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
So
Many Genes, SO LITTLE TIME, By Elise LeQuire Nothing
Ventured, Nothing Gained, By Elise LeQuire WATER
MARKS, By Elise LeQuire Staff
Citings
So Many Genes, So
Little Time
Customizing medical therapies to the genetic makeup of individual patients,
determining drug resistance of certain cancer therapies, and exploring the
effects of nanoparticles on aquatic species are a few of the many research
pathways that will benefit from a new facility on the campus of the University
of Tennessee (UT).
The UT Affymetrix Core Facility, located in the Department of Nutrition, is using GeneChip technology developed by the California-based company Affymetrix to speed research across a number of disciplines. The facility, which offers rapid analysis of differential gene expression in more than a dozen species, from yeast to humans, is the result of a multi-disciplinary effort spearheaded by UT’s Department of Nutrition in the College of Education, Health, and Human Sciences, and supported by the Institute of Agriculture, the College of Veterinary Medicine, the Agricultural Experiment Station, the departments of microbiology and biochemistry, cellular and molecular biology, the College of Nursing, and the UT Medical Center, Knoxville, Division of Surgical Research.
“We wanted a core facility for all these departments and other institutions so each one did not have to buy its own expensive equipment,” says Julia Gouffon, who manages the laboratory. This faster, more comprehensive analysis of gene expression allows researchers with little or no background in genetics to explore basic research in fields such as biochemistry and plant pathology, and applied research in clinical health and epidemiology.
Previous gene-array technologies deposited droplets of DNA on glass slides, and only a few hundred to a thousand genes could be represented. The new facility, which has been fully operational since June 2004, represents a revolution in genomic research.
“It’s like going from monks transcribing books by hand to the printing press,” says Gouffon, who brings her expertise in microbiology to the facility. The silicone chip technology combined with photolithography makes analysis of an entire genome comprised of thousands of genes on one chip possible in a matter of one to a few days.
BIRD’S EYE VIEW
Each Affymetrix GeneChip contains an entire genomic sequence of a particular
species, whether zebrafish or mouse or human. This allows researchers to see
beyond what is happening at the individual gene level.
“As a screening tool, it’s like looking at the Mississippi River from a bird’s eye view. You can see which tributary is responsible for the flooding rather than standing at one creek and guessing,” says Jay Whelan, professor and head of UT’s department of nutrition. Whelan’s research explores the effects of omega-3 fatty acids—found in some vegetable and fish oils—and arachidonic acid— found in all animal products—on intestinal, pancreatic, and prostate cancers.
All cancers are the result of a mutation in one or more genes increasing or decreasing their expression, thereby influencing the growth or death of the tumor cells. “You can tweak the expression of these genes up or down like a dimmer switch,” Whalen says.
If researchers want to examine cancer cell proliferation or interventions to inhibit tumor growth, the Affymetrix system allows them to look at both sides of the equation, the genes that regulate cell division and replication in relationship to those genes that regulate programmed cell death, or apoptosis.
“Since the technology can look at all the genes in the cell, you can see what effect a certain intervention has in a number of genes in multiple signaling pathways,” Whalen says.
Isolating the RNA from any specimen, such as a tumor or liver or brain, mouse or human, is easy, Whelan says. “Essentially, a novice can be trained to isolate RNA.”
MOLECULES AND ZEBRAFISH
Researchers in UT’s Center for Biotechnology (CEB) are using the Affymetrix
Core Facility to expand their genomic and nanotechnology research efforts.
Though CEB has been at the forefront of genomic research, much of that work
has been conducted on microorganisms. Theodore B. Henry, an adjunct assistant
research professor with a background in aquatic toxicology, is exploring the
potential effects on zebrafish (Danio rerio) of nanoparticles and endocrine
disrupting chemicals.
“The zebrafish is an excellent model organism for research,” says Henry, who directs CEBs new zebrafish culturing facility. The fish is easy to raise in the lab, the transparent egg shell allows clear observation of embryonic developmental stages, and experiments can be conducted at a fraction of the cost of other vertebrate model organisms.
The use of nanoparticles, especially in electronic applications, is expected to increase dramatically in the future, and the U.S. Environmental Protection Agency wants to know what the potential adverse effects may be. “We are trying to get some understanding of the toxicity of nanoparticles by investigating the effects of C60, a soccer-ball shaped molecule made of 60 carbon atoms joined to form a hollow sphere,” Henry says.
One approach is to expose the fish to C60 molecules, also known as fullerenes, and look for differences in gene expression. “Affymetrix has a GeneChip for zebrafish, so we can expose the fish at different concentrations, durations, and life stages, then extract the RNA and send it to the facility, where they can analyze the differential gene expression based on the RNA sample to determine which genes are turned on or off and compare that to fish that were not exposed to C60,” he says.
Gary S. Sayler, a distinguished professor of microbiology and CEB’s director, is using the Affymetrix Core Facility to study E coli bacterial genes expressed on contact with toxic chemicals. “We want to understand the patterns of genes expressed and then compare selected genes measured by bioluminescence from a collection of 400 lux marked bioreporter strains,” Sayler says.
The facility will also be useful in determining which genes of yeast and bacteria turn on in the presence of saxitoxin, a naturally occurring aquatic algal toxin. “One of our Ph.D. students, Kathleen Daumer, hopes to find a way to produce a bioluminescent sensor organism for this toxin in marine water,” Sayler says. Such a sensor would be useful in detecting toxicity threats of naturally occurring algal blooms, or human introduction of the toxin in a natural or synthetic form as a biological weapon.
In addition, the new facility will facilitate the research of faculty in UT’s College of Veterinary Medicine. Terry W. Schultz, for example, a professor in the Department of Comparative Medicine, is exploring the effects of polycyclic aromatic hydrocarbons (PAH) on human cells. (See InSites, Winter 2003.) PAHs are found in diesel particulates, among other substances, and can lead to atherosclerosis and chronic respiratory diseases associated with urban environments.
“Having access to the Affymetrix center means personnel in our laboratory can focus on the interpretation of the genomics results as they relate to toxicology, rather than being concerned with the actual techniques of handling and analyzing the RNA,” Schultz says.
TAMING THE FAT CELL
Like cancer, obesity also has a genetic component. For Michael B. Zemel, a
professor in the Department of Nutrition, the Affymetrix Core Facility will
be useful in research on molecular and cellular nutrition, from basic to applied
research.
Zemel’s work has focused on the transport and metabolism of calcium and its effects on obesity and diabetes. Calcium signaling controls fat cell function. “Once we understand the pathways better, we can design new strategies to coax fat cells to do their work less well,” Zemel says.
The Affymetrix Core Facility allows researchers in nutrition to identify patterns of gene expression in response to manipulation in human fat cells as well as in mouse studies. “Ours is a vertically integrated lab, from fundamental research to clinical evaluation,” Zemel says. “The Affymetrix facility serves as a screening tool to help our lab in new hypothesis development.”
DOUBLE-EDGED SWORD
This type of technology could result in the development of pharmaceutical
or medical therapies tailored to the individual’s gene expression patterns.
This would be important for those susceptible to or suffering from chronic
diseases such as cancer, obesity, or diabetes.
This gene expression fingerprint could eventually help determine which intervention would be preferable. For example, these expression patterns have been used to help diagnose certain types of brain tumors. “Wouldn’t it be interesting if we could find a biomarker that tells you whether your child has Attention Deficit Hyperactivity Disorder and whether the genetic marker or expression pattern could help determine if a pharmaceutical intervention or a nutritional intervention is preferentially effective?” Whelan says.
From a broader perspective, while this technology could boast multiple publichealth applications, it will also introduce a new set of challenges. If we use it as a screening tool, how do we regulate this information? Would it affect the ability of someone to get health insurance if our tests indicate he or she is predisposed to a disease we can’t yet cure?
“There is always a problem with cutting- edge technology,” Whelan says. “We have to move slowly and demonstrate benefit outweighs any risk.”
Nevertheless, the Affymetrix Core Facility is essential in helping the university remain competitive as it greatly enhances the ability of researchers at UT to obtain funding to generate new knowledge and to train the next generation of scientists. The low cost of the chips, at around $400 apiece, and the convenience of having the facility on campus, allow researchers to take greater research risks and pose broad research hypotheses.
“As a level-one research institution, if we are to be leaders in the field and compete for grants, we have to have the latest technology. This enhances our ability to think outside the box,” Whelan says.
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Contact Julia Gouffon, Facility Director, Affymetrix Core Facility, The University of Tennessee, 234 Jessie Harris Hall, 1215 W. Cumberland Ave., Knoxville, TN 37996-0000, or call 865-974-5244.
Nothing Ventured, Nothing
Gained
THE ECONOMY OF A REGION DEPENDS ON more than the infrastructure of office
space, airports, interstates, and Internet connectivity. Intellectual resources
and entrepreneurial courage are also crucial for growth.
“This region’s greatest strengths are the technology resources and intellectual capacity that exist at the University of Tennessee (UT) and Oak Ridge National Laboratory (ORNL),” says Tom Rogers, president and chief executive officer of Technology 2020, a public-private partnership with the goal of moving technological invention to the marketplace.
“We bring management expertise and access to capital to the table,” says Rogers. “Ten years ago, it was very diffi- cult to find the capital needed to launch a company.” Today, thanks to a wide web of partnerships, technology transfer in East Tennessee is becoming routine.
Traditionally, when people think about economic development, they think about manufacturing companies that are not headquartered locally.
“We are now able to demonstrate the importance of growing our own companies,” Rogers says. In fact, Technology 2020 client companies have created 1,300 jobs with an average salary of $50,000 a year, which is double the national average, equivalent to a $90 million annual payroll.
To promote the growth of area technology companies, the ninth annual Tennessee Valley Venture Forum will be held in Knoxville October 6-7, 2005. The Forum is a venture capital conference sponsored this year by Technology 2020, the city of Knoxville, and Knox County.
“The Venture Forum is becoming a major way for us to showcase our promising technology companies for the venture-capital community,” Rogers says. “Tennessee used to be a fly-over state for venture capital, but that is changing.” Last year, five out of 13 companies that presented at the Forum, held in Chattanooga, found venture capital. “We started our own private venture capital fund in partnership with Kentucky Highlands Investment Corporation, so now other venture capital firms in the region are willing to co-invest with us,” he says.
To Market to Market
Innovation in research at UT Knoxville plays a significant role in economic
development, business creation, and technology innovation in the region, says
Gary Sayler, director of UT’s Center for Environmental Biotechnology (CEB).
“Access to unique facilities and instrumentation at research institutes and
centers such as CEB, the Waste Management Research and Education Institute,
and the Energy, Environment and Resources Center contribute to new start-up
companies,” Sayler says.
Moreover, intellectual property in the form of new patents and other licensable technology is created from the funded research efforts of these centers. For example, the Bioluminescent Bioreporter Integrated Circuit (BBIC) sensor technology pioneered at CEB has been licensed to MicroSystems Technology, a start-up company based in Ohio that may expand to Tennessee. BBICs are genetically engineered bioreporter organisms engineered to luminescence—or light up—in the presence of a targeted substance.
In addition, the Knoxville Utilities Board and state agencies such as the Tennessee Department of Environment and Conservation have benefited from advances in environmental remediation and wastewater treatment developed at CEB.
Homegrown Talent
A 2001 graduate of the master’s program in business administration at UT is
a prime example of local talent and entrepreneurial spirit at work in the
regional marketplace. Chuck Witkowski, president and CEO of Protein Discovery,
Inc., launched his venture from the platform of a graduate class through the
Tennessee Technopreneurial Leadership Center (TLC), a joint effort of UT,
ORNL, and the Tennessee Department of Economic and Community Development.
“Basically, I founded the company out of that class, leveraging some of the core principles taught by Lee Martin and Dan Kuban, including how to license technologies from a national lab or university and how to bootstrap a company with equity-free research-and-development grants from the Small Business Administration,” Witkowski says. Martin and Kuban are co-founders of TLC and members of Clarity Resources, a mentor capital firm in Knoxville.
Protein Discovery, Inc. is developing a marketable technology for the discovery and identification of unique disease markers—biomarkers—that may be useful in the diagnosis, prognosis, and treatment of complex diseases such as cancer. The technology is based on fundamental discoveries made at ORNL and licensed exclusively to the company. “Our device enables the discovery of suites of biomarkers that, when taken together, may lead to an improved ability to diagnose diseases in their earliest stages, when treatment is most likely to be successful. These biomarkers may also be better predictors for how aggressively the disease may progress and how well it may respond to particular treatments,” Witkowski says.
Witkowski also credits Technology 2020 with providing business advice, financial support, and affordable office space. His company is now closing on its second round of financing and will have a product in the market place this year.
Plasma Matters
Technologies forged by UT researchers are also moving from the pre-product
stage to the marketplace at Atmospheric Glow Technologies, Inc. (AGT) in Knoxville.
AGT has licensed six patents from UT with potential applications in environmental
decontamination, air purification, reduction of diesel soot emissions, sterilization
of medical instruments, detection of biological agents, and improvements in
aerodynamics.
The technology is based on the fourth state of matter after solids, liquids, and gases: plasma. “Plasma is a high-energy state of matter, a collection of electrically charged particles mixed with a gas,” says Tom Reddoch, AGT’s chairman and CEO. The air filtration system consists of a killing agent blown from a plasma generator made up of wire electrodes. A filters traps microorganisms like bacteria, mold, viruses, or anthrax. “The chemistry of the plasma kills the microorganisms trapped on the filter,” Reddoch says.
AGT recently trademarked its technology for atmospheric plasma One Atmosphere Uniform Glow Discharge Plasma (OAUGDP®). The technology was originally developed in the department of electrical and computer engineering at UT.
Reddoch credits Kimberly Kelly-Wintenberg, a UT microbiologist and lead founder of the company, with the energy and courage to leave the academic community and launch the company. Also making the leap to the business world were researchers from UT’s department of microbiology and the College of Engineering.
Reddoch sees technology transfer and development in East Tennessee as relying on four powerful entities: UT, ORNL, private industry, and the Tennessee Valley Authority (TVA). “We look at the knowledge base of UT and the national resources of ORNL as pinnacles in terms of preparing people and raising skill levels,” he says.
In March, TVA released a study aimed to improve recruitment of participants in the life-sciences industry across the state of Tennessee. The agency contracted with Fluor Global Location Strategies to identify eight population clusters and tailor the assessment to address the strengths and opportunities of each specific region in terms of infrastructure, quality of life, educational resources, and other critical parameters for growth, says Heidi T. Smith, general manager of marketing development with TVA.
The study also identifies areas where there is room for improvement. “One segment of the life sciences industry, the pharmaceutical market, is approaching $500 billion in investments globally, and the American share of that is about $230 billion,” Smith says. “We will use this study as a marketing tool to reveal the Valley’s many life-sciences assets,” she says.
Room to Grow
Tennessee has been identified by the National Science Foundation (NSF) as
one of the states that needs a little help applying for NSF grants supporting
scientific research, says Joel Rolwing, executive director of the Tennessee
Biotechnology Association (TBA). With headquarters in Nashville, TBA is an
organization of researchers, biotech companies, business leaders, and legislators
that promotes the development of the life sciences in the state and works
to attract both local and outside investment.
Tennessee has responded by forming a state chapter of the NSF Experimental Program to Stimulate Competitive Research (EPSCoR) and submitting a planning grant to pull together the resources to help the state do a better job. EPSCoR has identified thematic areas—including biomedical/health sciences, environmental matters, natural sciences and engineering, and computational sciences—eligible for federal funding. Tennessee’s university-based researchers and scientific staff from ORNL and UT’s Arnold Engineering Development Center are leading this effort.
Further support for moving innovation to the marketplace is provided by a business incubation program, the Center for Entrepreneurial Growth, a joint venture of Technology 2020, the UT Research Foundation, and ORNL, with the support of the lab’s managing contractor, UT-Battelle.
“I am really encouraged that UT is beginning to work more and more closely with ORNL. The UT-Battelle venture is really beginning to take off,” says Technology 2020’s Tom Rogers. “The fact that UT and ORNL have demonstrated their commitment to using their technology resources to start new companies really bodes well for the future of the economy of this region.”
* * *
Contact Gary Sayler, Center for Environmental Biotechnology, 676 Dabney Hall, University of Tennessee, Knoxville, TN 37996- 1608, call 865-974-8080, or email sayler@utk.edu. Visit the Web sites of NSF EPSCoR at http://epscor.tennessee.edu, the Tennessee Biotechnology Association at www.tnbio.org, and Technology 2020 at www.tech2020.org.
Each spring since 1995, students and volunteer organizers have gathered for an annual festival on the banks of the Tennessee River in Knox County. Water- Fest is a county-wide educational event, held at Ijams Nature Center, that focuses on kids, says Ruth Anne Hanahan, senior research associate with the Water Resources Research Center (WRRC), a unit of the University of Tennessee’s Waste Management Research and Education Institute.
WaterFest partners bring about 750 students together, offering a range of engaging activities to introduce the ABCs of watershed health. Students compete in poetry and art contests, make models showing the effects of water pollution, and participate in activities that demonstrate what they can do to protect their streams and rivers.
“Our target is elementary students,” Hanahan says. The kids also engage in activities that are just plain fun, such as water rockets and the dunking booth. The day-long, annual festival is cosponsored by the Water Quality Forum (WQF), a consortium of partners with the mission of improving water quality in Knox County and its surrounding counties. On hand to lead or assist with many of the activities are members of the Community Action Committee (CAC) AmeriCorps, which was created in 1995 to engage volunteers in improving urban environments.
CORPS OF VOLUNTEERS
AmeriCorps volunteers, who receive a small stipend in exchange for 11 months
of service, come from all ages and backgrounds and from across the United
States.
“We now have people coming from as far away as Oregon and California,” says Tim Gangaware, assistant director of WRRC, which trains the volunteers to conduct many of the WQF’s educational and outreach activities and assist with its watershed remediation projects.
This year, six volunteers comprise the Water Quality Team, which also assists with the WQF’s Adopt-A-Watershed (AAW) Program. Based on a nationally implemented program, AAW involves students in projects that help protect, monitor, and restore local watersheds. WRRC staff also train AmeriCorps volunteers to work in the field on research activities with biologists from the Tennessee Valley Authority (TVA) and the Tennessee Department of Environment and Conservation (TDEC), doing stream assessments in the Tennessee Valley, Gangaware says. In addition, WRRC trains Knox County teachers who participated in AAW through a Water Quality Boot Camp held in June.
DO NOT DISTURB
While bacterial contamination, acid mine drainage, industrial effluents, and
sewerage treatment problems contribute to the degradation of waterways, 28
percent of the impairment of Tennessee’s streams and rivers can be tracked
to erosion and sedimentation from residential and industrial development and
road building, says Paul Schmeierbach, environmental program manager with
TDEC’s Division of Water Pollution Control.
Amendments to the Clean Water Act have imposed increasingly strict permitting requirements for anyone engaged in land-disturbing activities with the potential to degrade water quality, including contractors and developers.
“The state has a training program to enlighten people on Best Management Practices (BMPs) for erosion and sediment control,” Schmeierbach says. In addition, over the past four years, TDEC has issued 1,500 permits required by law in the 16-county eastern district alone.
“This is an indication of our educational program, our enforcement, and to some degree the increase in development activities,” he says.
Anyone disturbing an acre or more of land, or developers whose larger projects affect an acre or more, need a Storm Water Construction Permit issued by TDEC, which is responsible for statewide enforcement of the U.S. Environmental Protection Agency’s (EPA) National Pollutant Discharge Elimination System (NPDES). According to TDEC, permitted activities include housing subdivisions, commercial and industrial buildings, golf courses, utility lines, sewage treatment plants, and roads.
CLEANER DEVELOPMENT
To help contractors, developers, engineers, and other professionals involved
in land-disturbing activities understand BMPs and permit requirements, WRRC
has organized two tiers of training workshops. The Level I Fundamentals workshop
is a one-day course introducing the basics of Storm Water Pollution Prevention
Plans (SWPPP). The course targets contractors, developers, engineers, and
inspectors involved in land-disturbing activities. Level II training, a two-day
advanced course, is aimed at professionals who have completed Level I certification
and addresses the engineering technologies for preventing erosion and managing
sediment at construction sites, including stable channel design and the proper
use of vegetative and structural controls.
WRRC’s Gangaware has noticed a sharp increase in voluntary participation in the workshops and interest in implementing BMPs. In the future, Tennessee may make the training mandatory. The Tennessee Department of Transportation already requires its contractors to take the certification program, and the training is mandatory for contractors in the cities of Cleveland and Dyersburg. “The workshops are always full,” Gangware says.
WALMART WEIGHS IN
In addition, some high-profile businesses such as WalMart are putting the
pressure on their contractors to comply with BMPs, in part due to liability
concerns, such as dangerous road conditions from muddy runoff.
“WalMart was involved in a multimillion dollar enforcement action by EPA and now has written contracts with 185 firms and more than 300 contractors requiring daily sediment- and erosion- control reports to headquarters,” Gangaware says. “They can penalize contractors $5,000 a day for mud on the streets.” There are additional penalties for not filing a daily report.
Now the challenge is to increase awareness among subcontractors and small developers. In May, for example, WRRC will conduct a hands-on demonstration of devices at the Williamson County Agricultural Exposition outside of Nashville.
Gangaware says WRRC plans to expand the program to provide recertification after three years to keep construction professionals current on the latest in BMPs and to train inspectors. The future training courses will include up-to-date detailed information on advanced control methods such as jute, coconut, and synthetic nets, the rolled erosion products that are available in addition to siltation fences and other conventional practices. “There are a lot of new products available now to protect waterways during storm events,” Gangaware says.
READY, SET, GROW
To accommodate growth without impairing streams and rivers, community planners
need to understand how land-use patterns affect water quality. TVA, with support
from the Tennessee Department of Agriculture’s Nonpoint Source Program and
the assistance of WRRC, is leading a multi-agency effort launched in 2001
to help communities learn how to reduce the impact of land-use decisions on
water quality and comply with the NPDES Stormwater Phase II requirements.
The Tennessee Growth Readiness (TGR) program is assisting 85 communities that must meet the criteria of Phase II, including public education, public involvement, and post-construction development rules, says Joel Haden, sustainable development project manager with TVA. “WRRC’s Gangaware and Hanahan have been instrumental in developing and delivering the workshops,” Haden says. “They have been part of the team from day one.”
The pilot communities represent a mix of urban, suburban, and rural areas that confront the range of challenges faced across the state. TGR used the early results of the program—piloted in Knox County, Blount County, and the cities of Alcoa and Maryville—to roll out a major statewide thrust in the fall of 2003 and winter of 2004.
“In those six months we reached 270 cities and counties,” Haden says. “About 180 have evaluated their existing development rules, and 10 to 20 percent have started making changes. These are the early adopters.”
TVA also provides data on growth patterns and the effects on water quality of stormwater runoff, which increases with the area of paved surfaces, buildings, and compacted soil. By measuring and forecasting the percent of impervious surface in a growth area, a community can gauge the point at which impairment of streams will be serious or even irreversible.
“We have created maps for each county to determine how land-use changes affect the imperviousness of the ground,” Haden says. This indicator is a good measure of how growth in a community and changes in land use affect water quality.
“TGR gives communities a choice of best practices, legitimized at a national level, so they can grow and maintain water quality, too,” he says.l
*
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Contact Tim Gangaware, WRRC, The University of Tennessee, 311 Conference Center Building, Knoxville, TN 37996-4134, or call 865-974-3938.
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