Science and technology may not be one’s first thoughts at the mention of Colombia, the Latin American country that is emerging from more than half a century of armed conflict. Much about Colombia is lost in stereotypes, including its robust educational system, according to King Jordan. “Colombia has consistently defied my expectations arising from what we hear in the news,” he says.
An associate professor in the School of Biology and the director of Georgia Tech’s Bioinformatics Graduate Program, Jordan is poised to contribute to the country’s education and development of a knowledge-based economy. For six weeks beginning on June 20, 2016, he will conduct a Fulbright-supported workshop at Universidad Tecnológica del Chocó (UTech) to train Colombians in the use of databases and computer programs to analyze genomic information. He will also help develop a curriculum for a post-Bachelor specialization in bioinformatics.
Bioinformatics is where computer science and biology intersect. Scientists in the field develop and apply computational tools to address fundamental biological problems. Bioinformatics analyses of human genome sequences can uncover individuals’ genetic ancestry, as well as traits such as predisposition to disease. At Georgia Tech, Jordan uses bioinformatics to investigate the relationship between human genetic variation and health.
This summer trip continues Jordan’s years-long collaboration with Colombia and other Latin America countries as they strive to build national capacity for bioinformatics research.
Latin American populations have a mixture of ancestry from Africa, Europe, and the Americas, and Colombia’s ancestry is particularly diverse, Jordan says. The genetic mixing that occurred in the region over the past 500 years has created genome sequences that, Jordan says, “are novel in containing combinations of ancestry-specific alleles that never previously existed on the same genomic background. We want to understand the health-related implications of the emergence of this novel set of admixed genomes in Latin America.”
Colombia has about 11 million inhabitants of African descent, making it the country with the third highest population of African descendants in the Americas, after Brazil and the U.S. Located on the Pacific Coast, the state of Chocó has a uniquely African genetic heritage with admixture from Europe and the Americas, Jordan says.
The people of Chocó have an intense interest in both genetic ancestry and predisposition to disease, says Miguel Medina. The UTech professor of biology first met Jordan in 2014 at a conference where Jordan presented bioinformatics analyses of genomes from inhabitants of Medellín, who are predominantly of European descent. Medina invited Jordan to do similar work on the inhabitants of Chocó, 94% of whom are of African descent. To help establish bioinformatics formally in UTech, Medina and Jordan applied for a Fulbright grant to support Jordan’s visit this summer as a Fulbright Specialist in Biology Education.
Despite a number of studies on the genetic ancestry of Colombians, little research has focused on the Afro-Colombian population. Characterizing the genetic heritage of Chocó would a fuller picture of the scope of ancestry in Latin American populations, Jordan says, as well as reveal connections between genetic ancestry and health.
Working with the National Institutes of Health, Jordan and Medina have built a database of genomic sequences from samples provided by 100 inhabitants of Chocó. This pilot project was funded by the Denning Global Engagement Seed Fund, from Georgia Tech’s Office of the Vice-Provost for International Initiatives. That funding flowed from Georgia Tech’s strategic goal to expand its global footprint, Jordan explains. However, he emphasizes, the samples and the data generated by that funding belong to the people of Chocó.
For data analysis, UTech has formed a collaborative research partnership with BIOS, Colombia’s Center for Bioinformatics and Computational Biology; Georgia Tech; and the PanAmerican Bioinformatics Institute. Called ChocoGen, the project aims discover and characterize the genetic heritage of the people of Chocó. ChocoGen researchers are analyzing the genomic sequences of donors from Chocó to characterize their genetic ancestry; the quantity and nature of admixture between ancestral populations; and the possible relationship between ancestry, admixture, and genetic determinants of health and disease.
Over the course of six weeks this summer, Jordan will be training a diverse group of Colombian bioinformatics enthusiasts, teaching, and developing curriculum. And with Medina, Jordan will meet with government leaders to secure funding for future research and development in bioinformatics. His hope is not only to set the stage for a new research activity to take root but also to ensure that it grows strong.
For plants and animals fleeing rising temperatures, varying precipitation patterns and other effects of climate change, the eastern United States will need improved “climate connectivity” for these species to have a better shot at survival.
Western areas of the U.S. provide greater temperature ranges and fewer human interruptions than eastern landscapes, allowing plants and animals there to move toward more hospitable climates with fewer obstacles. A new study has found that only 2 percent of the eastern U.S. provides the kind of climate connectivity required by species that will likely need to migrate, compared to 51 percent of the western United States.
The research, reported June 13 in the journal Proceedings of the National Academy of Sciences, for the first time quantifies the concept of climate connectivity in the United States. The paper suggests that creating climate-specific corridors between natural areas could improve that connectivity to as much as 65 percent nationwide, boosting the chances of survival by more species. The issue is especially critical in the Southeast, which could provide routes to cooler northern climates as temperatures rise.
“Species are going to have to move in response to climate change, and we can act to both facilitate movement and create an environment that will prevent loss of biodiversity without a lot of pain to ourselves,” said Jenny McGuire, a research scientist in the School of Biology at the Georgia Institute of Technology. “If we really start to be strategic about planning to prevent biodiversity loss, we can help species adjust effectively to climate change.”
Creating and maintaining connections between natural areas has long been thought critical to allowing plants and animals to move in search of suitable climate conditions, she explained. Some species will have to move hundreds of kilometers over the course of a half-century.
McGuire and her collaborators set out to determine the practicality of that kind of travel and test whether these human initiatives could improve migration to cooler areas. Using detailed maps of human impact created by David Theobald at Conservation Partners in Fort Collins, Colorado, they distinguished natural areas from areas disturbed by human activity across the United States. They then calculated the coolest temperatures that could be found by moving within neighboring natural areas.
Co-authors Tristan Nuñez from the University of California Berkeley, Joshua Lawler from the University of Washington, Brad McRae from the Nature Conservancy and others created a program called Climate Linkage Mapper. They then used this program to find the easiest pathways across climate gradients and human-disturbed regions to connect natural areas.
“A lot of these land areas are very fragmented and broken up,” McGuire said. “We studied what could happen if we were to provide additional connectivity that would allow species to move across the landscape through climate corridors. We asked how far they could actually go and what would be the coolest temperatures they could find.”
With its relatively dense human population and smaller mountains, the eastern part of the United States fell short on climate connectivity. The western part of the country – with its tall mountains, substantial undisturbed natural areas and strict conservation policies – provided much better climate connectivity.
Improving connectivity would require rehabilitating forests and planting natural habitats adjacent to interruptions such as large agricultural fields or other areas where natural foliage has been destroyed. It could also mean building natural overpasses that would allow animals to cross highways, helping them avoid collisions with vehicles.
Not only will animals have to move, but they’ll also need to track changes in the environment and food, such as specific prey for carnivores and the right plants for herbivores. Some birds and large animals may be able to make that adjustment, but many smaller creatures may struggle to track the food and climate they need.
“A lot of them are going to have a hard time,” said McGuire. “For plants and animals in the East, there is a higher potential for extinction due to an inability to adapt to climate change. We have a high diversity of amphibians and other species that are going to struggle.”
The negative impacts of climate change won’t affect all species equally, McGuire said. Species with small ranges or those with specialist diets or habitats will struggle the most.
“Not all plants and animals will have to move,” she explained. “There is a subset of them that will be able to hunker down where they are. There will be some species that are really widespread and will end up just having some population losses. But especially for species that have smaller ranges, there will be some loss of biodiversity as they are unable to jump across agricultural fields or major roadways.”
The Southeast, especially the coastal plains from Louisiana through Virginia, could create a bottleneck for species trying to move north away from rising temperatures and sea levels. “The Southeast ends up being a really important area for a lot of vertebrate species that we know are going to have to move into the Appalachian area and even potentially farther north,” she added.
In future work, the researchers hope to examine individual species to determine which ones are most likely to struggle with the changing climate, and which areas of the country are likely to be most impacted by conflicts between humans and relocating animals.
“We see a lot of species’ distributions really start to wink out after about 50 years, but it is tricky to look at future predictions because we will have a lot of habitat loss predicted using our models,” McGuire said. “Change is perpetual, but we are going to have to scramble to prepare for this.”
The research was supported by the U.S. National Park Service and by the Packard Foundation.
CITATION: Jenny L. McGuire, Joshua J. Lawler, Brad H. McRae, Tristan Nuñez, and David Theobald, “Achieving climate connectivity in a fragmented landscape,” (Proceedings of the National Academy of Sciences, 2016). www.pnas.org/cgi/doi/10.1073/pnas.1602817113
Georgia Institute of Technology
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Writer: John Toon
College of Sciences Dean Paul M. Goldbart has appointed J. Todd Streelman to serve as the chair of the School of Biological Sciences, effective August 15, 2016. The School of Biological Sciences is a new unit within the College of Sciences, effective July 1, 2016.
A professor and associate chair for graduate studies in the School of Biology, Streelman joined Georgia Tech in 2004. Previously, he did research at the University of New Hampshire, where he was the recipient of an Alfred P. Sloan Foundation Postdoctoral Fellowship in Molecular Evolution. Since joining Georgia Tech, he has been honored as a Sloan Foundation Research Fellow in Computational and Evolutionary Molecular Biology and with a National Science Foundation CAREER Award.
Streelman’s research is focused on the relationship between genotype and phenotype in wild vertebrates, often via studies of cichlid fishes from Lake Malawi, in Africa. Major themes include aspects of the genomic and cellular circuitry of complex behavior, tooth and taste bud patterning and regeneration, and developmental diversification of the brain. Streelman served as associate editor for the journal Evolution and is a standing member of the National Institutes of Health Study Section on Skeletal Biology Development and Disease.
For the past four years, Streelman has played a pivotal role in defining the research themes for the Engineered Biosystems Building I, Georgia Tech’s inspiring new venture to catalyze interactions between life scientists and life engineers. He also co-chairs an Institute task force charged with developing Georgia Tech’s strengths in the field of neuroscience.
“My colleagues in the College of Sciences team and I are excited to be partnering with Todd and our colleagues in the School of Biological Sciences,” says College of Sciences Dean Paul M. Goldbart.
The new School of Biological Sciences combines the Schools of Applied Physiology and of Biology. The single entity is designed to capitalize on and add coherence to Georgia Tech’s broad strengths in the life sciences, both in research and in the suite of educational opportunities that the school will offer.
In taking on the role of chair, Streelman will be building on the outstanding leadership of Professors T. Richard Nichols and Terry W. Snell, says Dean Goldbart. “Richard and Terry have led their respective schools, Applied Physiology and Biology, with distinction, and they have guided the fusion of the schools with sensitivity and vision. I thank them for their critically important contributions.”
“I am thrilled to be named chair, on behalf of my colleagues in the School of Biological Sciences,” Streelman says. “I am excited to continue progress made under Richard and Terry, to both sustain and propel innovative research and teaching in the life sciences.”
Streelman’s appointment follows a national search conducted by Georgia Tech faculty members Linda E. Green, Brian K. Hammer, Julia Kubanek, Garrett B. Stanley, Joshua S. Weitz, Loren D. Williams, and Soojin Yi. Leading the search committee was Hang Lu, of Georgia Tech's School of Chemical and Biomolecular Engineering.
The National Institute of Environmental Health Sciences has awarded Dr. Francesca Storici, Associate Professor in the School of Biological Sciences, a new five-year grant entitled “Ribose-seq profile and analysis of ribonucleotides in DNA of oxidatively-stressed and cancer cells”. This $1.4 million project will focus on ribonucleoside monophosphates (rNMPs), the subunits of RNA, that are the most common non-canonical nucleotides found in genomic DNA with several thousands in the yeast genome and more than a million in mouse DNA. These rNMPs distort the DNA double helix, altering DNA function and increasing DNA fragility and instability. There is a pressing need to determine where rNMP sites are in DNA, especially in cells that are under stress and/or with abnormal genome stability, like cancer cells. Storici’s team developed a method to map rNMPs in genomic DNA ‘ribose-seq’ and applied it to the yeast cells. They discovered a widespread, but not random distribution of rNMPs with several hotspots in nuclear and mitochondrial DNA. This new project, together with collaborators Dr. Fred Vannberg from the School of Biological Sciences and Dr. Gianluca Tell from the University of Udine in Italy, will investigate how the profile of rNMP incorporation into genomic DNA changes upon oxidative stress, and whether there is any link with cancer phenotypes.
Timothy C. Cope, a professor in the School of Biological Sciences and the Wallace H. Coulter Department of Biomedical Engineering and a member of the Parker H. Petit Institute for Bioengineering and Bioscience, has been appointed to the Clinical Neuroplasticity and Neurotransmitters (CNNT) Study Section at the Center for Scientific Review, a branch of the National Institutes of Health (NIH).
According to NIH, the CNNT Study Section “reviews applications describing small animal and subhuman primate models of epilepsy, neurodegeneration (Parkinson’s disease, Amyotrophic Lateral Sclerosis, diabetic neuropathies) and spinal cord injury.”
"I see study section service as an important responsibility,” Cope says. “It's also a valuable opportunity to learn how fields are trending and to stay up with conceptual and technical advances.”
Cope will serve on the study section until June 30, 2020. During his tenure, he will review grant applications submitted to the NIH, make recommendations on these applications to the appropriate NIH national advisory council or board, and survey the status of research in the field.
“These functions are of great value to medical and allied research in this country,” says Richard Nakamura, the director of the Center for Scientific Review. “Membership on a study section represents a major commitment of professional time and energy, as well as a unique opportunity to contribute to the national biomedical research effort.”
“We’re proud every time one of our faculty members is chosen for study section service,” says J. Todd Streelman, chair of the School of Biological Sciences. “For Tim in particular, it means that he is well-respected by his peers and by the NIH. Study section service is hard work, but it’s rewarding to be part of the process.”
Streelman himself serves on the Skeletal Biology Development and Disease (SBDD) Study Section. Other School of Biological Sciences faculty members who serve on NIH study sections are Hang Lu, Enabling Bioanalytical and Imaging Technologies (EBIT) Study Section; Eric A. Gaucher, Genetic Variation and Evolution (GVE) Study Section; Lewis A. Wheaton, Risk, Prevention and Health Behavior (RPHB) Integrated Review Group; and M.G. Finn, Nanotechnology (NANO) Study Section.
College of Sciences
Dr. Francesca Storici, associate professor in the School of Biological Sciences, was awarded $690,000 for a 3 year project to study the mechanisms of RNA-DNA recombination. This project is funded by the National Science Foundation’s Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences. Dr. Storici and collaborators recently discovered a novel mechanism of genetic recombination and DNA damage repair via exchange of genetic information from RNA to DNA in budding yeast cells, yet little is known about how this process is activated and regulated. The proposed research will enable mechanistic characterization of this newly discovered phenomenon and describe how RNA participates in DNA repair. The study also will provide important biological insights to better understanding the physiological role of RNA in DNA stability and its impact on genome maintenance and evolution. The work is significant because it will provide molecular understanding how cells repair their DNA and how this process goes wrong in diseases like cancer. The expected discoveries will be integrated into classroom topics and activities for many graduate and undergraduate students. Through the inclusion of a Research Experience for Teachers (RET), the project will engage numerous students from a local, 100%-minority high school in lab experiences, and will support student participation in Science, Technology, Engineering and Math (STEM) programs, particularly in molecular biology.
Will Ratcliff is having a moment in the spotlight for getting yeast and algae to jump through hoops to new evolutionary heights.
The magazine Popular Science has heaved the researcher from the Georgia Institute of Technology into its annual list “The Brilliant 10,” a select roster of “the 10 most innovative young minds in science and technology.” Ratcliff was praised for advancing the study of cellular evolution.
PopSci cited his work demonstrating how single-cell organisms may have transitioned into simple multicellular organisms ages ago. It’s widely seen as an arduous evolutionary leap, since single cells had to forfeit a lot of their own fitness for the greater good of creating viable cell groups.
“William Ratcliff revealed surprising insights into what might have been necessary for this transition to occur,” Popular Science wrote in its September/October edition. He has illuminated “one of the greatest mysteries of life.”
The needs of the many
Ratcliff, an assistant professor in Georgia Tech's School of Biological Sciences, has put thousands of generations of yeast and many generations of algae cells through stresses in the lab devised to get them to evolve better survival strategies around forming cohesive groups.
“We’re figuring out kind of clever ways to get them to form groups and then for those groups to become more complex,” he said.
The idea is to end up with a rudimentary multicellular being with cells taking on specialized roles, a very early step on the pathway to organ development. But the first advantage to group formation is simple -- size. Bigger is often better.
“A lot of small predators have small mouths that are great at eating single-cells,” Ratcliff said. But big multicellular cell clusters are too big for these predators to get their mouths around. Clustered cells survive to pass on their genes.
Race to the bottom
To accelerate the evolution of yeast from individuals cells into cell groups called “snowflakes,” one of his signature achievements, Ratcliff has selected for yeast cells that sink more quickly. There, again, big clusters sink better than single cells.
Once clusters are done outcompeting the unicells, they compete against each other. “It’s remarkable how quickly snowflake yeast clusters evolve new traits that let them win this race,” he said.
While the group gains various strengths, it sacrifices the viability of individual cells. “They evolve a division of labor in the group, in which some of them commit suicide,” Ratcliff said. That changes reproductive patterns, which makes the clusters’ progeny more competitive.
The loss of individual cell fitness is extensive.
The more robust a cluster gets, the less likely its individuals are to survive if they are caused to revert back to individual cells. It’s like an odd twist on the traditional marriage vows: Part, and you will die.
Much of Ratcliff’s research is funded by NASA’s Exobiology program and the National Science Foundation.
Felt it coming
Before Popular Science called for an interview for its four-paragraph nod, Ratcliff had sensed something was coming. For a few months, while the magazine cemented its list, it asked around at scientific societies about noteworthy up-and-coming researchers.
As a result, Ratcliff received some veiled tips.
“A couple of colleagues of mine said, ‘Hey man, I got a call from a reporter. I can’t tell you anything about it, but you may be hearing something soon,’” he said.
When PopSci called, a reporter told Ratcliff that many scientists had mentioned him, strongly influencing the decision to name him one of "The Brilliant 10." “That was very touching that people within the research community said to them they should look at my lab,” Ratcliff said.
Hail Mary pass
Life’s small coincidences have helped guide Ratcliff’s academic strivings down the path of evolutionary research.
His career in biology spawned from childhood, when his parents carted him and his brother Felix off in their summers to woodland family cabins next to craggy Pacific Coast cliffs near Mendocino, California. “There was really nothing to do except to run around the forest and the ocean checking out the lives of plants and animals,” Ratcliff said.
They got hooked; both brothers became biologists.
Plants became Ratcliff’s passion at an early age, which led to a bachelor of science in plant biology from the University of California, Davis, but that threw his career a serendipitous curve. “I thought it would have a lot to do with ecology, but it turned out to be mostly cellular biology.”
The decision to see if yeast cells could be coaxed into making the leap to multicellularity was also slightly capricious. “There was a lot of doubt surrounding it, but I thought, ‘Why not just give it a try and see,’" said Ratcliff, whose Ph.D. is in ecology.
He was astonished when that longshot worked. “It was a kind of Hail Mary pass,” he said. It led to a dedicated research specialization and a notable body of continuing work.
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Writer and contact: Ben Brumfield