Duke Research Blog

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

Author: Kara Manke (Page 1 of 4)

How A Zebrafish’s Squiggly Cartilage Transforms into a Strong Spine

A column of green cartilage cells divides into an alternating pattern of green cartilage and red vertebra

Our spines begin as a flexible column called the notochord. Over time, cells on the notochord surface divide into alternating segments that go on to form cartilage and vertebrae.

In the womb, our strong spines start as nothing more than a rope of rubbery tissue. As our bodies develop, this flexible cord, called the notochord, morphs into a column of bone and cartilage sturdy enough to hold up our heavy upper bodies.

Graduate student Susan Wopat and her colleagues in Michel Bagnat’s lab at Duke are studying the notochords of the humble zebrafish to learn how this cartilage-like rope grows into a mature spine.

In a new paper, they detail the cellular messaging that directs this transformation.

It all comes down to Notch receptors on the notochord surface, they found. Notch receptors are a special type of protein that sits astride cell membranes. When two cells touch, these Notch receptors link up, forming channels that allow messages to rapidly travel between large groups of cells.

Notch receptors divide the outer notochord cells into two alternating groups – one group is told to grow into bone, while the other is told to grow into cartilage. Over time, bone starts to form on the surface of the notochord and works its way inward, eventually forming mature vertebrae.

X-ray images of four zebrafish spines

Meddling with cellular signaling on the notochord surface caused zebrafish spines to develop deformities. The first and third image show healthy spines, and the second and fourth image show deformed spines.

When the team tinkered with the Notch signaling on the surface cells, they found that the spinal vertebrae came out deformed – too big, too small, or the wrong shape.

“These results demonstrate that the notochord plays a critical role in guiding spine development,” Wopat said. “Further investigation into these findings may help us better understand the origin of spinal defects in humans.”

Spine patterning is guided by segmentation of the notochord sheath,” Susan Wopat, Jennifer Bagwell, Kaelyn D. Sumigray, Amy L. Dickson, Leonie F. Huitema, Kenneth D. Poss, Stefan Schulte-Merker, Michel Bagnat. Cell, February 20, 2018. DOI: 10.1016/j.celrep.2018.01.084

Post by Kara Manke

Duke Scholars Bridge Disciplines to Tackle Big Questions

A visualization showing faculty as dots that are connected by lines

This visualization, created by James Moody and the team at the Duke Network Analysis Center, links faculty from across schools and departments who serve together on Ph.D. committees. An interactive version is available here.

When the next big breakthrough in cancer treatment is announced, no one will ask whether the researchers are pharmacologists, oncologists or cellular biologists – and chances are, the team will represent all three.

In the second annual Scholars@Duke Visualization Challenge, Duke students explored how scholars across campus are drawing from multiple academic disciplines to tackle big research questions.

“I’m often amazed at how gifted Duke faculty are and how they can have expertise in multiple fields, sometimes even fields that don’t seem to overlap,” said Julia Trimmer, Director of Faculty Data Systems and Analysis at Duke.

In last year’s challenge, students dug into Scholars@Duke publication data to explore how Duke researchers collaborate across campus. This year, they were provided with additional data on Ph.D. dissertation committees and asked to focus on how graduate education and scholarship are reaching across departmental boundaries.

“The idea was to see if certain units or disciplines contributed faculty committee members across disciplines or if there’s a lot of discipline ‘overlap.’” Trimmer said.

The winning visualization, created by graduate student Matthew Epland, examines how Ph.D. committees span different fields. In this interactive plot, each marker represents an academic department. The closer together markers are, the more likely it is that a faculty member from one department will serve on the committee of a student in the other department.

Epland says he was intrigued to see the tight-knit community of neuroscience-focused departments that span different schools, including psychology and neuroscience, neurobiology, neurology and psychiatry and behavioral Sciences. Not surprisingly, many of the faculty in these departments are members of the Duke Institute for Brain Sciences (DIBS).

Duke schools appear as dots and are connected by lines of different thicknesses

Aghil Abed Zadeh and Varda F. Hagh analyzed publication data to visualize the extent to which faculty at different Duke schools collaborate with one another. The size of each dot represents the number of publications from each school, and thickness of each line represents the number of faculty collaborations between the connected schools.

Sociology Professor James Moody and the team at the Duke Network Analysis Center took a similar approach, creating a network of individual faculty members who are linked by shared students. Faculty who sit on committees in only one field are bunched together, highlighting researchers who bridge different disciplines. The size of each marker represents the extent to which each researcher sits “between” two fields.

The map shows a set of strong ties within the natural sciences and within the humanities, but few links between the two groups. Moody points out that philosophy is a surprising exception to this rule, lying closer to the natural sciences cluster than to the humanities cluster.

“At Duke, the strong emphasis on philosophy of science creates a natural link between philosophy and the natural sciences,” Moody said.

Duke graduate student Aghil Abed Zadeh teamed up with Varda F. Hagh, a student at Arizona State University, to create elegant maps linking schools and departments by shared authorship. The size of each marker represents the number of publications in that school or department, and the thickness of the connecting lines indicate the number of shared authorships.

“It is interesting to see how connected law school and public policy school are. They collaborate with many of the sciences as well, which is a surprising fact,” Zadeh said. “On the other hand, we see Divinity school, one the oldest at Duke, which is isolated and not connected to others at all.”

The teams presented their visualizations Jan. 20 at the Duke Research Computing Symposium.

Post by Kara Manke

 

Farewell, Electrons: Future Electronics May Ride on New Three-in-One Particle

“Trion” may sound like the name of one of the theoretical particles blamed for mucking up operations aboard the Starship Enterprise.

But believe it or not, trions are real — and they may soon play a key role in electronic devices. Duke researchers have for the first time pinned down some of the behaviors of these one-of-a-kind particles, a first step towards putting them to work in electronics.

A carbon nanotube, shaped like a rod, is wrapped in a helical coating of polymer

Three-in-one particles called trions — carrying charge, energy and spin — zoom through special polymer-wrapped carbon nanotubes at room temperature. Credit: Yusong Bai.

Trions are what scientists call “quasiparticles,” bundles of energy, electric charge and spin that zoom around inside semiconductors.

“Trions display unique properties that you won’t be able to find in conventional particles like electrons, holes (positive charges) and excitons (electron-hole pairs that are formed when light interacts with certain materials),” said Yusong Bai, a postdoctoral scholar in the chemistry department at Duke. “Because of their unique properties, trions could be used in new electronics such as photovoltaics, photodetectors, or in spintronics.”

Usually these properties – energy, charge and spin – are carried by separate particles. For example, excitons carry the light energy that powers solar cells, and electrons or holes carry the electric charge that drives electronic devices. But trions are essentially three-in-one particles, combining these elements together into a single entity – hence the “tri” in trion.

A diagram of how a trion is formed in carbon nanotubes.

A trion is born when a particle called a polaron (top) marries an exciton (middle). Credit: Yusong Bai.

“A trion is this hybrid that involves a charge marrying an exciton to become a uniquely distinct particle,” said Michael Therien, the William R. Kenan, Jr. Professor of Chemistry at Duke. “And the reason why people are excited about trions is because they are a new way to manipulate spin, charge, and the energy of absorbed light, all simultaneously.”

Until recently, scientists hadn’t given trions much attention because they could only be found in semiconductors at extremely low temperatures – around 2 Kelvin, or -271 Celcius. A few years ago, researchers observed trions in carbon nanotubes at room temperature, opening up the potential to use them in real electronic devices.

Bai used a laser probing technique to study how trions behave in carefully engineered and highly uniform carbon nanotubes. He examined basic properties including how they are formed, how fast they move and how long they live.

He was surprised to find that under certain conditions, these unusual particles were actually quite easy to create and control.

“We found these particles are very stable in materials like carbon nanotubes, which can be used in a new generation of electronics,” Bai said. “This study is the first step in understanding how we might take advantage of their unique properties.”

The team published their results Jan. 8 in the Proceedings of the National Academy of Sciences.

Dynamics of charged excitons in electronically and morphologically homogeneous single-walled carbon nanotubes,” Yusong Bai, Jean-Hubert Olivier, George Bullard, Chaoren Liu and Michael J. Therien. Proceedings of the National Academy of Sciences, Jan. 8, 2018 (online) DOI: 10.1073/pnas.1712971115

Post by Kara Manke

Glitter and Jell-O Reveal the Science of Oobleck

A black and white image showing a circular disk dropping into a container of oobleck

Mixing black glitter with oobleck allowed researchers to track the movement of individual cornstarch particles after a sudden impact. A computer program locked onto pieces of glitter and illustrated their motion. Credit: Melody Lim.

What do gelatin and glitter have to do with serious science? For some experiments, a lot! Duke alumna Melody Lim used jiggly Jell-O and a just a pinch of glitter to solve a scientific mystery about the curious goo many like to call oobleck.

To the uninitiated, oobleck is almost magic. The simple mixture of cornstarch and water feels solid if you squeeze it, but moments later runs through your fingers like water. You can dance across a bathtub full of oobleck, but stand still for too long and you will be sucked into a goopy mess. Not surprisingly, the stuff is a Youtube favorite.

Oobleck is an example of what scientists call a non-Newtonian fluid, a liquid whose viscosity – how easily it changes shape and flows – depends upon the force that is applied. But exactly how it is that this material switches from solid to liquid and back again has remained a mystery to scientists.

A piece of gelatin being squeezed viewed through a circular polarizer

This blogger mixed up a batch of jello to see the photoelastic effect for herself. When viewed with polarized light – from an iPhone screen and a circular polarizer – the jello changes color when squeezed.

“Water is simple to understand, and so is cornstarch,” said Lim, ’16, who is currently a graduate student at the University of Chicago. “However, a combination of the two produces this ‘liquid’ that ripples and flows, solidifies beneath your feet if you run on it, then turns back into a liquid if you stop running and stand still. I wanted to know why.”

The question beguiling scientists was whether sudden impact causes the cornstarch particles to “jam” into a solid like cement, or whether the suspension remains liquid but simply moves too slowly for its liquid-like properties to be apparent — similar to what happens if you skip a rock off the surface of a lake.

“There are these two opposing pictures,” said Robert Behringer, James B. Duke Professor of Physics at Duke. “Either you squish the material and turn it into cement temporarily, or you simply transmit the stress from the impactor straight to the boundary.”

Lim did two sets of experiments to find out which way oobleck works. In one experiment, she mixed black glitter into a transparent channel filled with oobleck, and then used a high-speed camera to watch how the material responded to the impact. The glitter let her track the motion of individual particles after the disc hit.

A piece of gelatin changes color when you squeeze it.

The photoelastic effect in gelatin.

Her video shows that the particles near the impact site jam and become solid, forming what the researchers call a “mass shock” wave that travels slowly through the suspension.

In a second set of experiments, Lim placed the oobleck in a container lined with gelatin, the main ingredient in Jell-O – besides sugar and food dye, of course. Gelatin is what is called a photoelastic material, which means that applying pressure bends light that travels through it, like a prism.

“Next time you eat Jell-O, get out your sunglasses and get somebody else’s sunglasses and look between them,” Behringer said. “Because if you give it a shake you should see all these stress patterns bouncing around.”

After the metal disc hit the oobleck, the gelatin let Lim see how fast the resulting pressure wave traveled through the material and reached the boundary.

A black and white image showing pressure waves traveling through a transparent material after impact

The researchers poured oobleck into a clear container lined with gelatin, a material that bends light when a pressure is applied to it. They saw that the force of a sudden impact is rapidly transmitted through the oobleck and to the boundary with the gelatin. Credit: Melody Lim.

They found that when the impact is sudden, the pressure wave traveled to the gelatin boundary faster than the “mass shock” wave. This means that the reason oobleck appears solid after a sudden impact is because the force of the collision is quickly transmitted to a solid boundary.

“If you are running across the water, that actually puts you into an impact velocity range where the pressure wave is significantly faster than the mass shock,” Behringer said. “Whereas if you try to walk across it, the impact speeds are slow, and the system actually doesn’t have the ability to transport the momentum quickly through the material and so you just sink in.”

“If you’d told me when I started that I would line a narrow container with Jell-o, add cornstarch, water, and black glitter, drop a piece of metal on it, then publish a paper on the results, I would have laughed at you,” Lim said.

CITATION: “Force and Mass Dynamics in Non-Newtonian Suspensions,” Melody X. Lim, Jonathan Barés, Hu Zheng and Robert P. Behringer. Physical Review Letters, Nov. 3, 2017. DOI: 10.1103/PhysRevLett.119.184501

Post by Kara Manke

Cheating Time to Watch Liquids do the Slow Dance

Colorful spheres simulating liquid molecules shift around inside a cube shape

The team’s new algorithm is able to simulate molecular configurations of supercooled liquids below the glass transition. The properties of these configurations are helping to solve a 70-year paradox about the entropy of glasses. Credit: Misaki Ozawa and Andrea Ninarello, Université de Montpellier.

If you could put on a pair of swimming goggles, shrink yourself down like a character from The Magic School Bus and take a deep dive inside a liquid, you would see a crowd of molecules all partying like it’s 1999.

All this frenetic wiggling makes it easy for molecules to rearrange themselves and for the liquid as a whole to change shape. But for supercooled liquids — liquids like honey that are cooled below their freezing point without crystallizing – the lower temperature slows down the dancing like Etta James’ “At Last.” Lower the temperature enough, and the slow-down can be so dramatic that it takes centuries or even millennia for the molecules to rearrange and the liquid to move.

Scientists can’t study processes that last longer than their careers. But Duke chemists and their Simons Foundation collaborators have found a way to cheat time, simulating the slow dance of deeply supercooled liquids. Along the way, they have found new physical properties of “aged” supercooled liquids and glasses.

A droplet rises above a surface of water

Credit: Ruben Alexander via Flickr.

To understand just how slow deeply supercooled liquids move, consider the world’s longest-running experiment, the University of Queensland’s Pitch Drop Experiment. A single drop of pitch forms every eight to thirteen years — and this pitch is moving faster than deeply supercooled liquids.

“Experimentally there is a limit to what you can observe, because even if you managed to do it over your entire career, that is still a maximum of 50 years,” said Patrick Charbonneau, an associate professor of chemistry and physics at Duke. “For many people that was considered a hard glass ceiling, beyond which you couldn’t study the behavior of supercooled liquids.”

Charbonneau, who is an expert on numerical simulations, said that using computers to simulate the behavior of supercooled liquids has even steeper time limitations. He estimates that, given the current rate of computer advancement, it would take 50 to 100 years before computers would be powerful enough for simulations to exceed experimental capabilities – and even then the simulations would take months.

To break this glass ceiling, the Charbonneau group collaborated with Ludovic Berthier and his team, who were developing an algorithm to bypass these time constraints. Rather than taking months or years to simulate how each molecule in a supercooled liquids jiggles around until the molecules rearrange, the algorithm picks individual molecules to swap places with each other, creating new molecular configurations.

This allows the team to explore new configurations that could take millennia to form naturally. These “deeply supercooled liquids and ultra-aged glasses” liquids are at a lower energy, and more stable, than any observed before.

“We were cheating time in the sense that we didn’t have to follow the dynamics of the system,” Charbonneau said. “We were able to simulate deeply supercooled liquids well beyond is possible in experiments, and it opened up a lot of possibilities.”

Two columns of blue and red spheres represent simulations of vapor-deposited glasses.

Glasses that are grown one layer at a time have a much different structure than bulk glasses. The team used their new algorithm to study how molecules in these glasses rearrange, and found that at low temperatures (right), only the molecules at the surface are mobile. The results may be used to design better types of glass for drug delivery or protective coatings. Credit: Elijah Flenner.

Last summer, the team used this technique to discover a new phase transition in low-temperature glasses. They recently published two additional studies, one of which sheds light on the “Kauzmann paradox,” a 70-year question about the entropy of supercooled liquids below the glass transition. The second explores the formation of vapor-deposited glasses, which have applications in drug delivery and protective coatings.

“Nature has only one way to equilibrate, by just following the molecular dynamics,” said Sho Yaida, a postdoctoral fellow in Charbonneau’s lab. “But the great thing about numerical simulations is you can tweak the algorithm to accelerate your experiment.”

Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling.” Ludovic Berthier, Patrick Charbonneau, Daniele Coslovich, Andrea Ninarello, Misaki Ozawa and Sho Yaida. PNAS, Oct. 24, 2017. DOI: 10.1073/pnas.1706860114

The origin of ultrastability in vapor-deposited glasses.” Ludovic Berthier, Patrick Charbonneau, Elijah Flenner and Francesco Zamponi. PRL, Nov. 1, 2017. DOI: 10.1103/PhysRevLett.119.188002

Post by Kara Manke

Designing Drugs Aimed at a Different Part of Life’s Code

Individual RNA molecules fluoresce inside a breast cancer cell.

Individual RNA molecules fluoresce inside a breast cancer cell. Credit: Sunjong Kwon, Oregon Health & Science University, via Flickr.

Most drugs work by tinkering with the behavior of proteins. Like meddlesome coworkers, these molecules are designed to latch onto their target proteins and keep them from doing what they need to do.

If a protein is responsible for speeding up a reaction, the drug helps slow the reaction down. If a protein serves as a gatekeeper to a cell, regulating what gets in and what stays out, a drug changes how many molecules it lets through.

But proteins aren’t the only doers and shakers in our bodies. Scientists are finding that strings of RNA — known primarily for their role in shuttling genetic information from nucleus-bound DNA to the cell’s protein-manufacturing machinery — can also play a major role in regulating disease.

A portrait of Amanda Hargrove

Amanda Hargrove is an assistant professor of chemistry at Duke University.

“There has been what some people are calling an RNA revolution,” said Amanda Hargrove, assistant professor of chemistry at Duke. “In some diseases, non-coding RNAs, or RNAs that don’t turn into protein, seem to be the best predictors of disease, and even to be driving the disease.”

Hargrove and her team at Duke are working to design new types of drugs that target RNA rather than proteins. RNA-targeted drug molecules have the potential help treat diseases like prostate cancer and HIV, but finding them is no easy task. Most drugs have been designed to interfere with proteins, and just don’t have the same effects on RNA.

Part of the problem is that proteins and RNA have many fundamental differences, Hargrove said. While proteins are made of strings of twenty amino acids that can twist into myriad different shapes, RNA is made of strings of only four bases — adenine, guanine, cytosine and uracil.

“People have been screening drugs for different kinds of RNA for quite a while, and historically have not had a lot of success,” Hargrove said. “This begged the question, since RNA has such chemically different properties than proteins, is there something different about the small molecules that we need in order to target RNA?”

To find out, graduate student Brittany Morgan and research associate Jordan Forte combed the scientific literature to identify 104 small molecules that are known interact with specific types of RNA. They then analyzed 20 different properties of these molecules, and compared their properties to those of collections of drug molecules known to interact with proteins.

The team found significant differences in shape, atomic composition, and charge between the RNA-active molecules and the protein-active molecules. They plan to use the results to compile a collection of molecules, called a library, that are chosen to better “speak the language” of the RNA-active molecules. They hope this collection of molecules will be more likely to interact with RNA in therapeutically beneficial ways.

“We found that there are differences between the RNA-targeted molecules and the protein-targeted drugs, and some of them are pretty striking,” Hargrove said. “What that means is that we could start to enrich our screening libraries with these types of molecules, and make these types of molecules, to have better luck at targeting RNA.”

Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA-Targeted Bioactive Ligands.” Brittany S. Morgan, Jordan E. Forte, Rebecca N. Culver, Yuqi Zhang and Amanda Hargrove. Angewandte Chemie, Sept. 18, 2017. DOI: 10.1002/anie.201707641

Kara J. Manke, PhDPost by Kara Manke

Lab-Made Protein Chomps Co-Factor Like a Big Ol' Gator

A protein is illustrated to look like an alligator mouth

The synthetic protein clamps down on the porphyrin like the jaws of an alligator. Credit: Nicholas Polizzi.

Proteins have the power to turbo-charge biochemical reactions inside the body.

Without the help of types of proteins called enzymes, the reaction that builds DNA could take over 130,000 years to complete. Enzymes cut that time down to just a few milliseconds.

To rev up chemical reactions, many proteins team up with smaller molecules or metals called cofactors. Chemists would like to design proteins that bind to non-biological cofactors in order to speed up chemical reactions not found in nature. But first, they have to figure out how to create man-made proteins that attach to new cofactors in exactly the right way, and that is no easy feat.

A team of chemists at Duke and UC San Francisco is the first to solve this protein design puzzle. The team created a synthetic protein that tightly binds a non-biological catalyst, a type of molecule called porphyrin that is capable of stealing electrons from other molecules when it absorbs light.

“To be able to combine man-made catalysts with proteins would be really big in the chemistry field because then you could combine the power of an enzyme with that of a reaction that isn’t found in nature,” said former Duke graduate student Nicholas Polizzi, who is now a postdoctoral researcher in William DeGrado’s lab at UCSF.

“We were able to figure out the design criteria necessary to place that porphyrin in a protein to within a very high accuracy,” Polizzi said. “That was a really big stepping stone to be able to design new protein-cofactor combinations not seen in nature.”

Proteins are made of chains of hundreds or thousands of smaller amino acids that twist and loop into complex 3-D shapes that can interlock with other molecules like pieces of a jigsaw puzzle. To catalyze chemical reactions, protein-cofactor combinations hold two or more molecules in precisely-shaped pockets that keep the molecules in just the right positions, and provide the right environment, for a chemical reaction to occur.

An illustration of a protein jigsaw puzzle

Chemists at Duke and UCSF designed a synthetic protein that tightly binds a non-biological molecule. Credit: Nicholas Polizzi.

Millions of years of evolution have created proteins that fold into the shapes that tightly grip specific cofactors and provide the perfect environments to catalyze chemical reactions.

For over 25 years, chemists have used what they know about protein folding to design synthetic amino acid sequences that twist up into useful shapes. But so far, they have been unable to design a protein that binds a non-biological cofactor with the precision necessary to power complex new chemical reactions.

Polizzi said this may be because these designs focused primarily on the “binding site” where cofactors and reacting molecules fit into the protein, while ignoring the rest of the structure. “What I did differently is that I considered essentially the entire interior of protein as the binding site for the porphyrin, as opposed to just a few amino acids that touch the porphyrin,” Polizzi said.

To understand how this works, you can think of the protein as the mouth of an alligator, said Michael Therien, William R. Kenan Jr. Professor of Chemistry at Duke. The protein latches onto a cofactor in the same way that an alligator uses its front teeth to chomp down on dinner. But for the front teeth to get a strong grip, the jaw and back teeth also have to be designed correctly.

“The new concept here is that the non-binding region of the protein is held in a shape that allows the binding region to work,” Therien said.

“We called the protein ‘gator’ in the lab,” Polizzi said.

The jaws of the gator protein actually clamp down so hard on the porphyrin cofactor that the whole structure is too rigid to catalyze a reaction, Polizzi said. But with a few tweaks to loosen up the structure, he thinks he can get it to work.

“In this reaction, often times you need a little bit of wiggle room in the protein for it to move. And there was no wiggle room in our protein, everything fit too perfectly,” Polizzi said.

CITATION: “De novo design of a hyperstable non-natural protein-ligand complex with sub-A accuracy.” Nicholas F. Polizzi, Yibing Wu, Thomas Lemmin, Alison M. Maxwell, Shao-Qing Zhang, Jeff Rawson, David N. Beratan, Michael J. Therien and William F. DeGrado. Nature Chemistry, Aug. 21, 2017. DOI: 10.1038/nchem.2846

Kara J. Manke, PhDPost by Kara Manke

Durham Traffic Data Reveal Clues to Safer Streets

Ghost bikes are a haunting site. The white-painted bicycles, often decorated with flowers or photographs, mark the locations where cyclists have been hit and killed on the street.

A white-painted bike next to a street.

A Ghost Bike located in Chapel Hill, NC.

Four of these memorials currently line the streets of Durham, and the statistics on non-fatal crashes in the community are equally sobering. According to data gathered by the North Carolina Department of Transportation, Durham county averaged 23 bicycle and 116 pedestrian crashes per year between 2011 and 2015.

But a team of Duke researchers say these grim crash data may also reveal clues for how to make Durham’s streets safer for bikers, walkers, and drivers.

This summer, a team of Duke students partnered with Durham’s Department of Transportation to analyze and map pedestrian, bicycle and motor vehicle crash data as part of the 10-week Data+ summer research program.

In the Ghost Bikes project, the team created an interactive website that allows users to explore how different factors such as the time-of-day, weather conditions, and sociodemographics affect crash risk. Insights from the data also allowed the team to develop policy recommendations for improving the safety of Durham’s streets.

“Ideally this could help make things safer, help people stay out of hospitals and save lives,” said Lauren Fox, a Duke cultural anthropology major who graduated this spring, and a member of the DATA+ Ghost Bikes team.

A map of Durham county with dots showing the locations of bicycle crashes

A heat map from the team’s interactive website shows areas with the highest density of bicycle crashes, overlaid with the locations of individual bicycle crashes.

The final analysis showed some surprising trends.

“For pedestrians the most common crash isn’t actually happening at intersections, it is happening at what is called mid-block crossings, which happen when someone is crossing in the middle of the road,” Fox said.

To mitigate the risks, the team’s Executive Summary includes recommendations to install crosswalks, median islands and bike lanes to roads with a high density of crashes.

They also found that males, who make up about two-thirds of bicycle commuters over the age of 16, are involved in 75% of bicycle crashes.

“We found that male cyclists over age 16 actually are hit at a statistically higher rate,” said Elizabeth Ratliff, a junior majoring in statistical science. “But we don’t know why. We don’t know if this is because males are riskier bikers, if it is because they are physically bigger objects to hit, or if it just happens to be a statistical coincidence of a very unlikely nature.”

To build their website, the team integrated more than 20 sets of crash data from a wide variety of different sources, including city, county, regional and state reports, and in an array of formats, from maps to Excel spreadsheets.

“They had to fit together many different data sources that don’t necessarily speak to each other,” said faculty advisor Harris Solomon, an associate professor of cultural anthropology and global health at Duke.  The Ghost Bikes project arose out of Solomon’s research on traffic accidents in India, supported by the National Science Foundation Cultural Anthropology Program.

In Solomon’s Spring 2017 anthropology and global health seminar, students explored the role of the ghost bikes as memorials in the Durham community. The Data+ team approached the same issues from a more quantitative angle, Solomon said.

“The bikes are a very concrete reminder that the data are about lives and deaths,” Solomon said. “By visiting the bikes, the team was able to think about the very human aspects of data work.”

“I was surprised to see how many stakeholders there are in biking,” Fox said. For example, she added, the simple act of adding a bike lane requires balancing the needs of bicyclists, nearby residents concerned with home values or parking spots, and buses or ambulances who require access to the road.

“I hadn’t seen policy work that closely in my classes, so it was interesting to see that there aren’t really simple solutions,” Fox said.

[youtube https://www.youtube.com/watch?v=YHIRqhdb7YQ&w=629&h=354]

 

Data+ is sponsored by Bass Connections, the Information Initiative at Duke, the Social Science Research Institute, the departments of Mathematics and Statistical Science and MEDx.

Other Duke sponsors include DTECH, Duke Health, Sanford School of Public Policy, Nicholas School of the Environment, Development and Alumni Affairs, Energy Initiative, Franklin Humanities Institute, Duke Institute for Brain Sciences, Office for Information Technology and the Office of the Provost, as well as the departments of Electrical & Computer Engineering, Computer Science, Biomedical Engineering, Biostatistics & Bioinformatics and Biology.

Government funding comes from the National Science Foundation. Outside funding comes from Accenture, Academic Analytics, Counter Tools and an anonymous donation.

Community partnerships, data and interesting problems come from the Durham Police Department, Durham Neighborhood Compass, Cary Institute of Ecosystem Studies, Duke Marine Lab, Center for Child and Family Policy, Northeast Ohio Medical University, TD Bank, Epsilon, Duke School of Nursing, University of Southern California, Durham Bicycle and Pedestrian Advisory Commission, Duke Surgery, MyHealth Teams, North Carolina Museum of Art and Scholars@Duke.

Writing by Kara Manke; video by Lauren Mueller and Summer Dunsmore

Not Your Basic Bench: Zebrafish Reveal Secrets of the Developing Gut

Our intestine is a highly complex organ – a tortuous, rugged channel built of many specialized cell-types and coated with a protective, slimy matrix. Yet the intestine begins as a simple tube consisting of a central lumen lined by a sheet of epithelial cells, which are smooth cells that lie on the surface of the lumen. These intestinal epithelial cells are central players in many human diseases.

A portrait of Daniel Levic

Daniel Levic, a postdoctoral research associate in the department of cell biology at the Duke University Medical Center.

Daniel Levic of the Bagnat Lab is using zebrafish as experimental models to understand how intestines are formed in hopes of finding new ways to combat disease. He wants to learn how the intestinal lumen forms during early development, and how intestinal epithelial cells take on their physiological functions.

Levic, a postdoctoral research associate in the department of cell biology at the Duke University Medical Center, focuses on projects in both basic and translational science. Daniel uses zebrafish to analyze the formation of the lumen and the polarity of epithelial cells — how specialized they are for carrying out different functions —  at the genetic and cellular level. He focuses on how membrane proteins are sorted into different, specialized domains of the cell surface and how this process affects intestinal formation. Additionally, Daniel studies how inflammation is evaded in intestinal epithelial cells in Crohn’s disease using a combination of patient biopsy samples and animal studies in zebrafish. This project is a collaborative effort aided by clinicians and human geneticists at the Duke University Medical Center.

A microscope image of a zebrafish gut

The developing gut of a zebrafish, magnified.

Though complex human diseases can’t be fully mimicked in animal models like zebrafish, this type of research can be extremely useful. These model organisms can be used to study the basic, fundamental cellular mechanisms that ultimately underlie disease. An example is Daniel’s work on Crohn’s disease, where he is trying to understand how inflammatory signaling networks become activated, specifically in intestinal epithelial cells. This problem is difficult, if not impossible, to address using exclusively human biopsy samples.

Overall, Daniel hopes that his translational research will provide new knowledge of the role of intestinal epithelial cells in Crohn’s disease and provide biomarkers that will aid clinicians in predicting how patients will respond to therapeutic interventions. Daniel’s research and basic science research are rapidly changing the way we diagnose disease, treat patients, and interact with the world around us.

Guest post by Vaishnavi Siripurapu

From Solid to Liquid and Back Again

A black and white moving image of a ball being pulled out from under a pile of circular discs

Force chains erupt as an “intruder” is yanked from beneath a pile of circular discs, which are designed to simulate a granular material. The entire process takes less than one second. Credit: Yue Zhang, Duke University.

You can easily walk across the sand on a beach. But step into a ball pit, and chances are you’ll fall right through.

Sand and ball pits are both granular materials, or materials that are made of collections of much smaller particles or grains. Depending on their density and how much force they experience, granular materials sometimes behave like liquids — something you fall right through — and sometimes “jam” into solids, making them something you can stand on.

“In some cases, these little particles have figured out how to actually form solid-like structures,” said Robert P. Behringer, James B. Duke Professor of Physics. “So why don’t they always just go squirting sideways and relax all the stress?”

Physicists do not yet understand exactly when and how jamming occurs, but Behringer’s team at Duke is on the case. The group squishes, stretches, hits, and pulls at granular materials to get a better picture of how and why they behave like they do. The team recently presented a whopping 10 papers at the 2017 Powders and Grains Conference, which occurred from July 3-7, 2017 in Montpellier, France.

Many of these studies use one of the lab’s favorite techniques, which is to create granular materials from small transparent discs that are about half an inch to an inch in diameter. These discs are made of a material which, thanks to the special way it interacts with light, changes color when squished. This effect allows the team to watch how the stress within the material changes as various forces are applied.

A blue and green moving image of spinning discs

As the wheels turn, shear strain between the discs creates a dense web of inter-particle forces. Credit: Yiqiu Zhao, Duke University.

In one experiment, graduate student Yue Zhang used a high-speed camera to catch the stress patterns as a ball on a string is yanked out from a pile of these discs. In the video, the ball first appears to be stuck under the pile, and then suddenly gives way after enough force is applied — not unlike what you might experience pulling a tent stake out of the ground, or opening the lid on a pesky pickle jar.

“The amusing thing is that you start trying to pull, you add more force, you add more force, and then at some point you pull so hard that you hit yourself in the head,” Behringer said.

The team was surprised to find that the stress patterns created by the ball, which Behringer says look “like hair all standing on end,” are almost identical to the stress of impact, only in reverse.

“What you see is even though you are just gradually gradually pulling harder and harder, the final dynamics are in some sense the same dynamics that you get on impact,” Behringer said.

In another experiment, the team examined what happens in granular materials under shear strain, which is similar to the force your fingers exert on one another when you rub them together.

Graduate student Yiqiu Zhao placed hundreds of these discs onto a circular platform made of a series of flat, concentric rings, each of which is controlled by a separate motor. As the rings turn at different speeds, the particles rub against one another, creating a shear stress.

An image of an experimental set up in a lab

Beneath the small transparent discs lie a series of concentric wheels, each attached to its own motor. By turning these platforms at different speeds, Yiqiu Zhao can observe how shear strain affects the discs.

“We have about twenty stepper motors here, so that we can rotate all the rings to apply a shear not only from the outside boundary, but also from everywhere inside the bulk of the material,” Zhao said. This ensures that each particle in the circle experiences a similar amount of shear.

“One of the key intents of this new experiment was to find a way that we could shear until the cows come home,” Behringer said. “And if it takes a hundred times more shear than I could get with older experiments, well we’ll get it.”

As the rings turn, videos of the material show forces snaking out from the inner circle like lightning bolts. They found that by applying enough shear, it is possible to make the material like a solid at much lower densities than had been seen before.

“You can actually turn a granular fluid into a granular solid by shearing it,” Behringer said. “So it is like you don’t put your ice in the refrigerator, you put it in one of these trays and you shear the tray and it turns into ice.”

Kara J. Manke, PhDPost by Kara Manke

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