The amazing ability of sidewinder snakes to quickly climb sandy slopes was once something biologists only vaguely understood and roboticists only dreamed of replicating. By studying the snakes in a unique bed of inclined sand and using a snake-like robot to test ideas spawned by observing the real animals, both biologists and roboticists have now gained long-sought insights.

In a study published in the October 10 issue of the journal Science, researchers from the Georgia Institute of Technology, Carnegie Mellon University, Oregon State University, and Zoo Atlanta report that sidewinders improve their ability to traverse sandy slopes by simply increasing the amount of their body area in contact with the granular surfaces they’re climbing.

As part of the study, the principles used by the sidewinders to gracefully climb sand dunes were tested using a modular snake robot developed at Carnegie Mellon. Before the study, the snake robot could use one component of sidewinding motion to move across level ground, but was unable to climb the inclined sand trackway the real snakes could readily ascend. In a real-world application – an archaeological mission in Red Sea caves – sandy inclines were especially challenging to the robot.

However, when the robot was programmed with the unique wave motion discovered in the sidewinders, it was able to climb slopes that had previously been unattainable. The research was funded by the National Science Foundation, the Army Research Office, and the Army Research Laboratory.

“Our initial idea was to use the robot as a physical model to learn what the snakes experienced,” said Daniel Goldman, an associate professor in Georgia Tech’s School of Physics. “By studying the animal and the physical model simultaneously, we learned important general principles that allowed us to not only understand the animal, but also to improve the robot.”

The detailed study showed that both horizontal and vertical motion had to be understood and then replicated on the snake-like robot for it to be useful on sloping sand.

“Think of the motion as an elliptical cylinder enveloped by a revolving tread, similar to that of a tank,” said Howie Choset, a Carnegie Mellon professor of robotics. “As the tread circulates around the cylinder, it is constantly placing itself down in front of the direction of motion and picking itself up in the back. The snake lifts some body segments while others remain on the ground, and as the slope increases, the cross section of the cylinder flattens.”

At Zoo Atlanta, the researchers observed several sidewinders as they moved in a large enclosure containing sand from the Arizona desert where the snakes live. The enclosure could be raised to create different angles in the sand, and air could be blown into the chamber from below, smoothing the sand after each snake was studied. Motion of the snakes was recorded using high-speed video cameras which helped the researchers understand how the animals were moving their bodies.

“We realized that the sidewinder snakes use a template for climbing on sand, two orthogonal waves that they can control independently,” said Hamid Marvi, a postdoctoral fellow at Carnegie Mellon who conducted the experiments while he was a graduate student in the laboratory of David Hu, an associate professor in Georgia Tech’s School of Mechanical Engineering. “We used the snake robot to systematically study the failure modes in sidewinding. We learned there are three different failure regimes, which we can avoid by carefully adjusting the aspect ratio of the two waves, thus controlling the area of the body in contact with the sand.”

Limbless animals like snakes can readily move through a broad range of surfaces, making them attractive to robot designers.

"The snake is one of the most versatile of all land animals, and we want to capture what they can do," said Ross Hatton, an assistant professor of mechanical engineering at Oregon State University who has studied the mathematical complexities of snake motion, and how they might be applied to robots. "The desert sidewinder is really extraordinary, with perhaps the fastest and most efficient natural motion we've ever observed for a snake."

Many people dislike snakes, but in this study, the venomous animals were easy study subjects who provided knowledge that may one day benefit humans, noted Joe Mendelson, director of research at Zoo Atlanta.

“If a robot gets stuck in the sand, that’s a problem, especially if that sand happens to be on another planet,” he said. “Sidewinders never get stuck in the sand, so they are helping us create robots that can avoid getting stuck in the sand. These venomous snakes are offering something to humanity.”

The modular snake robot used in this study was specifically designed to pass horizontal and vertical waves through its body to move in three-dimensional spaces.  The robot is two inches in diameter and 37 inches long; its body consists of 16 joints, each joint arranged perpendicular to the previous one.  That allows it to assume a number of configurations and to move using a variety of gaits – some similar to those of a biological snake.

“This type of robot often is described as biologically inspired, but too often the inspiration doesn’t extend beyond a casual observation of the biological system,” Choset said. “In this study, we got biology and robotics, mediated by physics, to work together in a way not previously seen.”

Choset’s robots appear well suited for urban search-and-rescue operations in which robots need to make their way through the rubble of collapsed structures, as well as archaeological explorations. Able to readily move through pipes, the robots also have been tested to evaluate their potential for inspecting nuclear power plants from the inside out.

For Goldman’s team, the work builds on earlier research studying how turtle hatchlings, crabs, sandfish lizards, and other animals move about on complex surfaces such as sand, leaves, and loose material. The team tests what it learns from the animals on robots, often gaining additional insights into how the animals move.

“We are interested in how animals move on different types of granular and complex surfaces,” Goldman said. “The idea of moving on flowing materials like sand can be useful in a broad sense. This is one of the nicest examples of collaboration between biology and robotics.”

In addition to those already mentioned, co-authors included Chaohui Gong and Matthew Travers from Carnegie Mellon University; and Nick Gravish and Henry Astley from Georgia Tech.

This research was supported by the National Science Foundation under awards CMMI-1000389, PHY-0848894, PHY-1205878, and PHY-1150760; by the Army Research Office under grants W911NF-11-1-0514 and W911NF1310092; and by the Army Research Lab MAST CTA under grant W911NF-08-2-0004; and by the Elizabeth Smithgall Watts endowment at Georgia Tech. The opinions expressed are those of the authors and do not necessarily represent the official views of the sponsoring agencies.

CITATION: Hamidreza Marvi et al., “Sidewinding with minimal slip: snake and robot ascent of sandy slopes,” Science 2014).

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The sheer volume of cyanobacteria in the oceans makes them major players in the global carbon cycle and responsible for as much as a third of the carbon fixed. These photosynthetic microbes, which include Prochlorococcus and Synechococcus, are tiny – as many as 100 million cells can be found in a single liter of water – and yet they are not the most abundant entities on Earth. That distinction goes to viruses, up to 100 million of which can be found per 1 mL of seawater. However, researchers know very little about the viruses in the water, other than that there are three kinds of viruses, and that they are capable of drastically decreasing cyanobacterial populations, affecting the global regulation of biogeochemical cycles.

Owls are mostly nocturnal animals that depend on stealth to catch their prey. With the help of their wing structure, they also helped create the world’s most famous high-speed train by making it less noisy.

Flamingos are famous because of their pink color, which comes from the tiny creatures they filter from the water and eat. But it’s their fast-moving, mysterious beaks that may provide practical uses for people as they contemplate the kitchen faucets of the future.

Highlighting these unexpected similarities between what animals do and what people are trying to do is a new strategy Georgia Institute of Technology researchers are using to hopefully increase public awareness about animals and encourage conservation. They’ve created an iPhone app based on biologically inspired design, highlighting two dozen species that have helped engineers solve problems or invent new solutions.

“Learning that owls eat rodents is interesting, but explaining how they’ve helped us invent new technologies is a more effective way of getting us interested in the natural world,” said Marc Weissburg. The Georgia Tech professor led the app project and is co-director of the Institute’s Center for Biologically Inspired Design.

Owl wings are built to disperse air pressure, which allows them to fly silently to sneak up on their watchful prey. Engineers used the same principle to design the super-fast, and super-quiet, Shinkansen bullet train. Flamingos pump water in and out of their mouths at a speed of four pumps a second while eating. They use their beaks to strain water and trap their food. Researchers are studying their bills to construct water filters of the future.

The app also features zebras (keeping ships cool), elephants (transforming floors and walls into speaker systems) and rattlesnakes (all-terrain robots).

The ZooScape app, which also includes a game that tests a user’s knowledge of the animals and their contributions, can be used by anyone, anywhere. It becomes interactive at Zoo Atlanta. The app uses GPS to send notifications to the guests’ smartphones whenever they visit an exhibit of an animal that has contributed a biologically inspired design.

“There’s so much we have learned and still have to learn about animals. They’re experts at navigating their environments successfully, and it turns out that sometimes all we have to do to improve our own systems and efficiency is to sit back and watch them do what they already do so well,” said Joe Mendelson, a Georgia Tech adjunct professor and Zoo Atlanta’s director of herpetological research. “Zoo Atlanta is proud to partner with Georgia Tech on groundbreaking studies that elevate the profile of wildlife while also helping people.”

Zoo Atlanta is the first facility to use ZooScape, although creators built it with other zoos and aquariums in mind. The app was developed and designed by Weissburg,  Leanne West and Brian Parise from the Georgia Tech Research Institute, with funds from the Smithgall Watts endowment to the School of Biology. Proceeds will fund further development of similar materials for outreach and public education.

Microbes of interest to clinicians and environmental scientists rarely exist in isolation. Organisms essential to breaking down pollutants or causing illness live in complex communities, and separating one microbe from hundreds of companion species can be challenging for researchers seeking to understand environmental issues or disease processes. 

A new National Science Foundation-supported project will provide computational tools designed to help identify and characterize the gene diversity of the residents of these microbial communities. The project, being done by researchers at the Georgia Institute of Technology and Michigan State University, will allow clinicians and scientists to compare the genomic information of organisms they encounter against the growing volumes of data provided by the world’s scientific community.

The tools will be hosted on a web server designed to be used by researchers who may not have training in the latest bioinformatics techniques. A prototype system containing a limited number of computational tools is already available at http://enve-omics.ce.gatech.edu and is attracting more than 500 users each month.

“Across many areas of science, we are dealing with communities of microorganisms, and one challenge we’ve had is to identify them because we haven’t had good tools to tell apart individual microbes from the mixtures,” said Kostas Konstantinidis, an associate professor in the School of Civil and Environmental Engineering at Georgia Tech and the project’s principal investigator. “Our tools will be designed to deal with the genomes of whole communities of organisms.”

Current techniques identify individual microbes by examining their small subunit ribosomal RNA (SSU rRNA) genes, but the new tools will allow scientists to analyze entire genomes and meta-genomes.

“With the dawn of the genomic era, we can now get the whole genome of these organisms to see not only the ribosomal RNA, but also all the genes in the genome to get a better understanding of what the each organism’s potential might be,” said Konstantinidis. “There will be many advantages for looking at all the genes instead of just one, the SSU rRNA, such as to identify which organisms encode toxins or the enzymes for breaking down pollutants.”

Collaborators on the three-year project include scientists who operate the Ribosomal Database Project at Michigan State University: Jim Tiedje, director of Michigan State University’s Center for Microbial Ecology and James Cole, a Michigan State University research assistant professor and director of the Ribosomal Database Project.

The ability to identify and enumerate the organisms in complex communities using culture-independent, genomic technologies and associated bioinformatics algorithms is becoming more important as scientists study organisms that can’t be grown in the lab. The majority of the world’s organisms resist traditional lab culture, meaning they have to be studied in the field and identified through genetic information.

Konstantinidis and his research group are studying such communities in the water of lakes in Chattahoochee River system in Georgia and elsewhere. They are examining how these communities respond to perturbations, such as oil or pesticide spills, and the role that different members of the community play in breaking down pollutants.

“These tools actually come from our research practice,” said Konstantinidis. “We came to the point where we couldn’t process the data to answer the questions we wanted to ask. That led us to this new project to develop the tools we and others need to interrogate the data and get the information we are looking for.”

A single liter of lake water may contain as many as 500 different species, and together, their genomic information can total tens of billions of gene-coding letters. From Lake Lanier alone, the team has generated 200 gigabytes of genomic data.

“We want to figure out what organisms are there, and what genes they encode,” Konstantinidis explained. “The tools we are developing will allow us to do this.”

The tools developed in the project will be useful to both clinical microbiologists and environmental researchers. “This will not be specific to any one discipline,” he said. “As long as people are working with microbes, this will be helpful to them because some of the questions are universal.”

The system will also be built to provide user-friendly help to scientists who may not have training in the latest genomic and bioinformatics techniques. “There is a big need for big data analysis, and there are not many trained people right now,” Konstantinidis said. “These tools will make the lives of researchers easier.”

Among the challenges ahead is building an infrastructure able to handle the growing amounts of genomic information produced worldwide.

“We will have to develop some computational solutions for the problems of keeping up with all the new data becoming available,” said Konstantinidis. “We need to make tools that have high throughput to keep up with data volumes that are increasing geometrically.”

The system will initially operate on servers at Georgia Tech and Michigan State University, but if demand and data grow, additional resources may be sought, such as the National Science Foundation’s XSEDE supercomputer.

This research is supported by the National Science Foundation under award DBI-1356288. The opinions expressed in this article are those of the authors and do not necessarily reflect the official views of the National Science Foundation.

Kostas Konstantinidis is the Carlton S. Wilder Junior Faculty Professor in the Georgia Tech School of Civil and Environmental Engineering.

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A species of small fish uses a homemade coral-scented cologne to hide from predators, a new study has shown, providing the first evidence of chemical camouflage from diet in fish.

Filefish evade predators by feeding on their home corals and emitting an odor that makes them invisible to the noses of predators, the study found. Chemical camouflage from diet has been previously shown in insects, such as caterpillars, which mask themselves by building their exoskeletons with chemicals from their food. The new study shows that animals don’t need an exoskeleton to use chemical camouflage, meaning more animals than previously thought could be using this survival tactic.

“This is the very first evidence of this kind of chemical crypsis from diet in a vertebrate,” said Rohan Brooker, a post-doctoral fellow in the School of Biology at the Georgia Institute of Technology in Atlanta. “This research shows that you don’t need an exoskeleton that for this kind of mechanism to work.”

The study was published December 10 in the journal Proceedings of the Royal Society B. The study was sponsored by the ARC Centre of Excellence for Coral Reef Studies and the Ecological Society of Australia. The work was done as a part of Booker’s doctoral research at James Cook University in Australia. 

Anyone who has watched a nature documentary has seen insects that camouflage themselves as sticks, protecting the insects against predators that use vision to hunt for prey. But many animals see the world through smell rather than sight, and cunning critters from among them have adapted clever ways of smelling like their surroundings. A certain species of caterpillar, for example, smells like the plant that it lives on and eats. The caterpillar incorporates chemicals from the plant into its exoskeleton. Ants hunting for the caterpillar will walk right over it, none the wiser.

For the new study, researchers traveled to Australia’s Lizard Island Research Station in the Great Barrier Reef, where they collected filefish. To show that filefish smelled like their home coral, the researchers recruited crabs to sniff them out. The filefish were fed two different species of coral; each species of coral is home to a unique species of crab. The crabs were given a choice between a filefish that had been fed the crab’s home coral and a filefish that had been fed a coral that is foreign to the crab. The crabs always sought the filefish that had been feeding on the crabs home coral. The filefish smelled so strongly of coral that sometimes the crabs were attracted to the fish instead of coral, when given a choice between the two.

“We can tell that there is something going through the filefish diet that’s making the fish smell enough like the coral to confuse the crabs,” Booker said.

To see if the chemical camouflage gives the filefish an evolutionary advantage to evade predators, the researchers tested cod to see how they responded to filefish that had been fed various diets. Cod, filefish and corals were put in a tank, with the filefish hidden from the cod. When the filefish diet didn’t match the corals in the tank, the cod were restless, suggesting that they smelled food. When the filefish diet matched the corals in the tank, the cod stayed tucked away in their cave inside the tank.

The next step in the project is to learn how filefish can smell like coral without the benefit of an exoskeleton. Some evidence shows that amino acids in the mucus of fish – where much of their smell originates – will match their diet, but much work remains to tease apart this pathway.

“We have established that there is some kind of pathway from filefish diet to filefish odor,” Booker said. “This is just the first study. There’s a lot of work still to be done to understand how it works.”

Booker is now working in the lab of Danielle Dixson, an associate professor of biology at Georgia Tech.

This research is supported by the ARC Centre of Excellence for Coral Reef Studies and the Ecological Society of Australia. Any conclusions or opinions are those of the authors and do not necessarily represent the official views of the sponsoring agencies.

CITATION: Rohan Brooker, et al., “You are what you eat: diet-induced chemical crypsis in a coral-feeding fish.” (Proceedings of the Royal Society B, December 2014). http://rspb.royalsocietypublishing.org/content/282/1799/20141887

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Ribonucleotides, units of RNA, can become embedded in genomic DNA during processes such as DNA replication and repair, affecting the stability of the genome by contributing to DNA fragility and mutability. Scientists have known about the presence of ribonucleotides in DNA, but until now had not been able to determine exactly what they are and where they are located in the DNA sequences.

Now, researchers have developed and tested a new technique known as ribose-seq that allows them to determine the full profile of ribonucleotides embedded in genomic DNA. Using ribose-seq, they have found widespread but not random incorporation and “hotspots” where the RNA insertions accumulate in the nuclear and mitochondrial DNA of a commonly-studied species of budding yeast. Ribose-seq could be used to locate ribonucleotides in the DNA of a wide range of other organisms, including that of humans.

“Ribonucleotides are the most abundant non-standard nucleotides that can be found in DNA, but until now there has not been a system to determine where they are located in the DNA, or to identify specifically which type they are,” said Francesca Storici, an associate professor in the School of Biology at the Georgia Institute of Technology. “Because they change the way that DNA works, in both its structure and function, it is important to know their identity and their sites of genomic incorporation.”

A description of the ribose-seq method and what it discovered in the DNA of the budding yeast species Saccharomyces cerevisiae were reported January 26 in the journal Nature Methods. The findings resulted from collaboration between researchers in Storici’s laboratory at Georgia Tech – with graduate students Kyung Duk Koh and Sathya Balachander – and at the University of Colorado Anschutz Medical School with assistant professor Jay Hesselberth.

The research was supported by the National Science Foundation, the Georgia Research Alliance, the American Cancer Society, the Damon Runyon Cancer Research Foundation, and the University of Colorado Golfers Against Cancer.

Because of the extra hydroxyl (OH) group in the ribonucleotides, their presence distorts the DNA and creates sensitive sites where reactions with other molecules can take place. Of particular interest are reactions between the OH and alkaline solutions, which can make the DNA more susceptible to cleavage.

Ribose-seq takes advantage of this reaction with the hydroxyl group to launch the process of identifying the genomic spectrum of ribonucleotide (rNMP) incorporation. Researchers first cleave the DNA samples at the ribonucleotides, then take the resulting fragments through a specialized process that concludes with generation of a library of DNA sequences that contain the sites of ribonucleotide incorporation and their upstream sequence. High-throughput sequencing of the library and alignment of sequencing reads to a reference genome identifies the profile of rNMP incorporation events.

“Ribose-seq is specific to directly capturing ribonucleotides embedded in DNA and does not capture RNA primers or Okazaki fragments formed during DNA replication, breaks or abasic sites in DNA,” Storici noted.

“For this reason, ribose-seq has application for rNMP mapping in any genomic DNA, from large nuclear genomes to small genomic molecules such as plasmids and mitochondrial DNA, with no need of standardization procedures,” she said. “It also allows mapping rNMPs even in conditions in which the DNA is exposed to environmental stressors that damage the DNA by generating breaks and/or abasic sites.”

The extra hydroxyl group found in the ribonucleotides is key to the ribose-seq technique, said Koh, the paper’s first author. “The OH group is specific to the ribonucleotides,” he explained. “That allowed us to build a new tool for recognizing specifically where the ribonucleotides are located.”

The high-throughput sequencing and initial data analysis were done in the Hesselberth laboratory in the Department of Biochemistry and Molecular Genetics at the University of Colorado Anschutz Medical School.

To validate their method, the researchers tested ribose-seq on the much-studied yeast species. The analyses revealed a strong preference for the cytidine and guanosine bases at the ribonucleotide sites.

“The ribonucleotides are not randomly distributed, and there is some preference for specific base sequences and specific base composition of the ribonucleotide itself,” said Koh. “By looking at the non-random distribution, we found several hotspots in which the ribonucleotides are incorporated into the genome.”

Knowledge of where the ribonucleotides cluster could help identify areas of greatest potential for genome instability and lead to a better understanding of how they affect the properties and activities of DNA.

“The fact that we see biases in the base compositions of the ribonucleotides allows us to tell which base is more likely to be incorporated into the DNA,” Koh explained. “If there are specific signatures of genomic instability that are caused by the ribonucleotides, this will allow us to narrow down the locations and know where they are more likely to be found.”

A next step will be to test ribose-seq on other DNA, Koh said. “Our technique could potentially be applied to any genome of any cell type from any organism as long as genomic DNA can be extracted from it,” he added. “It is independent of specific organisms.”

Beyond repair and replication processes, ribonucleotides can also be created in DNA as a result of damage caused by drugs, environmental stressors and other factors. The ribose-seq method could also allow scientists to study the impact of these processes.

“Ribose-seq should allow us to better understand the impact of ribonucleotides on the structure and function of DNA,” said Storici. “Identifying specific signatures of ribonucleotide incorporation in DNA may represent novel biomarkers for human diseases such as cancer, and other degenerative disorders.”

This material is based upon work supported by the National Science Foundation (NSF) under grant number MCB-1021763, by the Georgia Research Alliance under award number R9028, by the American Cancer Society, by the Damon Runyon Cancer Research Foundation and by the University of Colorado Golfers Against Cancer. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the sponsoring agencies.

CITATION: Kyung Duk Koh, Sathya Balachander, Jay Hesselberth and Francesca Storici, “Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA,” (Nature Methods, 2015). http://dx.doi.org/10.1038/nmeth.3259

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For swimming through sand, a slick and slender snake can perform better than a short and stubby lizard.

That’s one conclusion from a study of the movement patterns of the shovel-nosed snake, a native of the Mojave Desert of the southwest United States. The research shows how the snake uses its slender shape to move smoothly through the sand, and how its slippery skin reduces friction – both providing locomotive advantages over another sand-swimmer: the sandfish lizard native to the Sahara Desert of northern Africa.

The study provides information that could help explain how evolutionary pressures have affected body shape among sand-dwelling animals. And the work could also be useful in designing search and rescue robots able to move through sand and other granular materials.

Using X-ray technology to watch each creature as it moved through a bed of sand, researchers studied the waves propagating down the bodies of both the snakes and sandfish lizards. Granular resistive force theory, which considers the thrust provided by the body waves and the drag on the animals’ bodies, helped model the locomotion and compare the energy efficiency of the limbless snake against that of the four-legged lizard – which doesn’t use its legs to swim through the sand.

“We were curious about how this snake moved, and once we observed its movement, how it moved so well in the sand,” said Dan Goldman, an associate professor in the School of Physics at the Georgia Institute of Technology. “Our model reveals how both the snake and the sandfish move as fast as their body shapes permit while using the least amount of energy. We found that the snake’s elongated shape allowed it to beat the sandfish in both speed and energy efficiency.”

Information about the factors enabling the snake to move quickly and efficiently could help the designers of future robotic systems. “Knowing how the snake moves could be useful, for instance, in helping robots go farther on a given amount of battery power,” Goldman said.

Supported by the National Science Foundation and the Army Research Office, the research was published online December 18, 2014, in the Journal of Experimental Biology. The study is believed to be the first kinematic investigation of subsurface locomotion in the long and slender shovel-nosed snake, Chionactis occipitalis.

Measurements made by former Ph.D. student Sarah Sharpe revealed that the snake propagates traveling waves down its body, from head to tail, creating a body curvature and a number of waves along its body that enhance its movement through the sand. As a consequence of the kinematics, the snake’s body travels mostly in the same “tube” through the sand that is created by the movement of its wedge-shaped head and body.

Because the snake essentially follows its own tracks through the sand, the amount of slip generated by its motion is small, allowing it to move through the sand using less energy than the sandfish (Scincus scincus), whose movement pattern generated a larger fluidized region of sand around its body.

Overall, the research showed that each animal had optimized its ability to swim through the sand using its specific body plan.

“For each body wave the snake generates, it moves farther than the sandfish does within a single wave of motion of its body,” Goldman noted. “Having a long and slender body allows the snake to bend its body with greater amplitude while generating more waves on its body, making it a more efficient sand swimmer.”

The snake’s skin is also more slippery than that of the sandfish, further reducing the amount of energy required to move through the sand.

Scientists had suspected that long and slender animals would have a sand-swimming advantage over creatures with different body shapes. The research showed that the advantage results from a high length-to-width ratio that allows the formation of more waves.

“If you have the right body shape and slick skin, you can get a very low cost of transport,” explained Goldman.

To study the snakes as they moved through sand, Sharpe – from Georgia Tech’s Interdisciplinary Bioengineering Program – and undergraduate Robyn Kuckuk, from the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, glued tiny lead markers onto the scales of the snakes. The markers, which fall off when the snakes shed their skin, allowed the researchers to obtain X-ray images of the snakes moving beneath the surface of the sand. Sharpe, now a biomechanical engineer with a research and consulting firm in Phoenix, created detailed videos showing how the snakes moved.

Associate professor Patricio Vela and graduate student Miguel Serrano, both from Georgia Tech’s School of Electrical and Computer Engineering, developed software algorithms that allowed detailed analysis of the wave-forms seen on the X-ray movies as a function of time.

Stephan Koehler, a research associate in applied physics at Harvard University, applied Resistive Force Theory to obtain data on the snakes’ movement and energy efficiency. Animals swimming in sand can only move if the thrust provided by their bodies exceeds the drag created. The theory predicted that the snakes’ skin would have about half as much friction as that of the sandfish, and that prediction was verified experimentally.

Joe Mendelson, director of research at Zoo Atlanta, assisted the research team in obtaining and managing the snakes.

Understanding how animals move through granular materials like sand could help the designers of robotic systems better understand how to optimize the use of energy, which can be a significant limiting factor in robotics.

“This research is really about how body shape and form affect movement efficiency, and how we can go between experiment and theory to improve our understanding of these issues,” said Goldman. “What we are learning could help search and rescue robots maneuver in complex terrain and avoid obstacles.”

Beyond the robotics concerns, the work can help scientists understand biological issues, such as how the body plans of desert-dwelling lizards and snakes converge to optimize their ability to move through their environment.

“These granular swimming systems turn out to be quite useful for understanding fundamental questions about evolutionary biology, biomechanics and energetics because they are simple to analyze and they can describe a good number of systems,” Goldman added.

This material is based upon work supported by the National Science Foundation (NSF) under grant number PHY-0749991 and PHY-1150760, and by the Army Research Office (ARO) under grant number W911NF-11-1-0514. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or the Army Research Office.

CITATION: Sarah Sharpe, et al., “Locomotor benefits of being a slender and slick sand swimmer,” (Journal of Experimental Biology, 2014). http://www.dx.doi.org/10.1242/jeb.108357

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When oil from the Deepwater Horizon spill first began washing ashore on Pensacola Municipal Beach in June 2010, populations of sensitive microorganisms, including those that capture sunlight or fix nitrogen from the air, began to decline. At the same time, organisms able to digest light components of the oil began to multiply, starting the process of converting the pollutant to carbon dioxide and biomass.

Once the lightest fractions of the oil had been consumed, the organisms that had been digesting those compounds declined, replaced by others able to chew up the remaining heavier materials. Ultimately, a year after the spill, the oil had mostly disappeared and microbial populations buried in the beach sands looked much like they had before the spill, though there were as-yet unexplained differences.

That's the scenario observed by scientists who have studied the oil’s impact on the complex microbial communities – which contain hundreds of single-celled organisms – on this one Gulf Coast beach. Using advanced genomic identification techniques, they saw a succession of organisms and identified population changes in specific organisms that marked the progress of the bioremediation. They also identified the specific genes contained in the oil-eating microbes and the enzymes they used at different stages of the process.

The research, reported online this week in The ISME Journal, could help scientists better understand the microbial succession process that results from such environmental perturbations, and perhaps lay the groundwork for research aimed at accelerating bioremediation. The project represents a collaboration between professors at the Georgia Institute of Technology and Florida State University: Kostas Konstantinidis from the Georgia Tech School of Civil and Environmental Engineering, Joel Kostka from the Georgia Tech School of Biology, and Markus Huettel, professor of Earth, Ocean and Atmospheric Sciences at Florida State.

The research was supported by the National Science Foundation, and by the BP/Gulf of Mexico Research Initiative to the Deep-C Consortium.

“We observed the succession of organisms whose populations rose and fell as the degradation of the oil proceeded,” said Konstantinidis. “We also identified the indicator organisms that show the ecosystem’s response at different stages in the process. Knowing these indicators could help those who must manage these kinds of spills in the future.”

Oil began flowing into the Gulf of Mexico from the Deepwater Horizon rig in mid-April of 2010, but did not reach the Pensacola Municipal Beach until June 22. That allowed time for scientists from Georgia Tech and Florida State University to obtain samples of beach microorganism communities well before the oil began arriving.

Much of the oil reaching the beaches was cleaned up mechanically, though some became buried in the sand. Digging trenches in the beach, Huettel from Florida State took samples at regular intervals for one year after the oil came ashore, and quantified the petroleum hydrocarbon compounds present in the beach sand.

Using advanced meta-genomics technology, which studies the entire community, members of the team from Georgia Tech determined the relative abundances of certain organisms and how they changed over time, providing a clear view of the succession process. As many as ten species of microbes participated at each stage of the bioremediation.

“What is really special about this study is that we provide a robust meta-genomic time series that shows how shifts or changes in microbial populations closely paralleled the chemical evolution of the petroleum hydrocarbons,” said Kostka. Added Konstantinidis: “We have identified which organisms and which genes are important at every stage of the biodegradation process on the beaches.”

Beach communities contain hundreds of different microbes, and as many as 20 percent of them responded to the oil, Konstantinidis said. Those organisms for which the oil was toxic declined dramatically when the oil began reaching the beaches, but had mostly returned a year later.

“When we looked at the microbial communities a year after the spill and compared them to what we saw before the spill, we saw differences, but the communities were very similar to what we saw before the oil arrived,” he said. “You could tell confidently that the system had recovered, but it was not exactly the same community or same state. That’s something we’d like to study further and examine on other beaches.”

Other researchers have evaluated the fate of oil that remained in the Gulf waters.

Konstantinidis said it’s likely the oil washing up on the beaches had significantly different degradation kinetics than the oil that remained in the water columns. Oil containing lighter fractions would be easier to digest by the microbes that normally exist as part of beach communities.

Researchers had expected to see the oil favoring the growth of microbes specific to particular parts of the oil degradation process. While the researchers saw dramatic changes in the communities over time, they saw that “generalist” microbes – those that were the most flexible metabolically – were most successful in expanding their populations.

“These generalist microbes are always around on the beaches or in the water, so you will always have them to break down oil spills,” he said.

In future work, the team would like to study how key ecosystem services like nutrient cycling are directly impacted by microbial community changes from oiling as well as the factors that limit the growth of biodegrading organisms. Important controls for biodegradation include oxygen levels, available nutrients and even competing microbes. If these factors are better understood, the process of digesting oil from spills might be accelerated.

“It took almost a year for the oil to disappear,” Konstantinidis said. “We want to know what are limiting factors for the process that might be addressed. These microbes can take a long time, so if we can figure out how to make the process faster, it would be very helpful.”

This work was supported in part by the National Science Foundation award numbers 1241046, OCE-1057417 and OCE-1044939, an NSF graduate research fellowship to Will Overholt, and by grant SA-12-12, GoMRI-008 from the BP/Gulf of Mexico Research Initiative to the Deep-C Consortium. Any opinions expressed in this article are those of the authors and do not necessarily reflect the official views of the sponsoring organizations.

CITATION: Rodrigues-R, Luis M., et al., “Microbial community successional patterns in beach sands impacted by the Deepwater Horizons oil spill,” (The ISME Journal, 2015).

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When a Lake Malawi cichlid loses a tooth, a new one drops neatly into place as a replacement. Why can't humans similarly regrow teeth lost to injury or disease?

Working with hundreds of these colorful fish, researchers are beginning to understanding how the animals maintain their hundreds of teeth throughout their adult lives. By studying how structures in embryonic fish differentiate into either teeth or taste buds, the researchers hope to one day be able to turn on the tooth regeneration mechanism in humans – which, like other mammals, get only two sets of teeth to last a lifetime.

The work, which also involved a study of dental differentiation in mice, shows that the structures responsible for growing new teeth may remain active for longer than previously thought, suggesting that the process might be activated in human adults.

The research was conducted by scientists from the Georgia Institute of Technology in Atlanta and King’s College in London, and published October 19 in early edition of the journal Proceedings of the National Academy of Sciences. The research was supported by the National Institute of Dental and Craniofacial Research, part of the U.S. National Institutes of Health.

“We have uncovered developmental plasticity between teeth and taste buds, and we are trying to understand the pathways that mediate the fate of cells toward either dental or sensory development,” said Todd Streelman, a professor in the Georgia Tech School of Biology. “The potential applications to humans makes this interesting to everybody who has dealt with dental issues at one time or another in their lives.”

Worldwide, approximately 30 percent of persons have lost all their teeth by the time they reach the age of 60. Beyond the painful dental health issues, this can causes significant medical and nutritional problems that can shorten life.

To understand more about the pathways that lead to the growth and development of teeth, Streelman and first author Ryan Bloomquist – a DMD/PhD student at Georgia Tech and Georgia Regents University – studied how teeth and taste buds grow from the same epithelial tissues in embryonic fish. Unlike humans, fish have no tongues, so their taste buds are mixed in with their teeth, sometimes in adjacent rows.

The Lake Malawi cichlids have adapted their teeth and taste buds to thrive in the unique conditions where they live. One species eats plankton and needs few teeth because it locates its food visually and swallows it whole. Another species lives on algae which must be scraped or snipped from rocky lake formations, requiring both many more teeth and more taste buds to distinguish food.

The researchers crossed the two closely-related species, and in the second generation of these hybrids, saw substantial variation in the numbers of teeth and taste buds. By studying the genetic differences in some 300 of these second-generation hybrids, they were able to tease out the genetic components of the variation.

“We were able to map the regions of the genome that control a positive correlation between the densities of each of these structures,” Streelman explained. “And through a collaboration with colleagues at King’s College in London, we were able to demonstrate that a few poorly studied genes were also involved in the development of teeth and taste buds in mice.”

By bathing embryonic fish in chemicals that influence the developmental pathways involved in tooth and taste bud formation, the researchers then manipulated the development of the two structures. In one case, they boosted the growth of taste buds at the expense of teeth. These changes were initiated just five or six days after the fish eggs were fertilized, at a stage when the fish had eyes and a brain – but were still developing jaws.

“There appear to be developmental switches that will shift the fate of the common epithelial cells to either dental or sensory structures,” Streelman said.

Though they have very different purposes and final anatomy, teeth and taste buds originate in the same kind of epithelial tissue in the developing jaws of embryonic fish. These tiny buds differentiate later, forming teeth with hard enamel – or soft taste buds.

“It’s not until later in the development of a tooth that it forms enamel and dentine,” said Streelman. “At the earliest stages of development, these structures are really very similar.”

The studies in fish and mice suggest the possibility that with the right signals, epithelial tissue in humans might also be able to regenerate new teeth.

“It was not previously thought that development would be so plastic for structures that are so different in adult fish,” Streelman said. “Ultimately, this suggests that the epithelium in a human’s mouth might be more plastic than we had previously thought. The direction our research is taking, at least in terms of human health implications, is to figure out how to coax the epithelium to form one type of structure or the other.”

But growing new teeth wouldn’t be enough, Streelman cautions. Researchers would also need to understand how nerves and blood vessels grow into teeth to make them viable.

"The exciting aspect of this research for understanding human tooth development and regeneration is being able to identify genes and genetic pathways that naturally direct continuous tooth and taste bud development in fish, and study these in mammals,” said Professor Paul Sharpe, a co-author from King’s College. “The more we understand the basic biology of natural processes, the more we can utilize this for developing the next generation of clinical therapeutics: in this case how to generate biological replacement teeth."

As a next step, Streelman and research technician Teresa Fowler are working to determine how far into adulthood the plasticity between teeth and taste buds extends, and what can trigger the change.

In addition to those already mentioned, the research included Nicholas Parnell and Kristine Phillips from Georgia Tech, and Tian Yu from King’s College.

This research is supported by the National Institute of Dental and Craniofacial Research, part of the U.S. National Institutes of Health, under grants 2R01DE019637 (to J.T.S.) and 5F30DE023013 (to R.F.B.). Any opinions or conclusions are those of the authors and may not necessarily represent the official views of the NIH.

CITATION: Ryan F. Bloomquist, et al., “Co-Evolutionary Patterning of Teeth and Taste Buds,” (Proceedings of the National Academy of Sciences, 2015). http://www.pnas.org/content/early/2015/10/15/1514298112

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Writer: John Toon

When teaching Introduction to Organismal Biology (BIO 1520), Linda Green likes to tap into students’ curiosity by taking a fresh look at familiar occurrences.

“There are a lot of things in biology that people never think about,” said Green, senior academic professional in the School of Biology. “We see it every day, but most people never consider that the way a plant on a windowsill bends toward the light is a function of a hormone in the shoot and the cells elongating. In class, we pick apart why the plant is growing sideways and discuss what is involved in the process. That’s something that the students may not come in wanting to know, but it’s a way that I can connect with their curiosity.”

This is Green’s eighth year at Georgia Tech. Before coming to Tech she was already familiar with the campus because she grew up in Norcross, Georgia, and both of her parents are Tech alumni. Her dad earned a B.S. in chemical engineering and a master’s in nuclear engineering and was a practicing nuclear engineer, and her mom majored in and taught mathematics.

Read More: Go 'In the Classroom' with Linda Green.