Category: science

Genome analysis creates tree of life for modern birds

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Long long ago in a land far far away not so far from here at all, crocodiles, dinosaurs, and birds all arose from early reptiles called thecodonts.

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Using new computational methods developed by assistant professor of statistics Liang Liu, Travis Glenn of the College of Public health and others, an international team of scientists has shed more light on an obscure period of avian evolution and further untangle the bird family tree.

Members of the Avian Phylogenomics Consortium—composed of 200 researchers from 80 institutions and 20 countries—have sequenced and analyzed the genomes of 48 species of birds and three species of crocodiles to better understand the fundamental evolutionary events that led to feathers, flight and song.

The consortium simultaneously published 28 papers this past week—eight papers in a special Dec. 12 issue of Science and 20 more in Genome Biology, GigaScience and other journals.

Glenn, an associate professor of environmental health science in the College of Public Health; Liu, an assistant professor in the department of statistics and Institute of Bioinformatics in the Franklin College of Arts and Sciences; and John Finger Jr., a doctoral student in the Interdisciplinary Toxicology Program and College of Public Health, were co-authors on two of the eight papers published in Science.

The first of these two papers, "Whole genome analyses resolve the early branches to the tree of life of modern birds," creates the most reliable tree of life for birds to date.

Fantastic work by our faculty and all members of the consortium, all celebrated in a special issue of Science. This is the kind of atmosphere that attracts the best graduate students, among other interested parties. So we celebrate this marvelous achievement and all the other indicators it provides, campus-wide and beyond.

Uma Nagendra Dances her Ph.D.

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This is a quite visionary joining of art and science:

University of Georgia doctoral student Uma Nagendra flipped and twisted her way to the top prize in the seventh annual Dance Your Ph.D. contest for her video explaining biology research through an aerial dance performance.

The contest, sponsored by Science Magazine, the Association of the Advancement of Science and HighWire Press, challenged scientists around the world to explain their Ph.D. research through the art form of dance. Nagendra's video was chosen from 12 finalists as the overall winner by an expert panel of scientists and artists. Her video also won first place in the biology category.

Nagendra, a student in the Franklin College of Arts and Sciences department of plant biology, studies how forests regenerate after severe disturbances like tornadoes.

n 2005, Nagendra's home city of New Orleans was devastated by Hurricane Katrina. This piqued her interest in studying how the natural world recovers from disasters. Nagendra began her doctorate at UGA in 2011 and set out to research tornadoes, a more readily occurring disaster.

Nagendra attended the New Orleans Center for Creative Arts part time as a high school student but later shifted her attention to science as an undergraduate at Swarthmore College.

"From the moment I first saw a Dance Your Ph.D. video, I knew I would enter the contest someday," she said. "I really think that art can help communicate scientific ideas and fuel creative thinking."

Anthropocene: Economics of the transition

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renewable_energy.jpgSomething that often goes missing in conversations on, much less debates about, what to do about climate change is optimism. If, for example, a discussion of the economics of the transition to an industrial model from the agricultural age had occured, there would have been great gnashing of teeth but a convincing case could have been made, though likely with some strict limitations toward eventual consequences, if these could have been imagined. The point is, the same dynamics are at play when trying to imagine the transition away from a dependence on fossil fuels; we're limited by how things work now - travel, food production, growth, defense - and that present bias makes any transition all the more unimaginable, optimism evaporates and we choose to do nothing as though it's an preferable option. The next Anthropocene Lecture takes on this very question:

The lives of six out of the seven billion people now living on Earth are dependent on a combination of technology and fossil fuels.  Green Revolution crops have greatly increased food production, but only when supplied with plentiful fossil fuel inputs.  Supporting an even larger world population without using fossil fuels will pose a major technological challenge.  Transitioning away from fossil fuels on a global scale is a huge challenge but deploying new technologies is our best hope.  This lecture assembles a variety of data to present a coherent, quantitative view of both the challenges and the opportunities.  It concludes by examining the current state of the art of using markets to drive the transition to carbon-free energy systems. 

These are the discussions we need to have, led by the folks who need to lead them. Come be a part of the discussion. Knowledge is power and the switch gets flipped at 7 pm Thursday Oct. 9 in the Chapel. Free and open to the public.

Jessica Kissinger: making research usable

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Jessica_Kissinger.jpgGreat opportunity to feature not just one of our star faculty members, but also an emerging challenge for all researchers everywhere in this era of big data:

Jessica Kissinger is a molecular geneticist whose research on the evolution of disease and the genomes of eukaryotic pathogenic organisms—Cryptosporidium, Sarcocystis, Toxoplasma andPlasmodium (malaria) among them—has led her to perhaps the emerging issue among research scientists: managing data.

"To solve a complex problem like a disease, whether you're looking for a new drug target or just trying to understand the basic biology of an organism, how it interacts with its host, you have to bring together a lot of data sets," Kissinger said. "You want to be able to take the expertise of the community at large, with individually generated pieces of the puzzle, and then try to stitch them into a quilt that creates a better picture."

Kissinger's local community at UGA includes the genetics department, the Center for Tropical and Emerging Global Diseases and the Institute of Bioinformatics, where she serves as director. But her focus is the wider world of scientists and helping make the data they produce more accessible, sharable and reusable.

"So many resources go into generating some of these highly specialized data sets, with very difficult to work with and hard to culture organisms, and publishing your results doesn't necessarily make the data usable," she said. "I work on that usability part-taking data generated elsewhere and integrating it to help others access it and use it well."

Our researchers and those around the U.S. world now produce mountains of publicly available data that must be managed and archived properly in order to be utlized by other researchers. It's the way we build on scientific discovery now - whether it is about DNA of nutirents in deep ocean plumes or T-cells in the body - and the shoulders of giants now include alot of 1s and 0s. Kudos to Kissinger for maintaining her own lab investigations while also giving full force attention to bioinformatics practices that are the steps to the next great heights.

 

 

UGA discovery: building better plants

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xylan.jpgThe complexity of natural materials has long been a point of fascination for scientists, and has only increased as the technology to look closer has itself evolved. The structure and development of sea shells, for example, holds great potential for nanotechnology and building light weight materials of great strength. So, too, the cell walls of plants, whose flexibility and strength depend on two critical proteins. Now UGA scientists have discovered how these fundamental components of plant life might one day help scientists engineer improved plants for biofuels, construction materials, medicine and food production:

"The scientific community has identified a large number of proteins that the plant uses to assemble its cell walls, but it has been very difficult to identify those few proteins that are directly involved in the construction of key polysaccharides like xylan," said Will York, professor of biochemistry and molecular biology in UGA's Complex Carbohydrate Research Center and principal investigator of a CCRC research team that recently published the paper describing its results in The Plant Journal.

"The work we've done gives us the fundamental knowledge we need to manipulate plants for industry and agriculture," said York, who is a member of the Bioenergy Science Center, a partnership of Oak Ridge National Laboratory, the University of Georgia and other university and industry partners. It is one of three bioenergy research centers established by the Department of Energy in 2007 to accelerate progress toward development of liquid biofuels that add an affordable, sustainable, domestically produced option to the nation's energy supply.

Understanding how and why plants don't make enough xylan and so do not grow normally and thus cannot transport life-giving water from the roots to the leaves is potentially major breakthrough. The complexity evinced by millions of years of evolution holds unlimited promise, and as scientists continue to unlock different rooms in the grand, mysterious mansion of life on Earth, unimaginable connections, products and processes become possible. The force of great research is as humbling as the wonders of life it seeks to understand. Congratulations to the teams at the CCRC and the national research centers who support their work. 

Image: Electron micrograph scan shows a dried film of polymeric xylan isolated from Arabidopsis thaliana stems.

Next Science Cafe subject - Vaccinations

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SciCafe Vaccines.jpegAre vaccinations controversial? And what does that even mean when the vast majority of physicians are troubled by the so-called anti-vaccination movement. There is little doubt that the administration of antigenic material (aka vaccines) to stimulate an individual's immune system to develop adaptive immunity to a pathogen is responsible for the worldwide eradicaiton of smallpox and the diminution of polio, measles and tetanus. So... what's the controversy about? 

On Tuesday, September 16th at 7pm at Hendershot's Coffee Bar, the Athens Science Cafe presents "Immunize This! The Challenges of Vaccine Communications," led by Grady College professor Glen Nowak. Doors open at 6:30pm, and the event is free and open to the public. Athens Science Cafe is supported by the UGA President's Venture Fund, UGA Office of Academic Programs, UGA Science Library, UGA Public Service and Outreach, and UGA Biological Sciences. The Franklin College fully supports public discussions of science and/or any other topic where campus expertise can broaden confidence and understanding.

In the service of learning more about vaccines prior to next week's science cafe the NOVA special, "Vaccines -- Calling the Shots," premieres in the U.S. on Wednesday, September 10th at 9pm. Dr. Nowak was involved as a technical advisor in the production of this documentary. Check it out, get up to speed, come to Hendershot's and be a part of the discussion.

Science Learning Center: breaking ground

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UGA-ScLC-rendering.jpgThe D.W. Brooks mall on South Campus is about to [begin to] change for the better, with much-needed science instruction space in the new Science Learning Center:

The University of Georgia will break ground on its newest building-the 122,500-square-foot Science Learning Center-on Aug. 26 at 11:30 a.m. at the south end of the S10 parking lot located just off Carlton Street.

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The Science Learning Center will be situated on South Campus adjacent to Pharmacy South and across from the Miller Plant Sciences Building. Funded by Deal and the Georgia General Assembly, the center will cost $44.7 million and be designed around an environment that promotes active learning.

The building's 33 instructional labs will be designed specifically for interactive learning in core undergraduate science courses. The Science Learning Center also will contain two 280-seat lecture halls and two 72-seat SCALE-UP classrooms. SCALE-UP stands for Student-Centered Active Learning Environment for Undergraduate Programs, a learning model that focuses heavily on group-work class participation and technology-making student-to-student and student-to-teacher interaction easier in a larger class setting.

The building is scheduled to open in fall 2016.

Okay, that seems like a long way off but it will be here before you know it. Great news for students and faculty in the sciences, which more than ever, venture into many more disciolines than we have traditional associated with only chemistry or biology. But definitely for all our science majors, this new building is a welcome new addition to the campus learning environment.

Image: A rendering of the Science Learning Center shows how the new building will be situated on UGA's South Campus.

 

Microscopic photos spotlight the art of science

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thale cressWhile they are often identified as poles, a spectrum or even a line of demarcation from one kind of investigation into another, science and art can and occasionally do cohabitate, as in the case of UGA research scientist Stefan Eberhard, who utilizes scientific instrumentation for creative purposes:

2014 CURO Symposium

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Once again the best in UGA undergraduate research, heavy with Franklin College students, will be presented at the annual symposium by the Center for Undergraduate Research Opportunities March 31 and April 1 at the Classic Center in downtown Athens:

Since its inception in 1999, the CURO Symposium has provided a public space for students from all academic disciplines to share their research with their peers, the UGA research community and others.

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Among the more than 150 student research projects to be presented at the CURO Symposium are:

• "Perceptions about Global Development," a poster by Alexa DeAntonio, a third-year biological sciences major. DeAntonio has been examining the public's awareness, attitude and knowledge of the developing world and the role the media plays in shaping those perceptions.

• "Octopaminergic Gene Expression and Flexible Social Behavior in the Subsocial Burying Beetle Nicrophorus vespilloides," an oral presentation by Mary Douthit, a fourth-year biology major. The project looks at how genetics influences the social behavior of the burying beetle species Nicrophorus vespilloides.

Great work by many talented students. The opportunity to conduct research during the undergraduate years allows students to test out a variety of career paths within and outside of the laboratory. The symposium is open to the public, so be sure to check it out.

AAAS on Climate Change: What We know

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photo-consensus-senseThe American Association for the Advancement of Science launched a big climate change initiative today, "What we Know":

At the heart of the initiative is the AAAS's "What We Know" report, an assessment of current climate science and impacts that emphasizes the need to understand and recognize possible high-risk scenarios.
"We're the largest general scientific society in the world, and therefore we believe we have an obligation to inform the public and policymakers about what science is showing about any issue in modern life, and climate is a particularly pressing one," said Dr. Alan Leshner, CEO of AAAS. "As the voice of the scientific community, we need to share what we know and bring policymakers to the table to discuss how to deal with the issue."

The Nobel laureate Mario Moilina, Diana Wall and James McCarthy, along with the 10 panelists spanning climate science specialties, will engage in the initiative in various ways, from speaking engagements to testimonial on a forthcoming interactive web site to knowledge sharing with other professionals. The initiative encourages Americans to think of climate change as a risk management issue; the panel aims to clarify and contextualize the science so the public and decision-makers can be more adequately informed about those risks and possible ways to manage them. 

Emphasis mine, as these 10 panelists of course include our own J. Marshall Shepherd. Good for the AAAS for not sitting on their hands any longer, but actually getting to work. It's a rare intervention by the group, but the stakes couldn't be higher and this debate demands a much higher profile.