Duke Research Blog

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

Category: Field Research (Page 1 of 16)

A Summer Well-Spent In and Around Toxic Waste Sites

Edison, NJ is just 40 miles from Manhattan and 70 miles from Philadelphia. It’s also home to the US EPA’s Emergency Response Team (ERT), where I spent the summer as an intern.

Stella Wang and an EPA contractor used lifts to test oil being pumped out of these huge tanks. It was found to be contaminated with mercury, benzene and lead.

At the start of my internship, I had little idea of how ERT functioned. Unlike the 10 regional offices of the Environmental Protection Agency, ERT is a “headquarters” or Washington, DC-based group, which means it responds to incidents all over the country such as oil spills, train derailments, and natural disasters.

For example, my mentor, an air specialist who generally works from his cubicle in Edison, aided in the immediate aftermath of Hurricane Katrina by employing equipment to analyze air for hazardous pollutants. Other ERT team members have conducted sediment sampling to expedite the hazardous waste removal process, given consultation advice to other EPA members for long-term remedial site work, and led the innovation of new technology.

I was able to shadow and help my mentor and fellow ERT members with their Superfund site removal work. I created accurate maps showing injection well locations, learned how to use air monitoring instruments, and helped perform chemical lab experiments that will be employed for future site analysis.

Perhaps my favorite part of the internship was traveling to a myriad of active sites. At these sites, I not only got to see how ERT members worked with EPA’s on-scene coordinators, but also observed the physical removal and remediation processes. I was fortunate to visit a particular site multiple times — I witnessed the removal of contaminated oil from an abandoned lot as the summer progressed.

Stella Wang (left) and an EPA air specialist calibrating a air monitoring instrument before a public event.

At another site, I saw the beginning of an injection process intended to prevent the contamination of underground drinking water by hexavalent chromium. By pumping sodium lactate into underground wells, the hexavalent is converted into the insoluble and benign chromium-3 ion. If the injection process works, the community will no longer be threatened by this particular hazardous material.

ERT also acts in anticipation of possible contamination to protect the public. At largely attended events like the Democratic National Convention, a few ERT members will arrive with monitoring equipment. They pride themselves in their real-time data collection for a reason: throughout the event, they can detect whether a contaminant has been released and immediately instigate an emergency response to protect attendees.

Thanks to various ERT members, I felt accepted and welcome. They were open and patient with my never-ending questions about their career paths and other things. They’ve graciously taken me out to lunch so that they could get to know me better, ensuring my inclusion in their small community.

Of course, the experiences I had this summer, while brief, have taught me a tremendous amount and I have a clearer sense of how this division of the US federal government functions. But, it would be inaccurate and unjust to omit the impact that its people made on me.

Stella Wang, Duke 2019Guest post by Stella Wang, Class of 2019

Science on the Trail

Duke launches free two-week girls science camp in Pisgah National Forest.

Duke launches free two-week girls science camp in Pisgah National Forest.

DURHAM, N.C. — To listen to Destoni Carter from Raleigh’s Garner High School, you’d never know she had a phobia of snails. At least until her first backpacking trip, when a friend convinced her to let one glide over her outstretched palm.

Destoni Carter

Destoni Carter from Raleigh’s Garner High School was among eight high schoolers in a new two-week camp that combines science and backpacking.

Soon she started picking them up along the trail. She would collect a couple of snails, put them on a bed of rocks or soil or leaves, and watch to see whether they were speedier on one surface versus another, or at night versus the day.

The experiment was part of a not-so-typical science class.

From June 11-23, 2017, eight high school girls from across North Carolina and four Duke Ph.D. students left hot showers and clean sheets behind, strapped on their boots and packs, and ventured into Pisgah National Forest.

For the high schoolers, it was their first overnight hike. They experienced a lot of things you might expect on such a trip: Hefty packs. Sore muscles. Greasy hair. Crusty socks. But they also did research.

The girls, ages 15-17, were part of a new free summer science program, called Girls on outdoor Adventure for Leadership and Science, or GALS. Over the course of 13 days, they learned ecology, earth science and chemistry while backpacking with Duke scientists.

Duke ecology Ph.D. student Jacqueline Gerson came up with the idea for the program. “Backpacking is a great way to get people out of their comfort zones, and work on leadership development and teambuilding,” said Gerson, who also teamed up with co-instructors Emily Ury, Alice Carter and Emily Levy, all Ph.D. students in ecology or biology at Duke.

Marwa Hassan of Riverside High School in Durham studying stream ecology as part of a two-week summer science program in Pisgah National Forest. Photo by Savannah Midgette.

Marwa Hassan of Riverside High School in Durham studying stream ecology as part of a two-week summer science program in Pisgah National Forest. Photo by Savannah Midgette.

The students hauled 30- to 40-pound loads on their backs for up to five miles a day, through all types of weather. For the first week and a half they covered different themes each day: evolution, geology, soil formation, aquatic chemistry, contaminants. Then on the final leg they chose an independent project. Armed with hand lenses, water chemistry test strips, measuring tapes and other gear, each girl came up with a research question, and had two days to collect and analyze the data.

Briyete Garcia-Diaz of Kings Mountain High School surveyed rhododendrons and other trees at different distances from streambanks to see which species prefer wet soils.

Marwa Hassan of Riverside High School in Durham waded into creeks to net mayfly nymphs and caddisfly larvae to diagnose the health of the watershed.

Savannah Midgette of Manteo High School counted mosses and lichens on the sides of trees, but she also learned something about the secret of slug slime.

“If you lick a slug it makes your tongue go numb. It’s because of the protective coating they have,” Midgette said.

High schoolers head to the backcountry to learn the secret of slug slime and other discoveries of science and self in new girls camp

High schoolers head to the backcountry to learn the secret of slug slime and other discoveries of science and self in new girls camp

The hiking wasn’t always easy. On their second day they were still hours from camp when a thunderstorm rolled in. “We were still sore from the previous day. It started pouring. We were soaking wet and freezing. We did workouts to keep warm,” Midgette said.

At camp they took turns cooking. They stir fried chicken and vegetables and cooked pasta for dinner, and somebody even baked brownies for breakfast. Samantha Cardenas of Charlotte Country Day School discovered that meals that seem so-so at home taste heavenly in the backcountry.

“She would be like, ugh, chicken in a can? And then eat it and say: ‘That’s the most amazing thing I’ve ever had,’” said co-instructor Emily Ury.

Savannah Midgette and Briyete Garcia-Diaz drawing interactions within terrestrial systems as part of a new free summer science program called Girls on outdoor Adventure for Leadership and Science, or GALS. Learn more at https://sites.duke.edu/gals/.

Savannah Midgette and Briyete Garcia-Diaz drawing interactions within terrestrial systems as part of a new free summer science program called Girls on outdoor Adventure for Leadership and Science, or GALS. Learn more at https://sites.duke.edu/gals/.

The students were chosen from a pool of over 90 applicants, said co-instructor Emily Levy. There was no fee to participate in the program. Thanks to donations from Duke Outdoor Adventures, Project WILD and others, the girls were able to borrow all the necessary camping gear, including raincoats, rain pants, backpacks, tents, sleeping bags, sleeping pads and stoves.

The students presented their projects on Friday, June 23 in Environment Hall on Duke’s West Campus. Standing in front of her poster in a crisp summer dress, Destoni Carter said going up and down steep hills was hard on her knees. But she’s proud to have made it to the summit of Shining Rock Mountain to see the stunning vistas from the white quartz outcrop near the top.

“I even have a little bit of calf muscle now,” Carter said.

Funding and support for GALS was provided by Duke’s Nicholas School of the Environment, Duke ecologist Nicolette Cagle, the Duke Graduate School and private donors via GoFundMe.

2017 GALS participants (left to right): Emily Levy of Duke, Destoni Carter of Garner High School, Zyrehia Polk of East Mecklenburg High School, Rose DeConto of Durham School of the Arts, Briyete Garcia-Diaz of Kings Mountain High School, Marwa Hassan of Riverside High School, Jackie Gerson of Duke, Daiana Mendoza of Harnett Central High School, Savannah Midgette of Manteo High School, Samantha Cardenas of Charlotte Country Day School and Alice Carter of Duke.

2017 GALS participants (left to right): Emily Levy of Duke, Destoni Carter of Garner High School, Zyrehia Polk of East Mecklenburg High School, Rose DeConto of Durham School of the Arts, Briyete Garcia-Diaz of Kings Mountain High School, Marwa Hassan of Riverside High School, Jackie Gerson of Duke, Daiana Mendoza of Harnett Central High School, Savannah Midgette of Manteo High School, Samantha Cardenas of Charlotte Country Day School and Alice Carter of Duke.

 

Marine Parasites — Little Guys That Make a Big Difference

If you’re anything like me, the first images that come to mind when you hear the words “marine biology” are singing whales, dolphins racing each other, sharks flying out of the water, maybe a swordfish brawl or two — all the big, flashy stuff.

Of all the things “marine biology” invokes, parasites are probably at the very bottom of my list.

Not so for Joe Morton, a PhD student at the Nicholas School of the Environment and self-taught expert on the parasites that inhabit marine organisms. In fact, Morton posits that parasites play one of the most important roles in all of ecology, by modifying the behavior of ecologically influential host species. And he’s got the research to back it up.

Once back at the lab, Morton takes his place behind the microscope to study his research subjects: marine parasites. Courtesy: Joe Morton.

Morton’s academic quest into the world of marine parasites began about six years ago when he was a master’s student at UNC’s Institute of Marine Sciences — just down the road from Duke’s own Marine Lab, where he’s now stationed. Having just read Carl Zimmer’s pop-science book Parasite Rex, Morton wondered whether the marsh periwinkle snails (Littoraria irrorata) he was studying could be infected.

“In my spare time, I would go into the lab at night with a hammer and crack open a bunch of snails to see what I would find,” Morton said. “I didn’t find anything in the literature at the time about Littoraria harboring parasites, which I thought was really unusual because they’re really well-known, important marsh gastropod.”

Morton began to systematically collect Littoraria from local salt marshes, determine their infection status, then examine how the parasites affected the behavior of infected individuals and, in turn, how these behavioral changes affected the ecological health of the salt marsh. This way, Morton figured out that Littoraria infected with digenean trematodes (a class of parasite) climbed and grazed on marsh grass less often than uninfected Littoraria. He also noticed that infected Littoraria congregated at salt marsh “die-off borders,” the edges where marsh grasses stop growing sparsely and start growing in healthy amounts.

A microsopic view of digenean trematodes, the parasites that infect marsh periwinkle snails. Courtesy: Joe Morton.

Based on these observations, Morton designed an experiment to test whether the prevalence of infection among Littoraria correlated with marsh grass health.

“I found that, even under drought stress conditions, parasites could effectively slow the rate at which the marsh died off and help maintain marsh ecosystem structure,” Morton said. “More structure means more nursery habitat for fish. It means more nursery habitat for fiddler crabs. Increased filtration rate of water into the sediment because of crab burrows. The point is, parasites help to increase ecosystem resistance to drought stress.”

Joe Morton traipses through the salt marsh on a windy day. Courtesy: Joe Morton.

Morton was the first to demonstrate this relationship between parasites and marsh health in a behavioral experiment. It’s been a major focus of his research ever since.

“Parasites constitute more than half the life on the planet, but until very recently, parasites were somewhat ignored by ecologists,” Morton said.

Indeed, Morton’s former advisor once told him “never study anything smaller than your thumb.” According to Morton, this was a very widely-held view in ecology up until the last few decades.

“That was very much the idea at the time: these are small things; they probably mean a lot to individual organisms, but they’re may not be important to ecosystems. And now we know that’s just not the case,” Morton said. “Almost everywhere we look, parasites are there; they’re ubiquitous. And they have an important role to play.”

Though parasites are a hot topic in ecology nowadays, Morton, a self-declared “lifelong contrarian,” has a very distinct memory of a childhood moment foreshadowing his current research focus.

“I remember sitting in a barber shop and reading Popular Science magazine, which has an annual list of the ten worst jobs in science. I remember right at the top of the list was ‘parasitic worm biologist.’ And something in my head was just like ‘yeah, I’ll do that,’” Morton said.

Post by Maya Iskandarani

Scientists Engineer Disease-Resistant Rice Without Sacrificing Yield

Researchers have developed a way to make rice more resistant to bacterial blight and other diseases without reducing yield. Photo by Max Pixel.

Researchers have successfully developed a novel method that allows for increased disease resistance in rice without decreasing yield. A team at Duke University, working in collaboration with scientists at Huazhong Agricultural University in China, describe the findings in a paper published May 17, 2017 in the journal Nature.

Rice is one of the most important staple crops, responsible for providing over one-fifth of the calories consumed by humans worldwide. Diseases caused by bacterial or fungal pathogens present a significant problem, and can result in the loss of 80 percent or more of a rice crop.

Decades of research into the plant immune response have identified components that can be used to engineer disease-resistant plants. However, their practical application to crops is limited due to the decreased yield associated with a constantly active defense response.

“Immunity is a double-edged sword, ” said study co-author Xinnian Dong, professor of biology at Duke and lead investigator of the study. “There is often a tradeoff between growth and defense because defense proteins are not only toxic to pathogens but also harmful to self when overexpressed,” Dong said. “This is a major challenge in engineering disease resistance for agricultural use because the ultimate goal is to protect the yield.”

Previous studies have focused on altering the coding sequence or upstream DNA sequence elements of a gene. These upstream DNA elements are known as promoters, and they act as switches that turn on or off a gene’s expression. This is the first step of a gene’s synthesis into its protein product, known as transcription.

By attaching a promoter that gives an “on” signal to a defense gene, a plant can be engineered to be highly resistant to pathogens, though at a cost to growth and yield. These costs can be partially alleviated by attaching the defense gene to a “pathogen specific” promoter that turns on in the presence of pathogen attack.

To further alleviate the negative effects of active defense, the Dong group sought to add an additional layer of control. They turned newly discovered sequence elements, called upstream open reading frames (uORFs), to help address this problem. These sequence elements act on the intermediate of a gene, or messenger (RNA, a molecule similar to DNA) to govern its “translation” into the final protein product. A recent study by the Dong lab in an accompanying paper in Nature has identified many of these elements that respond in a pathogen-inducible manner.

The Dong group hypothesized that adding this pathogen-inducible translational regulation would result in a tighter control of defense protein expression and minimize the lost yield associated with enhanced disease resistance.

To test this hypothesis, the researchers started with Arabidopsis, a flowering plant commonly used in laboratory research. They created a DNA sequence that contains both the transcriptional and translational elements (uORFs) and fused them upstream of the potent “immune activator” gene called snc1. This hybrid sequence was called a “transcriptional/translational cassette” and was inserted into Arabidopsis plants.

When plants have snc1 constitutively active, they are highly resistant to pathogens, but have severely stunted growth. Strikingly, plants with the transcriptional/translational cassette not only have increased resistance, but they also lacked growth defects and resembled healthy wild-type plants. These results show the benefits of adding translational control in engineering plants that have increased resistance without significant costs.

The Dong group then sought to apply these findings to engineer disease-resistant rice, as it is one of the world’s most important crops. They created transgenic rice lines containing the transcriptional/translational cassette driving expression of another potent “immune activator” gene called AtNPR1. This gene was chosen as it has been found to confer broad spectrum pathogen resistance in a wide variety of crop species, including rice, citrus, apple and wheat.

The dry yellowish leaves on these rice plants are a classic symptom of bacterial blight, a devastating disease that affects rice fields worldwide. Photo by Meng Yuan.

The transgenic rice lines containing the transcriptional/translational cassette were infected with bacterial/fungal pathogens that cause three major rice diseases — rice  blight, leaf streak, and fungal blast. These showed high resistance to all three pathogens, indicating broad spectrum resistance could be achieved. Importantly, when grown in the field, their yield — both in terms of grain quantity and quality per plant — was almost unaffected. These results indicate a great potential for agricultural applications.

This strategy is the first known use of adding translational control for the engineering of disease-resistant crops with minimal yield costs. It has many advantages, as it is broadly applicable to a variety of crop species against many pathogens. Since this strategy involves activating the plants’ endogenous defenses, it may also reduce the use of pesticides on crops and hence protect the environment.

Additionally, these findings may be broadly applicable to other systems as well. These upstream elements (uORFs) are widely present in organisms from yeast to humans, with nearly half of all human transcripts containing them. “The great potential in using these elements in controlling protein translation during specific biological processes has yet to be realized,” Dong said.

Corresponding author Xinnian Dong can be reached at xdong@duke.edu or (919) 613-8176.

CITATION:  “uORF-Mediated Translation Allows Engineered Plant Disease Resistance Without Fitness Costs,” Guoyong Xu, Meng Yuan,   Chaoren Ai, Lijing Liu, Edward Zhuang, Sargis Karapetyan, Shiping Wang and Xinnian Dong. Nature, May 17, 2017. DOI: 10.1038/nature22372

 

Guest post by Jonathan Motley

Students Share Research Journeys at Bass Connections Showcase

From the highlands of north central Peru to high schools in North Carolina, student researchers in Duke’s Bass Connections program are gathering data in all sorts of unique places.

As the school year winds down, they packed into Duke’s Scharf Hall last week to hear one another’s stories.

Students and faculty gathered in Scharf Hall to learn about each other’s research at this year’s Bass Connections showcase. Photo by Jared Lazarus/Duke Photography.

The Bass Connections program brings together interdisciplinary teams of undergraduates, graduate students and professors to tackle big questions in research. This year’s showcase, which featured poster presentations and five “lightning talks,” was the first to include teams spanning all five of the program’s diverse themes: Brain and Society; Information, Society and Culture; Global Health; Education and Human Development; and Energy.

“The students wanted an opportunity to learn from one another about what they had been working on across all the different themes over the course of the year,” said Lori Bennear, associate professor of environmental economics and policy at the Nicholas School, during the opening remarks.

Students seized the chance, eagerly perusing peers’ posters and gathering for standing-room-only viewings of other team’s talks.

The different investigations took students from rural areas of Peru, where teams interviewed local residents to better understand the transmission of deadly diseases like malaria and leishmaniasis, to the North Carolina Museum of Art, where mathematicians and engineers worked side-by-side with artists to restore paintings.

Machine learning algorithms created by the Energy Data Analytics Lab can pick out buildings from a satellite image and estimate their energy consumption. Image courtesy Hoël Wiesner.

Students in the Energy Data Analytics Lab didn’t have to look much farther than their smart phones for the data they needed to better understand energy use.

“Here you can see a satellite image, very similar to one you can find on Google maps,” said Eric Peshkin, a junior mathematics major, as he showed an aerial photo of an urban area featuring buildings and a highway. “The question is how can this be useful to us as researchers?”

With the help of new machine-learning algorithms, images like these could soon give researchers oodles of valuable information about energy consumption, Peshkin said.

“For example, what if we could pick out buildings and estimate their energy usage on a per-building level?” said Hoël Wiesner, a second year master’s student at the Nicholas School. “There is not really a good data set for this out there because utilities that do have this information tend to keep it private for commercial reasons.”

The lab has had success developing algorithms that can estimate the size and location of solar panels from aerial photos. Peshkin and Wiesner described how they are now creating new algorithms that can first identify the size and locations of buildings in satellite imagery, and then estimate their energy usage. These tools could provide a quick and easy way to evaluate the total energy needs in any neighborhood, town or city in the U.S. or around the world.

“It’s not just that we can take one city, say Norfolk, Virginia, and estimate the buildings there. If you give us Reno, Tuscaloosa, Las Vegas, Pheonix — my hometown — you can absolutely get the per-building energy estimations,” Peshkin said. “And what that means is that policy makers will be more informed, NGOs will have the ability to best service their community, and more efficient, more accurate energy policy can be implemented.”

Some students’ research took them to the sidelines of local sports fields. Joost Op’t Eynde, a master’s student in biomedical engineering, described how he and his colleagues on a Brain and Society team are working with high school and youth football leagues to sort out what exactly happens to the brain during a high-impact sports game.

While a particularly nasty hit to the head might cause clear symptoms that can be diagnosed as a concussion, the accumulation of lesser impacts over the course of a game or season may also affect the brain. Eynde and his team are developing a set of tools to monitor both these impacts and their effects.

A standing-room only crowd listened to a team present on their work “Tackling Concussions.” Photo by Jared Lazarus/Duke Photography.

“We talk about inputs and outputs — what happens, and what are the results,” Eynde said. “For the inputs, we want to actually see when somebody gets hit, how they get hit, what kinds of things they experience, and what is going on in the head. And the output is we want to look at a way to assess objectively.”

The tools include surveys to estimate how often a player is impacted, an in-ear accelerometer called the DASHR that measures the intensity of jostles to the head, and tests of players’ performance on eye-tracking tasks.

“Right now we are looking on the scale of a season, maybe two seasons,” Eynde said. “What we would like to do in the future is actually follow some of these students throughout their career and get the full data for four years or however long they are involved in the program, and find out more of the long-term effects of what they experience.”

Kara J. Manke, PhD

Post by Kara Manke

Where Some Ski, Others Do Science

For most people, Lost Trail is a ski spot located at 7,000 feet in the Rocky Mountains on the border of Idaho and Montana. Skiers and snowboarders descend down steep slopes, past forests and alpine meadows that get more than 25 feet of snow each year. But for a team of researchers led by Duke biology professor Thomas Mitchell-Olds, buried beneath the snow is a hidden population of native plants on the cusp of dividing into two new species.

Molly Rivera-Olds shovels snow at Lost Trail Pass.

Studying a spindly North American wildflower called Boechera stricta, Mitchell-Olds and colleagues suspected that a process called chromosomal inversion — in which part of a chromosome breaks off and reattaches itself upside down — plays a central role in speciation. To test the idea, they planted Boechera stricta seedlings in a mountaintop meadow near the Lost Trail resort.

To reach the meadow, the researchers carried thousands of seedlings up the mountain in specially constructed backpacks. They also lugged up nine empty garbage cans and filled them with snow to water the plants throughout the summer.

Once the seedlings matured, the researchers measured flowering time, seed production, and survival. They found that plants with the chromosomal inversion had a leg up on the steep slopes of the Rocky Mountains. Eventually, the researchers say, this can lead to plants with the inverted DNA splitting off and forming a new species.

The findings were published April 3, 2017 in the journal Nature Ecology & Evolution.

# # #

CITATION:  “Young Inversion with Multiple Linked QTLs Under Selection in a Hybrid Zone,” Cheng-Ruei Lee, Baosheng Wang et al. Nature Ecology & Evolution, April 3, 2017. DOI:10.1038/s41559-017-0119.

Guest post by Molly Rivera-Olds

 

 

 

 

 

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