Periodic elements - Spring 2014

Inside:Fragmented Forests: Decades of Data

Crash Test Geniuses

Spit Take, No Laughing Matter

Spring 2014 No. 11 A Magazine from the College of Science

On the Cover

InsidePeriodic ElementsA Team Approach to Head Injury Research 1

New Center Works to Improve Transportation Safety 2

Oil Spills, Shipwrecks, and the Environment 4

NanoNotes 6

Space Weather 7

Jungle Seminar from Amazonas 8

Computer Simulations and Alzheimer’s Research 12

Dean’s Message 13

Patty SnellingsDirector of College Relations

College of Science703-993-8783

[email protected]

AdministrationPeggy Agouris, Dean

Evans Mandes, Senior Associate Dean, Finance and Personnel

Kevin Curtin, Associate Dean, Academic Affairs

Gregory Foster, Associate Dean, Research and Computing

Donna Fox, Associate DeanStudent Affairs andSpecial Programs

Martha Wescoat-Andes, Associate Dean, Administration

Newsletter Editors:Home Row Editorial

Sharon Ritchey, Liesl Wiederkehrwww.homerowed.com

Layout Designer:Beth Moorcones, EWM Design

www.ewmdesign.com

Lily pads in the Amazon rainforest

Story page 8

A publication of the George Mason University College of Science

cos.gmu.edu

COS cares about the environment – please recycle

Photo: Beth Cabrera

Christine H. Fox, acting deputysecretary of defense, U.S. Department of Defense, will deliver the keynote address.She has spent three decades in the defense industry as ananalyst and research manager,with a special emphasis on operations. Fox is a two-timeMason alumna, holding a master’s degree in appliedmathematics and a bachelor’s degree in mathematics.

Join us for the College of Science ConvocationWednesday, May 14, 2014, 2 p.m., at the Patriot Center

Spring 2014 • Periodic Elements • 1

Recent high-profile illnesses andsuicides of NFL players and

other professional athletes who havesuffered concussions have broughtthe seriousness of traumatic brain injury (TBI) to the public’s attention. A concussion occurs when thehead is hit so hard and so suddenlythat the brain slams up against theskull and is injured.And while thetrauma to the brain can be severe, itcan go unnoticed.A person sufferinga head injury may have cuts andbruises and may lose consciousness,but not always. In our get out thereand play, shake it off sports culture,coaches, athletes, and their familieshave misunderstood the severe im-pact of a concussion on long-termhealth. TBI can lead to depression, suicide, Alzheimer’s disease, Parkin-son’s disease, and chronic traumaticencephalopathy (CTE), a degenerativebrain disease.

“When a patient comes into anemergency room with a head injury,there is no objective clinical test to diagnosis a concussion.And there is no way to objectively determinewhen someone has sufficientlyhealed,” says Shane Caswell, associateprofessor in the College of Education

and Human Development and execu-tive director of its Sports Medicine Assessment, Research & Testing(SMART) Laboratory. Caswell is working to change allthat. He has partnered with Emanuel(Chip) Petricoin III, codirector of theCenter for Applied Proteomics andMolecular Medicine in the College of Science. Caswell and Petricoin are developing the first ever salivarybiobank to test for unique brain pro-teins that show up after a head injury.“We know that there are specificmarkers, tau protein, S100B, and GFAP,that if you find them in a patient’sblood are not good and indicate abrain trauma. One of the questionswe want to investigate is whetherthese markers also show up in saliva,”says Petricoin.The short answer isyes, but that is just the beginning. Caswell has developed a study totrack Mason athletes as well as a localyouth football team throughout theirentire ten-week playing season.Theplayers’ helmets are fitted with sensorsthat determine when a player hasbeen hit. But more important to thestudy is the player’s spit. Each week,Mason researchers collect the players’saliva and transport it to the lab,where it is analyzed for biomarkersusing nanoparticles developed in Petricoin’s lab.The sample collectionis easy, painless, and noninvasive. A nanoparticle is an engineeredpolymer, a microscopic substancethat is synthesized in a beaker andacts like a sponge, explains Petricoin.“The particles are simple to make andcan be tuned for specific uses, such as our salivary research.” Petricoin and his codirector,Lance Liotta, are using nanoparticlesin research projects, such as breastcancer research, and are excitedabout the applications. “We can use

them in vivo—on living material—tocollect information. For instance, youcan put them on a patch to collectbiomarkers from your skin or on atumor when it’s removed,” says Liotta. For the concussion project, Petricoin says, “We have documentedsixty concussive events and have samples from half of those athletes.We now have enough data to performa biomarker discovery analysis.” Caswell and Petricoin realize thatthey have years of research ahead.Many factors have to be examined, including age and gender differences.The long-term hope is that a mouthguard can be developed that reacts,possibly with a change in color, if aplayer were to suffer a concussion.The work has applications for playersreturning safely to play, soldiers returning safely to combat, as well as the general population who sufferconcussive events every day. “Shane’s dedication and detail to this study are tremendous,” saysPetricoin. “We couldn’t do this type ofresearch without such a well-thought-out collection method.” “We’re bringing our labs out tothe community,” says Caswell. “We areproviding direct care to athletes andhelping students conduct researchand see how clinically meaningful diagnostics are created.” This interdisciplinary researchmay help develop a new therapeuticapproach to preventing and treatingtraumatic brain injuries.

Using Their Heads:Research into Traumatic Brain Injury

An atomic force microscope imageof nanoparticles used to analyzebiomarkers found in saliva.

Photo: Courtesy of CAPMM

© iStockphoto.com

Spend some time with Cing-Dao(Steve) Kan, director of the new

Center for Collision Safety and Analysis(CCSA) in the College of Science(COS), and you’ll never look at a carcrash, road, or car the same way again. Kan and his staff of ten vehicleresearch experts and two studentsrun computer simulations to crashcars and trucks into each other, walls, guardrails, and other stationaryobjects, such as trees. Kan admits it’sfun but also serious work in an effortto improve transportation safety. Although the National Highway TrafficSafety Administration reports that traffic fatalities dropped by 4.2 percent for the first half of 2013, Kanis concerned this may change as theeconomy improves. More people willbe buying new cars and getting onthe road, and there will be an unpre-dictable mix of newer, fuel-efficientcars, like the tiny Fiat 500 and theSmart Car, and older, legacy modelcars and trucks.

CCSA partners with the National Center for Manufacturing Sciences(NCMS), a nonprofit member-basedgroup that has helped small manufac-turers safety test and perfect theirproducts before releasing them to themarket for more than thirty years. Kanexplains that automobile companiessuch as General Motors and Ford require their suppliers to test and certify that the parts they sell passsafety and quality standards. Many of these companies are small, withoutin-house testing expertise or resources.The small companies turn to NCMS,who partners with CCSA, to help. CCSA also works directly with car and parts manufacturers, researchuniversities across the globe, and government agencies, including theFederal Highway Administration, the National Highway Traffic SafetyAdministration, and the U.S. Departmentof Defense.After 9/11, CCSA workedwith the U.S. State Department to design protective anti-ram bollards,

those ubiquitous posts that surroundgovernment buildings and gate systemsfor U.S. buildings and embassies overseas. Highway and road safety is a national and an international concern,and CCSA has research collaborationprojects with schools across thecountry and as far away as Australia,Japan, and China.The center alsoworks directly with car manufacturerssuch as Ford, Toyota, Hyundai, andHonda, as well as parts manufacturerssuch as Johnson Controls. The CCSA facility is housed near the Fairfax Campus in a formeradministration building.The ground-floor garage lab is full of sophisticatedtesting equipment and a new car donated by Volkswagen that researchers are scanning inch-by-inchto reverse engineer into a completesimulated computer model. It’s ameticulous and time-consumingprocess but necessary to have this typeof vehicle in the simulation library.

2 • Periodic Elements • Spring 2014

Crash Test

Geniuses

© iStockphoto.com


The upstairs office area includesa conference room, NCMS officespace, and space for the researchers.As you walk through CCSA, posters of real and simulated vehicle crashesand data line the walls. It’s morevideo game-esque than roadsidemacabre. Kan admits that the space is quiet now, but it is just what he hadhoped for—room to grow. Plans arealready underway to bring in morestudent researchers. CCSA is alsoworking with Mason to raise moneyto build an outdoor test track wherethey can run real collisions to augmentthe computer simulations.

Simulation InvestigationCCSA’s simulation data is eerily accurate when compared to actualcollision images and videos. One ofthe most important tools the groupdeveloped was a series of computersimulations of more than twenty standard cars, vans, crossovers, andlight and heavy trucks, all now in the database.These virtual vehiclesrepresent standard models found inmost car inventories.The vehicles canrun on any road surface and in anyweather, contain virtual people of different sizes and weights, run at different speeds, and carry differentloads. Kan explains that the governmentwants to see trucks with increasedfuel efficiency by March 2016. Currently, cars and trucks have different safety and fuel efficiencystandards. However, one of the onlyways to increase fuel efficiency is to decrease the weight of a vehicle.Trucks are designed to carry materials,so it is difficult to assess whether a lighter truck with a heavy load is actually meeting fuel standards.Also, a lighter truck may not be as safe onthe road.These are all questions thatcan be investigated by changing theweight and running hundreds of simulations in almost unlimited scenarios.

Kan and many of his staff members worked together for morethan twenty years at the NationalCrash Analysis Center (NCAC) at TheGeorge Washington University. Hecredits NCAC’s work for many of ourcurrent vehicle and safety standards.

Driving the DataUnderstanding and interpreting datais at the heart of CCSA’s work. Whileit may be interesting to see virtualcars navigate icy roads or what happens in a side impact collisionfrom the safety of a computer screen,this is just the beginning. For instance, Kan explains thatten percent of car accidents involve a car rolling over.And while that indicates that ninety percent are fromother types of collisions, the fatalityrate for rollovers is thirty percent. Additionally, rollovers are inherently aproblem in the United States “becausewe have more open roads,” says Kan.

He explains that analyzing carcrashes and driving trends also involvesa bit of psychology. “Americans are casual drivers,” says Kan. “An American-made car is full of cup holders,

entertainment systems, and gadgets. Drivers in Europe are more seriousabout their cars, and driving in partsof Asia is like driving in Disneylandwith few rules or regulations.” CCSA’s simulations are differentfrom government crash tests. Inthose, a car is crashed head-on into a wall. Kan explains that this is thesame force as if the car were crashedinto itself. However, most crashes—and the most dangerous ones—areside-impact collisions and head-on impacts that skew to one side of thefront wheelbase. Government crashtesting also doesn’t test how a carwill survive if hit by a heavy car ortruck, or if it strikes a guardrail orbuilding.Additionally, crash test dummies are all one size and sit in one standard position. With the simulation, anything can be programmed to mirror real life. Kan explains all these detailswith intense interest, and he wants to grow CCSA and expose it to morestudents. His personal collisionknowledge is encyclopedic; by train-ing, Kan is a mechanical engineer. He says that in the beginning, CCSA’sresearch was more computer science-based because there was a need tobuild the simulations. But now thattechnology is readily available, thefocus is interdisciplinary. He jokesthat because crash testing involvesphysics, geography, biology, and psychology, CCSA’s home in the College of Science is a good fit and a great resource for students and researchers. In addition to settling into theirnew home, deconstructing a Volkswa-gen, working to finance a test track,and bringing in new researchers, theCCSA team is also studying jet enginecontainment scenarios to see how engine safety can be improved usingnew materials and designs. Vehicles are always evolving, and governmentstandards are always changing: CCSA hasno shortage of research opportunities.

”

“One of the most importanttools the group developedwas a series of computer simulations of more thantwenty standard cars, vans,crossovers, and light andheavy trucks, all now in the database. The vehiclescan run on any road surface

and in any weather, contain virtual people of different sizes and weights,run at different speeds, and carry different loads.

The 2010 Deepwater Horizon oil spill in the Gulf of Mexico affected marine mammals, fish, waterfowl—and the tiniest of marine life, microbes. Leila Hamdan, associate director of the

Microbiome Analysis Center (MBAC) in the College of Science (COS) and assistant professor ofmolecular microbial ecology in the Department of Environmental Science and Policy (ESP), isworking to understand the effects of this oil spill on microbial life on shipwrecks in the northernGulf of Mexico. “When a shipwreck happens,” Hamdan explains, “the first organisms on the sceneare microbes. They help transform…human structures into a hotspot for life in the deep ocean.” Hamdan is leading researchers in exploring the ecological role that shipwrecks play in the deepocean (deeper than 200 meters). Funded by the Bureau of Ocean Energy Management (BOEM),this is the first study to assess how this oil spill affected deep-ocean microbial communities onshipwrecks. Hamdan and her team, including ESP professor and MBAC director Patrick Gillevet, selectedsix shipwrecks at varying distances from the Macondo wellhead, the epicenter of the DeepwaterHorizon spill. Each area has one wooden-hulled and one steel-hulled shipwreck so that researcherscan compare their findings on different hull materials. The first expedition occurred in March of this year. Hamdan, Gillevet, and their team workedfrom the research vessel Pelican, operated by the Louisiana Universities Marine Consortium, outfitted for oceanographic study in coastal areas. Because the shipwrecks are at depths too extreme for diving, researchers use a remotely operated vehicle (ROV) to collect samples fromthe ocean bottom. Hamdan explains, “A shipwreck is a hard surface, rarely found in the deep ocean, and it createsa perfect environment for organisms large and small to attach to.” The study has implications for


Photo: Courtesy of Leila Hamdan

Research Examines How Oil Spills Affect Deep-Ocean Microbeson Shipwrecks

recovery from the environmentaldamage caused by the DeepwaterHorizon spill. “To understand howthese environments exist naturallyand how they’ll be affected,” explainsHamdan, “we have to get our brainsaround the microbial communitiesthat are present…and how resilient[they are] to change.” “Decades of study of aquatic microorganisms show us that when a chemical insult to the local environ-ment happens, in this case, an oilspill, the first organisms to respondare microorganisms,” Hamdan says.“That response could have been quitedetrimental. We need to understandwhat’s happened to the base of thisfood web so that we can evaluate howit has affected these artificial reefs.” Hamdan and her colleagues are seeking to learn whether the spill contamination had a specific, different effect on wood-degrading organisms than on metal-degradingorganisms.The answer could meanthat preservation of one or the othertype of ship hull may be affected differently, which could then affectBOEM’s work of evaluating how these shipwrecks hold up over time. Another goal is to examine the effects of the chemical dispersants(COREXIT 9500) that were used tomitigate the oil spill’s effects, for example, on microbe growth whichcould be harmful to the biota of anecosystem. As far as implications for science,government, and the private sector,Hamdan says, “Because of wherethese ecosystems are and their highbiodiversity compared to the sur-rounding ocean floor, they can serveas ecological monitoring platformsfor contaminants in the deep ocean. I think we’ll be able to contributequite a bit of knowledge about how oilinteracts at the ecosystem level there.”

(Left) Life in the deep – the wreckage of the steamship Anona provides afoundation for micro and macro marine life in the deep, dark biosphere.


Leila HamdanDuring summers at the Jersey Shore, Leila Hamdan saw a place that was entirely transformed by blue water. “The landscape is shaped by water, andthe attitudes of everyone there were moved by oceans,” Hamdan says. “Andthe oceans moved me, too.” She planned to study aquatic systems in graduate school but wasn’t sureexactly what discipline. She found her calling when she came to Mason andlearned about aquatic microorganisms. “My microbial ecology professortalked about how integral microbes are to ecosystems but how little we knowabout them,” Hamdan explains. “Studying microbes takes a lot of imaginationand creativity because you never see what you’re studying with the naked eye.It hit me like a thunderbolt, and I just had to study that. It’s been my passionever since.” Hamdan earned two degrees from COS: a master’s in biology and a doctoral degree in environmental science and public policy. In her previouswork as a research microbiologist at the U.S. Naval Research Laboratory, she researched bacterioplankton in major U.S. estuaries and studied microorganisms in hydrocarbon-rich environments on continental marginsaround the world. For Hamdan, Mason provides collaboration among the people in her department. She says, “I’m part of a team that’s trying to understand the environment in innovative and evolving ways.” Now a molecular microbial ecologist, she has expanded her research interests to include coastal, continental shelf, and deep ocean studies. To prospective students, Hamdan recommends, “Find something you’re passionate about and stop at nothing to understand it.”

Hamdan standing on the stern of the Pelican with the remotely operatedvehicle (ROV) used for this study.

Photo: Courtesy of Leila Hamdan


NanoNotesElements of Distinction about the College of Science,its Faculty, Staff, Students, and Alumni

Emanuel F. Petricoin III, Center for Applied Proteomics and MolecularMedicine, was appointed to the boardof directors and the scientific advisorycommittee of Egenix, Inc., a New York-based biotechnology company focused on the development of innovative cancer therapeutics.

Paul A. Dirmeyer, Department of Atmospheric, Oceanic, and Earth Sciences, was named a 2014 Fellowof the American Meteorological Society,the leading professional organizationfor atmospheric and related oceanicand hydrological sciences.

Gavin Sampey, a doctoral student inthe Biosciences program, received atwo-year funding award in the amountof $66,500 from the National Instituteof Neurological Disorders and Stroke,part of the National Institutes ofHealth. His application for the Ruth L.Kirschstein National Research ServiceAward Individual Pre-doctoral Fellow-ship, “Effects of Exosomes Derivedfrom HIV-1 Infected Cells on ViralSpread,” earned an outstanding scoreof one percent, placing it at the top of all similar applications evaluated inthat study section. Sampey’s researchwill be performed under the mentor-ship of Fatah Kashanchi, director ofresearch, at the National Center forBiodefense and Infectious Diseases in the College of Science.

Abul Hussam and Timothy Born, Department of Chemistry and Biochemistry, received a U.S. patentfor their application titled “RemovingViruses from Drinking Water.”

Dann Sklarew, Department of Environmental Science and Policy,served a one-year term as the Potomac River Goodwill Ambassadorto the Potomac’s sister river, theArakawa River in Tokyo, Japan. He

shared his expertise about the Potomac River watershed, its ecologicalchallenges, stewardship, and sustain-able development at an internationalgreen infrastructure workshop, aKantō Plain rivers workshop, and seminars at Hosei University andTokyo University of Agriculture.

Thomas Lovejoy, Department of Environmental Science and Policy, received the International Award of Excellence in Conservation from theBotanical Research Institute of Texas forhis lifelong work to protect biodiversity.

Iliriana Mushkolaj, PhD EnvironmentalScience and Public Policy ’13, hasbeen named the climate change planning advisor in the Senior ClimateChange Unit of the Ministry of ForeignAffairs and International Cooperationfor the Republic of Fiji.

Luis Nieves, PhD Environmental Science and Public Policy ’99, hasbeen appointed chancellor of the University of Puerto Rico at Humacao.He oversees more than 4,000 studentsand approximately 300 faculty membersat the university’s third-largest campus.

Carla Milagros Mere Roncal, a graduate student in the Departmentof Environmental Science and Policy,was selected to receive a Sidney ByersScholarship for Wildlife Conservationfrom the Wildlife Conservation Network.

Ryan Valdez, a doctoral student in theDepartment of Environmental Scienceand Policy, was awarded a dissertationscholarship from the Society of HispanicProfessional Engineers Foundation.

Christine H. Fox, MS Applied Mathe-matics ’80 and BS Mathematics ’76,was appointed acting deputy secre-tary of defense by President BarackObama. She is the highest-ranking female official in history to serve inthe U.S. Department of Defense.

Dieter Bilitza, School of Physics, Astronomy, and Computational Sciences, was honored with the 2013International Kristian Birkeland Medalfor Space Weather and Space Climate,awarded by the Norwegian Academyof Science and Letters. He was recog-nized for his work on the InternationalReference Ionosphere, a widely usedstandard for Earth’s ionosphere.

Kirk Borne, School of Physics, Astronomy,and Computational Sciences, was oneof twenty-nine researchers selectedfrom across the United States to participate in a National ScienceFoundation-sponsored Ideas Lab at Emory University. The program focused on big data in education,specifically, intensive research to improve teaching and learning.

Faculty, staff, students, and alumniare encouraged to send theirNanoNotes to [email protected].

COS Alumni Chapter EstablishedThe College of Science (COS)Alumni Chapter was recently accepted into the George MasonUniversity Alumni Association. Walter McLeod, MS Chemistry ’94,serves as president of the newchapter, which represents alumniwho graduated in or prior to 2006with a science degree from the former College of Arts and Sciencesor the former School of Computa-tional Sciences. McLeod says the purpose ofthe chapter is to enhance the senseof community and connection between the university and COSalumni. “One of the goals,” he adds,“is to strengthen the professionallink between alumni and graduateand undergraduate students.” For more information, contactMcLeod at [email protected].


Recently, the astronomical community was in a bit of a

buzz as the Sun flipped its polarity.“Rotating plasma in the Sun generatesa magnetic field” says associate professor Bob Weigel, director of theSpace Weather Lab in the College ofScience (COS).“Because the Sun rotatesfaster at the equator than at the poles, the magnetic field is constantlymigrating from the pole to the equator.”Weigel explains that this somehowcauses the Sun to flip its polarityabout every eleven years.This latestturn also marks the Sun’s halfwaypoint in its twenty-fourth solar cycle. “The Sun has been quiet in recentyears,” says Weigel.This cycle has beenthe weakest in 170 years. An activecycle is characterized by increasedsunspots and solar flares—events thatcontribute to space weather—literallyout-of-this-world conditions causedby changes coming from the Sun. “But even in an active solar cycle, most of us wouldn’t realize the change,” says Art Poland, a formerNASA researcher and one of the scientists responsible for establishingthe Space Weather Lab in 2003.Thebest known effect of space weather is the aurora borealis, the northernlights, usually only visible toward theNorth Pole.The light show is a result ofthe Sun’s magnetic storm interactingwith the Earth’s magnetic field; explosions on the Sun shoot chargedparticles into space and to the Earth.The Earth’s magnetic field capturesthe particles and pushes them to the poles. When the particles collidewith gas molecules in the Earth’s atmosphere, the energy produces the

light show. Poland says that both theEarth’s magnetic field and its atmos-phere protect us from the constantwind that comes from the Sun. Although most people aren’t lookingup the daily space weather forecast(you can at the National Weather ServiceSpace Weather Prediction Center,www.swpc.noaa.gov), space weatheris becoming increasingly important. Poland explains, “Our current understanding of space weather is the same as our understanding of the Earth’s weather was back in the 1950s.” Advances in technologyenable us to understand more.Andit’s precisely because of technologythat we care about space weatherforecasts. For instance, it is bothcheaper and faster for airlines to flyplanes over the poles when travelingbetween continents. However, increased solar activity brings largeamounts of radiation that can disruptcommunication systems and GPS, andincrease radiation exposure to theflight crew and passengers. Spaceweather forecasts allow carriers to decide when to reroute flights tolower latitudes. Utilities are concerned too. InMarch 1989, a powerful geomagneticstorm hit Earth, causing circuit breakersin Canada’s Hydro-Quebec’s powergrid to trip, causing a blackout. Withspace weather forecasts, power gridscan now be decoupled to prevent extensive blackouts. NASA and themilitary monitor space weather, too.Solar storms can affect the accuracyof missiles during warfare, disruptsatellites, and delay space walks orlaunches.

The Space Weather Lab is affiliatedwith the School of Physics, Astronomy,and Computational Sciences in COS.The lab, like its history, is unique.Poland says that in the early 2000s, heand several fellow space researchersworking at NASA and the U.S. Naval Research Laboratory (NRL) wereready to retire from their governmentjobs but not from their research orwork.The scientists had substantialgovernment grants that they wereable to bring to Mason with the hopethat the university would see a needfor their work and could support a program with several youngertenured faculty members. With additional funding from the NationalScience Foundation (NSF), the labwas established.Today, the lab attractsresearchers from all over the country,including NASA, NASA Goddard, andNRL. While there is no space weatheracademic degree currently offeredby COS, the lab is a place wherestudents develop an understandingof the Sun, the heliosphere, geospace,and how they interact. The Space Weather Lab has a variety of projects including the SolarEruptive Event Detection System(SEEDS), which automatically detectsand classifies solar events, and thespace weather forecasting contest, in which participants can test theirforecasting skills against models, algorithms, and other space weatherforecasters from around the world.

Today’s Space Weather Forecast:Solar Storm Yesterday, Watch for Northern Lights Tonight

This composite image presents thethree most visible elements of spaceweather: a storm from the Sun, aurora as seen from space, and aurora as seen from the Earth.

Photo composite: Courtesy of NASA


Last December, Mason President

Ángel Cabrera, his wife, Beth, an

d

their two children, Alex (16)

and Emily (14), took a dif

ferent

type of family camping tr

ip.

Itold Beth and the kids that I was taking them on an exotic

vacation, but it wasn’t going to be toa fancy resort,” says Cabrera. “Theywere going to be sleeping in a ham-mock in the middle of the Amazonrainforest.They were game for it.” The Cabreras were not alone.They were traveling with famed con-servation biologist Thomas Lovejoy to Camp 41, a unique and remote research facility that serves as the permanent home base for one of the oldest and largest conservationprojects in Brazil. Lovejoy, who holds a joint appointment as University Professorin the College of Science and the College of Humanities and Social Sciences and is a Senior Fellow at theUnited Nations Foundation, has ledscores of trips to Camp 41 to show

people the dramatic and real effectsof deforestation. For nearly fourdecades, he has been overseeing thisecological experiment in the heart of the Amazon rainforest. “I’ll take anybody down I can,”says Lovejoy. “These are my jungleseminars. I want as many people as

possible to see what is happening. I’dlike more Brazilians to see it, too. Ourhope is to get the board of the WorldWildlife Fund-Brazil there soon.” His tours have included celebrities,politicians, and researchers, anyoneinterested in sustainability.The morepeople who experience the Amazonand see how deforestation is causingthe loss of so many of the world’sspecies, the better the chance to save it. It also teaches about biodiversity and the living planet. In the 1970s, Brazil had a Forest Code requiring farmersand ranchers to maintain a fifty-percent legal preserve of theirproperty (today’s version iseighty percent). However, it wasnot known how large or whatshape these artificial environ-ments (habitat islands) neededto be to support the same typeof healthy ecological environ-ment found in natural forests.This set-aside gave Lovejoy an idea: What if the preservedareas could be arranged together to form a number of

islands of different sizes that could bemeasured for changes in biodiversity? Prior to this idea, starting in the1970s, there was a major controversycalled the SLOSS Debate (single largeor several small reserves). Not all scientists trusted the theory becauseit hadn’t been tested. Many ecologistsbegan running studies on already existing fragmented ecosystems, but the original conditions of the

fragments were undocumented andunknown. Lovejoy designed the first and,still to this day, the largest fragmenta-tion experiment, specifically in thiscase, to measure the effects of habitat fragmentation on the Amazontropical rainforest. Originally named theMinimum Critical Size of EcosystemsProject, it began in 1978 and was endorsed in 1979 by the National Institute of Amazonian Research

(INPA) and a small monthly grantfrom the World Wildlife Fund (WWF).Today, the project, now called the Bio-logical Dynamics of Forest FragmentsProject (BDFFP), is a collaborativeproject between INPA and the Smith-sonian Institution. Mason will soon be a partner. The original fragmented land was cleared, and the study was basedon one- and ten-hectare fragments.Researchers started collecting data,but the ranchers had not cleared therest of the land so the experimentwas not fully developed.Two yearslater in 1983, Lovejoy received newfunding from WWF to create two newfragments.


Postcardsfrom Camp 41

(Left) Exploring the Amazon jungle.(Above right) Houses along the Amazon River.

“

continued on page 10

“I’ll take anybody down I can,” says Lovejoy.“These are my jungle seminars. I want as manypeople as possible to see what is happening.”

All photos for this article: Courtesy of Beth Cabrera

10 • Periodic Elements • Fall 2013

The Edge EffectIt did not take long to document significant changes, specifically alongthe edges of the fragmented forest.Big trees and other plants, now exposed to strong sunlight and winds blowing down from the AndesMountains, died.This edge effect extends at least one hundred metersinto the fragmented area.Additionally,Lovejoy explains, “Anything that has a large home range, such as spidermonkeys and jungle cats, does notstay. Birds that prefer darkness andshade and avoid open areas disappear.A one hundred-hectare fragmentloses about half its bird species, about fifty types of birds.” The task of counting and docu-menting different animals and plants is immense, but what is often noticedis what is lacking. For instance, it’snot uncommon to find colonies ofarmy ants covering the jungle floor. A typical colony could contain onemillion or more of the insects. Birdsoften follow the ants as the insectsturn up the area and act as beaters,helping the birds find food. However,a one-hectare area is too small to sustain the immense ant colony, andthe insects die.The birds die or leave,as there is no food. Army ants need at least thirty hectares to survive.

Another significantproblem is water. Lovejoy says, “TheAmazon makes half its own rainfall.Whentrees die, the waterruns off and threatensthe entire rain cycle.The deforestationcan lead to severedrought.”

A Multi-JungleView

Lovejoy likes visitors to experiencethe Amazon from different levels, sothe Cabreras began their tour on theriver.The trip to Camp 41 begins inManaus, the capital city of the state of Amazonas in northern Brazil,

where the Rio Negro and the AmazonRiver come together at a famousplace called the Meeting of the Waters.“These rivers are bigger than anyriver you’ve seen,” says Cabrera. “Solarge that you can’t see across themat times.” The meeting is remarkable for itssize but, also, for a unique phenomenon.The Rio Negro is black, and the Amazon is a light brown. Where thetwo come together, the waters do not mix because of different densitiesand temperatures.The two massivewaterways flow separately side-by-sidefor many miles. “This is an incrediblesight to see,” says Lovejoy, “and wewere also lucky to see pink dolphinsthat are native to the area. I also likepeople to experience traveling on theriver because this is how people got

around before planes.” Not that trans-portation is still easy.There is onlyone main road in Manaus that travelsthrough the jungle and eventuallynorth to Venezuela. To get to Camp 41, you travel byJeep until you reach the jungle and a smaller dirt road.That eventuallyends. “You grab your things and hikethe rest of the way into camp,” saysCabrera. After touring the Meeting of theWaters, Lovejoy took the group to an early-morning visit to a tower thatextends above the level of the junglecanopy.“From there you see the jungle wake up. You see things thatyou have trouble seeing from theground,” says Lovejoy. Johan Rockström and his family

also joined the Cabreras. Rockström is the executive director of the Stockholm Resilience Centre and an international expert in global sustainability. “The party was half children and half adults,” says Lovejoy.He likes it when family memberscome on the trips.The adults becomeparents and see the research and thejungle through their children’s eyes. “Tom is a teacher and hangs back,letting his students guide visitorsthrough the site,” says Cabrera. “Youcan tell as you are walking through thejungle that he has dozens of stories to share, but he doesn’t interrupt. His researchers are experts, and eachwalk into the jungle exposes you toplants and animals you would nevernotice.”

Fragmented jungle. The edge e

ffect, where vegetation

and species exposed to

hot drying air and sunlig

ht die.

Postcards, from page 9

Learn more about the Biological Dynamicsof Forest Fragments Project at

amazonbiodiversitycenter.org. The website featuresphotos of the research and an eye-opening

deforestation video created from satellite imagery.

Fall 2013 • Periodic Elements • 11

Lovejoy explains that one of thetop researchers, Mario Cohn-Haft, isan ornithologist who could easilyhave become a musician. He has theability to hear the bird song and iden-tify the species.This is particularlyuseful because birds hide in the jungle. With these experts, it is all tooeasy to see the differences in the fragmented area compared to theundistributed control areas and Camp41, which is in the heart of the jungleand not in the fragmented sites. Cabrera and Lovejoy agree that it is depressing to see the loss ofspecies and the dramatic death of the forest and understand that if itcontinues, countless species will goextinct and the entire weather systemand ecology of Brazil and the worldmay be affected. Cabrera adds that he does feel a bit of hope becauseLovejoy is working so hard to bringattention to this problem with credible research and outreach. “Optimism is the only option,”Lovejoy says. If you are pessimistic,you won’t do anything.The challengeis much greater than it was forty-nineyears ago. But this country has thebiggest level of public awarenessabout biodiversity in the world. Half ofthe Amazon is now under protection.It’s not enough to protect the hydro-logical cycle.The forest is at a tippingpoint, it’s not an experiment we wantto see.” Lovejoy travels to Brazil aboutfour times a year. Many times he stays only in Manaus to oversee administrative work.A team of full-time researchers, both Brazilian andAmerican, work to document theproject and maintain the barrier thatcreates the jungle fragment. Lovejoysays, “The jungle keeps encroachingon the fragmented area, and itchanges depending on how the landis cleared.” He explains that if the areais cleared for cattle pasture, more natural forest will regrow. One of the

first trees to return is the Cecropia, a tree with distinct paddle-like leavesthat can reach heights of thirty feet. If the area is cleared by fire, what happens is that only a single speciescomes back usually through sendingout suckers. What you end up with is a “thicket of toxic plants.” Though the camp is remote, itcan only be reached on foot, andthere are no amenities orcomforts, Lovejoy loves therhythm of the jungle. “I lovethe sounds of the Amazon,it’s almost like home to me,”he says. “You never know allthe sounds you are hearing,but there is one sound thatyou hear every singlemorning, you can set yourwatch to it.” He recallshaving the actor TomCruise at camp, and earlyone morning, Cruiseasked him what time itwas. Minutes earlier the familiar animal callbroke through the jungle cacophony, andhe said, “Oh, it’s 5:30.”

Researcher to Researcher Cabrera’s interest in Lovejoy’s work is more than mere curiosity.The twoeducators met in the summer of 2012 while they were both in Rio deJaneiro. Cabrera, a recognized interna-tional expert in global leadership,higher education, and corporate citi-zenship, was chairing a set of sessionsat the Rio+20 United Nations Confer-ence on Sustainable Development;Lovejoy was announced as winner of the prestigious Blue Planet Prize,considered the most important international environmental award.A fast friendship based on mutual interests and goals was forged. Since that first meeting and thisAmazon trip, the two are working

together through the university to effect positive global environmentalchange. Cabrera says, “The type ofwork Tom does is an example of thetype of research we want to seeacross the university. His work showshow science can inform action andcan contribute to solving problems that matter.” Cabrera also is workingwith other science leaders at Mason,

such as Jagadish Shukla, University Professor of Atmospheric, Oceanic,and Earth Sciences, president of theInstitute of Global Environment andSociety, and a member of the 2007Nobel Prize–winning Intergovern-mental Panel on Climate Change, ondeveloping a sustainability researchinitiative. Lovejoy adds that Mason, alongwith colleagues at the University ofBrasília and King’s College, Cambridgethe United Kingdom, are developing a reforestation project. “The Braziliansare upbeat and warm people. If yougo halfway, they will meet you. Myheart beats according to the Samba.”

The Meeting of the Waters, the Rio Negro and Amazon River.


Alzheimer’s disease is the mostcommon form of dementia,

accounting for up to eighty percentof reported cases. Disease risk sharplyincreases with age, and it is estimatedthat more than half of individualsover eighty-five suffer from someform of Alzheimer’s. Despite urgencyand decades of research, Alzheimer’sdisease currently has no cure. To develop a therapeutic approachagainst Alzheimer’s, it becomes increasingly evident that concertedefforts of doctors, molecular biologists,and computational modelers areneeded. Dmitri Klimov, an associateprofessor in the School of Systems Biology, represents this new categoryof researchers who attempt to address this challenge through computational means. “Computer simulations—numeri-cal experiments that are important research tools—are constructed onsome known theoretical model,” explains Klimov. “The power of thesimulation comes from its ability toanalyze hundreds, if not thousands, of options for how molecules interactand behave.” Computational biology is an interdisciplinary science pullingfrom chemistry, computer science,and biology to build and understandmodels. Klimov and his graduate student,Chris Lockhart, are seeking the molec-ular origin of Alzheimer’s disease withthe hope that a therapeutic solutionor a biomarker-based diagnostic toolcan be developed.They are looking to tackle two specific problems.Thefirst is research on the small Abetapeptide, an agent that kills neuron

cells in Alzheimer’s patients. Theyhope to explore why the Abeta peptide, when it joins with others, becomes toxic to cells.The secondstudy is to see if a biomarker can beidentified for the disease. Currently,the disease is diagnosed using behav-ioral tests.These tests are unreliable andunable to quantify the occurrenceand progression of the disease. Solving these problems throughmolecular modeling requires an extraordinary amount of computingresources, which are not readily available. Klimov believes he hasfound an opportunity that may offerthe level of computations he needsby partnering with a local softwarecompany.

“We all have powerplants sitting on ourdesks,” says Steven Armentrout, founderand CEO of Reston, Virginia-based ParabonComputation, as he describes the untappedpotential of moderncomputers. “About ninety to ninety-five percent of computing capacitygoes to waste.” Parabon Computation is a softwarecompany specializing in distributedcomputing solutions.The company’sflagship program, Frontier, is used byorganizations to transform existing ITinfrastructures into a single, centrallymanaged computing network, pooling

resources to work on specific problems. Scientists and researchers whoare seeking answers to computationallychallenging questions use the Frontierplatform to distribute calculationsacross potentially thousands of computers to dramatically reduce thetime required to produce answers.Parabon has previously used Frontierfor its Compute Against Cancer program and is now partnering withKlimov on a new research project,Compute Against Alzheimer’s Disease. Any computer, even the one youmay be using to read this article, canbe connected to the Frontier platformvia the Internet.When the computersits idle, say in the middle of the nightor during the user’s lunch break, itcan be used to crunch datasets. If youcan string together several hundredcomputers or even thousands, the potential to analyze the data increasesproportionally.“Volunteering comput-ing” was popularized by the Universityof California, Berkeley, and itsSETI@home project. People aroundthe world volunteer to connect theircomputers through the Internet totackle many types of research problems. Klimov and Parabon are nowseeking volunteers who will connect

their computers to seek a cure forAlzheimer’s disease.The research ispartially funded through a Small Business Technology Transfer (STTR)grant from the National Institutes ofHealth (NIH), a special program thatrequires a small business to partnerwith an academic research institu-tion.The program goal is to transformscientific studies and results into

ComputingAgainstAlzheimer’s Disease

Interested in joining the fightagainst Alzheimer’s disease?Visit ComputeAgainstAlzheimers.org to learn howyou can connect your computer to the Frontierplatform. It’s safe, secure, noninvasive, and meaningful.

continued on page 13

Computer simulations showing Aβpeptide penetrating a cellular membrane.

Image: Courtesy of Dmitri Klimov

Fall 2013 • Periodic Elements • 13

Dean’s Message

Peggy AgourisDean, College of Science

As the new permanent dean of the College of Science, I’m excited to be in a place that mirrorsthe diversity of our society, captures the amazing

talent available in students, scientists, and educators, and becomes theplace where they find their intellectual home. My new role also gives me aunique opportunity to continue to examine and learn about the countlessopportunities to include science in the daily lives of people around us. In this issue of Periodic Elements, we take you into the field and insidethe lab to explore the spectrum of projects happening here every day. Onesuch special journey was taken by Mason President Ángel Cabrera and hisfamily when they visited the remote Amazon jungle with world-renownedconservation biologist Thomas Lovejoy, also a Mason professor. Their confluence of thoughts, ideas, and energy is as powerful as the confluenceof the Rio Negro and the Amazon rivers that they toured. Cabrera says the work of science at Mason shows “how science can inform action andcontribute to solving problems that matter to the world.” I couldn’t agreemore. Our new Center for Collision and Safety Analysis uses complex computer simulations to improve transportation safety, and researchers at the Prince William Campus are using nanoparticles to determine if anathlete has suffered a concussion. Our scientists are also investigatingecosystems that form around shipwrecks in the deep ocean, as well as the weather in space. We invite you to become involved, too, and donateyour computer’s downtime to help find a cure for Alzheimer’s disease. The university’s ten-year strategic plan is committed to elevating research at the university and promoting research of consequence. The College of Science will be a crucial part of that plan.

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innovative commercial products. “I’veknown Parabon for many years,” saysKlimov. “When I had the idea to applyfor the NIH funding, it was a naturalfit to partner with them.” Klimov will serve as the primaryinvestigator on the project but says,“Without this software company, wecan’t do this research.They providethe infrastructure.”The Alzheimer’s research is a good fit for Parabon, too.In addition to using the distributedcomputing grid for Klimov’s research,Parabon researcher Ellen McRae will belooking at the genetic underpinningsof the disease. This project is currently in itsfirst phase. Parabon has set up a web-site, ComputeAgainstAlzheimers.org,and the goal now is to solicit volun-teers who are willing to connect theircomputers through Frontier to beused to perform these extensive calculations. Armentrout explains that connecting to the project is easy. Volunteers download an applicationthat will run unobtrusively like ascreen saver.When a user is active,typing or surfing, the program remainsdormant.When user activity ceasesfor a period of time, the programcommunicates with the Frontierserver and is put to use to run thesimulations.The application is undercomplete control of the volunteer,and it can be turned off at any time.It’s also secure.The Frontier system is used by government agencies suchas the U.S. Department of Defense. “We would like to have at least1,000 computers to have a meaningfulimpact,” says Armentrout. “Of coursethe more we have the better.” Thewebsite will also publish updatesabout the project for anyone interested. This Alzheimer’s project is a non-invasive way to become involved inmedical research to help solve one of the most devastating diseases ofthe twenty-first century.

Alzheimers, from page 12

Career achievements are recognized in many ways: Actors vie for Oscars, musicians listen for the beat

of Grammys, and environmentalists dig clams. R.Christian Jones, director of the Potomac EnvironmentalResearch and Education Center and a professor in theDepartment of Environmental Science and Policy, hasearned his own clam—the Venerable Clam. This annual award from the Atlantic Estuarine ResearchSociety (AERS), the oldest scientific group of itskind in the United States, honors lifetime serv-ice and achievement for major contributionsto estuarine ecology and society. For nearly three decades, Jones and hiscolleagues have been monitoring the health ofthe Potomac River and its surrounding waters andecosystems in Northern Virginia. Committed to sharing his environmental passion beyondMason, he works with K-12 studentsand teachers to identify field experiencesthat instill the importance of stewardship,partners with community organizations to promote environmental education, and collaborateswith local governments to study and monitor ecosystemsand water quality. His work with the Fairfax County Department of PublicWorks and Environmental Services has resulted in partialrestoration of the ecosystems in Gunston Cove, a bay of the tidalPotomac. For his long-time involvement with monitoring thewater quality in the cove, Jones was recently honored by thecounty with a Champion Award, cited in the Partnering categoryfor his leadership, community outreach, and support of countyprojects. Jones also shares his passion through philanthropy to helpmake environmental education more accessible to students. Because of his generosity, AERS established the Ann C. PowelFund, named in honor of Jones’ deceased wife, to enhance theAERS Endowment and provide support for student travel andparticipation at AERS meetings. In addition, he is working withother organizations to create similar pathways to accessible environmental opportunities.

The Venerable Clam

R. Christian Jones

Periodic elements - Spring 2014

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