Dr. Marc Weissburg Professor of Biology, along with a team of multidisciplinary investigators have been awarded $2.5 million dollar grant to develop approaches for sustainable and resilient infrastructure. A key feature of the plan is to use, and compare, ecological and engineering approaches and principles for increasing cycling, reducing waste, and maintaining function in the face of perturbation. The team will examine complex interactions between infrastructure (e.g. water, transportation and energy systems) that traditionally have been ignored. Atlanta will provide both data and a possible test case for the principles developed. This proposal represents a unique and powerful interdisciplinary research and educational initiative, with graduate students from many fields being co-mentored by faculty from different disciplines. Along with Dr. Weissburg, the investigators consist of Dr. John Crittenden (PI, CEE), Dr. B. Ashuri (COA), Dr. J Clark (Ivan Allen) and Dr. R. Fujimoto (CS). Senior personnel come from many other units, including Mechanical Engineering, Industrial Systems Engineering and GTRI.
Researchers have sequenced the genomes and transcriptomes of five species of African cichlid fishes and uncovered a variety of features that enabled the fishes to thrive in new habitats and ecological niches within the Great Lakes of East Africa.
The study helps explain the genetic basis for the incredible diversity among cichlid fishes and provides new information about vertebrate evolution. The genomic information from the study will help answer questions about human biology and disease.
"Our study reveals a spectrum of methods that nature uses to allow organisms to adapt to different environments,” said co-senior author Kerstin Lindblad-Toh, scientific director of vertebrate genome biology at the Broad Institute of Harvard and MIT, a biomedical and genomic research center. “These mechanisms are likely also at work in humans and other vertebrates, and by focusing on the remarkably diverse cichlid fishes, we were able to study this process on a broad scale for the first time.”
The new study was published in the September 3 advance online edition of the journal Nature. The work was a collaboration between the Broad Institute of MIT and Harvard, the Georgia Institute of Technology, and the Eawag Swiss Federal Institute for Aquatic Sciences, in addition to more than 70 scientists from the international cichlid research community.
African cichlid fishes are some of the most diverse organisms on the planet, with over 2,000 known species. Some lakes are home to hundreds of distinct species that evolved from a common ancestral species in the Nile River. Like Darwin’s finches, the cichlids are a dramatic example of adaptive radiation, the process by which multiple species radiate from an ancestral species through adaptation.
In the new study, the researchers sequenced the genomes and transcriptomes – the protein-coding RNA - from ten tissues of five distinct lineages of African cichlids. The sequenced species include the Nile tilapia, representing the ancestral lineage, and four East African species: a species that inhabits a river near Lake Tanganyika; a species from Lake Tanganyika colonized 10-20 million years ago; a cichlid species from Lake Malawi colonized 5 million years ago; and species from Lake Victoria where the fish radiated only 15,000 to 100,000 years ago.
The researchers found a number of genomic changes at play in the adaptive radiation. Compared to the ancestral lineage, the East African cichlid genomes possess an excess of gene duplications, alterations in regulatory elements in the genome, accelerated evolution of protein-coding elements in genes for pigmentation, and other distinct features that affect gene expression.
“It’s not one big change in the genome of this fish, but lots of different molecular mechanisms used to achieve this amazing adaptation and speciation,” said Federica Di Palma, co-senior author of the Nature study and director of science in vertebrate and health genomics at The Genome Analysis Center in the UK.
Some changes in the genome appear to have accumulated before the species left the rivers to colonize lakes and radiated into hundreds of species. This suggests that the cichlids were once in a period of reduced constraint. During this time, the fishes accumulated diversity through genetic mutations, and the relaxed constraint – in which all individuals thrived, not just the fittest – allowed genetic variation to accumulate. As the fish later inhabited new environmental niches within the lakes, new species could form quickly through selection. In this way, a reservoir of mutations – and resultant phenotypes – represented a genomic toolkit that allowed quick adaptation.
More work remains to fully dissect the mutations that cause each of the varying phenotypes in cichlid fish, which could help explain how similar forms or traits evolved in parallel in different lakes.
"By learning how natural populations, such as fishes, adapt and evolve under selective pressures, we can learn how these pressures affect humans in terms of health and disease,” Di Palma said.
Todd Streelman, professor in the School of Biology at Georgia Tech and a co-author of the study, studies Lake Malawi cichlid species to address biological questions that are difficult to study in traditional model organisms.
"These fishes provide a great way to identify the genes that control traits in natural populations," Streelman said. “Now that we understand the genome sequences of some of these species, it’s a lot easier to interpret all of the new genetic and genomic data we collect in the lab.”
His lab studies natural mechanisms of lifelong tooth replacement and the genomics of complex social behavior using closely-related Malawi cichlids. The new genome sequence of the Lake Malawi cichlid will allow Streelman’s lab to investigate which genes are turned on or off during these processes.
Streelman's research group cultures roughly 25 different Malawi cichlid species in aquatic facilities at Georgia Tech, through research funded by the National Institute of Dental and Craniofacial Research (NIDCR) and the National Institute of General Medical Sciences (NIGMS).
This work was funded in part by the National Human Genome Research Institute (NHGRI), the Swiss National Science Foundation, the German Science Foundation, Biomedical Research Council of A*STAR, Singapore, the European Research Council, US National Institute of Dental and Craniofacial Research (NIDCR), and the Wellcome Trust.
CITATION: David Brawand, et al."The genomic substrate for adaptive radiation in African cichlid fish." (Nature, September 2014) http://dx.doi.org/10.1038/nature13726
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Writer: Leah Eisenstadt, Broad Institute of Harvard and MIT
Each team to receive $100K for two years to kick-start new research.
Three interdisciplinary teams with wide-ranging goals at the Parker H. Petit Institute for Bioengineering and Bioscience have gotten off to a fast start on pioneering explorations in biotechnology, thanks to a homegrown program that supports innovative early-stage research.
The winning teams of the 2014 Petit Bioengineering and Bioscience Collaborative Seed Grant are working to improve the prediction of disease (Hang Lu and Patrick McGrath), design better drug delivery strategies to fight cancer (M.G. Finn and Susan Thomas), and unveil (and better understand) the processes through which cell receptor signaling is initiated (Robert Dickson and Cheng Zhu).
Each of these fledgling collaborative teams was awarded $100,000 for two years to kick-start new research en route to long-range aspirations.
“The seed grant program is fantastic, because it supports bold ideas that don’t have preliminary data,” says Lu, a professor in the School of Chemical and Biomolecular Engineering. “Patrick and I have been wanting to work on this particular idea of evolving model systems to study multigenic diseases. We are extremely happy to have the support to pursue it now. We’re hoping to garner preliminary data to seek NIH funding in the long run.”
The program, now in its third year, gets to the heart of the Petit Institute mission, as it encourages a multidisciplinary approach to cutting-edge research, with each team bringing together an engineer and a scientist in a collaborative research endeavor, addressing complex biotech challenges by combining the distinct strengths of each lab. For example, as Lu and McGrath (assistant professor in the School of Biology) explain in their proposal, “Technologically and conceptually, what we propose here has never been done before. This pilot is truly enabled by the genomics know-how of the McGrath lab and the technological advancement of the Lu lab, which is a unique combination not found elsewhere.”
By applying a directed evolutionary approach, they expect to eventually be able to identify interacting genes that can be used as biomarkers for lifespan and age-related diseases, “and also as synergistic drug targets that can be used to ameliorate side-effects by lowering dose-levels of pharmaceuticals.”
Zhu, professor in the Wallace H. Coulter Department of Biomedical Engineering, he and Dickson, professor in the School of Chemistry and Biochemistry), are “trying to develop methods that allow in situ measurements of protein-protein interactions in live cells,” says Zhu. “The lacking of such methods hinders the development of a broad field in biology.” Currently, no method allows this kind of crucial measurement, Zhu and Dickson say in their proposal.
Meanwhile, Finn (professor and chair in the School of Chemistry and Biochemistry) and Thomas (assistant professor in the George W. Woodruff School of Mechanical Engineering) are working on a project with what they say will ultimately “impact the drug delivery field by introducing a new chemical means to temporally control drug release,” according to their proposal.
“In some ways, this approach runs counter to the prevailing drive in the field toward ever more sophisticated ways to respond to environmental cues,” the researchers say, adding, “While such technologies are undoubtedly valuable, there is also value in a cleavage mechanism that one can use like an alarm clock.” Stretching the analogy a bit further, they describe an alarm clock in which the start and end times, and intensity (and composition of the alarm) are all programmable.
“Results from this study,” Finn and Thomas say in their proposal, “will form the basis of numerous collaborative grant applications and a long-term collaboration between two labs with distinct but synergistic expertise aimed towards the design and effective drug delivery strategies for cancer therapy.”
Funding for the seed grants comes mainly from the Petit Institute’s endowment as well as contributions from the College of Sciences and the College of Engineering. Each research team receives $50,000 a year for two years, with the second year of funding contingent on submission of an external collaborative grant proposal.
The increasing acidification of ocean waters caused by rising atmospheric carbon dioxide levels could rob sharks of their ability to sense the smell of food, a new study suggests.
Elevated carbon dioxide levels impaired the odor-tracking behavior of the smooth dogfish, a shark whose range includes the Atlantic Ocean off the eastern United States. Adult sharks significantly avoided squid odor after swimming in a pool of water treated with carbon dioxide. The carbon dioxide concentrations tested are consistent with climate forecasts for midcentury and 2100. The study suggests that predator-prey interactions in nature could be influenced by elevated carbon dioxide concentrations of ocean waters.
“The sharks’ tracking behavior and attacking behavior were significantly reduced,” said Danielle Dixson, an assistant professor in the School of Biology at the Georgia Institute of Technology in Atlanta. “Sharks are like swimming noses, so chemical cues are really important for them in terms of finding food.”
The study is the first time that sharks’ ability to sense the odor of their food has been tested under conditions that simulate the acidity levels expected in the oceans by the turn of the century. The work supports recent research from Dixson and other research groups showing that ocean acidification impairs sensory functions and alters the behavior of aquatic organisms.
The study was published August 11 the journal Global Change Biology and was sponsored by the National Science Foundation (NSF).
Carbon dioxide released into the atmosphere is absorbed into ocean waters, where it dissolves and lowers the pH of the water. Acidic waters affect fish behavior by disrupting a specific receptor in the nervous system, called GABAA, which is present in most marine organisms with a nervous system. When GABAA stops working, neurons stop firing properly.
Dixson’s previous research has shown that fish living on coral reefs where carbon dioxide seeps from the ocean floor were less able to detect predator odor than fish from normal coral reefs. Study co-author Philip Munday, from James Cook University in Australia, has shown in previous work that a tiny coral reef predator fish, the dottyback,also loses interest in food in waters that simulate ocean acidification conditions forecast for the future.
In the experimental part of the new study, conducted at Woods Hole Oceanographic Institute in Cape Cod, Massachusetts, 24 sharks from local waters were studied in a 10-meter-long flume. The flume resembled two lanes of a swimming pool. Odor from a squid was pumped down one lane of the flume, while normal seawater was pumped down the other side.
Sharks tend to prefer one side of a tank over the other, so researchers first assessed each sharks’ side preference. Then the research team ran control experiments under normal ocean conditions to ensure that the sharks were tracking the food cue. Under present-day water conditions, sharks adjusted their position in the flume to spend a greater amount of time on the side containing the squid odor plume, regardless of the individual shark’s natural side preference.
Next, sharks spent five days in holding pools of three different carbon dioxide concentrations: local water concentration today (405 ± 26microatmospheres (µatms) CO2), projected midcentury concentration (741 ± 22 µatms CO2),projected concentration for 2100 (1,064 ± 17 µatms CO2). Sharks were not fed while in the holding pools to ensure they were motivated to track a food odor. The sharks were then released into the flume and their tracking behavior was observed.
Sharks from the normal seawater pool and mid-level carbon dioxide pool spent more than 60 percent of their time in the water stream containing the food stimulus. Sharks from the high carbon dioxide pool spent less than 15 percent of their time in the water stream containing the food stimulus. These sharks avoided the odor plume even when it was on the side of the flume that the sharks’ naturally prefer.
The food odor stream was pumped through bricks to make the plume flow better and to give the sharks a target to attack. Sharks treated under mid and high CO2 conditions also reduced their attack behavior.
“They significantly reduced their bumps and bites on the bricks compared to the control group,” Dixson said. “It’s like they’re uninterested in their food.”
Exposure to carbon dioxide did not significantly affect the sharks’ overall activity levels. The gill rate of the sharks – an indicator of heart rate – held in different water conditions was not significantly different, suggesting that differences in stress to the sharks was not likely affecting the experimental results.
Dixson noted that the study was carried out under laboratory conditions and thus does not allow for the full evaluation of the potential effects of ocean acidification on predatory abilities of the smooth dogfish.
Live food was not used as the odor cue because sharks can detect prey with their other senses, such as hearing and their ability to detect electrical impulses. By using an odor cue, the researchers were focusing on only the chemical sensing of sharks. Dixson’s future work will explore how sharks’ other senses might be affected by ocean acidification.
Sharks are an ancient species, and in the past have adapted to ocean acidification conditions projected for the future. But they’ve never had to adapt to changes happening as quickly as they are today.
“It’s the rate of change that’s happening that’s concerning. Sharks have never had to deal with it this fast,” Dixson said.
This research is supported by the National Science Foundation (NSF) under award number NSF-IOS-0843440. Any conclusions or opinions are those of the authors and do not necessarily represent the official views of the sponsoring agency.
CITATION: Danielle L. Dixson, et al., “Odor tracking in sharks is reduced under future ocean acidification conditions.” (Global Change Biology, August 2014) http://onlinelibrary.wiley.com/doi/10.1111/gcb.12678/full
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The amazing ability of sidewinder snakes to quickly climb sandy slopes was once something biologists only vaguely understood and roboticists only dreamed of replicating. By studying the snakes in a unique bed of inclined sand and using a snake-like robot to test ideas spawned by observing the real animals, both biologists and roboticists have now gained long-sought insights.
In a study published in the October 10 issue of the journal Science, researchers from the Georgia Institute of Technology, Carnegie Mellon University, Oregon State University, and Zoo Atlanta report that sidewinders improve their ability to traverse sandy slopes by simply increasing the amount of their body area in contact with the granular surfaces they’re climbing.
As part of the study, the principles used by the sidewinders to gracefully climb sand dunes were tested using a modular snake robot developed at Carnegie Mellon. Before the study, the snake robot could use one component of sidewinding motion to move across level ground, but was unable to climb the inclined sand trackway the real snakes could readily ascend. In a real-world application – an archaeological mission in Red Sea caves – sandy inclines were especially challenging to the robot.
However, when the robot was programmed with the unique wave motion discovered in the sidewinders, it was able to climb slopes that had previously been unattainable. The research was funded by the National Science Foundation, the Army Research Office, and the Army Research Laboratory.
“Our initial idea was to use the robot as a physical model to learn what the snakes experienced,” said Daniel Goldman, an associate professor in Georgia Tech’s School of Physics. “By studying the animal and the physical model simultaneously, we learned important general principles that allowed us to not only understand the animal, but also to improve the robot.”
The detailed study showed that both horizontal and vertical motion had to be understood and then replicated on the snake-like robot for it to be useful on sloping sand.
“Think of the motion as an elliptical cylinder enveloped by a revolving tread, similar to that of a tank,” said Howie Choset, a Carnegie Mellon professor of robotics. “As the tread circulates around the cylinder, it is constantly placing itself down in front of the direction of motion and picking itself up in the back. The snake lifts some body segments while others remain on the ground, and as the slope increases, the cross section of the cylinder flattens.”
At Zoo Atlanta, the researchers observed several sidewinders as they moved in a large enclosure containing sand from the Arizona desert where the snakes live. The enclosure could be raised to create different angles in the sand, and air could be blown into the chamber from below, smoothing the sand after each snake was studied. Motion of the snakes was recorded using high-speed video cameras which helped the researchers understand how the animals were moving their bodies.
“We realized that the sidewinder snakes use a template for climbing on sand, two orthogonal waves that they can control independently,” said Hamid Marvi, a postdoctoral fellow at Carnegie Mellon who conducted the experiments while he was a graduate student in the laboratory of David Hu, an associate professor in Georgia Tech’s School of Mechanical Engineering. “We used the snake robot to systematically study the failure modes in sidewinding. We learned there are three different failure regimes, which we can avoid by carefully adjusting the aspect ratio of the two waves, thus controlling the area of the body in contact with the sand.”
Limbless animals like snakes can readily move through a broad range of surfaces, making them attractive to robot designers.
"The snake is one of the most versatile of all land animals, and we want to capture what they can do," said Ross Hatton, an assistant professor of mechanical engineering at Oregon State University who has studied the mathematical complexities of snake motion, and how they might be applied to robots. "The desert sidewinder is really extraordinary, with perhaps the fastest and most efficient natural motion we've ever observed for a snake."
Many people dislike snakes, but in this study, the venomous animals were easy study subjects who provided knowledge that may one day benefit humans, noted Joe Mendelson, director of research at Zoo Atlanta.
“If a robot gets stuck in the sand, that’s a problem, especially if that sand happens to be on another planet,” he said. “Sidewinders never get stuck in the sand, so they are helping us create robots that can avoid getting stuck in the sand. These venomous snakes are offering something to humanity.”
The modular snake robot used in this study was specifically designed to pass horizontal and vertical waves through its body to move in three-dimensional spaces. The robot is two inches in diameter and 37 inches long; its body consists of 16 joints, each joint arranged perpendicular to the previous one. That allows it to assume a number of configurations and to move using a variety of gaits – some similar to those of a biological snake.
“This type of robot often is described as biologically inspired, but too often the inspiration doesn’t extend beyond a casual observation of the biological system,” Choset said. “In this study, we got biology and robotics, mediated by physics, to work together in a way not previously seen.”
Choset’s robots appear well suited for urban search-and-rescue operations in which robots need to make their way through the rubble of collapsed structures, as well as archaeological explorations. Able to readily move through pipes, the robots also have been tested to evaluate their potential for inspecting nuclear power plants from the inside out.
For Goldman’s team, the work builds on earlier research studying how turtle hatchlings, crabs, sandfish lizards, and other animals move about on complex surfaces such as sand, leaves, and loose material. The team tests what it learns from the animals on robots, often gaining additional insights into how the animals move.
“We are interested in how animals move on different types of granular and complex surfaces,” Goldman said. “The idea of moving on flowing materials like sand can be useful in a broad sense. This is one of the nicest examples of collaboration between biology and robotics.”
In addition to those already mentioned, co-authors included Chaohui Gong and Matthew Travers from Carnegie Mellon University; and Nick Gravish and Henry Astley from Georgia Tech.
This research was supported by the National Science Foundation under awards CMMI-1000389, PHY-0848894, PHY-1205878, and PHY-1150760; by the Army Research Office under grants W911NF-11-1-0514 and W911NF1310092; and by the Army Research Lab MAST CTA under grant W911NF-08-2-0004; and by the Elizabeth Smithgall Watts endowment at Georgia Tech. The opinions expressed are those of the authors and do not necessarily represent the official views of the sponsoring agencies.
CITATION: Hamidreza Marvi et al., “Sidewinding with minimal slip: snake and robot ascent of sandy slopes,” Science 2014).
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The sheer volume of cyanobacteria in the oceans makes them major players in the global carbon cycle and responsible for as much as a third of the carbon fixed. These photosynthetic microbes, which include Prochlorococcus and Synechococcus, are tiny – as many as 100 million cells can be found in a single liter of water – and yet they are not the most abundant entities on Earth. That distinction goes to viruses, up to 100 million of which can be found per 1 mL of seawater. However, researchers know very little about the viruses in the water, other than that there are three kinds of viruses, and that they are capable of drastically decreasing cyanobacterial populations, affecting the global regulation of biogeochemical cycles.
Owls are mostly nocturnal animals that depend on stealth to catch their prey. With the help of their wing structure, they also helped create the world’s most famous high-speed train by making it less noisy.
Flamingos are famous because of their pink color, which comes from the tiny creatures they filter from the water and eat. But it’s their fast-moving, mysterious beaks that may provide practical uses for people as they contemplate the kitchen faucets of the future.
Highlighting these unexpected similarities between what animals do and what people are trying to do is a new strategy Georgia Institute of Technology researchers are using to hopefully increase public awareness about animals and encourage conservation. They’ve created an iPhone app based on biologically inspired design, highlighting two dozen species that have helped engineers solve problems or invent new solutions.
“Learning that owls eat rodents is interesting, but explaining how they’ve helped us invent new technologies is a more effective way of getting us interested in the natural world,” said Marc Weissburg. The Georgia Tech professor led the app project and is co-director of the Institute’s Center for Biologically Inspired Design.
Owl wings are built to disperse air pressure, which allows them to fly silently to sneak up on their watchful prey. Engineers used the same principle to design the super-fast, and super-quiet, Shinkansen bullet train. Flamingos pump water in and out of their mouths at a speed of four pumps a second while eating. They use their beaks to strain water and trap their food. Researchers are studying their bills to construct water filters of the future.
The app also features zebras (keeping ships cool), elephants (transforming floors and walls into speaker systems) and rattlesnakes (all-terrain robots).
The ZooScape app, which also includes a game that tests a user’s knowledge of the animals and their contributions, can be used by anyone, anywhere. It becomes interactive at Zoo Atlanta. The app uses GPS to send notifications to the guests’ smartphones whenever they visit an exhibit of an animal that has contributed a biologically inspired design.
“There’s so much we have learned and still have to learn about animals. They’re experts at navigating their environments successfully, and it turns out that sometimes all we have to do to improve our own systems and efficiency is to sit back and watch them do what they already do so well,” said Joe Mendelson, a Georgia Tech adjunct professor and Zoo Atlanta’s director of herpetological research. “Zoo Atlanta is proud to partner with Georgia Tech on groundbreaking studies that elevate the profile of wildlife while also helping people.”
Zoo Atlanta is the first facility to use ZooScape, although creators built it with other zoos and aquariums in mind. The app was developed and designed by Weissburg, Leanne West and Brian Parise from the Georgia Tech Research Institute, with funds from the Smithgall Watts endowment to the School of Biology. Proceeds will fund further development of similar materials for outreach and public education.
Microbes of interest to clinicians and environmental scientists rarely exist in isolation. Organisms essential to breaking down pollutants or causing illness live in complex communities, and separating one microbe from hundreds of companion species can be challenging for researchers seeking to understand environmental issues or disease processes.
A new National Science Foundation-supported project will provide computational tools designed to help identify and characterize the gene diversity of the residents of these microbial communities. The project, being done by researchers at the Georgia Institute of Technology and Michigan State University, will allow clinicians and scientists to compare the genomic information of organisms they encounter against the growing volumes of data provided by the world’s scientific community.
The tools will be hosted on a web server designed to be used by researchers who may not have training in the latest bioinformatics techniques. A prototype system containing a limited number of computational tools is already available at http://enve-omics.ce.gatech.edu and is attracting more than 500 users each month.
“Across many areas of science, we are dealing with communities of microorganisms, and one challenge we’ve had is to identify them because we haven’t had good tools to tell apart individual microbes from the mixtures,” said Kostas Konstantinidis, an associate professor in the School of Civil and Environmental Engineering at Georgia Tech and the project’s principal investigator. “Our tools will be designed to deal with the genomes of whole communities of organisms.”
Current techniques identify individual microbes by examining their small subunit ribosomal RNA (SSU rRNA) genes, but the new tools will allow scientists to analyze entire genomes and meta-genomes.
“With the dawn of the genomic era, we can now get the whole genome of these organisms to see not only the ribosomal RNA, but also all the genes in the genome to get a better understanding of what the each organism’s potential might be,” said Konstantinidis. “There will be many advantages for looking at all the genes instead of just one, the SSU rRNA, such as to identify which organisms encode toxins or the enzymes for breaking down pollutants.”
Collaborators on the three-year project include scientists who operate the Ribosomal Database Project at Michigan State University: Jim Tiedje, director of Michigan State University’s Center for Microbial Ecology and James Cole, a Michigan State University research assistant professor and director of the Ribosomal Database Project.
The ability to identify and enumerate the organisms in complex communities using culture-independent, genomic technologies and associated bioinformatics algorithms is becoming more important as scientists study organisms that can’t be grown in the lab. The majority of the world’s organisms resist traditional lab culture, meaning they have to be studied in the field and identified through genetic information.
Konstantinidis and his research group are studying such communities in the water of lakes in Chattahoochee River system in Georgia and elsewhere. They are examining how these communities respond to perturbations, such as oil or pesticide spills, and the role that different members of the community play in breaking down pollutants.
“These tools actually come from our research practice,” said Konstantinidis. “We came to the point where we couldn’t process the data to answer the questions we wanted to ask. That led us to this new project to develop the tools we and others need to interrogate the data and get the information we are looking for.”
A single liter of lake water may contain as many as 500 different species, and together, their genomic information can total tens of billions of gene-coding letters. From Lake Lanier alone, the team has generated 200 gigabytes of genomic data.
“We want to figure out what organisms are there, and what genes they encode,” Konstantinidis explained. “The tools we are developing will allow us to do this.”
The tools developed in the project will be useful to both clinical microbiologists and environmental researchers. “This will not be specific to any one discipline,” he said. “As long as people are working with microbes, this will be helpful to them because some of the questions are universal.”
The system will also be built to provide user-friendly help to scientists who may not have training in the latest genomic and bioinformatics techniques. “There is a big need for big data analysis, and there are not many trained people right now,” Konstantinidis said. “These tools will make the lives of researchers easier.”
Among the challenges ahead is building an infrastructure able to handle the growing amounts of genomic information produced worldwide.
“We will have to develop some computational solutions for the problems of keeping up with all the new data becoming available,” said Konstantinidis. “We need to make tools that have high throughput to keep up with data volumes that are increasing geometrically.”
The system will initially operate on servers at Georgia Tech and Michigan State University, but if demand and data grow, additional resources may be sought, such as the National Science Foundation’s XSEDE supercomputer.
This research is supported by the National Science Foundation under award DBI-1356288. The opinions expressed in this article are those of the authors and do not necessarily reflect the official views of the National Science Foundation.
Kostas Konstantinidis is the Carlton S. Wilder Junior Faculty Professor in the Georgia Tech School of Civil and Environmental Engineering.
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A species of small fish uses a homemade coral-scented cologne to hide from predators, a new study has shown, providing the first evidence of chemical camouflage from diet in fish.
Filefish evade predators by feeding on their home corals and emitting an odor that makes them invisible to the noses of predators, the study found. Chemical camouflage from diet has been previously shown in insects, such as caterpillars, which mask themselves by building their exoskeletons with chemicals from their food. The new study shows that animals don’t need an exoskeleton to use chemical camouflage, meaning more animals than previously thought could be using this survival tactic.
“This is the very first evidence of this kind of chemical crypsis from diet in a vertebrate,” said Rohan Brooker, a post-doctoral fellow in the School of Biology at the Georgia Institute of Technology in Atlanta. “This research shows that you don’t need an exoskeleton that for this kind of mechanism to work.”
The study was published December 10 in the journal Proceedings of the Royal Society B. The study was sponsored by the ARC Centre of Excellence for Coral Reef Studies and the Ecological Society of Australia. The work was done as a part of Booker’s doctoral research at James Cook University in Australia.
Anyone who has watched a nature documentary has seen insects that camouflage themselves as sticks, protecting the insects against predators that use vision to hunt for prey. But many animals see the world through smell rather than sight, and cunning critters from among them have adapted clever ways of smelling like their surroundings. A certain species of caterpillar, for example, smells like the plant that it lives on and eats. The caterpillar incorporates chemicals from the plant into its exoskeleton. Ants hunting for the caterpillar will walk right over it, none the wiser.
For the new study, researchers traveled to Australia’s Lizard Island Research Station in the Great Barrier Reef, where they collected filefish. To show that filefish smelled like their home coral, the researchers recruited crabs to sniff them out. The filefish were fed two different species of coral; each species of coral is home to a unique species of crab. The crabs were given a choice between a filefish that had been fed the crab’s home coral and a filefish that had been fed a coral that is foreign to the crab. The crabs always sought the filefish that had been feeding on the crabs home coral. The filefish smelled so strongly of coral that sometimes the crabs were attracted to the fish instead of coral, when given a choice between the two.
“We can tell that there is something going through the filefish diet that’s making the fish smell enough like the coral to confuse the crabs,” Booker said.
To see if the chemical camouflage gives the filefish an evolutionary advantage to evade predators, the researchers tested cod to see how they responded to filefish that had been fed various diets. Cod, filefish and corals were put in a tank, with the filefish hidden from the cod. When the filefish diet didn’t match the corals in the tank, the cod were restless, suggesting that they smelled food. When the filefish diet matched the corals in the tank, the cod stayed tucked away in their cave inside the tank.
The next step in the project is to learn how filefish can smell like coral without the benefit of an exoskeleton. Some evidence shows that amino acids in the mucus of fish – where much of their smell originates – will match their diet, but much work remains to tease apart this pathway.
“We have established that there is some kind of pathway from filefish diet to filefish odor,” Booker said. “This is just the first study. There’s a lot of work still to be done to understand how it works.”
Booker is now working in the lab of Danielle Dixson, an associate professor of biology at Georgia Tech.
This research is supported by the ARC Centre of Excellence for Coral Reef Studies and the Ecological Society of Australia. Any conclusions or opinions are those of the authors and do not necessarily represent the official views of the sponsoring agencies.
CITATION: Rohan Brooker, et al., “You are what you eat: diet-induced chemical crypsis in a coral-feeding fish.” (Proceedings of the Royal Society B, December 2014). http://rspb.royalsocietypublishing.org/content/282/1799/20141887
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Ribonucleotides, units of RNA, can become embedded in genomic DNA during processes such as DNA replication and repair, affecting the stability of the genome by contributing to DNA fragility and mutability. Scientists have known about the presence of ribonucleotides in DNA, but until now had not been able to determine exactly what they are and where they are located in the DNA sequences.
Now, researchers have developed and tested a new technique known as ribose-seq that allows them to determine the full profile of ribonucleotides embedded in genomic DNA. Using ribose-seq, they have found widespread but not random incorporation and “hotspots” where the RNA insertions accumulate in the nuclear and mitochondrial DNA of a commonly-studied species of budding yeast. Ribose-seq could be used to locate ribonucleotides in the DNA of a wide range of other organisms, including that of humans.
“Ribonucleotides are the most abundant non-standard nucleotides that can be found in DNA, but until now there has not been a system to determine where they are located in the DNA, or to identify specifically which type they are,” said Francesca Storici, an associate professor in the School of Biology at the Georgia Institute of Technology. “Because they change the way that DNA works, in both its structure and function, it is important to know their identity and their sites of genomic incorporation.”
A description of the ribose-seq method and what it discovered in the DNA of the budding yeast species Saccharomyces cerevisiae were reported January 26 in the journal Nature Methods. The findings resulted from collaboration between researchers in Storici’s laboratory at Georgia Tech – with graduate students Kyung Duk Koh and Sathya Balachander – and at the University of Colorado Anschutz Medical School with assistant professor Jay Hesselberth.
The research was supported by the National Science Foundation, the Georgia Research Alliance, the American Cancer Society, the Damon Runyon Cancer Research Foundation, and the University of Colorado Golfers Against Cancer.
Because of the extra hydroxyl (OH) group in the ribonucleotides, their presence distorts the DNA and creates sensitive sites where reactions with other molecules can take place. Of particular interest are reactions between the OH and alkaline solutions, which can make the DNA more susceptible to cleavage.
Ribose-seq takes advantage of this reaction with the hydroxyl group to launch the process of identifying the genomic spectrum of ribonucleotide (rNMP) incorporation. Researchers first cleave the DNA samples at the ribonucleotides, then take the resulting fragments through a specialized process that concludes with generation of a library of DNA sequences that contain the sites of ribonucleotide incorporation and their upstream sequence. High-throughput sequencing of the library and alignment of sequencing reads to a reference genome identifies the profile of rNMP incorporation events.
“Ribose-seq is specific to directly capturing ribonucleotides embedded in DNA and does not capture RNA primers or Okazaki fragments formed during DNA replication, breaks or abasic sites in DNA,” Storici noted.
“For this reason, ribose-seq has application for rNMP mapping in any genomic DNA, from large nuclear genomes to small genomic molecules such as plasmids and mitochondrial DNA, with no need of standardization procedures,” she said. “It also allows mapping rNMPs even in conditions in which the DNA is exposed to environmental stressors that damage the DNA by generating breaks and/or abasic sites.”
The extra hydroxyl group found in the ribonucleotides is key to the ribose-seq technique, said Koh, the paper’s first author. “The OH group is specific to the ribonucleotides,” he explained. “That allowed us to build a new tool for recognizing specifically where the ribonucleotides are located.”
The high-throughput sequencing and initial data analysis were done in the Hesselberth laboratory in the Department of Biochemistry and Molecular Genetics at the University of Colorado Anschutz Medical School.
To validate their method, the researchers tested ribose-seq on the much-studied yeast species. The analyses revealed a strong preference for the cytidine and guanosine bases at the ribonucleotide sites.
“The ribonucleotides are not randomly distributed, and there is some preference for specific base sequences and specific base composition of the ribonucleotide itself,” said Koh. “By looking at the non-random distribution, we found several hotspots in which the ribonucleotides are incorporated into the genome.”
Knowledge of where the ribonucleotides cluster could help identify areas of greatest potential for genome instability and lead to a better understanding of how they affect the properties and activities of DNA.
“The fact that we see biases in the base compositions of the ribonucleotides allows us to tell which base is more likely to be incorporated into the DNA,” Koh explained. “If there are specific signatures of genomic instability that are caused by the ribonucleotides, this will allow us to narrow down the locations and know where they are more likely to be found.”
A next step will be to test ribose-seq on other DNA, Koh said. “Our technique could potentially be applied to any genome of any cell type from any organism as long as genomic DNA can be extracted from it,” he added. “It is independent of specific organisms.”
Beyond repair and replication processes, ribonucleotides can also be created in DNA as a result of damage caused by drugs, environmental stressors and other factors. The ribose-seq method could also allow scientists to study the impact of these processes.
“Ribose-seq should allow us to better understand the impact of ribonucleotides on the structure and function of DNA,” said Storici. “Identifying specific signatures of ribonucleotide incorporation in DNA may represent novel biomarkers for human diseases such as cancer, and other degenerative disorders.”
This material is based upon work supported by the National Science Foundation (NSF) under grant number MCB-1021763, by the Georgia Research Alliance under award number R9028, by the American Cancer Society, by the Damon Runyon Cancer Research Foundation and by the University of Colorado Golfers Against Cancer. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the sponsoring agencies.
CITATION: Kyung Duk Koh, Sathya Balachander, Jay Hesselberth and Francesca Storici, “Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA,” (Nature Methods, 2015). http://dx.doi.org/10.1038/nmeth.3259
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