiorespiratory fitness and the length of the telomeres—protective caps at the end of chromosomes that have been found to shorten with age.

Based on a subset of these biomarkers, the research team set a “biological age” for each participant, which ranged from under 30 to nearly 60 in the 38-year-olds.

According to Science News, “The finding tapped into a mystery that has long captivated scientists and the public alike…”

Iridescent Beauty: Development, function and evolution of plant nanostructures that influence animal behavior

By Anika Radiya-Dixit

On October 27, 2015

In Animals, Behavior/Psychology, Biology, Chemistry, Field Research, Genetics/Genomics

Iridescent wings of a Morpho butterfly

Creatures like the Morpho butterfly on the leaf above appear to be covered in shimmering blue and green metallic colors. This phenomenon is called “iridescence,” meaning that color appears to change as the angle changes, much like soap bubbles and sea shells.

Iridescent behavior of a soap bubble

In animals, the physical mechanisms and function of structural color have been studied significantly as a signal for recognition or mate choice.

On the other hand, Beverley Glover believes that such shimmering in plants can actually influence animal behavior by attracting pollinators better than their non-iridescent counterparts. Glover,Director of Cambridge University Botanic Garden, presented her study during the Biology Seminar Series in the French Family Science Center on Monday earlier this week.

Hibiscus Trionum

The metallic property of flowers like the Hibiscus Trionum above are generated by diffraction grating – similar to the way CD shines – to create color from transparent material.

In order to observe the effects of the iridescence on pollinators like bees, Glover created artificial materials with a surface structure of nanoscale ridges, similar to the microscopic view of a petal’s epidermal surface below.

Nanoscale ridges on a petal’s epidermal surface.

In the first set of experiments, Glover and her team marked bees with paint to follow their behavior as they set the insects to explore iridescent flowers. Some were covered in a red grating – containing a sweet solution as a reward – and others with a blue iridescent grating – containing a sour solution as deterrent. The experiment demonstrated that the bees were able to detect the iridescent signal produced by the petal’s nanoridges, and – as a result – correctly identified the rewarding flowers.

Bees pollinating iridescent “flowers”

With the evidence that the bees were able to see iridescence, Glover set out for the second experiment: once the bees find a specific type of flower, how long does it take them to find the same flower in a different location? Using the triangular arrangement of shimmering surfaces as shown below, Glover observed that iridescence produced by a diffraction grating leads to significant increase in foraging speed as compared to non-iridescent flowers.

Triangular formation of iridescent disks used for experimentation on bees

While iridescence in plants is difficult to spot by a casual stroll through the garden, pollinators such as bees definitely can see it, and scientists have recently realized that insect vision and flower colors have co-evolved.

In order to ensure that pollen is transferred between flowers of the same species, these flowers have developed a unique structure of iridescence. As scientists work on understanding which plants produce these beautiful colors and how the nanoscale structure is passed down through reproduction, we can only look at our gardens in wonder at the vast amount of nature that still remains to be explored and learned.

Wonders of nature in an everyday garden

Beverley Glover is the Director of Cambridge University Botanic Garden and is currently accepting applications for PhD students.

Post written by Anika Radiya-Dixit

Pinpointing the Cause of Coughs and Sneezes

By Robin Smith

On July 30, 2015

In Biology, Data, Genetics/Genomics, Medicine, Statistics, Students

Duke students are trying to help doctors find a faster way to pinpoint the cause of their patients’ coughs, sore throats and sniffles.

The goal is to better determine if and when to give antibiotics in order to stem the rise of drug-resistant superbugs, said senior Kelsey Sumner.

For ten weeks this summer, Sumner and fellow Duke student Christopher Hong teamed up with researchers at Duke Medicine to identify blood markers that could be used to tell whether what’s making someone sick is a bacteria, or a virus.

More than half of children who go to the doctor for a sore throat, ear infection, bronchitis or other respiratory illness leave with a prescription for antibiotics, even though the majority of these infections — more than 70% — turn out to be caused by viruses, which antibiotics can’t kill.

The end result is that antibiotics are prescribed roughly twice as often as they should be, to the tune of 11.4 million unnecessary prescriptions a year.

“It’s a big problem,” said Emily Ray Ko, MD, PhD, a physician at Duke Regional Hospital who worked with Sumner and Hong on the project, alongside biostatistician Ashlee Valente and infectious disease researcher Ephraim Tsalik of Duke’s Center for Applied Genomics and Precision Medicine.

Prescribing antibiotics when they aren’t needed can make other infections trickier to treat.

Fast, accurate genetic tests may soon help doctors tell if you really need antibiotics. Photo from the Centers for Disease Control and Prevention.

That’s because antibiotics wipe out susceptible bacteria, but a few bacteria that are naturally resistant to the drugs survive, which allows them to multiply without other bacteria to keep them in check.

More than two million people develop drug-resistant bacterial infections each year.

A single superbug known as methicillin-resistant Staphylococcus aureus, or MRSA, kills more Americans every year than emphysema, HIV/ AIDS, Parkinson’s disease and homicide combined.

Using antibiotics only when necessary can help, Ko said, but doctors need a quick and easy test that can be performed while the patient is still in the clinic or the emergency room.

“Most doctors need to know within an hour or two whether someone should get antibiotics or not,” Ko said. “Delaying treatment in someone with a bacterial infection could have serious and potentially life threatening consequences, which is one of the main reasons why antibiotics are over-prescribed.”

With help from Sumner and Hong, the team has identified differences in patients’ bloodwork they hope could eventually be detected within a few hours, whereas current tests can take days.

The researchers made use of the fact that bacteria and viruses trigger different responses in the immune system.

They focused on the genetic signature generated by tiny snippets of genetic material called microRNAs, or miRNAs, which play a role in controlling the activity of other genes within the cell.

Using blood samples from 31 people, ten with bacterial pneumonia and 21 with flu virus, they used a technique called RNA sequencing to compare miRNA levels in bacterial versus viral infections.

So far, the researchers have identified several snippets of miRNA that differ between bacterial and viral infections, and could be used to discriminate between the two.

“Hopefully it could be used for a blood test,” Sumner said.

“One goal of these types of assays could be to identify infections before symptoms even appear,” Ko said. “Think early detection of viral infections like Ebola, for example, where it would be helpful to screen people so you know who to quarantine.”

Sumner and Hong were among 40 students selected for a summer research program at Duke called Data+. They presented their work at the Data+ Final Symposium on July 23 in Gross Hall.

Data+ is sponsored by the Information Initiative at Duke, the Social Sciences Research Institute and Bass Connections. Additional funding was provided by the National Science Foundation via a grant to the departments of mathematics and statistical science.

Writing by Robin Smith; photos and video by Christine Delp and Hannah McCracken

Undergrads Share Results, and Lack Thereof

By Karl Bates

On July 24, 2015

In Behavior/Psychology, Biology, Computers/Technology, Genetics/Genomics, Guest Post, Science Communication & Education

Arts & Sciences Dean Valerie Ashby and Associate Dean for Undergraduate Research Ron Grunwald got the big picture of the poster session from an LSRC landing.

Dozens of Duke undergrads spent the summer working in labs, in part to learn why science is called “research” not “finding.”

“About a third of these students ended up without any data,” said Ron Grunwald, associate dean for undergraduate research, during a Friday poster session in the atrium of the LSRC building for three of the summer research programs.

Biology junior Eric Song gets it now. He spent the summer trying to culture one specific kind of bacteria taken from the abdomens of an ant called Camponotus chromaiodes, which he collected in the Duke Forest. All he got was

Eric Song’s poster featured a photo of the ant and the mysterious white stuff.

“this white stuff showing up and we don’t even know what that is.” His faculty mentor in the Genomics Summer Fellows Program, Jennifer Wernegreen, was hoping to do some genetic sequences on the bacteria, but the 10-week project never made it that far. “We’re only interested in the genome basically,” Song said good-naturedly.

Christine Zhou did get what she set out for, mastering the art of arranging E.coli bacteria in orderly rows of tight little dots, using a specially adapted ink jet printer. Working with graduate student Hannah Meredith and faculty mentor Linchong You, she was able to lay the bugs down at a rate of 500 dots per minute, which might lead to some massive studies. “In the future, we’re hoping to use the different colored cartridges to print multiple kinds of bacteria at the same time,” she said.

Sean Sweat (left) discusses her mouse study.

Neuroscience senior Sean Sweat also got good results, finding in her research with faculty mentor Staci Bilbo, that opiate addiction can be lessened in mice by handling them more, and identifying some of the patterns of gene expression that may lie behind that effect.

Neuroscience senior Obia Muoneke wanted to know if adolescents are more likely than children or adults to engage in risky behaviors. Muoneke, who worked with mentor Scott Huettel, said her results showed the influence of peers. “Adolescents are driven to seek rewards while with a peer,” said Muoneke. “Adults are more motivated to avoid losing rewards when they are by themselves.”

The new dean of Trinity College, chemist Valerie Ashby, worked the room asking questions before addressing everyone from a landing overlooking the atrium. “How many of you wake up thinking ‘I want nothing to happen today that I am uncertain about?’” she asked. Well, Ashby continued, scientists need to become comfortable with the unexpected and the unexplainable – such as not having any data after weeks of work.

“We need you to be scientists,” Ashby said, and a liberal arts education is a good start. “If all you took was science classes, you would not be well-educated,” she said.

_ post by Shakira Warren and Karl Leif Bates