1

Offi ce of the Senior Vice President for Research Annual Report of Research Activity

FISCAL YEAR 2009 2

Welcome

ENN STATE ENTERS THE SECOND DECADE of the twenty-first century standing on a platform of re- markable growth and accomplishment. Since 2000, the University’s research expenditures have grown P74 percent, with the total for this past year reaching $765 mil- lion. In aggregate, these numbers are reflective of a faculty that is competitive at the highest levels, and of an elite cadre of students and postdocs who join these talented professors in conducting exceptional research and scholarship. The Penn State intellectual climate embraces interdisci- plinarity, an approach that has fostered the development of many creative initiatives. In this report you will read about a new imaging facility designed to explore cognition and be- havior, a result of collaboration among life and social scien- tists and engineers. You will also learn of a partnership be- tween the College of Medicine and faculty in the Department of Physics who are using network science to tackle the molec- EDITOR’S NOTE: In January ular biology of cancer. 2010, Eva J. Pell left Penn State Among the University’s major research trajectories is a after thirty-seven years of service multipronged effort in energy-related science. Articles follow to take the position of Undersec- that describe a major Department of Energy–funded Energy retary of Science at the Smithso- nian Institution. Her successor as Frontier Research Center in cellulosic biofuels and the trans- Vice President for Research and lation of a long-term initiative to develop microbial fuel cells Dean of the Graduate School is into practice in a pilot plant in the Napa Valley. Henry C. Foley. Penn State is a top-tier research university as measured by our research expenditures, but what truly distinguishes the University is the heterogeneity of its strengths. It is the breadth of quality research and scholarship—in sciences, so- cial sciences, and the arts—and the way we bring these di- vergent fields together that create the character of this great institution.

Eva J. Pell, Senior Vice President for Research and Dean of the Graduate School

CONTENTS Cover: Root system of a maize plant forty days after germination, showing the metabolic cost of root main- Statistical Snapshot 3 tenance (in units of g carbon per day, with warmer col- Research Highlights 6 ors representing greater cost) as visualized by the com- puter simulation model SimRoot. Research of Johannes Contacts back cover Postma, Department of Horticulture, Penn State. For more on root biology, see page 11.

CREDIT: JONATHAN LYNCH/JOHANNES POSTMA 3

Statistical Snapshot

Total Research Expenditures, Industry-Sponsored Research, 1990–2009 2000–2009 Federal Non-federal

millions of dollars millions of dollars ’00 ’ 90 137 126 263 70.6 ’01 ’ 91 147 128 275 73.3 ’0 ’ 9 2 72.6 2 154 134 288 ’ 0 03 ’ 93 75.9 163 130 293 ’0 ’ 4 9 82.3 4 174 143 317 ’0 5 ’

95 83.7 190 154 344 ’0 6 ’

9 91.8 6

192 156 348 ’07

’ 98.2 9 7

186 167 353 ’08

’ 104.8 9 8

188 186 374 ’09

’ 103.6 99 201 192 393 ’ 00 228 212 440 ’ 01 248 224 472 ’ 0

2 284 223 507 ’ 03 307 238 545 ’ 0 4 350 257 607 ’0 0 5 365 273 638 ’ 0 6 372 285 657 ’ 07 375 290 665 ’ 0 8 411 306 717 ’ 09 446 319 765

Penn State’s research expendi- Funding from federal agencies Despite a small reduction in tures in fi scal 2009 reached accounts for $445 million, and industry-sponsored research a record $765 million, a 6.7 per- has grown 95 percent since fi s- over the last year attributable cent increase over the previous cal 2000. Federal dollars came to the economic downturn, year and a 74 percent increase from a wide variety of agencies, Penn State continues to rank since fi scal 2000. including the Department of third nationally in this impor- Defense, Department of Health tant category. and Human Services, and Na- tional Science Foundation. 4

Expenditures from Federal Agencies

Department of Defense ...... $178,939,000 Department of Health and Human Services . . . . . 105,508,000 National Science Foundation ...... 52,604,000 USDA ...... 19,419,000 NASA ...... 18,220,000 DOE ...... 16,586,000 Education ...... 10,562,000 Other ...... 43,423,000 Transportation ...... 7,140,000 Interior ...... 1,706,000 Commerce ...... 1,254,000 EPA ...... 796,000 Other Federal ...... $32,527,000

Total ...... $445,261,000

Expenditures by Performing Unit

Defense Related Research Units ...... $186,594,000 Applied Research Lab ...... 154,931,000 Electro-Optics Center ...... 31,663,000 Engineering ...... 104,929,000 Agricultural Sciences ...... 96,828,000 Eberly College of Science ...... 91,660,000 Medicine ...... 91,552,000 Earth and Mineral Sciences ...... 73,409,000 Health and Human Development ...... 40,273,000 Liberal Arts ...... 25,250,000 Education ...... 22,431,000 Information Sciences and Technology ...... 10,323,000 Other ...... 14,457,000 Altoona College ...... 801,000 Behrend College ...... 4,362,000 Berks College ...... 202,000 Capital College ...... 4,056,000 Great Valley ...... 187,000 Penn College ...... 1,622,000 Other Commonwealth Campuses ...... 3,227,000 Other Schools and Colleges ...... 7,331,000 Arts and Architecture ...... 900,000 Communications ...... 155,000 Dickinson School of Law ...... 470,000 School of Nursing ...... 674,000 Smeal College of Business ...... 5,132,000

Total ...... $765,037,000 5

Sources of Research Funding

Federal ...... $445,261,000 University ...... 130,710,000 Industry and other ...... 105,301,000 Commonwealth of Pennsylvania ...... 83,765,000

Total ...... $765,037,000

The Graduate School

Applications, ten-year history, 2000–2009 Total Enrollment, 2009

Resident Instruction (Fall only) ’00 13,101 World Campus (Calendar year) ’01 13,439

’02 15,202 ’06 9,793 1,967 11,760

’03 16,482 ’07 9,707 2,,429 12,136

’04 13,296 ’08 9,206 3,035 12,241

’05 13,609 ’09 9,088 3,426 12,514

’06 15,246

’07 15,915

’08 15,960

’09 17, 071

Degrees Conferred, ten-year history, 2000–2009 International Students, ten-year history, 2000–2009

Masters degrees Doctoral degrees Returning Students New Students

’99–’00 2,013 542 2,555 ’00 1,609 630 2,239

’00–’01 1,962 541 2,503 ’01 1,679 698 2,377

’01–’02 2,123 541 2,664 ’02 1,884 599 2,483

’02–’03 2,101 550 2,651 ’03 1,984 555 2,539

’03–’04 2,293 580 2,873 ’04 1,981 513 2,494

’04–’05 2,145 606 2,751 ’05 1,889 498 2,387

’05–’06 2,089 674 2,763 ’06 1,,856 577 2,433

’06–’07 2,093 685 2,778 ’07 1,862 543 2,405

’07–’08 2,197 658 2,855 ’08 1,797 611 2,408

’08–’09 2,278 679 2,957 ’09 1,883 520 2,403 6

Secrets of Cellulose

Stimulus funding from the American Recovery The main limitation in existing biomass-to-biofuel and Reinvestment Act of 2009 (ARRA) is meant production is the high cost of dissolving the tough to advance scientifi c research that will make a fi brous plant material, such as corn stover, switch- meaningful difference in the nation’s future, grass, and fast-growing trees. Currently, the best particularly in the area of renewable energy. treatment is to soak the fi bers in enzymes, adding 30 A perfect example is the Department of Energy’s to 50 cents per gallon to the cost of the ethanol fuel award of $21 million over fi ve years to Penn State to produced. fund the new Center for Lignocellulose Structure “Even after decades of research, cellulose synthe- and Formation. sis is not very well understood,” Catchmark notes. One of forty-six Energy Frontier Research Centers “We don’t know how the cells assemble this chemical (EFRC) established nationwide, Penn State’s center barrier to weather, insects, and other organisms. The (which will collaborate with North Carolina State cell wall is very diffi cult to degrade.” University and Virginia Polytechnic Institute and A decade ago, the Cosgrove lab discovered a new State University) is part of a major effort to acceler- group of proteins, dubbed “expansins” for their role ate the scientifi c breakthroughs required to create a in allowing plant cell walls to expand as the plant new twenty-fi rst-century energy economy. grows. These “wall-loosening” proteins show prom- Says Daniel J. Cosgrove, professor of biology ise in speeding the breakdown of cellulose material and the center’s director, the Penn State center will into sugars. The expansins strip off surface polymers use cutting-edge approaches and an interdisciplinary so the cellulose layers can be pulled apart to allow team—including physicists, material scientists, the enzymes to act on all of the layers of material at computational modelers, and engineers—to study once, explains Cosgrove. The hope? That expansins the molecular biology of cellulose. will help transform the industrial process for making Cellulose, says Cosgrove, is vital to future fuels. cellulosic biofuels into a cost-competitive, cleaner, re- “The biggest solar collectors on Earth are plants that newable energy source. use sunlight to convert atmospheric carbon dioxide “This is the most abundant biomass on the plan- into complex structural materials like cellulose and et,” says Cosgrove. “This is the material in which lignin,” he explains. “These make up wood, paper, most of the organic carbon on Earth is found and cotton, and many other everyday materials; globally, that the DOE wants to convert back into simple sug- they represent a huge untapped reserve of biorenew- ars and then into ethanol.” able energy. Our new center will try to pry loose the Virendra Puri, Distinguished Professor of Agri- secrets of how these molecules interact to form these cultural Engineering and one of the Penn State re- substances that have so many practical uses as an en- searchers involved in the center, comments, “Once ergy source.” we unlock the mystery of how the materials go to- Cosgrove and colleagues—including Jeffrey gether—how they are intertwined—and learn to take Catchmark, associate professor of agricultural and them apart, the possibilities are vast.” biological engineering in Penn State’s College of Penn State’s center is moving forward with energy Agricultural Sciences and co-director of the new and a shared vision to help the United States—with center—are working to understand the structure and its vast agricultural and forest-based resources—un- formation of plant cell walls, or lignocellulose. Such lock the full potential of its lignocellulosic materials. information will be important for transforming TO LEARN MORE, SEE: www.lignocellulose.org cellulose into a more affordable and sustainable feedstock for ethanol production.

Cellulose, found in the cell walls of plants, provides the rigidity and support that gives leaves their shape. Its synthe- sis is not well understood. 7

The Critical Zone

Nestled in a quiet hollow in the Stone Valley Southeast Asia, Africa, and Australia whose goal is experimental forest south of State College lies to develop collaborations in rapidly developing a twenty-acre tract that’s been studied by Penn interdisciplinary areas of global signifi cance. Penn State researchers since the 1970s. Now the so- State is a founding member of the alliance, which called Shale Hills watershed is part of a growing began in 2000. global network of sites that are boosting understand- “When we started talking about Critical Zone ing of the Critical Zone, that life-sustaining region science a number of years ago,” Brantley remem- of Earth’s surface from the top of vegetation to the bers, “some of our European colleagues heard about bottom of groundwater. it and I was invited to do a WUN seminar on the “I like to say it’s where rock meets life,” says subject.” A series of workshops at some of the other Susan Brantley, professor of geosciences and director WUN universities followed, along with student and of the Penn State Earth and Environmental Systems faculty exchanges. Says Brantley, “I think all that ac- Institute. “It includes soil, water, plants—everything tivity slowly led to the point where four Critical Zone we see at the surface of the Earth.” observatories are going to be established next year in In 2007, Brantley and Chris Duffy, professor of Europe, along with one proposed in Australia. Our civil engineering, with colleagues at the University of Chinese colleagues are talking about it as well.” Colorado and University of California, went to the In September of 2009, Penn State hosted a WUN National Science Foundation with proposals to estab- workshop at University Park. Attendees from the lish a number of observatories where interdisciplin- United States, United Kingdom, Australia, and Chi- ary teams of scientists could exhaustively study geol- na visited the Shale Hills Observatory. By building a ogy, hydrology, and ecology, creating a coordinated global network of fi eld sites like Shale Hills, Brantley picture of Critical Zone processes. Shale Hills was says, researchers hope to develop models to predict named one of three observatories, along with sites in the impacts of human activities on Critical Zone pro- the Sierra Nevada Mountains and the Rockies, and cesses and thereby determine how best to protect Brantley and Duffy were awarded a fi ve-year, $4.2 this vital region from threats including desertifi ca- million NSF grant. tion, loss of soil fertility, and soil erosion. In the fall of 2008, Brantley reports, three more “We are encouraging researchers to share data NSF observatories were established in the rainforest across sites so that we can begin to quantitatively of Puerto Rico, a coastal watershed along the Dela- predict how the Critical Zone is responding to natu- ware–Maryland border, and in the Sonoran desert ral and human perturbation,” said Tim White, senior of Arizona. And, she says, thanks in part to the activ- research associate at Penn State, who organized ity of the Worldwide Universities Network (WUN), the meeting. the Critical Zone concept is spreading to Europe TO LEARN MORE, SEE: www.psiee.psu.edu/ and beyond. research/project_details/60TN The WUN is a partnership of fi fteen research- intensive universities from Europe, North America,

BETH HERNDON doesn’t hesi- Now, under Brantley’s tutelage, Herndon is enrolled in the dual- tate when asked what brought Herndon is investigating man- title Ph.D. program in Geosci- her to Penn State’s Department ganese cycling in the Shale Hills ences and Biogeochemistry, of Geosciences. “It’s one of the watershed, “ quantifying the which draws students from sev- best programs in the country,” amount of excess manganese en participating departments at she says. and fi guring out where it comes Penn State. “I like being able to from, and how widespread an- cross these boundaries and un- Herndon was a senior at Wash- thropogenic manganese addi- derstand different perspectives ington University in St. Louis, tion is to the soils.” She recently and ways to approach a prob- Missouri, double majoring in spent a month in England at lem,” she says. “In this program earth and planetary sciences and the University of Sheffi eld, one we have students not only talk- biochemistry, when her adviser of Penn State’s partners in the ing across departments, but invited Susan Brantley to speak Worldwide Universities Network, doing research together.” at a colloquium series. “That was learning techniques to mimic in my introduction to Penn State,” the laboratory some of the min- she remembers. eral-weathering processes she has observed in the fi eld. 8

Thin-fi lm Fellow

“A piezoelectric material,” Susan Trolier- McKinstry explains, “is one that has a coupling between electrical and mechanical energies. If I take such a material and apply an electrical fi eld to it, I can make it change shape. If I squeeze it—apply mechanical stress—I can generate an electrical fi eld. “We use these materials all the time without know- ing it,” adds Trolier-McKinstry, professor of ceramic science and engineering at Penn State. “Medical ul- trasound is a good example.” An ultrasound probe, she explains, contains piezoelectric crystals, which vibrate (i.e., change shape) when an electric current Thin-fi lm accelerometer is applied. These vibrations produce sound waves that travel outward into the body until they reach the boundaries among fl uid, soft tissue, and bone. Some amorphous, like glass,” she says. “And it’s not piezo- of the sound waves are then bounced back to the electric until we crystallize it.” That usually requires probe, where the crystals emit an electrical current. 600 to 700 degrees Celsius, however—a heat much Most bulk piezoelectric devices, however, operate too intense for integrated circuits and other poten- at fairly high voltages—often more than 60 volts. Says tial components to withstand. “So instead of heating Trolier-McKinstry, “It would be really nice to make an up the whole fi lm and everything it sits on, we’re us- actuator that you could drive with really low voltage, ing laser adsorption to target just the fi lm.” like that produced by a silicon chip.” The materials she’s working to perfect have lots of She recently received major support to do just potential applications, both defense-related and not. that. Last fall, Trolier-McKinstry was selected as one “DOD is very interested in switches for high-speed of six distinguished researchers from U.S. universi- communications,” she says. “For radar applications, ties to form the inaugural class of the Department of they need to be able to switch parts of the circuit in Defense’s new National Security Science and Engi- and out. This is hard to miniaturize. neering Faculty Fellows Program. The program pro- “The same generic technology is useful in lots of vides long-term funding to scientists and engineers sensors for condition-based maintenance,” she con- to pursue basic research of crucial importance to tinues. “These allow you to tell when a bridge or a next-generation DOD technologies. The six Fellows big industrial tool is in need of repair—before dam- will receive grants of up to $3 million each over a age is being done.” fi ve-year period. Trolier-McKinstry also envisions a thin-fi lm ver- Trolier-McKinstry’s proposal to the DOD con- sion of an ultrasound system. “Our long-term goal tained three parts. Her fi rst objective is to improve would be to make something small enough that you the piezoelectric response of the thin-fi lm materials could swallow it. So you could maybe replace the that are crucial to increasingly miniaturized devices. colonoscopy with a pill that just passes through.” “I want to be able to create a big change of shape As director of the W. M. Keck Smart Materials In- with just a little bit of voltage,” she says. tegration Laboratory and the Center of Excellence Next, Trolier-McKinstry is looking at ways to cre- in Piezoelectric Materials and Devices at Penn State, ate usable structure on the surfaces of thin fi lms she says the DOD fellowship “gives me a tremendous without ruining them. “The materials we use are amount of fl exibility to address the key science and rather complicated in their chemistry,” she explains. engineering challenges in piezoelectrics for micro- “They usually contain at least four different types electromechanical systems. This kind of sustained of atoms, and inevitably these don’t all etch at the funding allows us to explore deeper, fundamental same rate. So it’s often easy to induce damage when problems. you etch into these materials. Instead, we’re trying “What we’d really like to do is move beyond the to print the patterns we want directly, using a stamp. incremental and make big improvements in the We’re the fi rst group that has ever done this.” functionality of these materials.” Her third goal, she says, is to be more precise in TO LEARN MORE, SEE: www.matse.psu.edu/fac/ applying the high temperatures necessary for crystal- profi les/mckinstry.htm lization of thin fi lms. “We start out with a fi lm that’s 9

Virtuosi Visit

For a couple of hours on the evening of March The all-Mendelssohn concert program celebrated 20, 2009, Penn State was arguably the epicenter the bicentennial of Felix Mendelssohn’s birth. The of the classical music world. Three of today’s most distinguished trio performed Mendelssohn’s Piano renowned musicians—pianist Emanuel Ax, violinist Trio No. 1 in d minor, Opus 49, and Piano Trio No. 2 in Itzhak Perlman, and cellist Yo-Yo Ma—made their c minor, Opus 66, as well as a sampling of the German world-premiere performance as a trio at Penn State’s composer’s Songs Without Words. Eisenhower Auditorium. Their only other perfor- “What we experienced that evening was not only mance together took place the following night at some of the fi nest music, played by three of the New York’s Carnegie Hall. most distinguished virtuosi of our time,” Tacconi en- The sold-out concert and medal ceremony were thused. “It was, in essence, a celebration of the pow- planned jointly by George Trudeau, director of the er of music, an example of the ability the arts have to Center for the Performing Arts, and Marica Tacconi, bring joy and to transport our minds and souls to a director of Penn State’s Institute for the Arts and loftier place. With each stroke of the key and draw of Humanities (IAH). the bow, these distinguished musicians spoke to our “Trudeau and his staff secured the performance humanity by reminding us that music, like the oth- and worked out the arrangements,” explains Tac- er arts, has the power to transcend differences and coni. “Then we, at the institute, offered the three bring us together as citizens of the world.” virtuosi the honor of our medal, which they gladly The evening was a highlight in a year in which accepted.” the IAH presented more than seventy events, many The award, presented by Penn State President as part of the institute’s Moments of Change initia- Graham Spanier at the end of the concert, is the tive, focused in 2008–09 on the turn of the twentieth 2009 Institute for the Arts and Humanities Medal for century (1889–1914). The multidisciplinary program Distinguished Contributions to the Arts and Human- included lectures, roundtable discussions, perfor- FRED WEBER ities, bestowed in past years upon novelist Salman mances, exhibitions, the second annual Josephine Rushdie; architect Daniel Libeskind; and novelist, es- Berry Weiss interdisciplinary humanities seminar, sayist, and political activist Mario Vargas Llosa. and even a halftime show at a football game in Bea- Established in 2006, the IAH Medal honors in- ver Stadium. Tacconi says, “It was a remarkably stim- dividuals whose work has reached a wide public au- ulating year that brought together faculty, students, dience while maintaining the highest standards of and community members to explore one of the most scholarship, creativity, and originality. As Tacconi remarkable periods of transformation in the arts, explains, “In choosing these three extraordinary mu- culture, and society.” sicians as the recipients of the 2009 IAH Medals, we TO LEARN MORE, SEE: live.psu.edu/album/2009 celebrated not only their individual and collective contributions to the arts, but also their commitment to uniting the peoples of the world through music.”

For MIA TOOTILL, “interdisci- mentor” in her academic adviser, “I’m looking at Saint-Saëns’ op- plinary” is more than a buzz- Marica Tacconi; and a thesis era Hélène, Lili Boulanger’s can- word—it’s the main reason she adviser, Charles Youmans, whom tata Faust et Hélène, and Richard came to Penn State for graduate she calls “a top Strauss scholar— Strauss’ opera Die Ägyptische studies. “The Institute for the Arts what an opportunity to work Helena, and am interested in the and Humanities was one of the with him!” ways mythology can be interpret- big draws for me,” says Tootill, a ed through the combination of One of eight graduate students native of England and clarinetist. music and text,” explains Tootill. chosen for a summer residency “Yet I wasn’t sure what to expect at the institute this past summer, Says Tootill, “I certainly never when I started here.” Tootill says her attendance at could have anticipated the What she found: a “wide variety” the Moments of Change events level of support that I’ve been of courses across the disciplines; helped her defi ne a master’s the- given here.” an “inspiring and supportive sis topic: musical depictions of the Helen of Troy story from the turn of the twentieth century. Wine into Hydrogen?

It’s been several years since Bruce Logan showed the world how to produce electricity from wastewater. Logan’s microbial fuel cell uses bacteria to turn the trick, and cleans up the wastewa- ter to boot. But there’s yet another twist. By applying a small electrical current, he can reconfi gure the cell to produce not electricity, but hydrogen. Now the fi rst demonstration of a renewable meth- od for hydrogen production from wastewater using Logan’s microbial electrolysis system is under way at the Napa Wine Company in Oakville, California. Bruce Logan checks demon- Last September, a refrigerator-sized hydrogen stration wastewater proces- generator began taking a fraction of the winery’s sor at Napa Wine Company. wastewater and, using bacteria and a small amount of electrical energy, converting the organic mate- rial it contains into hydrogen, according to Logan, voltage produced by the bacteria is slightly increased, Kappe Professor of Environmental Engineering hydrogen gas is produced electrochemically on the at Penn State. stainless steel cathode. “This is a demonstration to prove we can continu- “There is almost ten times more energy in the ously generate renewable hydrogen and to study wastewater than we currently use to treat it,” Logan the engineering factors affecting the system perfor- told ABC News. “If we get out a tenth of that ener- mance,” he says. “The hydrogen produced will be gy, we could run the treatment system by itself, but vented except for a small amount that will be used in we’ve still got nine times more energy in there that a hydrogen fuel cell.” Eventually, Napa Wine Com- we could extract. We’re wasting that; we’re throwing pany would like to use the hydrogen to run vehicles it away.” and power systems. The demonstration plant is made up of twenty- Like any large agricultural operation, Napa Wine four modules, each with six pairs of electrodes. “The Company generates millions of gallons of wastewa- composition of the wastewater will change through- ter per year. Water is used for cleaning equipment, out the year,” says Logan. “Now it is likely to be rath- grape disposal, wine making, and other processes. er sugary, but later it may shift more toward the rem- The company already has on-site wastewater treat- nants of the fermentation process.” The bacteria that ment and recycling and the partially treated water work in the electrolysis cells will consume either of from the microbial electrolysis system will join other these organic materials. water for further treatment and use in irrigation. “This is the fi rst time that a reactor of this size has “It is nice that Napa Wine Company offered up been attempted either in the laboratory or the fi eld,” their winery and facilities to test this new approach,” Logan told the LiveScience Web site in early Novem- says Logan. “We chose a winery because it is a natu- ber. “Performance continues to improve,” he added, ral tourist attraction. People go there all the time to though “we are not yet at our goal of daily produc- experience wine making and wine, and now they can tion of one liter of hydrogen per liter of reactor. We also see a demonstration of how to make clean hy- hope to generate more energy in the form of hydro- drogen gas from agricultural wastes.” gen than was used to treat the wastewater, thus mak- The demonstration microbial electrolysis plant ing the winery a net power producer.” is a continuous fl ow system that will process about The project is supported by Air Products and 1,000 liters of wastewater a day. Microbial electroly- Chemicals, Inc.; the Water Environmental Research sis cells consist of two electrodes immersed in liquid. Foundation’s Paul L. Busch Award; and other donors. Logan uses electrode pairs consisting of one carbon Brown and Caldwell, an environmental engineering anode and one stainless steel cathode in his system, consulting fi rm, was contracted to build the demon- rather than an electrode coated with a precious met- stration plant. The Napa Wine Company is donating al like platinum or gold. Replacing precious metals its facilities and wastewater for the demonstration. keeps down costs, he explains. The wastewater enters the cell where naturally occurring bacteria convert TO LEARN MORE, SEE: www.engr.psu.edu/ce/ enve/logan the organic material into electrical current. If the 11

A farm in Africa

Jonathan Lynch gets to the root of things. food supply, Lynch notes. When Buffett read about A professor of horticulture at Penn State, Lynch Lynch’s work in a Midwestern farm publication, believes that understanding plant root architecture “he called me,” says Lynch. The two met at the end may be the key to producing enough food to feed of 2008, and in early 2009 Lynch and members of the world’s 6 billion people. his lab visited Buffett’s 6,000-acre farm in South Af- “One of the main problems (in global agricul- rica. When Lynch pronounced the sandy, low-fertility ture) is low yields of plants because of drought, low African soil ideal for his research, Buffett offered soil fertility, and lack of access to fertilizer and irri- him the use of a fi fty-acre fi eld, along with a $1.5 gation in many parts of the world,” he explains. His million research grant. The Ukulima Root Biology research over the past twenty-fi ve years with collabo- Center was born. rators in the United States, Asia, Latin America, and Having an experimental base in the southern Africa has shown that root architecture plays a criti- hemisphere, Lynch says, will give him access to two cal role in determining plant yields under stressful growing seasons and the ability to study drought and soil conditions. Correlated with genetic information, other stress factors on a large scale. In addition, “we root traits can be harnessed to create higher-yield can wash nitrogen out of the sandy soil and create varieties of important crops like corn, bean, and low nitrogen conditions very easily,” he says. “And the soybean, he says. “We can then give farmers seeds sandy soil makes it easy to dig out roots for study.” that will do well in poor soils, without fertilizer and Lynch says he is amazed at how rapidly the irrigation.” Ukulima Center has taken off. “Howard Buffett is In the developed world, Lynch adds, stronger a man of action,” he says. “He built us a very nice, roots can have economic and environmental ben- fully equipped laboratory, with housing and efi ts. “The biggest cost in growing corn is nitrogen Internet access.” fertilizer,” he explains. “Nitrogen is also the biggest In January 2010, several of Lynch’s graduate pollutant, since half of the fertilizer gets leached into students and postdoctoral researchers will deploy the soil before the roots can get it.” He is currently to South Africa to begin a large and complex fi eld working on developing corn varieties with roots that planting of thousands of corn and bean genotypes. absorb the nutrient more effi ciently. “This new partnership has created an additional re- Recently, Lynch’s work received an important source to add to our existing projects,” Lynch says. boost with a grant from the Howard G. Buffett “It will allow us to work faster and better.” Foundation. Howard Buffett, a farmer, photogra- TO LEARN MORE, SEE: roots.psu.edu/ukulima pher, conservationist, and philanthropist, is inter- ested in improving crop yields as a means to increase

JAMES BURRIDGE worked on “Working with Dr. Lynch gives traveled earlier this year to help a small farm in Ohio for four me the opportunity to work with lay the groundwork for what has years while majoring in interna- critically important foods like become the Ukulima Root Biol- tional relations at the University corn and bean,” he explains, ogy Center. of Dayton. Later he worked in and to work toward a sustain- After graduation, Burridge hopes Mexico and Chile, where he ex- able food supply. He values the to continue to use his expertise perienced fi rsthand the intimate diverse opportunities offered by in root biology to impact global connection between agriculture his Penn State experience. development. “If we can learn to and development. Burridge’s de- “I have had the ability to work control the factors involved,” he sire to contribute to global de- with projects in many different says, “we can have dramatic im- velopment eventually drew him places,” he says. Those places pact all over the world.” James Burridge at to graduate study in Penn State’s include South Africa, where Bur- Ukulima Root Biology Department of Horticulture. Center, South Africa. ridge and other lab members Across the Galaxy

With tremendous advances in DNA sequencing and the advent of microarray technology in the 1990s, biology embarked on a new age of dis- covery. Researchers suddenly had access to unprec- edented amounts of data—and faced unprecedented complexity in its analysis. Necessity sparked the rise of a whole new fi eld: the hybrid of biology and computer science now known as bioinformatics. But as sequencing technol- ogies continue to evolve more and more rapidly, the challenge has grown more and more acute. “Biology is in a state of shock,” says Anton Nek- rutenko, assistant professor of biochemistry and mo- lecular biology at Penn State. “We have biochemistry and biology labs that are generating mountains of data, and then they say, ‘What do we do now?’” Anton Nekrutenko (top “Computational biologists write the programs right) and his Galaxy team. they need to solve their own problems,” Nekrutenko adds, “but they are generally not interested in pro- viding interfaces for experimental biologists.” That’s where Galaxy comes in. Developed by Nek- As with most of the software in this rapidly evolv- rutenko and others at Penn State, along with James ing fi eld, Galaxy is completely open source. “That’s Taylor at Emory University, Galaxy is a Web-based how biology works these days,” Nekrutenko explains. framework that pulls together a variety of tools that “There are commercial solutions, but they’re a waste allow for easy retrieval and analysis of large amounts of money, because the technology changes so often.” of data, simplifying the process of genomic analysis. He and his collaborators continue to work on im- Galaxy “combines the power of existing genome an- provements. One is to make computational analyses notation databases with a simple Web portal to en- transparent and reproducible, a basic tenet of exper- able users to search remote resources, combine data imental research. Nekrutenko points to one of his from independent queries, and visualize the results.” own papers, recently published in the journal Genome “Essentially we are providing a unifi ed interface Research. With the aid of Galaxy, every stage of the to many different tools,” Nekrutenko explains. As a analysis that he and his co-authors conducted is pub- trade review puts it, Galaxy “amplifi es the strengths lished as supplementary data, alongside the online of existing resources.” version of the article. The response has been gratifying. “Since last year The pace of change keeps things interesting, he the project has really taken on legs,” Nekrutenko says. “There are emerging technologies that will pro- says. The Galaxy Web site now has 10,000 registered duce 100 times more data than the so-called next- users. It runs 4,000 to 5,000 analyses daily. generation sequencing. We’re already at next-next- “It’s also available as software, so people can generation sequencing. It’s reaching the point where download and run it on their own hardware,” Nek- storage becomes an issue, never mind analysis.” rutenko says. “We encourage this because there’s a It’s exciting to be in the middle of such ferment, limit to how much data our computers can handle. he allows, and also stressful. “But we have a very “Our goal is proliferation,” Nekrutenko adds, good team assembled, and a lot of momentum. We “and right now we are really the only genomic so- have had generous early support from the Huck In- lution. We allow biologists to do very complicated stitutes at Penn State, and we are now well funded by analyses quite easily. And we have all sorts of cool NSF and NIH. features,” including an automated workfl ow man- “The funding agencies have fi nally recognized agement tool and a host of short video tutorials. that they need to pay not only for data generation, “There’s even an iPhone app so you can check your but also for data management,” Nekrutenko con- analysis as it’s running,” he says. cludes. “I think we’re in a really good place.” TO LEARN MORE, SEE: galaxy.psu.edu 13

Sharper Imaging

2009 was an exciting year for Penn State’s “Our near-term goals,” says Gilmore, “are to ex- Social, Life, and Engineering Sciences Imaging pand our user base, facilitate successful grant appli- Center (SLEIC). In mid-April, the center celebrated cations by principal investigators (PIs), and train PIs the opening of its new multidisciplinary research and students in the use of imaging methodologies.” facility, housed in the basement and fi rst fl oor of Noting that Penn State has particular strength in the renovated Chandlee Laboratory on the Univer- the biological sciences, engineering, and behavioral sity Park campus. sciences, Gilmore says that SLEIC will capitalize on The newest component of the SLEIC facility is these strengths and serve as a catalyst for the next an MRI machine, a Siemens Magnetom Trio 3T, generation of interdisciplinary research projects in that records a human body’s structure and measures these and related disciplines. brain function via blood fl ow. The machine is a twin Doctoral candidate Sarah Karalunas represents of the MRI machine at the Center for Nuclear Mag- that next generation of researcher. In collaboration netic Research at the Penn State Milton S. Hershey with Professors Lisa Gatzke-Kopp in Human Devel- Medical Center, and will permit the two centers to opment and Family Studies and Cynthia Huang- collaborate more effectively. Pollack in Psychology, Karalunas designed a study SLEIC has three components, explains Rick that involves collecting behavioral and brain wave Gilmore, associate professor of psychology and the measures during a cognitively demanding task in center’s acting director. “There is a high-fi eld facil- children with and without ADHD, to determine how ity with two MRI scanners used for biomedical and children with ADHD differ from those without the materials imaging; a 3T human MRI facility; and the disorder in terms of basic cognitive and neural func- Human Electrophysiology Facility (HEF) focusing on tion (see sidebar for more). EEG and psychophysiological studies.” Gilmore notes that Karalunas’ project is typical of “Penn State has a strongly collaborative intellectu- those that use the center’s facilities in that it involves al environment, and our center’s facilities are specifi - teams of investigators from multiple University de- cally designed to be shared,” says Gilmore. partments. “Imaging requires specialized expertise The center is a partnership of the Huck Institutes across a range of disciplines that no single person of the Life Sciences and the Social Science Research can really master,” he says. ”The center’s staff have Institute, with co-funding from the Colleges of Engi- come to be expert generalists in a variety of scien- neering, Health and Human Development, and the tifi c fi elds, and they enjoy the challenge of learning Liberal Arts, as well as the Offi ces of the Provost about new fi elds in order to help investigators effec- and the Senior Vice President for Research. It has tively answer their specifi c scientifi c questions.” a long-range goal of fostering outstanding multidis- “Although our center is new relative to other ciplinary research of all kinds, from engineering to universities,” concludes Gilmore, “we are poised for materials science, from biology to the social and be- rapid growth.” havioral sciences. TO LEARN MORE, SEE: www.imaging.psu.edu

SARAH KARALUNAS is an Her project aims to determine mance can help us understand articulate person. But when the how children with ADHD differ these differences, so we can, in doctoral candidate in Psychol- from those without the disorder time, design more customized ogy recently learned she had re- in terms of basic cognitive and interventions for each child.” ceived a National Research Ser- neural function. To do so, she’ll Karalunas is collaborating vice Award (NRSA) grant from use SLEIC’s Human Electrophysi- with Lisa Gatzke-Kopp in Human the National Institutes of Health, ology Facilities (HEF) lab to col- Development and Family Stud- the e-mail she sent off to her ad- lect behavioral and brain wave ies and Cynthia Huang-Pollack viser simply read, “YES YES YES measures on child subjects while in Psychology, as well as sev- YES YES YES YES YES!” they perform cognitively de- eral consulting faculty members manding tasks. Says Karalunas, “The process of across the disciplines. “Without applying, then reapplying, and “Not all kids with ADHD have SLEIC,” she says, “collecting then waiting took more than a the same issues,” Karalunas EEG data would have been im- year, so fi nding out that all that notes. “Looking at the brain ac- possible for me.” work paid off was pretty great.” tivity associated with perfor- 14

Switching off Leukemia

Thanks to research that combines molecular explain why some T-cells never receive the crucial biology with computer modeling, we may “self-destruct” message. To unravel the mystery of be several steps closer to winning the battle these rogue killer-T cells, Loughran called on Reka against a rare form of blood cancer known as Albert to construct an intricate computer model of large granular lymphocyte leukemia. the signaling network involved in the activation of Thomas Loughran, director of Penn State Her- the T-cells as well as their programmed death. shey Cancer Institute, and Reka Albert, professor of Albert brought impressive knowledge to bear on physics and biology at the University Park campus, the problem. A disciple of acclaimed network re- worked together to better understand the molecular searcher Albert-László Barabási and co-author with pathways and hundreds of genes and proteins inside him of the concept now known as the Barabási-Al- a cell that determine its life cycle. bert model, she explains her work as an attempt “to Their study—published in October 2008 in fi nd the mathematical model that will most accurate- the Proceedings of the National Academy of Sciences ly describe how a system changes over time.” (PNAS)—suggests that there are two key proteins Albert notes that when researchers investigate controlling “the on/off switch” in the malfunction- a complex problem in a biological system, such as ing killer T-cells that cause this type of leukemia. Says drought stress in plants or diseases in animals or peo- Albert, “Our model suggests that if we keep a specifi c ple, a computational representation can help them signaling protein called NfxB in the ‘off’ state, we predict likely outcomes. In this case, says Albert, “the can reverse the disease.” biggest challenge for constructing the computational The study, funded by the National Institutes of model was to think about the disease as a state that Health and the National Science Foundation, fi rst includes the deregulation of the signaling network took shape because Loughran and his colleagues at that guides activation-induced cell death in T-cells.” the Cancer Institute wanted to investigate why, in It took several years of effort by a very talented rare cases, the body’s normal immune response to graduate student, Ranran Zhang (the fi rst author fi ghting infection goes awry and causes disease. of the PNAS paper), guided by two mentors, to In a normal immune system, explains Loughran, make this crucial step. “Afterward, we were able to the body produces large numbers of a type of white use methodology that my group has developed and blood cell called cytotoxic T-cells or killer T-cells. used successfully in the context of other biological These cells are “programmed” by the body for a very regulatory networks. Nevertheless, this is the most narrow and specifi c mission: to kill infected cells and complex dynamic model we have constructed so far,” then die themselves. says Albert. Occasionally, Loughran says, these killer cells fail Among the billions of possibilities projected by to follow their scripted lifecycle. “When these cells the model, the researchers determined that two don’t die as expected, they expand gradually over proteins—IL-15 and PDGF—appear to be crucial in time and start attacking the body itself,” he notes. keeping the T-cells alive and growing. “You need the “They can attack the joints to cause autoimmune presence of both these proteins, as well as the signal- diseases such as rheumatoid arthritis and attack the ing protein NfxB, to create conditions in which the bone marrow to cause leukemia.” cytotoxic T-cells can proliferate,” explains Loughran. Loughran knew that, to fi nd answers, he’d need Essentially, says Loughran, “we are looking for the to zero in on the exact location of the malfunction- master control switches that keep these cells alive. ing signaling system. This system is the way cells send When we used drugs to block NfxB in cells from leu- and receive instructions—and a broken system might kemia patients, we found a signifi cant increase in mortality among the abnormal T-cells,” he adds. Loughran hopes that someday our control of A human T lymphocyte or these “master switches” may allow us to turn off the T cell, magnifi ed 2,600x. long-lived killer T-cells that cause leukemia, as well as Such precursors develop into harness their errant behavior to combat other deadly killer T cells, which are “pro- grammed” by the body to infectious diseases. kill infected cells and then TO LEARN MORE, SEE: www.phys.psu. die themselves. edu/~ralbert 15

Presidential Awards

Sean Hallgren Adam D. Smith Michael A. Hickner Susan E. Parks

This summer, four Penn State re- economy. Nine Federal depart- cal systems for computation. polymer photovoltaics, antifoul- searchers were named recipients ments and agencies join together Quantum computers can break ing surfaces, and water treat- of the prestigious 2009 Presiden- annually to nominate the most widely used cryptosystems, in- ment membranes. tial Early Career Award for Scien- meritorious young scientists cluding those used to protect e- Parks’ primary research interest tists and Engineers (PECASE). and engineers—researchers commerce transactions. Hallgren is in bioacoustics, integrating the whose early accomplishments is exploring new applications for SEAN HALLGREN and ADAM D. fi elds of biological oceanography, show the greatest promise for these computers and seeking to SMITH, both assistant professors behavioral ecology, and physi- strengthening America’s leader- determine which cryptosystems in computer science and engi- ology to address questions re- ship in science and technology are secure against them. neering; MICHAEL A. HICKNER, lated to acoustic communication. and contributing to the awarding assistant professor of materials Smith studies cryptography and She studies the use of sound for agencies’ missions.” science and engineering, and information privacy and their communication, hearing abili- SUSAN E. PARKS, assistant “These extraordinarily gifted connection to such diverse fi elds ties, and the impacts of noise on professor of acoustics and re- young scientists and engineers as quantum mechanics, combi- both sound production and re- search associate at the Univer- represent the best in our coun- natorics, information theory, and ception. Her current research fo- sity’s Applied Research Laborato- try,” President Obama said. statistics. He looks at preserving cuses on the use of sound by the ry, were among 100 researchers “With their talent, creativity, and privacy in the publication of sta- North Atlantic right whale, study- named by the White House to dedication, I am confi dent that tistical data, cryptography based ing behavioral aspects of sound receive this honor, the highest they will lead their fi elds in new on noisy secrets, and quantum production, perceptual abilities, presented to beginning scientists breakthroughs and discoveries cryptography. His CAREER award and impacts of noise on acoustic or engineers in the United and help us use science and tech- focuses on the problems stem- communication. States. They will be recognized nology to lift up our nation and ming from confl icts between data The PECASE program is coordi- at a White House ceremony our world.” access and privacy in collections nated by the Offi ce of Science in January 2010. of personal and sensitive data Recipients are nominated by and Technology Policy within the such as census surveys, social The PECASE program was es- the National Science Foundation, Executive Offi ce of the President. networks, and public health data. tablished in 1996 to identify and NASA, and the Departments of Awardees are selected on the ba- His work addresses the need for honor outstanding researchers Health and Human Services, sis of two criteria: pursuit of in- formal privacy guarantees that who are beginning their indepen- Defense, Energy, Agriculture, novative research at the frontiers remain meaningful even against dent research careers and pro- Education, Commerce, and of science and technology, and a an intruder with partial knowl- vide recognition of their potential Veterans Affairs. commitment to community ser- edge of the sensitive data. for leadership across the fron- vice as demonstrated through The NSF nominated two of tiers of scientifi c knowledge in Hickner and Parks were among scientifi c leadership, public edu- Penn State’s recipients, Hallgren the twenty-fi rst century. the forty-one recipients nominat- cation, or community outreach. and Smith, from among the re- ed by the Department of Defense. Winning scientists and engineers According to a White House cipients of its 2008 Faculty Early Hickner’s research interests in- receive up to a fi ve-year research statement, “The Presidential Career Development Program clude polymer chemistry, poly- grant to further their study in Early Career Awards embody the (CAREER) awards. The Founda- mer micro- and nanostructure, support of critical government high priority the Administration tion also nominates twenty of the transport properties in hetero- missions. places on producing outstand- PECASE recipients. geneous materials, electrochem- ing scientists and engineers to Hallgren works in the area of istry, and new materials for en- advance the nation’s goals and quantum computation, which ergy applications. He has active contribute to all sectors of the aims to use quantum mechani- research programs in fuel cells, 16

Contacts

Henry C. Foley Graduate School Interdisciplinary Research Publications Vice President for Research Regina Vasilatos-Younken Peter Hudson David Pacchioli Dean of the Senior Associate Dean Director, The Dorothy Foehr Associate Director, Graduate School 114 Kern Building Huck and J. Lloyd Huck Research Communications Institutes of the Life Sciences 304 Old Main 814-865-2516 University Relations University Park, PA 814-863-3650 814-865-3478 16802-1504 [email protected] [email protected] 814-863-9580 Suzanne Adair [email protected] Assistant Dean of Edward G. Liszka Graduate Student Affairs Director, Applied Peter E. Schiffer Senior Director of Graduate Research Laboratory Educational Equity Programs For more information, 814-865-6343 Associate Vice visit our Web sites: President for Research Director, egl4 @psu.edu Offi ce of Postdoctoral Affairs Director of Strategic Initiatives 114 Kern Building Research 304 Old Main Susan McHale www.research.psu.edu 814-865-2516 814-863-9658 Director, Social Science [email protected] Research Institute Graduate School Technology Transfer 814-865-2647 www.gradsch.psu.edu Daniel A. Notterman [email protected] Vice Dean for Research Stephen P. Brawley and Graduate Studies, President/CEO, Ben Franklin Tech- Carlo G. Pantano College of Medicine nology Center of Central and Director, Associate Vice President Northern Pennsylvania, Inc. Materials Research Institute for Health Sciences Research 814-865-8669 814-863-8407 717-531-7199 [email protected] [email protected] [email protected] Ronald J. Huss Padma Raghavan Ronald J. Huss Director, Director, Associate Vice President Intellectual Property Offi ce Institute for Cyber Science for Research and 814-865 6277 814-865-9233 Technology Transfer [email protected] [email protected] 113 Technology Center 814-865-6277 Daniel R. Leri Thomas L. Richard [email protected] Director, Innovation Park and Director, Penn State Institutes Research Commercialization of Energy and the Environment David W. Richardson 814-863-6301 814-865-3722 Associate Vice President [email protected] [email protected] for Research, Director of Sponsored Programs Tanna M. Pugh Marica S. Tacconi 110 Technology Center Director, Industrial Executive Director, Institute 814-865-3396 Research Offi ce for the Arts and Humanities [email protected] 814-865-2878 814-865-0495 [email protected] [email protected]

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