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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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.

A century ago, being an explorer meant trekking across icy wastelands, scaling impossibly high mountains or spending months at sea in search of new lands, unseen creatures and new scientific knowledge. Today’s explorers may travel by airliner, but the organisms they see, what they explore and the scientific data they bring back are no less important.

Understanding what's killing the world's coral reefs has been the life work of Mark Hay, the Teasley Professor in the School of Biology at the Georgia Institute of Technology. During the past 35 years, he's made more than 5,000 dives, worked weeks at a time underwater in both the Caribbean and Pacific – and each year spends as much as five months with villagers on the Fiji Islands.

On November 7, he received the Lowell Thomas Award from the New York-based Explorers Club, which cited his pioneering of innovative and effective new approaches for coral reef conservation. “Dr. Hay’s research and discoveries have influenced the foundations in the field of marine chemical ecology and created new procedures for effective conservation and management of the world’s coral reefs,” the organization said.

Hay notes that over the last 40 years, the world has lost 80 percent of coral reefs in Caribbean and 50 percent of the reefs in the Pacific. That loss has broad impacts.

“For about a billion people around the world in the tropics, coral reefs are one of the major sources of protein, so the loss affects food security for these areas,” he noted. “Reefs also provide storm protection for low-lying villages, absorbing big waves coming into shore. And coral reefs are kind of the underwater version of tropical rain forests because they have significant unexplored potential as a source of new therapeutic drugs.”

Hay’s research has focused on the complex interactions between species, communicated by chemical signals emitted by the plants and animals that are part of the reef community. For instance, seaweeds harm coral by emitting poisonous chemicals, by shading the coral, and by mechanically damaging it. Certain fish protect coral by controlling the seaweeds, but overfishing has allowed seaweed to get out of control on many reefs.

“We have asked which fish can get rid of those chemically-rich seaweeds, so we can tell villagers which species they can catch without harming the reefs, and which species they may want to protect,” he said. “We are trying to understand enough of the pieces and parts to know how we can work with local villagers. We can’t mandate what they do, but we can inform them and their culture will take care of it from there.”

The demise of coral reefs likely has many causes, and Hay acknowledges that he cannot address them all. But he believes that by understanding the details of the ecosystem, tweaking some factors – such as which fish to protect – can have an impact.

“We want to switch from cataloging the demise to asking how we can fix things,” he said. “We are looking at it more or less like a molecular scientist or human health researcher would. We’re asking what are the chemical signals involved, and whether there are opportunities to make minor adjustments that can have huge benefits.”

Among recent examples, Hay and collaborators have learned that degraded reefs produce chemicals that tell baby fish and baby corals to stay away. Unless those signals can somehow be changed, damaged reefs won’t have a chance to recover.

Many coral reef organisms lack hearing or vision. Instead, they must rely for their information on chemical signals provided by other organisms.

“We’ve realized that many of these species are behaving based primarily on chemical cues,” he explained. “They are perceiving the world chemically and reacting to that. Simple phytoplankton in the ocean can smell their neighbors being attacked, and from the smell, can identify who’s attacking and then respond in appropriate ways – by changing their shape or chemistry.”

At Georgia Tech, Hay keeps an office and lab. But the majority of his experiments are conducted in the wild, on the coral reef, building cages to determine what happens when certain species are excluded and to learn about interactions between plants and animals.

“I really have Georgia Tech’s biggest lab – the world,” he explained. “We try not to extract things from nature to ask how species are interacting. We try to find that out in nature. We spend huge amounts of time underwater. We’re wearing wet suits and we’re up to our necks in mud and water all day.”

Previous winners of the Lowell Thomas award, named after the noted broadcaster, have included Edwin “Buzz” Aldrin, Jr., Isaac Asimov, Sir David Attenborough, Robert Ballard, Eugenie Clark, Sylvia A. Earle, Sir Edmund Hillary, Carl Sagan, Kathryn D. Sullivan and Charles E. “Chuck” Yeager. The organization has 3,200 members worldwide.

The Explorers Club was founded in 1904, and boasts a membership that was first to the North Pole, the first the South Pole, the first to the summit of Everest, the first to the deepest point of the ocean – and first to the surface of the moon. With all those accomplishments on record, does that mean the time of exploration is past?

“I think this is the time of maximal exploration,” said Hay. “There is more exploration going on right now than has ever gone on before. I’ve been to more places around the world than any pirate. The amount of information we’re gathering – which is exploration and finding out new things about the world – is tremendous.”

What keeps him going after all these years?

“I love being underwater and seeing new things,” Hay said. “Everybody is trying to get lunch without becoming lunch. I’m always wondering about who eats who, what goes on, and the intricacies of the ecology and evolution.”

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Media Relations Contact: John Toon (jtoon@gatech.edu) (404-894-6986).
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The Center for Integrative Genomics (CIG) isn’t new. It just feels that way.

“We’re rebooting,” says CIG Director Greg Gibson, professor in the Georgia Institute of Technology’s School of Biology and faculty member of the Parker H. Petit Institute for Bioengineering and Bioscience. “We’ve got critical mass now, so the time is right for a reboot.”

Gibson is kind of like a head football coach rebuilding his game plan around a new combination of talented core personnel. But instead of a multi-threat quarterback, nimble wide receivers and tenacious offensive linemen, CIG is counting on a diverse team of biologists, engineers and other researchers to carry out work that can impact the future of medicine.

“Over the past several years we’ve attracted about half a dozen people who have expertise in quantitative genetics and analysis of human genomes, and that’s in addition to another half a dozen who were already here,” says Gibson.

The CIG team is comprised mostly of faculty from the School of Biology, including Gibson, King Jordan, Joe LaChance, Annalise Paaby, Todd Streelman, Fred Vannberg and Soojin Yi. CIG’s other faculty members are Melissa Kemp, Peng Qiu, Eberhard Voit and May Wang from the Wallace H. Coulter Department of Biomedical Engineering.

Gibson’s research collaborators include the Predictive Health Institute and multiple pediatric autoimmune disease experts at Emory University, the Georgia Tech Center for Computational Health (headed by Jimeng Sun and Jim Rehg in the School of Computational Science and Engineering) and Bruce Weir's statistical genetics team at the University of Washington.  Other CIG investigators similarly engaged in dozens of national and international collaborators are expanding the reach of the Center.

They bring a wide-range of interest areas and skill sets to the CIG mix, including but not limited to bioinformatics, machine learning, single cell imaging, computational modeling, the evolution of behavior, infectious disease, human population genetics, cardiovascular disease, electronic medical records, and cryptic genetic variation, or CGV, which refers to unexpressed, bottled-up genetic potential that can fuel evolution – nature’s curveball, served up under abnormal conditions, and a concept that interests researchers like Gibson and Paaby, for example.

“It’s not a theme you find commonly in human genetics right now,” says Gibson. “But it’s something we feel is a very important part of personalized medicine.”

Gibson figures that the CIG’s multi-disciplined team of pioneering scientists and engineers will also serve as an excellent recruiting tool – to attract graduate students, as well as future grant opportunities.

“We have a strong nucleus to carry out the real objective of the center, which is to provide a genetics focus for the systems biology and genomics initiatives on campus. It’s pretty much what I envisaged when I first got here,” says Gibson, who came to Georgia Tech in 2009 following a professorial fellowship at University of Queensland in his native Australia.

“Genetics is a big part of contemporary biology,” he adds. “And if we’re looking ahead, it’s a big part of anything to do with predictive health and personalized medicine.”

Center for Integrative Genomics

CONTACT:

Jerry Grillo
Communications Officer II
Parker H. Petit Institute for
Bioengineering and Bioscience

Georgia Institute of Technology researchers combed through more than two dozen studies and did surface measurements for 27 mammals and insects to better understand how animals are able to clean themselves. The findings could have implications for keeping manmade structures – such as sensors, robots and unmanned aerial vehicles – free from pollutants, pollen and dirt. The review study is published in the Journal of Experimental Biology.  

The research team focused on the many ways hair allows animals to both get dirty and remain dirt-free. The researchers found that a honeybee has the same amount of hairs as a squirrel: 3 million. That’s nothing compared to butterflies and moths – each have nearly 10 billion hairs. The human head, as a comparison, has just 100,000.

“Animals likely evolved with hair in order to stay warm. But it also brings a burden,” said David Hu, a Georgia Tech associate professor who co-led the study. “More hair means more surface area that can trap dirt, dust and pollen.”

Hu and his mechanical engineering Ph.D. student, Guillermo Amador, ran calculations to find the true surface area of animals, or the surface area that includes every location where dirt can be collected. The hairier it is, the larger the creature’s true surface area. In fact, the team says it’s 100 times greater than its skin surface area.

“A honeybee’s true surface area is the size of a piece of toast,” said Hu. “A cat’s is the size of a ping pong table. A sea otter has as much area as a professional hockey rink.”  

And with all that surface area comes the challenge of keeping away all the dirt. It turns out that animals use a variety of ways to stay clean. Some depend on non-renewable strategies and use their own energy.

“Dogs shake water off their backs, just like a washing machine,” said Amador, who recently graduated. “Bees use bristled appendages to brush pollen off their eyes and bodies. Fruit flies use hairs on their head and thorax to catapult dust off of them at accelerations of up to 500 times Earth’s gravity.”

Other animals and insects use more efficient, renewable cleaning tactics.

“They don’t do anything extra to stay clean. It just happens,” said Amador.

Eyelashes, for example, protect mammals by minimizing airflow and funneling particles away from eyes. Cicadas have sharp points on their wings that act as pincushions, essentially popping airborne bacteria like water balloons.

It’s these renewable cleaning tactics that have the Georgia Tech team thinking about applications for technology.

“Understanding how biological systems, like eyelashes, prevent soiling by interacting with the environment can help inspire low-energy solutions for keeping sensitive equipment free from dust and dirt,” said Hu. “Drones and other autonomous rovers, including our machines on Mars, are susceptible to failure because of the accumulation of airborne particles.” 

The study, “Cleanliness is next to godliness: mechanisms for staying clean,” appears in the current issue (Vol. 218/Issue 20) of Journal of Experimental Biology.

This work is partially funded by the National Science Foundation (PHY-1255127). Any conclusions expressed are those of the principal investigator and may not necessarily represent the official views of the funding organizations.

Using large-scale computer modeling, researchers have shown the effects of confinement on macromolecules inside cells – and taken the first steps toward simulating a living cell, a capability that could allow them to ask “what-if” questions impossible to ask in real organisms.

The work could help scientists better understand signaling between cells, and provide insights for designing new classes of therapeutics. For instance, the simulations showed that particles within the crowded cells tend to linger near cell walls, while confinement in the viscous liquid inside cells causes particles to move about more slowly than they would in unconfined spaces.

The research is believed to be the first to consider the effects of confinement on intracellular macromolecular dynamics. Supported by the National Science Foundation, the results are reported November 16 in the journal Proceedings of the National Academy of Sciences.

The study is an interdisciplinary collaboration between Edmond Chow, an associate professor in the Georgia Tech School of Computational Science and Engineering, and Jeffrey Skolnick, a professor in the Georgia Tech School of Biology. Their goal is to develop and study models for simulating the motions of molecules inside a cell, and also to develop advanced algorithms and computational techniques for performing large-scale simulations.

“We are setting the stage for what we need to do to simulate a real cell,” said Skolnick. “We would like to put enough of a real cell together to be able to understand all of the cellular biochemical principles of life. That would allow us to ask questions that we can’t ask now.”

Earlier simulations, which produced much less fidelity, had assumed that movement within a cell was the same as movement in an unconfined space.

Skolnick compared the interior of a living cell to a large New Year’s Eve party, perhaps even in Times Square.

“It’s kind of like a crowded party that has big people and little people, snakes – DNA strands – running around, some really large molecules and some very small molecules,” he said. “It’s a very heterogeneous and dense environment with as much as 40 percent of the volume occupied.”

The simulations showed that molecules near the cell walls tend to remain there for extended periods of time, just as a newcomer might be pushed toward the walls of the New Year’s Eve party. Motions of nearby particles also tended to be correlated, and those correlations appeared linked to hydrodynamic forces.

“The lifetimes of these interactions get enhanced, and that is what’s needed there for biological interactions to occur within the cell,” said Skolnick. “This lingering near the wall could be important for understanding other interactions because if there are signaling proteins arriving from other cells, they would associate with those particles first. This could have important consequences for how signals are transduced.”

For particles in the middle of the cell, however, things are different. These molecules interact primarily with nearby molecules, but they still feel the effects of the cell wall, even if it is relatively far away.

“Things move more slowly in the middle of the cell than they would if the cell were infinitely big,” Skolnick said. “This may increase the likelihood of having metabolic fluxes because you have to bring molecules around partners. If they are moving slowly, they have more time to react because intimate interactions by accident are unavoidable.”

While the rate of activity slows quantitatively, qualitatively it is the same kind of motion.

“Slowed motion is a double-edged sword,” Skolnick explained. “If you happen to be nearby, it is likely that you are going to have interactions if you are slower. But if you are not nearby, being slower makes it difficult to be nearby, affecting potential interactions.”

The researchers also compared the activities of systems of particles with different sizes, finding that having particles of different sizes didn’t make an appreciable difference in the overall behavior of the molecules.

While the simulations didn’t include the DNA strands or metabolite particles also found in cells, they did include up to a half-million objects. Using Brownian and Stokesian physics principles, Skolnick and Chow considered what the particles would do within the confined spherical cell a few microns in diameter.

“From the results of the computer simulations, we can measure things that we think might be interesting, such as the diffusion rates near the walls and away from the walls,” said Chow. “We often don’t know what we are looking for until we find something that forces us to ask more questions and analyze more data.”

Such simulations take a lot of computational time, so the algorithms used must be efficient enough to be completed in a reasonable time. The “art” of the algorithms is trading off fidelity with processing time. Even though the simulations were very large, they managed to study the actions of the confined particles for no more than milliseconds.

“Part of the art of this is guessing what will be a reasonable approximation that will mimic the system, but not be so simple to be trivial or too complicated that you can’t take more than a few steps of the simulation,” Chow explained.

Scientists, of course, can study real cells. But the simulation offers something the real thing can’t do: The ability to turn certain forces on or off to isolate the effects of other processes. For instance, in the simulated cell Skolnick and Chow hope to build, they’ll be able to turn on and off the hydrodynamic forces, allowing them to study the importance of these forces to the functioning of real cells.

Results from the simulation can suggest hypotheses to be confirmed or rejected by experiment, which can then lead to further questions and simulations.

“This becomes a tool you can use to understand real cells,” said Chow. “It’s a virtual system, and you can play all the games you want with it.”

This research was supported by the National Science Foundation under grant ACI-1147834. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Science Foundation.

CITATION: Edmond Chow and Jeffrey Skolnick, “Effects of confinement on models of intracellular macromolecular dynamics,” (Proceedings of the National Academy of Sciences, 2015). www.pnas.org/cgi/doi/10.1073/pnas.1514757112

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

Media Relations Contact: John Toon (jtoon@gatech.edu) (404-894-6986).
Writer: John Toon