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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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.”
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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
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Jeffrey Skolnick and coworkers at the Georgia Tech School of Biology have shown that the ability to catalyze biochemical reactions is an intrinsic property of protein molecules, defined only by their structure and the principles of chemistry and physics. Their study was published on Feb. 23, 2016, in the open-access journal F1000Research.
The finding suggests that where proteins exist, life is possible because biochemical transformations are possible. And because biochemical transformations are required for life, life as we know it could be ubiquitous in the universe.
Life on Earth depends on myriad biochemical reactions mediated by proteins. The conventional wisdom is that the biochemical properties of proteins arise from evolutionary selection. According to the new study, evolution is not necessary for the existence of proteins’ biochemical functions, although evolutionary selection may have optimized proteins for specific roles.
The study’s conclusion is profound, said Terry Snell, chair of the School of Biology, in the College of Sciences. That’s because “the impression of design pervades biology,” he explained. “All the exquisite structures in biology—such as the complex anatomy of the vertebrate eye or the molecular structure of enzymes—are thought to have arisen by adaptation directed by natural selection. The new paper suggests that a considerable portion of the design in biology can be attributed to physical and chemical laws that dictate the function and structure of proteins.”
Ron Elber concurs. He is the W.A. “Tex” Moncrief Chair in Computational Life Sciences and Biology at the University of Texas at Austin. The work “suggests that physical principles assist nature in selecting proteins for specific functions,” he said. “While selection is necessary, it is useful to reduce the number of possibilities, and the Skolnick study suggests a mechanism of how that might happen.”
Skolnick and coworkers Mu Gao and Hongyi Zhou at the Center for the Study of Systems Biology studied the properties of a library of artificially generated proteins selected only for their intrinsic stability, not any type of function. They found that a remarkable number of the artificial proteins have the unique features of functional proteins, including binding pockets to accommodate small molecules. These pockets are necessary for biochemical catalysis to take place.
Although Skolnick and coworkers studied only a small ensemble of protein-like molecules, Elber observed, “it nevertheless includes features that resemble active sites even though it was generated on the basis of physical principles only.”
The researchers further predicted computationally that some members of the artificial, nonfunctional protein library would have strong protein-protein and protein-DNA interactions. Such interactions are essential in the machinery of life as we know it.
“The biochemical seeds of life could be prevalent,” Skolnick said. “If you rain meteorites containing amino acids and somehow these polymerize to form small proteins, then a subset of these would fold to stable structure and a small subset of these could engage in rudimentary metabolism, all without any selection for biochemical function. Thus, the background probability for function is much larger than had been previously appreciated.”
In a manuscript in preparation, Skolnick and coworkers have built on this finding to propose a mechanism for the emergence of chirality in biology. Many compounds can have the same structure and physical properties but differ only in their right- or left-handed orientation. In the presence of other biological molecules, such as proteins, usually only the compounds with one type of handedness—or chirality—can react. In nature, one type of handedness prevails. And how this prevalence emerged has been the subject of years of research.
During the spring 2016 round of tenure and promotion decisions at Georgia Tech, 15 faculty members from the College of Sciences made the list.
The following were promoted to full professor:
School of Applied Physiology
School of Biology
School of Earth and Atmospheric Sciences
School of Mathematics
School of Physics
School of Psychology
The following were promoted to associate professor and awarded tenure:
School of Earth and Atmospheric Sciences
School of Mathematics
School of Physics
Joseph Sadighi, of the School of Chemistry and Biochemistry, was awarded tenure.
“On behalf of the College of Sciences community, I am pleased to offer my warmest congratulations to our most recent promotion and tenure recipients,” says Dean Paul M. Goldbart. “You, and colleagues like you, are truly pivotal to the future of mathematics and the sciences at Georgia Tech.
“The knowledge and understanding that you are creating and imparting – via your scholarship, teaching and service – are the fuel that ensures the continued rise in the appreciation of the college, across our campus, nationally and worldwide.
“I look forward with tremendous excitement to your future accomplishments as researchers, educators and builders whose vision and activities will shape and strengthen the Georgia Tech of the future.”
About 30 miles west of Atlanta lies the town of Douglasville. Described variously as “charming,” having a “small-town ambiance,” and “historic,” this town of close to 32,000 people away from the frenzy and busyness of the big city would not be an obvious site for a TEDx event. And yet for the second year in a row, TEDxDouglasville is happening, thanks to two Georgia Tech students driven by a deep sense of gratitude to their hometown: Joshua Barnett, a third-year physics major, and Mahdi Al-Husseini, a third-year biomedical engineering and public policy major.
For the two undergrads, TEDxDouglasville is a means to give back to a town and community that supported them as they began their undergraduate studies at Georgia Tech. Looking ahead to their graduation from Georgia Tech, Barnett and Al-Husseini regard TEDxDouglasville as a way to stay connected to their community of origin even as they might move farther away in search of their individual futures.
Barnett and Al-Husseini have known each other since their freshman days in Douglas County High School. “By the time we graduated, we were best friends and bound for Georgia Tech,” Barnett says. Al-Husseini masterminded the creation of TEDxDouglasville, asking Barnett to join soon after the TED license was approved. Barnett did not hesitate to take the role of co-organizer. “Both of us were deeply affected by a philosophy course we had taken in high school,” he says. “And we were convinced by the power of ideas and the impact of how ideas are conveyed.”
A big surprise of the event last year was how much younger the audience was than the organizers had expected. “A large number of high school students attended,” Barnett says. “This year we have made tickets more accessible to these students, and we’re even holding the event in a school that many of them attend.”
That would be Douglas County High School. When TEDxDouglasville 2016 is held there on April 9, two College of Sciences faculty members will speak:
Brian Hammer, from the School of Biology, will talk about cooperation and conflict in the microbial world. “Microbes are ubiquitous on Earth and interact with one another and their surroundings in diverse associations that maintain the health of our planet and all of its inhabitants,” Hammer says. His research is helping to explain how bacteria cooperate and compete. And he hopes the knowledge “will allow us to monitor and manipulate these behaviors to prevent and treat human diseases and to mitigate perturbations to global ecological systems.”
Laura Cadonati, from the School of Physics, will describe the discovery of gravitational waves. “Gravitational waves are ripples in the fabric of space and time that are produced by cataclysmic astrophysical events,” Cadonati explains. One hundred years after Albert Einstein predicted their existence, one such wave was detected for the first time on Sept. 14, 2015; the wave came from the merging of two gigantic black holes 1.3 billion years ago. Cadonati will explain how gravitational waves open a new way to probe the universe.
“Events like TEDxDouglasville speak to Georgia Tech’s and the College of Sciences’ tradition of educating and nurturing the whole person and not just the engineering or the physics aspects,” says College of Sciences Dean Paul M. Goldbart. “They also underscore the College’s commitment to sharing with nonscientists everywhere the excitement and promise of our researchers’ breakthrough discoveries.”
With an average age of 21, Barnett, Al-Husseini, and the organizing team of TEDxDouglasville are on a steep learning curve to achieve their aspirations for TEDxDouglasville. Following are edited excerpts from a Q&A conducted by e-mail. Responses are from both Barnett and Al-Husseini except where indicated.
Why is Douglasville a good venue for a TEDx program?
It’s hard to resist Douglasville’s southern charm, incredible past, beautiful parks, and strength of community. Douglasville is where history meets modernity. This little, big city rests on the fringes of Atlanta, but remains far enough to stay humble.
This event is a way to engage our community. It would give people a chance to meet and converse with individuals with whom they might never interact otherwise. Diverse interactions is important in the development of a wholesome, interconnected community.
Who are the people you are trying to reach with TEDxDouglasville?
Students, construction workers, teachers, businessmen, janitors, social workers, doctors, lawyers. Anyone with a sense of curiosity. We seek to get people thinking, dreaming, and achieving.
What is your measure of success for TEDxDouglasville?
Exposing our audience to different people and new ideas was one of our goals from the beginning. But we must also consider the impact on the wider community. TEDxDouglasville inspired a new level of civic engagement: It led to a proposal for the Douglas Youth Department and catalyzed the creation of a service organization, Progressive Action Towards the Health of Douglasville, a lasting legacy.
It is also great to have scientists from Georgia Tech speak to a general audience, especially to high school students. TEDxDouglasville not only gives the audience a chance to connect with scientists on a tangible, accessible level, but it also helps to steer youth who are considering majoring in the sciences by providing a realistic snapshot of what scientific research looks like on the collegiate level.
Give us a preview of TEDxDouglasville 2016.
Our theme for this year is “Laying the Tracks,” which is rooted in the city’s origins from a railroad track. TEDxDouglasville 2016 will explore the intricacies of pioneering and building in the sciences, arts, education, and business. The event is laying tracks for ideas worth spreading, in hopes of building something extraordinary.
What happens to TEDxDouglasville when you graduate from Georgia Tech?
Al-Husseini: We aim to transform TEDxDouglasville from an annual event into a continuous platform for creative thinking and community outreach. The proceeds from this year’s event will be stored in a scholarship fund dedicated to high school students in Douglas County.
I intend to spend four years on active-duty with the US Army, after a spring 2018 Georgia Tech graduation. Upon completing my service contract, I hope to attend graduate school and eventually return to Douglasville.
Barnett: I hope to take an advisory role for a successor who will come to organize the event. With plans to attend graduate school, I must commit more and more time to research and my courses. Meanwhile, we will explore various options.
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