Category: Research

Brain Cells Use A Telephone Trick To Report What They See

DURHAM, N.C. — “How many fingers am I holding up?”

For vision-sensing brain cells in a monkey’s visual cortex, that answer depends on whether the digits are next to each other or partially overlapping.

A new study from Duke University finds that single neurons conveying visual information about two separate objects in sight do so by alternating signals about one or the other. When two objects overlap, however, the brain cells detect them as a single entity.

The new report is out Nov. 28 in the journal eLife.

The findings help expand what is known about how the brain makes sense of its complicated and busy world. Most research on sensory processing, be it sounds or sights, sets the bar too low by testing how brain cells react to a single tone or image.

“There are lots of reasons to keep things simple in the lab,” said Jennifer Groh, Ph.D., a faculty member of the Duke Institute for Brain Sciences and senior author of the new report. “But it means that we’re not very far along in understanding how the brain encodes more than one thing at a time.”

Making sense of complicated sensory information is somewhat of a specialty for Groh. In 2018, her lab was the first to show that single auditory brain cells efficiently transmit information about two different sounds by using something called multiplexing.

“Multiplexing is an idea that comes from engineering,” Groh said. “When you have one wire and a lot of signals, you can swap the signals out, kind of like a telephone party line.”

The telecommunications technology works by rapidly switching back-and-forth between relaying information from one phone call and the other using just one wire. In the brain, the switching is probably happening much more slowly, Groh said, but the general idea is similar.

Na Young Jun, a graduate student in neurobiology at Duke and the lead author of the paper, first learned about how auditory neurons do this telephone wiring trick during a lecture Groh gave as part of a neuroscience boot camp course.

“I thought the concept of multiplexing was fascinating,” Jun said. “I wanted to talk more with Dr. Groh about it out, so I went to her office and ending up working in her lab.”

During her time in the Groh lab, Jun was given a valuable dataset from Groh’s collaborator Marlene Cohen, Ph.D., a professor of neurobiology at the University of Chicago and co-author on the paper. Cohen’s group had collected brain activity data from macaques while they watched pictures on a screen in an effort to study attention.

“Collecting data from monkeys is super hard,” Jun said. “It can take seven years of a grad student’s life to collect just a few gigabytes of data.”

The shared dataset proved to be just as efficient as the brain cells Jun then analyzed.

With help from Groh’s collaborator Surya Tokdar, Ph.D., a professor of statistical sciences at Duke and co-author on the paper, Jun found that a subset of cells in the visual cortex, considered a “higher order” brain region in the visual processing pathway, switch between reporting on two different images across trials.

“Say you have a visual cortex neuron,” Jun said. “When it just sees a backpack, it fires 20 times a second. When it just sees a coffee cup, it fires five times a second. But when that same neuron sees the backpack and the coffee cup next to each other, it alternates firing 20 times a second and five times a second.”

A sample set of images macaques saw during the study. Pictures of black and white diagonal lines and more naturalistic images produced similar multiplexing behavior. (Marlene Cohen, U. Chicago) However, if two objects overlap, like placing a coffee cup in front of a backpack, the brain cells fire the same way each time the eclipsing objects are presented. This suggests that the neurons treated overlapping images as a single object rather than separate ones.

While the real world is much busier than just two side-by-side objects, this work starts to move sensory research to better reflect everyday perception for the brain.

“Considering how the brain preserves information about two visual stimuli presented is still a far cry from understanding how the myriad details present in a natural scene are encoded,” Jun and her co-authors write in their report. “More studies are still needed to shed light on how our brains operate outside the rarefied environment of the laboratory.”

Support for the research came from the U.S. National Institutes of Health (R00EY020844; R01EY022930; Core Grant P30 EY008098s; R01DC013906; R01DC016363), the McKnight Foundation, the Whitehall Foundation, the Sloan Foundation, and the Simons Foundation.

CITATION: “Coordinated Multiplexing of Information About Separate Objects in Visual Cortex,” Na Young Jun, Douglas A. Ruff, Lily E. Kramer, Brittany Bowes, Surya T. Tokdar, Marlene R. Cohen, Jennifer M. Groh. eLife, Nov. 29, 2022. DOI: 10.7554/eLife.76452.sa0

Online – https://elifesciences.org/articles/76452

Mom’s Dietary Fat Rewires Male And Female Brains Differently

DURHAM, NC — More than half of all women in the United States are overweight or obese when they become pregnant. While being or becoming overweight during pregnancy can have potential health risks for moms, there are also hints that it may tip the scales for their kids to develop psychiatric disorders like autism or depression, which often affects one gender more than the other.

What hasn’t been understood however is how the accumulation of fat tissue in mom might signal through the placenta in a sex-specific way and rearrange the developing offspring’s brain.

To fill this gap, Duke postdoctoral researcher Alexis Ceasrine, Ph.D., and her team in the lab of Duke psychology & neuroscience professor Staci Bilbo, Ph.D., studied pregnant mice on a high-fat diet. In findings appearing November 28 in the journal Nature Metabolism, they found that mom’s high-fat diet triggers immune cells in the developing brains of male but not female mouse pups to overconsume the mood-influencing brain chemical serotonin, leading to depressed-like behavior.

The researchers said a similar thing may be happening in humans, too.

People with mood disorders like depression often lose interest in pleasurable activities. For mice, one innately pleasurable activity is drinking sugar water. Since mice preferentially sip sugar water over plain tap when given the choice, Ceasrine measured their drink preference as an estimate for depression. Males, but not females, born by moms on a high-fat diet lacked a preference for simple syrup over tap water. This rodent-like depression suggested to Ceasrine that mom’s nutrition while pregnant must have changed their male offspring’s brain during development.

One immediate suspect was serotonin. Often called the “happy” chemical, serotonin is a molecular brain messenger that’s typically reduced in people with depression.

Ceasrine and her team found that depressed-like male mice from high-fat diet moms had less serotonin in their brain both in the womb and as adults, suggesting these early impacts have lifelong consequences. Supplementing mom’s high-fat rodent chow with tryptophan, the chemical precursor to serotonin, restored males’ preference for sugar water and brain serotonin levels. Still, it was unclear how fat accumulation in mom lowered serotonin in their offspring.

To get at this, the team investigated the resident immune cells of the brain: microglia.

Microglia are the understudied Swiss Army knives of the brain. Their jobs include serving as a security monitor for pathogens as well as a hearse to haul away dead nerve cells. Microglia also have ample space and appetites to consume healthy brain cells whole.

To see if microglia were overindulging in serotonin, Ceasrine analyzed the contents of their cellular “stomach”, the phagosome, with 3D imaging, and found that males born by moms on high-fat diets had microglia packed with more serotonin than those born to moms on a typical diet. This indicated that elevated fat accumulation during pregnancy somehow signals through the male but not female placenta to microglia and instructs them to overeat serotonin cells. How fat can signal through the placental barrier remained a mystery, though.

One thought was that bacteria were to blame.

“There's a lot of evidence that when you eat a high fat diet, you actually end up with endotoxemia,” Ceasrine said. “It basically means that you have an increase in circulating bacteria in your blood, or endotoxins, which are just parts of bacteria.”

To test if endotoxins could be the critical messenger from mom to enwombed males, the team measured their presence and found that, indeed, high-fat diets during pregnancy beefed up endotoxin levels in the placenta and their offspring’s developing brain. Ceasrine said this may explain how fat accumulation triggers an immune response from microglia by increasing the presence of bacteria, resulting in overconsumed brain cells in male mice.

To see whether this may be true of humans as well, Ceasrine teamed up with Susan Murphy, Ph.D., a Duke School of Medicine associate professor in obstetrics and gynecology, who provided placental and fetal brain tissue from a previous study. Just as the researchers observed in mice, they found that the more fat measured in human placental tissue, the less serotonin was detected in the brains of males but not females.

Bilbo and Ceasrine are now starting to work out how and why female offspring are impacted differently when mom amasses high levels of fat during pregnancy. Fat doesn’t lead to depression in female mice, but it does make them less social, perhaps due to an overconsumption of the pro-social hormone oxytocin, instead of serotonin.

For now, this research highlights that not all placentas are created equally. This work may one day help guide clinicians and parents in better understanding and possible treatment or prevention of the origins of some mood disorders by considering early environmental factors, like fat accumulation during gestation.

So, why would the placenta treat male and female fetuses differently? Ceasrine was initially stumped when a student asked a similar question after a talk she gave to Bilbo’s class. Bilbo laughed and reiterated the question. But now they think they have it figured out.

 “I was hugely pregnant at the time, and I was like, ‘Oh, wait. Pregnancy!’” Ceasrine recalled. “Men never have to carry a fetus, so they never have to worry about the kind of immune response of self versus non-self that you have to do when you're a woman and you carry a baby.”

Support for the research came from the US National Institutes of Health (F32HD104430, R01ES025549), the Robert and Donna Landreth Family Foundation, and the Charles Lafitte Foundation.

CITATION: “Maternal Diet Disrupts the Placenta-Brain Axis in a Sex-Specific Manner,” Alexis M. Ceasrine, Benjamin A. Devlin, Jessica L. Bolton, Lauren A. Green, Young Chan Jo, Carolyn Huynh, Bailey Patrick, Kamryn Washington, Cristina L. Sanchez, Faith Joo, A. Brayan Campos-Salazar, Elana R. Lockshin, Cynthia Kuhn, Susan K. Murphy, Leigh Ann Simmons, Staci D. Bilbo. Nature Metabolism, Nov. 28, 2022. DOI: 10.1038/s42255-022-00693-8

Human Evolution Wasn’t Just the Sheet Music, But How it Was Played

DURHAM, N.C. — A team of Duke researchers has identified a group of human DNA sequences driving changes in brain development, digestion and immunity that seem to have evolved rapidly after our family line split from that of the chimpanzees, but before we split with the Neanderthals.

Our brains are bigger, and are guts are shorter than our ape peers.

“A lot of the traits that we think of as uniquely human, and human-specific, probably appear during that time period,” in the 7.5 million years since the split with the common ancestor we share with the chimpanzee, said Craig Lowe, Ph.D., an assistant professor of molecular genetics and microbiology in the Duke School of Medicine.

Specifically, the DNA sequences in question, which the researchers have dubbed Human Ancestor Quickly Evolved Regions (HAQERS), pronounced like hackers, regulate genes. They are the switches that tell nearby genes when to turn on and off. The findings appear Nov.23 in the journal CELL.

The rapid evolution of these regions of the genome seems to have served as a fine-tuning of regulatory control, Lowe said. More switches were added to the human operating system as sequences developed into regulatory regions, and they were more finely tuned to adapt to environmental or developmental cues. By and large, those changes were advantageous to our species.

“They seem especially specific in causing genes to turn on, we think just in certain cell types at certain times of development, or even genes that turn on when the environment changes in some way,” Lowe said.

A lot of this genomic innovation was found in brain development and the GI tract. “We see lots of regulatory elements that are turning on in these tissues,” Lowe said. “These are the tissues where humans are refining which genes are expressed and at what level.”

Today, our brains are larger than other apes, and our guts are shorter. “People have hypothesized that those two are even linked, because they are two really expensive metabolic tissues to have around,” Lowe said. “I think what we’re seeing is that there wasn’t really one mutation that gave you a large brain and one mutation that really struck the gut, it was probably many of these small changes over time.”

To produce the new findings, Lowe’s lab collaborated with Duke colleagues Tim Reddy, an associate professor of biostatistics and bioinformatics, and Debra Silver, an associate professor of molecular genetics and microbiology to tap their expertise. Reddy’s lab is capable of looking at millions of genetic switches at once and Silver is watching switches in action in developing mouse brains.

“Our contribution was, if we could bring both of those technologies together, then we could look at hundreds of switches in this sort of complex developing tissue, which you can't really get from a cell line,” Lowe said.

“We wanted to identify switches that were totally new in humans,” Lowe said. Computationally, they were able to infer what the human-chimp ancestor’s DNA would have been like, as well as the extinct Neanderthal and Denisovan lineages. The researchers were able to compare the genome sequences of these other post-chimpanzee relatives thanks to databases created from the pioneering work of 2022 Nobel laureate Svante Pääbo.

“So, we know the Neanderthal sequence, but let's test that Neanderthal sequence and see if it can really turn on genes or not,” which they did dozens of times.

“And we showed that, whoa, this really is a switch that turns on and off genes,” Lowe said. “It was really fun to see that new gene regulation came from totally new switches, rather than just sort of rewiring switches that already existed.” 

Along with the positive traits that HAQERs gave humans, they can also be implicated in some diseases.

Most of us have remarkably similar HAQER sequences, but there are some variances, “and we were able to show that those variants tend to correlate with certain diseases,” Lowe said, namely hypertension, neuroblastoma, unipolar depression, bipolar depression and schizophrenia. The mechanisms of action aren’t known yet, and more research will have to be done in these areas, Lowe said.

“Maybe human-specific diseases or human-specific susceptibilities to these diseases are going to be preferentially mapped back to these new genetic switches that only exist in humans,” Lowe said.

Support for the research came from National Human Genome Research Institute – NIH (R35-HG011332), North Carolina Biotechnology Center (2016-IDG-1013, 2020-IIG-2109), Sigma Xi, The Triangle Center for Evolutionary Medicine and the Duke Whitehead Scholarship.

CITATION: "Adaptive Sequence Divergence Forged New Neurodevelopmental Enhancers in Humans," Riley J. Mangan, Fernando C. Alsina, Federica Mosti, Jesus Emiliano Sotelo-Fonseca, Daniel A. Snellings, Eric H. Au, Juliana Carvalho, Laya Sathyan, Graham D. Johnson, Timothy E. Reddy, Debra L. Silver, Craig B. Lowe. CELL, Nov. 23, 2022. DOI: 10.1016/j.cell.2022.10.016

Watch Lemurs Fatten up for Winter's Slumber

Video of Tubby tails v2

Holiday weight gain: It’s a real thing in this season of bread stuffing and pumpkin pie.

Many of us haven’t yet looked up from the pantry or holiday table to consider what all those extra calories can do to our waistlines. But one group of creatures at the Duke Lemur Center has been overindulging and plumping up for weeks already, and they’re not the least bit guilty about it.

Since August, the center’s 42 fat-tailed dwarf lemurs have been busy gorging themselves to pack on the pounds they need to survive their winter hibernation.

These squirrel-sized primates are our closest genetic relatives known to hibernate for extended periods of time. By studying how they withstand months of inactivity and yo-yo weight gain with no ill effects, researchers hope to find lessons for humans dealing with prolonged bed rest, diabetes and other challenges to metabolic health.

Fat-tailed dwarf lemurs get their name from their sausage-like tails (shown poking out while its owner explores a tunnel). Photo by David Haring. Some of us carry extra weight in our thighs. Others stash the stuff in a muffin top or a beer belly. As its name suggests, the fat-tailed dwarf lemur stores surplus fat in its sausage-like tail. After two months of feasting, a healthy dwarf lemur’s well-padded appendage can blimp out to 40% of its body weight.

Every week, Duke Lemur Center scientists have been monitoring the lemurs’ girth and watching the numbers creep up on the scale. Now the lemurs are the heaviest they’ve been all year. Nine-year-old Francolin is this year’s champion, having layered on enough fat to boost his weight by some 60% and double the chub in his tail.  

All this weight gain is a good thing, says research scientist Marina Blanco, who leads the project. It’s a matter of survival in their native habitat of Madagascar, where their fat reserves help sustain them through the leanest months of the year.

Soon, the animals will curl up and enter a state of suspended animation, dropping their heart rate from 180 beats per minute to as few as eight in order to stretch their onboard fuel for the months-long food coma ahead.

But for now, the lemurs still have business to attend to: breakfast.

On a crisp November morning, they smack and slurp as they wolf down what’s in their bowls: sweet bits of melons, peaches and nectarines, sprinkled with dried cranberries.

Nine-year-old Kiwi is the first to scurry to the food, followed by her daughter, Starling.

“As usual, Jaeger the dad is the last one to get up,” says researcher Lydia Greene.

A fat-tailed dwarf lemur feasts on figs at the Duke Lemur Center. Photo by David Haring.

Their breakfast menu is part of a new project: to steer them towards a more ‘natural’ seasonal diet. The idea is to see if the researchers can make the physiological swings and cycles these lemurs experience in captivity closer to what their counterparts experience in the wild.

Blanco has been ferreting out their wild counterparts in slumber chambers in Madagascar for years to understand how they pull it off.

While we might gain weight overdosing on cookies and eggnog, dwarf lemurs get fat on fruit. Wild dwarf lemurs fill up on persimmons, Grewia berries, and other sugar-rich fruits during the rainy season, in preparation for the subsequent dry season when such foods are in short supply.

It’s not possible to feed North Carolina’s lemurs exactly what they would eat in the tropical forests of Madagascar, so the researchers come up with alternatives that come close in terms of nutritional content.

A typical menu at the Duke Lemur Center might include 12 grams of fruits and veggies, 6 grams of monkey biscuits and a couple of mealworms. But their fall fattening diets follow a different recipe: half the protein, and twice as much sugar in the form of finely chopped pears, figs, kiwi, mangos, papayas. Topped with dried apricots, raisins, dates and the occasional drizzle of honey, this bounty is delivered each morning and midday by their keepers.

“I feel like that's the only time I cook, basically — preparing the food for the lemurs,” Blanco said.

Both diets contain the same number of calories. But they’ve found that dwarf lemurs fattened on a diet high in sugary fruit prior to hibernation followed more natural patterns of weight ups and downs, building up and then burning through their tail fat more like their wild peers. Their fat tissue was also more similar to the wild lemurs in composition.

Most of us want to get off the weight roller coaster. But for dwarf lemurs, such seasonal swings are the norm.

“I love the fattening. It’s one of my favorite times of year,” Greene says.

The findings were published this summer in the journal Proceedings of the Royal Society B.

Love handles of the lemur kind: For fat-tailed dwarf lemurs, bulking up is a survival strategy for when food is in short supply. Photo credit: Sara Clark Sorraia, Duke Lemur Center.

CITATION: "Of Fruits and Fats: High-Sugar Diets Restore Fatty Acid Profiles in the White Adipose Tissue of Captive Dwarf Lemurs," M. B. Blanco, L. K. Greene, L. N. Ellsaesser, B. Schopler, M. Davison, C. Ostrowski, P. H. Klopfer, J. Fietz and E. E. Ehmke. Proceedings of the Royal Society B, June 15, 2022. DOI: 10.1098/rspb.2022.0598

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Artemis Launches With Two Duke Experiments

Video of Duke Study Aboard Artemis I

NASA's return to the Moon began at 1:47 a.m. Wednesday with the launch of Artemis I, a giant rocket carrying two experiments from Duke researchers. 

While the uncrewed Orion capsule orbits the moon for the next three weeks, two instrumented dummies, Zohar and Helga, will collect data on radiation and other factors that may affect crew health. The human stand-ins were created by researchers at the Carl E. Ravin Advanced Imaging Laboratories at the Duke School of Medicine with researchers at NASA, the German Aerospace Center, the Israeli Space Agency and an instrumentation company called CIRS. 

Zohar wears a prototype radiation-proof vest, while Helga takes the full dose of space radiation.

Zohar wears a protective vest while Helga (foreground) takes one for the team.

Also aboard is a "Fuel to Mars" study designed by Dr. Tim Hammond of Duke Medicine and Dr. Holly Birdsall of the Durham VA and Baylor Medicine that will look at the genes and gene pathways enacted by a population of fuel-producing algae aboard the capsule as it experiences space radiation and microgravity. 

The Artemis launch had been delayed by technical difficulties and two hurricanes before finally reaching space Wednesday morning. The capsule, with algae and dummies, is expected to return to Earth for splash down in 25 days. 

'Some Places Will Not Be Livable'

Climate change is already forcing people to leave their homes, and millions more will follow in the years to come.

The Intergovernmental Panel on Climate Change found 3.3 to 3.6 billion people are highly vulnerable to climate change because of their location and circumstances.

Duke University is responding. Reflecting the Duke Climate Commitment, scholars have launched a new Program on Climate-Related Migration, working on transdisciplinary research to better understand the complex links between climate change and human mobility, and to inform policies that can help.

The co-directors of the new program, Sarah Bermeo and Kerilyn Schewel, joined fellow Duke scholars scholars Erika Weinthal and Drew Shindell in a conversation moderated by immigration reporter Dara Lind.

 

Here are excerpts:

WHY CLIMATE-RELATED MIGRATION RESEARCH IS IMPORTANT

Sarah Bermeo: “With the amount of climate change we are experiencing, some places will not be livable. Lives will be affected. Often the poor and disadvantaged will be affected most. We have to define the problem of climate-related migration and then get to solutions.”

Keriyn Schewel: “We need to get over the question of whether migration is good or bad, but rather how we deal with it.”

 

FACTORS INFLUENCING CLIMATE-RELATED MIGRATION

Erika Weinthal: “It is easy to fall into the narrative and assume that only climate-related events drive people to move, but it is important to understand how they interact with political economy considerations, such as in Syria.”

Schewel: “It can be hard to decipher slow climate risk onsets and ways to assist migrants in those settings. In cases of natural disaster, it’s more clear how to respond. We need to think of all of the legal pathways to facilitate people on the move and holistic strategies to respond to changing migration systems.”

Bermeo: “People leave their homes because of climate, but that is not why they leave their countries. There is external migration (outside of a country) when affected persons cannot find internal solutions (inside a country). One of the big problems is we don’t know how to quantify this migration. We don’t have data on climate-related migration. How do you build systems, then? We need to bring in natural sciences combined with social sciences and demographers; an interdisciplinary approach is the only pathway forward.”

 

TOOLS THAT CAN ADDRESS CLIMATE-RELATED MIGRATION

Drew Shindell: “We need to use a combination of earth systems observations and model projections to quantify areas that are more vulnerable. There are systems to look at polar ice sheets that can be used to look at climate-related migration. Through projections, we can also see that some areas are increasingly becoming too hot for people to live. We can use projections and data on current trends for policy and economic analysis.”

Weinthal: “There have been consistent warning trends and prediction from climate data for decades. But we are not quantifying how many people are on the move. Depending on politics at the time in a place, numbers can shift at any time. There are more variables that come into play with climate-related migration data. We should analyze climate data alongside information about economic resources and policies.”

Schewel: “Qualitative data is important to understand the decision criteria for migrants to support adaptation strategies. This means gathering information about how populations affected perceive climate change and how they decide where to stay or go.”

Sarah Bermeo, middle, speaks at the panel on climate-related migration

POLICY SOLUTIONS FOR CLIMATE-RELATED MIGRATION

Schewel: “Participatory approaches involving local communities are important to learn about effective adaptation strategies. Partnerships with local think tanks who have knowledge of countries can craft more practical policies.”

Bermeo: “We need to think about long-term solutions as well as policy quick wins. For example in Central America, invest in rural farmers and climate-smart agriculture to reduce the need to migrate from that region. Investing in adaptation in fragile regions could have short-term impacts for those who do not want to leave but are forced to go.”

 

Panelists:

Sarah Bermeo
Sarah Bermeo is a political economist and associate professor of public policy and political science in the Sanford School at Duke University, director of Graduate Studies (DGS) in the Master of International Development Policy (MIDP) program and co-director of PCRM. Her research lies at the intersection of international relations and development.

Kerilyn Schewel
Kerilyn Schewel is co-director of PCRM, a lecturing fellow at the Duke Center for International Development and senior researcher at the International Migration Institute. Her research examines how processes of development reshape patterns of human migration. 

Erika Weinthal
Erika Weinthal is professor of environmental policy and public policy at the Nicholas School of the Environment and professor of environmental policy at Duke Kunshan University. Weinthal specializes in global environmental politics and environmental security with a particular emphasis on water and energy.

Drew Shindell
Drew Shindell is Nicholas Distinguished Professor of Earth Science at the Nicholas School of the Environment. He studies climate change, air quality, and links between science and policy.

The Duke Program on Climate-related Migration is coordinated through the Duke Center for International Development (DCID) with support from the Duke Office of Global Affairs.

 

Watch a Virus in the Moments Right Before it Attacks

Video of How to Catch a Virus

DURHAM, N.C. — When Courtney “CJ” Johnson pulls up footage from her Ph.D. dissertation, it’s like she’s watching an attempted break-in on a home security camera.

The intruder cases its target without setting a foot inside, looking for a point of entry. But this intruder is not your typical burglar. It’s a virus.

Filmed over two and a half minutes by pinpointing its location 1,000 times a second, the footage shows a tiny virus particle, thousands of times smaller than a grain of sand, as it lurches and bobs among tightly packed human intestinal cells.

For a fleeting moment, the virus makes contact with a cell and skims along its surface but doesn’t stick before bounding off again. If this were an actual home break-in, Johnson says, “this would be the part where the burglar has not broken the window yet.”

Johnson is part of a Duke University team led by assistant chemistry professor Kevin Welsher. Together with Welsher’s postdoctoral associate Jack Exell and colleagues, they have come up with a way to capture real-time footage of viruses as they approach their cellular targets.

We inhale, ingest and take in millions of viruses every day. Most of them are harmless, but some of them — such as the viruses that cause the flu or COVID-19 — can make us sick.

Infection starts when a virus binds to and enters a cell, where it hijacks the cellular machinery to make copies of itself.  But before it can break in, a virus has to reach the cell first, Johnson said.

That often means getting through the protective layer of cells and mucus that line the airways and the gut — one of the body’s first lines of defense against infection.

The researchers wanted to understand how viruses breach these frontline defenses. “How do viruses navigate these complex barriers?” Welsher said. But these critical early moments before infection begins have long been difficult if not impossible to watch with existing microscopy methods, he added.

Part of the reason is that viruses move two to three orders of magnitude faster in the unconfined space outside the cell, compared with its crowded interior. To make things even trickier from an imaging perspective, viruses are hundreds of times smaller than the cells they infect.

“That's why this is such a hard problem to study,” Johnson said. Under the microscope, “it's like you're trying to take a picture of a person standing in front of a skyscraper. You can’t get the whole skyscraper and see the details of the person in front of it with one picture.”

So the team developed a new method called 3D Tracking and Imaging Microscopy (3D-TrIm), which essentially combines two microscopes in one. The first microscope “locks on” to the fast-moving virus, sweeping a laser around the virus tens of thousands of times per second to calculate and update its position. As the virus bounces and tumbles around in the soupy exterior of the cell, the microscope stage continuously adjusts to keep it in focus.

While the first microscope tracks the virus, the second microscope takes images of the surrounding cells. The combined effect, Welsher said, is akin to navigating with Google Maps: it not only shows your current location as you drive, it also shows the terrain, landmarks and the overall lay of the land, but in 3D.

“Sometimes when I present this work people ask, ‘is this a video game or a simulation?’” said Johnson, now a postdoctoral associate at the Howard Hughes Medical Institute Janelia Research Campus. “No, this is something that came from a real microscope.”

With their method the researchers can’t just, say, watch a healthy person breathe in virus particles from an infected person’s cough or sneeze. For one, they have to attach a special fluorescent label to a virus before they can track it — what the microscope follows is the movement of the glowing spot. And currently they can only track a virus for a few minutes at a time before it goes dim.

“The biggest challenge for us now is to produce brighter viruses,” Exell said.

But Welsher said he hopes the technique will make it possible to follow viruses in action beyond the coverslip, and in more realistic tissue-like environments where infections first take hold.

“This is the real promise of this method,” Welsher said. “We think that's something we have the possibility to do now.”

This work appeared online Nov. 10 in the journal Nature Methods.

This research was supported by a grant from the National Institutes of Health (R35GM124868).

CITATION: "Capturing the Start Point of the Virus-Cell Interaction With High-Speed 3D Single-Virus Tracking," Courtney Johnson, Jack Exell, Yuxin Lin, Jonathan Aguilar, and Kevin D. Welsher. Nature Methods, Nov. 10, 2022. DOI: 10.1038/s41592-022-01672-3

Mysterious Outbreak of Bone-Eating TB Resembled an Ancestral Form

Video of Blebbing Macrophages

DURHAM, N.C. –  Tuberculosis is usually encountered as a disease of the lungs, but in 2 percent of cases in the U.S. it can also be found in the bones. The 9,000-year-old skeletons of some Egyptian mummies show signs of having tuberculosis infection in their bones, a painful condition that leaves the bones looking like they’ve been gnawed. 

So it was a weird puzzle when Duke physician Jason Stout M.D. encountered a Wake County TB outbreak in the mid-2000s in which the infection had spread beyond the lungs in six people. “Four out of six were in the bone,” Stout said. “That’s way more than 2 percent.”

The index case, the first person in Raleigh to have this strain of the disease, apparently contracted the bacterium in Vietnam, but he wasn’t feeling very sick and had been working around 400 people in his workplace.

“So it was prolonged exposure in a workplace,” said Stout, a Duke professor of medicine who tracked down and identified seven subsequent infections through contact tracing and health department records.

All eight people were treated with antibiotics and other co-workers received preventative care and then the strange outbreak went away. But the mystery was never really solved. “I’m an epidemiologist and clinical trial specialist and I was left scratching my head,” Stout said.

Until several years later when Stout had a chance conversation with his colleague and TB researcher David Tobin, Ph.D., an associate professor in molecular genetics and microbiology and immunology at Duke.

“We met up and we're having coffee one day, and we're talking about this,” Stout recalls. Academic medical centers like Duke routinely keep biological specimens, and Stout still had samples of the puzzling bug. “David said, ‘Well, give it to me and we'll take a look.’ And then this amazing science came from that,” Stout said.

The amazing science is that Tobin’s lab, with several colleagues at Duke, Notre Dame, and the University of Texas, figured out precisely how and why these particular TB bacteria were so mobile. Their findings appear online Nov. 9 in the journal Cell.

“Certain infections tend to go certain places,” Stout said. “And the question is always, why does it do that?” In TB strains found in the Americas and Europe, the bacteria seem more likely to stay put in the lungs. But this strain was highly mobile.

Tobin’s team, led by Joseph Saelens, Mollie Sweeney and Gopinath Viswanathan, ran genetic sequencing on the Raleigh bug and found it most resembled an ancestral strain from a group of strains called lineage 1. In the U.S. we tend to see the modern strains, lineages 2, 3, and 4, but lineage 1 is still out there, mostly in South and Southeast Asia.

Mycobacterium tuberculosis generally infects a type of white blood cell called a macrophage, a highly mobile street sweeper cell that moves around looking for invaders and then engulfs them and chews them up. (Macrophage is Latin for big eater.) One part of the pathogenic bacteria’s toolkit is a set of unique chemical signals – secreted factors — to protect itself from the immune system and tell its macrophage host what to do.

Tobin’s team wanted to find the difference that allowed the Wake County bug’s macrophages to be more mobile and leave the lungs.

They compared genetic variants from 225 different strains of TB with particular attention to the genes for their secreted factors. What they found is a secretion factor called EsxM that was active in the Raleigh bacteria, but had been inactivated by a mutation in the modern strains.

Then, working with Craig Lowe, an evolutionary biologist and assistant professor of molecular genetics and microbiology at Duke, they looked at genetic sequencing from 3236 different strains of TB and found the pattern persisted: the modern strains have a silenced version of the EsxM secretion factor. “Over a few thousand strains, that really holds up,” Tobin said. “They’ve maintained that and presumably it’s something that’s evolutionarily advantageous to them.”

To further prove their point, the researchers put active versions of EsxM into safely attenuated versions of modern strains and watched as their macrophage hosts in a lab dish became more active and mobile. “We can see these changes in macrophage shape and structure and they become more migratory,” Tobin said. They also knocked out EsxM in a strain with the ancestral version and made the infected macrophages less mobile.

While being careful not to overstate their findings, Tobin said it would appear that the broadly distributed modern strains of TB benefit from staying within the lungs because of the way they spread through the air by breathing. Staying in the lungs would presumably give them a better launching pad to a new host.

Fortunately, the migratory TB strain hasn’t been seen again locally, Stout said, “hopefully because we did good work and got a lot of people preventative therapy.” But the mystery of its strange mobility has been solved.

“This may well have ended with me saying, ‘Wow, that was weird. There’s got to be something about the strain because all these patients had healthy immune systems,’” Stout said. “But the kind of science that I do is not the kind of science that David does. This is a wonderful example of people from different disciplines coming together to answer a really interesting clinical problem.”

This research was supported by the National Institutes of Health (AI-125517, AI-130236, AI-127115, AI-142127, AI-149147, AI-106872, 1DP2-GM146458-01, UC6-AI-058607).

CITATION: “An Ancestral Mycobacterial Effector Promotes Dissemination of Infection,” Joseph W. Saelens, Mollie I. Sweeney, Gopinath Viswanathan, Ana María Xet-Mull, Kristen L. Juric Smith, Dana M. Sisk, Daniel D. Hu, Rachel M. Cronin, Erika J. Hughes, W. Jared Brewer, Jörn Coers, Matthew M. Champion, Patricia A. Champion, Craig B. Lowe, Claire M. Smith, Sunhee Lee, Jason E. Stout, David M. Tobin. Cell, Nov. 9, 2022. DOI: 10.1016/j.cell.2022.10.019

Media Moments: Ashley Ward On Discussing Research With Reporters

Video of Ashley Ward | Media Moments

Many of Duke University’s faculty members often are called upon by the media for their expertise. It’s an opportunity to connect and educate not only members of the media, but through them, they connect and educate the public. Duke’s subject matter experts also benefit from the exchange in a number of ways. Ashley Ward, senior policy associate for engagement and outreach for the Internet of Water in the Nicholas Institute for Energy, Environment & Sustainability kicks off a new series we have dubbed Media Moments to discuss her experiences working with the media and why others should as well.

Three of 25 Science Diversity Leadership Awards Come to Duke

Two researchers from Duke University School of Medicine and one from Duke’s Department of Biology have been named recipients of the 2022 Science Diversity Leadership Awards from the Chan Zuckerberg Initiative.

Lawrence David, PhD, associate professor of molecular genetics and microbiology; Chantell Evans, PhD, assistant professor of cell biology; and Gustavo Silva, PhD, assistant professor of biology, were among 25 awardees named nationwide. Each grant recipient will be awarded a total of $1.15 million over five years.

Launched this year in partnership with the National Academies of Sciences, Engineering, and Medicine, The Science Diversity Leadership program recognizes the leadership and scientific accomplishments of excellent biomedical researchers who — through their outreach, mentoring, and teaching — have a record of promoting diversity, equity, and inclusion in their scientific fields.

Lawrence David’s project, “Sharing Open Source Software for Biomarker-Based Analysis of Diet,” will distribute open source bioinformatic tools and resources for analyzing biomarkers of food intake. These biomarkers can in turn can be used to study the origins and management of autoimmune, metabolic, and cardiovascular diseases.

“We are developing diet-tracking tools that are designed to overcome some of the barriers that underserved communities can face when completing traditional dietary surveys, like age, literacy, cultural background, potential anxiety due to stigmas around body weight, and time burdens,” David said. His project will bring these tools to researchers around the world through a series of workshops.

Chantell Evans’ project, “Investigating the Role of Mitochondrial Dysfunction in Neurodegenerative Diseases,” will investigate the breakdown of energy-producing mitochondria in neuron cells, hopefully offering new insights into neurodegenerative diseases such as Parkinson’s, ALS, and Alzheimer’s.

“This unique award gives me the opportunity to not only advance my research, it also supports my equity and inclusion efforts at Duke,” said Evans, who is also a Duke Science & Technology scholar.

Gustavo Silva’s project, “Deciphering the Functional Ubiquitinome in Health and Disease,” focuses on the cellular underpinnings of Nascimento Syndrome, a recently described and poorly understood set of symptoms including severe learning disabilities and motor coordination issues. Nascimento syndrome is known to be associated with a mutation in a gene called UBE2A, which is a regulator of cellular health.  

“When we look at an affected individual, we only see the final stage, the effect of all the integrated cellular processes that culminated in these particular symptoms,” Silva said. “But we don't know how we got there, what are the key events, or how the initial steps in this downstream cascade affect the whole organism.”  

Silva, who is the director of a Provost-sponsored and faculty-led initiative at Duke called Black Think Tank, said he is humbled and excited to be part of the CZI Initiative’s inaugural cohort in this diversity, equity and inclusion (DEI) program. 

“It’s really good to see the work that I've done in the DEI space also being professionally valued and appreciated, not only because I do it, but because I care about it,” Silva said.