HHMI Bulletin November 2009 Vol. 22 No. 4

HHMI

BULLETIN N OV. ’09 VOL.22 t NO.04

4000 Jones Bridge Road r

Chevy Chase, Maryland 20815-6789 Howard Hu www.hhmi.org HHMI BULLETIN g hes Medical Institute

Going Tubular Your spinal cord, the bundle of nerves that carries messages between your brain and the rest of your body, is housed in a hollow tube that started out flat as a

pancake. During embryonic development, the flat sheet of cells folds in on itself r

and closes up by the fourth week after conception. The same cellular orchestra- tion happens in most vertebrate embryos, including the frog embryo shown here. www.hhmi.or Movement of these cells involves contraction of filaments called actin (green). On the right, they’ve contracted and begun forming a tube, so the green is more concentrated. When genetic control of the rolling process is perturbed, as it has been on the left side of this embryo, actin does not contract and the sheet stays g flat. Failure to form the so-called “neural tube” lies at the root of several human birth defects, including spina bifida. Read about research on neural tube formation and more in “The Most Vulnerable Patients” (page 12).

IN THIS ISSUE Kerry Ressler Fights Fear Membrane Awakening Training TAs

TO FULL

vol. POTENTIAL 22 / no. Chanjae Lee / Wallingford lab Chanjae Lee / Wallingford Researchers aim to protect babies from

04 the complications of prematurity. OBSERVATIONS

24 Like lips around a straw, the membranes around the channels that control water flow into and out of a cell must form a tight seal. Using electron crystallography, researchers produced this image of the water channel called aquaporin-0. The amino acid residues that make up the protein (blue) are arranged in a unique configuration that allows water molecules (red) to pass through. Hydrophobic lipids (yellow) form snug belts around each protein, creating moisture-repellent barriers ©2009

that help channel the water. Nature

VISUALIZE THIS

You could say membrane channels really caught Rod MacKinnon’s eye. was clear. The conservation of the signature sequence amino acids Trained as a physician, MacKinnon abandoned medicine for a life in in K+ channels throughout the tree of life, from bacteria to higher science after studying, during a medical residency, how potassium eukaryotic cells, implied that nature had settled upon a very special channels enable the heart to contract and relax. A desire to see those solution to achieve rapid, selective K+ conduction across the cell channels—to see how they physically do their job—pushed him into membrane. For me, this realization provided inspiration to want to structural biology, a field of research that proved providential. In 1998, directly visualize a K+ channel and its selectivity filter. I began to he produced the first high-resolution three-dimensional image of a study crystallography, and although I had no idea how I would obtain potassium channel, a feat that garnered MacKinnon the 2003 Nobel funding for this endeavor, I have always believed that if you really Prize in Chemistry. want to do something then you will find a way.

Ion selectivity is critical to the survival of a cell. How does nature accomplish high conduction rates and high selectivity at the same From Roderick MacKinnon’s Nobel Prize Lecture. ©The Nobel Foundation time? The answer to this question would require knowing the atomic 2003. Reprinted with permission of the Nobel Foundation. structure formed by the signature sequence amino acids, that much Mike Perry Courtesy of Tamir Gonen and Thomas Walz. Reprinted with permission from Macmillan Publishers Ltd: Gonen and Thomas Walz. Courtesy of Tamir november ’o9 vol. 22 · no. o4

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Visit the online Bulletin to see an audio slideshow of new teaching assistant Joe DePalma as he goes into his first day as a chemistry lab instructor at the University of Delaware and an audio slideshow of Catherine Drennan’s MIT training class for TAs on student diversity. Listen to Charles Sawyers give his view on the value of translational research and watch him move through a typical work day at Memorial Sloan-Kettering Cancer Center. Read about how a model bacterium is showing scientists how pathogens go from harmless to deadly: Pascale Cossart is building a library of knowledge on Listeria, and her methods are informing studies of viral and parasitic infections as well. All of this and more at www.hhmi.org/bulletin/nov2009. 30 24 Features Departments COVER STORY PRESIDENT’S LETTER LAB BOOK THE MOST VULNERABLE PATIENTS 03 Season of Change 40 Removing Radiation Roadblock 12 Problems during pregnancy burden 41 Starving for GABA CENTRIFUGE too many newborns with lifelong 42 Blue Baby Blues disabilities. Researchers are 04 From the Outside Looking In finding clues to a safer nine months, 05 Where Past Meets Future ASK A SCIENTIST and a brighter future. 06 Leapin’ Lizards 43 Does the anatomy of freshwater and saltwater fish differ? UPFRONT TAMING FEAR, RISING CALM 08 TOOLBOX 18 A social conscience rooted in the Piecing Together Rotavirus’s Deep South moves Kerry Ressler, Unique Approach 44 Freeze Frame 10 Seeing Spots a psychiatrist and neuroscientist, NOTA BENE to try to ease the consequences of PERSPECTIVES AND OPINIONS 46 News of recent awards and inner city trauma. 34 Terrence Sejnowski other notable achievements 36 MEMBRANE AWAKENING Q&A: What grade in school was OBSERVATIONS 24 your most formative and why? Researchers are taking a more Visualize This holistic look at cell membranes and CHRONICLE the proteins embedded in them— SCIENCE EDUCATION and the surprises keep coming. 38 Rummaging for Science 39 2009 Holiday Lectures on Science: ENHANCING TA PERFORMANCE Exploring Biodiversity 30 Instead of letting teaching assistants sink or swim, risking their failure and the ire of the undergrads, some schools are prescribing a class in how to teach before they get in front of a class.

VISIT THE BULLETIN ONLINE FOR ADDITIONAL CONTENT AND ADDED FEATURES: www.hhmi.org/bulletin COVER IMAGE: JASON HOLLEY 2 HHMI contributors

Fiduciary Trust CompanyInternational Director, RetiredChairman&CEO Anne M.Tatlock Law Dean /HowardUniversitySchoolof Kurt L.Schmoke, Esq. Former HeadofGlobalInvestmentBanking,J.P. Morgan&Co. Senior Lecturer,HarvardBusinessSchool Clayton S.Rose, Ph.D. The UniversityofCambridge Vice-Chancellor Alison F. Richard, Ph.D. President /TheRockefellerUniversity Paul Nurse, F.R.S. The PrudentialInsuranceCompanyofAmerica FormerInvestment Officer Vice Chairman&Chief Chairman /SeaBridgeInvestmentAdvisors,L.L.C. L.KeithGarnett The UniversityofChicago Distinguished ServiceProfessorofHistory President Emeritus&HarryPrattJudson Hanna H.Gray, Ph.D., University ofTexas SouthwesternMedicalCenteratDallas Regental Professor&Chairman,DepartmentofMolecularGenetics Joseph L.Goldstein, M.D. WilmerHale Senior InternationalPartner Ambassador CharleneBarshefsky Senior Partner /BakerBottsL.L.P. James A.Baker, III,Esq. HHMI TRUSTEES BULLETIN

November 2oo9 Chairman sense to trim online—and expanded, insomecases.Itmade you are accustomed to seeing,it’s just moved by eightpages.We haven’t lost thecontent the better, Ithink,andhopeyou’ll agree. we’re goingthrough somechanges,too. All for to embrace thanothers.Here atthe the way we live, work, andplay—some easier now, we’ve beenexperiencing adjustments in Change isintheair. For whatseemslike awhile boost intheform oftraining courses andboot novice teaching assistants, orTAs, awelcome presents theefforts by someuniversities to give some addedextras ontheWeb. That feature Cancer Center. typical work day atMemorialSloan-Kettering tional research andwatch himmove through a Sawyers give hisview onthevalue oftransla- In thisshortaudioslideshow, you canlisten to piece by HHMIinvestigator CharlesSawyers. example, you’ll findamultimediaperspective content andthensomeontheWeb. ing theprintversion, whileoffering existing With thisissue, we’ve gonealittleshorter, One ofourfeature articlesisshorter, with By visitingtheonlineversion ofthisissue, for Bulletin costs by slightlyreduc- Maya Pines Sarah C.P. Williams for Web &SpecialProjects Patricia Foster Andrea Widener Jim Keeley Cori Vanchieri Mary BethGardiner HHMI BULLETINSTAFF Landis Zimmerman Gerald M.Rubin,Ph.D. Edward J. Palmerino Avice A.Meehan Joan S.Leonard, Esq. Jack E.Dixon, Ph.D. Peter J. Bruns,Ph.D. Craig A.Alexander Robert Tjian, Ph.D. HHMI OFFICERS&SENIORADVISORS or officialpoliciesoftheHoward HughesMedicalInstitute. HHMI Bulletin The opinions,beliefs,andviewpoints expressed by authorsinthe ©2009 Howard HughesMedical Institute BSZS^V]\S! #&&##4Of! #&&$!eeeVV[W]Ù Finlay Printing VSA Partners, NYC Nicole Kresge, HeatherMcDonald Cay Butler, MichelleCissell, ADDITIONAL CONTRIBUTORS Bulletin donotnecessarily reflect theopinions, beliefs,viewpoints, /ScienceEditor , /ContributingEditor /StoryEditor we’re doing. inspires. Drop mealineandletknow how duce engagingcontent thatbothinforms and cation efforts. Our goal,asal more aboutHHMI’s research andscience edu- zine, andvisittheonlineversion to learneven hope you’ll continue to enjoy ourprintmaga- tional stories andinteractive multimedia.We to expand ourWeb extras, intheform ofaddi- video ofhow thebacteria infect acell. biology of tional research scholarPascale Cossart onthe about therecent discoveries ofHHMIinterna- cles. With thisissue, you cangoonlineto read including oneofourusualtrioUpfront arti- Delaware TA’s first day aslabinstructor. other you getto tagalongonaUniversity of MIT training course ondiversity, andinthe slideshows—one gives you aglimpseinto an camps. Onourwebsite you’ll findtwo audio /Printing&Binding /AssociateDirectorofCommunications /ScienceEducationEditor /V.P. forCommunications&PublicAffairs In coming editionsofthe Other stories are moving onlineaswell, / President /Concept&Design /V.P. &GeneralCounsel /V.P. &ChiefInvestmentOfficer /AssistantEditor /Editor /V.P. &ChiefScientificOfficer /V.P. forGrants&SpecialPrograms /V.P. forFinance &Treasurer /SeniorCounseltothePresident /V.P. &Director,Janelia Farm ResearchCampus Listeria infection—and watch ashort Bulletin ways, isto pro- , we intend

Paul Fetters Barbara Ries charter andthe work ofmanyinvestigators.Visit theonline worth asking:themedical importofHHMI researchiscentraltoour scientific culture? thatdefineHHMI’s thehighethicalstandards tion whilemaintaining useful therapiesforpeople?Can weencourageappropriatecollabora- hinder thetranslationofdiscoveries madeinHHMIlaboratoriesinto cies, whichhave beensubjecttothoughtfulrevisionovertime,helpor scientists and theprivatesectorshouldbestreamlined.Dothesepoli- whether HHMIpolicies thatgoverntheinteractionsbetweenour more pressingissues. toaddress on researchwhileenablingtheInstitute’slegalstaff talented paperwork. ThisapproachshouldfreeHHMIinvestigatorsto focus materials transferagreementisnecessary, wehopetosimplifythe agreements tosharenonhumanbiologicalmaterials;ifandwhen a conditions aremet,ourscientists willnolongerneedmaterialtransfer rials withinthenonprofitandacademic sectors.Aslongascertain reduce thepaperworkthathasslowed theexchangeofresearch mate- Universityhas joined andothersinaninitiative withStanford to community andseednewdiscoveries. Toward thatend,theInstitute can speedthedispersal ofideas throughtheacademic research Champagne. I’mthinkingaboutthefuture,waysthatHHMI receive theNationalMedalofScience. Wow. Elaine FuchsoftheRockefellerUniversity wasattheWhiteHouseto churns outtheproteins necessaryforlife.Andonthatverysameday, function oftheribosome—thecomplexcellularmachinerythat Institute ofScience fordiscoveries thatelucidated thestructureand Laboratory ofMolecularBiology, andAdaE.Yonath oftheWeizmann with Venkatraman RamakrishnanoftheMedical ResearchCouncil days later,Tom Steitz ofYale University sharedtheChemistry Prize cell division, andhow theyareprotectedagainstdegradation.Two are synthesized,how theycanbecopiedinacompletewayduring School ofMedicine. Thetrioshowed how theendsofchromosomes San Francisco, andCarolGreider oftheJohnsHopkinsUniversity Medicine withElizabethBlackburnoftheUniversity ofCalifornia, sharedtheNobelinPhysiologyor of MassachusettsGeneralHospital that twoHHMIcolleaguesreceived 2009NobelPrizes.JackSzostak occurs throughouttheyear. Thisisseriousfun—enlivenedbynews from themandtothelivelyinterchangeofscientific thinkingthat able promise, joined ourcommunity. We’re lookingforwardtohearing 40-plus earlycareerscientists, whoseresearchdemonstratesconsider- find anechointhepatternsofourwork. headwaters.Theseseasonalrhythmsinthenaturalworld in coldnatal whirring seedsdisperse intotheair;steelheadfightupstreamtospawn activity allaroundus:cloudsofbirdsseekdistantnestinggrounds; ago. Yet thesoftlightoftheseautumndayscontrastswith intense as EnglishRomanticpoetJohnKeatsdescribeditnearlytwocenturies FALL MAY BETHE“SEASONOF MISTSANDMELLOW FRUITFULNESS,” Season ofChange These important questionsThese important lack simpleanswers,buttheyare I havealsoaskedmyscientific andlegalcolleaguestoconsider But I’mdoing morethanlistening togreatscience andpopping An entirelynewflockofbirdsalightedatHHMIinSeptember: Bulletin the worldinallitsgloriouscomplexity. have much tolearnfromothers:afterall,thepoetalsolaborsexplain expanding thereach,scale,andsophisticationofanyendeavor. We similar philosophicalgoalsandcommitment toexcellence,thereby opportunities todevelopnewprogramswithpartnerswhodemonstrate four highlyregardedorganizations. Ilookforwardtofinding other our expandedsupportforpostdoctoralscientists incollaborationwith challenging biologicalquestions—into their newenvironments. ence—specifically, thevalueofgivingresearchers freedomtopursue like tothinkthattheycarryanappreciation fortheir HHMIexperi- Institutes ofHealth.We’re happy toseeouralumni succeed.Andwe being Francismost notable Collins,thenewdirector oftheNational roles ingovernment,academia, andpharmaceuticalresearch,the flow ofpeopleandideas. Former investigatorsholdmajorleadership are regulatedbuthighlyporous;webenefit mightily fromaconstant inthisissueofthe that starts monolith. Likethecellmembrane—thesubjectofatwo-partseries therapyforleukemia. targeted B. Lydon,formerlyofNovartis,forthesuccessfulidentificationa Lasker-DeBakey Clinical Medical ResearchAward withNicholas Brian DrukerattheOregonHealthSciences University sharedthe new attentionearlierthisfallwhenSawyers andHHMI colleague strengths ofacademic andpharmaceuticalindustryscientists received cancer. Indeed,theimpactofresearchthatcallsonspecifictate discuss translationalresearchand apromising treatmentforpros- HHMI investigatoratMemorialSloan-KetteringCancerCenter, (www.hhmi.org/bulletin/nov2009) tohearCharlesSawyers, an “ flow ofpeopleandideas. ROBERT TJIAN We benefitmightilyfromaconstant HHMI gains from collaboration and interchange, as witnessed by HHMI gainsfromcollaborationandinterchange,aswitnessedby butwearenoscientific HHMI islargeandwellestablished, Bulletin —the boundaries of the Institute —the boundariesoftheInstitute November 2oo9 president ”

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BULLETIN 3 4 HHMI Italy,” says Bischofberger. external view ofwhatishappeningin situation. around theworld aboutItaly’s political tions ofnewspaper articlesfrom Abroad.” Itwould post Italiantransla- “ItaliaDallEstero.info,” or“Italyfrom They would buildawebsite named in theUnited States, Fabio Parisi. Restivo,Gaetana andafriendbased hatched aplan withhisgirlfriend, Polytechnic SchoolofLausanne, Gisou van derGootattheFederal of HHMIinternational research scholar membrane biologyinthelaboratory doctoral student studying cell could have access to thesearticles.” done systematically sothatallItalians him. “Istarted thinkingthisshouldbe and hermother, whowere traveling with to Italian for hisSicilian-borngirlfriend He translated thearticlefrom German their voices heard through localmedia. how prominent Italianscould notmake an articleinaSwiss newspaper about Swiss father, Bischofberger was reading up withanideafor awebsite. March 2008,Mirko Bischofberger came On atrain From theOutsideLookingIn centrifuge “The general concept isto have an That evening Bischofberger, a The son ofanItalianmotherand

BULLETIN from Switzerland to Italy, in

November 2oo9 have to share.” it. The more you know, the more you science have aresponsibility to explain says. “Those ofuswhounderstand misunderstandings aboutscience,” he Neue ZürcherZeitung section ofthemajorSwiss newspaper is aregular contributor to thescience spent hischildhoodvacations) and village Castrignano deiGreci, where he certain partsofItaly(includingthe tary aboutaGreek dialectspoken in communicator. Hefilmedadocumen- ased,” explains Bischofberger. for themoment,to becompletely unbi- funding. “We keep thesite free ofads article. The site accepts noexternal contains alinkbackto theoriginal the translations’ accuracy. Eachposting translate thearticles;othersconfirm than 40countries. Over 50volunteers include over 2,000 articlesfrom more ItaliaDallEstero.info hasgrown to and Freedom House, agree withhim. including Reporters withoutBorders several independent organizations, most standards,” he says, addingthat The government isnot transparent by “There isalotofcensorship inItaly. control over most news outletsinItaly. media magnate SilvioBerlusconi, has led by primeminister andbillionaire says, becauseItaly’s governing party, Bischofberger seemsto beaborn Since itsApril2008launch, That outsideview is necessary, he . “There are many the situation.” and thendoessomethingto improve when someoneidentifiesaproblem says van derGoot.“Ithinkit’s great Dutch andfound themvery interesting,” read someoftheoriginalarticlesin Bischofberger’s Ph.D. advisor. “Ihave movement.” contributed alittlepiece to that Bischofberger. “We like to thinkwe about Berlusconi’s honesty,” says is amovement thatisbuildingmistrust prominent Italianbloggers.“Now there has alsohadpositive reviews from articles carrylinksto hiswebsite, which Those politicians’Web pagesandnews journalists inItaly,” says Bischofberger. “have beencited by politiciansand 5,000 visitors every day, itsarticles had themost obvious impact.With over FOR MOREINFORMATION: italiadallestero.info Among thewebsite’s visitors is ItaliaDallEstero.info hasperhaps . —Laura Bonetta Ifyou canread Italian, visit

Peter Arkle Andrew Cutraro conditions, thefight for freedom,” he is bred into you—the exposure of to benarrowly definedby race alone. in Jamaicaandamotherwho refused African Americanoriginsto hischildhood wider audience,” hesays. grew, Ifelt itshouldbepresented to a the subjectmatter, butasthecollection slowly. careers inbiomedicalresearch. from thishistorically blackcollege for a five-year period,100selected students directs aprogram thatwillprepare, over support asanHHMIprofessor, healso cancer, amongothersubjects.With of actionandbiomarkers for breast Anderson studies estrogen’s mechanism full flower,” hesays. when thecivilrightsmovement was in sure for racial equalitywas escalating. University. Itwas thelate 1950s,andpres- at 17to beginstudies atHoward arrived intheUnited States from Jamaica story ofrace inAmericabeganwhenhe Michael Anderson. Ronald McNair, MaeJemison,and and engineersincludesastronauts a display ofAfrican Americanscientists lawn, whileinsidethetwo-story museum Africa to theNew World stands onthe ship thattransported slaves from ation. Acut ship,” says Anderson,withoutexagger- history from slave “the shipto thespace Washington, D.C. north ofhislabatHoward University in inruralArt Gallery Maryland,20miles Sandy SpringSlave MuseumandAfrican Now anyone canseehiscollection atthe slaves andtheirAmericandescendants. ments tracing thehistory ofAfrican filled hisgarage withobjectsanddocu- Over three decades Meets Future Where Past “A different kindofconsciousness Anderson traces hisawareness of “At first, Iwas simplyinterested in The ideafor themuseumgerminated Now abiologyprofessor atHoward, “I’m fortunate to have grown up Winston Anderson’s interest inthe Exhibits cover African American away r away eplica ofaclipper ,

Winston Anderson garage isnow nearlyempty.) Heand opened itfor visitors in2004. (His museum buildingin1999, andﬁnally in 1995,broke ground for themain 1992, reconstructed aslave cabin in 1988,builttheslave shipdisplay in He boughttheproperty inSandy Spring in stages, ashescraped together funds. in science, thearts,politics,andlaw. the achievements ofAfrican Americans a lucky few. The museumalsodisplays and “letters of manumission” thatfreed slave auctions,bills ofsalefor slaves, engine. There are advertisements for reminder oftheOldSouth’s economic build America.Abasket ofcotton isa by black workers—slave andfree—to Another room displays handtools used slave’s passage through densebrush. shoulders, designedto slow arun hooked rods thatreach outpast the including aniron neckringwiththree and hobblesusedto restrain slaves, one wall ofthemuseumhangshackles and estate salesaround theU.S. On to Africa andvisitsto antique shops visitors whocome to themuseum.” says. “Mymission isto enlighten the Anderson constructed hismuseum He builthiscollection from travels away away the future.” a far distance, andthere ishopefor it’s partofthepast, butwe have come positive feelings,” hesays. “They know meaning. “Ithinkpeoplego Anderson seeshismuseumandits Spring discouraged. Butthat’s nothow be easy for avisitor to leave Sandy the JimCrow era thatfollowed, itmight ﬂee to Canadaandfreedom. and escaperoutes thathelpedslaves Railroad, thenetwork ofsafe houses became astop ontheUnderground and buildhouses.SandySpringalso tated there andwere ableto buyland Free blacksandformer slaves gravi- many ofwhomrefused to own slaves. town was founded in1728 by Quakers, black community inSandySpring.The appointment. which isopenonweekends andby 3,000 visitors ayear tour themuseum, from theState ofMaryland.About funding, alongwith$150,000 ingrants private donorsprovided most ofthe With allthehorrors ofslavery and One room shows thehistory ofthe WEB EXTRA: Slave Museumat November 2oo9 —Aaron Levin See more photos oftheSandySpring www.hhmi.org/bulletin/nov2009

HHMI away away

BULLETIN with . 5 6 HHMI can reproduce by parthenogenesis,a research: investigating how somelizards he alsoparlayed itinto anew avenue of and theirbacksagainst theother. But their feet against onewall ofthecanyon shimmied over asecond oneby bracing ter: they leaptover thesnake—and then a foot-and-a-half wide!” 30 feet deepandamilelong—butonly not easy whenyou’re inacanyon that’s and terraces withhiswife Diana.“That’s upon onewhilehikingtheruggedcliffs says Peter Baumann,whohappened see arattlesnake, give itawideberth,” way for wildlife. “slot” canyons—and sometimesmaking involves wrigglingthrough itsnarrow National MonumentinsouthernUtah Navigating Leapin’ Lizards centrifuge The Baumanns survived theencoun- “The guidebookstell you: whenyou

BULLETIN pypg the Grand Staircase-Escalante

November 2oo9 keeping reptiles canbeachallenge— and marineinvertebrates. Andthough species offish,amphibians,reptiles, into adepartmentthathouses20 lizards inplastic kiddiepoolshasgrown guidance. Whatstarted outasafew up abreeding facility underDiana’s by Neaves, whojoinedinthefun. slips itinto abag—amethodfashioned hold thecreature whilesomeoneelse uses anooseontheendofflyrod to in to pullthemout.” Instead, oneperson “So it’s now anHHMIearlycareer scientist. the sameholesaslizards,” says Baumann, discovered that rattlesnakes canlive in study subjects.“Onourfirst trip, we and headedto New Mexico to collect So theBaumannsgrabbed theirgear search suggested nooneelsedideither. how exactly are they made? its cells? Or, iftheeggshave afullset, number ofchromosomes astherest of reproducing animal, withhalfthe Are they like theeggsofasexually dering: whatdotheireggslooklike? never occurs. SoBaumanngotto won- that reproduce thisway, fertilization lizards asagraduate student. Inanimals Neaves hadstudied parthenogenic rattlesnake tale—anddiscovered that Neaves, theBaumannsshared their dinner withStowers CEOWilliam of bringinghislizards to thelab. Over Medical Research thatPeter thought they joinedtheStowers Institute for reptiles asahobby. Butitwasn’t until lawn mower,” hesays. tended muchbetter by asheepthan see thatoursuburbanyard could be showed upwithalamb. “They didn’t says, were “very tolerant”—until he and rodents. Hisparents, Baumann his fair share ofsnakes, lizards, frogs, the aidofsperm. process inwhicheggsdevelop without Back atthelab, the Baumannsset Neaves didn’tknow—and aliterature For years, the Baumannshave kept As akid,Baumannbrought home not advisableto stick your hand with us.” “We don’ttake any more animalshome leave theirlassos behind,says Baumann. each year. Onthosetrips,though,they when they visitfriendsinWest Texas they enjoy photographing rattlesnakes handful ofseedsevery morning.And pamper withsaladgreens they anda Saharan spiny tailedlizards, which Baumann laughs. a colony ofwhiptaillizards,” Peter someone withexperience maintaining they hire anew labtech. “Just tryto find their accumulated wisdomwhenever the reptiles andaquaticsfacility, shares Now Diana,asmanagingdirector of captured inNew Mexico survived. Baumann says thatallthelizards they temperature, humidity, andlighting— when itcomes to nutritionandto the animalshave pretty specificneeds “ pull themout. stick yourhandinto So it’snotadvisableto same holesaslizards. snakes canliveinthe discovered thatrattle- PETER BAUMANN On ourfirsttrip,we At home, theBaumannsfavor WEB EXTRA: studies ( photos andlearnmore aboutthelizards Baumann —Karen Hopkin www.hhmi.org/bulletin/nov2009 Visit the Bulletin ” online to see ).

Illustration: Peter Arkle Photo: Don Ipock upfront

08 PIECING TOGETHER ROTAVIRUS’S UNIQUE APPROACH An extra protective layer primes this virus to do its harm, mainly in children in the developing world.

10 SEEING SPOTS Relying on old-fashioned techniques allowed these researchers to make a surprising discovery.

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Dangerous Agent A model bacterium is showing scientists how pathogens go from harmless to deadly. Pascale Cossart is building a library of knowledge on Listeria, and her methods are informing studies of viral and parasitic infections as well (www.hhmi.org/bulletin/nov2009).

Sometimes it takes a while for a modern technique to prove its worth. But taking a risk on the novel method might yield a Eureka finding. Other times, it’s better to go with the old standard, or maybe even wipe the dust off a method that’s been nearly forgotten. Occasionally, both old and new methods have something important to offer. The scientists in this issue reached deeper into their bag of research tricks. Good thing. They learned unexpected things about gene silencing and unsilencing, and they got a much better view of a particularly quirky and dangerous virus.

November 2oo9 | HHMI BULLETIN 7 upfront

Piecing Together Rotavirus’s Unique Approach An extra protective layer primes this virus to do its harm, mainly in children in the developing world.

FOR A VIRUS TO INFECT THE CELLS OF ITS HOST, IT MUST FIRST find a way in. For some viruses, the strategy is to fuse membranes with the target cell, often after hitching a ride in a vesicle with an entry

ticket. In the case of viruses with no membranes of their own, such as into progeny particles. The outermost rotavirus, the story is more complicated. Using two complementary layer, acquired before the virus emerges techniques of structural biology—x-ray crystallography and electron from one infected cell and searches for another, consists of two proteins—VP4 and cryomicroscopy—HHMI researchers have uncovered some impor- VP7. The spike-shaped VP4 is thought to tant details about how rotavirus manages to make its way into a cell. perforate the membranes of host cells, but the role of VP7 in penetration has been Rotavirus particles surround their appropriate candidates for a vaccine because less clear. RNA genomes with three protein layers. immune system antibodies recognize them. In work published in the June 12, 2009, Understanding the structure and behavior Despite its multilayered configuration, issue of Science, Harrison and his team of the proteins that constitute those layers rotavirus lacks a lipid membrane, or enve- (which included student Scott Aoki, HHMI could help scientists design better vaccines lope, that can fuse with lipid-containing postdoctoral fellow Ethan Settembre, and for a disease that yearly kills half a million membranes of host cells. Entry of the so- collaborator Philip Dormitzer) crystal- people, most of them children in the devel- called nonenveloped viruses is not as well lized VP7 in the clutch of an antibody and, oping world. Current vaccines, based on a understood as that of their enveloped coun- using x-ray crystallography, determined live, attenuated form of the virus, may be terparts. They use a diverse, and still largely the molecular structure of the complex. It impractical in the world’s poorest regions. unexplored, range of strategies to infiltrate showed both how calcium ions hold VP7 A protein-based vaccine would be easier host cells. together as a trimer of three identical mole- to ship, store, and combine with other Unlike the genomes of simpler viruses, cules and how an antibody can prevent vaccines, says HHMI investigator Stephen rotavirus RNA always remains enclosed it from coming apart. The investigators Harrison of Harvard Medical School and within two of the three protein layers that concluded that the VP7 trimer must come Children’s Hospital, Boston. With this surround it in the infectious virus particle. apart during viral entry and that a loss of goal in mind, Harrison studies the virus’s Enzymes packaged with the genome make calcium ions in the host environment outermost coat proteins, which he says are and export new RNA for incorporation might trigger this process.

8 HHMI BULLETIN | November 2oo9 Ian Wright with anarrow beamofelectrons.Thethou- particles canbeimagedfrom every angle Toolbox, page44).Onceimmobilized, rapidly inabathofliquid ethane(see macromolecular complexby freezingit microscopy (cryo-EM). emerging technique calledelectroncryo- at Brandeis University andexpertinan Nikolaus Grigorieff,anHHMIinvestigator virus particle,Harrisonpartneredwith the outer-coatproteins onanintact in isolationfromthevirus.To visualize In cryo-EM,scientists preservealarge The studyofferedapictureofVP7 issue of published thestructureinJune 30,2009, the surfaceofvirus. VP4 proteins inaninterlinkedwebacross VP7 proteins encircling thespike-shaped near atomic resolution—four angstroms— multiple angles. reflects whatthestructurelookslikefrom Grigorieff explains,becauseeachimage helps, The symmetricalnatureofrotavirus high-resolution three-dimensional picture. sands ofimagesarethenaveragedintoa Harrison, Grigorieff,andcolleagues The resultwasapicturethatshowed at Proceedings ofthe NationalAcademy to donext.” we know thekindsofexperiments weneed know alotaboutwhatitmust involve,and “We don’tknow theanswer yet,butwe ask, how doesVP4actually doit?”hesays. entering livingcells.“We’re now poised to light microscopy toimagevirusparticles crystallography, withcryo-EM,andusing step. Heplanstoinvestigateitwithx-ray protein VP4 carriesoutthispuncturing how, andwherewithinthe cell,thespike cellular membrane. and preventingVP4frompuncturingthe by clampingVP7ontothevirusparticle with VP7apparentlypreventsinfection cell.Theantibodycrystallized of atarget freeing VP4topuncturethemembrane tion. TheVP7proteins arethenreleased, virus particle—primetheparticleforinfec- host cellvesiclesurrounding the engulfed ably adropincalcium concentrationinthe hold VP4inplaceuntilconditions—prob- of Sciences Harrison now wishestounderstand . TheVP7proteins appearto W November 2oo9

–SARAH GOFORTH

HHMI

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November 2oo9 Relying onold-fashioned techniques allowed these Skirmantas KriaucionisandNathaniel Heintzfound anew piece ofDNA’s researchers tomakeasurprising discovery. genetic code and energized thefieldofepigenetics research. Seeing Spots

Elizabeth Weinberg THE HISTORY OF SCIENCE GLITTERS WITH ACCIDENTAL DISCOVERIES, FROM Roentgen’s x-rays to Fleming’s penicillin. And despite what some would consider a creeping loss of flexibility in the modern scientific process, researchers from time to time still stumble across finding. Hydroxymethylcytosine, they reported, is present in mouse embryonic something truly surprising. Just ask HHMI investigator Nathaniel stem cells and is converted from mC by an Heintz and his postdoctoral associate Skirmantas Kriaucionis. enzyme found in humans as well as mice. “Her discovery of an enzyme that actually Their serendipitous finding of a DNA the experiment numerous times with does this hydroxylation is critically impor- constituent called hydroxymethylcyto- different controls, however, the researchers tant, for it tells us that there’s a dedicated sine—roughly akin to the discovery of a new realized that the mystery spot marked a biochemical mechanism for producing this letter of the AGCT genetic code—has ener- nucleotide known as hydroxymethylcyto- modification,” Heintz says. gized the fast-growing field of epigenetics, sine (hmC). Previously, hmC had been The two papers appeared together in the study of the all-important mechanisms considered a rare DNA modification found Science on May 15, 2009, and both labs that maintain genes in an “on” or “off” state only in primitive, bacteria-infecting viruses. are now trying to understand hmC’s func- within cells. Its relative abundance in a mammalian tions in different cell types. Some evidence “Our finding of this nucleotide in animal brain cell strongly suggested that it could be already suggests that hmC can reverse mC’s cells was completely unexpected,” says a major epigenetic player. usual gene-silencing function, although Heintz, whose lab is based at Rockefeller That its presence had been overlooked Heintz thinks it could have other, more University in New York City. for so long also suggested that molecular interesting epigenetic roles. To help clear It began with a dark spot on a glass chro- biologists needed to rethink some of their up the mystery, he and Kriaucionis are first matography plate—a spot that shouldn’t have been there. Under Heintz’s guidance, “ Kriaucionis had been trying to measure Our finding of this nucleotide in animal levels of a known epigenetic marker, a cells was completely unexpected. gene-silencing nucleotide known as methyl- NATHANIEL HEINTZ ” cytosine (mC), in a sample of DNA from mouse Purkinje cells. These large neurons, located in the experimental methods, according to trying to map hmC’s distribution in the movement-coordinating cerebellum, are Heintz. The Heintz lab had long empha- DNA of various cell types—a goal compli- difficult to harvest in large quantities, says sized the use of cells taken from animals, cated by the lack of a high-resolution Heintz: “To get enough DNA to do the but if Kriaucionis had instead relied on method that can separate hmC from mC. analysis was difficult, so we used a very immortalized neuronal cell lines, which “It is critical to develop a new chemical sensitive, old-fashioned methodology for are more convenient to use but differ subtly strategy to allow us to precisely map the detecting DNA nucleotides.” from normal neurons, he would have found locations of both of these marks in the The experiment yielded a chromato- no hmC. He also determined that the stan- genome,” says Heintz. The two researchers gram, in which separate spots of clustered dard sequencing technique for mapping also have begun collaborating with Rao’s material indicate the presence of unique mC in cellular genomes could not distin- group to manipulate hmC levels in different DNA nucleotides within the sample. But guish hmC from ordinary mC. types of mouse neurons to see how it affects near the expected spot for mC Kriaucionis As it turned out, other researchers had their gene expression. saw another spot in a surprising location, been on a similar epigenetic quest. A week The apparent significance of hmC has suggesting an unknown nucleotide. after Heintz and Kriaucionis submitted drawn keen interest from other researchers, Was it an experimental artifact? “We their paper to Science, a group led by too. Based on queries she’s had from other were suspicious,” Kriaucionis remembers. Harvard Medical School scientist Anjana scientists, Rao says “at least fifty other labs After searching the literature and repeating Rao submitted their own closely related are interested in this now.” W –JIM SCHNABEL

November 2oo9 | HHMI BULLETIN 11 THE MOST VULNERABLE PATIENTS Heather Weston / Getty Images Heather Weston

12 HHMI BULLETIN | November 2oo9 Problems during pregnancy burden too many newborns with lifelong disabilities. Researchers are finding clues to a safer nine months, and a brighter future. by Kendall Powell

November 2oo9 | HHMI BULLETIN 13 YOU CAN ALMOST HEAR A WOMAN BREATHE A SIGH OF RELIEF

when she reaches her 24th week of pregnancy. If delivery comes Advances in neonatal care have dramatically improved the this early—well before the normal 40 weeks of gestation—a baby survival rates of babies born between 24 and 26 weeks of pregnancy. has a 50:50 chance of surviving outside the womb with the help But, Rowitch explains, about half will have lasting neurological of modern medicine. But neonatologist David Rowitch knows damage—from mild learning impairments to cerebral palsy, a life- that extremely premature delivery is far from ideal. His tiniest long physical disability. “We don’t know the root causes of these patients face tough odds. neurological injuries,” says Rowitch, a neonatal pediatric specialist. “They don’t look like a normal baby,” Rowitch explains. None About 800,000 people in the United States have cerebral palsy of their major organs—lungs, heart, intestines—is finished (CP), which can cause loss of muscle coordination, sensory prob- forming. “They aren’t able to carry out the basic life-sustaining lems, and mental impairment. And because more extremely functions,” he says. Instead, doctors must support these babies premature infants are surviving, the incidence is increasing, with ventilators, intravenous fluids, and tube feeding. Rowitch explains. In one country that keeps national figures, the The research of several HHMI investigators is aimed at these United Kingdom, a recent study found that, between 1994 and most vulnerable patients—developing fetuses and babies that 2005, the survival of babies born at 24 and 25 weeks increased by are born too early. They want to prevent and treat conditions 17 and 11 percent, respectively. that lead to a lifetime of disability for affected babies: defects in “Is it the stress of being delivered early, infection, and/or the the formation of the spinal cord, a hypertensive disorder in preg- inflammatory response that happens in these babies? We don’t nant women called pre-eclampsia, and brain damage in know,” he says. Rowitch speaks with the reserved demeanor of premature infants. someone who has consoled countless families, and he talks about Rowitch, an HHMI investigator at the University of California, his patients as if they were fully formed adults. His tone reveals San Francisco (UCSF), and the other researchers who are trying his commitment to see them reach their full potential. to solve some of the most persistent problems of pregnancy face an uphill battle. No one really understands, for example, why the Boosting Brain Repair third trimester is so important for normal brain development. It’s Something about the third trimester of pregnancy—which these difficult for scientists to make observations in utero, and medical babies experience in the alien environment of a neonatal intensive research to test treatments on pregnant women, their fetuses, and care unit (NICU)—is critical for brain development. Because of newborns is often considered too risky. their limited ability to peer inside the newborn brain, Rowitch’s However, researchers have begun to gain traction on some of laboratory group has turned to some clever research models to gain these problems. Using advanced techniques in genetics and a better view of brain damage and the brain’s repair processes. molecular and developmental biology, they are making progress Using mouse models of brain damage similar to CP and without poking or prodding pregnant bellies or newborn babies. looking at other cases of human neurological damage, Rowitch’s They’ve found clues to the causes of pre-eclampsia, neural tube group has identified problems in two sets of precursor cells in the defects, and cerebral palsy. Their insights may lead to better, brain. One precursor becomes the oligodendrocytes, which act noninvasive diagnostic tests for the women and babies at highest like road crews repaving damaged surfaces along nerve tracts, the risk. The findings will also build the foundation for designing information highway connecting brain cells. The researchers treatments tailored to each patient’s genes and risk level. found that the cells in the brains of premature infants sometimes

14 HHMI BULLETIN | November 2oo9 remain stuck in the precursor stage—in part due to flawed other babies might be saved in the future. Surveying brain tissue signaling—and fail to repair. of premature babies is the only way to find out if the same cell Using a mouse model, Rowitch’s team investigated the neuron problems and faulty repair mechanisms that Rowitch sees in his precursors that drive the burst of growth in the cerebellum in healthy mouse models are present in the human brain. “It’s so important babies just before and after birth. The cerebellum is the part of the to do this. We can learn even when things don’t work out well.” brain that integrates coordination and motor control. His group found a key connection: They showed how steroid drugs, like those A Healthy Spinal Cord given to help premature lungs develop, can inhibit growth of these On a converted army base east of Denver, Lee Niswander’s sparkling cells. When the team artificially turned on a natural defense mecha- new University of Colorado laboratory building faces the sunny nism in the cells against the steroids, the problem was alleviated. downtown skyline and its mountain backdrop. But the HHMI inves- Both findings shifted Rowitch’s thinking. Boosting the brain’s tigator rarely looks up from her microscope. She’s usually too busy protective or repair mechanisms might be the best route for watching the neural tube—the structure that will become the brain rescuing premature brains from permanent damage. How to help and spinal cord—develop in real time in mouse embryos. the brain help itself “is not a well-established area of research,” “No one has ever watched this process in a mammal,” she says Rowitch. “In some ways we are swimming in a deep ocean says. “We’re seeing things that nobody has ever seen before.” where you cannot see the bottom.” But that doesn’t stop his group Niswander’s penchant for solving three-dimensional puzzles from pushing toward shore. emerges when she talks about the “beautiful complexity” of Although these key insights came from research models, neural tube closure. Rowitch believes it is absolutely necessary to chart what goes In all vertebrate embryos, the neural tube starts out as a flat wrong in the brains of premature infants. So when he became an plate of cells. That plate must buckle inward, creating a furrow HHMI investigator in 2008, he spent the first year wading and two opposing neural folds. The folds come together and fuse through the paperwork, red tape, and delicate negotiations to set to form the hollow tube that will become the central nervous up the first-of-its-kind pediatric brain tissue bank. system. These tissue movements are driven by complicated cell One-third of babies born with severe brain injury do not shifting and shuffling, which results in chunky parts becoming survive, Rowitch says, and this bank represents those tragedies. slimmer, bringing sections together at spots, and finally zipping But many families, he notes, take comfort in donating so that closed down the length of the embryo’s back.

Safer trisomy 21, which leads to Down “Sequencing is going through This work was published in syndrome, and trisomies 13 and an amazing revolution right now October 2008 in Proceedings of the Chromosome 18, which have very low survival and there is opportunity for great National Academy of Sciences. rates after birth. creativity in using it for things Quake says the simple blood Counting So when Quake read an article other than straightforward genome test could be available to doctors in about researchers trying to capture sequencing,” he says. Quake’s the next couple of years. He thinks Stephen Quake knows firsthand information from fetal DNA circu- group devised a method to amplify the test could work as early as the the wrenching decision parents lating in the mother’s blood, he fetal DNA from a mother’s blood 7th or 8th week of pregnancy—the face when a doctor recommends immediately saw a possibility for sample and sequence the millions time when most women have their an amniocentesis or chorionic making the invasive tests obsolete. of tiny DNA fragments. Next, they first prenatal doctor’s visit. Such a villus sampling test to check for Quake, an HHMI investigator matched up each fragment to its test would carry no risk to the fetus chromosomal abnormalities in a at Stanford University, had corresponding chromosome—as if and would allow families to make fetus. His wife underwent one of recently published the first single- each fragment gets to vote for a decisions about a trisomy pregnancy each test with her two pregnancies. molecule DNA sequencing particular chromosome. much earlier. The invasive tests use a needle to method. It occurred to him that “Then we look for ‘voter “What we went through as a collect fetal cells through the he could harness the power of fraud,’” he says. “In other words, is family definitely sensitized me to mother’s abdomen. Both tests modern sequencing techniques to any sequence overrepresented, the problem,” says Quake, the carry a low, but real, risk of miscar- solve what is essentially a problem indicating that there are three father of a 4-year-old boy and riage (about 1 in 400). They are of counting molecules. copies of that chromosome rather 7-year-old girl. “I still get e-mail most often used to find out if a than two?” In a 2008 pilot study, every day from people who want to fetus has abnormal copy numbers the method correctly identified the get the noninvasive test. It affects a of certain chromosomes, such as number of fetal chromosomes in lot of people.” —K.P. 18 pregnancies—there were 12 cases of trisomy—and it worked as early as the 10th week of pregnancy.

November 2oo9 | HHMI BULLETIN 15 In humans, the neural tube normally forms and closes by the “It’s totally daunting to think you could try to tackle NTDs,” she fourth week after conception, before most women even know they continues. “But as a developmental biologist, I think I can bring are pregnant. It is one reason women are encouraged to eat well my expertise to make an impact on a very real problem in and take vitamins such as folic acid (which helps to ensure the human biology.” neural tube closes correctly) long before they become pregnant. Like Niswander, HHMI early career scientist John Wallingford Failure of the tube to close properly causes a condition known as loves to watch development unfold. He also spends countless spina bifida, Latin for split spine—which exposes the spinal cord hours at the microscope, making videos of frog neural tubes as to the fluid in the womb. The resulting permanent neurological they curl and seal up. damage ranges from mild symptoms to partial paralysis. After The advantage of working with frogs? “Any kid who has gone heart defects, neural tube defects (NTDs) are the second most out and caught tadpoles in a pond can tell you,” he says. Frogs common type of serious birth defect. develop outside the womb in open, clear water, which makes it a “Because of the complexity, there are so many places where cinch for Wallingford’s group to watch the whole process at the it can go wrong,” Niswander says. She explains that it’s not just cellular, and even subcellular, level. They can also easily manip- the cell movements that have to come off correctly, but all of the ulate frog genes to find those critical to neural tube closure by underlying genetic programming, biochemical signaling, and microinjecting modifiers directly into embryos. This procedure incoming environmental influences that together conduct this lets Wallingford, at the University of Texas at Austin, screen choreography. “Based on how many genes we already know are hundreds of embryos at a time. required for neural tube closure in mice, I would not be “Ultimately we have to go to the mouse and then to humans surprised if there were 800–1,000 genes that, if disturbed, might to see if the genes we’re finding are relevant,” he notes. “But lead to a defect.” the frog work has allowed us to move the field forward very So far, Niswander and her collaborators are actively working quickly.” Wallingford has found two major groups of genes on about 30 genes in mice that lead to NTDs. Using a powerful critical for closing neural tubes. Recently, his group showed microscope, her lab members observe cellular changes in the that certain gene mutations prevented a key process called developing neural tubes of mouse embryos. In normal mice, convergent extension where neighboring cells cozy up and they’ve seen that some cells at the edges of the opposing neural slide between one another to bring the neural folds closer folds put out dynamic membrane extensions to communicate or together. At least one similar gene mutation has been found in firm up contacts across the gap. Although the data are very humans with NTDs. preliminary, Niswander says, at least some of the genetic muta- Finding more of those human genes is the real goal for both tions change this behavior of putting out feelers. Wallingford and Niswander. “I’m not out to solve the problem of Niswander has begun to give the mutant mice folic acid neural tube closure for frogs,” says Wallingford. These birth supplements to study how the vitamin acts to prevent some defects are almost never due to a single gene mutation in NTDs. “Folic acid is touted as preventing up to 70 percent of humans; they are most often the result of multiple gene varia- NTDs in women. I want to know, how is it doing that?” she says. tions and their interaction with the environment. What the BOOSTING THE BRAIN’S PROTECTIVE OR REPAIR MECHANISMS MIGHT BE THE BEST ROUTE FOR RESCUING PREMATURE BRAINS FROM PERMANENT DAMAGE.

16 HHMI BULLETIN | November 2oo9 Basic science to save babies: Lee Niswander, David Rowitch, Ananth Karumanchi, and John Wallingford are bringing their expertise in molecular science to study the causes of premature birth and developmental problems.

researchers would like to see in the future is a panel of known “We’ve identified biomarkers that, in a very simple blood test, neural tube closure genes for screening. Then, when a couple is could potentially replace a kidney biopsy down the line. The considering pregnancy, a blood test could determine whether markers could tell us who has pre-eclampsia, who doesn’t, and they would be at high risk for a NTD pregnancy. From there, maybe even how severe it is,” says Karumanchi. physicians might even personalize a woman’s dose of folic acid. Karumanchi, whose early research focused on blood vessel Niswander’s early findings suggest that an average dose may not formation, or angiogenesis, brought a new approach to the riddle be right for all genetic situations. For some mutations, a higher of pre-eclampsia. The placenta is just a bag of blood vessels, after dose is needed to rescue the NTD; for other mutations, a lower all. “No one had looked at it from the angle of blood vessels and dose works better. I thought, here is a disease where I could have a 200 percent impact—on both the baby and the mother.” But as a young inves- Taking the Premature Out of Pre-Eclampsia tigator at the time, he wanted to run his idea by his mentor down Work from another HHMI investigator’s lab might also lead to a the hall, a kidney expert named Frank Epstein. blood test to assess a woman’s risk for a common complication of “He grabbed me and said, ‘Let’s go down right now to the pregnancy that puts both mom and baby in harm’s way. Five to 10 labor and delivery floor and see these patients,’” Karumanchi percent of all expectant mothers develop pre-eclampsia, charac- recalls. There, it dawned on him that every day doctors threw terized by high blood pressure and “leaky” blood vessels that can away placentas from both healthy and pre-eclamptic women. lead to kidney damage, liver damage, and even seizures and coma. He obtained those tissues and used gene microarrays to look at In the developing world, pre-eclampsia kills an estimated which gene expression levels were turned up higher or squelched in 75,000 women each year. In the United States, the total health pre-eclampsia placentas compared with normal ones. Karumanchi’s care costs for pre-eclampsia treatment for both mothers and research team found that two proteins, sFlt-1 and soluble endoglin, babies run about $7 billion a year. The only treatment available are pumped out by pre-eclamptic placentas. The proteins appear to today is to deliver the baby and placenta, the real root of the disrupt the health of a mother’s blood vessels, which damages her problem, as early as possible after severe pre-eclampsia develops. organs and makes her blood pressure rocket upward. Pre-eclampsia therefore contributes significantly to the problem Karumanchi says that clinical trials of a blood test to measure of premature births. How and why the placenta becomes destruc- sFlt-1 levels as a way to detect pre-eclampsia are ongoing in the tive in some pregnancies has remained an enigma since the U.S. He predicts such a test will be available in two or three years. condition was first described some 2,000 years ago. As evidence piles up that sFlt-1 not only indicates pre-eclampsia As a kidney specialist at Beth Israel Deaconess Medical Center but also causes much of the problem, Karumanchi is developing in Boston, HHMI investigator Ananth Karumanchi diagnoses antibodies to sFlt-1 as a potential treatment. tricky cases of pre-eclampsia, ruling out other possible kidney Although the work is still in early stages, he says that finding problems to ensure no baby is delivered unnecessarily early. His women to help test such a drug will not be hard. Severe pre- research, however, may soon make this duty obsolete. eclampsia results in babies being delivered at 24–26 weeks, when

Niswander: Anthony D. Kapp Rowitch: Andy Kuno / PR Newswire, ©HHMI / PR Newswire, ©HHMI Andy Kuno Anthony D. Kapp Rowitch: Niswander: Sasha Haagensen / PR Newswire, ©HHMI Wallingford: Kaye Evans-Lutterodt Karumanchi: (continued on page 48)

November 2oo9 | HHMI BULLETIN 17

IT STARTS IN THE LAB In late 2007, Ressler became the first psychiatrist named an HHMI investigator since Eric Kandel, who was selected in 1984. Kandel went on to win the Nobel Prize in 2000 for insights into learning and memory he acquired by studying Aplysia, a sea slug that looks like a cross between a tree fungus and a football. hen Kerry Ressler “Kerry Ressler strikes me as a role model for the future of walks briskly from his car to his laboratory on a steamy July psychiatry,” says Kandel, who is director of the Kavli Institute for morning, the rasp of cicadas fills the air. Inside, his fifth floor Brain Science at Columbia University. He laments “disappoint- office at Emory University’s Neuroscience Research Facility is ingly slow” progress in treating mental health disorders, which he quiet and overlooks the wooded grounds of the venerable Yerkes blames on a shortfall of basic science and translational research National Primate Research Center. The building is new, the in psychiatry. A new generation of scientists, he believes, can help atmosphere suburban; grad students tapping smartphones wait close the gaps. for a shuttle to the main campus. Ressler made his mark in translational research as a second- The next morning, Ressler’s in a different world. He stacks his year resident, shortly after joining the Emory laboratory of car in a deck atop a McDonald’s and lopes alongside the tower- renowned amygdala expert Michael Davis. In the almond-shaped ing, tawny bulk of Grady Memorial Hospital. Perennially amygdala, a structure found deep in the brain, the binding of the teetering on the edge of financial ruin, Grady remains the hospi- excitatory neurotransmitter glutamate to the N-methyl-D- tal of first and last resort for Atlanta’s urban poor. Across from the aspartate (NMDA) receptor strengthens synaptic connections main entrance, men leaning on “No Smoking” signs exhale when fear is learned or extinguished. Ressler and Davis predicted plumes of smoke and raise their voices over the roar of the they could speed the extinction of fear in rats by using an oppressively close Interstate. Although an architectural facelift approved human tuberculosis drug, D-cycloserine, which binds has smoothed and tightened Grady’s façade, look more closely and activates the NMDA receptor, thereby increasing glutamate and this massive, 21-story structure is marked by more than 50 binding in the amygdala. The experiment was a success. years of hard use. “As soon as we knew it was working, I went to Barbara Ressler—a physician and a basic scientist—has been shaped Rothbaum and asked if we could combine this with psychother- by both places, and he’s resolved not only to move what he learns apy in people,” Ressler recalls. Rothbaum is an Emory psychiatry from “bench to bedside” but to take it all the way to the violent professor who specializes in treating a spectrum of anxiety disor- and chaotic streets where Grady patients live. ders. They launched a small study comparing the response of “My scientific goal is understanding the biology of fear,” says acrophobic patients to behavioral exposure therapy with or Ressler, a Harvard-educated M.D./Ph.D. who came to Emory without a dose of D-cycloserine. Patients given the drug immedi- University, in Atlanta, a dozen years ago to train in psychiatry. ately before virtual or real exposure to heights clearly became less Now an associate professor of psychiatry and behavioral sciences, fearful than those not given the drug. Before the Emory team he is known for developing rodent models that help reveal what published these results in the November 2004 Archives of General happens in the amygdala—the brain’s command center for panic Psychiatry, there was nothing in the literature about pharmaco- attacks and fight-or-flight responses—when fear is learned, logic enhancement of fear extinction. remembered, and sometimes overcome. The idea that pharmacologic agents can alter brain plasticity, Ressler was the lead author on a 2004 article reporting that a thereby mediating fear extinction, is no longer novel. Ressler’s drug can boost the effectiveness of exposure therapy that uses team is experimenting with other mediators of synaptic strength. virtual reality—a simulated glass elevator—to desensitize patients In the July 2006 Nature Neuroscience, they reported that activa- who have acrophobia, or fear of heights. These findings, which tion of the receptor for brain-derived neurotrophic factor is have been replicated in patients with social phobia, panic disor- essential for extinguishing fear. His group has also determined der, and obsessive compulsive disorder, are steps toward what he that the protein ß-catenin is essential for stabilizing synapses and characterizes as his ultimate “social and political” goal: develop- forming fear memories, findings they reported in Nature ing ways to lift weight off poor people who are worn down, held Neuroscience in 2008. down, and made sick by post-traumatic stress disorder (PTSD) In Ressler’s neuroscience lab at Emory, nine graduate and other trauma-related disorders. students and postdocs study fear with tools including small But that, he admits, may be a long time coming. molecules and viral vectors that deliver modified genes to

20 HHMI BULLETIN | November 2oo9 specific brain regions in transgenic mice. By observing how worked part-time to get her through college,” Ressler recalls. mice react to environmental cues, such as a sudden noise or an Some nights he helped her clean the doctors’ offices where she elevated maze, researchers can tell whether genetic modifica- did desk work during the day. Finances eased when she gradu- tions have changed how animals handle fear. Meanwhile, at ated, got a nursing job, and remarried. Grady Hospital, Ressler leads a massive search for genetic poly- In the 1970s, “you could not grow up in Mississippi and not be morphisms, or variations, that might predict which individuals extraordinarily aware of race,” Ressler says about his childhood. who were abused as children will be especially vulnerable to But his mother taught him that “people are often different PTSD as adults—and which ones will prove resilient. because of what life has dealt them, not because of different abilities.” His mother’s lessons helped him at Grady Hospital, where A KNACK FOR CONNECTING patients have experienced oceans of disrespect. Growing up in Mississippi in the 1970s, Ressler had no clue he “Using a lot of jargon and big words just doesn’t work around would become a behavioral neuroscientist with a social conscience. here,” says Grady chief psychologist and Emory psychiatry profes- He certainly never thought Nobel laureates would know his name. sor Nadine Kaslow, who supervised Ressler when he was a Ressler is an only child whose parents divorced when he was first-year resident in the hospital. From the start, Ressler had a young. When he was 12, he and his mother relocated from Jackson knack for connecting with people of all descriptions: “Female to Ocean Springs, a small town between Biloxi and Pascagoula. “It patients see him as not sexist; male patients see him as someone was a wonderful place: you could bike to the Gulf and crab and they can bond with,” says Kaslow. fish and go canoeing in the bayou,” Ressler recalls with delight. Besides his mother, the other influential woman in Ressler’s Ocean Springs schools were also better than most in Mississippi. young life was his advanced placement math teacher, who When puberty hit, Ressler scored the geek trifecta. He had no encouraged him to excel in mathematics competitions and to gift for sports, he played tuba in the high school band, and he apply to the Massachusetts Institute of Technology (MIT). excelled at math and computers. About this time, his mother quit When the MIT acceptance packet arrived, Ressler had been her office job to pursue her dream of becoming a nurse. “We both working the night shift at Delchamp’s Superstore in Ocean

KERRY RESSLER HOPES HIS BASIC SCIENCE RESEARCH CAN HELP LOW-INCOME MEN AND WOMEN RISE ABOVE THE TRAUMA HE’S FOUND TO BE SO COMMON AMONG THE INNER CITY POOR.

November 2oo9 | HHMI BULLETIN 21 – K E R RY R E S S L E R

Springs for several years. He swept and stocked shelves in the wee he was keeping company with Betsy Craig, a Wellesley student hours, when customers were rare. When he told his Delchamp’s from Atlanta. The two are now married and have three sons. coworkers that he was quitting and heading for college, they were As an MIT senior, Ressler was certain he and Craig belonged amazed he would leave such a good job. And when he said that together and that he wanted to delve into the biology of thinking his destination was MIT, the puzzled response was “MIT? That and learning. He was less sure about clinical medicine, but when stands for Mississippi what?” he was accepted to the Medical Scientist Training Program at Ressler left Ocean Springs knowing that computer science Harvard Medical School, he could not refuse. was his destiny. Wasn’t it obvious? “I enjoyed computers and I was going to MIT.” But he was nervous about moving to a strange DAZZLED BY SCIENCE city where he had no friends and might be a total misfit. He The first two years of medical school at Harvard went well, but worried that MIT felt compelled to accept someone from Ressler still needed the right mentor for his Ph.D. work. He knew Mississippi, and he was it. he wanted to use molecular biology and genetics to address a His anxiety was short-lived. Within weeks he joined a fraternity, significant, clinically relevant problem in neurobiology—but which was cheaper than living in a dorm because the residents did what problem? At just this moment, a friend invited him to tag much of their own cooking rather than pay a chef. (“Many of our along to a lecture by Linda Buck, a Columbia University research meals were pretty awful,” he admits.) He worked hard and played associate being recruited by Harvard. hard with 40 other guys at Phi Kappa Sigma in Boston’s Back Bay. “I had never thought about smell a day in my life until I He also discovered that biology was every bit as compelling as heard Linda give her talk,” Ressler says, still jazzed by the computer science and wondered if medicine—which his mother memory, “and I was absolutely blown away.” Buck had methodi- exposed him to—might be his calling. Then Ressler fell in love with cally identified about 1,000 odorant receptor (OR) genes and an advanced genetics lab taught by Drosophila biologist Hermann she outlined an orderly plan for decoding their function. Her Steller, now an HHMI investigator at Rockefeller University. work was “a beautiful example of using science to explain Steller had his students create transgenic fruit flies and observe biology,” Ressler says. phenotypic changes. “That’s what really sold me on being a biolo- He immediately wrote to Buck, asking for a research rotation gist and a scientist,” Ressler recalls. Polymerase chain reaction and in her lab if she did indeed join the Harvard faculty. Helping other new techniques had slashed the time needed to identify and figure out how ORs are arrayed and how they integrate informa- clone a gene, introduce it into an animal, and examine the results. tion to detect and identify smells—that was exactly the kind of Years’ worth of work could be accomplished in a semester. difficult quest Ressler had been hoping for. Ressler asked to stay on with Steller and remained in the fly lab In early 1992, Buck, Ressler, and a truckload of equipment until he graduated. Long hours earned him the nickname “the converged on the Harvard Medical School quadrangle. “My lab biologist.” When he wasn’t at the lab or hanging out with the guys, was full of boxes and crates of equipment when Kerry came in.

22 HHMI BULLETIN | November 2oo9 So I unpacked with him and we set up the lab in about a week,” The three launched the Grady Trauma Project (GTP), today says Buck. led by Ressler, which has been assessing environmental and She went to work writing grant proposals while Ressler set genetic risk factors for PTSD in a broader sample of Grady about creating a library of mouse OR genes and then determining patients since 2005. A team of trained interviewers, most of them where they are expressed in the lining of the nose. “That gave us students from Atlanta area colleges and universities, have the first inkling of how information from 1,000 different receptors collected saliva samples and conducted extensive interviews is organized in the nose,” recalls Buck, an HHMI investigator with more than 2,500 low-income, primarily African American, now at the Fred Hutchinson Cancer Research Center. men and women waiting for primary care or ob-gyn appoint- Over the next three years, Ressler’s dissertation work contrib- ments at the hospital. uted to the accomplishments that earned Buck the 2004 Nobel Nearly 90 percent of GTP participants have been exposed to Prize in Physiology or Medicine, which she shared with HHMI significant trauma, mostly interpersonal violence, at some point investigator Richard Axel. Prominently displayed in Ressler’s in their lives. Rates of emotional, sexual, or physical abuse during Emory office is a framed picture of him with Buck at the childhood are high; later in life, assaults by intimate partners or Stockholm ceremony, both grinning broadly in formalwear. “I others are commonplace. The lifetime prevalence of PTSD is was in a numb fog the whole time,” Ressler says with the goofy 46.2 percent among these Grady patients—as high as in combat laugh that is his signature. veterans—Ressler’s team reports in the November 2009 General The two have a mutual admiration society: Buck calls Ressler Hospital Psychiatry. “a fantastic scientist and a wonderful, compassionate person.” For As these findings indicate, however, not every traumatized Ressler, Buck’s lab will always be where he initially experienced child or adult develops PTSD. With support from the National the joy of being the first to know something. Other epiphanies Institutes of Health, Ressler and his colleagues are searching for would come later, but in places nothing like the beaux-arts splen- gene-environment interactions that may help explain why some dor of the Harvard Medical School quad. During his first weeks suffer more than others. They started with some of the “usual of clinical training at Grady Hospital, Ressler helped stabilize suspects,” including genes involved in the glucocorticoid-mediated gunshot victims and debride wounds colonized by maggots. stress response. So far they’ve identified four single-nucleotide polymorphisms, tiny variations in the FKBP5 gene that appear to URBAN WAR ZONE interact with severe child abuse trauma to predict adult PTSD Within weeks, Ressler was rotated to Grady’s psychiatric emer- symptoms. These findings were reported inThe Journal of the gency room and from there to the hospital’s outpatient psych American Medical Association in March 2008. Additional studies clinic, where the wounds were equally grim but less visible. None are under way to identify novel genes that affect who develops of the patients he evaluated matched the neat diagnostic check- PTSD and who does not. lists in DSM-IV, the standard reference for coding mental Although Ressler can offer no guarantees, he is hopeful that disorders. “Diagnostic messiness” is the norm, clinical veterans basic science findings—taken to the streets—could have an say, because Grady’s typical psychiatric patient is poor, black, uses enormous public health impact. PTSD is associated with inter- drugs, and has multiple health problems. generational violence, poverty, teen pregnancy, broken families, As a fear biologist, Ressler saw something different. These and a host of maladies both physical and mental. Therapies that patients carried “enormous amounts of trauma,” as a result of unshackle people from some of their worst fears and help them living in the urban equivalent of a war zone, and he reasoned establish new emotional habits might relieve some of the human that PTSD might be as common among them as among combat misery that Ressler confronted as a resident in the Grady Hospital veterans. But PTSD was not high on the index of suspicion for emergency room. Grady doctors because they don’t treat vets, who are cared for by There’s little doubt that Ressler’s experiences at this battered private doctors or at the large VA Medical Center across town. landmark helped forge who he is today. As a raw newcomer, he Ressler couldn’t shake the feeling that trauma was important began each shift “with a sense of dread, because there would be here, and in 2003 he teamed with psychiatrist Ann Schwartz and so much work to do and some of the stories would be so hopeless. psychologist Bekh Bradley to determine the prevalence of undi- But I always left in a really good mood, because we did help agnosed PTSD among mental health patients at Grady. Although people and it was not all hopeless.” PTSD was noted in only 6 percent of the charts, they found that Today, knowing what he knows, he still says “I am a pretty 40 percent of patients met criteria for lifetime or current PTSD. optimistic person.” W

November 2oo9 | HHMI BULLETIN 23 membrane awakening

Researchers are taking a more holistic look at cell membranes and the proteins embedded in them—and the surprises keep coming.

Picture a neatly groomed hedge between two houses. On one side, a grassy yard is strewn with jumbles of sandbox toys, half- buried dog bones, and plastic cars. On the other side, neat rows of pansies frame a manicured garden. The hedge is a barrier between two worlds. Look closer though, and the border is a busy place. Insects buzz through the branches without hesitation and a rabbit has traveled through the underbrush so often that a tunnel has formed. Hands reach across a low gate from one side to the other, delivering cookies, wrongly addressed mail, and toys that have leapt the bushes.

by sarah c.p. williams illustration by Jillian Tamaki

The boundary of a living, metabolizing cell is surprisingly similar to that hedge.

The cellular membrane, once thought to have been solved and scientists are moving aligning themselves into double layers, be an inert barrier, is one of the most on to study the finer details of how the with the water-shy lipid tails sandwiched dynamic parts of the cell. The membrane proteins function and interact with the in the dry area between sheets of the phos- and the plethora of proteins that stud its membrane. phate headgroups. This is just how the surface direct the exchange of information MacKinnon and other HHMI investi- membranes in a cell are arranged. The between cells, tightly control the flow of gators, while still adding to the growing list strength of the unfavorable reaction materials from inside to outside the cell, of membrane protein structures, are also between the tails and water—termed a and provide surfaces for some of life’s most beginning to look at the membrane as a “hydrophobic effect”—holds the bilayer vital chemical reactions. whole. They’re studying proteins in the together with no other bonds. “We’re in a very, very primitive stage of membranes, rather than isolated in solu- Along with making up the cellular, or understanding the membrane,” says tion, and asking questions about how plasma, membrane, such bilayers also hold HHMI investigator Roderick MacKinnon different membrane elements interact together many organelles and compart- at Rockefeller University. “We’ve been with each other and with proteins. They’re ments, such as the DNA-containing looking at the membrane in a very hoping to uncover what goes on at the nucleus and the energy-producing mito- protein-centric way and we have to under- boundary of the cell. chondria. stand it with a more holistic view of all its “All metabolically active life relies on components.” water phobia membranes,” says Jay Groves, an HHMI For a long time, the immediate chal- investigator at the University of California, lenge was to figure out the structure and The simple fact that oil and water don’t Berkeley. Apart from various kinds of function of the membrane proteins, which mix guides much of membrane science. phospholipids, and related molecules like do most of the communicating and trans- The molecules that make up most of the cholesterol, plasma membranes teem with porting. But the proteins tend to fall apart membrane are phospholipids—water- proteins. Some proteins are inserted into when removed from the membrane for soluble phosphate-containing heads with only one side of the membrane, acting as study. In 1998, however, MacKinnon lipid tails that will do anything to avoid a beacon for other proteins that need to published the first structure of an ion water. Drop a small amount of phospho- find the membrane. Some jut all the way channel—a protein that acts as a conduit lipids into water, and they will through the membrane, such as receptors for potassium through the membrane. Ion spontaneously form membranes by that detect signals on one side of the channels allow cells to generate, and pass along, electrical signals by controlling the PART 1 OF 2 flow of charged potassium, sodium, and Membranes inside the cell are just as active and dynamic calcium molecules through the membrane. as those that surround cells. In the next issue of the MacKinnon’s structural breakthrough Bulletin earned him, along with Peter Agre of the , our two-part series on membranes will continue Johns Hopkins University School of with a closer look at the membranes that divide the Medicine, the 2003 Nobel Prize in insides of a cell into constantly shifting compartments. Chemistry and shattered the long-held In February, you’ll learn how membranes form bubbles, notion that determining the structure of stacks of sheets, and tubules, and how they can change channels was an insurmountable chal- shape at a moment’s notice. lenge. In the decade since, the structures of more than 200 membrane proteins

26 HHMI BULLETIN | November 2oo9 Gonen: Paul Fetters Groves: Noah Berger / AP, ©HHMI MacKinnon: Matthew Septimus Miller: Yiling Fang proteins withfattydetergentstokeepthem tricky. Researchersmust surround the embedded justsointhemembrane, thisis proteins tendtofallapartunlessthey’re Sincemembrane symmetrical crystal. isolated fromacellandarranged ina many copiesoftheprotein must be diffracted. For thistechnique towork, the protein and measurehow theyare arranged. Theyshineabeamofx-raysat together how theatomsinaprotein are topiece then relyonx-raycrystallography mined membrane protein structuressince nical one.” as much apsychologicaloneastech- through thisstructuralbarrier,whichwas changed whenRodMacKinnonbroke toral training. “Andthenthewholething during hisundergraduateandpostdoc- University andwhomentoredMacKinnon who studies ionchannelsat Brandeis says ChrisMiller,anHHMIinvestigator was, essentially, basicelectrophysiology,” when andhow theyfunctioned. channels andcalculatebasicpropertiesof currents todetectionsmovingthroughthe could useprobesthatmeasureelectric proteins couldbefullyimagined,scientists ciable behavior.” organisms fastenoughtomakeanyappre- couldn’t transferinformationacrossthe isms,” saysMacKinnon,“becauseyou have beenbiggerthansingle-celledorgan- difference theysenseacrossthemembrane. open andcloseddepending onthecharge firing ofneuronsbyswitchingbetween These channelsallow, forexample,the membrane, sending fastelectricalsignals. allow chargedionstopassthrougha focuses onstudyingthechannelsthat particles—across. materials—like water,nutrients, orcharged other. Andsomeproteins helpshuttle membrane andsendthemalongonthe Most ofthescientists whohavedeter- “At thebeginning, ionchannelwork Long beforethestructuresofthese “Without thisswitchlifecouldn’tever One branchofmembraneresearch pass signalsbetweencells. and membrane-embeddedreceptorsthat channels thatallow ionstomoveacross, membrane: poresthatallow waterthrough, some ofthemajorprotein playersinthe this method,scientists haveilluminated can playgamesfromthere,” hesays.Using day, andthenyou theprotein crystallizes luck asitishardwork,saysMiller. arranged correctlyinsolution.It’s asmuch protein structureremainunanswered. Some basicquestions aboutmembrane rather thangoing thetraditionalrouteofisolating individualproteins. membrane byzoomingouttolook atallitscomponentstogether, Christopher Miller,andRoderick MacKinnonarestudying the cell’s plasma HHMI investigators (clockwise fromtopleft)Tamir Gonen,Jay Groves, “If you’veprayedtotherightgodsthat the fullstory place again.Thishappensentirelyatthe the cellssothatsignalingcantake another, andthenmoppedupbyoneof released fromonecell,detectedby milliseconds. Neurotransmitters must be in theformofneurotransmitters, inmere cells ofthebrainmust passalongsignals, membrane proteins inthebrain.The between thestructuresofdifferent example, recentlyfoundsurprisinglinks acid sequence. protein willlooklikebasedonitsamino membrane andhow topredict whata picture ofhow proteins foldintothe Each newstructuregivesscientists abetter HHMI investigatorEricGouaux,for November 2oo9

HHMI

BULLETIN 27 membranes of the neurons. Understanding proteins illuminated the full story of the activated channel in Nature on September 3, how brain receptors work is vital to CLC protein family. 2009, Rees is frustrated by the limitations explaining learning, memory, and cogni- As the list of membrane protein struc- of typical x-ray crystallography for studying tive disorders. tures grows, and lessons are learned, membrane proteins and wants to find a Using x-ray crystallography, Gouaux scientists have also begun to toy more with better method. In 2008, he received a and his lab team at Oregon Health & other aspects of these proteins. Most Collaborative Innovator Award from Science University have shown unex- notably: how do membrane proteins HHMI to make membrane protein crys- pected similarities between different types interact with, and depend on, the mem- tals with colleagues at Caltech and of neurotransmitter receptors. While the brane that surrounds them? University of Colorado. His idea is to coax receptors have vastly different amino acid proteins into forming polyhedral arrange- sequences, which suggests different struc- safety valve ments embedded in membranes. Such a tures, his group found that each receptor shape—inspired by symmetrical 20-sided forms a similar shape. Piecing out these If a single-cell bacterium, full of molecules viruses—would allow proteins to interact unexpected details will help scientists and salts, fell into a puddle of water, the normally with the membrane while still better predict the shape of membrane water would rush through the membrane providing the sample homogeneity needed proteins from their amino acid sequences. into the cell. If this went on for too long, for x-ray crystallography. “At some point it will happen, maybe the membrane would rupture, unable to Tamir Gonen of the University of 10 years from now, that the next membrane stretch very far. Luckily for the cell, it has Washington, an HHMI early career scien- protein structure will come out and a way to bail itself out. tist, also studies stretch-activated channels, everyone will yawn because it starts to feel Doug Rees, an HHMI investigator at specifically the water channel aquaporin-0 like stamp collecting,” says Miller, at California Institute of Technology, studies (AQP-0), found in the lens of the eye. Brandeis University. But that hasn’t one type of stretch-activated, or mechano- “These channels are much more than just happened yet, he says. “The number of sensitive, channel. When these channels a hole,” Gonen says. “They let water structures is still small enough that each sense a membrane stretching too far, Rees through very efficiently, billions of mole- one has something novel to tell people says, they open, like the safety valve on a cules per second.” When they’re not about how these things are put together, pressure cooker. Their function depends working due to certain mutations, the how they sit in the membrane, or how on the membrane around them. Rees eye’s lens clouds over with cataracts. they fold.” focuses on bacterial versions, but stretch- In 2004, while working in the lab of Miller knows well, though, that some- activated channels play a role in HHMI investigator Thomas Walz at times it pays to look beyond the structure. maintaining the membrane’s tension in Harvard Medical School, Gonen deter- When MacKinnon published the struc- all organisms. In humans, other mechano- mined the structure of AQP-0. While x-ray ture of a chloride channel (CLC) in 2002, sensitive channels in the nervous system crystallography usually uses three-dimen- scientists thought they knew the basics of help convey a sense of touch by passing sional crystals of membrane proteins that how it worked—it appeared to be a typical along a signal when the pressure on a are enveloped by detergents, Gonen channel. But Miller took a closer look at membrane changes. analyzed the protein while it was the electrical behavior of the protein and To study these channels, Rees inserts embedded in a membrane, one of only a found, much to everyone’s astonishment, them into an artificial membrane and few successful attempts to do this. He’s that this particular CLC isn’t a passive sucks up part of the membrane with a convinced that observing a protein struc- channel. It’s a pump that uses protons to glass pipette, increasing membrane ture while it’s in a membrane gives the push chloride across the membrane. tension around the channels. As the best picture of how the protein really looks. “It ended up being somewhat of a tension increases, channels open and he “The way we need to look at membrane game-changer,” says Miller, “because can measure the molecules flowing proteins is not in isolation,” Gonen says. within a year, other labs following our through. His system is a simple way to “We need to look at them with the discovery tested the electrical properties of probe how membrane proteins can detect membrane, because in the cell they’re not other CLCs and found that this family of and respond to one type of variation— operating in a vacuum.” CLCs is split into two subtypes.” Some tension—in the membrane. HHMI investigator John Kuriyan has a CLCs are channels; others are pumps. Ultimately, Rees wants to determine story that illustrates Gonen’s point. Kuriyan, The structures hadn’t hinted at this. the structures of these channels. Although at the University of California, Berkeley, Pairing the function and structure of the he published the structure of one stretch- studies SOS, a signaling protein that,

28 HHMI BULLETIN | November 2oo9 “The single molecule approach will always be there, that’s essential, but we’re starting to have tools to go after the collective as well. We want to see the forest and the trees both.” –Jay Groves

when mutated, causes Noonan syndrome, when scientists dissolved membranes and description of membrane organization a developmental disorder that causes heart observed that they separated into distinct needs to capture this diversity.” malformation, mental retardation, and layers—one with phospholipids and one To probe how the organization of other problems. SOS sends signals by acti- with other lipid-like membrane mole- groups of membrane proteins affects their vating Ras, a membrane-associated protein. cules, including cholesterol. Proteins function, Groves has developed a tech- Researchers assumed that the Noonan separated into both layers, and the scien- nique called spatial mutations. He creates syndrome-causing mutation changed the tists hypothesized that the cholesterol artificial bilayers that impose organization interaction between SOS and Ras. wasn’t just scattered around the membrane on a cell, using miniscule tools designed But when Kuriyan placed mutated but was in distinct “rafts” where certain for nanoengineers who build things even SOS and its normal version in solution proteins localized. smaller than cells. His lab débuted the and compared how they interacted with So scientists began experimenting with strategy in a paper on T cell-receptor Ras, he saw no differences. When he whatever membrane proteins they studied, signaling in Science in 2005. T cells are repeated the experiment with Ras bound testing whether removing cholesterol from immune cells responsible for recognizing to an artificial membrane built by Groves, the membrane—a simple experiment— antigens in the body and eliciting a specific however, the mutated SOS kept Ras acti- altered the function of the protein. response. This process relies on a number vated. The interaction, Kuriyan realized, “Lo and behold, everyone who did that of receptors clustered on a cell membrane took place at the membrane and both experiment, no matter what they looked that must work closely together. SOS and Ras needed the membrane envi- at, messed up the function of the protein,” When Groves’s team used its artificial ronment to behave as they do in the cell. says Groves. “And so everything became membranes to move the components of The results appeared in Nature Structural ‘raft-associated.’ You can find hundreds of the T cell receptors around, the receptors & Molecular Biology in May 2008. papers with this in the title.” stopped working normally. “There were But Groves thinks those results suggest no genetic mutations, and no drugs,” says the forest and the trees something else: the structure and compo- Groves. “We just physically reorganized sition of the membrane are important for the membrane and could track differences Certain that membrane proteins are inex- all processes. “I think it’s really a mistake to in signaling.” orably linked in function to the lipids think there are only two types of things in Membranes, says Groves, provide around them, Jay Groves at UC Berkeley the membrane: rafts and everything else,” places where molecules can be organized studies how groups of proteins are arranged he says. “I think every process assembles in nonrandom ways, clustered where in membranes. The first theories on its own object. Cholesterol is important, they’re needed. His research continues to membrane organization arose in the 1980s lipids are important. And a truly useful (continued on page 48)

November 2oo9 | HHMI BULLETIN 29

Instead of letting teaching assistants sink or swim, risking their failure and the ire of the undergrads, some schools are prescribing a class in how to teach before Enhancing they get in front of a class. TA Performance

By Andrea Widener illustration by VSA Partners

After seven years, Catherine Drennan was best way to improve the class was to revamp papers, share ideas, and talk about the best finally happy with her lectures for her the TA experience. In 2007, she joined ways to help problem students. introductory chemistry class. She had with fellow instructor Elizabeth Vogel “It seems to defy the laws of thermody- integrated engaging techniques and Taylor, a recent graduate of the doctoral namics,” Drennan says. “The amount of worked hard to find meaningful examples program in chemistry at MIT, to expand time we’ve put into TA training is so little from biology for the 200-plus student class TA training by creating a TA “boot camp” compared to the time it saved with at the Massachusetts Institute of to be held the week before school began. complaints and issues later.” Technology (MIT). But the recitation The boot camp included everything While TA training itself isn’t new, more sections—the small groups where teach- from team building exercises to advice faculty like Drennan say comprehensive ing assistants (TAs) and undergraduate from former TAs to a discussion on teach- TA training improves large introductory students meet to reinforce lectures and ing students from diverse backgrounds. science courses for everyone involved: work problems—were hit or miss. What’s more, the TAs had to apply to undergraduates, TAs, and professors. While some TAs were dedicated teach- teach the class. The number of applicants Undergraduates get better instruction in ers, others thought that teaching freshmen for what had been a dreaded assignment labs and recitation sections where one-on- interested in engineering or life sciences surprised Drennan and Taylor: 11 of 44 one instruction most often occurs. TAs was beneath their abilities. That meant chemistry graduate students applied in learn from the beginning how to handle some undergraduates thought they 2007, the program’s first year, and 16 of 41 common classroom problems and present weren’t getting the support they needed to did the same in 2008. challenging material in an engaging way. pass the class. And that made Drennan The results have been better than And faculty can worry more about teaching miserable—especially when students Drennan imagined. Student complaints and less about complaints from students. showed up in her office to complain. “It have been replaced by enthusiasm about “I was actually very excited they were was very disheartening,” she says. chemistry. And, rather than grumbling giving this type of training because you So Drennan, an HHMI professor and about their teaching assignment, the really want to put your best self forward now an HHMI investigator, decided the class’s dozen TAs get together to grade when you’re teaching,” says Mike Morrison,

November 2oo9 | HHMI BULLETIN 31 who was a TA for Drennan’s class in fall Oregon State’s introductory biology class, What scared them wasn’t the subject 2008. That is especially important when with funding from an HHMI grant. The matter—it was how to deliver a lecture, teaching freshmen who are often scared class includes two immense lecture how to manage a classroom, how to write and overcommitted, he says. “You need to sessions of 650 students each—which a quiz. connect with these students early on, and doesn’t give the faculty much opportunity White agreed to help teach a course for to do that you really need to have a basis to reach out to individual students. But TAs who were assigned to run introduc- and a foundation to teach. I had never had Mason had at least 28 graduate students tory biology labs. But first she looked to that before.” serving as lab TAs, each meeting with see what was available elsewhere and Morrison used that connection to help undergraduates weekly in smaller lab learned that TA training nationwide varies bring one student back from the brink. She sections. When Mason asked around greatly. Some schools offer intensive had stopped coming to his recitation and about TA training, colleagues pointed him certificate programs that span years and her grades were dropping, so Morrison to Jessica White, an education professor. cover many types of classes and teaching tracked her down after lecture one day. Like White studies the factors that cause experiences. Others offer university-wide many MIT freshmen, she was bright and graduate students to stay in or drop out of courses for a few hours or a few days before driven, but as they talked she confessed that school, and she had heard a lot about the school starts, though some science TAs she was having trouble managing her time. TA experience. Some students were glad complain that those are often generic. He gave her advice on balancing commit- for the income from the paid position, Many schools, including Oregon State, ments, and soon she was back in recitation since it helped them finance their educa- had no organized training at all. and ended up doing well in the class. tion. But often, students cried during White wanted the TA course to begin “As long as you get to a student quick interviews when talking about teaching. with the practical: teaching TAs how to set enough, when you start seeing them slip a “They felt really unprepared and felt they expectations for the lab, work with stu- bit, you can get on the problem and show were being fed to the wolves,” White says. dents who have disabilities or otherwise that you care,” Morrison says. “I think they get a boost of confidence and are more likely to do better in the class.” Hal White University Focus on Critical Thinking of Delaware Robert Mason’s first experience with a TA was when he became one. In the 1980s, Mason went from College of the Holy Cross, a small liberal arts school in Massachusetts with no graduate students, to pursue a doctoral degree at the University of Texas at Austin, one of the largest schools in the nation. He remembers being told he was a TA, and that he’d have to report to the introductory biology classroom on Monday morning. “It was pretty much, ‘Knock ’em dead, kid!’” laughs Mason, who now heads the undergraduate biology program at Oregon State University. “I have a vivid memory of standing up in front of the class thinking, ‘Holy cow, three months ago I was over there, and now I’m over here.’” Mason thought back to that experience

when he began looking for ways to improve Fetters Paul

32 HHMI BULLETIN | November 2oo9 Catherine Drennan Massachusetts Institute of Technology

need special assistance, manage disrup- tive students, and deal with academic dishonesty. Then she moved on to subjects that would make the TAs better teachers: writing thoughtful quiz questions, address- ing different learning styles, and breaking the cycle of memorization and repetition. During the school year, White saw a notable increase in confidence among the graduate students that they could handle both the class and the material. “It became evident that many of the people were just craving this,” White recalls. “Even the veteran TAs were thrilled to have this opportunity because they had already had a year or two of really floundering.” Sarah Eddy, a veteran TA and zoology graduate student, says White’s course made her think about her class differently. She revised her introductory lectures to include more group activities and learned how to streamline her weekly grading duties. But the part she found most inter- A Jumping Off Point White’s goal in this science-specific TA esting was the focus on improving critical In a TA training course at the University of training is to get them past their personal thinking, both in lectures and on quizzes. Delaware, on a humid August day, about fears and these common problems quickly, “If you can give the students that skill, 60 new biology and chemistry graduate so they can move on to the serious busi- then they are much closer to becoming students gathered around tables debating ness of teaching. He wants them to think scientists,” she says. the best way to explain dependent and about how people learn—even if for just Within a few weeks after White’s class independent variables. They had just one hour a week. “What I‘m trying to do is began in fall 2008, other graduate students suffered through a video of an obviously take the focus from one’s self to a focus on were asking if they could join. Now faculty unprepared TA struggling to answer just the students,” he says. and graduate students in chemistry, that question. The TAs responded with Graduate students need to understand physics, and even departments outside the occasional groans or chuckles. that they can have a big impact on under- sciences want to find out what the class is Hal White, a biochemistry professor graduates, White says. College is a time about. The idea has been so popular that who has taught Delaware’s HHMI-funded when many students change how they Mason and White are creating a teaching “Introduction to Laboratory Instruction” think about the world, from a simple black certificate program for graduate students class for eight years, says that first-time TAs and white view to one that includes the at Oregon State. But what drives Mason to often fear they won’t know the material or shades of gray so common in science. The do this is the effect on the students. be able to answer questions like this one. TAs can also help students understand the “My responsibility is to make sure that But that usually isn’t the kind of problem importance of science—this science class these undergrads are taught as effectively they encounter. “There are more issues of might be the only one they take in their as possible,” Mason says. “Now we’re management than there are of content,” he college career. saying [to TAs] the onus is on us to make says. For example, how do you get students Graduate student Brad Bauer took the you an effective teacher. I can’t just say be to come to class on time? What do you do Delaware TA training course in 2006 an effective teacher. We have to teach if they are constantly texting or talking on when he started teaching an introductory

Leah Fasten them how.” a cell phone? (continued on page 48)

November 2oo9 | HHMI BULLETIN 33 34 HHMI

BULLETIN

November 2oo9 PERSPECTIVES &OPINIONS LEARNING ROBOTIC IF Terrence Sejnowski

YOU THINK

THINK

AGAIN

IT ’ S .

BAD ,

John Dole A new science of learning is in the offing, says HHMI investigator and Salk Institute researcher Terrence Sejnowski. He and others are tapping the disciplines of psychology, neuroscience, and machine learning to create innovative ways to engage even the youngest students. One goal: robotic assistants for tomorrow’s teachers.

We face a crisis in public education in America. In my state, One of the biggest challenges in designing social robots California, class sizes are up, budgets are down, and there is is getting children to interact with the machine as a peer. no clear idea how to improve learning as the system lurches A robot has to respond to the child within a human interval, on with more and more kids left behind. which turns out to be about two seconds. Science can help. New research on human and machine Javier Movellan has built a social robot named RUBI learning is extending our knowledge of how kids and computers and tests it daily in the classroom with 18- to 24-month-olds. can collaborate. This work goes far beyond video games and At first, he found that toddlers wanted to treat it like a toy keyboard or controller interfaces. I’m talking about some- and pull its arms off. The solution? Install pressure sensors thing much more human—and far more complex to deliver— in the arms and program RUBI to “cry” when mishandled. a social robot. Presented with this very human response, the children Research (and common sense) shows that the most effec- stopped tugging and hugged the machine instead. tive teaching happens one on one. Such directed instruction But robots need to do much more than cry—they have to can improve a student’s performance from midquartile to act human in key ways. One such golden behavior is shared top quartile. Unfortunately, the current ratio of 15 students attention. RUBI is programmed to follow a child’s gaze at a to 1 teacher in American schools doesn’t support this level of third object. Combine that with facial recognition (RUBI interaction. There just aren’t enough teachers—or enough smiles back when smiled at) and the little students become money to pay for more. enthralled with their new acquaintance. Let the learning begin. But something strange and wonderful is happening: as If you’re thinking this is all implausible, realize that teachers become rarer and more expensive, computers get RUBI consists of $500 worth of computer parts and motors. cheaper and more powerful. We’re on the verge of an era Her progeny will no doubt be cheaper to produce, and more where inexpensive robotic teaching machines can augment capable, but the real sticking point to future adoption of classroom learning. Imagine Ms. Smith’s science class with social robots in the classroom is humans. Teachers and an Albert Einstein at each desk to help kids grasp the theory unions are wary of mechanized aides and it will likely be a of relativity. Not a computer screen, but a fully interactive long, slow pull to get the technology accepted by school automaton that can talk, recognize facial expressions, antici- boards dubious that a “droid” can help a human instructor. pate needs, and learn from the student how to teach better. School administrators will no doubt be pushed by parents, What sounds like a Hollywood sci-fi flick is already being who tend to be intrepid, early adopters of technology that can refined in the laboratory. Underlying the effort is a new help their children learn. But we need a better system to get science of learning that combines psychology, neuroscience, innovations from the lab to the classroom faster. A National machine learning, and education, a concept I reviewed Science Foundation-sponsored group I codirect called The with colleagues Andrew Meltzoff and Patricia Kuhl of the Temporal Dynamics of Learning Center is working to do just University of Washington, and Javier Movellan of the that, bringing together researchers, teachers, administrators, and University of California at San Diego, in the July 17, 2009, policy makers to create a collaborative science of education. issue of Science. The classroom of the future may look quite different with We’re getting a much better idea how young children social robot assistants, but how do we get from here to there? come to understand the world around them. They follow We need an X Prize for education, just like the $10 million social and physical cues from adults and their peers, mirror competition now under way to build an automobile capable behaviors, and empathically connect with those around of reaching 100 miles per gallon. Let’s award $1 million to them. But what we do so naturally as humans is both second the schools that deliver the best improvements for teaching nature and enormously complicated. And it depends on reading, science, and math, and then $10 million to the the right cues at the right time. school that is best able to scale it up.

INTERVIEW BY RANDY BARRETT. Terrence Sejnowski is director of the Computational Neurobiology Laboratory at the Salk Institute.

November 2oo9 | HHMI BULLETIN 35 Q & A What grade in school was your most formative and why? While some of our early years remain fuzzy, holding no great resonance as we move into adulthood, others stand in sharp relief as the ones that shape us and help decide our futures. Here, four scientists recall the years most significant to them.

—EDITED BY SARAH C.P. WILLIAMS

Marta Miaczynska Gerald R. Crabtree Susan R. Wessler Peter Cresswell HHMI INTERNATIONAL HHMI INVESTIGATOR HHMI PROFESSOR HHMI INVESTIGATOR RESEARCH SCHOLAR STANFORD UNIVERSITY UNIVERSITY OF GEORGIA YALE SCHOOL OF MEDICINE INTERNATIONAL INSTITUTE SCHOOL OF MEDICINE OF MOLECULAR AND CELL “After graduating college “It wasn’t the grade as much BIOLOGY, POLAND “My most formative year was I was unable to decide as the national exam that probably 8th grade, when I “It was the 7th grade of whether to go to graduate everyone in the UK had to began scanning my older Polish primary school when school, as the prospect of take at 11 years of age. It well brother’s college chemistry chemistry appeared on the spending my life in the was called the Eleven Plus textbooks for clues to make program. I was fascinated proverbial ‘Ivory Tower’ was exam and was later found rockets and explosives and by simple but imaginative troubling. To help gain to be based on faked data. obtained my first glimpse of and colorful experiments, some perspective, I took a It was supposed to determine how the physical world the laboratory glassware and year off and worked as a whether you were qualified worked. This evolved into a tools. It was like magic! To secretary for a lingerie to attend a grammar school serious interest in chemistry, continue my fascination, in company on Fifth Avenue. or what was called a which later initiated my secondary school I chose a Riding the subway from the Secondary Modern school, interest in many areas of class with an extended pro- Bronx to Manhattan every designed basically to keep science. Socially, I remem- gram of chemistry—but it day helped convince me kids off the streets until ber taking the noon dance came at the same time with that being cloistered in the they were 15 years old and classes offered at our school. extended biology. There I Ivory Tower of academia could leave and get a job. I thought that it was pretty discovered that the two might be preferable! I have I passed the exam. If I had nice that there were 10 girls went hand in hand and my never regretted that decision.” failed, I would probably by to every boy. I needed those interest in molecular biology now be spending my time kinds of odds and hoped was born, determining my with other geezers in the that my newly acquired future career choices.” pub playing dominoes and dancing skills might impress wondering what I might a certain girl. They didn’t.” have been if I’d passed.” Miaczynska: David Rolls Crabtree: Caroline Tudor / Stanford University Wessler: Imke Lass Cresswell: Courtesy of Peter Cress Imke Lass Cresswell: Courtesy of Peter / Stanford University Wessler: Miaczynska: David Rolls Crabtree: Caroline Tudor

36 HHMI BULLETIN | November 2oo9 James Chen, Ethan Settembre, Scott Aoki, Xing Zhang, Richard Bellamy, Philip Dormitzer, Stephen Harrison, and Nikolaus Grigorieff. fish Doestheanatomyoffreshwaterandsaltwater differ? ASK ASCIENTIST 43 forGABA/BlueBabyBlues RemovingRadiation Roadblock/Starving 40 LAB BOOK LecturesonScience: ExploringBiodiversity RummagingforScience /2009Holiday 38 SCIENCE EDUCATION MedalofScience /Keio PrizeGoestoFriedman DrukerandSawyers WinLaskerAward /FuchsAwarded 46 NOTA BENE Freeze Frame 44 TOOLBOX how setsofthreeVP7molecules worktogether. by electroncloudsinblue,allowed researcherstodiscover This detailed structure,withproteininyellowsurrounded a rotavirusfromattacking itshostbeforeconditionsare right. VP7 proteins,liketheoneshownhereinatomicdetail,keep chronicle November 2oo9

HHMI

BULLETIN 37 38 HHMI concluded that they wouldnotbeexcited bylistening tomelecture, age. “Would theyliketheclass I’d beenteaching?”shewondered. “I lectures fiveyearsagoasherson anddaughterapproachedcollege grabbed apairofoldsoccersocks torepresentsisterchromatids. a vesiclestuddedwithspikypurple proteins. Inahurryoneday, she hydrogen ions,orherdaughter’s oldHalloween wigthatdoublesas reviews. Shemight infor arriveatclasstotingtennis ballsthatstand because that’s wheresheforagesformanyofhermaterials—earnrave anymore. Her“garagedemos”—socalled sweat overherpresentations room asthestudentsgraspedconcept. the partofamotorprotein traversingthecell,eyeslitupacross But whenshewalkedacrossthelarger-than-lifecelldrawing, acting her demonstration,thinkingitcondescending andgrade-schoolish. brought thegiantcelltoclass. DIANE O’DOWD REMEMBERSSWEATING THEFIRSTTIMESHE THE BEST TEACHING TOOLS INTHECLASSROOM. SOMETIMES EVERYDAY OBJECTS MAKE Rummaging forScience science education O’Dowd, who’s beenteachingfortwodecades,revamped her A professorattheUniversity ofCalifornia, Irvine,O’Dowd doesn’t She worriedthatherintroductorybiologystudentswouldsneer at

BULLETIN

November 2oo9 and uses the demos to reiterate important concepts. and usesthedemos toreiterate important testers fornewdemosbeforeunveiling them inclass. Styrofoam, andanoldhanger. Sherecruited herchildrenasbeta- pipe insulationandmembrane phospholipidsfromPVCpipes, tobuild:proteins from rummaged throughhergarage andstarted uted acrosssomanypoints, doesn’tbreaktheskin.So O’Dowd professor wholiesonabedofnailstoshow thattheforce,distrib- physics, wherelecturersroutinelyusedemonstrations,suchas the University, outinhermind. Oneisintroductory afewcoursesstand which arehitsnotonlyintheclassroombutalsoonYouTube. training programs. Amongthoseeffortsareherfamousdemos, she isdevelopingandtestingeducationaltechniques andteacher- Education inBiology. Now, withsupportasanHHMIprofessor, National Academies SummerInstituteonUndergraduate learning inlargeclassrooms,sheattendedtheHHMI-sponsored uninterrupted, for50minutes.” To learnaboutincorporatingactive She explainsclasscontentwith old-fashionedPowerPoint slides When O’Dowd thinksbacktoherown collegeyearsat Stanford

Andrew Rae “It puts an exclamation point on the sentence,” says Michael act as carbonic acid and bicarbonate ions buffering the blood’s pH. Leon, Irvine’s associate dean of undergraduate biology education. Three tennis balls “in solution”—that is, on the floor—represent the O’Dowd found that students can misunderstand key concepts ideal pH. The job of the student buffers is to pick up or drop tennis when they’re presented two-dimensionally. For example, many balls to maintain that perfect state. Once, O’Dowd set out five students perceive DNA plasmids as a flat circle, which is how they’re “hydrogens,” two too many. When three students reached for balls, typically drawn. But they are actually loops, with empty space in the she recalls, “The whole class yelled, ‘Nooo!’” The third bicarbonate middle. Her 3-D “plasmid,” manufactured from an old garden hose, quickly dropped his ball, keeping the blood pH at equilibrium. shows students the proper shape. In an anonymous survey, 90 percent of students rated the demos Students often become moving parts in her demos—for “helpful,” O’Dowd reported earlier this year in the journal CBE— example, they make great motor proteins. A volunteer in O’Dowd’s Life Sciences Education. Vivian Nguyen, a junior who works in lecture might portray a kinesin, carrying the vesicle-wig across O’Dowd’s lab, recalls that the textbook was crammed with details, the giant cell’s microtubule tracks, or one in a lineup of myosins, but the demos “went straight to the point.” Sophomore Marina pulling and pushing to simulate muscle contraction. Dozing off in Nemetalla says she thought back to demonstrations during exams class is dangerous—the sleepy undergrad could wind up starring and continues to do so now in her research. During a recent lab as the “resting neuron” in a one-act play on nerve cell stimulation. meeting, Nemetalla even launched into a demonstration of her O’Dowd tries to break through the invisible barrier between the own, using colored beads to represent DNA bases. lecturer droning at the podium and the students slouched in their The students are not the only ones to benefit. O’Dowd says she chairs. “They have to feel like they’re people in your class, not just gets more satisfaction from teaching than in years past. Inspiring one in a sea of faces,” she says. young people provides rewards that her research on learning and Even those who remain seated are engaged, shouting out instruc- memory in fruit flies cannot. No fellow neurobiologist has ever tions to their friends onstage. “They stop looking at their computers written her with the comment she occasionally hears from her and start looking at the lecture,” says graduate student Melissa students: “You changed my life.” W –AMBER DANCE Strong, who was a teaching assistant in the course. In one demonstration, O’Dowd uses tennis balls to represent hydrogen ions in the FOR MORE INFORMATION: To see some of Diane O’Dowd’s classroom demos, visit blood, and invites six students to come to the front of the room and www.researchandteaching.bio.uci.edu/lecture_demo.html.

2009 HOLIDAY LECTURES ON SCIENCE EXPLORING BIODIVERSITY

Sometimes it pays to look in unlikely Medicines” will introduce viewers to lab on the venomous cone snail, which places to uncover the secrets of the intriguing research of these two can produce up to 100 different toxins. biology. Researchers Bonnie Bassler biologists. ¶ Bassler, an HHMI investi- He is sorting through the molecules and Baldomero Olivera know from gator at Princeton University, studies that make up these toxins in search of experience that nature holds clues to glow-in-the-dark marine bacteria to compounds to treat human disease. medical science, and this winter they’ll learn how they communicate with each ¶ Both researchers’ work illustrates be sharing their insights in HHMI’s 2009 other. Understanding how they coor- the value in studying the diversity of Holiday Lectures on Science. Available dinate their actions could help improve organisms found off the beaten path. live by Webcast on December 3 and 4, treatment of bacterial infections in For more information on the 2009 the four-part lecture series “Exploring humans. ¶ Olivera, an HHMI professor, Holiday Lectures, visit www.hhmi.org/ Biodiversity: The Search for New focuses his University of Utah research biointeractive/hl.

November 2oo9 | HHMI BULLETIN 39 lab book

Removing Radiation Roadblock RESEARCHERS HAVE FOUND THE PROTEIN THAT MAKES SOME TUMORS UNRESPONSIVE TO RADIATION.

Almost half of all cancer patients receive radiation treatment. often show signs of oxygen depletion, Simon hypothesized that When it works, the high-energy rays damage genetic material HIF2 was inhibiting p53 in these cancers. So she tested cell lines inside tumor cells, causing them to self-destruct. But some tumors from renal cancers for HIF2 and p53 activity. She showed that when are resistant to the radiation. HHMI investigator M. Celeste Simon a tumor cell has increased HIF2, it has low p53 activity and is there- at the University of Pennsylvania School of Medicine has uncov- fore resistant to radiation. Moreover, when the lab decreased the ered one protein responsible for radiation resistance in some renal amount of HIF2 in a cell, it had increased cancers and likely implicated in other cancers as well. p53 activity and increased response to radia- Simon’s lab studies proteins involved in maintaining normal tion. The results appear in the August 25, oxygen levels throughout the body. Called hypoxia inducible factors 2009, issue of Proceedings of the National (HIFs), these proteins usually signal cells to conserve energy when Academy of Sciences. oxygen is depleted, promoting survival. But some types of cells, like If researchers can find a way to block those that form new blood vessels, need to grow more aggressively HIF2, Simon says, p53 would once more do when they sense an oxygen shortage. This is the job, Simon’s lab has its job of directing radiation-damaged cells shown, of HIF2—it encourages oxygen-depleted cells to grow by to die. HIF2 is not the only protein that activating growth factors and inhibiting p53, a protein that normally inhibits p53 in cancers, so while Simon’s induces cell death in the presence of DNA damage. approach would work for renal cancers with It has long been known that p53 is a tumor suppressor. When it’s active HIF2, there are likely multiple forms turned off, tumors can grow more aggressively. p53 inhibition also Radiation damages the of radiation resistance. Simon does, chromosomes inside leads to radiation resistance as it is responsible for telling cells with cells (lower panel), however, have evidence that HIF2 is linked radiation damage to die. normally causing the to some forms of radiation-resistant lung cells to die. Knowing this, as well as the fact that radiation-resistant tumors cancer. W –SARAH C.P. WILLIAMS

IN BRIEF

CUTTING BACTERIAL CHATTER interfere with the bacteria’s AHL receptors. Oligodendrocytes, the brain’s fix-it It’s a lesson learned by army generals In her latest work, which appears in the cells, normally can rebuild myelin. Rowitch throughout history: cut off communication July 31, 2009, issue of Molecular Cell, she and his lab group at the University of among soldiers, and their attack strategy took a promising chemical from this screen California, San Francisco, set out to under- goes haywire. It’s as true for bacteria as it and tweaked its structure to yield related stand why this didn’t happen effectively is for human armies—bacteria rely on chemicals. The most potent version, chlor- in MS patients. The researchers destroyed chemical signals to coordinate their activi- olactone, protected roundworms from a bit of myelin in the spinal cords of ties. HHMI investigator Bonnie Bassler, at death due to C. violaceum, without any healthy mice, and monitored the activity Princeton University, has used her work on side effects. This inhibitor could lead to of more than a thousand genes during the bacterial communication to develop chem- drugs that stop bacterial infections without repair process. icals that can stop a bacterial infection in relying on traditional antibiotics. The team showed that 50 genes its tracks. encoding transcription factors, which The bacteria in growing colonies DAMAGE REPAIR IN control the activity of other genes, were produce chemical signals called autoin- MULTIPLE SCLEROSIS active during myelin repair. They focused ducers. When the amount of autoinducer Damaged nerve cells cause the tingling, on one, Tcf4, a member of the Wnt reaches a threshold, the individual bacteria paralysis, and numbness in multiple scle- signaling pathway, which showed a local- simultaneously change their behavior—by rosis (MS) patients. In the early stages of ized increase in expression in white matter releasing a toxin when there are enough the disease, immune cells attack myelin— during myelin repair. They found that bacteria to have an impact on a host, for the protective coating surrounding nerve hyperactivation of the Wnt pathway in the example. Bassler’s lab group focused on cells—which begins to erode. An analo- oligodendrocytes of mice resulted in Chromobacterium violaceum, a bacterium gous situation resulting from lack of significantly delayed myelin repair that rarely infects humans but can be lethal myelin is seen in the major form of cere- compared with that in normal mice. to other organisms. When C. violaceum bral palsy that affects premature infants Testing also showed that, in humans, Tcf4 reaches a certain growth level, the colony with brain injury. Eventually, unprotected protein is found in areas damaged by MS produces an easily detectable purple dye. nerve cells die. New evidence from HHMI but not in healthy myelin. Furthermore, the The bacteria rely on an autoinducer called investigator David H. Rowitch suggests researchers discovered that many Wnt acyl-homoserine lactone (AHL) to commu- that progression of multiple sclerosis pathway signaling molecules are over- nicate their population density. involves not only initial myelin damage but active in patients with MS. The results Previously, Bassler had screened thou- also inhibition of the body’s normal myelin appear in the July 1, 2009, issue of Genes sands of chemicals to ﬁnd one that would repair mechanism. & Development. Omikron / Photo Researchers, Inc.

40 HHMI BULLETIN | November 2oo9 Starving for GABA A SMALL CHEMICAL IN THE BRAIN IS THE DIFFERENCE BETWEEN EATING AND WASTING AWAY.

Control of feeding behavior and body weight is a complicated busi- tively killing the AgRP/NPY ness. The field has been dominated by studies investigating the role neurons, Palmiter and of hormones and neuropeptides for the last 15 years. Yet the roles of colleagues observed that the glutamate and GABA, two major neurotransmitters in the brain, activity of many postsynaptic have been largely ignored. But now, HHMI investigator Richard neurons, in an area of the Palmiter has shown that GABA plays a critical role in maintenance brain called the parabrachial of feeding behavior. nucleus, was greatly elevated. A group of neurons in the arcuate nucleus, a part of the brain’s They postulated that the hypothalamus, has long drawn the attention of scientists looking for sudden loss of GABA from Whether or not a mouse eats food the neural circuits that control eating. These neurons synthesize AgRP/NPY neurons was placed in front of it depends on a protein messengers that promote eating, called agouti-related responsible and showed that complex circuit in the brain. peptide (AgRP) and neuropeptide Y (NPY). Though these peptides they could prevent starvation were strong candidates for eating regulators, there was a hitch: by supplementing mice with a drug that activates GABA receptors. animals without them eat normally. Yet killing the neurons that Conversely, blocking GABA receptors there led normal mice to starve. make them induces starvation; mice won’t even consume food put Although it’s unclear how hyperactivity in the parabrachial nucleus directly into their mouths. “So the neurons must be making some- halts eating, the results reveal a pathway critical for food consumption, thing that’s critical, and it’s probably not AgRP or NPY,” says one that Palmiter will further delineate by identifying the transmitters Palmiter, at the University of Washington. involved in activating the nucleus and the targets of the parabrachial In a series of experiments published in Cell on June 26, 2009, the nucleus. Judging by how quickly appetites can be suppressed, he may authors fingered GABA, a neurotransmitter that inhibits neuronal not have to look far. “I think this is a pretty short circuit,” he says. “But activity throughout the brain, as the missing ingredient. After selec- that would just be my gut feeling.” W –MICHELE SOLIS

IN BRIEF

IMMUNE SYSTEM OVERDRIVE normally, but when Veillette looked at diverse clinical disorders, including sickle Natural killer cells find and destroy natural killer cells from them, he discov- cell anemia. abnormal cells in the body, playing an ered something odd. The natural killer cells In 2001, Lifton discovered a pathway important role in preventing cancers. The could destroy some types of cancer cells that helps control blood pressure. Since pathway of molecules that allows them to but not cancerous blood cells. The results, then, as his group investigated the key do this, however, has not been fully eluci- which appear in the September 2009 issue players in the pathway—protein kinases dated. Now, HHMI international research of Nature Immunology, suggest that, called WNKs—they found that the WNKs scholar André Veillette has put one piece without SAP, natural killer cells don’t are involved in orchestrating the ﬂow of of the puzzle into place, by identifying a recognize damaged blood cells, allowing chloride ions in and out of cells. molecular switch that tells natural killer them to pile up. The standard treatment To explore this pathway, Lifton’s lab cells to attack. for XLP is bone marrow transplantation, group at the Yale School of Medicine used The results explain how a healthy and that’s unlikely to change, Veillette says. new tools of quantitative phosphopro- immune system works and give a better However, he thinks future research on teomics to identify key sites on chloride understanding of a rare genetic disease: SAP-related molecules could point toward cotransporters. These sites are phosphory- X-linked lymphoproliferative disease better therapies for other viral infections or lated under resting conditions, which (XLP), which causes the immune system autoimmune diseases. keeps the transporters inactive, but are to go into overdrive, making normally mild rapidly dephosphorylated in low-salt envi- viral infections fatal. In the late 1990s, MANAGING SALT ronments, activating transport. This phos- researchers discovered that a mutation in Researchers led by HHMI investigator phorylation depends on WNK activity, the an immune system protein called SAP Richard P. Lifton have uncovered clues to team concludes in the August 7, 2009, caused XLP. SAP mutations lead to defects how cells manage their delicate interior issue of Cell. With further research, they in many types of immune cells, including balance of salts and water and how that hope to reveal just how the pathway works. natural killer cells, the researchers found. affects cell volume. Too much salt inside a Veillette, based at the Clinical Research cell causes water to rush in, potentially RANKING SPECIES WITH GOOGLE Institute of Montreal and the University of bursting the cell, whereas too little salt can The same method Google uses to rank Montreal, decided to probe these ﬁndings make a cell shrivel up and die. Specialized the importance of Web pages can be further, examining just what happens to ion transporters regulate the flow of used to rank the importance of species natural killer cells when SAP is missing. He salts across a cell’s outer membrane. within an ecosystem, researchers have genetically engineered mice that lack the Abnormalities in the regulation of intracel- shown. Mercedes Pascual, an HHMI inves- SAP family of proteins. The mice developed lular chloride are believed to play a role in tigator at the University of Michigan, Phanie / Photo Researchers, Inc.

November 2oo9 | HHMI BULLETIN 41 lab book

Blue Baby Blues A CONGENITAL HEART DEFECT IS EXPLAINED BY NEW GENETIC CLUES

A deep blue tint in a newborn’s skin is the first sign that something’s linked to TOF, Seidman’s lab group hypothesized that TOF might wrong. Blood cells that should be bright red and full of oxygen, have its root in the number of copies of particular genes. This kind creating a baby’s typically rosy hue, instead lack oxygen due to a of genetic change can lead to incorrect amounts of protein being congenital heart defect. Known made by a cell. Down syndrome, one extreme example of a copy colloquially as blue baby syndrome, number variation, is caused by an entire duplicated chromosome. tetralogy of Fallot (TOF) occurs in Seidman’s team searched the genomes of 114 TOF patients and one in 3,000 live births and accounts found 11 segments of DNA that were present in too many or too few for nearly 10 percent of all serious copies. They then looked at these regions in the DNA of another congenital heart defects. Its cause 398 TOF patients and confirmed that seven of the copy number has largely been a mystery, as the variations were linked to TOF. The regions did not show incorrect parents of babies born with TOF copy number in the unaffected parents of the babies born with usually show no signs of heart defect. TOF, the scientists report in the August issue of Nature Genetics. Now, HHMI investigator Christine The team is now studying those seven regions to explore what Seidman of Brigham and Women’s particular genes may be implicated in TOF. Seidman also thinks Hospital and Harvard Medical that variation in copy number could be at play in other congenital School has found a genetic cause for heart defects, where researchers have been unable to pinpoint The x-ray of the chest of an some cases of TOF. specific mutations. infant with Fallot’s tetralogy, a congenital heart defect. After hitting dead ends when “Our work really reiterates the theme that the dosage of certain trying to pinpoint specific mutations genes is vital,” says Seidman. W –SARAH C.P. WILLIAMS

IN BRIEF

studies the tangled network of relation- investigator at Tufts University School of new strategies for targeting extracellular ships between species in a food web. To Medicine, have discovered a previously pathogens. determine how a species’ extinction unknown function of killer T cells in the would affect the rest of the web, scien- immune system. Scientists knew that killer SPOTTING OVARIAN CANCERS EARLY tists like Pascual must first rank all species T cells can attack cells that have been A new study by HHMI scientists reveals based on how codependent they are. A invaded by bacteria to thwart an infection. details on just how long early-stage ovarian postdoctoral fellow working in Pascual’s The new research shows that killer T cells tumors exist before they are detectable by lab realized that this was how Google’s can also attack cells with bacteria attached current tests. The researchers, led by HHMI “PageRank” system worked: it rates a page to their outer surfaces. investigator Patrick O. Brown at the as more important if it is linked to other Isberg’s team inoculated mice with a Stanford University School of Medicine, pages ranked important. strain of Yersinia pseudotuberculosis, a scoured existing data on ovarian tumors to Pascual’s lab group and their collabora- bacterium that attaches itself to the uncover the new statistics. tors tweaked PageRank to apply to their outside of cells in the gut. The inocu- They relied on details about ovarian ecosystem modeling. The new system lated mice had high levels of anti-Yersinia tumors discovered by chance in healthy performed better, they found, than tradi- antibodies and increased numbers of women who had their ovaries and fallo- tional algorithms. They then applied it to killer T cells—unexpected findings since pian tubes removed because they were at some real ecosystems, including the the bacteria generally live outside of high risk for cancer. Most of the tumors Chesapeake Bay and oceanic coral reefs. host cells. were microscopic and undetectable by the The researchers compared these results To investigate this finding, the scien- naked eye. None of the women showed from the new method with those calcu- tists injected weak forms of the bacteria symptoms of cancer. lated by a more computationally intensive into mice lacking killer T cells. The mice The study concluded that most ovarian method and found that it stands up well. died from this infection, whereas normal tumors exist for at least 4 years before The researchers say that this system, mice survived, suggesting that killer T cells they spread, and the typical cancer is less published online on September 4, 2009, in are vital to fighting off the infection. The than three millimeters across for most of PLoS Computational Biology, could also results were published September 4, this time. In addition, the researchers be made to analyze other biological 2009, in PLoS Pathogens. determined that these early tumors are networks, such as metabolic networks Further experiments showed that after more likely to be in the fallopian tubes within cells or interactions of cells within the killer T cells attack a cell carrying Y. than in the ovaries. The findings were organisms. pseudotuberculosis, other immune system published July 28, 2009, in PLoS Medicine. cells can engulf the dead cell and bacteria. Brown’s lab is now looking for ways to A NEW FUNCTION OF KILLER T CELLS The new mechanism sheds light on how detect such tumors earlier and intervene Researchers led by Ralph Isberg, an HHMI the immune system functions and suggests before the cancer spreads. Zephyr / Photo Researchers, Inc.

42 HHMI BULLETIN | November 2oo9 ask a scientist

Q A

Does the There are almost 28,000 species of fish balance ions and water between the in the world, more than the number of environment and the fish’s blood. anatomy of amphibian, reptile, bird, and mammal Two major osmoregulatory organs in freshwater species combined. Slightly more than fish are the gill and the kidney. Let’s focus half of these fish, including swordfish, on the gill. Both freshwater and saltwater and saltwater tuna, and angelfish live only in salt fish have specialized chloride cells in water. Another 40 percent, such as gold- their gills. These large round cells are rich ﬁsh differ? fish, guppies, and channel catfish, reside in mitochondria, to produce energy, and only in fresh water. The remaining few in ion transporters, which use that energy Eli, a high school student from Australia percent, like salmon, eel, and striped to pump salts across the membrane. In bass, can switch between fresh water marine fish, the chloride cells pump and salt water at various stages in their salts out of the gills into the surrounding life cycles. environment. In freshwater fish that are While fish have many adaptations to constantly trying to stay saltier than the their environments—such as body shape, surrounding water, however, the chloride size, and color—there are no general cells pump sodium, calcium, and chlo- anatomical differences that distinguish ride into the fish. freshwater fish from marine fish. The Which, where, and how many differences instead relate to how they ion transporters and channels are regulate water and salts in their cells. present in these chloride cells is under Ocean water has a salinity of roughly complex regulation by various genes. 35 parts per thousand (ppt), or 35 grams Expression of these genes may stay of dissolved salts per liter of water. Fresh constant throughout a fish’s life or may water varies but is usually less than 0.5 change in response to environmental ppt. However, all fish, no matter where shifts in salinity. Chloride cells in fish they live, have virtually identical salt migrating between fresh and salt water, concentrations in their blood—around for example, express different pumps in 10 ppt. Since this blood concentration the different environments. Studying falls between the salinity of salt water and what genetic makeup allows for adapta- fresh water, saltwater and freshwater fish tion to different salinity environments are constantly facing opposite osmotic will help us understand how freshwater pressures: In fresh water, the natural and saltwater fish evolved as well as tendency is for water to seep into the what mechanisms nature has selected FURTHER READING fish, and salt out. In salt water, though, for ion and water regulation, which “Why Can Some Fish Live in Freshwater, Some in Saltwater, and Some in Both?” W. A. Wurts environmental salt tends to diffuse into goes beyond fish and relates to human World Aquaculture 1998 29(1): 65 the fish and the water in the internal disease and heath.

“Molecular Biology of Major Components of fluid of the fish tends to be pushed out. Chloride Cells” S. Hirose et al. Comparative Biochemistry To adapt to these diverging physiological ANSWER RESEARCHED BY HAILI ZHANG, and Physiology Part B (2003) 136:593–620 demands, freshwater and saltwater fish postdoctoral fellow in laboratory of “Evolution of Blood Pressure Regulation differ in the function of their osmoregu- HHMI investigator David Kingsley, in Humans” J. H. Young Current Hypertension Reports (2007) 9(1):13–18 lation machinery—the organs that help Stanford University.

Science is all about asking questions, exploring the problems that confound or intrigue us. But answers can’t always be found in a classroom or textbook. At HHMI’s Ask a Scientist website, working scientists tackle your tough questions about human biology, diseases, evolution, animals, and genetics. Visit www.hhmi.org/askascientist to browse an archive of questions and answers, ﬁnd helpful Web links, or toss your question into the mix. What’s been puzzling you lately?

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Freeze Frame Cryo-EM is a way to view protein structures—now at atomic resolution—as they do their thing in the biological world. for an electron microscope, which needs a vacuum parts are made to move, and locking them into a static position gives to clear the air, water is the enemy. “It contaminates the sample, only one part of the story. Other structural biology techniques are makes the vacuum dirty, and essentially destroys the experiment,” limited in that they require dehydration, dyes, or harsh fixatives that says Nikolaus Grigorieff, an HHMI investigator at Brandeis can disrupt fragile chemical bonds. University. “Of course, in biology, water is the one substance that is Developed in the 1970s, cryo-EM has the advantage of being able present everywhere.” to preserve molecular structures in multiple states and hence to give The solution is to flash-freeze the sample and use the electron a more complete picture of a macromolecular machine in action. microscope, one of the most sensitive tools in science, to look at proteins or other biological structures trapped in a frozen matrix. In Refining Resolution electron cryomicroscopy, or cryo-EM, researchers freeze a sample It’s not easy to prepare a sample in this way, but the bigger challenge in liquid ethane so quickly that the watery environment becomes a for the cryo-EM community, says Grigorieff, has been getting to an glassy, vitreous solid before it can spoil the experiment or crystallize atomic-scale resolution of one to five angstroms (the average atom is into regular ice. The living structure is preserved whole, suspended roughly two angstroms). in time. “For a long time, people were getting around 20 angstroms reso- The technique has recently begun to achieve the degree of sensi- lution, where they might be able to distinguish different proteins but tivity that makes it useful for structural biologists who want to resolve not different amino acids within the proteins,” he says. “Then it was molecular structures at the atomic level. Increasingly, cryo-EM is six angstroms or so, which still isn’t good enough to show atomic- seen as a natural complement to—and sometimes a substitute for— level detail.” gold-standard methods such as x-ray crystallography for studying Grigorieff is intent on pushing that limit. In the rotavirus study, proteins, nucleic acids, and the complexes they form inside cells. his group achieved a resolution of about four angstroms. Grigorieff is a specialist in the field of cryo-EM. Working with There are two primary ways to get three-dimensional structures fellow HHMI investigator Stephen Harrison of Harvard Medical from cryo-EM images. Grigorieff uses an approach called single School and Children’s Hospital, Boston, he recently reported a particle reconstruction, taking two-dimensional images of thou- structural map of an outer-coat protein locked in place on an intact sands of copies of the virus particle and then averaging them with rotavirus particle (see Upfront, “Piecing Together Rotavirus’s computer algorithms into a three-dimensional picture. In the other Unique Approach”). The picture was not as detailed as Harrison’s approach, called computed tomography cryo-EM, a single molec- images of the protein captured by x-ray crystallography, but it ular structure is photographed in a series of pictures from many allowed the scientists to visualize the protein’s placement on the angles to arrive at a similar three-dimensional average, much like intact particle and infer its role in rotavirus infection. the CT-scan technology used by physicians. In both cases, the raw For almost any technique in structural biology, the trick is to images appear fuzzy, so the averaging step is key. achieve high resolution without losing the fuller picture of how a “Basically, you have a bunch of very snowy images, and then you structure looks and behaves inside a cell. That’s a big challenge for stack them up on top of each other and out comes a pattern,” says x-ray crystallographers, who must isolate, purify, and coax living Grigorieff. “When we do enough of these—100,000 or even a structures into an artificial crystalline lattice to study them. For one million—then we are suddenly able to see much more detail in the thing, crystallization is not always possible, especially for large struc- underlying pattern.” Or rather, computers see the pattern and inter- tures made of many interlocking molecules. In addition, the pret it, creating a color-mapped model that shows the orientation of crystallized form captures only one state of the structure: cellular molecules and the ways they interact with each other.

44 HHMI BULLETIN | November 2oo9 James Chen, Ethan Settembre, Scott Aoki, Xing Zhang, Richard Bellamy, Philip Dormitzer, Stephen Harrison, and Nikolaus Grigorieff. the virusisprimedfor infection. Ingreen isathird protein, VP6,found inthemiddlecoat. the viruspuncture themembranes oftarget cells, isheldincheckby theVP7 protein (gold) until proteins onthevirus’s temporary, outermost coat. The VP4spike protein (red), whichhelps This three-dimensional cryo-EM imageof a rotavirus enablesresearchers to infer therole oftwo to buildatomic models,” hesays.“Becausewenow haveproofof ofaveragingonemillion moleculesmuchtask easier,” heexplains. 20-faced solidcalledtheicosahedron. “Thesymmetrymakesthe whichhasthesamesymmetryas the rical particlelikerotavirus, structures. Ithelps,Grigorieffsays, toworkwithahighlysymmet- thousands ofpictures—andflexibleenoughtointerpretavariety of algorithms, whichmust bepowerful enoughtoanalyzeallthose “The rotavirus workshowed thatwecangetsufficient“The rotavirus resolution Grigorieff spendsmuch ofhistimecreatingandrefining those – GOFORTH SARAH messenger RNAintoamorereadable form. as thespliceosome,astructure made of150orsoproteins thatedits Eventually, cellularbehemoths such Grigorieffwouldliketotackle able togetsimilar resolutionwithmoredifficult samples.” concept …wehavemoreconfidencethatwilleventually be of rotavirus. of rotavirus. WEB EXTRA: www.hhmi.org/bulletin/nov2009

Visit theonline Bulletin to learn more about Grigorieff’s cryo-EMimages to learnmoreaboutGrigorieff’s November 2oo9 W

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BULLETIN 45 46 HHMI ROBERTIS American Society of HumanGenetics. won the2009CurtSternAward fromthe the University Cruz, ofCalifornia, Santa HHMI investigator stem cellresearch. Senateontestimony totheUnited States ety’s publicpolicycommittee andhasgiven Biology. Goldstein isamember ofthesoci- Award fromtheAmericanSociety forCell San Diego,wonthe2009PublicService investigator attheUniversity ofCalifornia, LAWRENCE S.B.GOLDSTEIN malaria. drug-resistant world’s topexpertsonthecharacterizationof Francophone world.Djimdéisoneofthe France tothetoppharmacist inthe by TheNationalAcademyofPharmacy Pharmacie Francophone,” aprizeawarded Bamako inMali,wonthe2009“Prixdela tional researchscholarattheUniversity of ABDOULAYE DJIMDÉ HHMI investigator tiation inearlyembryos. Scotland. DeRobertisstudies celldifferen- this yeartookplaceinEdinburgh, Biology,Society ofDevelopmental which years attheCongressofInternational Prize. Theprizeisawarded everyfour Los Angeles,wonthe2009RossHarrison SPOTLIGHT nota bene BRIAN DRUKER Druker andSawyersWin LaskerAward

BULLETIN of theUniversity ofCalifornia,

November 2oo9 DAVID HAUSSLER , anHHMIinterna- EDWARD M.DE CHARLES SAWYERS , anHHMI , of KATHERINE A.HIGH study thesequence. sequence andasetoftoolsresearchersuseto acompletedhumangenomecontains Genome Bioinformatics website,which Cruz, fortheir developmentoftheUCSC also oftheUniversity ofCalifornia, Santa Haussler sharestheaward withJamesKent, regulation ofgeneexpressionin plants. plant biology. Jacobsen studies epigenetic a youngscientist forpioneeringresearchin Award. TheShullAward isgivenannually to Los Angeles,the2009Charles Albert Shull investigator attheUniversity ofCalifornia, awarded The AmericanSociety ofPlantBiologists Society ofLondon. was electedasaforeign membertothe Royal the MassachusettsInstituteofTechnology HHMI investigator ited eyedisease. Leber’s amaurosis,arareinher- congenital their workdevelopingagenetictreatmentfor both attheUniversity ofPennsylvania, for award withJeanBennettandAlbert Maguire, Ronald McDonaldHouse.Shesharesthe Award ofExcellencefromthePhiladelphia Philadelphia, wonthefirst Audrey E.Evans gator attheChildren’sof Hospital STEVEN E.JACOBSEN and publicservice. the categories ofbasicmedicalresearch, clinicalmedicalresearch, cancer to amanageableone. The Lasker Awards are given annuallyin discoveries changedchronic myelogenous leukemia from afatal some patientsare resistant to thedrug.The researchers’ combined Gleevec, whileSawyers’ work was instrumental inunderstanding why Novartis AG. Druker’s andLydon’s research ledto thedevelopment of kemia. Alsosharingtheaward was NicholasB.Lydon, formerly of for theirwork onGleevec, atreatment for chronic myelogenous leu- Medical Research Award from theAlbertandMaryLasker Foundation Cancer Center, were awarded the2009Lasker-DeBakey Clinical University, and HHMI investigators H. ROBERTHORVITZ , anHHMIinvesti- Charles L.Sawyers , anHHMI Brian J. Druker of during embryonic development. studies how neuronsbecomespecialized neurons inthebrain,andYuh NungJan sium channelsregulatethesignalingof of neuroscience. LilyJanstudies how potas- honors outstandingcontributionstothefield prize, givenbytheSociety forNeuroscience, Gerard PrizeinNeuroscience. Theannual San Francisco, sharethe2009RalphW. HHMI investigator logical processes. blood pressure,amongmanyotherphysio- chemical signalsregulatingheartrate and for hisresearchonreceptorsthattransmit Achievement Award. Lefkowitz waschosen of theAmericanHeartAssociation Research gator atDukeUniversity, isthe2009recipient elected tothe Association ofAmerican University ofCalifornia, SanFrancisco, was NUNG JAN HHMI investigator of thebody. breast andlungcancersspreadto otherparts chosen forhisbodyofworkstudyinghow in thebiomedicine category. Massaguéwas Frontiers ofKnowledge andCultureAward Center, wonthefirstBBVA Foundation the MemorialSloan-KetteringCancer HHMI investigators ROBERT J. LEFKOWITZ , ofMemorial-SloanKettering , ofOregon Health&Science of theUniversity ofCalifornia, LOUIS J. PTÁC JOAN MASSAGUÉ IL Y J N JA Y. LY LI , anHHMIinvesti- ˇ and EK of the YUH , of

Druker: Courtesy of OHSU Sawyers: Liz Baylen / PR Newswire, ©HHMI Fuchs: Courtesy of Rockefeller University Friedman: Robert Reichert gator attheUniversity ofWashington School to sensoryexperiences. studies how theactivityofbraincircuits leads National Autonomous University ofMexico, Institute ofCellularPhysiologyatthe MICHAEL N.SHADLEN HHMI investigator rhythms offruitflies. University fortheir workonthecircadian and MichaelYoung ofTheRockefeller with JeffreyHalloftheUniversity ofMaine Gruber Foundation. Hesharestheaward Neuroscience PrizeofthePeter andPatricia at Brandeis University, received the2009 MICHAEL ROSBASH scholar awarded toHHMIinternationalresearch Argentine Society forNeurochemistry was The 2009RanwellCaputoAward fromthe basis ofparalysisdiseases. Physicians inApril.Ptác alter the state ofcells. alter thestate theepigenomeand molecules thattarget istry. Schreiber’s researchfocusesonsmall has madeoutstandingcontributionstochem- biannual award recognizes ascientist who Chicago’s DepartmentofChemistry. The 2010 WhelandMedalfromtheUniversity of of HarvardUniversity, received the2009– SPOTLIGHT research inmedicalscience. ally by Keio University, inJapan,for outstanding decrease appetite. The Keio Prize isgiven annu- found thatleptinrewires neurons inthebrain to animal to search for food. Inobesemice, he leptin concentrations fall andthiscausesthe discovered that whenananimallosesweight, cule linked to appetite andobesity. Friedman Rockefeller University, studies leptin,onemole- food intake andbodyweight. Friedman,ofThe nition ofhisresearch onhormonesthatregulate HHMI investigator The 2009Keio Science Prize was awarded to Keio PrizeGoestoFriedman RANULFO ROMO STUART L.SCHREIBER , anHHMIinvestigator ˇek studies thegenetic ˇek , anHHMIinvesti- Jeffrey M.Friedman . Romo,ofthe , diver HHMI-supported undergraduateandNCAA neural science. outstanding researchcontributionsto Kavli InstituteforBrainScience for Department ofNeuroscience andThe College ofPhysicians andSurgeons given annually bytheColumbiaUniversity Spencer Award. TheSpencerAward is of Medicine, wonthe2009W. Alden awarded the2009Walter ByersPostgraduate the University ofArizonainMay, was in recog- SPOTLIGHT deemed outstanding intheirﬁelds. as aPresidential Award to begiven to scientists established theNationalMedal ofScience in1959 defective stem cells cancausecancer. Congress inroads into understanding hairgrowth andhow become skinorhair. Herwork hasalready made of how askinstem cell chooseswhetherto skin stem cells. Shehopesto unravel thequestion distinct structures thatdevelop from thesame skin diseases.Fuchsstudies skinandhair—two honored for herresearch onmammalian skinand nation’s highest honorfor science. Fuchswas scientists were alsopresented medals—the at aceremony attheWhite House. Eightother Medal ofScience from President Barack Obama Rockefeller University, received theNational Elaine Fuchs Fuchs Awarded MedalofScience CRAIG SHEEDY JEFFREY FRIEDMAN , anHHMIinvestigator atThe , whograduatedfrom Louisiana State University,Louisiana State and science. scientific achievementsandhisleadershipin America 2009PresidentialAward forhis the Society ofChineseBiochemists in ANDRÉ VEILLETTE HHMI President of Medicine. attending theVanderbilt University School postgraduate education.Sheedyisnow college athleteinthecountrytofundtheir annually toonemaleandfemale arship, character,andleadershipisgiven Scholarship. Thisnationalaward forschol- class ofAmericanChemical Society Fellows. the 162scientists namedtotheinaugural HHMI professors immune cells. studies theactivationanddifferentiation of immunologist workinginCanada.Veillette annual award recognizes anoutstanding Canadian Society forImmunology. This 2009 BernhardCinaderAward ofthe Research InstituteofMontreal,received the tional researchscholarattheClinical ZARE , of Stanford University,, ofStanford wereamong November 2oo9 ELAINE FUCHS ROBERT TJIAN ISIAH M.WARNER , anHHMIinterna-

HHMI RICHARD N.

BULLETIN received , of 47 CONTINUED FROM PAGE 17 clock brainwave monitoring and magnetic resonance imaging for (THE MOST VULNERABLE PATIENTS) premature infants. With these tools, doctors and researchers are the chance of losing a baby can be as high as 80 percent in areas developing and testing supportive therapies for the most vulner- of the world where NICUs are lacking, and most babies who do able babies’ brains. survive will have long-term mental and physical disabilities. “These are the hardest patients, the ones with neurological “For a woman, that is like being told she has metastatic cancer. injuries. It’s extremely hard to see what families go through and to She’s willing to try anything to save her baby’s life,” Karumanchi routinely have to tell them there are no therapies available,” says says. A therapeutic agent that could prolong her pregnancy by Rowitch. “One way for doctors and nurses to combat emotional even a few weeks would increase the odds dramatically—babies exhaustion is by thinking toward the future. For me, that’s working born after 28 weeks have a greater than 90 percent chance of on a neuroprotective strategy for these very premature babies.” survival, with fewer complications. Rowitch now cares for babies born too soon in a new unit at

UCSF, the Neurointensive Care Nursery, which opened in April WEB EXTRA: To read about an HHMI professor’s efforts to refine inexpensive incubators, 2008. The nursery is the only one in the country with round-the- and to hear her describe her students’ work, visit: www.hhmi.org/bulletin/nov2009.

CONTINUED FROM PAGE 29 helices can stretch a little bit, and if they’re in a thin spot, the (MEMBRANE AWAKENING) helices will condense. probe the membrane as a complete system, rather than as isolated “That is just a theory, and using aquaporins we can actually proteins. “The single molecule approach will always be there, measure whether this is happening or not,” says Walz. By doing that’s essential,” Groves says, “but we’re starting to have tools to crystallography of aquaporins while they’re embedded in the go after the collective as well. We want to see the forest and the membrane, as he and Gonen did for the AQP-0 structure, Walz trees both.” can see how the structure changes in membranes of varying widths. Harvard’s Walz shares this view. He has moved from studying Innovative experiments like this, membrane scientists agree, the structure of aquaporins to looking at the broader view—probing will answer the questions raised by a decade of structural work. how the channels interact with the membrane around them. “It’s a little like the stage of biology back when collectors were His lab has been testing the theory that helix-shaped parts that going out and collecting things and sending them back to exist in many membrane proteins, including aquaporins, can museums,” says Rod MacKinnon. “We have a large collection adjust to the bilayer surrounding them by expanding and now. Which means we have to start figuring out the logic to how contracting like a spring. If they’re in a thick lipid membrane, the this all fits together.” W

CONTINUED FROM PAGE 33 Bauer says he would like to be a teacher some day and will use (ENHANCING TA PERFORMANCE) what he learned in White’s class. “He pushed the boundaries of chemistry lab at the university, which is consistently among the what else we could try [in class] and helped us get out of our 10 schools with the largest number of undergraduate chemistry comfort zones. I think it’s a good jumping off point,” Bauer says. and biochemistry majors in the country. Introductory classes are That’s what White hopes these biology and chemistry TAs often packed with 2,200 or so students each fall. The training learn: teaching well is a constant learning experience. In the rush helped him overcome his initial nervousness, and the support to get into graduate school, most graduate students haven’t spent structure was important when he encountered his first major time thinking about teaching, he says, and TA training can be the problem in the lab. first step toward becoming a great teacher one day—whether his In that instance, a nontraditional student in his 70s wasn’t students become professors or not. “It doesn’t come easily—and working well with the other students, most of them just 18, and it doesn’t happen in one semester.” W he ended up being a burden to his lab mates. Bauer brought the problem to his TA training class. After much discussion, they

concluded it might be best for the older student to rotate to a WEB EXTRA: Visit www.hhmi.org/bulletin/nov2009 to see an audio slideshow of a new different lab group each week. “I implemented that change in the TA as he prepares for his first time teaching a University of Delaware lab and an audio lab and it seemed to work,” he says. slideshow of Catherine Drennan’s MIT training class on diversity.

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48 HHMI BULLETIN | November 2oo9