InSites is a quarterly newsletter that highlights the personalities and projects of the Waste Management Research and Education Institute (WMREI) of The University of Tennessee. WMREI is an affiliate of the EERC.
WMREI was created in 1985 as a state-funded Center of Excellence. Research areas include solid-, hazardous-, and nuclear-waste management; waste minimization; and pollution prevention.
Biotechnology is the focal point of the institute's technical research, while issues involving public attitudes and federal/state policies related to waste-management issues are the primary concerns of the institute's policy research.
For additional information about InSites, or to be added to our mailing list, please write InSites, WMREI, The University of Tennessee, 311 Conference Building, Knoxville, TN 37996-4134, call 865-974-1156, or fax 865-974-1838. Or, if you prefer, email us.
Table of Contents
CRACKING the CELL CODE,
By Elise LeQuire
A SEMESTER for the ENVIRONMENT ,
By Elise LeQuire
Bilingual in Research
and Education ,
By Kris Christen
Appalachian
Mountain Man
,
By Kris Christen Call to Service 
CRACKING the CELL
CODE
It took scientists 13 years to map the human genome, but it could take longer
than that, decades perhaps, to simulate the cellular processes of a single
E. coli cell. To fuel the next revolution in the understanding of biological
systems, researchers will need faster computational tools and better analytical
methods that can unravel the complex behaviors of simple organisms.
With the help of funding from the National Academies and
the Keck Foundation, an interdisciplinary team of researchers at the University
of Tennessee (UT) hopes to accelerate the computational speed of traditional
computer software and hardware that simulate the action of the genetic circuits
and networks that enable cells to function.
SIGNALING SUBTLETIES
Their work targets the signaling processing that allows cells to perform crucial
functions, such as coordinating movement of cancer cells that leads to metastasis.
Seed money for innovative research on cell signaling comes from the National Academies Keck Futures Initiative. Among the first 11 research teams nationwide to receive the awards is a group of scientists led by Michael Simpson, Distinguished Scientist at Oak Ridge National Laboratory (ORNL) and UT professor of Materials Science and Engineering.
“The intent of this grant is to foster interdisciplinary research to get people in the physical sciences to bring their approach to questions of biological significance and to bring a quantitative mathematical background to the table of biological research,” Simpson says. The $75,000 Keck Futures Initiative award is being used to recruit graduate students and postdoctoral fellows, invest in equipment, and outline a research strategy.
Two graduate students will be involved on a full-time basis on the project.
Mike McCollum brings his expertise and past contributions
to the systems biology community in computer simulation. Derek Austin is a
high-level contributor to interdisciplinary research projects of the Molecular-Scale
Engineering and Nanoscale Technologies (MENT) Research Group at ORNL, directed
by Simpson. Michael Allen, the postdoctoral fellow in the project, has also
worked as part of the interdisciplinary MENT group and performed research
at UT’s Center for Environmental Biotechnology, directed by Gary Sayler.
SPEED THRILLS
With the computer simulations of today, Simpson says, “to analyze every
reaction in a cell such as E. coli during an entire cell cycle, if we went
flat out as fast as we could go with the best supercomputer in the world,
the simulation time would be decades. We have to make orders-ofmagnitude improvements
in computational speed and algorithm efficiency to allow simulations on a
time scale that makes sense.”
Simpson hopes such revolutionary advances in simulation speed will be to the systems biology community what the development of the computer chip was to the semiconductor industry.
Gregory D. Peterson, an assistant professor in the Department of Electrical and Computational Engineering at UT, is part of a team working on new techniques to speed up simulation time using reconfigurable computing, “building a custom circuit to solve a specific problem on the fly.”
This work involves using stochastic simulation algorithms with simple cell models. “Stochastic is a fancy way of saying random processes,” Peterson says. “Basically, we use statistics to figure out the random probability that the next reaction will be of a certain type, drawing random variables to see which reaction happens next at what time.”
In Vibrio fischeri, for example, a bioluminescent
marine organism, the process that makes it glow is regulated by quorum sensing.
“Individual cells don’t glow by themselves; they generate signaling
molecules,” Peterson says. “We are exploring the mechanisms that
turn the genome into a functional system—the nuts and bolts of how the
genome works.”
PARALLEL UNIVERSES
Chris D. Cox, an associate professor in UT’s Department of Civil and
Environmental Engineering, is helping provide a real biological context for
the computational simulations. The aim of systems biology is to apply mathematical,
computational, and engineering principles to the process of biological discovery.
“If we can understand on a more fundamental level the systems behavior of cancer or pulmonary disease, we are more likely to really streamline the testing of new drugs and therapies,”Cox says.
Cox is working to ensure that the computer simulations actually parallel processes in real biological models.
“Biological models have a certain architecture or
typology of how one gene is connected to another,” he says.
PATHWAYS OF DISCOVERY
Many disease processes—including cancer, diabetes, and cystic fibrosis—represent
a malfunction in the processing of cell communication. In diabetes, for example,
there are two signals, glucose and insulin, which are used by the body to
regulate the blood-sugar level.
“When the body reads these wrong, you may have plenty of insulin, but the body ignores it, and you don’t metabolize the glucose and cannot maintain a healthy blood-sugar level,” Peterson says.
Cell signaling is also the mechanism that allows cancer cells to grow. “In cancer, the cell does not process the information properly, and the control mechanisms of the cell aren’t working to keep them from growing wildly. Once you understand these basic processes, you can detect sooner when they have gone wrong,” Peterson says.
Understanding cell communication may allow therapeutic intervention in these processes to defeat deadly infections. The lungs of patients with cystic fibrosis, for example, are infected by a nasty bacterium Pseudomonas aeruginosa, which uses quorum sensing to coordinate group behavior leading to the formation of a biofilm that impedes respiration. Once established, P. aeruginosa cannot be completely defeated by antibiotics and other remedies.
“If you could devise a scheme to defeat the quorum system, you might keep the microorganism from forming a biofilm,” Simpson says, like jamming the radio of the enemy in battle to defeat its communications system.
* * *
Contact Michael Simpson, MENT Research Group,ORNL, P.O. Box 2008, MS 6006, Oak Ridge, TN 37831-6006, call 865-574-8588, or email simpsonML1@ornl.gov.
A SEMESTER for the ENVIRONMENT
With nearly 200 courses across almost 40 disciplines, the University of Tennessee
Knoxville (UTK) offers an impressive array of academic routes for students
interested in environmental studies, from fish physiology to philosophy.
To underscore the reputation of university faculty in environmental research, education, and outreach, and to foster environmental stewardship on the UTK campus, the University has established an Environmental Semester for spring 2005 and is planning a host of activities across campus. The effort was spearheaded by an interdisciplinary steering committee, with the full support of the administration.
“We are situated in one of the most environmentally diverse regions in the world to consider environmental issues,” says Loren Crabtree, chancellor of UTK. “This is a wonderful opportunity to make a difference among students, faculty, and staff on environmental concerns.” The university is backing the program with a $100,000 budget.
Not only does UTK boast research scientists with international reputations in a wide variety of environmental fields, including air pollution, ecosystem and species monitoring, and environmental bioengineering, its established ties to Oak Ridge National Laboratory give researchers unparalleled access to the lab’s supercomputer, which can model the global environment, Crabtree says.
“UT has a lot of capability, and we are going to celebrate that in the spring,” he says. The idea for the semester sprang from a UT President’s Salon, under the aegis of University Studies, in 2003. The brainstorming sessions quickly revealed the wealth of existing resources that could be tapped to further environmental awareness on campus.
The activities for Environmental Semester 2005, including lectures, gallery exhibits, conferences, and competitions, will center around seven priority areas: energy sources, oil and national security, the Clean Air Act, global climate change, species conservation, bioengineering, and Earth Day, says Mary English, research leader with the University’s Energy, Environment and Resources Center (EERC) and co-coordinator of the Environmental Semester’s steering committee.
“We have the backbone of the semester in place,” says Neil Greenberg, professor of Ecology and Evolutionary Biology, who co-coordinates the steering committee with English. Once the committee had collated the course offerings and areas of faculty expertise, it was impressed at what a powerhouse UTK is in environmental areas, from the hard sciences to the liberal arts.
MARK YOUR CALENDARS GREEN
To kick off the celebration in January, Robert F. Kennedy Jr., an environmental
lawyer with the Natural Resources Defense Council and UTK’s Environmental
Semester Distinguished Lecturer, will speak on the environmental destiny of
the United States.
February 18-20, Students Promoting Environmental Action in Knoxville (SPEAK) and the Southern Alliance for Clean Energy (SACE) will cosponsor the Second Annual Southeast Student Renewable Energy Conference, a collaborative effort to promote sustainable energy use on campuses in the region. And on March 15, sociobiologist E.O. Wilson, the Chancellor’s Distinguished Interdisciplinary Speaker, will speak on species conservation.
The Clean Air Act Conference, March 8-10, will provide a retrospective look at how the Clean Air Act (CAA) came about and how it has evolved in the decades since its enactment in 1970. Cosponsored by the Howard H. Baker Jr. Center for Public Policy, EERC, and the Joint Institute for Energy and Environment, the conference will host a colloquy consisting of key policy players in the creation and evolution of the CAA.
The Baker Center was named for the Tennessee senator who was a key force in creating the CAA.
“We hope to attract some heavy hitters in terms of how the Clean Air Act has been implemented and where it is today,” says Jack Barkenbus, EERC executive director.
Senator Baker, who has an international reputation as a nature photographer, is also the honorary chair of a panel of jurors for a nature photography show and nature conservation art exhibit to be held in the University Center Gallery.
The Frank H. McClung Museum, which houses one of the premier collections of archeology and anthropology in the Southeast, will hold a four-month exhibit titled “Lost Worlds: Discovering Past Environments.” Focused on the history of mankind, its ecosystems, and natural history, the exhibit will run from January 21 through May 22. The Museum will also host occasional speakers throughout the semester.
The College of Architecture and Design will host a retrospective of the work of environmental artist and conceptual designer Agnes Denes at the Ewing Gallery of Art and Architecture from January 10 to March 7.
The Ewing Gallery is also working with the American Institute of Architects to bring an exhibit titled “Top Ten Green Projects,” spotlighting the best of the nation’s sustainable architectural designs.
Throughout the semester, an energy competition, “Make Orange Green: The Residence Hall Conservation Challenge,” will raise awareness of practical approaches to energy conservation on campus.
“This is a student initiated program that was approved by the Housing Department. Our goal is to sponsor a competition within residence halls throughout the semester,” says Sarah Surak, UTK recycling coordinator. “The residence hall that conserves the most energy will win a big cookout in April.”
To wind up the semester with a celebration of “Earth Music,” the Paul Winter Consortium will perform in Cox Auditorium on April 15.
In addition, Career Services will hold a major conference for students interested in environmental careers, inviting potential employees from a number of sources, including the U.S. Forest Service, the U.S. Environmental Protection Agency, and big business.
“I am going to be very happy if students with concern for the environment will see that, whatever their major, whether law, business, art, English, or the sciences, they can help engage the immense problem of the environment at the career level, in their professional lives,” says Greenberg.
* * *
On events on the Environmental Calendar, visit the Environmental Semester 2005 Web site at <http://environmentalsemester.utk.edu/>.
Bilingual in Research and Education
RESEARCH ACADEMICS, PARTICULARLY those who work in education, are often criticized for being too cozily ensconced in ivory towers to be aware of what’s really going on in the public school system. Nobody can level that criticism at Rosalyn McKeown, director of the University of Tennessee’s (UT’s) Center for Geography and Environmental Education, a division of UT’s Energy, Environment and Resources Center (EERC).
Taking this message to heart, McKeown took a two-year hiatus from EERC to teach geography, earth science, and Spanish in the public high schools. The experience brought her face to face with the social issues—be they drugs, alcohol, physical and emotional abuse, divorce, or poverty—that impinge on schools today.
“Because adolescents are living in that world, they come to school with those issues sitting on their shoulders as part of their being,” McKeown says. And “if their family life is weighing so heavily on their minds, they’re probably not going to be able to come into your classroom and concentrate on your curriculum.”
Helping her students come to terms with such issues taught her a lot about teaching, curriculum, and the social context of schools. “I tell my colleagues now that I’m bilingual; I speak both high school and university,” McKeown says.
Now, back from the classroom, she’s looking to turn those experiences into research projects to develop better teaching methods, as well as to train teachers how to deal with diversity. And what she has to offer is of tremendous benefit to UT, says Jack Barkenbus, EERC’s executive director.
“She brings the perspective of an educator who understands the teaching requirements, guidelines, and frameworks that many of us scientists overlook, at our peril,” Barkenbus explains. “Her expertise and knowing how information is processed in the educational system is a significant contribution to getting our work accepted in the real world.”
Understanding Learning Styles
One project McKeown is working to get funded involves gaining a better understanding
of the different ways in which students learn. The findings could have both
curricular and policy implications.
The way McKeown puts it, she discovered that her students just weren’t picking up on the geographical locations of countries around the world. “I could be talking about India and pointing to it on a map, but when I gave my students a map test requiring them to identify countries with major landmasses, they couldn’t necessarily get countries other than the United States and Canada,” she says. “It didn’t make sense because they were bright students.”
Since people tend to learn through different channels—such as visual, auditory, or tactual-kinesthetic—she gave her students a learning modality inventory, which poses a series of questions surrounding one’s learning preferences. For example, questions might ask, do you start a project before reading the directions? Or, do your papers and notebooks seem messy? When you take a test, can you see the textbook page in your head? If you hear something, will you remember it?
She found that none of her students was visual, a big problem since geography is a visual discipline, enriched with maps, pictures of the world, charts, and diagrams.
“The question therefore was, how could I modify the curriculum to meet their learning needs better, and how could I support them in becoming more visual students,” McKeown says.
Further research showed that her auditory students weren’t turning in their reading assignments, so she started playing their textbook on CD/ROMs, allowing the students to follow along in the text or just listen.
Telling the students stories about a particular country during her lectures also seemed to help them retain more knowledge. So did giving them outlines of her lectures so that the students could see where she was headed. “I would leave blanks in the lecture outlines, so they’d have to stay on task, listening and then filling in the blanks. That way they could see how the material was organized,” she explains.
A host of questions arose through this experience in terms of whether this was just an unusual class or more a matter of tracking students. McKeown also wonders whether these things need to be addressed more formally in curriculums.
“The way you see these things play out in the classroom is just amazing,” she says, adding that she’s hoping to repeat this experience on a more widespread basis to determine if what she has learned can be generalized to a larger population.
Teaching Sustainability
Another project McKeown has been heavily involved with and that has helped
put UT on the map internationally is education for sustainable development
(ESD), which was called for at the 1992 United Nations (UN) Conference on
Environment and Development, also known as the Earth Summit, and again at
a UN Commission on Sustainable Development meeting in 1998.
Stated simply, sustainable development is defined in UN documents as “development that meets the needs of the present without compromising the ability of future generations to meet their own needs,” with education being crucial to meeting this goal.
McKeown’s work in this area, which has been part of a larger, worldwide ESD effort headed by UNESCO (UN Educational, Scientific, and Cultural Organization), culminated a couple of years back in a Web-based Education for Sustainable Development Toolkit, which was funded by UT’s Waste Management Research and Education Institute. The Toolkit is essentially an easy-to-use manual to help communities and school systems get started in developing a locally relevant and culturally appropriate educational strategy for sustainable development.
Used by education ministries, policymakers, higher education administrators, and non-profit organizations, among others, the Toolkit Web site (www.esdtoolkit. org) has so far gotten 40,000 hits, and UT has received requests to translate it into 11 different languages.
“Every place I or my co-authors go, people tell us that they’re using our Toolkit,” McKeown says, adding that some of the prose from the Toolkit is showing up in UN documents.
Now that the UN has declared 2005 to 2014 as the Decade of ESD, she’s continuing her focus in this area. As the Secretariat for the UNITWIN/UNESCO Chair on Reorienting Teacher Education to Address Sustainability and the UN University Chair on ESD, McKeown has helped create a network of some 40 teacher education institutions around the world. (UNITWIN is the abbreviation for universities twinning with UNESCO.)
Draft guidelines developed by this group are currently under revision. Additionally, McKeown is working on a paper for the UN University about the challenges and roles of higher education in promoting sustainable development. She’s also thinking about developing a training course complement to the Toolkit for educators and educational administrators.
* * *
Contact Rosalyn McKeown, EERC, The University of Tennessee, 311 Conference Center Building, Knoxville, TN 37996-4134, call 865-974-1835, or e-mail mckeowni@utk.edu.
AS A LONG-TERM RESEARCHER OF THE Southern Appalachian Mountain region, John Peine has built an international reputation in raising awareness of the ongoing assaults on fragile natural resources and developing more sustainable development strategies for minimizing adverse human impacts.
Over the years, as chief scientist for Great Smoky Mountains National Park (GSMNP) and later as adjunct professor in the University of Tennessee’s (UT) Forestry, Wildlife, and Fisheries Department, Peine has studied ecosystems management, sustainable development, land use and sprawl, environmental education, visitor use, and recreation planning, among other issues.
Peine recently joined UT’s Energy, Environment, and Resources Center (EERC), where his expertise adds another dimension “that is needed and useful to cover a wide range of environmental concerns here in the East Tennessee region,” says Jack Barkenbus, EERC’s executive director.
Peine has edited a book with 50 contributors on the principles and practices of ecosystem management in the Southern Appalachian Highlands. An important outgrowth of his efforts includes the GSMNP air-quality program, which has become one of the leading air-quality programs in the National Park Service system and serves as a model in other countries.
Peine’s current research focuses on establishing a network of individuals and institutions involved in environmental inventory and monitoring along the 2,167-mile Appalachian Trail as part of the U.S. Geological Survey’s National Biological Information Infrastructure.
Through a Web site, he’s developing a community of resource managers, scientists, and educators to collaboratively document environmental conditions and trends, with the overarching goal of creating data-collection protocols so that information can be compared along the entire trail corridor.
The idea, Peine says, is to get people talking to each other, engaging them in a more holistic way to better understand what the issues are and the advantages of research collaboration. And such collaboration is particularly urgent now because of the growing number of stressors on the environment.
“The more people are aware of largescale environmental change, the better the chance that some mitigation measures can take place,” Peine notes.
So far, the project encompasses 10 national forests, four National Park System units, a state forest, and several nongovernmental organizations, all of which are engaged in environmental monitoring. Once Peine’s network is up and running, the Appalachian Trail corridor has the potential of becoming one of the longest continental-scale environmental inventory and monitoring transects in the world.
Environmental Pulses
Peine and his colleagues have identified a host of potential inventory and
monitoring themes that best lend themselves to collaboration. They include
adjacent land-use changes and related impacts; forest health; water quality
in springs and first-order streams; air quality, including hiker health and
visibility; climate trends; forest fires; species of concern, including threatened
and endangered species, as well as those that are endemic; breeding birds;
black bears; and grassy balds and alpine meadows. They’ll also be tracking
the infestation status of various exotic pests and pathogens up and down the
trail and methods to control and/or mitigate them.
Through this scale of inventory and monitoring, the researchers and resource managers are hoping to better anticipate what might happen in the future by being more aware of what’s going on right now.
“By placing the state of the environment at any given site within a continental- scale context, there might be a better understanding of the implications of any given perturbation,” Peine explains.
Take the hemlock woolly adelgid, for example, an invasive pest that has devastated numerous groves of hemlock trees in Shenandoah National Park and more recently has begun to infiltrate GSMNP. “There’s a growing awareness of what people are doing to try to combat this pest,” Peine says. “Maybe through this tool, people will realize how important it is to understand the organisms associated with old-growth hemlock stands before it’s too late, because once the over-story forest is dead, the whole system breaks down.”
Climate change adds another dimension to the stressors affecting ecosystems, particularly in the high-elevation areas. But “there hasn’t really been any discussion or collaboration among those engaged in research and resource management concerning the various disparate alpine communities up and down the Appalachian region and the need for an interdisciplinary, landscape-scale risk assessment,” Peine says. He’s counting on the environmental inventory and monitoring system to change that.
Worldwide Application
Peine and his colleagues have chosen to focus their efforts on the Appalachian
region because it represents some of the richest temperate forest biota in
the world. The Southern Appalachians are internationally recognized as a Biosphere
Reserve and GSMNP as a World Heritage Site.
Peine wrote the application for the latter’s designation. More important though, the Appalachian Trail “is an iconic symbol that’s known globally,” Peine says. Consequently, if their plan works, the inventory and monitoring system being set up could serve as a paradigm and be applied globally along other internationally well-known trails.
“It’s valuable to have an iconic symbol that draws people together with a common interest,” he says, pointing out that the National Heritage Corridor initiative got started along similar lines. This concept in natural and cultural resources conservation, which Peine and others first devised, provides a mechanism for the protection and interpretation of resources that are more diverse and widely dispersed than what’s found in traditional national parks.
The Illinois & Michigan Canal, which President Abraham Lincoln lobbied to get built, became the nation’s first federally designated National Heritage Corridor. It has served as a model for the 25 additional National Heritage Corridors/Areas established since then in the United States and been applied abroad as well. The most recent National Heritage Area proposal is for western North Carolina.
* * *
Contact John Peine, EERC, The University of Tennessee, 311 Conference Center Building, Knoxville, TN 37996-4134, call 865-974-4056, or e-mail jpeine@utk.edu.
* * *
Contact Tim Ezzell, CPC, The University of Tennssee, 311 Conference Center Building, Knoxville, TN 37996-4134, call 865- 974-4251, or email tezzell@utk.edu. Contact Eric Ogle at 865- 974-4562 or eogle@utk.edu.
