If your ancestry in the United States stretches back more than 250 years, you may have Native American forbears. A new population genetics study shows that Americans with early European or early African ancestry can also have Native American gene groups.

Those Americans usually have family roots near the traditional homes of the respective tribes found in their genes, according to research led by the Georgia Institute of Technology. But where the descendants are today differs between these groups.

“People of Western European heritage have Native gene sequences from tribes that were located near where they now live,” said Andrew Conley, who led the study and is a research scientist in Georgia Tech’s School of Biological Sciences. “For African descendants, Native American ancestry looks like it came from regional groups of Native Americans in the southeastern United States.”

Many Americans descending from enslaved Africans later left the South in the Great Northward Migration, took those Native American sequences with them, and apparently no longer significantly reproduced with indigenous populations.

Americans with European heritage going back to Spain, mostly people who immigrated to the U.S. from Mexico, carry sequences from Native American ancestors who were traditionally located in what is Mexico today. This group also carries the most Native American genetic sequences by far, roughly 40% of their total genome, according to the study.

The researchers came to their conclusions by tracking haplotypes, patterns of genetic variants that are passed on by one parent, and that are typical for certain regions and peoples. They published their results in the journal PLoS Genetics on September 23, 2019.

“Haplotype combinations are very different between European, African and Native American ancestries and specific to locations,” Conley said.

The data was extracted from a much larger study, The Health and Retirement Study, sponsored by the National Institute on Aging (NIA) and conducted by the University of Michigan. That study also followed health and finance over time but included genomes and geography. Neither the NIA nor Michigan was part of the Georgia Tech study.

Americans of early African heritage have about 1.0% and of Western European heritage about 0.1% Native American haplotypes, though the difference in those numbers can be deceiving. The native ancestry probably lies a similar number of generations back for both groups.

“With African Americans, it correlates to about eight to nine generations back and probably ends there,” Conley said. “With Western European ancestors, we think about eight to 10 generations ago, and the contact with Native Americans could have also been more continuous.”

Further immigration from Europe likely dropped the percentage of Native American ancestry for the overall sample of Americans with Western European heritage.

“Particularly in the Mid-Atlantic and the Northeast there is almost no Native American ancestry among European descendants,” Conley said. “When you go out West, that’s where you have the most Native American ancestry in European populations.”

There was also an outlier group with European heritage from Spain.

“In parts of the Southwest, there are people of Spanish descent with also distinctive Native American ancestry. These groups call themselves Hispanos or Nuevomexicanos,” Conley said. “Their native American ancestry does not come from present-day Mexico. There were Spanish settlers in the region 400 years ago, and they could be the European ancestors of the Nuevomexicanos.”

The following coauthors from Georgia Tech collaborated on the study: King Jordan and Lavanya Rishishwar. Any findings, conclusions, or recommendations are those of the study’s authors.

Writer & Media Representative: Ben Brumfield (404-660-1408), email: ben.brumfield@comm.gatech.edu

Georgia Institute of Technology
177 North Avenue
Atlanta, Georgia  30332-0181  USA

Spasticity is a condition in which muscles are contract strongly, resulting stiffness or tightness, and quite often, pain. Usually caused by damage to the brain or spinal cord, it’s particularly common in people with neurological maladies like cerebral palsy or stroke.

Cerebral palsy (CP) is the most common cause of physical disability in children in most developed countries, and spastic CP is the most common form of the disorder. For these patients (and others), spasticity can be severely debilitating, negatively impacting their movement, speech, gait, and overall quality of life.

The lab of Lena Ting, professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory, and in the Division of Physical Therapy in Emory’s Department of Rehabilitation Medicine, is tackling the problem, shedding new light on issues underlying spasticity.

Ting’s lab is part of an international collaborative effort with a recently published research article in the open access scientific journal, PLOS One. She is corresponding author of, “Interaction between muscle tone, short-range stiffness and increased sensory feedback

gains explains key kinematic features of the pendulum test in spastic cerebral palsy: A

simulation study.”

The pendulum test is a sensitive clinical assessment of spasticity in which the lower leg is

dropped from the horizontal position and the features of leg motion are recorded. “This problem actually arose out of a homework problem for my Computational Neuromechanics class, where we simulate the leg as a pendulum,” said Ting.

In typically-developed people, the swinging leg behaves like a damped pendulum, with the angle of leg swing decreasing as it oscillates several times before coming to rest. In children with spastic CP, three key differences in the leg motion are observed: Reduced angle of leg swing in the first oscillation,  fewer oscillations, and the coming to rest at a less vertical angle.

Overall, the decrease in the first swing has been found to be the best predictor of spasticity severity, but why this is the case is has not been clear. Ting’s team hypothesized that increased muscle tone– the continual contraction of muscles while at rest­–accounts for both the reduced leg swing and the non-vertical resting leg angle. This idea contrasts with the clinical explanation of spasticity as an abnormal increase in the activation of reflexes as the leg is stretched with higher velocities. 

 “We were stumped because the clinical explanation of increased velocity-dependent reflexes didn’t generate realistic motion,” Ting said. “But we happened to be working on a different research project studying an interesting property of muscles called short-range stiffness, which increases when muscles are activated. We wanted to know if this very rapid rise and drop of resistive force in muscles when they are stretched could explain the parts of the pendulum test that were giving us a hard time in the simulation.”

So the researchers developed and tested a physiologically-plausible computer simulation of how muscle tone and reflexes would interact to reproduce key features of the pendulum test for spasticity across a range of severity levels. Their new model helps to explain a whole range of pendulum test kinematics in people with and without CP.

“Increased muscle tone plays a primary role in generating a key feature of the leg motion that is most closely related to the level of spasticity,” Ting explained. “Even when reflexes are increased,  can only account for pendulum test results across the spectrum of spasticity severity if we also increase muscle tone and short-range stiffness. This is exciting because the pendulum test is more objective than a clinician’s subjective assessment of leg stiffness. And with our model we can now begin to understand how multiple mechanisms of spasticity might interact to cause abnormal body motion, not just in the pendulum test, but in everyday movements.”

Lead author of the paper was Friedl De Groote, assistant professor in the Department of Movement Sciences at KU Leuven in Belgium. Other authors were both researchers from Ting’s lab, Kyle Blum and Brian Horslen.

Microbes live inside crowded communities in the environment and in hosts. Many wield a toxin-tipped harpoon called the Type 6 Secretion System (T6SS) to poke and kill competitors. The pathogenic bacterium Vibrio cholerae uses its T6SS weapon to survive in water and cause massive outbreaks of fatal cholera. In places like Yemen and Haiti, where water supplies are often contaminated and proper sanitation techniques are unavailable, cholera epidemics cause thousands of deaths. Only a few V. cholerae T6SS toxins have been described in prior studies that focused on outbreak strains, but the Hammer lab suspected novel toxins might be discovered by examining less-studied samples from environmental sources. In a collaborative study published in Genome Biology with Georgia Tech colleagues from the Jordan and Yunker labs, graduate students Cristian Crisan and Aroon Chande develop a computational tool, find several new T6SS toxins, and show that one of them is highly efficient at killing competitors. Currently, Cristian is studying the molecular mechanism by which another of the toxins can kill other cells.

True or false? Bacteria living in the same space, like the mouth, have evolved collaborations so generous that they are not possible with outside bacteria. That was long held to be true, but in a new, large-scale study of microbial interactions, the resounding answer was “false.”

Research led by the Georgia Institute of Technology found that common mouth bacteria responsible for acute periodontitis fared better overall when paired with bacteria and other microbes that live anywhere but the mouth, including some commonly found in the colon or in dirt. Bacteria from the oral microbiome, by contrast, generally shared food and assistance more stingily with gum infector Aggregatibacter actinomycetemcomitans, or Aa for short.

Like many bacteria known for infections they can cause – like Strep – Aa often live peacefully in the mouth, and certain circumstances turn them into infectors. The researchers and their sponsors at the National Institutes of Health would like to know more about how Aa interacts with other microbes to gain insights that may eventually help fight acute periodontitis and other ailments.

“Periodontitis is the most prevalent human infection on the planet after cavities,” said Marvin Whiteley, a professor in Georgia Tech’s School of Biological Sciences and the study’s principal investigator. “Those bugs get into your bloodstream every day, and there has been a long, noted correlation between poor oral hygiene and prevalence of heart disease.”

Unnatural pairing

The findings are surprising because bacteria in a microbiome have indeed evolved intricate interactions making it seem logical that those interactions would stand out as uniquely generous. Some mouth microbes even have special docking sites to bind to their partners, and much previous research has tightly focused on their cooperations. The new study went broad.

“We asked a bigger question: How do microbes interact with bugs they co-evolved with as opposed to how they would interact with microbes they had hardly ever seen. We thought they would not interact well with the other bugs, but it was the opposite,” Whiteley said.

The study’s scale was massive. Researchers manipulated and tracked nearly all of Aa’s roughly 2,100 genes using an emergent gene tagging technology while pairing Aa with 25 other microbes — about half from the mouth and half from other body areas or the environment.

They did not examine the mouth microbiome as a whole because multi-microbial synergies would have made interactions incalculable. Instead, the researchers paired Aa with one other bug at a time — Aa plus mouth bacterium X, Aa plus colon bacterium Y, Aa plus dirt fungus Z, and so on.

“We wanted to see specifically which genes Aa needed to survive in each partnership and which ones it could do without because it was getting help from the partner,” said Gina Lewin, a postdoctoral researcher in Whiteley’s lab and the study’s first author. They published their results in the Proceedings of the National Academy of Sciences.

Q & A

How could they tell that Aa was doing well or poorly with another microbe?

The researchers looked at each of Aa’s genes necessary for survival while it infected a mouse -- when Aa was the sole infector, when it partnered with a fellow mouth bacterium and when paired with a microbe from colon, dirt, or skin.

“When Aa was by itself, it needed a certain set of genes to survive – like for breathing oxygen,” Lewin said. “It was striking that when Aa was with this or that microbe that it normally didn’t live around, it no longer needed a lot of its own genes. The other microbe was giving Aa things that it needed, so it didn’t have to make them itself.”

“Interactions between usual neighbors — other mouth bacteria — looked more frugal,” Whiteley said. “Aa needed a lot more of its own genes to survive around them, sometimes more than when it was by itself.”

^{[Ready for graduate school? Here's how to apply to Georgia Tech.]} 

How did the emerging genetic marking method work?

To understand “transposon sequencing,” picture a transposon as a DNA brick that cracks a gene, breaking its function. The brick also sticks to the gene and can be detected by DNA sequencing, thus tagging that malfunction.

Every Aa bacterium in a pile of 10,000 had a brick in a random gene. If Aa’s partner bacterium, say, E. coli, picked up the slack for a broken function, Aa survived and multiplied even with the damaged gene, and researchers detected a higher number of bacteria containing the gene.

Aa surviving with more broken genes meant a partner microbe was giving it more assistance. Aa bacteria with broken genes that a partner could not compensate for were more likely to die, reducing their count.

Does this mean the mouth microbiome does not have unique relationships?

It very likely does have them, but the study’s results point to not all relationships being cooperative. Some microbiomes could have high fences and share sparsely. 

“One friend or enemy may be driving your behavior, and other microbes may just be standing around,” Lewin said.

Smoking, poor hygiene, or diabetes — all associated with gum disease — might be damaging defensive microbiomes and allowing outside bacteria to help Aa attack gum tissue. It’s too early to know that, but Whiteley’s lab wants to dig deeper, and the research could have implications for other microbiomes.

Also read: Test for Life-Threatening Nutrient Deficit Made From Bacteria Entrails

These researchers coauthored the study: Apollo Stacy from the National Institute of Infectious Diseases and the National Institute of General Medical Sciences, Kelly Michie from Georgia Tech, and Richard Lamont from the University of Louisville. The research was funded by the National Institutes of Health’s National Institute of Infectious Diseases (grants R01DE020100, R01DE023193) and the National Institutes of Health (grants F32DE027281, F31DE024931). Any findings, conclusions or recommendations are those of the authors and not necessarily those of the National Institutes of Health. Whiteley is also a Georgia Research Alliance Eminent Scholar and Co-Director of Emory-Children’s Cystic Fibrosis Center.

Writer & Media Representative: Ben Brumfield (404-660-1408), email: ben.brumfield@comm.gatech.edu

Georgia Institute of Technology
177 North Avenue
Atlanta, Georgia  30332-0181  USA

Serious nature lovers and forest hikers might keep track of wildlife by the shape of animal droppings on the trail. Deer leave a pile of pellets, a large tubular mass suggests a bear, whereas smaller tubules indicate a fox. What about scat that is shaped like ice cubes?

In southeastern Australia, cube-shaped scat is found around the home range of wombats. These marsupials have been likened to a hybrid between a pig, a bear, and a gopher. They have another distinction: They are the only known animals that excrete cubic feces.

How wombats produce the distinctively shaped poop has been of interest to the research teams of Georgia Tech mechanical engineering professor David Hu and Scott Carver, a lecturer in wildlife ecology in University of Tasmania, Australia. Wombats are poised to gain acclaim, because Hu, Carver, and their coworkers just received a 2019 Ig Nobel Prize, awarded by Improbable Research for research that initially makes people laugh and then think.

What seven-year-old would not be mesmerized by the idea of bringing a stop watch to the bathroom to check the claim that all mammals pee in about 20 seconds or tickled with the hilarity of a gif image of a wet dog shaking off water?

The 2019 Ig Nobel is the second for Hu, who also has appointments in the Georgia Tech School of Biological Sciences and School of Physics. Hu is a leading expert in the biomechanics of animal locomotion, from the wet-dog shake, to the lightning-fast tongues of frogs, to the wagging of elephant tails, and more.

Hu is also an expert in fluid dynamics, including of biological fluids like urine. With then-Ph.D. student Patricia Yang, Hu reported in 2015 that the average urination time of mammals is about 20 seconds. That finding earned Hu and Yang their first Ig Nobel Prize. 

FIRST WE LAUGH

Yang extended her studies to defecation. In one conference, she proposed a mathematical theory suggesting that the average time for mammals to move their bowels is 12 seconds. According to Hu’s account in Australasian Science last spring, “A scientist raised his hand and said that his 8-year-old children were fascinated by cubic wombat feces,” Hu wrote. “Could our theory account for that shape? This is the first time we heard of such a thing, so we searched for the feces on our phones and were amazed.”

Curious, Hu recruited students to research wombats. They found Carver, one of the world’s few experts on wombats, who studies them for conservation. “They face a lot of threats from animals, humans, and diseases,” he says.  Currently, he studies the wombats’ affliction with sarcoptic mange, or scabies, which can be fatal to whole populations. As such, Carver receives calls from a Tasmanian wildlife sanctuary when wombats have been humanely put down by a veterinarian.

Carver opens the cadaver with a slice from the mouth to the anus to gain access to tissues and organs for his biological work. The first time he did this, he was surprised by another wombat distinction: the extraordinarily long intestines, about 33 feet. In contrast, human intestines are only 23 feet long. Partially because of wombats’ long colons, Carver says, “wombat scat is dry. Human colons are not that long; we don’t pull as much water from feces.”

The dissections revealed something else: “My lab discovered that the cubes formed in the intestine,” Carver says. That discovery dismissed the idea that the cubes formed by passing through a square-shaped sphincter.

With wombat intestines supplied by Carver, Hu’s team began investigating. Before working on the specimen, they practice with pig intestine sourced from the Asian supermarket the Great Wall. They also create models made of cloth to try to mimic how the cubes are formed.

Last summer undergraduate researchers Kelly Qiu and Michael Kowalski joined the wombat team. A third-year biomedical engineering major, Qiu says she got interested in the work after reading about Yang’s research and “how they blew up intestines with balloons.” She says the research is “an enjoyable experience.”

As part of this research Kowalski, a fourth-year biomedical engineering major, has learned how to sew. “We’re sewing cloth to replicate the intestine. We do it in Paper & Clay. We put sewing lines to create the stiff regions of the intestine.” That’s because the team found that the wombat intestine is not uniformly flexible. Some parts are rigid. Some parts are soft.

As Hu writes in Australasian Science: “As brown slurry fills the intestine, a stiff zone would resist bending in that particular region. Four such stiff zones could create the tell-tale four walls of the cube. The corners of the cube would be a consequence of the intermediary soft zones.”

That’s the hypothesis for now. The cloth models are part of the process of testing the hypothesis. Alexander Lee, a Ph.D. student of Hu’s, is working on a theoretical model. “Can we also recreate cubic poop in a math simulation?” he asks. “Can we make other shapes come up? Right now, we mostly get potatoes.”

Not surprisingly, Hu’s research on animal locomotion and biological fluids has attracted much mainstream coverage. What seven-year-old would not be mesmerized by the idea of bringing a stop watch to the bathroom to check the claim that all mammals pee in about 20 seconds or tickled with the hilarity of a gif image of a wet dog shaking off water?

Alas, popularity is a double-edged sword. Those two studies, and another on eyelashes, caught the eye of then-Senator Jeff Flake, of Arizona. In Flake’s 2016 list of the top 20 most wasteful uses of government fund, three were work by Hu. 

"The easiest questions are still among the most difficult to answer."

THEN WE THINK

Hu rebutted with a guest blog, “Confessions of a Wasteful Scientist,” in Scientific American.

“[M]ost of what animals do is completely a mystery to scientists. When I was a student, I thought that 95 percent of all knowledge was already solved. But in fact, we only understand a small amount of the world around us, especially in the world of biology. For example, we can’t understand why a dog walks as easily as it does. Robots still cannot move as well as dogs, which have a complex interplay of tendons, bones and specially placed sensors that make it look like magic. The easiest questions are still among the most difficult to answer,” Hu wrote.

According to Hu, the wet-dog shake study is relevant to clothes drying, which takes up a lot of energy. The study of eyelashes could help explain how allergens enter the eye. And the urination study could be used as an early, noninvasive way to detect urinary malfunction as people age.

“This science helps us learn about the natural world. It’s extremely unusual to get a cube out of what looks like a tube. So there is a manufacturing side to this.” Carver says. “Pure science has been incredibly productive in finding something useful for humans that didn’t have a clear application. Lasers and many other useful things have come about because of people looking just out of curiosity.”

"Lasers and many other useful things have come about because of people looking just out of curiosity.”

“Not at all!” Yang says when asked whether winning two Ig Nobels might be a black mark on her professional record. “It actually promotes my science. It attracts people who are interested in my research. After the Ig Nobel, my paper got downloaded 10 times as much as before.”

In fact, Yang says, “the application side for this research could be an early screening for colon cancer. Because with colon cancer, the tissue starts getting harder. That will change the shape of feces.”

Editor's note: Here is an update on the information at minute 1:36 in the video: The Center for Relativistic Astrophysics, which currently occupies the next space to be renovated, is now slated to move into the Klaus Building to form a new interdisciplinary research neighborhood focusing on astrophysics and planetary sciences. 

Relentless construction in Georgia Tech makes it hard to keep track of what’s done and what’s just started. Earlier this year, the renovated first floor of the Gilbert Hillhouse Boggs building opened for business without fanfare. In the spring 2019 semester, upper-level laboratory courses in physics and biology quietly moved to spaces fashioned out of old offices and research labs.

On the outside, Boggs looks the same as it was in the 1970s, when it was built. But come in and you might exclaim, “Wow! I had no idea Boggs could look like this,” as Juan Archila says he has heard many people say. As the College of Sciences’ director of facilities and capital planning, Archila was heavily involved in the building’s makeover. 

Repurposed Mingles with State-of-the-Art

The main drivers of the Boggs first-floor upgrade are safety, accessibility, and sustainability. “We now have windows between the biology labs,” Archila says. All door also have windows, “to create transparency and to promote safety and accountability.” For students with disabilities, labs now have benches that are shorter than standard.

Budget for the project was tight, Archila says. In the spirit of sustainability and economy, usable materials were reused. “We didn’t completely gut the old spaces,” Archila says. “We repurposed and moved a lot of the cabinetry.”

Amid the repurposed cabinets are state-of-the-art equipment.

“Last year we received Tech Fee Funds to purchase nine Class II Biological Safety Cabinets,” says Alison Onstine, laboratory manager in the School of Biological Sciences. Each cabinet is six feet long and can accommodate two students working side by side. These equipment expand the hands on experience for students in handling cells, as well as organisms that require Biosafety Level 2.

More equipment is forthcoming, including an ultra-low-temperature freezer for specimen preservation, fluorescent microscopes, incubators for microbial work, and additional physiology equipment. 

Improvements in Learning and Instruction

Upper-level biology lab courses are now in Boggs, including genetics, microbiology, cell and molecular biology, anatomy, and physiology. Labs for advanced physics courses, as well as electronics and optics, also have moved to Boggs.

The advanced physics labs were previously taught in two small rooms in the Howey Building, says Claire Berger, a professor of the practice in the School of Physics who teaches the lab courses. In Boggs, “we have so much more space! It is clean and well-organized.

“It allows for more experiments to be set up and in better conditions. For example, the labs now have three separate dark rooms, equipped with water sinks, for the optical experiments.

“The labs are also less cluttered, therefore better in terms of safety. Because the teaching environment is less noisy, we can have one-to-one teaching on each of the individual experiments, as well as group teaching with a large, well-lit white board.”

The biology labs now in Boggs previously were taught in spaces spread across three floors of the Cherry Emerson Building. Now they are in one floor, sharing preparation rooms and equipment. “In Boggs, we have a strong nucleus that brings together the biology teaching lab community,” Onstine says.

“We have, for the first time, office spaces for teaching assistants and instructors to meet with students in close proximity to the labs,” Onstine says. “Additional benefits include two new shared equipment labs accessible to everyone, bringing our most advanced equipment within easy reach of students – including a bench-top flow cytometer, fluorescent plate readers, real-time PCR machines. These equipment spaces located between two teaching labs have promoted an open plan which we hope will create more connectivity between our core upper-level lab courses.” 

With the advanced chemistry labs in the second-floor, Boggs has become an interdisciplinary space for upper-level science majors, Archila says. “People who are focused on different majors see each other. That’s when you realize that a lot of people are attacking the same problem, just from different angles. It makes sense for Georgia Tech to establish that culture from the very beginning.”

“We are fortunate to share the floor with a new neuroscience teaching lab and to be one floor away from the chemistry teaching labs,” Onstine says. She thinks this layout will foster interaction and interdisciplinary research among students of different majors.