HHMI

BULLETIN February ’06 Vol. 19 • No. 01

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Howard Hughes Medical Institute

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www.hhmi.org ields L ab Courtesy of F

The thousands of interactions that take place between proteins Mapping How Parasite of the malaria-causing parasite Plasmodium falciparum are being tracked and mapped in the University of Washington laboratory of HHMI investigator Stanley Fields. In this depiction, Proteins Relate individual proteins are indicated by pink circles and the interactions by the lines that connect them. Understanding how the proteins relate to each other may illuminate vulnerabilities in the parasite’s defenses (see pG. 49).

nonprofit org. us postage paid 4000 Jones Bridge Road Hyattsville, md Chevy Chase, Maryland 20815-6789 permit no. 61 www.hhmi.org Change Service Requested A Cell’s

vol. 19 / no. Can a cell’sS developmentalecond Ahistoryct be erased, giving it a fresh start toward a new destiny?

01 01 IN THIS ISSUE: AFTER KATRINA / MICROSCOPY AT JANELIA / JOAN STEITZ major pursuitatJanelia Farm. methods suchasthisonewillbea Development ofinnovative imaging are labeledred, green, andyellow. mouse of anewborn bral cortex individual neurons from thecere - label intosinglecellsinvivo. Here, a geneticchangeandfluorescent Luo cansimultaneously introduce markers), HHMI investigator Liqun (mosaic analysiswithdouble Using amethodtermedMADM pg. 30

Courtesy of Liqun Luo; reprinted from Cell 121:479-492, with permission from Elsevier. © 2005.

Leif Parsons I Neur Te especially functionalimaging, work now proceeding inthe of clinicaldeath. With its accesstoimproving technologies, implications oflife-extending modalities for the definition technologicalcapabilities suchasthe attention becauseofnew approach. In the early days of bioethics, many issues attracted casethatobligea novelpeculiar aspectsofaparticular analytic issues cometowidespread awareness, itismainly becauseof To theextentthatthere isanappearanceofnovelty asethical conceptual schemestobeconsidered andrevised orreformed. precursors and therefore analogies to be drawn and prior Ethical problems seemnever there tobewhollynew; are always OBSERVATIoNS n Mo rm o s cience s r al

work inmoral aswell asscientificterms. increasingly bechallengedto explainthesignificanceoftheir colleagues innuclearphysicsandgenetics.Neuroscientists will ofpublicattentionpreviouslyof thesort experienced by their willfindthemselves thesubjects those engagedintheseefforts neurosciences provides richground forsuchcases.Many of Virginia andafellow attheCenter forAmerican Progress. Professor anddirector oftheCenter forBiomedical Ethics attheUniversity of A memberofHHMI’s BioethicsBoard, Advisory Jonathan Moreno istheKornfield here ofthepublisher, withpermission Indiana University Press. Bioethics, by Jonathan D.Moreno. ©2005by Jonathan D.Moreno. Reprinted From the bookIs There an Ethicist inthe House? On the Cutting Edge of vo1. 19 / february ’06 no. 01 3 36 51 departments President’s Letter Perspectives and Opinions Chronicle: In Memoriam Working backward to move forward Jeff Lichtman, Eric Betzig, and Q&A Lawrence C. Katz

4 42 52 Centrifuge Chronicle: Science Education Chronicle: Up-Close Nobelist’s cathedral of dreams / Hearing-impaired med student aims to Scientists crack code for motor What’s on your iPod? / A family’s enhance cochlear implants / Loudoun neuron wiring penchant for plants / From dropout County preschoolers indulge curiosity / to medical student Students captivated by evolution- religion debate

7 44 54 Upfront Chronicle: Institute News Chronicle: Nota Bene Split frog embryo yields twins— Science is a global enterprise / Craig News of recent awards and other nota- and knowledge / Dopamine’s role named General Counsel / HHMI ble achievements in depression, addiction / Today’s enters into agreements on mice / mouse models Partnership with Science sealed / Nurse elected Trustee

48 Inside Back Cover Chronicle: Lab Book Observations Cancers use “cellular bookmarks” / Neuroscience in moral terms Protein-pairing method may yield new drug targets / The immune system: imaged at last features 14 20 24 30

A Cell’s Second Act Trailblazer Turned A Way Station Optical [cover story] Superstar After Katrina Aspirations Researchers set out to understand Joan Steitz started up the scientific HHMI responds to help Xavier At Janelia Farm, researchers nuclear reprogramming to revert ranks when few women did. University retain its displaced will link mathematics, physics, adult cells to medically useful Today, Nobel laureates laud her faculty, support their professional engineering, and computing in the embryonic stem cells. research and scores of scientists growth, and ultimately benefit pursuit of better cellular pictures. praise her mentoring acumen. students.

WWW.HHMI.ORG/BULLETIN Visit the Bulletin Online for additional content and added features. Cover image: Jason Holley contributors president’s letter

(1) Working Backward to Move Forward (2) (3) Dan Ferber is a freelance journalist based in Indianapolis and a contributing correspondent for more than 20 years at the university of colorado, I spent for Science, where he covers biology, biotechnology, and biomedical research. His stories many hours in the classroom, sharing a lifelong interest in about science, technology, and medicine have also appeared in Reader’s Digest, Popular Science, New Scientist, and other magazines. In his former life as a microbiologist, he biochemistry with undergraduate and graduate students. Yet, like many of my colleagues, I may have tackled my teaching peered through many a microscope. (1) assignment from the wrong direction. I went forward when I Author of Alternative Treatments for Arthritis: An A to Z Guide (Arthritis Foundation, 2005) and should have been going backward—at least that’s the conclu- a contributing editor for Health and Arthritis Today magazines, Dorothy Foltz-Gray is currently (4) sion I’ve drawn after reading a handbook on “scientific teaching” writing a memoir about being and losing a twin, entitled With and Without Her. (2) written by an HHMI Professor. Richard Saltus is a science writer and editor at the Dana-Farber Cancer Institute in Boston. As Jo Handelsman and her colleagues at the University of He has been a staff science and medical writer for the Boston Globe, San Francisco Examiner, Wisconsin–Madison point out in their handbook, Scientific “We need to think broadly about how and Associated Press in Los Angeles. Saltus is a frequent contributor to the HHMI Bulletin, Teaching: A Guide to Transforming Undergraduate Biology we structure science education, with and his freelance articles have also appeared in The New York Times, Science, Popular Science, Education, the idea is deceptively simple: Decide what you Science Digest, Harvard School of Public Health Review, and Boston Globe Magazine. (3) want students to understand and determine how you will assess two goals in mind: generating a cadre A freelance education writer and editor based in Rockville, Maryland, Judy Saks was an whether they do, in fact, understand the material before deciding of creative scientific thinkers as well as education reporter for the Boston Globe and a senior editor of The American School Board how to teach it. In my experience, “backward design”—Grant an educated citizenry. Journal. When not at her keyboard, Saks enjoys such endeavors as teaching summer work- Wiggins and Jay McTighe coined the memorable description in shops for young writers and moderating focus groups on adult education issues. (4) 1998—is rare. Certainly, I wasn’t alone in first choosing a text- thomas cech book, deciding the order in which to cover the chapters, and ” seeing when and where I could fit in some demonstrations or well as an educated citizenry. When we choose those measurable experiments to enhance the course—without considering the results, applying the rubric of backward design, it becomes clear HHMI TRUSTEES HHMI OFFICERS impact the course would have on the same students a year later. that we must rethink the nation’s approach to science education. James A. Baker, III, Esq. Thomas R. Cech, Ph.D. / President Since the grants program commenced in 1988, HHMI A working paper issued by the National Bureau of Senior Partner / Baker & Botts Craig A. Alexander / V.P. & General Counsel has invested more than $1.4 billion in a variety of educa- Economic Research, which pulled together data from a variety Richard G. Darman Peter J. Bruns, Ph.D. / V.P. for Grants & Special Programs tional programs, among them the HHMI Professors initiative of sources, is illustrative. The demographics of U.S.-trained Partner / The Carlyle Group David A. Clayton, Ph.D. / V.P. & Chief Scientific Officer pioneered by Handelsman and 19 other teacher-scholars. Ph.D.s in science and engineering have changed substantially Chairman of the Board / AES Corp. Joseph D. Collins / V.P. for Information Technology Our efforts have ranged from research fellowships for medical over the past 40 years. On the positive side, more women and Frank William Gay Joan S. Leonard, Esq. / Senior Counsel to the President Former President & CEO / SUMMA Corporation Avice A. Meehan / V.P. for Communications & Public Affairs students and new graduate training programs to research expe- minorities are pursuing careers in science, but, on the negative, riences for undergraduates and outreach programs for K–12 the percentage of U.S. citizens receiving Ph.D.s has dropped Joseph L. Goldstein, M.D. Edward J. Palmerino / V.P. for Finance & Treasurer Professor & Chairman, Department of Molecular Genetics Gerald M. Rubin, Ph.D. / V.P. & Director, Janelia Farm Research Campus students. HHMI and its grantees now have considerable significantly. In 1966, 71 percent of Ph.D. graduates in science University of Texas Southwestern Medical Center at Dallas Landis Zimmerman / V.P. & Chief Investment Officer knowledge of what works and what doesn’t, and we’re placing and engineering were men born in the United States, 6 percent Hanna H. Gray, Ph.D., Chairman a renewed emphasis on extending the reach of our programs. were U.S.-born women, and 23 percent were foreign-born. By President Emeritus & Harry Pratt Judson HHMI BULLETIN STAFF But because we’re scientists, we’re also experimenting— 2000, the statistical picture had shifted: 36 percent of all science Distinguished Service Professor of History / The University of Chicago Mary Beth Gardiner, Stephen G. Pelletier / Issue Editors experimenting with a variety of approaches to engage the commu- and engineering Ph.D.s were U.S.-born men, 25 percent were Garnett L. Keith Cori Vanchieri / Story Editor nity in high-impact teaching. Right now, we’re in the midst of U.S.-born women, and 39 percent were foreign-born. SeaBridge Investment Advisors, L.L.C. Dean Trackman, Maya Pines / Contributing Editors evaluating applications for the second group of HHMI Professors, The recent Summit on National Competitiveness— Former Vice Chairman & Chief Investment Officer Jim Keeley / Science Editor The Prudential Insurance Company of America and I’m struck by the number of accomplished research scientists convened by U.S. Reps. Frank Wolf (R-Virginia), Sherwood L. Jennifer Donovan / Education Editor Jeremy R. Knowles, D.Phil. Patricia Foster / Associate Director of Communications for Web & Special Projects who have applied. We’re committed to the broad dissemination of Boehlert (R-New York), and Vernon J. Ehlers (R-Michigan)— Dean Emeritus & Amory Houghton Professor of Additional ContrIButors their experiments in education. In another initiative, HHMI and was spurred by an outcry from corporations both large and Chemistry & Biochemistry / Harvard University Cindy Allen, Laura Bonetta, Cay Butler, Steven Marcus, the journal Science have begun a collaboration that will bring small about the dearth of well-trained scientists and engineers. William R. Lummis, Esq. Kathy Savory, Katherine Wood information about innovative teaching approaches directly to The summit has called for nothing less than a transformation Former Chairman of the Board of Directors & CEO VSA Partners, NYC / Concept & Design The Howard Hughes Corporation scientists. In January 2006, the editorial staff at Science began of the U.S. educational system. High on the list is a doubling Paul M. Nurse, Ph.D. producing a monthly section about education. We hope it will of the number of undergraduate degrees in science and mathe- President, The Rockefeller University HHMI engage a broad array of scientists—beyond the life sciences and matics to 400,000 a year by 2015. It’s a tall order, particularly Kurt L. Schmoke, Esq. howard hughes medical institute beyond colleges and universities—with a lively selection of articles in an era when many technical jobs are being exported overseas Dean / Howard University School of Law Telephone (301) 215.8855 • Fax (301) 215.8863 • www.hhmi.org intended to pique interest and spark discussion. and federal research funding is being reduced. By defining the Anne M. Tatlock © 2006 Howard Hughes Medical Institute The challenge, of course, goes beyond how an individual goal—and working backward—the nation may, with contribu- Chairman & CEO / Fiduciary Trust Company International professor structures a course or even how an individual college tions from organizations like HHMI, move forward. The opinions, beliefs, and viewpoints expressed by authors in the HHMI Bulletin do not necessarily reflect the opinions, beliefs, viewpoints, or university organizes its science curriculum. In fact, we need to or official policies of the Howard Hughes Medical Institute. think broadly about how we structure science education, with two Paul Fetters Paul Ferber: Foltz-Gray: Foltz-Gray Courtesy of Dorothy Courtesy Ferber of Dan Saltus: Saks: Saltus Courtesy of Richard Saks Courtesy of Judy goals in mind: generating a cadre of creative scientific thinkers as

2 hhmi bulletin | February 2006 February 2006 | hhmi bulletin 3 president’s letter

Working Backward to Move Forward

for more than 20 years at the university of colorado, I spent many hours in the classroom, sharing a lifelong interest in biochemistry with undergraduate and graduate students. Yet, like many of my colleagues, I may have tackled my teaching assignment from the wrong direction. I went forward when I should have been going backward—at least that’s the conclu- sion I’ve drawn after reading a handbook on “scientific teaching” written by an HHMI Professor. As Jo Handelsman and her colleagues at the University of Wisconsin–Madison point out in their handbook, Scientific “We need to think broadly about how  Teaching: A Guide to Transforming Undergraduate Biology Education, the idea is deceptively simple: Decide what you we structure science education, with want students to understand and determine how you will assess two goals in mind: generating a cadre whether they do, in fact, understand the material before deciding of creative scientific thinkers as well as how to teach it. In my experience, “backward design”—Grant Wiggins and Jay McTighe coined the memorable description in an educated citizenry.

1998—is rare. Certainly, I wasn’t alone in first choosing a text- thomas cech book, deciding the order in which to cover the chapters, and ” seeing when and where I could fit in some demonstrations or well as an educated citizenry. When we choose those measurable experiments to enhance the course—without considering the results, applying the rubric of backward design, it becomes clear impact the course would have on the same students a year later. that we must rethink the nation’s approach to science education. Since the grants program commenced in 1988, HHMI A working paper issued by the National Bureau of Economic has invested more than $1.4 billion in a variety of educational Research, which pulled together data from a variety of sources, programs, among them the HHMI Professors initiative pioneered is illustrative. The demographics of U.S.-trained Ph.D.s in by Handelsman and 19 other teacher-scholars. Our efforts have science and engineering have changed substantially over the ranged from research fellowships for medical students and new past 40 years. On the positive side, more women and minori- graduate training programs to research experiences for under- ties are pursuing careers in science, but, on the negative, the graduates and outreach programs for K–12 students. HHMI percentage of U.S. citizens receiving Ph.D.s has dropped signifi- and its grantees now have considerable knowledge of what cantly. In 1966, 71 percent of Ph.D. graduates in science and works and what doesn’t, and we’re placing a renewed emphasis engineering were men born in the United States, 6 percent were on extending the reach of our programs. U.S.-born women, and 23 percent were foreign-born. By 2000, But because we’re scientists, we’re also experimenting— the statistical picture had shifted: 36 percent of all science and experimenting with a variety of approaches to engage the commu- engineering Ph.D.s were U.S.-born men, 25 percent were U.S.- nity in high-impact teaching. Right now, we’re in the midst of born women, and 39 percent were foreign-born. evaluating applications for the second group of HHMI Professors, The recent Summit on National Competitiveness—convened and I’m struck by the number of accomplished research scientists by U.S. Reps. Frank Wolf (R-Virginia), Sherwood L. Boehlert who have applied. We’re committed to the broad dissemination (R-New York), and Vernon J. Ehlers (R-Michigan)—was spurred of their experiments in education. In another initiative, HHMI by an outcry from corporations both large and small about the and the journal Science have begun a collaboration that will bring dearth of well-trained scientists and engineers. The summit has information about innovative teaching approaches directly to called for nothing less than a transformation of the U.S. educa- scientists. In January 2006, the editorial staff at Science began tional system. High on the list is a doubling of the number of producing a monthly section about education. We hope it will undergraduate degrees in science and mathematics to 400,000 a engage a broad array of scientists—beyond the life sciences and year by 2015. It’s a tall order, particularly in an era when many beyond colleges and universities—with a lively selection of articles technical jobs are being exported overseas and federal research intended to pique interest and spark discussion. funding is being reduced. By defining the goal—and working The challenge, of course, goes beyond how an individual backward—the nation may, with contributions from organiza- professor structures a course or even how an individual college tions like HHMI, move forward. or university organizes its science curriculum. In fact, we need to think broadly about how we structure science education, with two

Paul Fetters Paul goals in mind: generating a cadre of creative scientific thinkers as

February 2006 | hhmi bulletin  centrifuge

Nobelist’s that graced the church before, and when you enter, it’s full of light.” Another special feature is its cupola, which Blobel compares to the Duomo Cathedral in Florence. “Now the next generation too can love this skyline along a bend in the “They stayed true Günter Blobel saw a 60-year-old dream Elbe,” he says. come true this past October 30: the They’ll have at least one more reason to the baroque reopening of an 18th-century baroque to love it. Although the original Frauenkirche architecture—not cathedral he had first admired just 2 days was not built as a concert hall, its superb polluting it with before it was reduced to rubble during the acoustics drew legendary musicians, final European air raids of World War II. including Johann Sebastian Bach and additions from  Dresden’s Frauenkirche, or Church Richard Wagner. the 19th or 20th of Our Lady, with its cupola, turrets, and Apparently, that quality has been centuries—and did enormous stone dome, had been consid- restored as well. After returning to Dresden ered an architectural masterpiece and an to attend a concert of the New York a wonderful job. essential part of the city. But it lay in ruin Philharmonic on November 17, part of for decades. an extended celebration of the church’s ” When Blobel, an HHMI investigator at reconsecration, Blobel was ready to the Rockefeller University, won the 1999 pass an additional judgment: “The acoustics Nobel Prize in Physiology or Medicine, are outstanding!” –Cori Vanchieri he devoted most of his $1-million award günter blobel to rebuilding the Frauenkirche as close FOR MORE INFORMATION

To learn more about the Frauenkirche, Aidan O’Rourke to its original design as possible, and to visit http://www.frauenkirche-dresden.org/ reconstructing a Dresden synagogue. He also raised another $2 million in the Frauenkirche: United States for the project. The result is “better than I even expected,” he says. “They stayed true to the baroque architecture—not polluting it with additions from the 19th or 20th centuries—and did a wonderful job. Matthew Septimus

The colors are the true, vibrant colors Blobel:

 hhmi bulletin | February 2006 what’s on your ipod? Ask music lovers anywhere, and they’ll tell you the hottest gift in town is an iPod or MP3 player. That goes for HHMI investigators as well. After all, what’s a lab break for, if “I’d take my computer not a quick surf to a digital music store? to the greenhouse and Here’s what’s playing on the portable audio players of some HHMI scientists. work there. It was my Evan E. Eichler dream office. associate professor of genome sciences, university of washington school of medicine louis kunkel “At the moment, my portable MP3 player ” holds two albums from U2: Rattle and Hum and How to Dismantle an Atomic Bomb. There are a few odds and ends, too, including songs by AC/DC, Merle Haggard, and Tom Petty & The Heartbreakers.” Botanical Bloodline Dianne K. Newman In the midst of the civil war, President Abraham Lincoln created the National Academy of associate professor of geobiology, Sciences (NAS) as an honorific society of prominent scientists who would—and still do— california institute of technology advise the federal government on matters of science and technology. “On my iPod, there’s everything from merengue (Juan Luis Guerra) and opera Newly elected members by long tradition have penned their signatures in a large book (Jessye Norman) to tango (Astor Piazolla) that resides in the NAS building on the mall in Washington, D.C. In 1991, when HHMI and rap (C&C Music Factory). There’s investigator and Harvard geneticist Louis M. Kunkel was inducted and signed the volume, also ’80s music (Pretenders, U2, David he leafed through it in search of family. Bowie), Latin pop (Chi-Chi Peralta, Ana “I found my dad’s signature,” he says. That would be Henry George Kunkel, a clinical Belen, Shakira), and old classics (Frank immunologist born in 1916 and elected to the NAS in 1967. “But I couldn’t find my Sinatra). The only unifying theme is that granddad’s name.” Louis Otto Kunkel, who had a farm in Bucks County, Pennsylvania, and you can run or dance to most of them.” a lab at the Rockefeller Institute (now University) in New York City, was elected in 1932. David G. Schatz “He didn’t travel to the induction ceremony,” says Kunkel. “In those days it was a much bigger professor of immunobiology, deal to get to Washington.” yale university school of medicine Though no gene for NAS membership has yet been discovered, the three Kunkels have “I’ve got the full text of The Shadow of all shared two other traits: the drives to do outstanding science and to work the soil to bring , a bestseller in Spain by Carlos the Wind forth beautiful plants. Ruiz Zafón, the two most recent Harry “I spent hours and hours with my dad in the garden” at the family home in Yonkers, Potter books, and hundreds of classical and popular music tracks.” New York, recalls Kunkel. It had vegetables and flowers of all kinds. When Kunkel was 10 years old he began breeding irises there to obtain a variety of colors and shapes. “We had more Brenda A. Schulman than 40 varieties of irises and many more hybrids, only a few of which were kept,” he says. associate member, departments of structural His favorite was one his dad bred, nicknamed Big Blue, after its beautiful blue color and size. biology, and genetics and tumor cell biology, st. jude children’s research hospital Looking back, it was the beginning of his interest in genetics. “My iPod holds an eclectic mix of pop, jazz, Kunkel is based at Children’s Hospital Boston, where he cloned genes for muscular R&B, folk, country, and classical music. dystrophy and now studies complex traits such as human longevity and autism. He and his I listen to different genres, depending on wife and three daughters live west of the city on two acres of land, where he grows many kinds what I’m doing. One constant: I always of vegetables and flowers and continues to propagate irises—including Big Blue. He also has like a good dance beat when I’m doing 20 of the original irises he grew with his father, including a two-tone lavender iris, which came lab work or looking at crystal structures.” from his grandfather’s farm. mages

I Kunkel says one thing is still missing. “Our other house had a big greenhouse made with 32 old glass DNA sequencing plates,” he says. The plant-filled enclosure, 12 feet long and MENU Getty 8 feet high, was a treasured sanctuary. “I’d take my computer to the greenhouse and work there. It was my dream office,” says Kunkel. Has the NAS-botany gene combination been expressed in the next generation as well? There is always the possibility. Kunkel says, “My daughters have been great garden companions over Lily Lily illustration: the years and they share the same attitude toward the beauty of nature as I do.” Although they have found their own paths to take, only the future will tell whether their names will ever grace the pages of that NAS roster. Jason Grow Grow Jason There are additional tendrils of hope. “I had my sister’s teenage son in my lab two summers

Kunkel: ago—and he’s very interested in science. But alas, he isn’t very interested in flowers.”–Richard Saltus

February 2006 | hhmi bulletin  centrifuge

A Little Lab Music What a long, strange trip it’s been for Steve gave academia another—this time, highly Mickelsen, from high school dropout to 37- successful—try. year-old third-year student at the University He worked hard to overcome the dyslexia of New Mexico School of Medicine. Along by forcing himself to read. “I recognized the way, he was front man (including a brief that there was a vast resource of knowledge, stint with purple hair) for two successful entertainment, and inspiration in books,” he bands, developed into an accomplished says. “With much practice, either I learned painter, became a cardiac technician, then to overcome my obstacles or I just became a medical student, and most recently an less annoyed and more patient about them.” HHMI-NIH Research Scholar. Writing was no longer impossible, though he Mickelsen grew up in Clovis and credits computer spell-check for getting him Albuquerque, New Mexico. After struggling through college. “Writing and reading still mightily in high school, he decided to require great effort, but I can now keep up pursue music. “I wanted to go to college with most of my cohort in medical school.” and I was always interested in science,” Mickelsen’s creative side was evident in he recalls. “It’s just that schools weren’t his choice of HHMI-NIH research project really set up for me with my dyslexia.” at the National Heart, Lung, and Blood His band, The Bellyachers, got signed Institute. Working with animals, the guitarist to a record label and toured, visiting some went electric, showing that a tiny purposeful of the country’s best-known clubs— cardiac puncture—usually the thing to “A symphony or Hollywood’s Whisky A Go-Go and CBGB in avoid—could accommodate electrical leads a painting is a New York City, for example. Mickelsen also used in correcting arrhythmias (see Lab ‘solution’ to human painted, becoming good enough after 5 years Book, page 50). to sell some of his impressionistic work. “Many of the conversations I had with emotion like a math- Later, inspired by the jazzy music of the musicians when I was working as a tech ematical equation is beatnik era in the late 1950s, he formed a revolved around the interface between art a solution to natural band called Venus Diablo. During more than and science,” Mickelsen says of the one season, viewers of MTV’s The Real World connections between his various interests. phenomena. heard Mickelsen’s guitar riffs and what one “The creative drive is common to artistic reviewer called “sweeping baritone vocals.” and scientific endeavors. A symphony or a steve mickelsen ” Critical success in the music and art painting is a ‘solution’ to human emotion worlds can still require the oft-dreaded like a mathematical equation is a solution “day job” to make ends meet, so Mickelsen to natural phenomena. They are both worked as a technician in a cardiac abstractions that serve to communicate research lab at Lovelace Medical Center in efficiently a kind of beauty and under- Albuquerque. The cardiac lab stint, however, standing to others.” –Steve Mirsky truly inspired a change of heart. Encouraged by mentor Fred Kusumoto, now at the Mayo ouglas Merriam

Clinic in Jacksonville, Florida, Mickelsen D

 hhmi bulletin | February 2006 february ’06

SOLVING THE PUZZLE OF THE REsILIENT EMBrYO PG.8 A LIFE-ALTErING CHEMIcaL PG.10 NEW, IMprOVED MINI ME PG.12 Two types of regulatory proteins working in seesaw Researchers are beginning to get a handle on dopamine’s The latest mouse models can mimic human disease fashion ensure normal embryonic formation—even if role in depression and addiction. with greater precision. the embryo is split in half.

upfront The Key to Making a Perfect Baby. Write that book and you’ve got yourself a bestseller. One chapter might highlight the work of HHMI investigator Edward De Robertis, who has recently figured out how normal embryos develop. He can show you how to slice a frog embryo in half to yield identical twin tadpoles—and he can name the exact proteins that seesaw up and down during the process. We admit, the book likely wouldn’t bump Harry Potter from the top of the charts, but some biologists might want to give it a read.

February 2006 | hhmi bulletin 7 upfront Solving the Puzzle of the Resilient Embryo Two types of regulatory proteins working in seesaw fashion ensure normal embryonic formation—even if the embryo is split in half.

Facing off below, identical tadpole twins—generated by cutting an embryo in two equal halves—are indistinguishable from the typical tadpole above. obertis Lab R Courtesy of Hiroki Kuroda/De

 hhmi bulletin | February 2006 It was in 1903 that biologist Hans Spemann—using a loop of his baby including ADMP, in Xenopus embryos. The daughter’s hair and a newt egg—revealed the startling embryological entire surface of the embryo became neural tissue. “This is a major transformation of a mystery that would persist for more than a century. Testing the adapt- type you almost never see in embryos,” says ability of an embryo, Spemann deftly lassoed the egg with the hair and De Robertis. “It told us that BMPs play a crucial role in the establishment of a constricted it so that all nuclear divisions occurred only on one side. self-regulating morphogenetic field for Eventually, a nucleus would escape through the constriction to the other dorsoventral patterning.” In fact, when the scientists grafted material from either dorsal side and nuclear divisions would begin there as well. At this point, he or ventral BMP sources into embryos would tighten the lasso to completely separate the two sides. To his amaze- depleted of all BMPs, either of the grafts could restore normal embryo formation. ment, both halves developed into iden- that while the ventral half of the embryo “We think this finding is important tical, perfectly normal, half-sized embryos. requires specific BMPs for normal develop- in showing that the embryo is probably This embryonic fail-safe machinery ment, “It was rather shocking to us that the patterned by two gradients of BMP—one doesn’t only reside in amphibians, though. dorsal part of the embryo developed fairly from the dorsal side and one from the Identical twins often result when such egg normally,” says De Robertis. Indeed, further ventral,” says De Robertis. “The key to splitting occurs in humans. experiments revealed that normal dorsal devel- making a perfect baby every time, these Now, HHMI investigator Edward M. opment instead requires a different member experiments tell us, lies in the ability to De Robertis and graduate student Bruno of the BMP family, called anti-dorsalizing have a double gradient that will ensure a Reversade have made an important advance morphogenetic protein (ADMP). robust developmental system.” in revealing the molecular mechanism Importantly, De Robertis and Reversade This discovery could also have impor- underlying this remarkable resilience— discovered that the two kinds of proteins tant implications for efforts to use stem namely, the “morphogenetic fields” that in embryo halves are regulated in a seesaw cells to rejuvenate tissues lost to disease govern embryonic development. Such fashion. When the researchers decreased or trauma. When cultured in vitro, stem fields are gradients of regulatory proteins BMP signaling levels, they found that ADMP cells tend to differentiate into multiple cell that guide differentiation of embryonic cells levels would rise, and vice versa. This compen- types, as their self-regulatory systems work and organize the embryo’s overall shape. satory ability is a key to self-regulation in the to produce an embryo. De Robertis suggests Although researchers have long known that embryo, according to De Robertis. it might be necessary to shut down such self- such fields exist, little was known about the Another surprise came when the research- regulation in stem cells to induce them to molecular basis of their function. ers shut down all the relevant BMP proteins, produce specific tissues.–Dennis Meredith De Robertis and Reversade, both at University of California, Los Angeles, “It was rather shocking to us that the dorsal part of the sought to understand the possible role of the regulatory molecules called bone embryo developed fairly normally. morphogenetic proteins (BMPs). Other edward de robertis studies have shown BMPs to be key regu- ” lators in the dorsoventral (back-to-belly) patterning of embryos whereby dorsal cells differentiate into neural cells, and ventral cells become epidermal cells. Yet no one had been able to demonstrate their role by shutting down the system and eliminating such embryonic “self-regulation.” In their experiments with embryos of the African frog Xenopus, the researchers split the embryos into dorsal and ventral halves and used sophisticated molecular techniques to selectively inhibit BMP signaling in each half. They then observed the effects of their manipulations on embryonic development. The experiments, published in the December 16, 2005, issue of Cell, revealed

Edward De Robertis (right)

Hiroki Hiroki Kuroda and Bruno Reversade

February 2006 | hhmi bulletin  upfront A Life-Altering Chemical Researchers are beginning to get a handle on dopamine’s role in depression and addiction.

A lthough less than 1 percent of the bra i n’s neurons pro d u c e “Investigators have dopamine,­ the neurochemical exerts powerful effects on motiva- begun to focus  tion, reward, learning, memory, sexual desire, and pleasure. “To on the dendrite a large degree, dopamine is what makes us human,” says HHMI and its spines as investigator Li-Huei Tsai. Yet, scientists know relatively little about potential sites  how this neurotransmitter is so vital for many different behaviors. that are altered >> Neurotransmitters such as dopamine and serotonin are molecular during reward and addiction. messengers released by neurons to communicate information to neigh- boring neurons. Studies by two independent HHMI research teams are erin schuman ” helping to clarify the molecular events that occur after dopamine binds to its receptors. Their findings may lead to new treatment strategies for depression, Parkinson’s disease, and addiction. In studies published in the July 27, 2005, issue of Cell, a research group led by Tsai at Harvard Medical School discovered a molecule that links faulty dopamine signaling in the brain to the neural machinery that breaks down in people with depression. The findings may explain why commonly prescribed antidepressants are ineffective for some people and why, for others, they can take weeks to work. That long lag time has been one of the enduring puzzles in the treatment of depression, says Tsai. Antidepressants work by increasing levels of the neurotransmit- ters serotonin and/or noradrenaline in the brain. The efficacy of antidepressants, however, may depend more on changes to much later events that occur in the dopa- mine-signaling pathway. Tsai and lead author Sang Ki Park wanted to know more about those downstream events—which may involve little-known signaling pathways that are triggered when one type of dopamine receptor, D2, is activated. Park launched

Local stimulation of protein synthesis by dopamine may also modify synapses in the brain during

learning, says Erin Schuman. Misha Gravenor

10 hhmi bulletin | February 2006 Li-Huei Tsai believes her lab’s findings may lead to antidepressant drugs with improved efficacy.

the studies with a broad screen that turned up surprising information: A cell suicide molecule, prostate apoptosis response 4 (Par-4), interacted with a central regula- tory segment of the D2 receptor. The researchers then showed that Par-4 was produced in neurons where D2 receptors function. By knocking out Par-4 in mouse neurons or disrupting its interaction with the receptor, Tsai and Park caused striking behavioral changes in the mice. The knockout mice showed depression-like behaviors in multiple tests, easily giving up when faced with ordinary challenges. “These are very exciting results for two reasons,” Tsai says. “First, they indicate the importance of the signaling pathway mediated by the D2 receptor in depres- sive behavior. And second, this study pinpoints a specific pathway that impli- cates Par-4 in this process, which opens new possibilities for developing improved antidepressants.”

Synthesize Locally, Act Globally Approaching dopamine from a different direction, HHMI investigator Erin M. Schuman and her colleague Bryan Smith, both at the California Institute of Technology, discovered how dopamine stimulates the synthesis of proteins in neuronal processes, which may in turn “To a large degree, dopamine is what modify synapses in the brain during makes us human. reward-related learning. The brain’s reward circuitry is the top target of addic- li-huei tsai ” tive drugs. According to Schuman, scientists knew neurons, so that the neurons glow during that is protein synthesis-sensitive.” The that dopamine influenced the strength- protein synthesis. When the researchers findings were published in the March 3, ening of synaptic connections among activated dopamine receptors on the 2005, issue of Neuron. neurons. This strengthening, or plasticity, dendrites, they detected the glow in the According to Schuman, this research causes activation of protein synthesis dendrites, revealing that dopamine acti- could have implications for under- in the dendrites, which somehow leads vated local protein synthesis and, thus, standing and treating drug addiction. to enhanced activity of other kinds of promoted plasticity. “Over the past few years, investigators neurotransmitter receptors. However, Additional experiments indicated have begun to focus on the dendrite and Schuman says, no one knew how dopa- that activation of dopamine receptors its spines as potential sites that are altered mine influences local protein synthesis triggered immediate enhancement of during reward and addiction,” she says. and triggers plasticity. synaptic transmission in the neurons. “This raises the possibility that some of Schuman, Smith, and their colleagues “That’s a result that people have been the signaling that goes awry during addic- introduced the gene for a fluorescent seeking for years,” says Schuman. “It’s a tion may have to do with local protein

Sean Sean Kernan reporter molecule into cultured rat very rapid effect on synaptic transmission synthesis.” –Susan Gaidos and Jim Keeley

February 2006 | hhmi bulletin 11 upfront New, Improved Mini Me The latest mouse models can mimic human disease with greater precision.

K e v i n P. C a m p b e l l u s e d t o s t u d y m u s c u l a r d y s t r o p h y b y one can test the diaphragm to study the analyzing small pieces of thigh muscle from a child with the disease. Today, pathogenesis or the response to particular therapies.” there’s a better option. Campbell can now mimic the biochemistry of An astonishing 99 percent of mouse genes muscular dystrophy and test its effects in mice—rather than children strug- have comparable versions in the human genome, and many of them appear in the gling with disease—and evaluate tissues that could never be tested before. same order in the two organisms’ chromo- >> “With a patient,” says Campbell, an HHMI investigator at the somes. “We also have similar reproductive systems, similar physiology, very similar University of Iowa Roy J. and Lucille A. Carver College of Medicine, “you never biopsy the diaphragm, but it’s a very important muscle Mouse models of human cancer help Tyler Jacks explore biochemical pathways because most patients die from respiratory problems. With the mouse, regulated by cancer-associated genes. lynn Larsen F

12 hhmi bulletin | February 2006 Researchers

Kevin Campbell Mario Capecchi Richard Flavell Nathaniel Heintz HHMI investigator HHMI investigator HHMI investigator HHMI investigator University of Iowa University of Utah Yale University School Rockefeller University college of medicine School of medicine of Medicine nervous systems, and so forth,” says HHMI investigator Mario R. Capecchi, professor of human genetics at the University of Utah School of Medicine. “For all these reasons, the mouse model is a good representation of human biology.” In the last century, the mouse became the premier mammalian model system for genetic research. Now, the creation of mouse models is “like a cottage industry,” Mouse models helped Mario Capecchi has Humanized mouse To study neurological says Capecchi. “There are literally thou- Kevin Campbell’s team created mouse models models are getting function, Nathaniel discover that defective to study problems big support. Richard Heintz introduces large sands of labs all over the world making sarcoglycan complex as wide ranging as Flavell received a pieces of DNA—called mutations in mice.” causes constriction of limb skeletal defects; $17 million pledge bacterial artificial Capecchi pioneered “gene targeting,” a smooth muscle in the obsessive-compulsive in 2005 from the chromosomes, or vessels of the heart. disorder; and alveolar Bill & Melinda Gates BACs—into specific technology that has revolutionized scien- In addition, looking at rhabdomyosarcoma, Foundation to develop brain cell populations tists’ ability to use the mouse to model brain tissue from their an aggressive child- laboratory mice with in the mouse. Because human disease. This advance of the mice, they’ve found hood muscle cancer, immune systems the BACs contain that the dystroglycan for which the scientist similar enough to a gene and all the late 1980s allowed researchers, in their protein is a “major created the first mouse humans to allow regulatory information attempts to re-create the possible genetic player” in the abnor- model. testing of human necessary to express cause of a specific disease or study the malities in neuronal vaccines. that gene, they can migration and mental be used to introduce function of a particular gene of interest, retardation associ- human genes into mice. to “knock out” the function of that gene ated with muscular or modify its activity. dystrophy. Since then, researchers have refined gene targeting to create strains of mice with mutations in virtually any gene. They can direct gene mutation so that it occurs “Today, mice  in every cell of the body or only in certain tissues or cell populations. And they can are our test tubes. control when that mutation occurs—right away, or later in the animal’s life span. They nathaniel heintz can even inactivate combinations of genes, etters independently of each other, within the Jacks studies an oncogene called K-ras mutations in multiple genes, occurring F ” same animal. whose activation has been linked to many in particular tissues and at particular Paul different cancers. His group recently times in the animal’s life span—simulates Mimicking cancer developed two mouse models of lung what we know about cancer initiation Capecchi: These advances are critical to faithfully cancer involving K-ras that come close to in humans. mimic human cancer in the mouse, says mimicking spontaneous human disease. “That’s a powerful tool in the study Tyler Jacks, an HHMI investigator at the One strain of mice has an inactive K- of lung cancer,” says Jacks, “because we eichert R Massachusetts Institute of Technology, ras gene in its cells; a second strain has are interested in using these models to niversity niversity of Iowa obert U because the effects of cancer-associated an inactive K-ras gene plus a tampered- explore tumor progression, even from R mutations can depend on the specific with version of the tumor suppressor the earliest points.” In June 2005, his type of cell or tissue in which they occur. gene p53. The genes are engineered in group published a paper in Cell identi- Heintz: “Making accurate cancer models requires such a way that when triggered—by the fying a stem cell within the lung as the a good deal of subtlety,” says Jacks. “It’s introduction of a virus, for example— origin of non-small-cell lung cancers. important to match the relevant mutations the oncogenes can be turned on or the “We wouldn’t have been able to do

Creative Media Group, to the appropriate cancer and to pay atten- tumor suppressor can be turned off, that without use of sophisticated mouse Harold Shapiro tion to details ranging from the timing of thereby tripping the cellular overgrowth models to control the initiation of tumor

Campbell: Flavell: the mutations to the levels of expression.” characteristic of cancer. This scenario— development.” –Mary Beth Gardiner

February 2006 | hhmi bulletin 13

Researchers set out to understand nuclear reprogramming to revert adult cells to medically useful embryonic stem cells

by Richard Saltus // illustration by Jason holley cell’se a second act

February 2006 | hhmi bulletin 15 othing in nature is more elegant— or more humbling to scientists—than the transformation of a single-celled embryo into a unique and complex individual containing, in the case of an adult human, some 10 trillion cells with more than 200 different specialized functions. // Also astonishing, however, is that a cell’s career decision isn’t necessarily permanent. It can be reversed. When novelist F. Scott Fitzgerald said shortly before his death in 1940, “There are no second acts in American lives,” scientists had not yet discovered that committed, specialized humann cells could, in effect, go back and start again from scratch. “Reprogramming”—the erasure of a patient’s own body cells. The hope is to factors needed for reprogramming, and cell’s developmental history—enables it to improve treatments for neurodegenerative eventually free the cloning process from start over as an uncommitted embryonic diseases like Alzheimer’s and Parkinson’s, the need for unfertilized eggs or embryos, cell. The process is central to cloning, diabetes, heart disease, and spinal cord which are scarce and expensive, and raise which creates an exact copy of an adult injuries, for example. ethical concerns. organism from the genetic material in one Following the birth of Dolly, pigs, The ideal, says Melton, who is co- of its cells. A notable example was the mice, calves, and other animals have been director of the Harvard Stem Cell Institute, birth of Dolly the lamb in 1996, the first cloned through the transfer of adult-cell “would be if you could take a specialized, mammalian clone. She developed from a nuclei into unfertilized eggs. In addition differentiated cell from an individual fully differentiated adult cell whose to nuclear transfer, reprogramming can and use some chemical compounds to nucleus had been turned back in time, also be induced by the fusion of certain reprogram it, turning it into an embryonic developmentally speaking, so that its full cells. In 2005, biologist Kevin Eggan and stem cell” without having to resort to set of genes was once again in its original, HHMI investigator Douglas A. Melton nuclear transfer or cell fusion. “But we are embryonic state—and capable of giving at Harvard University succeeded in many steps and years away from that.” rise to a new animal genetically identical to reprogramming human adult skin cells Dolly’s donor. to revert to an embryonic state by fusing First observed and confirmed in a series them with stem cells removed from of experiments from the late 1950s to embryos. Evidently, the embryonic stem Dormant Genes the mid-1970s, reprogramming is still cells contained something that could Can Be Awakened something of a “black box” to scientists. reawaken the embryonic genes in the skin It appears that unknown factors in the cells. But there was a problem: The resulting egg’s cytoplasm signal the nucleus to embryonic cells contained a double set of erase its specialized genetic program and chromosomes, an abnormality that made ach of our cells contains reactivate previously silenced genes that them unsuitable for practical cloning. the full set of DNA support the development of a new embryo. Using his own approach, Yuri Verlinsky, instructions, or genome, But little is known about what these of the Reproductive Genetics Institute in for making all the proteins essential factors are or how they turn back Chicago, reported in the January issue of that build and operate a human being. the developmental clock. the journal Reproductive BioMedicine According to current estimates, the “It’s a wonderful problem and an Online that he had fused several types egenome of a human cell carries 25,000 incredibly fascinating subject,” says Allan of human somatic cells with human to 30,000 genes on its 46 chromosomes C. Spradling, a developmental biologist embryonic stem cells, and that in some within the nucleus. But the function of and HHMI investigator at the Carnegie instances the adult nuclei had completely any particular cell—skin, nerve, or blood, Institution of Washington in Baltimore. replaced the stem cell nuclei, leaving only for example—requires the activity of “You’re talking about one of the most one set of chromosomes. only a small subset of the genome. It fundamental of the processes that make These were patient-specific embryonic would be not only superfluous but also life possible.” stem cells, Verlinsky notes. But when harmful if a nerve cell made proteins, say, But limited understanding of the grown in culture, some of the cells had for bone or intestine. So how do cells process explains why cloning is still both donor and recipient nuclei, so they’ll prevent this from occurring? For many an inefficient and error-prone tech­ need further purification before they have years scientists pondered whether a cell ooher

nology. And that hampers the promise any practical value. specialized for one role permanently D of “regenerative medicine”—generating These studies and many other inactivates, or even loses, its genes for

rejection-free repair tissues by cloning a lines of research aim to elucidate the making other types of cells—as well as Kathleen

16 hhmi bulletin | February 2006 the genes that were essentially in its be reactivated to direct the development nothing had been discarded, and no part embryonic past. of a normal embryo—at least, up to a of the genetic sequence had been edited In 1975, John Gurdon and colleagues point. The reprogramming was clearly or rewritten. at the MRC Molecular Biology Laboratory induced by the cytoplasm of the egg, When Eggan was at the Whitehead in Cambridge, England, carried out and it was accomplished within a few Institute in Cambridge, Massachusetts, a series of experiments that built on hours after nuclear transfer. with Rudolf Jaenisch in 2004, they those first observations, in the 1950s, Before the work of Gurdon and partnered with HHMI’s Richard Axel of nuclear reprogramming. Gurdon others, “One might have thought that at Columbia University and brilliantly transferred the nuclei from adult-frog a cell is locked in—that a blood cell demonstrated this capacity for the rea­ skin cells into an egg whose own nucleus can only be a blood cell—and can wakening of genes in even the most had been removed. Of all the nuclei never be changed,” says Leonard I. Zon, specialized of cells. To be attuned to specific placed in the eggs, 4 percent generated an HHMI investigator and stem cell odors, mice have hundreds of different fully developed tadpoles, though none researcher at Harvard Medical School types of olfactory sensory neurons: In each of them led to adult frogs. Inefficient and Children’s Hospital Boston. But the nerve cell, just 1 of 1,500 olfactory genes and incomplete as the process was, it nuclear-transfer experiments suggested is turned on, while the rest are silenced. nailed an important point: Genes in that the differentiated cell’s chromosomal The researchers extracted one such cell the nuclei of differentiated cells could DNA hadn’t been permanently altered; from an adult mouse and cloned it, through nuclear transfer, to create a mouse that had a full repertoire of smell-sensitive neurons. Clearly, the process had reactivated the leonard zon, Hhmi investigator, harvard entire set of silenced olfactory genes. medical school and children’s hospital boston That’s why reprogramming can occur: The unexpressed DNA is dormant but intact, and can be awakened. These reversible changes in gene activity are due to so-called “epigenetic modifications.” Epigenetics, the study of changes in gene silencing that occur without changes in the genes themselves, has become a highly active field—a journal devoted entirely to the subject was just launched in January— and scientists are steadily discovering more about its role in development, reprogramming, and diseases. Most of the events that occur during development, they’ve learned, are orchestrated by epigenetic modifications triggered by signals from the cell’s environment. “Epigenetics explains many things that happen between development and death,” says Jeannie T. Lee, an HHMI investigator at Harvard Medical School and Massachusetts General Hospital. “Not only is epigenetics responsible for setting up a developmental program, it determines whether you are going to get cancer or develop autoimmunity, or get prion diseases such as mad cow.”

February 2006 | hhmi bulletin 17 Inducing Cellular Amnesia

hough epigenetic modification is not well understood, scientists have a broad outline view. “Inside the nucleus of each cell there are proteins that bind to DNA and tell particular genes to be activated or trepressed,” explains Zon. The accessibility of binding targets on the DNA molecule depends in part on the chromosomes’ shape and configuration at any given time. When the chromosomes are densely packed in the nucleus, they offer fewer binding targets. When they’re in a more threadlike stretched- out arrangement, chromosomes are 50,000 times longer and that much more accessible to regulatory binding proteins. Chromosomal DNA is packaged in a structure called chromatin, which contains small, spool-like proteins, or histones, around which the DNA is wrapped. These histone spools are like scaffolding that determines the configuration of the DNA and its availability for modification by regulatory proteins. Changes in yi zhang, HHMI investigator, university of north carolina–chapel hill chromatin structure caused by chemical modifications to the DNA or the histones are passed to successive generations of the same type of cell. Zon sums up the achieve the appropriate level of expression. and egg that had been silenced must big picture like this: “Development from One of these factors is methylation— be reactivated. a single cell into a multicellular organism the addition of a “tag,” recognizable by “Very rapidly they demethylate, erasing is regulated by environmental signals cellular proteins, onto one of the chem­ the entire adult cell program,” says David acting through changes in chromatin, ical bases, or nucleotides, that make up L. Garbers, an HHMI investigator at the affecting gene expression.” The chromatin the DNA code. In methylation, a methyl University of Texas Southwest Medical changes enable genes to be transcribed— group—a hydrocarbon unit notated as Center at Dallas. “It’s pretty cool, but that is, expressed—or to be repressed. “CH3”—replaces a hydrogen atom on none of this is well understood.” Last Appropriate genes are thus turned on or the base. Methylation generally represses November, Garbers reported on a method silenced in different types of cells. gene expression, whereas removing the of keeping rat sperm precursor cells from Conversely, Zon explains, “Repro­ tag, or demethylation, allows the gene to differentiating into sperm proper. He gramming is the undoing of the chro- be expressed. maintained them—even after freezing and matin changes back to the original Nuclear reprogramming occurs not rethawing them—in a nearly stem cell-like conformation of the DNA. It’s like a drug only in cloning, but as a natural process state. “We’re only one step removed from

that erases the cell’s memory of what it just after a sperm and egg—both highly pushing these cells back a level to a state HHMI . has been through.” committed, differentiated cells—join in that is similar to embryonic stem cells,” he . ©

Epigenetic regulation of gene expres­ conception to create an embryo. For the says. If that could be done, it might be a am/ AP sion is not a simple switch; many control embryo to take its first steps toward model for creating embryonic stem cells T

factors have to operate in concert to development, many genes in the sperm without harvesting them from embryos. Karen

18 hhmi bulletin | February 2006 Find Jaenisch and others in the cloning from DNA itself,” Yi says—adding he the Demethylase community are carrying out a range of wouldn’t be surprised, however, if this experiments aimed at exploring this issue turned out to be the case. If so, it would and, more broadly, trying to identify enable researchers to ask questions that exactly what factors in the unfertilized egg could open the door to “artificially nother question that are responsible for reprogramming. reprogramming” an adult cell without the weighs on the minds of Zon says the answer lies in the trigger need for a donated human egg. cloning experts is whether for demethylation. “The big prize is to “It could be that if you put this some of the inefficiencies figure out what the ‘demethylase’ is. If you demethylase enzyme into the donor cell, and abnormalities that plague the present could identify it, reprogramming research it would be all you’d need to carry out technology result from incomplete would take a major step forward.” reprogramming,” he says. “But I doubt a reprogramming of the donor nucleus. HHMI investigator Yi Zhang, at the that it will be that simple.” Perhaps not all of the essential genes are University of North Carolina–Chapel Harvard’s Melton doesn’t suggest wait- activated or deactivated when the nucleus’s Hill, is hot on the trail of this trigger. ing until one of these efforts to reprogram adult program is erased. Jaenisch holds Last December, he and his collaborators adult cells without the need for human this view and points to an important announced they had discovered in cul­ eggs or embryos pays off. “The hard fact is embryonic gene called Oct-4 that was tured human cells a family of proteins that, at this moment, the only way to create shown to be incompletely and randomly that demethylates not the actual DNA of an embryonic stem cell from a somatic reactivated when adult cells were repro­ genes, but sites on the spool-like histones cell is by nuclear transfer into oocytes,” grammed during cloning. This might be in chromatin that package the DNA. This he says. “Taking advantage of this current one of the reasons, he suggests, that most family of proteins is known as JHDM1. capability is critical if we hope to realize the embryos created through nuclear-transfer “We’re not sure if members of this extraordinary clinical potential of therapies techniques die. protein family can remove methyl groups based on stem cell technology.”

Searching for Wayward Germ Cells Developmental studies shed light on stem cell behavior

Germ cells, which give rise to sperm and eggs, must navigate epithelial cell layers that form its midgut. They have since shown from the tail end of an embryo, where they form, to a distant that the germ cells in mutants they call wunen and wunen2 cross reproductive organ where they will do their work. To discover cues the midgut, but then wander around the middle of the embryo in a the cells use to guide their journey, Ruth Lehmann, an HHMI seemingly random fashion, rarely reaching their proper destination investigator at New York University School of Medicine, searches in the developing gonads. • In separate studies, Lehmann’s group for mutant Drosophila embryos whose germ cells get lost along and Ken Howard’s group at University College in London, England, the way. • “Our long-term goal is to determine how germ cells showed that the wunen genes encode enzymes that remove are specified, how they are guided during their migration in the phosphates from phospholipids, which float in the spaces between embryo, and how a stem cell population is selected cells and help guide germ cells as they wander that gives rise to egg and sperm throughout the through the embryo. Recently, Lehmann’s team fly’s adult life,” says Lehmann. • By inserting a found that in germ cells Wunen appears to be part genetic element into the genome of developing of the apparatus that detects those phospholipids fruit flies, Lehmann and her colleagues can stain and uses the lipids for migration and survival. the germ cells blue and then search for wayward • “The same phospholipids that could be involved blue cells in thousands of developing fly embryos. in germ-cell migration have been shown to give Using this approach, Lehmann and her colleagues the timing signal for lymphocytes migrating out have identified gene mutations that interfere with of the lymph node,” Lehmann notes. If that is discrete steps of germ cell migration. • In 2003, true, Lehmann’s group may have stumbled onto Lehmann’s lab identified trapped in endoderm-1 a navigation mechanism used by many types of T homas (tre1), a mutant fly whose germ cells get stuck at cells as they migrate through different tissues.

Juliana Juliana the back end of the embryo and cannot cross the –Rabiya S. Tuma

February 2006 | hhmi bulletin 19

Trailblazer

Turned Superstar

Joan Steitz started up the scientific ranks when few women did. Today, Nobel laureates laud her research and scores of scientists praise her mentoring acumen. By Margaret A. Woodbury Photographs by Ethan Hill

February 2006 | hhmi bulletin 21 If anyone had told HHMI investigator Joan A. Steitz when she was an undergraduate chemistry major at Antioch College in Yellow Springs, Ohio, that she would someday run her own research lab, and that a Nobel laureate would call her a star scientist, she most likely would have exclaimed, “Come on!” It’s a phrase she uses often, usually meaning: Get real! >> A Minnesota native who came of age in the 1960s, Steitz says she was always interested in science and got plenty of encouragement from her parents, even though a far different model was everywhere around her. “Women of my day,” she recalls, “had six kids and a station wagon.” >> “At that time, there were no women professors in the natural sciences at any major university,” Steitz says. “Consequently, I never envisioned myself being where I am today: I never thought I would teach undergraduates. I never thought I would mentor graduate students. I never thought I would be on the faculty of a prominent university. I really thought I would be a research associate in someone’s lab—a man’s, of course.” But Steitz persevered, and now holds Steitz soon discovered, however, that high ranks in the world of molecular the door could just as easily swing shut. biology. She is Sterling Professor of During her first year at Harvard, she Molecular Biophysics and Biochemistry approached a male scientist she will only at Yale University and has served as chair identify as “famous, well-respected, and of her department and as scientific now deceased.” Steitz wanted to work director of the Jane Coffin Childs Fund with him for her graduate thesis. But Dr. Both Baserga and Doudna are vigorous for Medical Research. Moreover, Steitz Famous had other ideas, namely that men in their praise of Steitz as a scientist, but it has earned an international reputation belonged in the lab and women at home is with particular gratitude that they cite for her research on RNA—the chemical with those six kids and the station wagon. her mentorship in teaching them how to that delivers DNA’s genetic messages and Steitz recalls running from the room and navigate the system and the ins and outs performs an impressive repertoire of then dissolving into tears, but she now of starting one’s own lab. For her part, cellular functions. “Joan is looked up to looks back on the event as one of the best Steitz recalls what it was like not to have as one who has contributed to a cohesive things that ever happened to her: She other women around in her early days as view of RNA science,” says Thomas R. completed her thesis with Watson, and a scientist—lonely. So she has made it a Cech, HHMI president and a Nobel their professional relationship strength­ priority to give the Basergas and Doudnas laureate for his work on catalytic RNA. ened into a lifetime bond. of the next generation something she didn’t “When I became interested in RNA in These days, it’s hard to imagine Steitz have: a female network within the system. the early 1980s, she was already a star. Her running from anything. (She still counts work continues to evolve and remains at herself as a bit of a shrinking violet, but only the forefront.” because she dislikes being in the spotlight; Giant steps despite her status, she rarely grants media interviews and is an intensely private Steitz characterizes her rela­ o Pe nin g d o o r s person.) “Joan is extremely competitive in tionship with RNA as a “personal romance” her field, as are all good scientists,” says that dates back to her time in Watson’s In the early years, Steitz’s deci­ molecular biologist Susan J. Baserga, who lab and her initial work on bacteriophage sions clearly reflected her doubts. Thinking was a postdoc in Steitz’s lab from 1988 RNA. But her first major leap forward in her chances of autonomy in a laboratory to 1993 and is now a faculty colleague RNA science came during her postdoctoral setting were minimal, she set her sights on at Yale. “She is not afraid to offend, but years overseas. After finishing at Harvard, becoming an M.D. She was accepted to her manner is such that she gets done what the newly married Steitz traveled with her Harvard Medical School, but summer needs to get done in a way that usually husband, Tom Steitz (also an HHMI research in the laboratory of Joseph Gall at doesn’t offend.” investigator at Yale), to Cambridge, England. the University of Minnesota made her HHMI investigator Jennifer A. Doudna, There, in the division run by two more change her mind. Instead, in the fall of who was a junior faculty member in Steitz’s renowned scientists, Francis Crick and 1963 she became the only woman in a class department at Yale and is now at the Sydney Brenner, she focused her research of 10 incoming students in a new program University of California, Berkeley, recalls on determining the exact point on a strand in biochemistry and molecular biology at numerous times when Steitz “called a spade of messenger RNA (mRNA) that binds Harvard’s Graduate School of Arts and a spade”—times when it might have been a bacterial ribosome to begin the Sciences. James D. Watson—fresh from easier to let things pass. “If a faculty mem­ manufacture of a protein. (A ribosome is winning his Nobel Prize for solving the ber wasn’t being treated fairly, Joan spoke the machine that does protein synthesis in structure of DNA—became her mentor, up in a way that I really respected,” says the cell.) Success came in 1969 when she and the door to science opened a crack. Doudna. published a paper in Nature showing the

22 hhmi bulletin | February 2006 nucleotide sequences in bacteriophage lab ritual. Each is savored and signed by Technology (MIT), Richard Roberts at mRNA that act as such start points. a student who has successfully completed Cold Spring Harbor Laboratory, and She continued her work on bacterial a thesis. Steitz has a particular smile that many others coalesced into the realization and bacteriophage RNA upon her return flickers beneath her rosy, yet elegant in 1977 that the DNA in eukaryotic cells to the United States in 1970, when she cheekbones when talking about or with alternates between exons, which contain joined the Yale faculty as an assistant her students. It’s something her students gene sequences, and introns, which do professor of molecular biophysics and notice and appreciate. The smile plays not code for any protein (“junk DNA”). biochemisty (her husband also took a there as a message of encouragement, Yet the discovery of introns did not position at Yale). By 1975, her efforts endorsing their right to think aloud even explain the machinery or how all the were further rewarded when she published as they sometimes fumble with their noncoding introns were removed from how ribosomes identify the start site on biological formulations. a newly transcribed length of RNA. Steitz kept at the problem, and by analyzing blood samples from patients L e ft Joan Steitz gives high priority to teaching undergraduates and with an autoimmune disease, she and mentoring graduate students. b e l ow SnRNAs are part of the spliceosome, her student Michael Lerner discovered which splices introns from mRNA. They are the fourth class of RNAs, a novel entity—the snRNP. A snRNP essential for gene expression. (pronounced snurp) comprises a small length of RNA (about 150 nucleotides long) that is complexed with several proteins. “It turned out,” says Steitz, “that the blood samples we analyzed contained antibodies against snRNPs. “After we discovered snRNPs, we proposed they were involved in splicing [removing the introns from newly tran­ scribed RNA, or pre-mRNAs, as they’re now called] and we did the first experiments that showed they were, in fact, involved in splicing,” says Steitz. Her lab also determined that it is a particular small nuclear RNA (snRNA), U1, in a snRNP that defines one of the splice sites of an intron via base pairing with complemen- tary pre-mRNA. Later, other labs coined the term spliceosome for a large assembly made up of several different snRNPs as well as additional proteins. The big mystery— why so little transcribed RNA becomes a strand of mRNA: by complementary Although Steitz gives top ranking mRNA—was no longer so baffling. base pairing. to her work on ribosomes, it was her Shortly after Steitz published her That discovery remains a highlight of seminal 1980 paper in Nature, “Are celebrated snRNP paper in Nature, ribo­ her career—in fact, it tops the list, she snRNPs involved in splicing?”, that zymes were discovered by Thomas Cech says. But she rebuffs a request to rank clinched her scientific reputation. Steitz, and by Sidney Altman of Yale and past accomplishments, preferring to talk like many others in the early 1970s, had Norman Pace of Indiana University. As about what’s currently underway. It’s turned her attention to eukaryotic cells (a the name implies, these large molecules of clear this energetic woman would rather eukaryote is an organism whose genetic RNA actually have the ability to catalyze get on with her research than rehash material is located within a membrane- a reaction—namely, they can splice or cut “such ancient history.” Her cramped bound nucleus). Of particular interest to strands of RNA. And while it’s yet to be office—piled with papers and stacks of Steitz was the mystery of why so much proved, Steitz thinks that RNA catalysis is , June , 1998. June books everywhere—is a bit mazelike. She RNA was made in the nucleus, but so responsible for the cutting and rejoining apologizes for the mess, but in pro forma little—about 10 percent—ever made actions of the spliceosome. “Like a fashion that says, come back next year and it out to the cytoplasm to be translated standard enzyme, snRNPs come together it’ll look the same. into proteins. As she tried to figure and form a spliceosome, do their business,

Scientific American Dozens of empty champagne bottles line out the answer, experiments by Philip fall apart, and do the whole thing over

Image by Ian Worpole; reprinted with Image permission by Worpole; Ian from a top office shelf, remnants of an honored Sharp at the Massachusetts Institute of C o ntin u e d o n Pa g e 5 6

February 2006 | hhmi bulletin 23 A Way Station After Katrina

HHMI responds to help Xavier University retain its displaced faculty, support their professional growth, and ultimately benefit students.

24 hhmi bulletin | February 2006 by dorothy foltz-gray photographs by imke lass

February 2006 | hhmi bulletin 25 T h e m o r n i n g b e f o r e H u r r i c a n e Katrina bacteriologist Tanya McKinney and her 2-year-old daughter drove from the city to Mound Bayou, Mississippi, 5 hours away, where her mother lives. McKinney’s husband, First Lieutenant Steve L. McKinney of the Louisiana Air National Guard, stayed behind on duty. “I sat in front of my mother’s TV, watching Katrina devastate New Orleans,” says McKinney, an assistant professor of biology at Xavier University for the past 6 years. “And of course I was terrified for my husband. It was nerve-wracking.” Within a few days, McKinney had word from her husband that both her home and workplace—Xavier is located in the heart of Orleans Parish in New Orleans—were flooded, and that 5 years of scientific research had been destroyed. McKinney was creating mutant bacterial strains of Staphylococcus aureus, a bacterium that is the most common cause of food poisoning. “Although high salt concentra- tions kill most bacteria, S. aureus survives. If we could understand how, then we might be able to better control it.” She was investigating which staphylococcal genes are regulated in various salt concentra- tions. It was a time-consuming process, but by last summer’s end, she finally had identified certain genes and constructed the necessary mutant strains to begin exploring the role of specific proteins. “I was very excited,” she says, “but now I have to start over.” Many of McKinney’s colleagues at Tanya McKinney // Assistant Professor of Xavier—one of HHMI’s longtime under- Biology, Xavier University // University of AlabamA, Birmingham graduate science-education grantees—have McKinney was back at Xavier with the rest of the reported similar losses. Every research scien- returning faculty on January 12. Phone service has been in tist with frozen or refrigerated specimens and out, but she’s home. lost all they had, says Elizabeth Barron, the university’s vice president for academic affairs, and a lot of scientific equipment was damaged. Most Providing Safe Harbor heavily affected were faculty in the departments of biology and I t is n o su r p r is e that HHMI zeroed i n o n X av i e r , chemistry and the College of Pharmacy, says Tuajuanda Jordan, a historically black university that has received $7.6 million in former associate vice president for academic affairs. “They will HHMI grants since 1988. HHMI selects grantee institutions have to start over, though if their computers were not submerged, based on their success in sending students to medical school they should be able to save their data.” Throughout the campus, or graduate science programs—an area in which Xavier excels, however, floodwaters rose up to 6 feet, submerging the first says Peter J. Bruns, HHMI vice president for grants and special floors of 39 buildings and destroying any computers situated programs. “Xavier puts more African American undergraduates there. The school also lost its central power plant. into medical school than any other college or university of any Yet, Xavier stood to lose its most precious resource of all—its size in the country,” he says. “And it ranks in the top 50 of all faculty. Without salaries or homes, most would be forced to U.S. universities for graduating chemistry and physics majors.” find employment elsewhere. People at HHMI quickly grasped By September 16—fewer than 3 weeks after the storm— that problem, and within days of the storm, Hanna H. Gray, HHMI President Thomas R. Cech had sent a letter to HHMI chairman of the Board of Trustees, conferred with Institute staff investigators across the country, asking them to consider to see what they could do to help. including Xavier science faculty on their research teams. Just

26 hhmi bulletin | February 2006 ashley fornerette senior, biology-education, xavier university as rapidly, HHMI’s undergraduate grants texas tech University, lubbock staff—Director Stephen Barkanic and his Fornerette is back in class. The sidewalks near Xavier are colleagues, Program Officer Patricia Soochan piled high with debris from houses that have been cleared of their ruined contents. It’s a daily reminder, she says, of and Program Assistant Mary Bonds—set how hard it was to see her childhood memories thrown up a structure for matching Xavier faculty onto the sidewalk in a mountain of unidentifiable junk. with their scientific hosts. The Institute “Sure it’s garbage now, but before Katrina it wasn’t.” would fund the sabbaticals, for 9 months at $5,600 per month, of any Xavier science faculty who participated. It also extended offers to members of the staff and students who accompanied them, offering $3,600 and $2,000 per month, respectively, and would pay for expenses such as relocating computers or purchasing special supplies. Within a week, 200 HHMI investigators had offered places for as many as 360 faculty and 80 students in their labs and institutions. Xavier administrators were scattered around the country—President Norman C. Francis set up an office in his sister’s home in Grand Coteau, Louisiana, Vice President Barron was in Gatlinburg, Tennessee, and Jordan worked from HHMI headquarters in Maryland. Yet getting word to the now far-flung faculty, staff, and students was relatively easy because of an online faculty registry that Xavier already had in place for hurricane emergencies. HHMI posted investigators’ offerings on the Xavier Web site, updating it as opportunities opened or closed. The first faculty member signed up on September 22, and by October 10, Jordan and the HHMI team had been in touch with 75 Xavier science faculty who asked for support. Ultimately, 62 faculty, one staff member, and two students were placed. HHMI also was flexible about place- ments—approving some, for example, outside the HHMI investigators’ offerings. Such was the case for McKinney. When her former graduate school adviser Janet Yother, professor of microbiology at the University of Alabama, invited McKinney to work in her Birmingham lab, McKinney loved the idea. But sorting out the finances would take time. That’s when she learned about the HHMI program. “Other people had offered me opportunities that weren’t in my field, where I could make a contribution,” says McKinney. “But HHMI was Since early October, she has been attempting to isolate and flexible enough to say, ‘If you have someone in mind to work identify an enzyme from Bacillus circulans, which degrades with, just send us your work plan.’” the capsule around Streptococcus pneumoniae, a bacterium that causes pneumonia. Her collaboration with Yother has also intro- duced McKinney to new and effective procedures. For instance, Deep Loyalties a graduate student is showing her how to use a phage display A lth o u g h M c K i n n e y c o u l d n ’ t r e sum e h e r system, an easier and less expensive way to screen protein inter- research on staphylococci at the Alabama lab, she has nonethe- actions than any she has used before. “I’m going back to Xavier less found the work there stimulating and has been productive. a better teacher and researcher,” she says.

February 2006 | hhmi bulletin 27 27 their son had local friends and could easily slip into school. “Lou Messerle [an associate professor of chemistry], whose interests are very close to ours, said we were welcome in his lab,” says Goloverda, an organic chemist. “As soon as I learned about HHMI’s program, I wrote to Dr. Jordan, explaining Messerle’s offer. So she made it happen.” Darrell Eyman, an associate professor of chemistry at Iowa, convinced the university’s administration to allow Kolesnichenko, a materials chemist, to develop and teach a new graduate-level class in nanochemistry. Jordan again intervened constructively, by ensuring that Kolesnichenko received the difference between the Iowa salary and the higher HHMI stipend. Assured of income, the two scientists could get back to work. They were collabo- rators at Xavier, Kolesnichenko developing nanocrystals and Goloverda wrapping them into the shells of organic compounds that make the particles soluble and stable in water. “We target magnetic nanoparticles that can respond to an external magnet passed over the body, carrying drugs to a specific site,” she says. “The idea was not ours, but we are trying to improve the drug delivery.” They say their work and their colleagues at Iowa have been a gift during a very diffi- Ray Lang // associate professor and chair of cult time. “We dig through publications computer sciences and engineering, Xavier and do experimental work in the labs,” says

University // Washington University, St. Louis Kolesnichenko, who divides his time between Lang finally returned to his house when utilities were restored—on New Year’s Day. He started work at teaching and lab research. “Our work here Xavier on January 12, where he’ll continue the research he gives us the opportunity to get new ideas that began in Sean Eddy’s lab in St. Louis. might be applied to our research at Xavier.” Like McKinney, these two scientists have no doubts about returning to New Orleans. In fact, McKinney never considered not returning. Since “We have never felt like it was just a job,” says Goloverda. “It college, where she had few black science professors, she has was always a mission, where you have something to offer and the wanted to be a role model for minority students. “At Xavier I students are happy to accept it. Some of them never before had can mentor and encourage science students, and also do my a good opportunity to learn, and they are ready. That makes our research there with funding and equipment. It’s too valuable an efforts very rewarding.” asset to be lost or diminished. I want to help rebuild it.” Vladimir Kolesnichenko, an assistant professor of chemistry, and his wife, Galina Goloverda, an associate professor of chem- A Good Place During Personal Loss istry, have similar feelings about Xavier. The couple left New r A y l A n g , ass o c iat e p r o f e ss o r a n d c hai r o f Orleans the day before Katrina’s arrival with their 15-year-old computer sciences and engineering, never considered quitting son, Igor, and with friends who didn’t have a car, driving to Xavier either. “I felt very lucky to get a job there,” he says, “and Lafayette, Louisiana. A close friend in Iowa City, Iowa, Ronita after 12 years I’m very invested.” Lebeau-Meyerdirk, who knew they were camping near Lafayette, The Gulf Coast’s perennial hurricanes were almost ho-hum called campground after campground until she found them, for Lang, a New Orleans native. Despite dozens of tree-snapping whereupon she invited the family to her home. Kolesnichenko storms, he’d never felt the need to evacuate. But the night before and Goloverda were eager to return to Iowa City, where they Katrina hit, he and his partner Alex Sanabria realized that the had lived from 1996 to 1998. They knew professors at the hurricane was going to be a monster—and that it was too late University of Iowa—both of them had worked there—and to leave. Six days after the storm, the couple was evacuated by

28 hhmi bulletin | February 2006 boat. After 16 hours with tense and sometimes unruly mobs at Xavier, you can get to know your professors,” she says. “You’re the New Orleans airport, and a ride in a cargo plane to Austin, not just a name in a grade book. Xavier has molded me.” Texas, they finally flew with their cairn terrierC aesar to the home Among its 4,121 full-time students pre-Katrina, 3,118 said of a friend in St. Louis, Missouri. they planned to return when the campus reopened on January 17. When Lang heard about the HHMI program, he combed Two-thirds of the faculty said they would return; 50 of them are the offerings for a spot and found HHMI investigator Sean R. living temporarily in mobile homes or trailers on campus. About Eddy, an associate professor of genetics at Washington University one-third had to be laid off, though Xavier administrators hope in St. Louis, who praises both the HHMI program and his to rehire many of them next September. HHMI will continue to guest researcher. “Ray has research experience in an area of fund about 56 faculty at Xavier until September 2006. computational linguistics that we use extensively in DNA- and Of course, challenges remain. Reconstruction alone will cost protein-sequence analysis, so it was a really great fit,” saysE ddy. between $30 million and $40 million, says Xavier President Lang’s feelings are mutual. The placement and new Francis, but he is confident of Xavier’s survival. “We have a colleagues have provided him with both expanded opportuni- dedicated faculty overall. The science faculty teaches as a team, ties and a distraction from personal grief: Sanabria, ill with and they know what the students have been taught the semester liver disease before the storm, became weakened by the stress of before. It’s a very managed process, and it works. That’s why we Katrina and the move and died 6 weeks after the pair arrived in have the record we do. We teach students what academic life is St. Louis. Says Lang: “We’d been together 26 years.” about, and we graduate people who are ready to excel.” Lang was in a good place, however, at that difficult time. “Everyone at Washington rolled out the red carpet for me. I began by giving a presentation about my work. Since then, I’ve been writing a compiler [a program that translates code for a computer] to describe the secondary structures of RNA, an area somewhat connected to what I was The Storm doing at Xavier. And working here has been a fabulous opportunity to make the transi- Brought Her tion into computational biology, which uses techniques from mathematics, statistics, and Home computer science to solve biology problems Tuajuanda Jordan grew up in Forestville, Maryland. So after she like the alignment of gene sequences.” and her 15-year-old twins were evacuated to Dallas after Hurricane Katrina flooded New Orleans, the three decided to head back to Maryland, to her parents’ home, about 20 miles from HHMI Confidence in Xavier’s Future headquarters. Xavier University’s associate These Xavier faculty are acquiring • Learning that Jordan, new methods and directions and continuing to vice president for academic affairs, was in Maryland, Stephen do research in the face of huge losses—exactly Barkanic, director of HHMI’s undergraduate grants program, what HHMI and Xavier administrators hoped offered her office space and use of Institute facilities to do her work the program would offer. “We are a tuition- for Xavier. Meanwhile, her kids, Jordan and Patrice Starck, quickly dependent university, so right now we have no became ensconced at the Bullis School in Potomac. Not wanting income,” explains Vice President Barron. “Being to disrupt their education any further this year, Jordan planned to able to pay the salaries of the faculty allows us to return to her job at Xavier and commute to Maryland on weekends keep more of our teachers. But most significant to be with them. However, she realized this arrangement just is that HHMI found opportunities that allow wouldn’t work. • When word got out that Jordan intended to stay faculty to grow, which will enrich our students’ in Maryland, Peter Bruns, HHMI vice president for grants and research experiences as well.” special programs, offered her a position as HHMI’s senior program Xavier senior Ashley Fornerette, 21, a officer in charge of science education. “I was taken aback,” she biology-education major, is certainly real- says, “and happy that they had enough faith in my ability to make izing that benefit. After the hurricane, Xavier me an offer like that on the spot.” • The decision to leave Xavier biology professor Ray “Trey” Brown asked after 11 years wasn’t easy, though. “I don’t know anyone who’s Fornerette to join him in his lab at Texas worked long-term at Xavier who isn’t absolutely committed to the Tech University in Lubbock, and she was institution,” Jordan says. “Writing my letter of resignation was one delighted to do so. Although Brown is not of the hardest things I’ve had to do in my adult life.” On the other returning to Xavier, Fornerette—who plans hand, her relationship with the school may continue on a different to go to graduate school in environmental level. “There’s lots of science education going on at Xavier,” she

Paul Fetters Paul toxicology—wants her Xavier degree. “At says, “so I expect to work with the university again.”

February 2006 | hhmi bulletin 29 A s p i r a t i o n s At Janelia Farm, researchers will link mathematics, physics, engineering, and computing in the pursuit of better cellular pictures. b y d a n f e r b e r O p t i c a l

A s p i r a t i o n s

Mouse neurobl a s t o ma cells were sti m u l at e d t o d i ff e r e n t i ate in vitro, a n d t h e n l a b e l e d f luorescently. T h e i ma g e , c a ptured with a n e p i f luorescence m i c r o s c o p e , s h o w s a ctin (blue) a n d m icrotubules (green) in two such cells during the e a r ly s ta g e s o f neurite outgrowth ( d n A is yellow). I n d i v i d u a l c h a nnels were subsequently o v e r l a i d a nd colorized. P h o t o g r a p h C o u r t e s y o f T o r s t e n W i t t ma n n

February 2006 | hhmi bulletin 31 I n the world o f b i o m e d i c a l r e s e a r c h , there are big-idea guys and detail guys, microscopy methods and new computing tissue, so researchers could only see into and Nikolaus Grigorieff is a detail guy. He methods to analyze images. Nationally, the dead, chemically fixed cells. And electron doesn’t just sweat the details—he thrives organization is investing tens of millions microscopists like Grigorieff who wanted to on them. For the problems he addresses, of dollars each year in microscopy. That’s determine the atomic structures of protein details are everything. Grigorieff, an HHMI because imaging, Rubin says, “is the most complexes could not do it. So biologists investigator at Brandeis University, has been important technology that we need now.” filled textbooks with descriptions of what appointed one of the first group leaders at they could see, saying little about what HHMI’s new Janelia Farm research cam­ they couldn’t. pus, which opens later this year. He uses L i m i t e d V i s i o n electron microscopy to visualize tiny three- T h e h u ma n e y e dimensional protein structures inside cells. can readily distinguish objects as small Freeze Frame That means grappling with a sea of details. as 100 micrometers across, about the I n a d a r k , A single molecular machine may contain width of a human hair. A typical human high-ceilinged room near Grigorieff’s dozens of proteins, each with hundreds cell is about 10 micrometers in diameter laboratory, Carsten Sachse pours liquid of amino acids. To understand how it and therefore invisible to the naked eye. nitrogen into a stainless steel sample holder works, you need to “open it up, see what’s As of the early 1990s, even state-of-the- on the side of an electron microscope, a inside, and see how those bits and pieces art light microscopes could distinguish foot-thick gray column taller than an NBA fit together,” Grigorieff says. And that’s only objects larger than 0.2 micrometer star. It hisses and boils off an icy steam. where microscopy comes in. in diameter—half the wavelength of He points to a computer monitor next Since Theodor Schwann first peered blue light—which meant that smaller but to the microscope, to an image of gray inside animal cells in the 1830s, curious important structures like ribosomes and fibers packed tightly side by side. They’re biologists have sought to identify cellular spliceosomes were impossible to see in living lab-grown fibrils of amyloid beta peptide, components and comprehend how they cells. Biologists’ vision was restricted by the the molecule in the brain suspected of work together. But until recently, light light microscope’s resolution—its ability causing Alzheimer’s disease, magnified microscopes could not distinguish objects to create a sharp image by distinguishing 59,000 times. The regular packing of much smaller than a mitochondrion—an between two adjacent points. Optics dogma the fibrils means that Sachse, a visiting organelle about one-fiftieth the diameter dictated that resolution was limited to about graduate student who works with Marcus of a typical cell. Electron microscopes have half the shortest wavelength of light used, Fändrich at the Leibniz Institute for Age long helped scientists like Grigorieff make so many scientists thought it could get Research, in Jena, Germany, may well be out smaller objects, such as molecular no better. able to use electron microscope images of machines and small organelles—but only Cellular structures were also difficult to similar preparations to determine the three- in dead, chemically fixed cells. To better view because they’re usually transparent, dimensional atomic structure of amyloid understand such objects, biologists tried making it hard to distinguish them from peptide packed into fibrils. Understanding to obtain sharper images of them and see the watery cytoplasm in which they sit. that could be key to blocking tissue them in action. But until the last decade, Phase-contrast microscopes made that damage in Alzheimer’s patients. “It looks they had little luck. easier by using interfering light waves very promising,” he says. Now that’s changing. “Every 20 years or to distinguish cellular structures from Electron microscopy, Grigorieff says, so there’s a big technical advance that really background. And biologists developed a can help elucidate the molecular structures changes the way biomedical research is plethora of chemical stains and fluorescent of complexes too big to analyze by crys­ done,” says Gerald M. Rubin, vice president antibodies that bound to specific cellular tallography or nuclear magnetic resonance of HHMI and director of Janelia Farm. In structures, making them visible. But cells yet too small to see with a light microscope. the late 1950s, x-ray crystallography allowed usually had to be killed first, and scientists “EM is a good technique to bridge the gap biologists to see the atomic structure of then had to surmise what the structures did to high resolution,” Grigorieff says. proteins, which carry out most of the work when the cells were alive. But not just any electron microscope. of the cell; in the 1970s, cloning and DNA To see molecular machines and small Grigorieff’s $2 million microscope sequencing led to new insights into evo­ organelles, scientists used transmission contains a 300,000-volt field-emission lution, gene regulation, and the biochemical electron microscopes, which utilize electron gun to accelerate electrons workings of individual proteins. electromagnetic coils to focus electron through relatively thick samples, while At Janelia Farm, HHMI has focused a beams instead of glass lenses to focus light. ensuring they march in lockstep—a good deal of its efforts on developing new But electron beams destroy biological property needed to enhance contrast. It

32 hhmi bulletin | February 2006 has specialized CCD cameras—tricked-out the protein. The researchers obtained their neighbors, and, with Thomas Walz large-format digital cameras, essentially— thousands of electron microscope images of Harvard Medical School, a soccer-ball- to capture electron images and diffraction of single frozen spliceosomes and then shaped delivery structure called a clathrin patterns. The researchers run recently devel­ reconstructed the complex’s three-dim­ coat. “We need to know what these oped algorithms on high-powered clusters ensional shape on a computer. The result: molecules look like,” Grigorieff says. of computers to turn huge amounts of a cylinder on a hollow ovoid domain For particularly complex molecular electron microscopy data into three- with an armlike extension that seems machines, it’s often necessary to combine dimensional images. And the darkened optimized to perform the contortions methods. David A. Agard, an HHMI room where Sachse works contains a necessary to cut and splice a threadlike investigator at the University of California, $400,000 climate-control system that RNA molecule. San Francisco, uses a technique he’s opti­ prevents even the smallest drafts and shifts Grigorieff’s team has also determined mized called cryoelectron tomography that in temperature—all to keep their samples the structures of other cellular machines, takes images of particles from different extraordinarily steady, which they must do including, in collaboration with HHMI angles and then assembles those images to obtain good data. investigator Axel T. Brünger of Stanford into a three-dimensional model. He’s used Such attention to technology has paid University, a molecular machine called the method to visualize the centrosome, an dividends for Grigorieff. Working in col­ NSF that helps nerve cells export packets organelle that manages the cell’s internal laboration with HHMI investigator of molecules that enable them to signal skeleton. To show how the centrosome Melissa J. Moore of Brandeis University and former postdoc Melissa Jurica, the group got the first-ever glimpse of the three-dimensional structure of the spliceosome, a molecular machine that A t J a n e l i a F a r m , Nikolaus Grigorieff says, splices newly formed RNA to form messenger RNA, which in turn encodes he’ll try to push single-particle cryoelectron the correct amino acid sequence of microscopy methods to “routinely get to such high resolution that you can build an atomic model.”

carries out that task, he uses single- particle electron microscopy and x-ray crystallography to view its components at atomic resolution. Grigorieff and others also use electron microscopy to visualize two-dimensional crystals of membrane proteins in a lipid bilayer, much like that in the cell. He and others have even used electron microscopy to visualize membrane pro­ teins in atomic detail. In December, Walz reported using this technique, called electron crystallography, to determine the three-dimensional structure of a cellular water-pore protein called aquaporin; the resolution was high enough to spot discrete lipid molecules clinging to the side of the protein. Electron microscope images of single protein complexes (as opposed to crystals) have lower resolution, but they can distinguish parts of proteins, such A s p h e r i c a l r e g i o n o f i l l u m i n ation within a n o p t i c a l l at t i c e m i c r o s c o p e may c o n ta i n t h o u s a n d s o f p o i n t s o f l i g h t f o r ma s s i v e ly as helices and loops. At Janelia Farm, p a r a l l e l , r a p i d i ma g i n g o v e r a l a r g e v o l u m e w i t h i n a c e l l . Illustration Illustration courtesy of Eric Betzig Grigorieff says, he’ll try to push single-

February 2006 | hhmi bulletin 33 particle cryoelectron microscopy methods A closer view within a n o p t i c a l l a t t i c e m i c r o s c o p e to “routinely get to such high resolution r e v e a ls individu a l, tightly f ocused excit a t i o n p o i n t s ( r e d ) that you can build an atomic model.” a r r a n g e d i n a p e r i o d i c a r r a y.

G o i n g L i v e At J a n e l i a Fa r m , other scientists will press light-microscopy methods to observe cells or even entire brains at high resolution. Janelia Farm group leader Eugene W. Meyers, who wrote programs that dramatically sped the sequencing of the human genome, will design new computing methods to assemble three-dimensional reconstructions of working brains from two-dimensional microscope images. Group leader Karel Svoboda, currently an HHMI investigator at Cold Spring Harbor Laboratory, will use two- photon excitation microscopy, a form of fuorescence microscopy developed in the 1990s, to observe living neurons in mouse brains. “We need new imaging

k A r e l S v o b o d a a n d o t h e r researchers use two-photon excitation microscopy invading cells. Others had used electron microscopes to spot influenza virus in to peer into opaque tissues like the brain—an membrane-bound compartments called ability akin to Superman’s x-ray vision. coated vesicles and endosomes, indicating that cells engulfed the viruses in a process called receptor-mediated endocytosis. But no one knew whether the virus homed in on existing pits in the membrane or methods to fgure out how the brain investigator Roger Y. Tsien of the induced the cell to create new ones. works,” Rubin says. University of California, San Diego, Zhuang’s movies showed a red virus Janelia Farm biologists will make use of began working on a naturally fluorescent surrounded by a green coat of clathrin more than a decade of extraordinary advances jellyfish molecule called the green molecules, which coat membrane pits. in light microscopy. Until the early 1990s, fluorescent protein (GFP). Since then, he The pits then bud off to become coated some biologists examined cell shape and and others have developed GFP variants vesicles. “We actually saw pits grow right behavior by using light microscopy, while that glow red, yellow, and many other outside a virus,” she says. That means the others tried to understand their protein colors. Biologists quickly learned to tag virus most likely persuades the cell to take of interest by localizing it in cells that had proteins by fusing them with GFP or its it up by receptor-mediated endocytosis—a been killed and fixed, says Doug Murphy, cousins. Today biologists can follow several result she confirmed by statistical analyses. a cell biologist at Johns Hopkins School differently colored proteins simultaneously Until Zhuang made her movies, no one of Medicine in Baltimore who will move in live cells and in real time. “To see knew influenza viruses used this trick to to Janelia Farm to direct its shared light molecules zip around inside living cells and invade cells. Drugs that target key parts microscopy facility. “Now we don’t just want tissues—that’s been huge,” Svoboda says. of the process could one day help block to see where it is, but how it’s behaving.” Xiaowei Zhuang, an HHMI investigator viral infection. New fluorescent probes make at Harvard University, makes movies of Svoboda and other researchers use two-

that possible. In the mid-1990s, HHMI single fluorescently tagged influenza viruses photon excitation microscopy to peer into Illustration courtesy of Eric Betzig

34 hhmi bulletin | February 2006 opaque tissues like the brain—an ability reduces background. Recently, Svoboda’s stimulates the synapse to reshape itself—a akin to Superman’s x-ray vision. Optically, team watched single nerve endings fire phenomenon that underlies learning. brain tissue resembles milk, he says. The by combining the method with a second interface between fat and water “acts fluorescence method called fluorescence like little mirrors” that scatter light and resonance energy transfer (FRET). O ptical Advances make the substance appear white, which FRET works like this: One fluorescent R e c e n t a d va n c e s i n makes it impossibly murky under older dye emits light of a specific color that excites fluorescence microscopy occurred only fluorescent scopes. a nearby dye to glow a different color. By because microscope designers focused on In two-photon excitation microscopy, tagging one protein with the donor dye developing and adapting new technologies. however, a new type of laser emits bright, and a second protein with the acceptor dye, To see GFP and its cousins, for example, they synchronized pulses of infrared light that scientists can see when and where the two built new lenses from materials that allow for are focused on tiny volumes in the cell. proteins interact. Svoboda chose proteins brighter samples and greater contrast, created Tagged molecules fluoresce only when that would come together only when an thin-film interference filters that transmit they simultaneously absorb two such enzyme called Ras was activated. It turned only a specific color of light, and replaced photons. Outside of the zone of focus, out that activation of single synapses in film cameras with low-noise CCD cameras that’s rare, so the method dramatically the hippocampus activates Ras, which then to record very dim fluorescence. Two- photon excitation microscopy required new microscope objectives that were transparent to infrared light, and mode-locked pulsed lasers, developed in the 1980s, to create very short, very bright pulses of photons. T h e The past few years have seen an explosion of new microscopy methods, which some­ C h a l l e n g e s times read like alphabet soup: two-photon fluorescence correlation microscopy (TPFCM), which helped scientists trace o f i M A g i n g drug transport in tumors; three-dimensional live-cell microscopy, which helped identify never-before-seen threadlike transport lines between live cells; and the GRIN lens, a To bring cells into sharper focus, biologists need a world-class imaging facility, and that’s exactly what HHMI plans at Janelia Farm. But building such a facility offers needle-shaped, insertable lens that can create challenges of its own. For starters, developing new microscopes takes a broad microscopic images several centimeters deep range of expertise. For example, Eric Betzig, a physicist and Janelia Farm group leader, in the brain. has developed a blueprint for a new type of ultra-high-resolution light microscope (see But microscope designers are far from main story) by drawing on mathematics, theoretical and experimental physics, and done. At Janelia Farm, group leader Eric engineering. To make his blueprint a reality, he’ll work with experimental physicists; Betzig, a physicist, will see if he can build computer scientists; and electrical, optical, and mechanical engineers to build prototypes microscopes that use optical tricks to see and to develop them into reliable instruments. His long-term goal is “to make instruments objects far smaller than previous light that are widely used by biologists.” To develop better electron microscopes, microscopes. Betzig is developing what he Chen Xu, a physicist in HHMI investigator and Janelia Farm group leader Nikolaus calls the optical lattice microscope, in which Grigorieff’s lab who will manage Janelia Farm’s shared electron microscope facility, will collaborate with microscope manufacturers like FEI and JEOL to obtain the best electron multiple beams of light interfere with each beams, the best phase plates, and the most sensitive CCD detectors—and customize other to create a three-dimensional lattice them. Grigorieff’s team will develop fast new computer programs that choose particles to that will fill a sample with spots of light. analyze, align them, and piece together a three-dimensional structure. Developing new The result, according to his theories, would microscopes is only part of the challenge. “You also need a facility for [biologists] to do be a microscope that can image objects high-end microscopy with established techniques,” says Winfried Denk, a leading three times smaller than today’s best light microscopist who directs the department of biomedical optics at the Max Planck Institute microscopes and thousands of times faster. in Heidelberg, Germany. At Janelia Farm, HHMI plans to create several core facilities, Others in the small field of ultra-high- including Xu’s shared electron microscope facility, to provide expert technical support to resolution microscopy are pursuing the the biologists who use them. Research institutes like the Max Planck Institute same goals using different designs. and Janelia Farm are great places to develop new technologies, says Denk. “Developing new “The holy grail is to see dynamically technology involves taking risks,” he says. Academic scientists, with their eye on tenure and their next grant, can’t always do that. Research institutes also foster cross-disciplinary imaged living cells noninvasively, to see at collaboration, which is critical for developing new microscopes. At Janelia Farm, physicists the level of an individual protein molecule, will rub elbows with biologists, chemists will talk with computer scientists, and molecular and to see how the molecules interact in biologists will mingle with mathematicians, says Gerald Rubin, director of Janelia Farm. a cell,” Betzig says. “It’s many years away, “We’re going to have all those kinds of people working side by side,” he says. but you can dream about it.”

February 2006 | hhmi bulletin 35 perspectives & opinions

Jeff Lichtman Closely Watched Organisms Sean Sean Kernan

36 hhmi bulletin | February 2006 jeff lichtman likes to invoke baseball legend Yogi Berra’s famous line “You can observe a lot by watching” to describe his own work. Lichtman, who is a professor of molecular and cellular biology at Harvard University and has participated in planning for HHMI’s Janelia Farm Research Campus, is a self-described “neuronal ethologist.” He watches nerve cells in their native habitat—the animal. Powerful new microscopes are facilitating a trend toward observational biology, which Lichtman contends has some key advantages over experimental biology.

For me, an observational approach to biology is very when you have young colleagues, who bring fewer natural, but it’s not that common in my field. Most of biases to biological phenomena. Microscopes are partic- modern biology, and indeed science education from ularly valuable tools for this endeavor in neurobiology elementary school on up, is actually rooted in deduc- because they are a direct link between cell-biological tion: You start with an idea and use experimental tools phenomena and the visual system, our most sophisti- to manipulate variables to test that hypothesis. cated sensory mechanism. The aim of the deductive scientific method is to In the 1990s, neuroscience turned sharply toward try your hardest to prove the idea wrong. If you keep molecular genetics. Many remarkable technological failing at these attempts, the hypothesis stays alive, even advances have resulted, including the ability to make though you haven’t actually proved it. But where have mice that express fluorescent proteins from jellyfish. you gotten? Given that the idea was already out there, In our lab and others’, these animals have dramatically all you’ve done is maintain the status quo. Refuting a improved the ability to visualize neurons over time hypothesis, on the other hand, leads to paradigm shifts. in living animals (so-called intravital microscopy). But it requires compelling data against the hypothesis, Automated microscopes and computational tools also which is difficult to obtain, and when it is negative allow assessment of the structure of many individual data, it is even more difficult to publish. nerve cells in one preparation. Together, these innova- So with deduction, hypotheses tend to become tions may enable us to describe all the synaptic linkages entrenched as the weight of the published record in neuronal circuits, what I like to call “connectomics.” becomes progressively lopsided. You could provide By providing a complete description of the wiring a virtually limitless amount of evidence consistent of the brain, these maps may give us a window into with the hypothesis that Earth is flat, but that doesn’t the inner workings of the mind and may even yield make it so. insights into “connectopathies,” where the wiring has Observational, or inductive, science proceeds in a gone awry. different way. The researcher simply observes a biolog- Some optimists believed that knowing the complete ical system, and hypotheses emerge as a consequence genome sequences of animals meant it was just a matter of, rather than as the motivation for, the observation. of time before we would understand essentially all Nobel laureate Sydney Brenner said, “Progress in biological phenomena as molecular cascades. My sense science depends on new techniques, new discoveries, is that this optimistic view now holds less sway. So many and new ideas, probably in that order,” which is a good concurrent and interacting molecular reactions occur way to sum up how inductive science works. This within cells that scientists simply cannot reduce a living approach, however, has its own pitfalls. First, your cell, much less a multicellular organism, to just so many hypotheses are only as good as the observational tools bags of molecules, hoping to extrapolate the organism’s at your disposal. Second, your life experience molds full repertoire of behaviors. Observational approaches of your worldview and therefore your observational abili- neuronal behavior may provide a much-needed bridge ties. You see things that resonate in your mind as real between molecules and brains. Just as nature videogra- and interesting, and you ignore those things that don’t. phers working in the wild show us a far better view of The strength of inductive science, however, is that behavior than we could obtain by observing specimens new observational tools often reveal unexpected things in a museum case or even a zoo, intravital imaging helps that force you to confront the disconnect between the us move out of the culture dish and into the real jungle current worldview and the revealed world—especially of the brain. –Interview by Julie Corliss

February 2006 | hhmi bulletin 37 perspectives & opinions

Eric Betzig A Microscopist’s View A group leader at Janelia Farm hopes to do for biology what the Hubble Space Telescope did for astronomy. Paul Fetters Paul

38 hhmi bulletin | February 2006 physicist eric betzig made a dramatic contribution to the imaging field in the 1980s and 1990s with his work on the near-field microscope. This technology, which shattered the theoretical “diffraction limit” imposed on spatial resolution by the wavelength of light, imaged small structures at higher resolutions than scientists thought possible. Techniques to peer inside living cells at similar high resolutions are still too slow, however. So when Betzig comes to the Janelia Farm Research Campus, opening this fall, he plans to develop a new method—“optical lattice microscopy”— to rapidly image the constant activity within living cells.

Which fields of biology stand to benefit most from you can optimize them so that the fluorescence of a improvements to microscopy? labeling molecule is sensitive to a parameter of interest. eb: Basically, the interfaces between cell biology and Techniques like fluorescence lifetime imaging give you molecular biology. We understand the genetic sequences contrast based on how long it takes for a photon to be by which proteins are made, and we understand, in emitted from the molecule, which can act, say, as a pH many cases, the structures of the proteins. What we don’t sensor or a viscosity sensor. So this is an ongoing area understand in sufficient detail is when they’re expressed, of interest: both on the chemistry side, in how to create or not expressed, within the cell; how that relates to new and better labels, and on the technology side, in environmental factors; what other proteins are present how to get the information from the photons. within the cell right then; how the proteins interact On a biological level, there are dynamics happening on with one another; and how those areas of interaction are all time scales, from the femtosecond to the many, many localized to drive the cell and its function. tens of seconds. There’s a whole continuum of processes Conventional optical microscopy cannot provide high- happening, and you want to be able to study as many as enough resolution to address these questions. But if the you can. So the second goal is to increase the dynamics. techniques that are at the edge right now pan out, we’ve The reason we do optical microscopy (as opposed to only seen the tip of the iceberg. I make an analogy with electron microscopy)—despite the limited resolution—is astronomy: When people at the turn of the last century that we want to be able to look at living cells without looked at Mars through telescopes with inadequate resolu- pumping in so much energy that we perturb them. But tion to see any detail, the fuzzy lines they saw started them the more energy you pump into trying to interrogate thinking about built canals and Martian civilizations. your sample, the greater the chance of perturbing it. Similarly, when you crack open any issue of Cell The third goal, then, is to achieve the greatest dynamics or Biophysical Journal, you see tons of interpretive possible so that we can look at things in real time, yet do studies based on relatively low-resolution cell images. so noninvasively. Oftentimes, the interpretations are necessarily specula- Of course, the fourth area would be high resolution: tive. But as we begin to get higher resolutions, better trying to get to the diffraction limit and push beyond it. dynamics, and the ability to access deeper tissue, we’re And finally, deep-tissue imaging: We need to do better going to get vast improvements in understanding. With than diffraction-limited resolution, which confines us to factor-of-two or -four increases in each of those areas, really thin and idealized samples, and actually push into we’ll be creating this multidimensional space of infor- the brain and other areas. Those are the five main issues mation that can grow by orders of magnitude. All these that I see people working on in the field of optics. systems that we’ve looked at before very blurrily we will now see in greater detail. It’s going to be like the differ- Is there an ideal goal? ence between using those old telescopes and using the eb: In terms of resolution, once you get to the molec- Hubble Space Telescope. ular level, that’s pretty much it; there’s not much more to do there. But in terms of dynamics, you can always Which aspects of optical microscopy need to be improved? ask for more. In terms of slicing and dicing your signal eb: The first is new contrast mechanisms: To find and getting different contrast, you can always ask for out more about the cell optically, you need a wider more. In terms of how deep you can go, you can always and better set of labels. Single molecules are basically ask for more. There’s loads of room for improvement. exquisite reporters of their local environment, and C o n t i n u ed on Page 56

February 2006 | hhmi bulletin 39 39 perspectives & opinions

Q & A

What did see you through your first microscope ? Some scientists have been peering through microscopes for decades. Still, they often vividly remember their first glimpse through a lens, squinting at some otherwise imperceptibly tiny thing below. Here, a few HHMI investigators recall that seminal moment. –Edited by Kathryn Brown

DAVId A. AgARd PAMELA J. BjÖRKMANN NIKOLAUS GRIgORIEFFt TOM K. KERppOLA Professor of Biochemistry Max Delbrück Professor of associate Professor of Professor of Biological and Biophysics and of Biology, California Institute Biochemistry, Brandeis Chemistry, University of Pharmaceutical Chemistry, of Technology University, and incoming Michigan University of California, Janelia Farm group leader San Francisco

A: A: A: A: “I believe I was 7 or 8 when “I think it was during a “When I was about 12, my “When I was growing up I was delighted to receive 7th-grade science class parents gave me my first in Finland, experimental a microscope for my that I first looked at a drop microscope. In my excite- science was not a big part birthday. I immediately ran of pond water through ment to peer through it, I of school. At home, I out to the creek to collect a microscope and saw immediately began looking once discovered parts of some algae—and rather an amazing collection of for a suitable substance to my grandfather’s antique stagnant water—thinking strange creatures—hydra, study. Eventually, I plucked microscope. With some tape rigorieff: Kerppola: Fetters Fetters Paul Paul it would be full of bugs. rotifers, and other tiny a hair from my own head.” and cardboard, I managed I was right. I also looked organisms. I was fascinated to fashion these bits into a at onion cells and cells to think that there was a working scope, producing a from my own cheek. whole world out there we blurry image. I was unim- What a blast!” don’t usually see. Maybe pressed. It wasn’t until many that inspired me to want years later, after finding ways to know what else could be to study molecular events revealed by high-resolution by imaging, that the micro- imaging.” scope became one of my favorite tools.” Lab Björkman: Agard: Tabios/Agard G Mariano Gravenor Misha

40 hhmi bulletin | February 2006 chronicle SCIENCE EDUCATION PG.42 INSTITUTE NEWS PG.44 LAB BOOK PG.48 Hearing-impaired Med Student Aims to Enhance Science Is a Global Enterprise / Craig Named General Cancers Use “Cellular Bookmarks” / Protein-Pairing Cochlear Implants / Loudoun County Preschoolers Counsel / HHMI Enters into Agreements on Mice / Method May Yield New Drug Targets / The Immune Indulge Curiosity / Students Captivated by Partnership with Science Sealed / Nurse Elected Trustee. System: Imaged at Last Evolution-Religion Debate

IN MEMORIAM PG.51 UP-CLOSE PG.52 NOTA BENE PG.54 Lawrence C. Katz Scientists Crack Code for Motor Neuron Wiring: Three Scientists Win Cancer Research Prize / Understanding how a developing chick embryo assigns Whitehead Institute Taps Page as Leader / Researchers different functions to nerve cells in the spinal cord may Shine in Esquire yield payoffs for humans

HHMI researchers have deciphered a key part of the regulatory code that governs how motor neurons in the spinal cord connect to specific target muscles in limbs (pg. 52). This transverse section of a chick spinal cord is stained with antibodies against various transcription factors expressed in motor neurons.

February 2006 | hhmi bulletin 41 science education Improving Cochlear Implants A young researcher aims to make the technology responsive to pitch and widen deaf people’s perceptions of complex sound environments.

Experiencing the limitations of his own cochlear implant inspired Chad Ruffin to better the device.

Jay Rubinstein, director of the Bloedel Center, to test a speech-processing algo- rithm designed to do just that. Studies in animals show that this algorithm conveys a sound’s fine structure to the brain, Rubinstein says. And some people whose implants were reprogrammed with the new algorithm report improved speech perception. Ruffn is developing psycho- physical tests to prove that the algorithm is in fact allowing fne structure informa- tion to reach the brain. For the congenitally deaf, says Rubinstein, the earlier they receive an implant, the better. Older children and adults show a great deal of variability in how Cochlear implants have helped bring profoundly deaf individuals well they perform with implants. Ruffn still requires assistive listening devices at into the hearing world, but one HHMI fellow says the technology needs the movies and to hear lectures in a class- improvement. Chad Ruffn says users have a tough time understanding room environment, but he marvels at the changes he’s experienced since his implant. speech in noisy environments, largely because today’s implants transmit “My social circle expanded exponentially almost no information about pitch—the tone that allows the hearer after the implant,” and, he says, “Now I can converse in the dark with a friend; I don’t to distinguish one sound from another, as in picking one voice out of have to read lips.” the din. Ruffn knows frsthand; he received an implant 6 years ago. Ruffin began working in the field of implant research in 2004 after completing He hopes to correct the limitations of are sensitive mainly to the changes in ampli- his frst year of medical school at Louisiana cochlear implants through his research. tude in a series of spoken syllables or words. State University in Shreveport. His investi- An HHMI medical research training Although this feature gives “good speech gations took him to the University of Iowa fellow at the Virginia Merrill Bloedel perception in the quiet,” Ruffn says, “if in Iowa City, where he met Rubinstein. Hearing Research Center at the University you start to add complex sounds, such as When Rubinstein moved to the University of Washington in Seattle, Ruffn is studying music or noise, the perception goes down of Washington, Ruffin applied for the how cochlear implants can be programmed dramatically.” HHMI fellowship to join him. Although to transmit more information on frequency, For cochlear implants to give users a he plans to become a surgeon, Ruffin thereby enabling the user to discriminate better level of pitch perception, they must would also like to do long-term research. between the pitch of different voices. deliver information on the fne structure of “And I decided that if I was going to do Each implant contains a tiny com- the sound—the tiny and rapid changes research,” he says, “it’d be something that puter that receives sound information in frequency. Ruffin is working with I’m interested in.” –Melissa Lee Phillips from the environment and then uses speech-processing programs to relay this information—or at least some of it—to “I decided that if I was going to do research, it’d be  the brain. Current speech processors rely almost entirely on the intensity of sounds something that I’m interested in. within a few frequency bands; that is, they chad ruffin ” Brian Smale 42 hhmi bulletin | February 2006 Never Too Young for Science says Odette Scovel, science supervisor for the Loudoun County schools. To help A program aimed at preschoolers exploits children develop literacy skills, teachers their natural curiosity and hands-on predispositions. read them science-related books and encourage them to talk about what they For 4-year-olds, what could be vative preschool science program provides are doing as they work. more fun than playing with water? And such activities to help children begin to Supported by a 2-year, $50,000 grant from a science educator’s point of view, think critically and solve problems. The from HHMI, the program partners the what could be more powerful than tapping curriculum, steeped in research about how Loudoun County schools and Florida’s children’s fascinations? children learn, capitalizes on their natural Fairchild Tropical Botanic Garden, whose In a Head Start classroom at Dominion curiosity and trains teachers and parents to staff also work with preschool science High School in Loudoun County, Virginia, arouse that curiosity. teachers at the Miami site of the Children’s children dressed in purple smocks are Teachers can choose from 21 activities Home Society of Florida, which serves exploring the concept of volume by pouring in a toolbox that contains experiments, thousands of children eligible for adoption water from a bucket into another container questions, and suggestions. In one activity, or foster care. Selected preschool classes with a line marked by masking tape. Using students learn to observe and compare by in Harrisburg, Pennsylvania, also use the beakers and liter containers, they pour making a fruit salad, discussing the similari- program. The grantees collaborate with the water in or take water out, repeatedly ties and differences in the pieces of fruit, and curriculum’s developer, Cognitive Learning trying to judge how much liquid they need counting the number of pieces of each type Systems (CLS), also of Harrisburg. to fll the container to the mark. “They are of fruit they add to the salad. In another “So much is going on in children’s brains learning to use the tools in ways that were activity, children use a pan balance to weigh when they are doing something as simple intended—and maybe in ways that were objects, determine which are heavier or as pouring water,” says Joanna Garner, not intended. But they are excited about lighter, and sort them by weight. vice president for program development learning, and that’s wonderful,” says teacher The activities can be integrated seam- at CLS. She provides teachers and parents Kathleen Miller. lessly into the preschool day, allowing with a “science-behaviors checklist” to In Loudoun County public schools and teachers to take advantage of “teachable determine how well children are using select schools in two other states, an inno- moments” to reinforce or extend concepts, C o ntinued o n Page 5 6 Students Drawn to Debate on Evolution and Religion Must evolution and religion be at odds? A theologian, a philosopher, and two scientists help high school students grapple with tough questions.

Many people think science and (Left to right) Father James Wiseman, religion make uncomfortable bedfellows. philosopher Michael Ruse, and scientists Father James A. Wiseman isn’t one of Sean Carroll and David Kingsley them. “I am a believing Christian who evidence for biological evolution, which totally accepts evolutionary theory,” the Kingsley called “absolutely overwhelming.” Benedictine monk and theology professor “I don’t see a fundamental conflict at the Catholic University of America told between religion and evolution,” he said. a group of Washington, D.C.–area high “Evolution is a description of how life school students. The teenagers gathered changes. That’s different from addressing at HHMI headquarters for a discussion “Should evolution be taught with a where the whole universe came from. following the 2005 Holiday Lectures on disclaimer, presenting it as one theory Darwin says nothing about why the Science, which focused on evolution. among many?” universe exists. There is still the critically In addition to Wiseman, the panel “Could creationism and evolution be important ‘why’ question of how the included Michael Ruse, a philosophy different paths to the same answer?” universe came to be that isn’t addressed by professor at Florida State University, “Do you believe in God? If so, how do evolutionary theory.” and the two Holiday Lectures speakers, you reconcile that belief with the science Ruse observed, “I can’t see why one HHMI investigators Sean B. Carroll of that you do?” can’t be both an ardent Darwinian and a the University of Wisconsin–Madison Although the speakers brought different C o ntinued o n Page 5 6 and David M. Kingsley from the Stanford viewpoints to the discussion, they agreed for more information View the lectures and discussion at University School of Medicine. that it is possible to be an evolutionist and www.hhmi.org/biointeractive/evolution The high school students peppered the a Christian. They encouraged the students A free DVD of the Holiday Lectures on evolution and the discussion of evolution and religion will be available

Paul Fetters Fetters Paul speakers with challenging questions: to use the scientifc method to examine the in April 2006.

February 2006 | hhmi bulletin 43 institute news

“Science Is a Global Enterprise” New grants support top scientists abroad.

countries

Croatia Czech Republic Estonia HunGary Lithuania poland russia slovak republic

Tamás Freund, a talented scientist in Hungary, has been tempted by prestigious job offers in the West. In 1995, though, a grant from HHMI helped him decide to stay in his native country. A second grant in 2000 enabled him to build a well-equipped lab in Budapest. “For science to flourish, fresh ideas often come  Now, Freund has earned a third grant from fresh new scientists. from HHMI. He is 1 of 28 exceptional scientists in eight countries who were peter bruns ” selected in November to receive new inter- national research awards from HHMI. The new grants support research in his new HHMI grant to explore the role Each scientist will receive U.S. $75,000 Croatia, the Czech Republic, Estonia, in neuron signaling of a mind-altering a year for 3 years. HHMI will contribute Hungary, Lithuania, Poland, Russia, and compound naturally produced in the $50,000 per scientist, and EMBO and the Slovak Republic. Each scientist will human body. He hopes the research will participating member countries will provide receive $100,000 a year, and the 28 awards lead to new drugs to treat anxiety and new the additional $25,000. total $14 million over 5 years. Sixteen of ways to combat drug dependence. “HHMI already has an ongoing program the researchers have previously received Commenting about the awards, HHMI in support of established science in central HHMI international grants. President Thomas R. Cech said, “It is Europe, but we recognize that for science to In addition to supporting scientists in vital to invest in the scientifc capacity of fourish, fresh new ideas often come from the Baltics, central and eastern Europe, and economically less advantaged countries fresh new scientists,” said Peter J. Bruns, Russia, HHMI awards competitive grants because science is a global enterprise.” HHMI vice president for grants and special to researchers in Latin America and Canada In the same spirit of global science, programs. “This new program aims to help and supports infectious disease and parasi- HHMI and the European Molecular Biology promising new scientists get established tology research worldwide. The Institute Organization (EMBO) have singled out six with resources, space, and time in the early has awarded a total of $129 million to 353 outstanding central European scientists to years of their independent careers.” scientists in 39 countries since 1991. receive EMBO/HHMI Startup Grants—

Freund, now director of the Institute of awards to help the scientists establish their For more information Experimental Medicine of the Hungarian frst independent laboratories in the Czech For details about the new grants, including the names of the grantees, go to www.hhmi.org/news/122205.html Academy of Sciences in Budapest, will use Republic, Estonia, and Hungary. and www.hhmi.org/news/120605.html

44 hhmi bulletin | February 2006 institute news Craig Alexander Named as HHMI’s General Counsel The Trustees of the Howard Hughes As deputy general counsel, Alexander Medical Institute have elected Craig A. played a major role in formulating and Alexander as the Institute’s vice presi- implementing HHMI’s policies on “Science Is a dent and general counsel. He assumed intellectual property, in providing legal his new role in January. advice concerning the investment of the Alexander, 46, had served as HHMI’s endowment, and in guiding the devel- Global Enterprise” deputy general counsel since 1994. He opment of the Janelia Farm Research New grants support top scientists abroad. succeeds Joan Leonard, who retired as Campus in Ashburn, Virginia. general counsel after 11 years in that Alexander joined HHMI as an asso- post. She is now senior counsel to the ciate general counsel in 1992 from the countries Institute’s president, Thomas R. Cech. Indianapolis law firm of Sommer & Barnard, CROATIA “Over the past decade, Craig has P.C. Before that, he handled numerous in accounting from Butler University in CZECH REPUBLIC been Joan Leonard’s active collab- matters involving HHMI while an associate Indianapolis. He is also a certified public ESTONIA orator and partner in managing the in the Washington, D.C., office of Paul, accountant. Alexander is a member of HUNGARY Office of the General Counsel. His Weiss, Rifkind, Wharton & Garrison. the tax, science, and technology sections LITHUANIA broad legal expertise and deep famil- A magna cum laude graduate of the of the American Bar Association, the POLAND iarity with HHMI make him uniquely Georgetown University Law Center, National Association of College and RUSSIA qualified for this new assignment,” where he was editor of the law journal, University Attorneys, and a variety of SLOVAK REPUBLIC said Cech. Alexander received a bachelor’s degree other organizations.

“His broad legal expertise and deep Tamás Freund, a talented scientist in Hungary, has been tempted by prestigious familiarity with HHMI make him uniquely job offers in the West. In 1995, though, a qualified for this new assignment. grant from HHMI helped him decide to stay in his native country. A second grant in THOMAS CECH 2000 enabled him to build a well-equipped ” lab in Budapest. “For science to flourish, fresh ideas often come Now, Freund has earned a third grant from fresh new scientists. Spotlight | Janelia Farm Dinner from HHMI. He is 1 of 28 exceptional scientists in eight countries who were peter bruns ” selected in November to receive new inter- national research awards from HHMI. The new grants support research in his new HHMI grant to explore the role Each scientist will receive U.S. $75,000 Croatia, the Czech Republic, Estonia, in neuron signaling of a mind-altering a year for 3 years. HHMI will contribute Hungary, Lithuania, Poland, Russia, and compound naturally produced in the $50,000 per scientist, and EMBO and the Slovak Republic. Each scientist will human body. He hopes the research will participating member countries will receive $100,000 a year, and the 28 awards lead to new drugs to treat anxiety and new provide the additional $25,000. total $14 million over 5 years. Sixteen of ways to combat drug dependence. “HHMI already has an ongoing the researchers have previously received Commenting about the awards, HHMI program in support of established science HHMI international grants. President Thomas R. Cech said, “It is in central Europe, but we recognize that for In addition to supporting scientists in vital to invest in the scientific capacity of science to flourish, fresh new ideas often the Baltics, central and eastern Europe, and economically less advantaged countries come from fresh new scientists,” said Peter A MODEL EVENING: Members of the A FEW POINTERS: GERALD RUBIN, director INFORMAL BRIEFING: Loudoun County Russia, HHMI awards competitive grants because science is a global enterprise.” J. Bruns, HHMI vice president for grants Virginia House of Delegates visited the Janelia of Janelia Farm, uses a scale model to explain Supervisor LORI WATERS (right), whose district to researchers in Latin America and Canada In the same spirit of global science, and special programs. “This new program Farm Research Campus last November to the campus layout to Delegate VINCENT J. includes the Janelia Farm campus, joined and supports infectious disease and parasi- HHMI and the European Molecular aims to help promising new scientists get learn firsthand about HHMI’s investment in CALLAHAN (R-34th District), who is dean of other local officials for the evening. GERALD tology research worldwide. The Institute Biology Organization (EMBO) have established with resources, space, and time Northern Virginia. The dinner and reception the Northern Virginia delegation and chair of RUBIN and KEVIN MOSES (center), associate has awarded a total of $129 million to 353 singled out six outstanding central in the early years of their independent were part of the annual retreat for members of the Appropriations Committee. director for science and training at Janelia scientists in 39 countries since 1991. European scientists to receive EMBO/ careers.” the Appropriations and Finance committees. Farm, provided an update about recruitment

Freund, now director of the Institute of HHMI Startup Grants—awards to help For more information and the Janelia Farm graduate program. Experimental Medicine of the Hungarian the scientists establish their first indepen- For details about the new grants, including the names For more information of the grantees, go to www.hhmi.org/news/122205.html To learn more about Janelia Farm, visit

Academy of Sciences in Budapest, will use dent laboratories in the Czech Republic, and www.hhmi.org/news/120605.html Fetters Paul by Photos www.hhmi.org/janelia Estonia, and Hungary. 44 hhmi bulletin | February 2006 February 2006 | hhmi bulletin 45 institute news New Agreements on Mice HHMI aims to help manage the logistics and allay the cost of the ever more refined yet ubiquitous laboratory mouse.

With the use of laboratory mice Jackson Laboratory (TJL), the leading skyrocketing, it’s no surprise that scien- independent center for mouse genetics tists across the country face a murine in the United States, as well as one of housing crunch—and that’s just for three NIH-supported mouse repositories starters. Not only do the mice repre- and home to two HHMI investigators. sent a significant investment of time The agreement focuses on improving and laboratory resources but require- ways to archive and distribute valuable ments by organizations like HHMI and strains of mice and develop better tools the National Institutes of Health (NIH) for managing mouse colonies. Second, mean that researchers also have to fnd HHMI is running a short-term trial cost-effective ways to share mouse stocks program with Transnetyx, a Memphis- with their colleagues and preserve them based company, to outsource genotyping, “We’re always for future experiments. the important task of determining the looking for  “Because most institutions’ facilities genetics of a mouse. are bursting at the seams, any way that “This gives us an opportunity to ways we can you can more effectively maintain your invigorate our historic relationship with improve how mouse colonies will be a big benefit the Jackson Lab by funding projects that research is  to the community,” says Nathaniel are relevant to the aims of both TJL and Heintz, an HHMI investigator at the HHMI and are also cutting-edge,” says being done.

Rockefeller University. He ought to David Clayton, HHMI’s chief scientifc philip perlman know: Heintz has created hundreds of offcer, noting that HHMI has collabo- ” transgenic mice in studying the devel- rated with TJL since the 1980s. opment of the mammalian brain and About 75 percent of the nearly 3,000 facility is a necessary part of mouse deposited many of them in an NIH- mouse strains at TJL are stored as frozen research. This genotyping determines supported facility that makes them embryos or sperm. Cryopreservation which individual mice have certain available at nominal cost. is efficient, but recovering live mice mutant and wild-type genes. It is a time- More than one-third of HHMI’s 321 requires techniques not widely used consuming and costly activity, which investigators now use laboratory mice in HHMI labs. So part of the initia- is why HHMI is funding the pilot in their research, and that percentage tive focuses on training lab staff program with Transnetyx. More than 70 is likely to increase. With spending on and developing better cryopreserva- HHMI investigators are now trying out animal breeding and maintenance hitting tion approaches. Other goals include the company’s automated approach to an estimated $47 million between 2002 creating more effective ways to tag mouse genotyping. and 2004, an Institute-wide initiative individual mice and enhancing mouse “This is the kind of work that is was required. colony management software that was repetitious and not very interesting Enter Philip Perlman, one of largely developed by HHMI investi- for a researcher to do, but we have to HHMI’s senior scientifc offcers, whose gator Simon W.M. John. know the answer,” says Richard A. own research focused on mitochondrial Perlman says the Institute is planning Flavell, an HHMI investigator at genes in yeast—a more manageable another project to help defray the costs Yale University School of Medicine model organism. Perlman has spent the of archiving mutant mice developed and one of the scientists participating past 18 months identifying approaches in HHMI labs. With HHMI partially in the program. to improve the management of mouse covering the expenses, Perlman expects Each of these initiatives can make colonies in HHMI laboratories so the labs to break even in the frst year. mouse research in HHMI laboratories a that resources could be freed for more “We’re always looking for ways we can little more effcient and can potentially research. improve how research is being done,” reduce the cost of mouse breeding for After consulting with HHMI investi- he notes. research. Notes Perlman, “Whichever gators, several NIH scientists, and experts Because many mutant mice do not projects prove to be effective for in mouse genetics and animal care, the look any different from wild-type mice HHMI researchers will also be useful Institute has taken two steps. First, it has or from other mutant mice, DNA geno- for the wider community of mouse

entered into a new agreement with the typing of every mouse born in a mouse researchers.” Southwestern Medical Center at Courtesy Dallas of Texas the of University

46 hhmi bulletin | February 2006 HHMI and Science Partner to Improve Science Education

HHMI and the journal Science have begun a collaboration to showcase innovative approaches to teaching science. Sir Paul Nurse Elected A new monthly section of the journal will engage research scientists in thinking as HHMI Trustee about ways to improve education at all levels by providing a forum for sharing Sir Paul Nurse, president of the Nurse graduated from the University ideas and sparking discussion. Rockefeller University, has been elected a of Birmingham in 1970 and received his The new education section will be Trustee of the Howard Hughes Medical Ph.D. from the University of East Anglia produced by Science’s editorial staff. It Institute. He is one of 11 Trustees of the in 1973. He headed laboratories at the will feature peer-reviewed research as well Institute. University of Sussex, the Imperial Cancer as scholarly literature reviews, essays, and Nurse, 56, is a distinguished scien- Research Fund (ICRF), and Oxford other original writing on science education. tist who shared the 2001 Nobel Prize University before rejoining the ICRF in The section will focus on undergraduate in Physiology or Medicine with Leland 1996 as its director general. He presided and graduate level education but will also H. Hartwell and R. Timothy Hunt for over its merger with the Cancer Research showcase innovations in K–12 science fundamental discoveries concerning Council. education. control of the cell cycle. A geneticist who Nurse’s work has been recognized “Why Science?” asked Peter J. Bruns, uses fission yeast as a model system, he around the world. He is a fellow of the HHMI vice president for grants and continues an active research program that British Royal Society and, in 1995, special programs. “Because that’s where focuses on the cell cycle and how the cell became a foreign associate of the U.S. the scientists are. Science is read by scien- organizes its internal structures to prepare National Academy of Sciences. He tists, and scientists are an important key for cell division. has received the Gairdner Foundation to great science education. Good research A native of England, Nurse became International Award (1992), the Alfred P. and good teaching can go hand in hand Rockefeller’s ninth president in 2003. He Sloan Jr. Prize from the General Motors to the mutual benefit of both.” had been chief executive of Cancer Research Cancer Research Foundation (1997), In an editorial in the December 16, UK, the world’s largest cancer research and the Albert Lasker Award for Basic 2005, issue of Science, HHMI President organization outside the United States. Medical Research (1998). Thomas R. Cech and Science Editor- in-Chief Donald Kennedy argued that research scientists should care about the strength of science education in view of the “pipeline issue”—where we will get Awards Smooth Path the next generation of research leaders— and in view of the policymaking threat to Research Career posed by voters who do not under- stand science or the process of scientific The transition from advanced or are in the first 2 years of their first thinking. training to operating a self-sufficient lab independent positions are eligible to “If the electorate distrusts science and is difficult for any scientist. Physician- compete for the awards. doesn’t understand how scientists explore scientists, who are expected to handle The Institute will award 13 grants and interrogate the natural world,” the a clinical caseload while they are trying annually. Each award totals $150,000 authors asked, “how will they vote on issues to establish a research career, can find it over 3 years. Institutions employing the ranging from stem cell research and global especially challenging. awardees must agree to let them spend climate change to the teaching of intelligent To address the need for support 70 percent of their time on research. The design in our schools?” during that transition, HHMI is estab- funds may be used for research expenses, The new section in Science debuts this lishing a program of early career awards. such as supplies, technical support, and year. Former HHMI medical student fellows small equipment. and HHMI-NIH research scholars who HHMI will make its first early career

Courtesy of Rockefeller University are just finishing their advanced training awards in June 2006.

February 2006 | hhmi bulletin 47 lab book Cancers Use “Cellular Bookmarks” to Target Favorite Sites of Metastasis

HHMI researc h e r s a n d t h e i r colleagues h av e colonies—are recruited by tumors and aid in the growth of discovered that nonmalignant bone marrow cells establish “cellular new blood vessels. The generation of new blood vessels occurs bookmarks” in target organs that guide the spread of cancer cells through a process called angiogenesis. In previous studies, the to their predetermined destinations. researchers had shown that co-recruitment of hematopoietic The researchers say their findings could have a major impact BMDCs expressing an angiogenic factor receptor, VEGFR1, on how oncologists assess the likeliness of metastasis to specific along with the vascular cells accelerated the assembly of newly organs. Their discovery may also help identify subsets of high- formed blood vessels and tumor growth. risk cancer patients prone to distant metastases who would likely “In the current paper, we set forth another novel concept by beneft from a more aggressive therapy to prevent cancer relapse. demonstrating that a nonmalignant cluster of VEGFR1-positive Ultimately, understanding how cellular bookmarking works at hematopoietic BMDCs were recruited to a premetastatic niche, the molecular level could lead to information that may help thwart thereby establishing a permissive docking site prior to the arrival metastasis, a major cause of death among cancer patients, says one of the circulating tumor cells,” says Rafi. A “premetastatic of the study’s senior authors, Shahin Rafi, niche” is a cellular microenvironment an HHMI investigator at Weill Medical that is specialized for the development of College of Cornell University. metastatic tumor cells. The researchers, led by David Lyden In experiments with mice that had been and Rafi, published their fndings in the implanted with highly metastatic lung December 8, 2005, issue of the journal cancers or melanoma cells, the scientists Nature. Lyden is at Memorial Sloan-Kettering discovered that BMDCs arrived at the Cancer Center and Weill Medical College. premetastatic sites before the cancer cells Rafii and Lyden’s group had estab- did. They also found that such clusters lished that a specific subset of bone appeared before metastases developed in marrow–derived cells (BMDCs)—which mice genetically predisposed to developing CLUSTERS OF BONE MARROW-DERIVED CELLS are composed of hematopoietic progen- (GREEN) AND ANGIOGENIC FACTORS (RED) tumors—a system that closely mimics itor cells capable of dividing and forming MAY MARK AREAS FOR METASTASIS how cancers develop. –Dennis Meredith

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Breast Cancer Drugs May Slow To see if they could block this growth, the research scholar at the Institute of Biotechnology Growth of Lung Cancer team started with the enzyme aromatase. It in Vilnius, Lithuania, and chemists at the Institute A few years ago researchers discovered that, was a natural target because it converts testos- of Organic Chemistry in Aachen, Germany, much like breast tumors, some lung tumors terone into estradiol, a potent form of estrogen harnessed a group of essential enzymes also thrive on estrogen. Now a medical also used in hormone replacement therapy. to add various chemical groups to DNA, thereby student conducting research on an HHMI In addition, drugs that inhibit aromatase have altering its function. fellowship and colleagues have managed already made it to market as treatments for The enzymes at the heart of the study, to stop the growth of human lung cancer cells breast cancer. “The production of estrogen known as DNA methyltransferases, are one of

in mice with a class of breast cancer drugs takes several steps, and aromatase is the the tools cells use to turn genes on and off. ©2005. 438(7069):820-7. called aromatase inhibitors. key to the process,” said Weinberg. “Without In this study, the scientists demonstrated that “It was a natural progression of the work aromatase, you don’t get estrogen.” methyltransferases can be used to transfer Nature that had already been done linking estrogen The studies were reported in the sizable chemical groups to large DNA mole- and lung cancer,” said Olga Weinberg, who December 15, 2005, issue of the journal cules in a sequence-specific manner. delayed her fourth year at Vanderbilt University Cancer Research. Earlier studies had suggested that trans- School of Medicine to work on the project. ferring chemical groups larger than a methyl The findings suggest a new way to treat lung Biotechnology’s New Chemical Tool group was not feasible. “No one has really cancer in women—a group whose death rate Researchers have developed a new technique thought about possible applications [of from the disease is surging. that allows them to modify specific sequences this] before because no one thought it was “More women are dying now from lung cancer within a DNA molecule. The approach not only possible,” said Klimašauskas. He predicts than from breast cancer,” said senior author will reveal the impact of biochemical alterations that DNA methyltransferases will become a Richard Pietras, Weinberg’s research mentor to DNA but also could have far-reaching impli- standard laboratory tool like restriction endo- at the University of California at Los Angeles. cations for DNA-based medical diagnosis and nucleases. “We followed one of the clues as to why this is nanobiotechnology. The work was published in the January happening, namely that estrogen drives the growth Combining chemistry with biotechnology, 2006 issue of Nature Chemical Biology. of certain types of lung cancer in women.” Saulius Klimašauskas, an HHMI international Image Image reprinted by permission from Macmillan Ltd: Publishers

48 hhmi bulletin | February 2006 Protein-Pairing Method May Yield New Drug Targets

Plasmodium falci pa ru m , t h e protozoan t h at An illuminating fnding from the analysis is that some groups causes the most severe form of malaria, is one of the deadliest of of proteins with seemingly disparate functions may nevertheless human pathogens, killing up to 2.7 million people each year. But interact. One large cluster includes proteins implicated in chro- the parasite is particularly diffcult to study with standard genetic mosome modifcation, gene regulation, and protein and mRNA methods, thus hampering the search for drugs or vaccines, says Stanley stability. Another cluster includes proteins important in host-cell Fields, an HHMI investigator at the University of Washington. In invasion. “This shared function implies that in the second cluster, the hope of bypassing this bottleneck, researchers from his laboratory some uncharacterized proteins might also be involved in infec- and Prolexys Pharmaceuticals recently adapted a method that Fields tivity,” Fields says, and this offers hope that they could become invented, called the yeast two-hybrid assay, to map protein-protein targets for future antimalarial drugs. interactions in P. falciparum. The P. falciparum protein-interaction network developed by the The test, performed by expressing pairs of randomly chosen researchers has also yielded information about evolution. In a P. falciparum proteins in yeast cells, tells researchers whether the letter in the same issue of Nature, HHMI medical student fellow two proteins can physically touch one another, or “interact,” within Taylor Sittler and colleagues at the University of California, San the cell. “The utility of the assay is based on the principle of guilt Diego, compared P. falciparum network clusters with those in flies, by association,” Fields explains. Proteins that interact are likely to yeast, worms, and bacteria. P. falciparum is already recognized as participate in common cellular processes. If you know the function an evolutionary “oddball”—only about 40 percent of its proteins of one of the proteins, you can reason that the proteins it interacts have similar counterparts in other organisms. Sittler’s analysis with may be involved in the same process. found that the parasite’s protein networks are as unconventional Using robots and other high-throughput technologies, the as the proteins themselves. Only three P. falciparum networks researchers screened more than 32,000 protein combinations, had counterparts in yeast, and the protozoan had no networks in identifying 2,846 unique pairwise interactions in their study. common with the other organisms. Because some P. falciparum Even so, says Fields, “We’ve only scratched the surface of what’s proteins have counterparts in other species, the research suggests out there.” He and his colleagues published their results in the that similar proteins might serve distinct roles in different species November 3, 2005, issue of Nature. by making unique network connections. –Paul Muhlrad

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Technique Captures New Information paper, which was published in an early online in the journal Nature. The two groups were led About Protein Synthesis Machinery article in Science Express on December 1, by Craig Micchelli and HHMI investigator HHMI researchers have deduced the structure 2005. Another coauthor, Richard Hall, is at Norbert Perrimon, both at Harvard Medical of a molecule that orchestrates the early stages Lawrence Berkeley National Laboratory. School, and Benjamin Ohlstein and HHMI of protein synthesis. They used the newly solved investigator Allan C. Spradling, both at the structure to better understand protein synthesis Researchers Identify Fruit Carnegie Institution of Washington. and to learn how the hepatitis C virus may hijack the Fly Intestinal Stem Cells protein-synthesizing machinery in human cells. HHMI researchers have identified stem cells in Regenerating Worms Help The new view of the protein complex, known the gut of the fruit fly—a finding that may lead Elucidate Stem Cell Biology as eIF3, reveals a five-lobed structure, with to new insights into digestive diseases, intes- Using a flatworm known for its ability to regen- the lobes arranged much like a head, arms, tinal cancers, and the infection strategies used erate lost tissue, researchers have identified a and legs. The scientists’ findings help explain by insect-borne parasites. The discovery puts gene that controls the ability of stem cells to how eIF3 uses these appendage-like lobes to rest a scientific debate over whether inverte- differentiate into specialized cells. The gene to maneuver components of a cell’s protein- brates have gut stem cells. encodes a protein that is similar to the protein making factory, allowing the conversion of RNA The discovery of immature cells that differ- PIWI, an important regulator of stem cells in to protein to begin. Their findings also reveal entiate into multiple types of gut cells suggests organisms ranging from plants to humans. how hepatitis C virus (HCV) interacts with eIF3, that the digestive tract of the fruit fly is likely to The replacement of tissue lost to injury a finding that could yield new drug targets in be a more similar, albeit simpler, version of that or shed during the body’s normal activities is treating HCV, they said. found in humans. Scientists now envision using essential for the survival of most organisms. The The research involved a collaboration the fruit fly to explore normal and pathogenic study, published in the November 25, 2005, between the laboratories of HHMI investiga- regeneration of the digestive tract in ways that issue of Science, helps scientists understand tors Eva Nogales and Jennifer A. Doudna, were not available before. how stem cells make this process possible. The both at the University of California, Berkeley. The two HHMI research teams reported research, performed at the University of Utah Bunpote Siridechadilok and Christopher S. their independent findings on December 7, School of Medicine, was led by HHMI investi- Fraser were co-lead authors of the research 2005, in two online research articles published gator Alejandro Sánchez Alvarado.

February 2006 | hhmi bulletin 49 lab book The Immune System: Imaged at Last

I f th e t h o u gh t o f i n va si v e m e d i c a l p ro c e d u r e s into mice with tumors. The chemical, an analog of glucose, makes you queasy, HHMI investigator Owen N. Witte points concentrates in metabolically active tissues, allowing the PET out that “there’s a noninvasive trend in medical diagnosis—to apparatus to image its radioactive emissions. Tumors themselves, measure things inside the body without having to stick tubes in a composed of cells grown out of control, are also high-energy patient or do an operation.” Witte, a researcher at the University of tissues, and hospitals have used FDG for many years to monitor California, Los Angeles, has recently furthered this trend, leading tumor progression. “While we expected to see the cancer with a team from three medical institutions to develop a noninvasive FDG, it was a bit unexpected as to how well we saw the immune technique based on positron emission tomography (PET). The system at the same time,” Witte says. scientists captured three-dimensional views of one body compo- The team reported on its work in the November 29, 2005, issue nent never before seen from the outside—the immune system. of Proceedings of the National Academy of Sciences. The immune system is particularly challenging to image, Besides its utility in evaluating the immune systems of cancer Witte says, because “it’s everywhere in the body.” Thus, the patients, the technique may also help monitor other diseases, researchers targeted one contiguous aspect of the immune Witte says. “We’ve had contacts from a number of people who system—the primary immune response want to try this technology in to localized tumors, which they induced animal models of various autoim- experimentally in laboratory mice. They mune disorders, and eventually focused their PET scanning method on the in people.” –Paul Muhlrad increased metabolic activity of activated lymph nodes. Lymph nodes are relatively inactive in healthy mammals, but when they face foreign antigens, such as from a growing tumor, “it’s like cranking up a rheostat,” Witte says. “All the same meta- Whole-body sections of a mouse with cancer show bolic processes go on, but at a rate that’s 10 a radioactive analog of to 100 times higher.” glucose concentrated in highly metabolic tissues, The team injected trace amounts of a including activated immune 18 radioactive compound called [ F]FDG cells fighting the tumor.

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Grabbing Addiction by the Tail that has very few side effects,” said Wang, a wires that resynchronize the beating of the Canadian scientists have developed some neuroscientist. Although the initial studies are left and right ventricles—onto the heart. The clever molecular trickery that is helping reduce promising, Wang cautioned that the drug is in standard approach to lead placement on the the drug cravings of addicted rats. One problem the early stages of development and is years left ventricle is through a blood vessel on the in addiction is that neurons in some parts of away from testing in humans. heart’s surface, a technical challenge in some the brain lose glutamate receptors from the patients that limits lead placement to where cell surface, and those receptors are impor- Radical Approach to Cardiac blood vessels are. A substantial number of tant for communication between neurons. Resynchronization cardiac leads fail to work because they are The researchers sidestepped this problem by Correcting the timing of heart contractions positioned poorly, or they become dislodged. crafting a peptide that mimics a portion of the through cardiac resynchronization therapy When lead placement fails, the most common tail of the glutamate receptor and, once inside can be a lifesaver for people with advanced next step is open chest surgery to place the a neuron, serves as a decoy to prevent the loss heart failure. But the procedure, as it is done lead—an invasive procedure that requires a of glutamate receptors. today, fails in about 15 percent of patients. surgeon and general anesthesia. Yu Tian Wang, an HHMI international Steven Mickelsen, a third-year medical Mickelsen searched for a better way to posi- research scholar, and colleagues at the student at the University of New Mexico School tion the critical leads, testing his technique in University of British Columbia in Vancouver of Medicine, developed a minimally invasive small pigs whose hearts are about the size of a reported their findings in the November 25, technique that—at least in pigs—overcomes human’s. Using a catheter inserted through the 2005, issue of Science. the procedure’s main shortcomings. Mickelsen pig’s jugular vein, he implanted pacing leads In addicted rats, cell-to-cell communication conducted the research during a year away by puncturing the upper chamber of the heart is compromised as a result of certain long- from medical school as a Howard Hughes to reach the pericardium, the fluid-filled sac ©2005. 102(48): 17412-7.

term changes at the level of individual Medical Institute–National Institutes of Health around the heart. PNAS neurons. The group’s research produced research scholar at the National Heart, Lung, The work was reported in the October a targeted drug that tricks brain cells into and Blood Institute. 2005 issue of the journal Pacing and Clinical preventing those changes. “We think this is A critical step in cardiac resynchroniza- Electrophysiology. a good candidate for a drug against addiction tion therapy is the placing of leads—thin Image Image adapted from

50 hhmi bulletin | February 2006 in memoriam

Lawrence C. Katz 1956–2005

An HHMI investigator at Duke University Medical Center, he died of melanoma on November 26, 2005, at his home. He was 48 years old.

Larry Katz was a highly esteemed neurobiologist made several important contributions to the planning whose research on the development and function of the and development of Janelia Farm,” says HHMI President mammalian cortex was recognized internationally. The Thomas Cech. “The good advice he gave us will form at early part of Katz’s research career focused on identi- least a small part of his lasting legacy.” fying cellular events and cues used by the developing At Duke University Medical Center, Katz was the brain to form, maintain, and modify local neuronal James B. Duke Professor of Neurobiology. He published circuits in the primary visual cortex. more than 50 original scientific articles and received He pioneered the use of a variety of techniques, numerous professional awards for his research. Katz was including fluorescent tracers, optical imaging in brain also an avid and skilled fly fisherman. slices and in vivo, and combinations of optical and elec- Before moving to Duke, Katz did postdoctoral work trophysiological methods to help define the rules by with Torsten Wiesel at the Rockefeller University. “My which specific circuits in the cortex emerge and func- first encounter with Larry was when he was a graduate tion as neuronal assemblies. student in Masakazu ‘Mark’ Konishi’s laboratory at In recent years, Katz continued to investigate the Caltech,” Wiesel recently observed, “and I remember organization of the visual system, and his group had being struck by his enthusiasm for rather daring experi- begun to study the olfactory system. In particular, his ments. It was no surprise to me that, at graduation, his lab used the mouse as a model to examine how olfac- thesis was selected by the university as the best that tory signals important for basic, built-in behaviors are particular year. It was a sheer pleasure intellectually and encoded by the main olfactory system, which detects experimentally to have Larry in my laboratory, first as a airborne odors, and the vomeronasal system, which postdoc and later as a junior faculty member. Larry had detects species-specific chemical signals called phero- an unbounded energy and imagination; not one day mones. Katz’s long-term goal was to understand how would go by without lively discussions and arguments the neuronal circuits activated by the olfactory and about research questions and how a problem should be vomeronasal systems elicit species-specific behaviors. approached experimentally.” Katz and his colleagues used brain-imaging techniques Another colleague, HHMI investigator Rafael Yuste to visualize the representations of individual odorants at Columbia University, remembers Katz as both a and mixtures in space and time in the living brain. By mentor and a friend. “He supervised my Ph.D. thesis applying advanced microscopy techniques, they were and, even more importantly, first introduced me to able to visualize the microstructure of neuronal circuits my wife on a blind date,” Yuste says. “So he ‘fixed’ my in living mice and to follow changes in those circuits as professional and personal life. From the first time I met animals learned new olfactory tasks. him, I admired his unique combination of intelligence Katz was named an HHMI investigator in 1996. and creativity.” Recently, he was one of the Institute’s advisers in the Katz is survived by his wife, Doris Iarovici, of Durham, planning of its Janelia Farm Research Campus. “Larry North Carolina, and two children, Ariel and Justin. Courtesy of Duke University

February 2006 | hhmi bulletin 51 up-close Scientists Crack Code for Motor Neuron Wiring Understanding how a developing chick embryo assigns different functions to nerve cells in the spinal cord may yield clinical payoffs for humans.

As you turn the p a ges of this B u l l e t i n , motor neurons that project from your spinal cord are coordinating the precise actions of more than 50 muscles in each of your arms. Each muscle is indi- neuron, and Hox protein B may prevail vidually controlled by its own motor neuron cluster, which has a in another neuron,” says Jessell. “And distinct identity and pattern of connectivity. “Motor neurons repre- since the emergence of that final Hox pattern determines identity, the nature sent an extreme example of neuronal diversification,” says HHMI of the interactive circuit between Hox investigator Thomas M. Jessell, whose research group at Columbia proteins is in itself driving the diversifica- tion of neurons.” University Medical Center is seeking to understand how a devel- These findings may have broad impli- oping embryo delegates specialized functions to different nerve cells. cations. “We already know that the basic organization of the chick motor system “Its first task is to make motor neuron columns within the spinal cord. is conserved within higher vertebrates, neurons, as a class, different from all the That finding prompted the recent study, including humans,” Jessell says. “If you other classes of neurons,” says Jessell. in which Jeremy S. Dasen, an HHMI look at chick locomotor behavior, it’s “And once the embryo has solved that research associate in Jessell’s lab, painted strikingly similar to humans walking.” It’s problem it has to generate distinct chick embryos with a palette of fluores- possible, then, that understanding the Hox columns of motor neurons in the spinal cently tagged antibodies directed against code may one day help guide progress in cord, with each column controlling a many of the 39 Hox proteins. The exper- restoring motor neuron function in people particular body region, such as a limb. iments were painstaking and meticulous, whose spinal cords have been damaged by Then, within each column, the embryo says Jessell. Merely generating the anti- trauma or disease. –Paul Muhlrad has to generate motor neuron pools, each bodies was a 5-year effort by Bonnie of which activates one particular muscle.” C.Tice and Susan Brenner-Morton, Motor axons must then grow from the Dasen’s labmates and coauthors of the spinal cord into the limbs and elsewhere Cell paper. and target the right muscle. The hard work paid off. What has Jessell’s team recently deciphered the emerged from these experiments is a code that assigns unique identities to the detailed motor neuron atlas that shows motor neuron pools. This code, as the the locations of relevant Hox proteins in researchers explained in the November 4, the chick embryo at different times during 2005, issue of Cell, is written in the development. The appearance and disap- language of Hox proteins—a family pearance of the different protein types in of transcription factors (proteins that distinct motor neuron pools revealed the “Different Hox activate specific sets of genes) found in molecular logic at work to Dasen and his proteins have virtually all organisms. colleagues. “Different Hox proteins have

Scientists have long recognized that specific tasks that progressively determine specific tasks that Images by Dasen/JessellJeremy Lab Hox proteins, by orchestrating a cascade motor neuron identity,” Jessell explains. progressively  of gene expression in the early embryo, What’s more, it became clear from

determine motor page: Facing ensure animals’ overall body plan. They the pictures that certain pairs of Hox place the head at the top, the feet below, proteins exclude each other from an neuron identity. and the correct arrangement of ribs individual neuron, whereas other combi- in between. nations of Hox proteins can coexist. In ” Four years ago, the Columbia group effect, the Hox proteins wage a battle for discovered that Hox proteins also influ- dominance within the cells of each pool. Christopher Denney

ence the arrangement of the motor “Hox protein A may win out in one thomas jessell Jessell:

52 hhmi bulletin | February 2006 Outfitting Motor Pools

Researchers in Thomas For this set of images, Each panel shows cell The images demonstrate Jessell’s lab have created the researchers injected nuclei stained with red- that different combinations an atlas of images that different muscles in the tagged antibodies that bind of transcription factors shows the location chick forelimb with a to different transcription are present in different of various Hox-related green tracer, which then factors. The transcription motor neuron pools. proteins in the chick spread to the corresponding factors, shown clockwise embryo at different motor neuron pools in the from top left, are Runx1, developmental times. spinal cord. Pea3, Scip, and Pea3. nota bene

SPOTLIGHT Whitehead Institute Taps Page as Leader HHMI investigator David C. Page has been elected the fourth director of the Whitehead Institute for Biomedical Research. Page, who came to the nonprofit institute in 1984 as one of its first fellows and became a faculty member 2 years later, began his new post in December 2005, after a year’s appointment as interim director. “To my mind, the Whitehead Institute is an artist colony extraordinaire,” said Page in a press release. “My vision is that in the years ahead we will continue to attract the best young minds and provide them a place to realize dreams.” Page, also a professor of biology at the Massachusetts Institute of Technology, has spent his career examining the Y chromosome: tracing its evolution, determining its nucleotide sequence, and unraveling the mechanism that allows the compact chromosome to main- tain its genes. His work has led to an appreciation of the complexity of the Y chromosome and to a better understanding of male infertility.

The Irvington Institute for Immunological at Stanford University School of Medicine, Guy Caldwell, an associate professor of Research created a special award in honor one of the 2005 Scientific American 50, a biological sciences at the University of of Frederick W. Alt, an HHMI investi- designation recognizing people, teams, Alabama, was named Alabama’s 2005 gator at Children’s Hospital, Boston, and and organizations whose recent accom- Professor of the Year by the Carnegie chairman of Irvington’s Scientific Advisory plishments demonstrate leadership in Foundation for the Advancement of Board. The Frederick W. Alt Award for shaping both established and emerging Teaching and the Council for Advancement New Discoveries in Immunology will be technologies. Brown received the honor and Support of Education. Caldwell was presented to former Irvington Institute with Michael B. Eisen for founding the supported in his first 3 years at the univer- fellows who have shown outstanding Public Library of Science and for their sity by an HHMI undergraduate biological success in academia or industry. The continuing efforts to make scientific sciences education grant, beginning in first recipient will be announced in publications accessible to scientists and 1999, and he continues to participate in October 2006. the public. HHMI grant activities there.

Bonnie Bassler, an HHMI investigator SPOTLIGHT at Princeton University, won the 2006

Eli Lilly and Company Research Award, Left to right: Tyler Jacks, Scott W. Lowe, given to recognize fundamental research and Jeff L. Wrana of unusual merit in microbiology or immunology by an individual on the threshold of his or her career.

Two HHMI investigators received awards for outstanding scientific achieve- ment from the National Academy of Three Scientists Sciences (NAS). Ronald R. Breaker, Yale University, shared the 2006 NAS Award in Win Cancer Research Prize

Molecular Biology with Tina M. Henkin, Two HHMI investigators and one international research scholar have been © HHMI. Zack Seckler/AP. Ohio State University, for “establishing a honored with the 2005 Paul Marks Prize for Cancer Research. The prize, named

new mode of regulation of gene expres- after Paul A. Marks, president emeritus of the Memorial Sloan-Kettering Cancer Lowe: sion.” Frederick M. Rieke, University of Center, recognizes significant contributions to the basic understanding and treat- Washington School of Medicine, received ment of cancer by scientists no more than 45 years of age. a 2006 Troland Research Award for The winners are Tyler Jacks, of the Massachusetts Institute of Technology, Fetters Paul “experimental and theoretical analyses of for advancing our understanding of the pathogenesis of cancer; Scott W. Lowe, information coding in the central nervous of Cold Spring Harbor Laboratory, who studies how genes influence a patient’s Jacks: system and its relation to perception.” response to chemotherapy; and Jeff L. Wrana, of the University of Toronto and

the Samuel Lunenfeld Research Institute, for his work analyzing the impact of Courtesy of Wrana Jeff Scientific American magazine named cell-cell communication on tumor development. Stanley Rowin

Patrick O. Brown, an HHMI investigator Page: Wrana:

54 hhmi bulletin | February 2006 Kevin P. Campbell, an HHMI investi- SPOTLIGHT gator at the University of Iowa Roy J. and

Lucille A. Carver College of Medicine, Left to right: Bruce T. Lahn, Gregory J. was elected in 2005 as a member of the Hannon, and Joseph Derisi National Arthritis and Musculoskeletal and Skin Diseases Advisory Council.

Three students supported by HHMI’s undergraduate grants program are in the 2006 class of Rhodes Scholars. They are Adam D. Chandler and Rahul Satija, both students at Duke University, and Elizabeth Researchers Shine in Esquire W. Mayne, who is enrolled at Stanford Three HHMI investigators were listed among Esquire magazine’s “Best & Brightest” of University. Each of the three conducted 2005. The popular magazine’s picks appeared in the December 2005 “Genius Issue.” research projects supported by HHMI. Gregory J. Hannon, an HHMI investigator at Cold Spring Harbor Laboratory, was cited for his harnessing of RNA interference to silence genes, which Esquire named Two researchers were honored recently by the “Breakthrough of the Decade.” Bruce T. Lahn, an HHMI investigator at the the American Association of Immunologists University of Chicago, was hailed for his research on the factors driving evolution of the (AAI). Max D. Cooper, an HHMI inves- brain, which the magazine called the “Impolitic Idea of the Year.” tigator at the University of Alabama, HHMI investigator Joseph DeRisi was singled out for his work at the University Birmingham, received the 2006 AAI- of California, San Francisco, studying the molecular biology of infectious diseases, such Dana Foundation Award in Human as malaria, that disproportionately affect developing countries. The magazine dubbed Immunology Research for his “record DeRisi a “brilliant do-gooder” for his work and for making his research protocols and of significant achievement and sustained published articles freely accessible to other scientists and to the public, placing him accomplishment in immunology research.” among the “vanguard of scientists dedicated to open-source medical research.” Ruslan Medzhitov, an HHMI investigator at Yale University School of Medicine, won the 2006 AAI-BD Biosciences Wayne A. Hendrickson, an HHMI inves- Craig C. Mello, an HHMI investigator at Investigator Award for his “outstanding, tigator at Columbia University College the University of Massachusetts Medical early-career research contributions to the of Physicians and Surgeons, and Joan School, was awarded the 2005 Massry Prize field of immunology.” Massagué, an HHMI investigator at with colleague Andrew Z. Fire at Stanford Memorial Sloan-Kettering Cancer Center, University School of Medicine for their Cristoph G.F. Dehio, an HHMI interna- won 2005 Mayor’s Awards for Excellence discovery of RNA interference (RNAi). tional research scholar at the University in Science and Technology in the category Mello and Fire share the award with David of Basel, in Switzerland, shared the Pfizer of biological and medical sciences. The C. Baulcombe of the Sainsbury Laboratory, Research Prize 2006 in infectious disease awards are administered by the New York John Innes Centre, in Norwich, England, with his coworker Ralf Schülein. The prize Academy of Sciences. whose research in plants contributed to the

is awarded annually to young, outstanding discovery of RNAi. scientists for basic or clinical research done Arthur L. Horwich, an HHMI investigator in Swiss research centers or hospitals. at Yale University School of Medicine, Sergei A. Nedospasov, an HHMI interna- received the 2006 Stein and Moore Award tional research scholar at the Engelhardt Gregory J. Hannon, an HHMI investi- from the Protein Society. The award will Institute of Molecular Biology, Russian gator at Cold Spring Harbor Laboratory, be given jointly to Horwich and F. Ulrich Academy of Sciences, in Moscow, won received the 2005 American Association for Hartl, director of the Max Planck Institute the 2005 Helmholtz Humboldt Research Zack Seckler/AP. © HHMI. Zack Seckler/AP. Cancer Research Award for Outstanding for Biochemistry in Munich, for their Award from the Humboldt Foundation Achievement in Cancer Research. The discovery of and groundbreaking work on and the Helmholtz Association in

Hannon: award honors an accomplished investigator chaperone-assisted protein folding. Germany in recognition of his accom- in the field who is no more than 40 years plishments in research and teaching. old at the time the award is conferred. Eric R. Kandel, an HHMI investigator at Columbia University College of Physicians Michael K. Rosen, an HHMI investigator Stephen C. Harrison, an HHMI inves- and Surgeons, won the 2005 Austrian at the University of Texas Southwestern tigator at Harvard Medical School, Medal of Honor for Science and Art. Medical Center at Dallas, was one of three was awarded the 2005 Bristol-Myers researchers to receive an inaugural Edith Squibb Company Freedom to Discover David R. Liu, an HHMI investigator at and Peter O’Donnell Award from the

George Nitikin/AP. © HHMI. George Nitikin/AP. Distinguished Achievement Award in Harvard University, received the 2006 Academy of Medicine, Engineering, and Courtesy of the of University Chicago infectious diseases research for pioneering American Chemical Society Award in Science of Texas honoring the work of

Lahn: DeRisi: virus x-ray crystallography. Pure Chemistry. outstanding up-and-coming researchers.

February 2006 | hhmi bulletin 55 continued from page 23 ( Joan Steitz) recent participation in a committee that to develop internally. somewhere else,” says Steitz. If this turns wrote the National Academy of Sciences The problem with the near-field micro- out to be the case, the RNA portion of a report titled “Bio 2010” inspired her to scope—a device I was using fairly success- snRNP would be considered a ribozyme. completely revamp a course for advanced fully—was that there was no mechanism By this time, Steitz had already advanced undergraduates that teaches them, by for turning it into a good turnkey instru- up the Yale ladder to become a full pro­ group participation, how to read the ment. And it’s still too embryonic for fessor. Her lab subsequently discovered a literature. “Almost every time I lecture most biologists to consider using. There second spliceosome that eliminates a rare at another university, someone comes up are hundreds, if not thousands, of exam- class of “black sheep” introns that have to me and says, ‘I took your biochemistry ples in science and technology of good atypical sequences at their splice sites. course back in 19xx, and it was terrific.’ ideas that just languish because of the And with her discovery of another kind What more can one wish for?” gulf that exists between the conception/ of snRNP particle, small nucleolar RNPs Another passion is a desire for women demonstration of an idea and something (snoRNPs), she proved that the term junk scientists to be appreciated as men’s equals. that’s economically viable. DNA was a misnomer. Introns, the so- Steitz stands firmly by her 2001 comment My hope is that Janelia will be a step in called noncoding regions of DNA, some- in The New York Times that a woman the right direction, because mechanisms times code for the small nucleolar RNA scientist needs to be twice as good for half will be in place there to take ideas that found in a snoRNP. These molecules (pro- the pay, although, Thomas Cech points have been shown to work from a proof- nounced snow-RNPs by Steitz) chemically out, she doesn’t picket for change but of-principle standpoint to the point where modify ribosomal RNA and are essential rather leads by example. Steitz spends time they might be broadly applied. Right now, to its function. on oversight issues to remedy remaining that’s pretty damn rare. –Interview by Jennifer Currently, Steitz is exploring viral inequality problems—time she would far Michalowski snRNPs as well as the welter of effects rather devote to her science. splicing has on the downstream life of an She bristles when asked about Harvard continued from page 43 RNA message. “For instance,” she says, President Larry Summers’ recent suggestion (Never too young for science) “we know that in the process of splic- that women have less innate scientific tools, observing, drawing conclusions, and ing proteins are put on RNA that are ability. But she’s certainly circumspect in making predictions. important for getting the RNA out of the her reply: “What he said, and the sequelae at Evaluations show that the children’s nucleus to the cytoplasm.” Harvard and throughout the nation, is the vocabulary for the names and functions of While her work is on the bench side of best thing to happen for women in science science tools increased significantly over a science, others are translating her findings since the MIT report.” She is referring to 5-month period during the 2005 program in the clinic in ways Steitz finds “absolutely the report out of MIT in the late 1990s and that most were able to select the appro- amazing.” A recent paper in Science details that found women scientists at that insti­ priate tool to solve a new problem. The a way to use aberrant splicing to prevent tution suffered significant discrimination in results “tell us that children not only know the ravages of muscular dystrophy in dog terms of pay and stature. After that report how to use the tools but are also more models. “Basically, they designed a snRNP was made public, remedial changes were likely to transfer that knowledge into a to undo the drastic consequences of a initiated at many universities. Steitz says she new situation,” says Garner. mutation,” Steitz marvels. “I think that is is optimistic that Summers’ comments will “When we looked at outcomes,” adds just extremely cool!” again prompt positive change for women CLS president Keith Verner, a former in science. Regarding his continuation HHMI grantee at the Penn State College the pleasure of her as Harvard’s president, post-gaffe: “That’s of Medicine, “we saw increases that were company something I find very interesting,” replies not dependent on a particular teacher or Apart from the official kudos Steitz without expression. a particular class. We believe it was the Steitz has received, including the National It’s not hard to imagine how she program itself that made the difference.” Medal of Science, postdocs and graduate would respond to Dr. Famous today if he Loudoun County’s Scovel agrees, and students in her lab say it’s a genuine plea- questioned her place in and dedication to notes, “We don’t want to repeat what sure to be there. They rave, for example, science. She might show him her weighty children will learn in kindergarten, but about her “really great parties.” At their CV and invite him sailing with her we want to build skills they can use in most recent Halloween bash, Joan was beloved son and husband to remind him kindergarten and beyond.”–Judith B. Saks the Statue of Liberty and Tom was Uncle that a career in science does not exclude a Sam. And Doudna recalls delightful happy family life—even without the sta- continued from page 43 afternoons spent sailing with Steitz and tion wagon. (EVOlution/Religion debate) her husband, drinking wine, discussing nonbeliever like myself or a believer like science—or the wind. “Working as a Father Wiseman. It seems to me that continued from page 39 postdoc under Joan was such a fantastic (Eric Betzig) [science and religion] are two separate experience,” says Baserga, “that I spent Do you have thoughts on how to speed things.” He added, “The Bible is not a the first several years on my own wishing up progress? work of science.” I were still there.” eb: Well, that gets into the wider philo- “I find it beyond ironic that society While science itself is clearly Steitz’s sophical issues of how research is done, depends on DNA evidence for questions first priority, education is her second. “I which Janelia will try to address in some of life and death,” Carroll remarked, adore teaching undergraduates and con- ways. In particular, I’m hopeful that the “yet we’re not willing to contemplate sider it a privilege to interact with the innovative engineering group within the DNA record of natural history and fabulous students at Yale,” she says. Her Janelia will help, at least for stuff we start evolution.”–Jennifer Boeth Donovan

56 hhmi bulletin | February 2006 major pursuitatJanelia Farm. methods suchasthisonewillbea Development ofinnovative imaging are labeledred, green, andyellow. mouse of anewborn bral cortex individual neurons from thecere - label intosinglecellsinvivo. Here, a geneticchangeandfluorescent Luo cansimultaneously introduce markers), HHMI investigator Liqun (mosaic analysiswithdouble Using amethodtermedMADM pg. 30

Courtesy of Liqun Luo; reprinted from Cell 121:479-492, with permission from Elsevier. © 2005.

Leif Parsons I Neur Te especially functionalimaging, work now proceeding inthe of clinicaldeath. With its accesstoimproving technologies, implications oflife-extending modalities for the definition technologicalcapabilities suchasthe attention becauseofnew approach. In the early days of bioethics, many issues attracted casethatobligea novelpeculiar aspectsofaparticular analytic issues cometowidespread awareness, itismainly becauseof To theextentthatthere isanappearanceofnovelty asethical conceptual schemestobeconsidered andrevised orreformed. precursors and therefore analogies to be drawn and prior Ethical problems seemnever there tobewhollynew; are always OBSERVATIoNS n Mo rm o s cience s r al

work inmoral aswell asscientificterms. increasingly bechallengedto explainthesignificanceoftheir colleagues innuclearphysicsandgenetics.Neuroscientists will ofpublicattentionpreviouslyof thesort experienced by their willfindthemselves thesubjects those engagedintheseefforts neurosciences provides richground forsuchcases.Many of Virginia andafellow attheCenter forAmerican Progress. Professor anddirector oftheCenter forBiomedical Ethics attheUniversity of A memberofHHMI’s BioethicsBoard, Advisory Jonathan Moreno istheKornfield here ofthepublisher, withpermission Indiana University Press. Bioethics, by Jonathan D.Moreno. ©2005by Jonathan D.Moreno. Reprinted From the bookIs There an Ethicist inthe House? On the Cutting Edge of HHMI

BULLETIN February ’06 Vol. 19 • No. 01

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Howard Hughes Medical Institute

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www.hhmi.org ields L ab Courtesy of F

The thousands of interactions that take place between proteins Mapping How Parasite of the malaria-causing parasite Plasmodium falciparum are being tracked and mapped in the University of Washington laboratory of HHMI investigator Stanley Fields. In this depiction, Proteins Relate individual proteins are indicated by pink circles and the interactions by the lines that connect them. Understanding how the proteins relate to each other may illuminate vulnerabilities in the parasite’s defenses (see pG. 49).

nonprofit org. us postage paid 4000 Jones Bridge Road Hyattsville, md Chevy Chase, Maryland 20815-6789 permit no. 61 www.hhmi.org Change Service Requested A Cell’s

vol. 19 / no. Can a cell’sS developmentalecond Ahistoryct be erased, giving it a fresh start toward a new destiny?

01 01 IN THIS ISSUE: AFTER KATRINA / MICROSCOPY AT JANELIA / JOAN STEITZ