HHMI

BULLETIN F EB. ’09 VOL.22 s NO.01

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Howard Hu HHMI BULLETIN g hes Medical Institute

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www.hhmi.or g Lars Dietrich / Newman lab

A MUTATION IN A GENE FOR ANTIBIOTIC PIGMENTS Where’s My Snorkel? CALLED PHENAZINES MAKES BACTERIAL COLONIES GROW IN THIS SHRIVELED—BUT SURPRISINGLY SYMMETRICAL AND PREDICTABLE—PATTERN. DIANNE NEWMAN’S EXPLANATION: PHENAZINES USUALLY ACT AS SNORKELS, HELPING THE DEEPEST BACTERIA ILLUMINATING IN A THICK COLONY BREATHE WITHOUT OXYGEN. WITHOUT THESE MOLECULES, BACTERIA MUST ARRANGE THEMSELVES IN THIS UNUSUAL WAY SO THAT EACH BIOLOGY CELL HAS DIRECT ACCESS TO OXYGEN IN THE AIR A spectrum of fluorescent proteins (SEE PAGE 26). won Roger Tsien a Nobel Prize. Now he’s shining his light on cancer cells and memory formation.

In This Issue When Cells Grow Old MicroRNA Dianne Newman Introduces Geology to Microbiology

4000 Jones Bridge Road vol. Chevy Chase, Maryland 20815-6789 22 www.hhmi.org / no. 01

14 This brightbugmayglowlike organisms. Inthecaseofthis express fluorescent proteins like express fluorescentproteinslike cules localizewithin cellsand winner RogerTsien.Suchfluore- illuminated tick,scientists can been geneticallyengineeredto a firefly, butit’s actuallyadeer how andwheredifferentmole- pathogens likeLyme disease. probe howthecrittercarries those developedbyNobelPrize tick— scence lets researchers visualize scence letsresearchersvisualize Ixodes scapularis —that’s

Utpal Pal, Ruth R. Montgomery, Erol Fikrig

Alfred Russel Wallace: My Life (1905) that fillthehistory ofscience don’tal Tales from theTrenches the fieldofevolution, includinganovel concept ofnatural selection. dramatic setbackslike theonesdescribedhere, Wallace madeseminalcontributions to century scientist whovoyaged to theMalay Archipelago andtheAmazon. Despite some stories. At thestart ofChapter 2,thereader meetsAlfred Russel Wallace, anineteenth- which thehistory ofevolutionary science unfolds through someofitsmost memorable Sean B.Carroll wants to changethat.Sohewrote atextbook, publishedlast summer, in OBSERVATIONS | The| colorful characters, epicadventures, andpersonalstruggles ways ways find theirway into classrooms. HHMIinvestigator permission oftheauthor. ©2009 BenjaminCummings.Reprinted with the Search for Evolution From then the ered itwas leaking. salt water. Once inthelifeboat, hediscov- compounded whenhisinjured handshitthe seared hishandsontherope. Hispainwas to lower himselfinto alifeboat, slipped,and some notes, andadiary. Hegrabbed aline a smalltinbox andthrew insomedrawings, reentered hishot,smoky cabinandsalvaged scene was afeverish dream. Itwasn’t. He bout withyellow fever, looked onasifthe the lifeboats. Wallace, still weak from his smoldering blaze. The captain ordered down out ofthehold. cabin. Andrightfullyso—smoke was pouring was concerned enoughto visitWallace inhis east ofBermuda,thecaptain three weeks outofportandsomewhere see whatyou thinkofit.” Just after breakfast, and setsailfor England. animals, many boxes ofspecimensand notes, boarded thebrig comforts ofhome. OnJuly12,1852, he neat gardens, bread andbutter, andother for sale. he hadnotyet beenableto shipto England both withhimandstored downriver, that had acouple ofyears’ worth ofspecimens, was killinghim.Besidestheanimals,healso all theway to theLondon Zoo. Their upkeep parrots, andatoucan—that hehopedto take erie oflive animals—monkeys, macaws, died before hecould board aboatto England. Herbert was stricken withyellow fever and before turnedback.Unbeknownst to Wallace, panied himupto theRioNegro, hadlong His younger brother, Herbert,whoaccom- yellow fever. Hewas too exhausted to goon. had beenlaidupthelast three monthswith four years exploring andcollecting, but arriving inMay 1848,hehadspentnearly than any European hadever gone. Since dos UaupéstributaryoftheAmazon—further upriver from theAtlantic Ocean, ontheRio It was timeto packupandgohome. Wallace watched hisanimalsperish,and The crew tried,butcould notdousethe “I’m afraid theship’s onfire; come and Wallace beganto dream ofgreen fields, Wallace hadaccumulated alarge menag- Alfred Wallace was two thousandmiles Into theJungle:Great Adventures in Helen , along with all of his specimens. , alongwithallofhisspecimens. Helen with thirty-four live , by Sean B.Carroll. Helen vol. 22 february ’o9 no. o1

DEPARTMENTS

PRESIDENT’S LETTER 0 3 A Responsibility to Experiment

CENTRIFUGE 06 Rocket Man 0 7 Play On 0 8 Found in Translation

UPFRONT 1 0 Chasing Amyloid 1 2 Alter Ego

PERSPECTIVES AND OPINIONS 3 8 David Lopatto 4 0 Helen Hobbs 4 2 Q&A – If you could trade places with someone for a day, who would it be?

CHRONICLE

Science Education 4 4 Fire Ant! 4 5 2008 Holiday Lectures: Making Your Mind Institute News 4 6 A Call for Collaboration Lab Book 4 8 Probing Pigs 4 9 Avoiding Rupture 5 0 Sleep-Inducing Monsters Ask a Scientist 5 1 Why do injections hurt more on some parts of the skin than on others? Up Close 5 2 Crystal Clear Nota Bene 54 News of recent awards and other notable achievements

OBSERVATIONS Tales from the Trenches

FEATURES 14 2o 26 32

Luminosity The Macro World of Between a Rock When Cells Roger Tsien won a MicroRNA and a New Place Grow Old Nobel Prize for designing Short stretches of “junk DNA” With a wide-angle Just like a whole person, a rainbow of proteins are surprisingly influential in view of the world and a cells change as they age. that shine as they do preventing or limiting disease commitment to follow Clues about what controls their work within a cell. —so influential, they are now her fascination, this cellular aging are Now he’s using his fine- high on the agendas of many scientist is making revealing puzzles and tuned aesthetic to cure drug companies. imaginative connections possibilities for combating cancer and flag memory between rocks, bacteria, a host of diseases. formation. and medicine. [COVER STORY]

VISIT THE BULLETIN ONLINE FOR ADDITIONAL CONTENT AND ADDED FEATURES: www.hhmi.org/bulletin COVER IMAGE: RICCARDO VECCHIO contributors

Born near Milan, Italy, RICCARDO VECCHIO (cover and “Luminosity,” page 14) studied applied and fine arts at the University of Trier, Germany, and then spent a year at the European Institute (1) of Design in Milan. In l994, he received a Fulbright Scholarship to enroll in the master’s program at the School of Visual Arts (SVA), New York City. Since graduating, Vecchio has been a faculty member in the SVA illustration department. His work has been commissioned for a wide variety of magazines, books, and other media in the United States and abroad. (1)

Writer CATHY SHUFRO µ@]QYSb;O\¶^OUS$WaR`Oe\b]aQWS\bWabaPSQOcaS]TbVSW`W\bS\aS engagement in their work. She recently returned from the Thailand–Burma border, where she

wrote for Johns Hopkins Public Health about health workers who risk their lives to attend births (3) (2) in eastern Burma’s civil war zones. Shufro lives in Connecticut, where she teaches writing at Yale University. (2)

JIM SCHNABEL (“Found in Translation,” page 8), who has written features for Nature, New Scientist, and other publications, is embarking on his second career as a science writer. The first tailed off in the late 1990s when he fell in love with a certain beach in the tropical Pacific. Now, after ten years, two very bad typhoons, and a not-particularly-lucrative venture as a Third World real estate developer, he’s finally got paradise out of his system and is living and writing (4) back in the United States. (3)

JOÃO CANZIANI (“Chasing Amyloid,” page 10) was born and raised in Lima, Perú; spent his adolescence in Vancouver, Canada; and is now based in Los Angeles. A fascination for different cultures has led him to travel whenever and wherever he can, always with camera in hand. Named by Photo District News as one of 30 emerging photographers to watch in 2005, Can- ziani frequently shoots for W magazine, Spin, and Travel & Leisure, among others. (4)

HHMI TRUSTEES HHMI OFFICERS & SENIOR ADVISORS James A. Baker, III, Esq. Thomas R. Cech, Ph.D. / President Senior Partner / Baker & Botts Craig A. Alexander / V.P. & General Counsel Ambassador Charlene Barshefsky Peter J. Bruns, Ph.D. / V.P. for Grants & Special Programs Senior International Partner David A. Clayton, Ph.D. / V.P. for Research Operations WilmerHale Joseph D. Collins / V.P. for Information Technology Joseph L. Goldstein, M.D. Jack E. Dixon, Ph.D. / V.P. & Chief Scientific Officer Regental Professor & Chairman, Department of Molecular Genetics Joan S. Leonard, Esq. / Senior Counsel to the President University of Texas Southwestern Medical Center at Dallas Avice A. Meehan / V.P. for Communications & Public Affairs Hanna H. Gray, Ph.D., Chairman Edward J. Palmerino / V.P. for Finance & Treasurer President Emeritus & Harry Pratt Judson Gerald M. Rubin, Ph.D. / V.P. & Director, Janelia Farm Research Campus Distinguished Service Professor of History Landis Zimmerman / V.P. & Chief Investment Officer The University of Chicago HHMI BULLETIN STAFF Garnett L. Keith Chairman / SeaBridge Investment Advisors, L.L.C. Mary Beth Gardiner / Editor Former Vice Chairman & Chief Investment Officer Cori Vanchieri / Story Editor The Prudential Insurance Company of America Jim Keeley / Science Editor Paul Nurse, F.R.S. Andrea Widener / Science Education Editor President / The Rockefeller University Patricia Foster / Associate Director of Communications Alison F. Richard Ph.D. for Web & Special Projects Vice-Chancellor Sarah C.P. Williams / Assistant Editor The University of Cambridge Maya Pines / Contributing Editor Kurt L. Schmoke, Esq. ADDITIONAL CONTRIBUTORS Dean / Howard University School of Law Cay Butler, Michelle Cissell, Mark Farrell, Nicole Kresge, Steven Marcus, Heather McDonald, Anne Sommer Anne M. Tatlock Director, Retired Chairman & CEO VSA Partners, NYC / Concept & Design Fiduciary Trust Company International

BSZS^V]\S!  #&&##’4Of!  #&&$!’eeeVV[W]`U ©2009 Howard Hughes Medical Institute

The opinions, beliefs, and viewpoints expressed by authors in the HHMI Bulletin do not necessarily reflect the opinions, beliefs, viewpoints, or official policies of the Howard Hughes Medical Institute. Riccardo Vecchio, Cathy Shufro, Jim Schnabel, João Canziani João Cathy Shufro, Jim Schnabel, Riccardo Vecchio,

2 HHMI BULLETIN | February 2oo9 president’s letter

A Responsibility to Experiment

nearly 10 years ago, just after the trustees of the I ever could have anticipated in May 1999. I know that my successor, Howard Hughes Medical Institute elected me as the Institute’s Robert Tjian, can look forward to a similarly challenging and fourth president, I had the opportunity to meet with the staff in the rewarding journey during his tenure. auditorium at our headquarters in Chevy Chase. There was an air of So let’s step back briefly to that moment in the auditorium—the anticipation in the room, one that echoed the excitement I felt on scene of so many investigator meetings, the backdrop for the Holiday the cusp of my new responsibilities to HHMI. Lectures on Science, a space now named in memory of HHMI’s As a long-time HHMI investigator, I had great appreciation for legendary chief scientific officer, W. Maxwell Cowan. With the all that had been accomplished under the leadership of Purnell W. benefit of hindsight, the words with which I described HHMI’s Choppin, the man I was about to succeed. I thought—certainly at impact on my own research could just as easily apply to the role of the time—that I understood the opportunities ahead. Yet, the the Institute within the broader scientific community. As I said at

Erika Larsen journey has been more surprising, fascinating, and demanding than the time, “Howard Hughes has allowed us to go into some new

February 2oo9 | HHMI BULLETIN 3 president’s letter

directions that we otherwise wouldn’t have been able to. In fact, I porate medicine into their Ph.D. studies, to physician-scientists at a think really it is more the other way around. I almost felt a responsi- variety of career stages who seek to combine research with clinical bility to go in some new directions because we had the advantage of practice. On the biomedical research front, I first worked with vice not having to rely on traditional sources of funding.” presidents Gerry Rubin and David Clayton to expand the cadre of The responsibility to experiment has been a recurring theme of patient-oriented physician-scientists within the ranks of our investiga- the past decade of my leadership. But before I mention a few of the tors and later with Jack Dixon to open the investigator selection Institute’s recent experiments, I need to say that we experiment process to direct application from scientists. We have also taken steps within the confines of a set of values—including freedom, flexibility, to ensure that the results of our investigators’ discoveries will be creativity, and integrity—that define HHMI’s science-based culture. broadly shared within the scientific community. These values have never One of the Institute’s most been more important. The visible experiments is the Janelia public has begun to express Farm Research Campus, which deep concern about the loss of opened in 2006 along the objectivity that can occur at the Potomac River in Ashburn, intersection of science and Virginia. The notion of creating commerce. At HHMI, we have a freestanding campus with a remained tough-minded about distinct scientific culture arose Institute policies that reinforce in conversations I had with my our independence from colleagues Gerry Rubin and company-funded research. Also, David Clayton in 1999. We during this event-filled decade, touched on many subjects the nation has twice endured during those conversations, periods of great financial most notably the HHMI investi- upheaval. With the govern- gator program. That program ment’s attention focused on seemed to be just the right issues related to national secu- size—a much larger program rity, we have seen the impact of might have reduced quality and continued fiscal and political been difficult to manage—so we pressure on federal research concluded that additional agencies, particularly the Institute resources should be National Institutes of Health CBS reporter Leslie Stahl visited HHMI headquarters in 2003 to invested in a novel direction. (NIH). HHMI is hardly immune interview Tom Cech for a 60 Minutes story about the Institute. According to our analysis, from these currents. Many of the research opportunities most our investigators also conduct research that is supported by the NIH, challenged at U.S. academic institutions were in the area of inter- and they are based at medical schools, research universities, and disciplinary research—bringing physics, chemistry, computer institutes that are best served by steady year-to-year resources. The science, and engineering to bear on problems of biology. By Institute’s commitment to plan for long-term, consistent funding building a research facility without departmental barriers, we serves our scientists well. thought we could catalyze such collaboration. As we looked for a Given the opportunity to examine our own programs and activities suitable piece of property, we refined the scientific challenges that in the light of pressing national needs, I have worked with Peter Bruns an interdisciplinary campus might address. The initial goals of what to launch several new educational initiatives. The goal has been to is now the Janelia Farm Research Campus are to understand the expand opportunity in key areas: to promising college students who neural circuits that enable complex behavior and to create new come from disadvantaged or minority backgrounds, to graduate imaging and computational technologies. Already, the campus has students who want to study across disciplinary boundaries or to incor- become a hive of activity for the resident scientists as well as for our Paul Fetters Paul

4 HHMI BULLETIN | February 2oo9 investigators and their collaborators from around the world. Janelia of their independent careers, between years two and six of their Farm has added to—rather than subtracted from—the vibrant first academic appointments. We’re betting that unfettered finan- culture of HHMI’s investigator program and that, for me, is an cial support to these Early Career Scientists, coupled with the important touchstone. new interactions they’ll forge as part of the HHMI community, One area where HHMI charted an independent course concerns will have a big impact on their ability to develop full-fledged research involving human embryonic stem cells. HHMI enabled its research programs. investigators to work outside the constraints of a national policy that This issue of the HHMI Bulletin highlights another response limited the stem cell lines that could be used and barred the devel- by HHMI to the current research environment. Jack Dixon, our opment of new cell lines in federally funded research. We made our chief scientific officer, has led the creation of the Collabora- decision in consultation with tive Innovation Awards. Using outside advisors, including ethi- HHMI investigators as the cists, and with the support of our nucleus, we challenged them Trustees. The care with which to assemble teams of scientists to HHMI proceeded made the tackle transformational research initiative no less bold. Our stem projects that are too big or too cell investigators, who aim to risky for any single laboratory to cure some of our most devas- handle. If a quarter of these tating diseases, have estab- efforts succeed, HHMI will have lished new cell lines and have done something worthwhile. published important, sometimes That’s the whole point: we don’t surprising, findings on tissue want to be assured that these development and regeneration. teams of scientists will solve the Back in the 1980s, HHMI problem; we do want to ensure president Donald Fredrickson that they have the means to believed the Institute should explore big questions. locate its headquarters “inside As I prepare to return to my the Beltway” so that it would be laboratory at the University of proximate to the NIH and the Colorado at Boulder—to focus officials (elected and otherwise) more on some scientific ques- who make important decisions tions of my own—I am deeply about science policy in the Tom Cech presided over the 2003 groundbreaking of the Janelia Farm conscious of the fact that the United States. The decision to Research Campus. Since its 2006 opening, he has been a regular visitor Institute’s successes of the past base HHMI in the Washington, for science meetings, workshops, and public lectures. decade reflect the contributions D.C., area was prescient and made by HHMI employees has facilitated my interactions with the National Academy of around the country, the members of the Medical Advisory Board Sciences, NIH, National Science Foundation, American and other advisory groups, and, most particularly, the Trustees. Led Association for the Advancement of Science, and the numerous by Hanna H. Gray, the Trustees have ensured that HHMI remains scientific societies headquartered in Washington. Often we find true to its mission as a medical research organization and lives up to ourselves facing the same issues about biomedical research in the the highest standards of excellence. Thank you for the privilege of United States. These issues include the challenges early career leading this great organization. scientists face and the cumulative effect of conservative funding decisions on innovation in America. Last year, the Institute launched a new open-applicationn competition to identify talented researchers at the very beginningg Paul Fetters Paul

February 2oo9 | HHMI BULLETIN 5 centrifuge

Rocket Man

If you’re a serious surfer—and Steven F. Dowdy qualifies—you act nonchalant as you bob on your board, chatting with other surfers. You don’t let them see you scanning the ocean. “You’re just looking for the dark little sliver on the horizon and wondering if anyone else has noticed,” says Dowdy, an HHMI investigator at the University of California, San Diego. “You want to get that wave.”

You paddle on your stomach toward the incoming set of swells and choose your wave. As it rises in front of you, you turn toward shore. The water stacks up beneath your board as the belly of the swell meets the reef. When the swell begins to go vertical, you stroke once, maybe twice, to stay with it. The wave crests, then rolls, and you feel your board accelerate. “It’s an entirely different way of applying my brain. “It’s an entirely different way of You’re really focused. You do not want to get applying my brain,” says Dowdy, who largely devotes his intellect to slammed on a coral reef or get hit on the head inventing ways to transport cancer- by a 20-foot wave. fighting macromolecules across cell

membranes. “You’re really focused. STEVEN DOWDY You do not want to get slammed on ” a coral reef or get hit on the head by a 20-foot wave.” local surfer, who turned out to be a Sumba Island, Indonesia, where the chemist, showed them a better beach. two also volunteered at a malaria As your surfboard drops over the lip Dowdy later hired him. clinic. In July, he plans another gradu- of the breaking wave, you stand. At Most often, though, Dowdy surfs ation trip to Sumba, this time with the bottom of the wave, you turn your four blocks from home. He walks down Kelsey, who is captain of her high board parallel to the wall of water. The to South Bird Rock in La Jolla, carrying school surfing team. Of surfing with moving water grabs the surfboard fins one of nine custom surfboards under his kids, Dowdy jokes, “I’m getting and shoots you forward through the his arm. (He buys mostly blue boards, concerned, because they’re starting liquid tube. It’s like getting shot out of on the theory that his wife, computer to take waves that are my waves.” a rocket. Once you know you are free scientist Lisa Dowdy, might not notice Raised on Naples Island in southern and clear, you’re just screaming with joy. a new one when it shows up in the California, Dowdy first stood up on a “board room,” their converted garage.) surfboard when he was 7. By age 11, Dowdy has sought out that adrena- Dowdy often surfs with his son his parents let him leave the house at line rush all over the world—as far as and daughter. (Lisa gave up surfing dawn to surf with his buddies before New Zealand, Indonesia, and Europe. after a board broke her nose.) He school. The boys would let their motor- On a trip to Portugal, when his family celebrated Connor’s 2007 high school boat drift until they were far enough

hit a beach with lackluster waves, a graduation with a surfing trip to offshore to avoid waking the neighbors McGrath Ted

6 HHMI BULLETIN | February 2oo9 Play On

Lacing up his fútbol shoes, for biochemist Fernando Goldbaum, is the first step in rebooting his brain. After that, he may look like he’s just kicking a soccer ball. But as he dribbles, passes, and shoots, he’s uncluttering his mind, the better to concentrate when he gets back to the lab. “Soccer is very important for me,” says Goldbaum, an HHMI international research scholar at Leloir Institute in Buenos Aires. “Without any doubt, it clears my head.” That’s why, at least once a week, he and about a dozen researchers, fellows, and professors from the institute meet for an after-work match at a nearby indoor field. Other sports offer fitness, competition, and social interaction, but they’re mere exercise. Fútbol (we call it soccer) is one of Goldbaum’s two lifelong passions—and a family tradition. “My father played soccer and was also a referee,” he says. “And I have an uncle who played professionally, a goalkeeper in the Argentinean leagues for 20 years.” A devoted amateur player since childhood, Goldbaum has downshifted from the full outdoor field to the smaller indoor pitch without regret. At age 48, “The main thing is that, for 90 minutes, you can keep playing with people 10 or 20 years younger than you are. On the big field, that’s almost impossible.” Goldbaum’s second passion, of course, is science. As a small boy, “I used to make little experiments at home and at school.” He recalls masking the surface of a leaf with a disc of foil cut from the seal on a wine bottle. “You leave it on the leaf for a week, and when you remove it, you have a green leaf with a white circle where the chlorophyll has disappeared, due to the lack of sunlight. That was astonishing for me.” Decades later, sunlight still fascinates. He and his team are developing vaccines based on their discovery that blue wavelengths in sunlight acti- vate proteins that drive the spread of brucellosis, an infectious disease that costs the Brazilian and Argentinean cattle industry $100 million a year. The peak moments come, Goldbaum says, when the rewards of the lab and the playing field with the revving motor. The friends converge. “One match I’m still proud of was during have been reuniting to surf every year the first congress of the Protein Society’s Latin since one of the group died suddenly American chapter, in Angra dos Reis, Brazil. We at age 38. organized a match between the Brazilian and the Dowdy throws a summer beach Argentinean researchers. Brazil produces some of party for his research team and neigh- the best players in the world, so you can imagine boring labs, where novices line up for how my team felt when, at the end of the congress, lessons. Granted, a beginner may only they announced the final score: we beat Brazil, stay upright for a second, says Dowdy, 6 to 3, on their home ground.” but “once you get someone standing up, As a fan, he says, “I’ve always followed the Buenos they’re just howling, having a blast.” Aires team called Racing Club. They went for many, —Cathy Shufro many years without a championship. Finally, in November of 2001, they won the local cup for the first time in almost 40 years—exactly when I received

WEB EXTRA: Visit the Bulletin online to my first HHMI fellowship. Now, that was a time for see video footage of Steve Dowdy and his celebration.” —George Heidekat son surfing off Sumba Island. Wacso

February 2oo9 | HHMI BULLETIN 7 centrifuge

Found in Translation

Bringing the autobiography of a 26-year-old senior at the University of able about it than I am.” (Before he Jewish scientist, who narrowly escaped California, San Diego (UCSD). He calls emigrated, Jamshidi, at 20, was the the Holocaust, to a predominantly Shia his time in Kandel’s lab “a life-changing assistant conductor of the Tehran Muslim readership is not as quixotic a experience. I was surrounded by the Philharmonic Symphony Orchestra.) project as it might seem, insists Pouya most brilliant people, including Eric Jamshidi, who has been working in a Jamshidi. himself, who is a legend in neurosci- nerve growth factor lab at UCSD, spent “Anyone anywhere who is interested ence yet was very approachable and the summer studying similar growth in neuroscience will relate to Eric friendly.” factors in Kandel’s signature animal Kandel,” says Jamshidi, an Iranian-born Reading Kandel’s book, In Search of model, the giant sea slug Aplysia cali- college student who spent last summer Memory, Jamshidi sensed a connec- fornica, as part of HHMI’s Exceptional in Kandel’s lab at Columbia University tion. “Aside from having a tremendous Research Opportunities Program. He College of Physicians and Surgeons. intellect, he has a real passion for has been invited to return to Kandel’s “His contribution is one of a kind and science. I like to think that in my own lab after he graduates. Once there, he really, to a great extent, his life story perhaps naïve way I have that passion plans to start the translation project is also the story of neuroscience.” too.” He decided to translate the book and begin contacting academic pub- Jamshidi immigrated to California into Persian in the hope that others lishers in Tehran, from whom he expects with his parents in 2002 and is now a in Iran, Afghanistan, and the Persian- “a very positive reaction.” speaking diaspora will be inspired to Long term, he plans to apply to M.D./ choose a life in science. Ph.D. programs, with hopes of doing Kandel, a longtime HHMI investigator neuroscience within a neurosurgery who won the Nobel Prize in Physiology practice at a teaching hospital. At or Medicine in 2000, has genuine affec- UCSD’s Center for Neural Repair he’s tion for Jamshidi—“just a wonderful been participating in animal surgeries human being”—and, despite concern to optimize nerve growth factor gene that the translation venture could delivery; the techniques could one day absorb too much of Jamshidi’s time, lead to treatments for nerve injuries “Anyone anywhere says that “it seems perfectly innocuous, and even neurodegenerative diseases who is interested so I won’t stop him.” in humans. “In the future these kinds Kandel also admits to pleasant of therapies are probably going to be in neuroscience surprise that he and Jamshidi turned delivered by neurosurgeons,” notes lab will relate to Eric out to have so much in common: “He’s director Mark Tuszynski. extremely engaged in the science and Jamshidi feels the tug of pure Kandel. very serious. But he’s also very cultured. neuroscience but finds the blend with Unlike most kids of his generation, for a medical career a better fit with his POUYA JAMSHIDI example, he likes the music I like”— passions. “I love doing surgeries but I ” both are opera aficionados—“and not also love studying the brain,” he says.

only that, he’s much more knowledge- —Jim Schnabel Jamshidi Photo: Pouya Illustration: Wacso

8 HHMI BULLETIN | February 2oo9 upfront

10 Chasing Amyloid Though it’s taken decades, solving the mystery behind the structure of this errant protein has opened a door to new therapies.

12 Alter Ego One protein encourages prostate cancer and another stifles it. Both are encoded by the same gene.

He wrote the classic textbook on the properties of steam, ice, and liquid water in 1969, but David Eisenberg has always remembered his pediatrician father’s aspirations for him—to go into medicine. Moving closer to that dream, Eisenberg recently solved the structure of a disruptive protein called amyloid that accumulates in cells and appears to play a role in diabetes and several mind-robbing diseases, including Alzheimer’s. He’s training up-and-coming researchers in crystallography so they can make a difference as well, maybe even for patients. Dad would be proud.

February 2oo9 | HHMI BULLETIN 9 upfront

Chasing Amyloid Though it’s taken decades, solving the mystery behind the structure of this errant protein has opened a door to new therapies.

After solving the atomic structure of amyloid, David Eisenberg found the same zipper-like

conformation in similar segments of 30 disease-related proteins. Now he’s devising new therapies. Canziani João

10 HHMI BULLETIN | February 2009 SOLVING A PROTEIN’S STRUCTURE—THE THREE-DIMENSIONAL ARRANGEMENT and spacing of its atoms—is vital for understanding its behavior and is a major step in drug development. But coaxing balky proteins to form chains along which beta sheets assemble, crystals for x-ray analysis can consume months or years of frustrating forming a lengthening fiber as more units are added. The surprise was that side chains effort. Success requires doggedness and creativity; luck helps, too. ¶ emanating from the sheets interact closely David Eisenberg, an HHMI investigator at the University of California, with each other like the teeth of a zipper, locking the sheets tightly in place. Los Angeles, lives for such challenges. Using x-ray crystallography and “That was the ‘aha!’ moment,” Eisenberg computational methods, he has special- scattered through the brain. It is still unclear recalls. “That’s what causes molecules to form ized in determining the structural details whether the deposits directly kill nerve cells the fibers.” Moreover, this so-called “steric of how proteins bind to other proteins. or are the end result of a toxic process during zipper” seals the interface between sheets so Now, he is using that knowledge to develop fibril formation. that water is excluded, explaining why amyloid patient therapies. An important lead came, Eisenberg says, is so persistent and insoluble in tissues. About 10 years ago, Eisenberg began when HHMI investigators Susan Lindquist This landmark finding was a jumping-off to attack a particularly stubborn protein— (Massachusetts Institute of Technology) and point for Eisenberg. In a 2007 Nature paper, amyloid. A tough, fibrous substance that can Jonathan Weissman (University of California, he reported the discovery of similar cross- accumulate in cells like trash in a landfill, San Francisco) independently showed beta spines in amyloid-forming segments amyloid has been linked to at least two dozen that fibril formation could be initiated by a of 30 disease-related proteins, including the disorders, from Alzheimer’s and Parkinson’s segment made up of about 100 amino acid amyloid beta and tau proteins that make up diseases to type 2 diabetes and “mad cow” residues at one end of the protein. Following the characteristic plaques and tangles in the disease. These proteins—in fact, almost any up on this insight, Eisenberg and graduate brains of people with Alzheimer’s disease. protein, apparently—can lose their intricate student Melinda Balbirnie narrowed the Toxic fibrils formed by human islet amyloid folded configurations and form fine hair-like segment down to just seven essential fibril- polypeptide are found in the pancreas of amyloid “fibrils.” forming residues, publishing the discovery most patients with type 2 diabetes, but Understanding the pathology of amyloid in 2001. “Melinda and I realized that it their atomic structure wasn’t known until would be vastly aided by learning its atomic took only a tiny bit of the protein to form an Eisenberg reported it in September 2008 in structure, but for decades this goal was amyloid fiber,” says Eisenberg. “To me, that Protein Science. elusive. Amyloid isn’t soluble in water, was the paradigm paper.” While much remains to be learned about thereby confounding conventional anal- In the same paper, they reported that the role of amyloid fibers in disease, the infor- ysis methods; and it has proved extremely the seven-residue segment could also form mation gained from their atomic structure resistant to crystallization, which would illu- crystals—a huge breakthrough. “We were has already led to work in Eisenberg’s lab on minate its chemical bonds. thrilled,” he says, “but there was a big potential clinical applications. His group is As early as 1935, British scientist William problem: the crystals were 50,000 times designing molecular caps, for example, to Astbury, who studied the physics of textiles, smaller than the ones we usually work with. attach to the ends of amyloid fibers. “It is fired x-rays at strips of poached egg white They had beautiful faces and edges, but their conceivable that capping the end of a fiber that he stretched to form amyloid-like fibers. width was typically around 1 micrometer.” might stop it from lengthening and help to With the x-rays scattering in a pattern that No existing x-ray beam was narrow enough break it down,” he explains. he called “cross-beta,” Astbury inferred that to probe these “microcrystals.” The pursuit of amyloid and potential the protein was composed of “beta strands” Then, luck intervened. At a meeting in human therapies marks a departure for a (short stretches of amino acids) connected Greece in 2003, Eisenberg learned that the scientist at age 69 whose body of work has by hydrogen bonds to form flat and extended European Synchrotron Radiation Facility in leaned away from medicine (in 1969 he “beta sheets,” packed tightly against each Grenoble, France, had just launched a new published the definitive book on the proper- other. It was a good start, but it provided only “microfocus” machine that fired a beam of ties of ice and water). It’s a career move he a rough picture. “Astbury’s analysis tells you x-rays only 4 micrometers wide—the size of thinks would have pleased his father. that the protein is organized into beta sheets the largest amyloid crystals. By teaming with “He was a doctor and always wanted with certain spacing, but it doesn’t tell you European scientists, Eisenberg and graduate me to go into medicine,” Eisenberg says. “I where the atoms are,” explains Eisenberg. student Rebecca Nelson got permission to use thought it was about time I did something In the 1990s, pathologists began making the new beam line, and in a matter of weeks that had medical applications.” p the connection between amyloid deposits they had captured the elusive atomic structure. – RICHARD SALTUS in brain cells and several neurodegenera- Published in 2005, the research confirmed tive disorders—most famously Alzheimer’s in fine detail that amyloid fibrils contain a FOR MORE INFORMATION: To learn about Eisenberg’s disease, in which plaques of beta-amyloid are cross-beta “spine” made of short amino acid class on x-ray crystallography, see “Crystal Clear” on page 52.

February 2009 | HHMI BULLETIN 11 upfront

Alter Ego One protein encourages prostate cancer and another stifles it. Both are encoded by the same gene.

SOME GENES ARE LIKE STORIES THAT LET READERS CHOOSE BETWEEN

several endings. Take the gene KLF6, for instance. The way a person’s cells read KLF6 can result in a protein that drives growth or one that slows it. That decision makes a difference in prostate cancer, according some that includes KLF6. He dissected to research by Goutham Narla, a recent winner of an HHMI Early Career human prostate tumors and confirmed Physician-Scientist Award. ¶ Ten years ago, when Narla was an HHMI that most lacked one copy of KLF6 or had mutations in the gene. Moreover, when he medical research fellow, he made a discovery that helped characterize activated KLF6 in cultured tumor cells, the KLF6 as a tumor suppressor gene that is active. Although every cell in the body cells grew more slowly. blocked in prostate cancer. The work was expressed KLF6, Friedman wanted to know In human and mouse tumors, he an outgrowth of research on the liver; Narla the gene’s role in the liver. As an HHMI found four versions of KLF6 messenger trained, as a medical student and then as medical fellow, Narla engineered mice RNA (mRNA). Cells read the gene like an M.D./Ph.D. student, in the laboratory with overactive KLF6 in the liver. a choose-your-own-adventure story, skip- of Scott L. Friedman, a physician-scien- The mice were unusually small—with ping some parts and transcribing the tist at New York’s Mount Sinai School of small livers. At the time, “we thought, maybe others into mRNA. Medicine who studies liver disease. this gene actually tells cells to stop growing,” Protein made from the shortest version, With Friedman and colleagues, Narla, Narla recalls. He tested the idea and dis- called KLF6-SV1, drives cellular changes who launched his own lab at Mount Sinai covered that KLF6 engages well-known that speed the spread of tumor cells in mice. in 2006, recently revealed that KLF6 also cellular machinery for growth suppression— In 2005, the team studied the DNA encodes a protein that drives cancer devel- specifically, tumor suppression. of more than 3,400 men and found that opment and progression. On the basis of this Narla scoured the literature and found some have a hereditary variation in KLF6 discovery, they’ve proposed ways to predict that many patients’ prostate tumors have that changes how cells read the gene. As a man’s risk of developing prostate cancer DNA damage in a region of the chromo- a result, they make more KLF6-SV1 and and whether the disease, once diagnosed, is likely to recur. In 2008, they designed what “As a clinician I was struggling to may one day be a new treatment for the most aggressive forms of the disease. find a way to apply this informa- In 1998, Friedman was studying a class tion to the patients we see every of cells (hepatic stellate cells) involved in day with metastatic cancer. liver healing. His lab group had found that when these cells reproduced, KLF6 was GOUTHAM NARLA ” Mount Sinai Medical Center

12 HHMI BULLETIN | February 2009 less full-length mRNA. A man born with Narla and colleagues also managed to an independent scientist. The early career the variation is twice as likely to develop reverse the effects of KLF6-SV1 in the lab. physician-scientist award, part of HHMI’s prostate cancer as someone without it. “He After inducing prostate-derived tumors in effort to support young scientists working makes a little more KLF6-SV1, and over his mice, they injected the tumors with small to translate scientific discoveries into better lifetime that drives the process of cancer RNA segments, called siRNA, that attach treatments for patients, will provide five development forward,” Narla says. specifically to KLF6-SV1 and prevent it years of funding to Narla’s lab. Genetic testing for this variation may from being translated into protein. The Narla believes he’s finally getting close predict a man’s chance of developing pros- tumors regressed. These siRNA also killed to his goal of helping patients. “As a clini- tate cancer. prostate cancer cells in culture. The study cian I was struggling to find a way to apply The researchers also found, in 2008, that was published in the Journal of Clinical this information to the patients we see patients whose tumors had high concentra- Investigation in August 2008. every day with metastatic cancer. When we tions of KLF6-SV1 had a greater chance of “It was really Goutham’s work that led us identified KLF6-SV1 and were able to actu- disease recurrence. This finding may lead into an understanding of [the gene’s] role ally target it and see tumors shrink, I was to a test on a patient’s tumor biopsy that in cancer,” says Friedman, who adds that extraordinarily excited.” p

Paul Sahre Paul could inform treatment decisions. he’s gratified to see his student emerging as – OLGA KUCHMENT

February 2009 | HHMI BULLETIN 13

LUMINOSITY

BY ROBIN MEJIA AND CORI VANCHIERI ILLUSTRATION BY RICCARDO VECCHIO

February 2009 | HHMI BULLETIN 15 oger tsien is ready to move developing green fluorescent protein (GFP) markers to watch beyond his signature accom- proteins in action. By manipulating genes from a glowing jellyfish plishments. Specifically, the and from corals, Tsien created a set of genes that produce colors Nobel-prize winning bio- ranging from violet to deep red. These genes allow scientists to chemist, who devised a way to tag any of the tens of thousands of proteins at work in the body to use fluorescence to watch observe what they do, and, by marking multiple proteins, how proteins in action, wants to they interact. GFP’s utility goes far beyond human biology as change how cancer surgery is well; it’s been used to create bacteria that glow in the presence of done, among other things. But arsenic, a significant problem in well water in Southeast Asia, and a shift away from glowing to identify explosives such as TNT. proteins is turning out to be Tsien isn’t leaving visualizing of otherwise invisible processes harder than he expected. ¶ “Maybe it’s foolish,” says Tsien, an behind, but he’s set his sights on new targets: lighting up HHMI investigator at the University of California (UC), San cancerous tumors for surgeons and watching memories form. His Diego. It is rather late in his career, he admits, to delve into an results on both fronts are promising. At a recent lecture at a unfamiliar clinical problem. The impact of his work makes it Midwestern university, however, when he described his progress, easy to see why he feels like he’s swimming against the tide. the first question from the audience was about the work he’s been “There’s been this great transformation in biology because of trying to leave behind: “When are you going to devise infrared the tools that Roger developed,” says HHMI investigator Susan fluorescent proteins?” Taylor, a biochemist at UC San Diego who helped recruit Tsien to the school. They have provided “enormous extra information” CELLULAR VISION about how cells function, she says. At a November science meeting at HHMI’s Janelia Farm The 2008 Nobel Prize in Chemistry, which Tsien shared with Research Campus, Loren Looger wanted to set the stage for a

Osamu Shimomura and Martin Chalfie, recognized his work discussion of his own research on sensors to study molecular Fetters Paul

16 HHMI BULLETIN | February 2009 comes from a family of high-achieving engineers—his father was a mechanical engineer and his mother’s brothers were engi- neering professors at the Massachusetts Institute of Technology (MIT). Tsien’s brother Richard, originally an electrical engi- neering major at MIT, is now a prominent neurobiologist at Stanford University and former member of HHMI’s scientific review board. Roger Tsien says that it was a given he’d end up in science, too, but his path to chemistry and biochemistry was in part shaped by his role as the youngest of three brothers in search of his own niche. “Part of the reason [I pursued] chemistry is that it was one of the things that Dad and my brothers didn’t really like,” he says. “Dad’s idea of taking care of the lawn—since he was an impatient mechanical engineer—was to get on his hands and knees and dig up the weeds. I was allergic to them and wanted to pour herbicide on them from a distance.” Tsien explained that his work inventing calcium dyes at Cambridge was the fourth project within his dissertation; his first three efforts had run into dead ends. When he started work on the calcium indicator he didn’t tell his advisor, who surely would have vetoed the effort. The subterfuge paid off, and his career was launched. Today, researchers around the world rely on the dyes Tsien created to study calcium, pH, sodium, and other molecules. At the Janelia lecture, he showed an image sequence called the Blush of Conception. When a sperm fertilizes an egg, it initi- activity in the brain. So the Janelia Farm group leader described ates a wave of changes inside the cell, including creating an Tsien’s early work, which focused on calcium. intracellular wave of calcium. Tsien made those processes visible. Calcium is an important cellular messenger that controls As the sperm hit the egg, the calcium change was depicted as a neurotransmitter release from neurons, governs muscle cell wave of color—as if the egg were blushing—washing across it contraction, and plays a role in fertilization. When Tsien was a from the point of contact. graduate student at the University of Cambridge, researchers could Mark Ellisman, a professor of neurosciences and bioengi- measure calcium levels in only a few extremely large cells that neering at UC San Diego, notes that each time Tsien develops a could tolerate being poked with a needle. During his graduate and new tool, in the paper that introduces it he affirms its value by postdoctoral studies, Tsien developed fluorescent dyes to measure showing how it can be used to understand some substantive calcium in most animal cells without having to inject them. problem in biology. “As soon as that’s out, the world picks up on Later that evening, Tsien gave his own presentation, a last- it and starts to use the technology on a large number of prob- minute addition to the agenda at HHMI’s request, to celebrate his lems,” says Ellisman, who collaborates so closely with Tsien that Nobel win. Tsien himself was physically unassuming. Many of the two sometimes hold joint lab meetings. the slides were black and white bullet points put together in “He’s passionate about things that are useful to society,” Janelia’s library that afternoon. The presentation’s color came Ellisman adds. “He’s got a very beautiful orientation to what’s from Tsien’s passion for his work, a sense of humor about himself, important.” and an interest in others. He explained that he’d decided to speak primarily to the graduate students in the audience. BEYOND THE JELLYFISH “I wish to explain how you can screw up and be screwed up As a young faculty member at the University of California, and still, some day, accomplish something,” he began. Berkeley, Tsien’s personal insecurity drove his next big success. The first step? “Identify a big problem in biology, preferably Surely, he thought, the prestigious biochemists and molecular one whose solution would assuage a personal sense of inade- biologists at Berkeley were looking down their noses at a scientist quacy,” he said. Tsien, who grew up in Livingston, New Jersey, in the physiology department working on a “mere metal ion like

February 2009 | HHMI BULLETIN 17 calcium.” So he decided to find a way to use a process called agreed to send the DNA for GFP to Tsien. Another scientist, FRET to build indicators of the essential cellular messenger Martin Chalfie also contacted Prasher and received the DNA. cyclic AMP (cAMP). Would the gene only work in the jellyfish? If GFP needed to When two fluorescent dyes get close to each other, one steals interact with other chemicals in jellyfish cells in order to glow, it energy from the other, changing the color it emits. The process— wouldn’t solve Tsien’s problem; he needed a protein he could called fluorescence resonance energy transfer, or FRET—is add to any cell. Chalfie quickly answered that question by particularly useful in watching cAMP split apart the subunits of creating transgenic bacteria and worms that glowed, showing protein kinases that depend on cAMP. GFP would glow in other organisms as well. Tsien began collaborating with Susan Taylor at UC San Tsien immediately recognized the potential of GFP, but he Diego, the world’s expert on cAMP-dependent protein kinase. also saw its flaws—it gave a big peak in the UV spectrum where But sending samples by FedEx between Berkeley and San Diego scientists didn’t want to illuminate; the visible blue-green peak was wasn’t working, so Tsien moved south. much smaller. And in its native state, five-sixths of it was in a form “Even after the move, it took a year of my people being physi- useless to researchers. He modified the gene, creating a series of cally in the lab adjacent to Susan’s for us to make the cAMP highly effective fluorescent proteins in colors from blue to red. reporter work,” Tsien says. “It required laboriously growing And that Midwestern questioner will be happy to know Tsien’s bacteria, purifying two proteins, chemically labeling them in a lab has made progress toward producing an infrared fluorescent test tube with two different colors, recombining and repurifying protein for viewing cells and organs inside living animals without them, and then microinjecting them into the cells of interest”— having to open the animals. (The deep red color of blood obscures and the cells had to be large enough to handle microinjection. the current palette of fluorescent proteins.) Tsien fretted over these limitations. There had to be an easier way. The Nobel Prize can only be split three ways, but Tsien has With transgenic technologies, he could insert foreign genes into been adamant about recognizing the contribution of Prasher, a cell’s genome, making the cell create whatever protein the gene who eventually left science and now lives in Huntsville, Alabama. called for. Tsien searched for a gene that encoded a fluorescent “If there’s anyone who’s underappreciated, it’s Douglas protein he could monitor—a daunting challenge. He remembered Prasher,” Tsien says. “If he hadn’t cloned the GFP gene, progress reading a review of a protein called aequorin, which is produced by in the field would have been delayed indefinitely. I don’t know the Aequorea victoria jellyfish in the Puget Sound. “[The paper] anyone else who was working on the cloning.” Tsien and Chalfie said if you’re really careful, you can get rid of this awful contami- flew Prasher and his wife Virginia Eckenrode to Sweden for the nant, green fluorescent protein,” Tsien recalls. “In despair, I typed Nobel ceremony. green fluorescent protein into Medline in early 1992.” The rest, as they say, is history. He found that a scientist at the MARKER FOR MEMORY Woods Hole Oceanographic Institution, Douglas Prasher, had “Seeing things, that’s sort of buried in my psychic makeup,” says just cloned the gene for GFP. When Tsien contacted him, Prasher Tsien, explaining why his work is so focused on visualization. said his funding was ending and he was stopping work on it, but he Today, he’s applying that inner aesthetic to new problems. “How and where synapses adapt to create and preserve a memory is one of the most important problems in neurobiology right now,” says Michael Lin, a postdoctoral researcher in Tsien’s lab. When new memories form, unique neural connections, or synapses, grow in size. This process involves new protein produc- tion, so Lin and Tsien are working on ways to watch the proteins that are created during synapse growth. To do this, Lin fuses three genes in sequence: an easy to visu- alize tag, a protease from hepatitis C virus, and a synaptic protein of interest. The hepatitis viral protease likes to cut off anything attached to its own ends, so, left alone, the triple protein splits itself into its three constituents, leaving the synaptic protein untagged. If Lin administers an anti-hepatitis C drug that cripples the protease, all the fusion protein molecules made after that point remain intact with their tags still attached.

18 HHMI BULLETIN | February 2009 THE BARREL-SHAPED GREEN FLUORESCENT PROTEIN, GFP, WAS FIRST ISOLATED FROM A GLOWING JELLYFISH.

The work remains at an early stage, but Lin has used the system about the disease that claimed the lives of his father and his to create transgenic flies, labeling a protein that’s known to be a Ph.D. supervisor. major structural component of synapses. Neither he nor Tsien When surgeons remove a tumor, they rely on their knowledge thinks they’ve found the perfect marker for memory formation, of how cancer tissues look and feel to remove as much as they can but, says Lin, “We have a good enough candidate to begin work.” without taking out too much surrounding tissue. “The way we try Their “dream experiment” would be to find a master protein to tell whether we have gotten it all is to take samples of what’s left that is freshly made when a new synapse is born but is not being and send them to the pathology lab,” says Quyen Nguyen, a head continuously refreshed in existing synapses. They would then and neck surgeon at the UC San Diego School of Medicine who create an animal with that protein labeled and train it in some task also works in Tsien’s lab. Examining tissue for cancer can take 10 while giving it the anti-hepatitis C drug. All copies of the master or 20 minutes per sample, so that process can mean keeping a protein formed from that point forward would be labeled. By patient under anesthesia for an extra hour or longer. observing where those proteins accumulate, they could see where Fluorescent proteins don’t help here, because their main nerve synapses had formed or expanded. From a practical stand- advantage is that they can be delivered by gene transfer, which is point this process is a bit more daunting than it sounds. They still fine for experimental animals but not human patients. Nguyen don’t know all the proteins that help create synapses. Tsien hopes and Tsien have found a way to load tumors with synthetic other scientists will take up the memory question as well, so that nanoparticles that not only are visible by magnetic resonance they can divvy up the many potential protein candidates. imaging but also glow on the operating table, making the edge of the tumor visible to the surgeon. The technology holds promise GLOWING TUMORS as a way to detect tumors and improve the success of surgery and, The effort that Tsien calls “foolish,” but is taking most of his possibly someday, as a way to deliver drug treatment.

Tsien lab energy, is his foray into cancer. It reflects a wish to do something (continued on page 56)

February 2009 | HHMI BULLETIN 19 The Macro World of MicroRNA Short stretches of “junk DNA” are surprisingly influential in preventing or limiting disease— so influential, they are now high on the agendas of many drug companies. by Maya Pines illustration by IC4 Design

20 HHMI BULLETIN | February 2009

One reason most of us don’t get Underpinnings of Cancer microRNAs and cancer. (Led by HHMI cancer is that we are endowed with Cancer researchers in particular are excited investigators Todd R. Golub at the Dana- tumor suppressor genes. Until by recently uncovered connections Farber Cancer Institute in Boston and H. recently, scientists believed these between microRNAs and major pathways Robert Horvitz at MIT, the study showed genes operated through proteins of the disease. As many as 50 percent of all that microRNAs are expressed at a much that put the brakes on cell growth, cancers involve a cellular pathway lower level in various tumor cells than in thus preventing cancer’s develop- governed by the p53 gene, a tumor normal tissue, but it was not clear why.) ment. Now scientists realize that suppressor. When this gene is mutated and This time Jacks chose mice whose lung some tumor suppressor genes do fails to produce normal protein, malignant tumors looked like those of humans with not produce proteins at all. Instead, cells can grow wildly. In 2007, five lab advanced, non-small cell lung cancer. they make tiny snippets of RNA, groups independently reported that a When researchers in his lab activated let-7 called “microRNAs.” family of microRNAs called miR-34 sits in microRNAs that they had delivered into RNA, a nucleic acid, is still best known the middle of the p53 pathway. the animals’ lungs, “this dramatically inhib- for its role as a messenger, relaying One team, led by HHMI investigators ited the tumors’ development,” says Jacks. instructions from the DNA of genes to the Gregory J. Hannon and Scott W. Lowe at Unfortunately, the tumors later became parts of the cell that make proteins. But its Cold Spring Harbor Laboratory in New resistant to the microRNAs. His group is many other talents keep surprising York, found that when they switched on trying to analyze why that happened. researchers. MicroRNAs, for instance— these microRNAs in mouse cells there was Other researchers want to use short stretches of 21 to 22 nucleotides, a rise in cell senescence (a kind of genetic microRNAs as early markers of cancer. compared with the thousands of nucleo- death in which cells lose the ability to repli- Muneesh Tewari and his colleagues at the tides that contain the recipe for making a cate—see “When Cells Grow Old,” page Fred Hutchinson Cancer Research Center protein—come from parts of the genome 32). Other teams showed that miR-34 could in Seattle showed that microRNAs are once considered worthless. also promote apoptosis (cell death). Both of present in samples of plasma and serum “in When the human genome was these responses protect the organism when a remarkably stable form.” Thus, it may be sequenced, only a small fraction of it—the a particular cell’s DNA is damaged through possible to monitor tumor-derived “coding” part—seemed important. The environmental exposures. By contrast, microRNAs, which are present in different coding DNA is first transcribed into RNA when researchers decreased the activity of amounts in healthy individuals and cancer and then translated into proteins. Yet this miR-34 microRNAs, cancerous cells patients, the group reported in the July 29, part makes up only 1.2 percent of the 3 survived and proliferated. The scientists 2008, issue of Proceedings of the National billion nucleotides in our genome. The hope that before long these microRNAs can Academy of Sciences. rest was sometimes called “junk DNA” be medically delivered to living animals in Most promising, perhaps, are recent because it didn’t seem to do anything. As a safe and efficient manner, to disrupt findings that raise the possibility of stopping David P. Bartel, an HHMI investigator at cancer pathways. Their success could be a a cancer’s metastasis—the spread to other the Massachusetts Institute of Technology step toward preventing or treating the organs, which ultimately kills the patient. (MIT) points out, however, “You know it’s disease in humans. Last year, HHMI investigator Joan not junk if evolution has retained it.” In Tyler Jacks, a cancer researcher and Massagué and colleagues at Memorial fact, “noncoding” DNA is beginning to HHMI investigator at MIT, is also looking Sloan-Kettering Cancer Center identified look more like a gold mine—a source of into the therapeutic potential of two microRNAs (miR-126 and miR-335) many kinds of potent RNA, including microRNAs—particularly those of the let-7 that were missing in the most aggressive forms such as microRNAs (and the different family, which are extremely scarce in cells mouse and human breast tumors. When but structurally related small interfering from mice with lung tumors. To find out they delivered these critical microRNAs to RNAs) that help regulate gene activity. whether increasing these microRNAs would the breast cancer cells, the tumors lost the MicroRNAs influence nearly all aspects reduce the development of cancer, he ability to spread. And on December 12, of health and disease—the “stemness” of turned to a mouse model of lung cancer. He 2008, Arul M. Chinnaiyan, an HHMI stem cells, cancer, early development, had already used such a model in 2005 in a investigator at the University of Michigan diabetes, viral infections, schizophrenia, landmark study of the relationship between Medical School, reported in Science that heart disease, aging, and Alzheimer’s his team had discovered that a microRNA disease, for example. Bartel calculates that called miR-101 must be active to prevent more than half of human genes are regu- the spread of prostate cancer. When this lated by microRNAs. microRNA is lost, an enzyme called EZH2 that promotes the spread of cancer cells springs into action. Thus, “for treatment purposes,” Chinnaiyan says, “replacing miR-101 in solid tumors that have lost it could reduce

22 HHMI BULLETIN | February 2009 their metastatic properties.” This proce- Idiosyncratic No Longer that were supposed to behave as if they dure might apply not only to prostate No one realized that microRNAs would be belonged to older larvae got stuck at an cancer but also to breast, ovarian, and so important when the first one was discov- earlier stage, repeating cell-fate programs colon cancers as well as to certain forms of ered, in 1993, in the microscopic worm that they should have expressed only once. brain and lung cancers and leukemia. Caenorhabditis elegans. Since his time as a What lin-4 normally does is turn off “The problem is the delivery issue,” he postdoctoral fellow in Horvitz’s MIT lab, another gene, lin-14, as Ambros realized says. “Several drug companies are now Victor Ambros had been trying to deter- after studying the interactions between working on ways to put specific microRNAs mine how the mutant gene lin-4 made lin-4 and lin-14 mutations. Gary Ruvkun, into ailing cells while avoiding healthy worms develop abnormally. The gene also a postdoc in Horvitz’ lab, cloned lin-14 cells, where [the agents] might produce controlled developmental timing, Ambros and found that it encoded a protein which some damage.” (now on the faculty of the University of was expressed in juvenile worms. Try as Many other diseases besides cancer Massachusetts Medical School) and they might, however, Ambros and his have been linked to microRNAs. For Horvitz concluded. When lin-4’s function colleagues could not find any protein that example, at the Gladstone Institute of the was missing, this timing was off and cells corresponded to the lin-4 gene. University of California, San Francisco, Deepak Srivastava produced genetically engineered mice that lacked miR-1-2, a microRNA normally found in the animals’ heart cells. These mutants produced offspring with life-threatening holes in their hearts or fatal disruptions in their cardiac rhythms. Srivastava found that other microRNAs were deficient in mice with cardiac hypertrophy, a condition that can lead to heart failure. In diabetes, however, scientists see the opposite problem: an overabundance of microRNAs. The goal in that case is to silence the microRNAs involved. For instance, researcher Markus Stoffel of the Swiss Federal Institute of Technology in Zurich is collaborating with an American drug company, Alnylam Pharmaceuticals, to develop what they call “antagomirs”— small fragments of RNA that can travel through the body and reduce the expres- sion of certain microRNAs in specific organs. (HHMI investigators Phillip D. Zamore and Thomas Tuschl invented antagomirs in 2004. Zamore, Tuschl, and Bartel are among the founders of Alnylam.)

Tyler Jacks (top) is inhibiting lung tumors in mice by introducing the microRNA called let-7.

David Bartel: (bottom) calculates that more than half of human genes are regulated by

Jacks: Leah Fasten Bartel: Robert E. Klein / AP, ©HHMI Bartel: Robert E. Klein / AP, Leah Fasten Jacks: microRNAs.

February 2009 | HHMI BULLETIN 23 Phillip Zamore: (top) says that knocking out microRNAs in animals in the wild will instigate very different changes than in those raised in a controlled lab environment.

Robert Horvitz: (bottom) has shown in worms that microRNAs work in fami- lies; knocking out just one has little, if any, effect.

very ancient gene, conserved in a wide range of animals from flies and sea urchins to humans. (It is the same let-7 microRNA that MIT’s Jacks now hopes to use against lung cancer.) That discovery made scien- tists take notice. Shortly afterward, in 2001, a block- buster series of three articles was published in Science. In these articles, three separate labs headed by Ambros, Tuschl (then at the Max Planck Institute in Göttingen, Germany, and now an HHMI investigator at the Rockefeller University), and Bartel announced the existence of “a large class of tiny noncoding RNAs” with potentially broad regulatory functions in animals. This finding started a deluge of other newly identified microRNAs. “We keep discovering more of them,” says Bartel, who estimates that humans have at least 500 different microRNAs, which regulate thousands of genes. “Back in 2001, we were happy when we had sequenced 300 small RNAs, 55 of which were unique microRNAs. Now, with high- throughput methods, we can sequence 5 million small RNAs at a time, from humans or any animal we choose. This gives us the ability to find microRNAs that we’d missed earlier.” Those they found early on are Then came the breakthrough in 1993, act by preventing the translation of their highly conserved through evolution, recalls Horvitz. “In his own lab, Victor messenger target or targets.” according to Bartel. “As we dig deeper, we made the unexpected and remarkable “The biomedical world, however, get those that are expressed at lower levels discovery that lin-4 encodes a tiny, remained indifferent,” he notes. Most biol- and are less likely to be conserved in other 21-nucleotide RNA. He and Gary further ogists viewed these molecules as just “weird animals,” he says. showed that this RNA—later recognized as little idiosyncratic things, limited to devel- Nevertheless, in a paper published the first microRNA—is complementary in opmental timing in worms,” says Joan A. October 30, 2008, in Nature, Bartel and sequence to its target, lin-14.” This obser- Steitz, an HHMI investigator at Yale colleagues at MIT; the University of vation, Horvitz says, led them to establish University who studies other kinds of small California, Berkeley; and the University of “a common mechanism of microRNA RNAs and is now turning her eye to control of gene function—that microRNAs microRNAs. But seven years later, Ruvkun’s lab cloned another mutant gene, let-7, which also encoded a 21-nucleotide RNA,

and—most importantly—found that it is a Fetters ©HHMI Horvitz: Paul Zamore: Robert E. Klein / AP,

24 HHMI BULLETIN | February 2009 many genes at once. He points out that “We keep discovering more of animals in which researchers have knocked them,” says Bartel, who estimates out a gene—such as the fruit flies he studies in his own lab—are well fed and live in that humans have at least 500 temperature-controlled environments. But what if a fly that is less than perfect is put in different microRNAs, which a normal environment? “In real life, flies experience noonday sun and cold nights. regulate thousands of genes. And their proteins are distributed in gradi- ents that change with temperature,” he says. “Something may look like a small Queensland showed the influence of but imagine how difficult it would be to do defect in the lab, but you know what would microRNAs throughout history. it in a mouse!” happen in the wild? The fly would die.” “MicroRNAs have been available to regu- It takes much longer—about a year, as Everything depends, of course, on the late and shape gene expression as far back opposed to a week—and costs a great deal microRNAs’ targets. MicroRNAs cannot as we can go in animal evolution—they more to produce a mouse with a specific act until they have paired with complemen- might even predate animals,” he says. gene deletion. Nevertheless, the Sanger tary nucleotides on a cell’s messenger RNA. “They might have helped to usher in the Institute in Cambridge, England, is Once paired, they generally shorten the era of multicellular animal life.” creating a library of knockouts of each of lifetime of the messenger RNA, or block or the 500 microRNAs identified in the weaken its instructions, thus reducing the Exploring Biological Mechanisms mouse genome so far. This resource will output of protein. Now, one big push in To find out what microRNAs do biologi- serve as a counterpart to the National microRNA research is to find an efficient cally, scientists have been knocking out the Institutes of Health Knockout Mouse method of zeroing in on their targets. known microRNA genes in worms. In Project for protein-encoding genes. Several groups have developed December 2007, Horvitz, Ambros, Bartel, Eventually, stem cell lines of each mouse computer programs that predict which and their colleagues reported in PLoS in each library will be available to scientists genes are the most likely targets of each Genetics on a new collection of engineered who want to use these rodents as models for microRNA. To evaluate these programs worms in which 95 of the 115 microRNAs human diseases. and find targets that might be missed by the that had been clearly identified in C. Meanwhile two studies—one led by programs, researchers are also developing elegans were knocked out. Matthias Selbach and Nikolaus Rajewsky new methods for identifying targets. “To our surprise, the worms in general of the Max Delbrück Center for Molecular At Stanford University, for instance, seemed perfectly okay,” Horvitz says. The Medicine in Berlin, Germany, and the HHMI investigator Patrick O. Brown is researchers looked for worms with other by Bartel and Steven Gygi of Harvard using the kind of microarray chips he abnormal behavior or anatomy but, apart Medical School—have measured how pioneered 14 years ago to examine large from those with deletions in lin-4, let-7, or proteins change after a cell encounters a quantities of messenger RNA, looking for lsy-6 (identified earlier by Oliver Hobert, specific microRNA. Using a new technique targets. Brown’s results show that a program an HHMI investigator at Columbia called SILAC (an updated version of mass developed by Bartel and colleagues does a University), they could find only one—a spectrometry), they examined several thou- relatively good job of predicting the targets worm that was constipated. This worm’s sand proteins and concluded, in the of the microRNAs he examined. He “abnormally long defecation cycle” was September 4, 2008, issue of Nature, that a suggests that many segments of messenger caused by the deletion of two microRNA single microRNA can repress the produc- RNA are ready to be “tuned” by specific genes, miR-240 and miR-786, both of tion of hundreds of proteins—but for each microRNAs, as needed, in a “continuous which are conserved in other species. protein this repression is relatively mild. scale of regulation.” “The microRNAs are in families,” Yet even small changes in protein And former HHMI investigator Horvitz explains. “If you knock out the expression can make a huge difference, Jennifer A. Doudna (now at Genentech) entire family, defects can appear,” but says Phillip Zamore, an HHMI investigator is attacking the problem from a different knock out just one microRNA and in most at the University of Massachusetts Medical angle. Her UC Berkeley lab is looking at cases the worms look normal. To see a School. Zamore is comparing highly selec- what allows a specific microRNA to target change, he says, it takes not just single or tive microRNAs with those that control a specific messenger RNA in terms of even double knockouts, but at least triple, both nucleotide sequence and structure. and perhaps six or seven knockouts in a “We want to harness microRNAs and single animal. “We can do this in the worm, manipulate them for use in therapy,” she says. “Potentially, it could have a large impact on the way drug companies develop microRNAs.” p

February 2009 | HHMI BULLETIN 25 between a rock and a new place

With a wide-angle view of the world and a commitment to follow her fascination, this scientist is making imaginative connections between rocks, bacteria, and medicine.

by Sarah C.P. Williams photography by Leah Fasten

26 HHMI BULLETIN | February 2009

dianne k. newman grew up embracing two cultures. Born to American parents in Argentina (her father was a diplomat) she took to the transitions with ease: speaking English at home and fluent Spanish when

she stepped outside in her adoptive cities throughout plankton respond to silver. Beakers for Argentina, Venezuela, and Panama. ¶ She learned early these experiments needed to be washed to let her passions guide her, and she has a gift for repeatedly in acid baths to rid them of metal contamination. “I realized that convincing others that her ideas are worth pursuing. multiple acid-washing would probably With these talents, Newman, an HHMI investigator at drive me crazy after a while,” says Newman, “so I asked if I could switch.” the Massachusetts Institute of Technology (MIT), has Around that time, a senior student in become a scientific diplomat: an ambassador between the lab, who had gone all over Boston the once-disparate fields of geology and microbiology. collecting bacteria that could metabolize high concentrations of arsenic, cleared off She has mastered the languages, tech- to arsenic-contaminated streams. Learning her desk. “She gave me one of her bottles niques, and cultures of both fields to get to what keeps the bacteria alive could lead to of bacteria that was destined to be thrown the crux of her work: using modern novel ways to thwart their growth. away,” says Newman. “And it was this bacteria to understand how the first really bright yellow color, and the only bacteria on earth could have survived. thing I knew how to do—from my mate- The only way to extrapolate how—and follow the fun rials science background—was to figure when—early bacteria thrived is to study As an undergraduate at Stanford out what compound was making it yellow.” the relics they left behind: rocks. So University, Newman never guessed she’d That’s how Newman stumbled upon Newman is probing how bacteria interact end up as a microbiologist. She majored the molecules that allow bacteria to with minerals. She’s discovered how some in German studies and took a lot of envi- metabolize metals. These colorful com- bacteria produce energy from arsenic and ronmental and materials science classes. pounds guided her budding career. But iron and how they change their environ- “I loved everything, that was my problem,” the real pivot point came when Morel ments in the process. She thinks some of she says. “I was an advising nightmare.” moved his lab from MIT to Princeton. the oldest bacteria—those that existed She believed in doing what she loved, she Though Newman had planned on only before the atmosphere resembled its says. If one day that was German and the getting a master’s degree and then pursuing current, oxygen-dominated state—relied next engineering, why not? That’s still patent law, she decided to accompany him heavily on iron to drive their metabolisms. how she conducts research, following the and finish her Ph.D., for the fun of it. “I Today, the remnants of a long-ago iron-rich ever-winding path of her interests. was doing things because I enjoyed them environment are visible as striking red But as graduation loomed, Newman and I was lucky because the rest just took bands on ancient canyon walls, and had to nail down something to do next. care of itself,” Newman says. Newman’s work is relevant for explaining She chose environmental engineering—a She started seeking out courses in those patterns. combination of some of the things that genetics and quickly saw its potential for “Choosing bacteria that can be had fascinated her most at Stanford—and studying bacterial processes. Newman’s worked with genetically really set her began a graduate program at MIT. teacher of one short course, “Advanced apart from her peers in the geosciences,” With no real engineering experience, Bacterial Genetics” at Cold Spring says her former teacher Thomas Silhavy, she had to push to find a professor who Harbor, was Bonnie Bassler, now an a Princeton University microbiologist. would take her on. “Even though I said HHMI investigator at Princeton. Bassler “She realized that genetic analysis opens ‘No thanks’ six or seven times, she really says Newman caught her attention with all the doors for molecular sciences. You wanted to work with me,” says François her incredible energy. could argue that she created the field of Morel, who studies how microorganisms “She came with little background in geomicrobiology.” interact with metals—a topic that genetics but she knew she wanted to learn Newman’s work has crossed over into intrigued Newman. Her persistence paid it. She was incredibly hard working, and modern medicine and ecology as well, off and Morel finally became her advisor. unflappable. After long days of working helping explain how modern bacteria In Morel’s lab though, Newman says and studying, everyone else would be too thrive in unusual settings—from the she didn’t have the patience for the first exhausted to move, and she’d bound out mucus-filled lungs of cystic fibrosis patients project he gave her: studying how phyto- the door to go on a jog.”

28 HHMI BULLETIN | February 2009 That vitality and enthusiasm hasn’t The 36-year old Newman exudes not grant application that requires complex faded; Newman’s lab members nick- only energy, but confidence. She could chemical structures, he double checks to named her “The Catalyst” (like an easily be mistaken for a graduate student: make sure I’ve drawn the bonds right. enzyme that increases the rate of a chem- small with dark, untamed hair and glasses Sometimes he just draws them for me.” ical reaction). “She injects energy into perched on her nose, she’s dressed casu- any project,” keeping the lab both fun ally in brown and orange earth tones, and successful, says graduate student except for a purple plastic watch. But she geology goes genetic Alexa Price-Whelan. “Even when she was owns her lab like no graduate student That summer at Cold Spring Harbor exhausted on maternity leave, she’d come could. At a recent lab meeting, midsen- changed the direction of Newman’s into the lab and have more energy than tence talking about geology, she leans her research. the rest of us combined.” chair back and rests her clog-adorned feet “I realized this huge power in genetics Every lab member likes to mention the on the conference table. She’s perfectly at that could solve all these problems I lab bench with Newman’s name on it, a home here, leading a lab. was considering,” she recalls. Once at rarity among investigators who have teams Her one-year old son Ronen occasion- Princeton, she started characterizing the of students to collect data for them. ally makes the lab his home too. A pile of arsenic-metabolizing bacterium, which Though the countertop has become a stuffed animals and a rubber duck sit on she named Desulfotomaculum auripig- storage area for unneeded equipment, Newman’s office floor next to a thick text- mentum for its gold-colored pigments. At Newman insists that the area is hers, and book entitled “Principles and Applications that point, she couldn’t genetically modify she plans to hunker down at the bench any of Aquatic Chemistry.” Although married the microorganism, but she held on to that day. “She wants to be right there in the to inorganic chemist Jonas Peters, she says goal for later. thick of things, getting her hands dirty,” science talk is rare at home—especially Though she worked in a geosciences says Paula Welander, another postdoctoral now, with the baby dominating their time. lab, Newman frequented molecular biology fellow in the lab. “We tease her about her “Once in a blue moon we’ll talk about labs to absorb techniques and advice, says

Leah Fasten lab bench a lot, but really it’s very inspiring.” science,” she says. “Whenever I have a Princeton’s Silhavy, who had Newman as a

February 2009 | HHMI BULLETIN 29 student in his graduate genetics course. spare electrons. Other compounds—like forms rely on it. But 3.8 billion years “When there were things to learn, she took iron—can accept electrons too but the ago—when the earliest evidence of life is it upon herself to learn them,” he says. mechanism was unknown before Newman recorded in ancient rocks—oxygen was Newman thought that together micro- started studying iron-metabolizing bacteria. scarce. Nailing down exactly when, and biology and genetics could tackle questions Newman had an inkling that the how, the atmosphere transitioned to that geologists had been grappling with. bacteria produced molecules that acted oxygen requires probing the fossil record “A lot of geology-related microbiology outside the cell as electron shuttles— for the appearance of microorganisms that until then had been very descriptive, and carrying electrons from the cell and produced oxygen. “Dinosaur footprints here was finally a way to get at underlying dumping them on iron. Her suspicions only go back a short ways,” says Newman. mechanisms.” were right—she discovered evidence for “If you want to understand the evolution In 1998, Newman landed a postdoc such an electron shuttle by screening of life on earth billions of years before that, position in the microbiology lab of mutants that couldn’t metabolize iron. you need to understand microbiology.” Roberto Kolter at Harvard Medical With that finding, Newman suddenly had Typically, geologists have used mole- School. “Her background really caught a plethora of options for her future. cules called 2-methylhopanoids as my eye,” says Kolter, who prides himself in “She arrived in my lab in January, and markers of oxygen-generating life. They’ve having a diverse team. “I’d never had after she had been there less than a month, been found in rocks that some claim are anyone with a degree in German studies she came into my office and told me that 2.7 billion years old. But other geochem- apply to my lab.” She proposed to study she had three job interviews,” says Kolter. ical measurements do not find evidence bacteria that metabolize not arsenic, as “This is how impressive she was. Nobody for appreciable oxygen on the earth at that she’d studied with Morel, but iron. else at the time was thinking of combining time. At Caltech, and now at MIT, where “I must say that I had never thought of environmental microbiology and genetics. she moved her lab in 2007, Newman has studying this,” says Kolter. “When she first She paved the way for a new field.” probed this discrepancy by investigating brought it up I thought ‘What’s the big Newman stayed in Kolter’s lab for two the role of 2-methylhopanoids in modern deal? Why is this important?’ but after a years, though, learning everything she bacteria. Her lab has found that the ability few minutes with her I was convinced this could about genetics before accepting a job of modern bacteria to make these com- was the project she should do.” at the California Institute of Technology—a pounds is not related to their ability to Iron is noteworthy because it was much joint appointment in geological and plan- generate oxygen. Although more work more biologically available in the ancient, etary sciences and biology. needs to be done before ruling out 2-meth- oxygen-depleted earth than it is today. Most ylhopanoids as oxygen markers, Newman bacteria need oxygen to survive because says the “case doesn’t look very good.” chemical reactions that give bacteria ancient record, modern lungs The biggest focus in the Newman lab energy produce excess electrons. Oxygen, Today, oxygen makes up a fifth of the now is one that started as a side project: how

an electron acceptor, can collect these atmosphere of the earth and most life the bacteria Pseudomonas aeruginosa Image: Lars/ Newman lab Photo: Leah Fasten Dietrich

30 HHMI BULLETIN | February 2009 Bye-bye Biofilm. left: P. aeruginosa use phenazines to breathe in low-oxygen environments, like the mucus-filled lungs of cystic fibrosis patients. With no phenazines available, the bacteria form shriveled colonies (front, center) so that every bacterium has access to oxygen. right: One strain of P. aeruginosa makes green-pigmented phenazines. The bottles on the left contain bacteria engineered to lack the molecules.

fellow Lars Dietrich shows the drastic work, and she brings it back to her parents: effect of oxygen on phenazine production “I have to credit them as people who by pulling two beakers of murky bacterial always appreciated new things and soup off a shaking platform that keeps the encouraged my wide-ranging interests.” liquids constantly churned and exposed On weekends they drove her to high to oxygen. One beaker, filled with unmod- school debate tournaments, and helped ified P. aeruginosa, is the color of green her track down materials for science fair Kool-Aid (other natural P. aeruginosa projects that emitted horrible noises from strains produce blue, orange, red, and the basement, which she says they toler- yellow phenazines). The other beaker, ated happily. full of almost transparent fluid, is chock The way she charts her own path is a full of bacteria that were modified so they lesson that resonates strongly in her can’t produce phenazines. Dietrich sets students. Tanja Bosak, one of Newman’s the beakers on his lab bench and immedi- first students at Caltech and now an assis- ately the green in the first sample begins tant professor at MIT, says she tries to to fade. model parts of her own lab after Newman’s. metabolizes iron. P. aeruginosa produces “Since it’s not being shaken around to “She let me really develop my own colorful phenazines—compounds get lots of oxygen, it’s using up the phen- project the way I wanted but was always Newman identified in her search for mole- azines,” he explains. “Having phenazines there to support me and answer ques- cules that shuttle electrons to iron. But P. is like having a snorkel to breathe under- tions,” explains Bosak. “She taught me aeruginosa isn’t relevant only to the ancient water.” The bacteria are dumping extra that you can have fun and do science. And earth—it’s the bacteria that most often electrons onto the phenazines, which that it’s really important to run a lab the infect the lungs of people with cystic fibrosis. carry the electrons out of the cells. way you want—you don’t have to try to be The minuscule cellular brushes that Phenazines also affect whether P. aeru- something you’re not.” normally sweep the lungs clear of mucus ginosa can form biofilms—colonies of Whether it’s the quick switch from are missing in people with the disease. bacteria encased in a slimy goop of extra- English to Spanish to order a sandwich Their lungs build up layers of mucus, a cellular matrix. Bacteria banded together from a Latino cashier at an MIT café, her fertile place for bacteria to thrive. These into biofilms exist on unbrushed teeth, on ability to bridge geology and microbi- thick layers of mucus have low concen- slimy rocks, and in the lungs of cystic ology, or juggling her work life and home trations of oxygen, resembling the fibrosis patients. Since bacteria in the life, Newman moves with ease across oxygen-deprived atmosphere of the planet deepest layers of the biofilms don’t have several worlds. billions of years ago. access to oxygen, they need phenazines to “She’s gone from being a student, “Pseudomonads colonize the lungs breathe. In the bacterial strain that when I first met her, to the head of a huge just like they colonize other surfaces,” says Dietrich has blocked from making phen- lab and a leader in her field,” says Bassler. Newman. “They aggregate into multicel- azines, the colonies form not smooth films “But to me she seems exactly the same as lular communities that become increas- but curly, bumpy, surprisingly predictable that day she walked into Cold Spring ingly resistant to antibiotics with time.” shapes that expose every bacterium to Harbor. Her science has certainly grown Since Newman suspects that phen- oxygen. It’s another finding that links back and changed, but in her spirit, she’s one of azines are critical to P. aeruginosa’s to cystic fibrosis: if the bacteria without the brightest lights in the bacterial survival in these deep layers without phenazines can’t form normal biofilms community. Her modesty and enthusiasm oxygen, she hopes that blocking phen- when oxygen is limited, they can’t survive and talent are always a breath of fresh air.” azine cycling might be a way to combat in mucus-filled lungs as easily. As for the future, Newman hesitates to lung infections. Morel says Newman’s diverse back- predict where her next research projects ground is what allows her to make these will take her, beyond the obvious contin- imaginative connections. “Her back- uation of her foray into cystic fibrosis. “My a rainbow of bacteria ground gives her a lot of different things to hope is that in the longer term, my Thanks to the bright colors of phenazines, think about when she looks at a problem,” research will take me in directions I can’t it’s easy to see whether bacteria are he says. Ask Newman how she’s come to even imagine now,” she says, “because producing them. Newman’s postdoctoral make such creative connections in her that’s what makes this so fun.” p

February 2009 | HHMI BULLETIN 31

When Cells Grow Old by John Davenport illustration by Frank Stockton

Just like a whole person, cells change as they age. Clues about what controls cellular aging are revealing puzzles and possibilities for a host of diseases.

February 2009 | HHMI BULLETIN 33 Sometimes the evidence cells in a culture dish could split an indefinite number of times. But Hayflick found that after 50 or so divisions—now called the of aging Hayflick limit—cells stopped dividing. The cells turned into zombies. They didn’t die but remained in a kind of hibernation, a state known as cellular senescence. hits a Over the following decades, researchers elucidated the envi- ronmental conditions that push cells to senesce and defined many of the genes and molecules that control the process. little too Several signals can put cells to sleep. Accumulating DNA mutations can send cells into senescence. Fraying chromo- close somes also serve as a trigger. Protective caps of DNA called telomeres keep chromosomes from unraveling, but each time a cell divides, its telomeres get a little shorter. When telomeres to home. get too short, chromosomes can break or fuse with other chro- mosomes, shuffling the genome and possibly causing cancer. A HHMI investigator George Daley, of Harvard Medical School, third signal also links to cancer. In 1997, HHMI investigator saw signs of his own mortality as he peered into a Petri dish. Daley Scott Lowe of Cold Spring Harbor Laboratory, New York, and has been studying how to coax adult cells into stem cells, using his colleagues found that activating a cancer-causing gene lab members’ cells—and his own. forces cultured cells into senescence. Adding just four genes can turn adult cells back into embry- The cancer connection seems counterintuitive. Typically, onic-like cells, able to develop into any cell type in the body, cancer-causing genes spur cells to divide uncontrollably, not according to Daley’s studies. In culture dishes, cells from a grind to a halt. But Lowe’s result supports the idea that senes- younger postdoctoral fellow in Daley’s group were “youthful and cence is a cancer-prevention tactic. Cells must accumulate vigorous,” he says; many of them morphed into stem cells. But multiple mutations before turning into full-blown cancer. When Daley’s cells were stubborn, refusing to reverse their clocks. It a cancer gene turns on, senescence might help cells shut down seems as a person ages, cells get increasingly stuck in their ways. before additional mutations push the cell to become cancerous. Daley isn’t taking it too personally. “I’m deficient in a lot of However, shutting down cells to fight cancer could hamper things, and reprogramming seems to be one of them,” he says. He health in other ways. For instance, senescence might deplete the plans to use the observation to understand how to reprogram cells pools of cells that replace damaged ones and keep liver, bone, most efficiently. blood, and other tissues working properly. An accumulation of His finding points out an important concept: cells might not malfunctioning cells and a loss of new ones to replace them sprout gray hair, get achy joints, or forget where they put their car could underlie some of the effects of aging. So is senescence good keys, but they do age. Several HHMI researchers are just begin- or bad for the body? ning to learn what happens to cells as they grow old, and they’re In a sense, cancer and senescence are opposite sides of the making connections between those changes and cancer, deficien- same coin. To remain robust, tissues rely on dividing cells for cies in wound healing, and other problems that increase in replenishment; yet, left unchecked, cell division leads to cancer. likelihood as a person ages. Thus, it might seem a Faustian bargain to guard against cancer now at the expense of decrepit tissues later. a help or a hindrance? Evolution should favor the anti-cancer mechanism, Lowe The first inkling that cells might grow old came in the early says. Genes that improve survival early in life should help ensure 1960s, when gerontologist Leonard Hayflick was playing with that an organism reproduces, and thus the genes tend to be cells in culture. The conventional wisdom at the time held that passed down to the next generation. That’s true even if the same

34 HHMI BULLETIN | February 2009 genes compromise health late in life. “We didn’t evolve during a period when we lived 80 years,” says Lowe. “The system isn’t built to last that long.” Some studies on the tumor suppressor gene p53 have supported this idea of a trade-off between cancer and aging. The p53 gene acts as a master controller of anti-cancer mechanisms, including senescence, particularly when DNA incurs damage or telomeres erode. The gene also governs other processes such as a regulated cell death pathway called apoptosis. Several groups of researchers have shown that producing certain forms of p53 dramatically reduces cancer in mice, but those animals age more rapidly than normal.

sending signals For decades, cellular senescence was thought to be an oddity seen only in the lab. Few studies provided any evidence that senes- cence influenced aging or cancer in a living creature. “[Researchers in the] cancer biology field felt it was a cell culture artifact,” says Lowe. “Senescence hadn’t been observed in tissues.” But starting in the mid 1990s, researchers discovered ways to track senescent cells in living tissues, not just in cell culture. For instance, senescent cells produce an enzyme called beta galacto- sidase. When bathed in a particular sugar compound, cells with this enzyme turn blue, providing a way to spot senescent cells. Since then, researchers have used this method to show that tissues from people, as well as from animals such as rodents and monkeys, carried blue cells. And, “the older you got the more blue cells you had,” says Lowe. Other markers exist, and although none of the markers is exclusive to senescent cells—they tag other things too—these studies have provided robust evidence that senescence is important beyond the culture dish. Recent research supports the notion that senescence helps divert cells when they start down the path toward cancer. Four studies in 2005 revealed that senescent cells accumulate in precancerous growths such as moles, and quieting senescence pathways suffices to trigger melanoma and prostate cancer. “Premalignant tumors are chock full of senescent cells,” says Lowe. The studies’ findings settled the controversy about whether senescence works to prevent cancer in people, he adds. Senescent cells might seem to be introverted wallflowers, but George Daley (top) aims to efficiently reprogram cells, with help from lessons new work suggests that they are rather social, communicating learned on cellular senescence. Michael Green (bottom) is using senescence-

Daley: Leah Fasten Green: Leah Fasten Daley: Leah Fasten and influencing their neighbors. HHMI investigator Michael inducing proteins to stop cancer cells from dividing.

February 2009 | HHMI BULLETIN 35 Melanoma cells don’t make IGFBP7, says Green, but his studies suggest that they still respond to the molecule. Bathing cancer cells in IGFBP7 prodded them to die. Green is exploring the idea of using IGFBP7 as an anti-cancer drug. He will collabo- rate with scientists at the National Cancer Institute to conduct preclinical studies that will lay the foundation for clinical trials.

fending off fibrosis With mounting evidence that senescence is a cancer counter- measure, Lowe and his team wondered if senescence played a part in another disorder: liver disease. Previously, researchers had noticed senescent cells in diseased livers, and Lowe wondered whether they were harmful or beneficial. Hepatitis infection, alcohol abuse, and fatty liver disease can bring on cirrhosis, a permanent scarring that undermines the liver’s normal function. A buildup of connective tissue, known as fibrosis, presages cirrhosis. When a liver is damaged, particular liver cells Scott Lowe thinks senescence might be a cell’s strategy to cope with an called stellate cells churn out extracellular matrix, the protein immediate threat—even if that tactic proves detrimental later on. structure that forms fibrous tissue. If the cause of liver damage disappears, the stellate cells help other cells grow, repair, and Green, of the University of Massachusetts Medical School in replenish the liver. But a chronic drinking problem or untreated Worcester, made the discovery after looking deeper into how infection puts a liver under constant stress. Under these conditions, senescence prevents melanoma from taking hold. A cancer- fibrosis spreads, cirrhosis sets in, and, ultimately, the liver fails. causing mutation in a gene called BRAF occurs frequently in Lowe’s recent studies suggest that senescence helps put a melanoma; most benign mole cells also carry the mutation. Like damper on fibrosis. His team injected mice with an agent that other oncogenes, BRAF spurs cells in culture to senesce. Green damaged their livers, spurring fibrosis. In the animals’ livers, wondered what spurred cells carrying BRAF to senesce rather senescent stellate cells peppered fibrotic regions, the team than grow into tumors. reported in August 2008 in Cell. In animals that can’t undergo He and his colleagues identified a set of genes that appear to cellular senescence because they lack p53, fibrosis was more hold mole cells in senescence; when they shut down any of these pervasive. Lowe posits that senescence hampers fibrosis by genes, the cells grew like crazy. Green was surprised to discover preventing stellate cells from growing too heartily and manufac- that one of the genes makes a protein called IGFBP7 that gets turing a flood of extracellular matrix. discharged out of the cell. “We were expecting it to be a purely Fibrosis is part of the normal response to repair an injury, and intracellular event,” he says. The team reported its findings in the unless a liver suffers continuous insults, fibrosis eventually dissi- journal Cell in February 2008. Mole cells didn’t need to make pates. Lowe also found that senescence not only prevents fibrosis, this protein themselves to stay quiet. Applying IGFBP7 to the it also helps clear fibrosis once it starts. In normal animals, fibrosis outside of mole cells was enough to keep cells in senescence. The subsided and eventually disappeared once the liver-damaging findings suggest that, by spewing IGFBP7, one cell could help its injections stopped. But in animals without p53—and therefore neighbors from turning cancerous. deficient in senescence—fibrosis persisted. At about that time, other groups also showed that other types Researchers have known for a while that senescent cells exude sets of senescent cells discharge proteins that stall cell division. The of molecules that deplete extracellular matrix. His findings suggest results of all the studies are striking, says Lowe. “Senescent cells one possible reason for this behavior. “It fits nicely with this puzzling

aren’t just sitting there.” gene expression pattern that’s been around for some time,” he says. ©HHMI / AP, Seckler Zack

36 HHMI BULLETIN | February 2009 We didn’t evolve during a period when we lived 80 years. The system long haul, quieting cells creates havoc. The body “can’t stop isn’t built to everything,” says Lowe. Once an obscure artifact of cell culture, cellular aging is emerging as a key force that shapes tissue health. And those who last that long. want to help patients are taking note. Harvard’s Daley, for scott lowe instance, wants to understand how to make stem cells and use them to repair malfunctioning tissues. But he’s proceeding with Lowe adds that cirrhosis puts patients at increased risk for caution. “Reprogramming is, in a sense, reversing senescence,” liver cancer, and he’s trying to understand why, in light of the he says. Researchers must face the “sobering possibility” that new findings. Opposing Green’s IGFBP7 finding, previous doing so will accelerate cancer. Still, Daley is optimistic that studies have found that senescent cells produce molecules that “we can harness the process in a way that’s productive.” spur cancer, rather than prevent it. Senescence might be built Hopefully, he won’t have to age much more before the answers to cope with an immediate insult, says Lowe, even if, over the become clear. p

CONNECTING DOTS

As the role of senescence in health and She is now collaborating with Yale cell split and join, allowing them to mix disease gains prominence, researchers colleague Daniel DiMaio to understand and redistribute copies of mitochondrial new to the phenomenon are beginning to how microRNAs work in senescent cells. DNA, which means any particular cell is look for connections to their own work. “Would the same kind of controls be unlikely to remain stuck with a large HHMI investigator Joan Steitz of Yale going on in senescent cells?” she asks. number of faulty mitochondria. “Fusion University has been fascinated by how “Would it be a different protein that is is potentially a protective mechanism,” small RNA molecules control the activity associated? We don’t know.” In addition says Chan. Chan suggests that a of genes. Now, she’s starting to look at to the activity of genes, senescence connection between mitochondrial how this capability ties to senescence. might tie to the activities of mitochondria. dynamics and cellular aging could exist. One particular type of small RNA These structures generate power in cells, Old cells may have deficiencies in molecules, called microRNAs, control and David Chan at the California Institute mitochondrial fusion that help mutations how much protein a cell makes from a of Technology, who was named an HHMI build up, he says. Faults in this process messenger RNA (see “The Macro World investigator in spring 2008, scrutinizes could be particularly important in of MicroRNA,” page 20). In an actively how mitochondria merge and divide. He’s neurodegenerative diseases. Evidence growing and dividing cell, microRNAs curious how this dance influences energy already links problems in mitochondria dampen the amount of protein the cell production and how missteps might to Alzheimer’s disease, Parkinson’s makes. But microRNAs do the opposite trigger illness. Mitochondria accumulate disease, and Lou Gehrig’s disease and amplify protein production when mutations in their DNA over a lifetime. As (amyotrophic lateral sclerosis). Recent cells are in a state called quiescence, the glitches pile up, they can cause studies even suggest that a gene Steitz’s group has found. Like senescent mitochondria to produce less energy or involved in mitochondrial dynamics is cells, quiescent cells don’t divide. But, work less efficiently. It’s particularly crippled in some inherited forms of unlike senescent cells, they can reactivate troublesome for the brain and muscles, Parkinson’s disease. Chan plans to dig and start growing and dividing again. heavy users of energy. A blackout in deeper into these disease connections. “We want to know why microRNAs do cellular energy production may also With this new scrutiny, cellular aging one thing when cells are rapidly contribute to gray hair, weak bones, and could step farther into the spotlight as proliferating and another thing when they other age-related changes. Chan has a key component of many withdraw from the cell cycle,” says Steitz. found that the many mitochondria in a diseases. —J.D.

February 2009 | HHMI BULLETIN 37 PERSPECTIVES & OPINIONS

David Lopatto IMPACT FACTOR ASK STUDENTS WHAT KEEPS THEM IN SCIENCE– THEY JUST MIGHT TELL YOU. Mark Kegans

38 HHMI BULLETIN | February 2oo9 What draws students to science? David Lopatto aims to find out. Since joining the faculty at Grinnell College, this professor of psychology has designed surveys to learn how under- graduate students respond to summer and classroom research experiences. His findings reveal best practices for creating programs that sustain students’ interest in science.

The number of undergraduate science students doing career paths; the more they hear professionals talk about summer research has grown steadily for nearly 20 years. themselves and what they do, the more they understand And from what their faculty mentors tell us, most of them what a science career is really like. Ethics seminars are also are enjoying themselves as they are learning about the important; students need to know about the broader impli- research process. But for me, these anecdotes aren’t enough. cations of conducting research. Organized social activities, I want to know how and why research experiences enhance such as picnics and trips to the ball park, can help students education and attract students to science. What’s more, feel like they’re part of a learning community. Above all, how can we optimize these programs in ways that maximize mentoring by the research supervisor has the most dramatic learning and sustain a student’s interest in a science career? effect on the student experience. About 10 years ago, I began developing research tools We’ve found that a good way to turn students off of to investigate these questions systematically. The tool I use science is to give them a bad mentor. But good mentors— now, developed in 2003 with HHMI support, is called the who are supportive, aware of personal goals, and listen as Summer Undergraduate Research Experiences (SURE) much as they talk—can be a powerful factor in making survey. This detailed questionnaire allows me to quantify the research experience a positive one. student responses to a variety of topics, such as learning Finally, we’ve found that students who close the experi- gains in specific areas, the impact of summer research on ence with a poster session, a research paper, or some other future academic plans, and the influence of mentors. During final production hone key skills—such as science writing each of the last two years, more than 2,000 undergraduate and oral presentation—that serve them well in the future. students have responded, representing more than 60 colleges The take-home message is that a research experience isn’t and universities. like a summer job. Whether these experiences are HHMI- In part, their answers validate what we knew already from funded or not, they involve continuous interaction between anecdotal reports. Students in undergraduate research report students, who learn to work and think independently, and a that they learn how to do science, clarify their career plans, faculty member who provides structure and oversight. and are very satisfied with their experiences. More than A similar philosophy applies in the classroom. A related 90 percent rate their experiences positively, and most claim survey instrument—the Classroom Undergraduate Research they would have another research experience if they could. Experience, or CURE—found that “research-like” classes I’ve also seen something unexpected in the data: the produce response patterns similar to those seen with experience for so many students is defined more by personal SURE. Successful research-like courses aren’t organized development than by professional growth. Most students around stock lectures and canned labs. Instead, they build give high marks for professional factors, such as learning learning around a shared research problem that students laboratory techniques and how to analyze data. But for those and instructors solve together. As with the best summer who report a successful undergraduate experience, attain- programs, these classroom experiences foster indepen- ing personal benchmarks—such as enhanced tolerance dence and teach research skills. for obstacles, a readiness for more demanding research, In short, the capacity to excel in science is tied closely and gaining a better understanding of how scientists really to personal development. Students who make their own work—is particularly important. discoveries feel valuable in research, and that sense of worth When science educators ask about best practices for generalizes across their character in many positive ways. We summer undergraduate research programs, I emphasize often hear that what this country needs in terms of science the need to promote personal as well as professional goals. and technology is more innovation, invention, and transfor- Cumulative data from the SURE survey reveal specific mation. If we want our students to advance those goals, measures that optimize student experiences. For instance, then the research programs we design should encourage seminars given by visiting scientists help students clarify self-authorship, confidence, and creative thinking.

INTERVIEW BY CHARLES SCHMIDT. David Lopatto is also a professor of natural science and mathematics at Grinnell College.

February 2oo9 | HHMI BULLETIN 39 PERSPECTIVES & OPINIONS

Helen Hobbs HEART OF THE MATTER Brian Harkin

40 HHMI BULLETIN | February 2oo9 Helen Hobbs, who thrives in the fast pace and intensity of medicine, did not settle easily into the more measured world of research. Now chief of human genetics at the University of Texas Southwestern Medical Center at Dallas, her desire for better treatments drives her to pore over susceptibility factors to learn who develops disease and who does not—and why.

What affects a person’s disease susceptibility? In this case, genotype seems to be especially important? The expression of a person’s genes over time, in the context of These results show how a genotype can provide information environmental factors such as exercise, diet, aging, and stress, that is not captured in phenotype. The PCSK9 genotypes we produces susceptibility or resistance to certain diseases. The identified tell us about the level of LDL in the blood over a term phenotype is used to capture the physical and biochem- lifetime rather than at one moment in time. Individuals with ical characteristics that result from this interplay of genes and mutations in PCSK9 have lower levels of LDL starting at the environment. Phenotype in humans includes not only birth so the arteries feeding the heart are exposed to cumu- overt effects, like a heart attack or stroke, but the more subtle latively fewer LDL particles over time. We have known for changes we uncover through blood tests and imaging studies. years that high levels of LDL are sufficient to cause heart disease, even in the absence of other risk factors. These new How are you using phenotype analysis in your research? data tell us that the reverse is also true; low levels of LDL We’ve used sophisticated imaging together with more con- starting early in life provide protection from heart disease, ventional medical testing to develop very precise phenotypes even in those individuals who have other risk factors. in a large study population. In the Dallas Heart Study, we enrolled 3,500 individuals—African American, Hispanic, How do mutations in PCSK9 cause lower levels of LDL in and Caucasian—between 30 and 65 years of age, and obtained the blood? a series of phenotypes for each participant, including imaging PCSK9 expression causes degradation of LDL receptors, studies to visualize the heart, blood vessels, liver, and other which are proteins on the surfaces of cells that bind and tissues and blood tests to measure the levels of many different remove LDL from blood. Mutations that interfere with the proteins and lipids. synthesis of PCSK9 result in an increase in the number of LDL receptors, which leads to lower levels of LDL in the blood. What have you found? Our work with a gene called PCSK9 is the most significant con- Is there more to come? tribution of the Dallas Heart Study. We discovered that variant Soon it will be possible to sequence entire genomes of study forms of PCSK9 are associated with lower levels of low-density subjects. A major challenge will be to link the sequence lipoproteins (LDL), the “bad” cholesterol. We found that differences identified in genes to traits and diseases. We will one out of every 50 African Americans has a PCSK9 variant need large collections of very carefully phenotyped individuals associated with a 28 percent reduction in LDL; Caucasians with of different ancestries. The Dallas Heart Study was designed a different variant experience a 15 percent reduction in LDL. specifically to address this need. We assessed these PCSK9 variations in more than 12,000 Very few population studies include large numbers of samples collected in the Atherosclerosis Risk in Communities individuals whose ancestors are not from Europe. Genomes Study across 15 years. The findings were unequivocal: low differ depending on ancestry. For example, we showed LDL is remarkably cardioprotective. The African Americans that Hispanics tend to deposit more fat in the liver, which with the PCSK9 mutations had an 88 percent decrease in heart can lead to liver injury and, ultimately, liver failure. In disease risk—and this included many individuals with hyper- September 2008, we reported that sequence variations in tension or diabetes, or those who smoked. The Caucasians a gene of unknown function called PNPLA3 are responsible with the other PCSK9 sequence variation had a 50 percent for a large fraction of the differences in liver fat between disease risk reduction. These are much greater reductions Hispanics and other groups. Now we are exploring in coronary heart disease than we see when we lower plasma whether those sequence variations in PNPLA3 predispose LDL to similar levels with a statin drug in adults. individuals to liver injury after exposure to alcohol, drugs, We published those results in 2006. It now seems reason- or infection. able to consider lowering LDL during early adulthood in individuals who have other risk factors. The NIH is consid- ering a trial to test this, and pharmaceutical companies are INTERVIEW BY RICHARD CURREY. HHMI investigator looking at PCSK9 as a drug target. Helen H. Hobbs is director of the Dallas Heart Study.

February 2oo9 | HHMI BULLETIN 41 Q & A If you could trade places with someone for a day, who would it be? Scientists are a curious bunch, and how better to satisfy curiosity about the world than glimpse things from someone else’s perspective? Four HHMI scientists offer their picks on how they’d spend a day in another person’s shoes.

— EDITED BY SARAH C.P. WILLIAMS

Leslie A. Leinwand Alejandro Sánchez Alvarado Elaine Fuchs David J. Anderson HHMI PROFESSOR HHMI INVESTIGATOR HHMI INVESTIGATOR HHMI INVESTIGATOR UNIVERSITY OF COLORADO UNIVERSITY OF UTAH SCHOOL THE ROCKEFELLER CALIFORNIA INSTITUTE AT BOULDER OF MEDICINE UNIVERSITY OF TECHNOLOGY “My top pick is Alice Waters, “I’d love to trade places for a “It would have to be the “Jonathan Miller, the British the chef and co-owner of day with either of my two Flemish painter Pieter humorist, neurologist, writ- Chez Panisse in Berkeley, children. As a father and a Bruegel on the day he fin- er, and theater director. Gravenor California. Alice Waters scientist, I am often struck by ished The Triumph of There’s nobody else I know champions the use of local, the genuine, unencumbered, Death, which now hangs who has so successfully just-picked ingredients and and fresh ways my children see in the Prado museum in combined an interest in sci- appears to have a generous and question the world around Madrid. My introduction ence/medicine and the per- spirit. My first meal at Chez them. From the mundane— to Bruegel came when I forming arts. During a day Panisse was a revelation; Where do dreams come was 6 years old and became in Miller’s shoes, I’d meet like nothing else I had ever from?—to the mysterious— fascinated by a reproduction lots of interesting, talented eaten. Her food appears What’s outside of outer space? of one of his paintings in people in fields I would simple, but has layers of My children’s natural interro- my uncle’s home. As I got normally never encounter. complex tastes and textures. gation of their world is always older and learned to appre- And I’d exercise the right Since I can’t actually be a fresh reminder of why I fell ciate art, I became passion- half of my brain, the part her for a day, I’d sure like in love with science in the ate about seeing Bruegel’s that tends to atrophy during to be able to spend a day first place.” paintings whenever and a career in science.” with her in the kitchen.” wherever I had the chance. My favorite is the master- piece in the Prado, although The Beggars and The Fall of Icarus are also right up there. What a creative genius Bruegel was, whose pulse was on sixteenth century Europe in a unique and extraordinary way!” Leinwand: Jack Dempsey / WWP, ©HHMI Alvarado: Yvonne B.L. Jenkin / Sánchez Alvarado lab Fuchs: Elaine Fuchs Anderson: Elaine Fuchs Misha lab Fuchs: Alvarado / Sánchez Yvonne B.L. Jenkin ©HHMI Alvarado: Dempsey / WWP, Jack Leinwand:

42 HHMI BULLETIN | February 2oo9 chronicle

44 Science Education Fire Ant!

46 Institute News A Call for Collaboration

48 Lab Book Probing Pigs / Avoiding Rupture / Sleep-Inducing Monsters

51 Ask a Scientist Why do injections hurt more on some parts of the skin than on others?

52 Up Close Crystal Clear

54 Nota Bene Seven Elected to Institute of Medicine / Tsien Awarded Wilson Medal / HHMI Graduate Fellow Wins a ll Grand Prize in Inventors Competition

The fluid shapes of Trypanosoma brucei shown here become distorted when treated with one immuno- Antonio Barqui d suppressant (see page 49). The parasite, which causes African sleeping sickness, spends part of its life cycle in the tsetse fly before infecting mammals. Navarro an Navarro l ue g Miguel Navarro and Antonio Barquilla Miguel Navarro Mi

February 2oo9 | HHMI BULLETIN 43 science education

Fire Ant!

MISSISSIPPI HIGH SCHOOL STUDENTS ARE GETTING UP CLOSE AND PERSONAL WITH THIS PERVASIVE PEST—ALL IN THE NAME OF BIOLOGY.

KATHY MCKONE KNEW SHE WAS FALLING BEHIND. BY 2005, THE sting has disrupted many a family picnic or football game. It leaves veteran high school biology teacher in rural Bogue Chitto, its victims with a distinctive white blister and, on occasion, a life- Mississippi, couldn’t recognize many biotechnology topics threatening allergic reaction. Swarms have been known to kill covered in the newest textbooks. Even the products listed for sale livestock and invade nursing homes. in teacher catalogues—everything from thermal cyclers to ampli- “The fire ant is a unique point of interest, especially among fication primers—were unfamiliar. children,” explains Rob Rockhold, a scientist and administrator at “It was all foreign to me,” McKone says. the University of Mississippi Medical Center who has studied fire But not for long. McKone took action and, using the Internet, ant venom and conjured the Muse of Fire name from his college found teacher workshops in molecular biology that brought her literature classes. “It also became obvious to us that fire ants just to the campuses of some of the nation’s premier universities, opened up a world of scientific disciplines.” including Princeton, Harvard, and Cornell. Her newfound excite- Rockhold, who oversees the fire ant project with colleague ment and knowledge are having a big impact in Bogue Chitto, Donna Sullivan and MBL scientist William Reznikoff, says the a crossroads community an hour south of Jackson that consists Muse of Fire project speaks directly to students and will enable of a post office, two country stores, two gas stations, and a few them to learn about subjects ranging from molecular biology and churches. Now they are spreading elsewhere in the state. environmental science to toxicology and human health. McKone is one of five Mississippi high school teachers collabo- Teams of scientists and teachers met last summer in Jackson to rating with scientists from the University of Mississippi Medical develop the coursework and a variety of experiments. Then each Center in Jackson and the Marine Biological Laboratory (MBL) of the five high school teachers tested one part of the curriculum in Massachusetts to develop a biology curriculum centered on a in a class to make sure the lessons moved students beyond fire pervasive Southern pest—the fire ant Solenopsis invicta. HHMI ants to wider biology concepts. Some teachers took their students has supported development of the curriculum, and Millsaps to fields filled with tall grass to observe how fire ants affect other College in Jackson is also part of the team. insects in their local environment. Others devised experiments “Most everybody in the South has been stung by a fire ant,” that allowed students to understand how fire ants prey on their McKone says. As a child, McKone was often a victim as she played victims—in this case, crickets—by using venom substitutes to outside or worked in the family garden. And it hasn’t stopped now determine the concentration of a fatal dose. that she’s an adult: she was stung around eight times earlier this This past fall, McKone incorporated elements from Muse school year when she stood too close to a fire ant mound outside of Fire in Bogue Chitto’s first biomedical research course. One her K–12 school. September afternoon, she led seven seniors to a sandy area just With apologies to William Shakespeare—who invoked “a outside the cafeteria that serves the school of 630 students. muse of fire” in seeking inspiration for Henry V—the Muse of Although they searched for fire ants, their real quarry that day Fire project draws its inspiration from a venomous creature whose was a type of bacteria called Wolbachia, which lives inside the ant. Their goal? To determine whether Mississippi fire ants are Left: Teacher Kathy McKone quizzes Bogue Chitto infected with Wolbachia and, if so, the prevalence of the bacteria. high school seniors Britney Saucier and Blake Sasser about extracting fire ant DNA. Right: Senior Wolbachia are complicated critters. They infect spiders and

Tracy Adams concentrates on pipetting the DNA. many insects, influencing their reproductive behavior in a variety Roster Tom

44 HHMI BULLETIN | February 2oo9 of ways. For example, the bacteria can cause all an insect’s many types of ants,” says student Jerry Fry. “I thought an ant was offspring to develop as females or allow only infected insects to just an ant.” reproduce. The bacteria live inside insect cells and are passed So far, four ants from Bogue Chitto have tested positive for from generation to generation through the eggs. Wolbachia may the Wolbachia parasite, all from the mound outside the cafeteria. also play a complex role in human diseases such as river blindness. Ants from another mound at the school and from two mounds off “The interesting thing is that one can use fire ants and other campus had no evidence of the parasite. When the students get the insects as investigative tools to find out if only some of them are full Wolbachia DNA sequence back from MBL, McKone hopes it infected with Wolbachia and why,” says Reznikoff, who helped will tell them how these fire ants are related to those elsewhere or McKone design the Wolbachia portion of the fire ants project. provide some insight into how the bacteria might manipulate fire Back in McKone’s large, bright classroom, the seven students ants’ reproduction. huddle in three groups, smashing ants with the sealed end of a This summer, McKone, her fellow teachers, and the scientists pipette tip. They make sure to crush the ant’s abdomen, where will assess what they have learned and then finalize the five-part Wolbachia are typically found. The next step comes straight from curriculum. They plan to make it available to teachers wherever a molecular biology textbook: finding the bacterial DNA (if it is fire ants are found. present) inside the fire ant cells. Using polymerase chain reac- Rockhold hopes the students’ Wolbachia research can eventu- tion machines borrowed from Florida A&M University—the same ally be combined with that from other students throughout the thermal cyclers that so puzzled McKone in 2005—the students go South to help scientists find out what makes fire ants infected with through the step-by-step process of extracting the DNA samples. the bacteria different from those not infected. “If there are enough McKone occasionally stops to quiz the students on what they’re folks doing the work at different sites, it might ultimately become doing, making sure they know what each chemical does or why a comprehensive and meaningful addition to the science,” he says. they are heating up the sample. “They love it. They like under- Meanwhile, McKone is happy her students have learned about standing why.” molecular biology using a subject close to home. Perhaps it will Getting her students interested in fire ants has been easy, inspire them to become researchers—and find a solution to a local McKone says. She doesn’t have to push them to read research problem, she says. “They would love for somebody—and I would love papers or ask questions. They are motivated to learn because they for them to be a part of it—to find a way to control fire ants.” p are already interested in fire ants. “I didn’t know there were so —ANDREA WIDENER

2008 Holiday Lectures: Making Your Mind

HHMI investigators Eric Kandel (left) and Thomas Jessell (second from left) headlined the 2008 Holiday Lectures on Science, an annual December seminar that welcomes Washington, D.C.-area high school students to the Institute’s headquarters in Chevy Chase, Maryland. This year’s lectures delved into the complexities of the mind, memory, and movement. For fun, the students got to dabble in the ancient, now debunked, art of phrenology (far right). To learn more, visit www.hhmi.org/biointeractive/. Paul Fetters Paul

February 2oo9 | HHMI BULLETIN 45 institute news

A Call for Collaboration

PILOT PROGRAM FROM HHMI AWARDS $40 MILLION TO EIGHT MULTIDISCIPLINARY TEAMS. P, ©HHMI P, ©HHMI

UNTIL FOUR YEARS AGO, DANNY REINBERG’S RESEARCH COMFORT- undertake projects that are new and so large in scope that they ably revolved around molecules and cells, just what Reinberg—a require a team covering a range of fields. In Reinberg’s case, biochemist and HHMI investigator at New York University—had that means collaborating with Berger as well as Juergen Liebig been trained to study. But then, at a scientific meeting, colleague of Arizona State University, a leader in studying the complicated Shelley Berger of the Wistar Institute mentioned her recent fasci- social dynamics of insect societies. The team hopes to explain how nation with ant behavior, after observing leafcutter ants in Costa gene expression—rather than gene sequence—is passed to gener- Rica. She suggested that ants might be a perfect organism for ations of ants, affecting their behavior, social roles, and aging. studying gene expression and behavior. HHMI’s vice-president and chief scientific officer, Jack Dixon, That encounter led to a unique, multidisciplinary collaboration says the newly funded projects represent an important step for the that calls on the expertise of everyone involved. It’s one of eight Institute. “This award permits our investigators to assemble the such collaborative projects that HHMI is funding as part of a $40 team of experts they need to attack these complex scientific prob- million pilot program. lems,” he says. “We were looking for projects that could represent The Collaborative Innovation Awards represent the first time breakthroughs—those that could really change the way we think.” the Institute will provide funding for specific research projects At the Jackson Laboratory, in Bar Harbor, Maine, HHMI inves- rather than funds for investigators to take their science in any tigator Simon John has spent more than a decade using mouse number of directions. The new funds are intended to encourage models to study glaucoma—a major cause of vision loss and HHMI investigators to join with scientists outside HHMI to blindness. Glaucoma researchers desperately need new tools for

Left to right: Catherine Dulac, Harvard University; Susan Lindquist, measuring intraocular pressure, according to John. High intraoc- Whitehead Institute for Biomedical Research; Douglas Rees, California ular pressure, which damages nerve cells in the eye, is a common Institute of Technology; Danny Reinberg, New York University School cause of glaucoma. of Medicine; Simon John, Jackson Laboratory; Peter Walter, University of California, San Francisco; Xiaowei Zhuang, Harvard University; With the help of a Collaborative Innovation Award, John will

Huda Zoghbi, Baylor College of Medicine. work with two Purdue University engineers to develop the world’s / AP, ©HHMI Reinberg: Bizuayehu Tesfaye ©HHMI Rees: Rene Macura / AP, Cheryl Senter / AP, Dulac: Matt Kalinowski Lindquist: ©HHMI Zoghbi: Bob Levey / A ©HHMI Zhuang: Cheryl Senter / AP, George Nikitin / AP, ©HHMI Walter: / AP, C. York Michael John:

46 HHMI BULLETIN | February 2oo9 first ultraminiature pressure-sensing device that can be implanted in neuronal function and behavior,” she says. “This has triggered the the eyes of mice that have—or are at risk of developing—glaucoma. interest of several colleagues with very different fields of expertise, “This program requires the investigators to step outside their who can now brainstorm and test key hypotheses together.” normal comfort zone and expertise,” says John. “We thought our HHMI plans to evaluate the progress of the eight collabora- plan was a good match.” tive projects selected for this pilot phase and expects to expand the Only slightly thicker than a human hair, and capable of trans- program in coming years. Philip Perlman, a senior scientific officer mitting the data it collects to the researchers via a tiny wireless at HHMI who oversees the program, stresses that such funding antenna, the sensor could have other applications, says John— is valuable because scientists often hesitate to undertake large monitoring blood pressure or cerebrospinal fluid, for example. collaborations, which can be seen as detracting from a lab’s primary HHMI investigator Catherine Dulac, of Harvard University, focus. “Many research groups find it difficult to allocate resources to will use the new funding to lead a team of neuroscience experts in allow one or more members to devote years to a project that could studying the impact of gene imprinting—a phenomenon in which yield important results but may never directly further the lab’s own only a single gene copy is expressed rather than both chromosomal mission,” says Perlman. copies—on behavior and brain development. She’s collaborating Reinberg, who now has to make room in his lab for boxes of with three other Harvard researchers who specialize in how ants frozen in liquid nitrogen and shipped from Arizona, loves his neurons make decisions, the role of genetics in neurological disor- new collaboration because it allows him to study new areas—like ders, and the evolutionary role of imprinting in the embryo. By neuroscience. “I have been working in cells for more than 20 some estimates, the team could find 600 or more genes controlled years,” he says. “And now I have the opportunity to work on whole by imprinting, but Dulac doesn’t really know what they’ll find. organisms and move into neurobiology. This project has opened “I have been thinking for many years about the mechanisms the door for my next 20 years of science.” p of gene regulation—such as imprinting—and the coevolution of —SARAH C.P. WILLIAMS

OTHER COLLABORATIVE INNOVATION AWARD PROJECTS

DOUGLAS REES, of the California Institute of Technology, is personalized treatments for patients. Partners include stem leading a team of three experts in structural biology and protein cell expert Rudolf Jaenisch and colleagues at the University of chemistry to develop a novel way to solve the three-dimensional Alabama, Boston University, and Purdue University. structures of proteins embedded in membranes. Such proteins HUDA ZOGHBI has a plan for speeding up drug discovery. are vital to cells—they act as gatekeepers between compartments Her team, at Baylor College of Medicine and the University of and between the cell and its surroundings—but they are notori- Minnesota, is working on a rapid way to identify hundreds of genes ously hard to work with. involved in clearing disabled proteins from the brain—a process PETER WALTER, at the University of California, San Francisco, that goes awry in Parkinson’s disease. “If we can figure out the an expert in protein folding, will enlist five collaborators in San neurobiology for one of these diseases, it can then be applied to Francisco and Chile to probe whether it’s possible to target many of the other neurodegenerative disorders,” says Zoghbi. drugs to different steps of the pathway that guards cells against XIAOWEI ZHUANG, whose Harvard University lab develops misfolded proteins. imaging techniques, is taking a closer look at the brain. By SUSAN LINDQUIST, at the Whitehead Institute for Biomedical collaborating with creators of some of the most powerful and Research, wants to find strategies to target the biological innovative methods for imaging, data analysis, and sample mechanisms that break down in Parkinson’s disease and other preparation, Zhuang seeks to map out all the neural connections neurodegenerative disorders. Her long-term goal is to develop in mammalian brains.

February 2oo9 | HHMI BULLETIN 47 lab book

Probing Pigs A PORCINE MODEL OF CYSTIC FIBROSIS HELPS RESEARCHERS STUDY THE DISEASE.

A new line of genetically altered piglets offers scientists a novel testing Affected humans and ground for the causes, progression, and treatments of cystic fibrosis. piglets are born healthy but In the past, researchers relied on mice to study the disease, which in develop increasing symp- humans is caused by a mutation in the cystic fibrosis transmembrane toms as they age. Having the conductance regulator (CFTR) gene. The mutation causes pancre- pig model will allow atic failure, lung infections, and liver disease, among other problems. researchers to study how But mice with the flawed gene don’t show humanlike symptoms of cystic fibrosis progresses over the disease, says HHMI investigator Michael J. Welsh. time, says Welsh. “This is a “Mice just don’t develop cystic fibrosis,” he says. “There are 20 disease that affects a whole theories as to why, but what it all comes down to is that if these organism and now we can animals don’t get the symptoms, you can’t use them to study the study it in a whole organism.” progression of the disease; you can’t use them to test whether some- By comparing the thing treats the disease.” affected pigs to mice with So Welsh, at the University of Iowa, and collaborators turned to the same mutations, In humans, cystic fibrosis clogs the pigs—closer to human in terms of anatomy, physiology, biochem- researchers may also be airways of the lungs with mucus. istry, size, lifespan, and genetics. They engineered pig cells with able to figure out why mice mutations in CFTR to make piglets with one bad copy of the gene, don’t get symptoms of cystic fibrosis. “We can look at what’s and then mated those pigs to produce offspring with both copies different in mice and pigs that causes the mutation to have such of CFTR mutated. These piglets show many of the hallmarks of different effects,” says Welsh. “Is it gene differences? human cystic fibrosis. The results appear in the September 26, Physiological differences? Anatomical? Maybe the answer will 2008, issue of Science. lead us to a therapy.” p —SARAH C.P. WILLIAMS

IN BRIEF

IT TAKES TWO tions—that were engineered to express They placed the mice in water and used The symptoms of most Listeria monocyto- human E-cadherin, the placenta was the forced-swim test, an animal model of genes infections are often mild—a fever or susceptible to the bacteria. depression in which, after awhile, animals stomachache at worst. But in pregnant Cossart and her colleagues conclude in show signs of behavioral despair and stop women, the bacteria can be deadly to the October 23, 2008, issue of Nature that swimming. growing fetuses. Scientists long assumed for Listeria to infect human placenta—and “We found that the mice trained for that Listeria posed this heightened risk to therefore risk harming a fetus—the safety could overcome their sense of a fetus because of a pregnant woman’s bacteria must express both InlA and InlB, hopelessness in the swim test and weakened immune system. Several years and that the pregnant woman’s epithelial continued swimming,” says Kandel. In fact, ago, however, researchers found evidence cells must express E-cadherin. the mice performed similarly to mice that the bacteria actively target the Understanding this interaction could lead treated with fluoxetine (Prozac). human placenta. Now, HHMI international to ways to combat Listeria. Antidepressants such as fluoxetine research scholar Pascale Cossart and mediate part of the action by regulating colleagues at the Pasteur Institute have LEARNING HOW NOT TO BE AFRAID the production of new neurons in adult- pinpointed two proteins involved in this Like people able to keep their inner calm hood in an area of the hippocampus. The targeted attack. during stressful times, mice can be condi- scientists therefore next looked at how The team already knew that when tioned to feel safe in normally anxiety- learned safety affects the production of Listeria infect the intestine, the organisms causing situations. Researchers led by new neurons in adulthood. The condi- rely on an interaction between internalin HHMI investigator Eric Kandel of Columbia tioned mice had more new cells in this (InlA), a protein on the bacterial surface, University have probed the brain chem- area. Using radiation to blunt the birth of and E-cadherin, a receptor on human istry associated with this “learned safety.” neurons here diminished the antidepres- epithelial cells. To see whether this held The researchers first taught mice fear sant effects of the conditioning. true in the placenta, the team infected by associating a particular sound with a In their paper published October 9, pieces of human placenta with the mild shock to their feet. Then, they 2008, in Neuron, the team also reported bacteria. They discovered that not only changed the training conditions so mice that learned safety ramped up expression InlA was involved, but also a related bacte- never received the shock along with the of a factor involved in neuron growth and rial protein, InlB. noise. These mice learned to associate the differentiation, and affected key compo- Moreover, the researchers found that in tone with the absence of danger, and nents of the brain’s dopamine system. pregnant gerbils, Listeria that lacked InlA, acted calmer in their surroundings than InlB, or both, couldn’t infect placental those that had learned fear. A MOUNTAIN OF CANCER MUTATIONS tissue. And in mice—where the proteins do Kandel’s team next asked whether The most detailed genetic survey yet of not normally play a role in placental infec- learned safety has antidepressant actions. human tumors has revealed a multitude of CNRI / Photo Researchers, Inc.

48 HHMI BULLETIN | February 2oo9 Sleep-Inducing Monsters A DRUG FOR TRANSPLANT PATIENTS ALSO KILLS THE PARASITES THAT CAUSE AFRICAN SLEEPING SICKNESS BY GROSSLY DISTORTING THEIR SHAPE AND BLOCKING CELL DIVISION.

A drug that helps transplant patients fight tissue rejection may lead the team’s surprise, it did more than that. Rapamycin-treated para- to new therapies for African sleeping sickness. The disease is fatal sites enlarged, sprouting multiple nuclei and other cell parts, and if left untreated, and current therapies have severe side effects. then they died. “They look so weird and grotesque we call them HHMI international research scholar Miguel Navarro of the monsters,” Navarro says. Institute of Parasitology and Biomedicine at the Spanish National The drug doesn’t cause the same cell deformities in the human Research Council in Granada, Spain, and colleagues have found that immune system. In humans and all other previously studied the immunosuppressant drug rapamycin kills Trypanosoma brucei, the organisms, rapamycin slows the rate of cell growth. In T. brucei, parasite that causes African sleeping sickness. These parasites contain however, the drug inhibits cell division, the team discovered. proteins similar to those that rapa- Their results appeared in the September 23, 2008, issue of mycin inhibits in humans. Proceedings of the National Academy of Sciences. Studying how T. brucei The different effects come about because humans have one evades the immune system, TOR gene and most single-celled organisms have one or two TOR Navarro’s group realized that genes, but T. brucei have four. Navarro’s group found that rapa- four genes of the TOR family mycin inhibits different TOR proteins in T. brucei than in humans. enable the parasite to make The differences could be exploited to design better drugs to treat evasive maneuvers. The genes African sleeping sickness. are called TOR because their Because it suppresses the immune system, rapamycin could not protein products are “targets of be used directly to treat sleeping sickness in humans. But rapa- rapamycin.” The researchers mycin-derived drugs that ignore immune cells are being tested as Trypanosoma brucei infects the wanted to see if rapamycin could anticancer agents in clinical trials, and Navarro plans to test them tsetse fly, found only in Africa. inhibit these TOR proteins. To on T. brucei. p — OLGA KUCHMENT

IN BRIEF

broken, missing, and overactive genes— “Instead, we should be thinking about the Using fluorescent tracers, the team some of which were previously unknown. functional pathways in which these genes was able to observe the myosin Vb motor HHMI investigator Bert Vogelstein and operate.” proteins actually carrying the cargo to the colleagues at the Johns Hopkins Kimmel tips of the neurons that had been stimu- Cancer Center, in collaboration with MOLECULAR MOTOR FOR MEMORY lated. When the researchers shut down researchers elsewhere, sequenced 20,661 IDENTIFIED myosin Vb, the cellular steps of memory genes in cells from 24 patients with Building new memories takes raw molec- formation were blocked, they reported in pancreatic cancer and 22 patients with ular materials and a cellular vehicle to truck Cell on October 31, 2008. glioblastoma—the most common form of the goods where they’re needed within a Scientists suspect that breakdowns in brain tumors. cell. When new memories are stored, the this transport process may contribute to The team identified hundreds of gene junctions between neurons in the brain are deficits in learning and memory, so under- mutations associated with the cancers. rapidly reconfigured and rebuilt so they standing their molecular basis could lead to They also found numerous cases where can respond more readily in the future. treatments for disorders such as addiction the tumor cells had too many or too few Researchers led by Michael Ehlers, an and Alzheimer’s disease. copies of a gene. The typical pancreatic HHMI investigator at Duke University cancer, they discovered, contains 63 Medical Center, have identified the motor CANCER’S KEEPER genetic alterations and the typical brain protein that carries new receptors and Although many cancer cells remain at tumor contains 60. other molecules to the synapse when their site of origin, some escape to lodge The researchers say that the results— they’re needed. in distant organs, a process called metas- which appear in two reports published Scientists had already established that tasis. These metastases cause most September 26, 2008, in Science—indicate certain myosin proteins haul cargo in the cancer-related deaths. Scientists have that a small number of commonly mutated cell. Ehlers’ team showed that one specific found a systematic way to identify genes genes (“mountains”) and a much larger myosin—myosin Vb—resides within micron- that might keep cancers from spreading number of rarer gene changes (“hills”) sized dendritic spines of neurons, the sites and in the process have identified a gene cause the cancers. that respond to memory signals. When that suppresses melanoma metastasis in “If you have 100 patients, you have 100 neurons receive signals that trigger long- mice. different diseases,” says Vogelstein. The term potentiation—the repeated signaling at The team, led by HHMI investigator number and variability of tumors poses a a synapse that enhances nerve cell connec- Michael Green, confined mouse mela- challenge to developing drugs. “It’s tions during the creation of a memory— noma cells in a matrix that mimics the suggesting that maybe we shouldn’t be myosin Vb attaches itself to cellular cells’ natural surroundings in the body focusing so much on the individual genes containers full of the necessary materials, and then administered RNA fragments to that are mutated,” Vogelstein says. including new neurotransmitter receptors. silence genes one at a time. They identi- Miguel Navarro and Antonio Barquilla Miguel Navarro

February 2oo9 | HHMI BULLETIN 49 lab book

Avoiding Rupture GENETIC CLUES COULD PROVIDE ADVANCE WARNING OF BRAIN ANEURYSM RUPTURE.

A ruptured brain aneurysm can kill with the speed and surprise of same amount as known nongenetic factors such as high blood pres- an assassin’s bullet: before rupture, most intact brain aneurysms— sure, smoking, and age. The results were published in the distended areas in blood vessel walls—do not cause symptoms. A December 2008 issue of Nature Genetics. lucky patient will have an intense headache before the aneurysm The study compared the genomes of more than 10,000 bursts; this warning can alert doctors to check for an aneurysm people—2,100 with intact or ruptured brain aneurysms and 8,000 using a brain scan so that they can correct the problem surgically. controls. Specifically, the scientists examined over 300,000 single Now, an international study nucleotide polymorphisms (SNPs)—areas in the genome known to has found three genetic clues vary in the human population. They were looking for any SNPs to help anticipate and prevent more commonly found in individuals with aneurysms. brain aneurysm rupture. The subjects were Finnish, Dutch, and Japanese. These coun- HHMI investigator tries’ populations are relatively genetically homogeneous, which Richard P. Lifton and Murat helped the researchers distinguish only the relevant genetic patterns. Gunel, of the Yale School of The three genetic markers the scientists found will increase Medicine, led an interna- understanding of the biological causes of brain aneurysms and tional team in the first help doctors to identify people at risk. Two variants lie near genes genomewide search for that function in the formation and maintenance of blood vessels. common genetic markers for The third, which had previously been linked to brain aneurysms, brain aneurysms. They lies near a gene associated with arterial diseases. uncovered three genetic vari- “We ought to be able to identify more variants that contribute as ations that together can we study more patients,” Lifton says. Both lifestyle and genetic A three-dimensional CT scan shows a bulging aneurysm (red) in an increase the risk of the condi- factors would then help doctors identify individuals who should artery in the brain. tion threefold—by about the receive regular brain scans. p —OLGA KUCHMENT

IN BRIEF

fied 22 genes that, when “knocked down” receptor called SR-BI is scarce, infection neurodegenerative disease in mice, with RNA interference, allowed tumors to levels drop dramatically. researchers have found. metastasize but had no effect on the Malarial liver infection had already The team, including HHMI international growth of the original tumors. Further been linked to the organ’s filtering of research scholar Freda Miller, had previously study showed that one gene, called Gas1, lipids. To learn more, a team led by HHMI discovered that the p73 gene keeps neurons keeps melanoma from metastasizing in international research scholar Maria M. alive in growing mice. But its function in living mice. The team tested human meta- Mota studied how removing different adult mice was unclear, because most static melanoma cells and discovered that lipoprotein receptors from liver cells animals that lack the p73 protein die young. Gas1 was often present at substantially affects infection. When cells’ SR-BI “We had a number of hints that p73 reduced levels than normal. production (or function) was blocked, might be doing something throughout the “We can use this approach to find infection levels fell 50–70 percent. lifetime of the animal, but we hadn’t metastasis suppressor genes for virtually Besides allowing Plasmodium in, SR-BI suspected that it had anything to do with any type of cancer,” says Green, who is at may supply cholesterol for the parasites’ neurodegeneration,” Miller says. the University of Massachusetts Medical membranes. Her team found that while mice with School. The team published its work on The results were published in the one good copy of p73 develop normally, November 1, 2008, in Genes and September 2008 issue of Cell Host & they lose neurons—and cognitive skills—as Development. Microbe. Now Mota, at the University of they age. Their brains develop tangles of Lisbon, Portugal, and collaborators are the nervous-system protein tau, as seen in SHUTTING THE DOOR ON MALARIA working to design better SR-BI inhibitors; Alzheimer’s disease. The researchers When malaria-causing parasites enter a brief treatment may be able to stop infec- reported their results on September 11, human body through the bite of an tion without significantly impairing liver cell 2008, in Neuron. infected mosquito, they must enter liver function. The team is also searching for Other studies have found that some cells and mature there before enacting other Plasmodium doorways. Alzheimer’s patients have just one func- full-blown disease. Researchers have tional copy of p73. Miller, at the Toronto found that these parasites, called LOST GENE SPELLS Hospital for Sick Children, and colleagues Plasmodium, enter liver cells through a NEURODEGENERATION are now testing the link between p73 and “door” used by cholesterol, which the liver Losing one working copy of a specific neurodegenerative disease in human filters from blood. When a cholesterol gene causes major symptoms of human populations. CHU Poitiers / Photo Researchers, Inc CHU Poitiers

50 HHMI BULLETIN | February 2oo9 ask a scientist

Q A

Why do The skin contains millions of nerves More importantly, needles stuck in that respond to a myriad of sensa- these areas are less likely to injure injections tions, including touch, temperature, internal structures. Unlike the back, hurt more and pain. The number of nerves that the shoulder, buttock, and thigh are cover the skin varies from one part of relatively distant from vital organs. on some the body to another. Areas that need Attempts have been made to reduce to discriminate fine sensations have the pain felt during injections. A parts of the more nerves than areas that do not commercially available option is a skin than require this ability. Your hands and gel patch containing lidocaine, a fast- fingers, for example, have many more acting numbing medication. Applied on others? nerves than your back, because hands to the skin, the patch numbs the nerves. and fingers need to do more intricate This patch is sometimes used for espe- Patience, tasks, such as writing or threading cially anxious children to minimize or an undergraduate student a needle. You feel more pain from eliminate the pain from needles. injections to the more sensitive parts Researchers are also working on of your skin because there are more an experimental system called trans- nerves reacting to the “insult.” dermal injection, which eliminates You can test how many nerves are the need for needles. Just as Star Trek’s in an area of skin by closing your Enterprise crew members received eyes and having someone pretend to injections via “hyposprays,” trans- write on that area with a finger. Most dermal injections force medications people instantly know the letters into the bloodstream by pushing them drawn on their hand but have a harder through the tiny pores of the skin. time figuring out a message written on However, most drugs are too big to their back. push through the skin, so researchers To minimize pain, injections have more work to do. In the mean- are typically given in the shoulder, time, we will have to bear with the buttock, or thigh. These areas are like brief pain that occurs when we receive the back in that they have fewer nerve a medically necessary injection. endings than other parts of the body but are convenient and safe to inject. ANSWER RESEARCHED BY PETER JUN, M.D. Rolling up your sleeve to expose your a former HHMI medical student fellow, shoulder is much easier than taking now a diagnostic radiology resident at the off your shirt to expose your back. University of California, San Francisco.

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

February 2oo9 | HHMI BULLETIN 51 up close

Crystal Clear A master practitioner initiates young scientists into the arcane craft of crystallography.

a crystal is a thing of beauty, but to a protein three decades, puts a great deal of thought, personal experience, scientist it is that and much more. The crystal form of a material and enthusiasm into his course, which is taken by about 20 embodies its essence—the unique framework of atoms and researchers—mostly graduate students—each year. chemical bonds that determines the molecule’s function and “We feel that x-ray crystallography is an extremely impor- how it interacts with other molecules. tant tool for young scientists to acquire—it is no longer the But growing the crystal from a protein involves an uncommon province of specialists,” says Eisenberg, who is director of blend of science, art, and tenacity—qualities that HHMI inves- UCLA’s Institute for Genomics & Proteomics. The multi- tigator and protein biochemist David Eisenberg strives to convey instructor course includes the history of x-ray diffraction in his course on x-ray crystallography at the University of techniques, their theoretical underpinnings, hands-on prac- California, Los Angeles. tice in crystallizing a protein, “shooting” it with x-rays, and “At any of several steps, you can get stuck for months at a interpreting the data. time,” says Howard Chang, a student in the course. “All you First-year graduate students Chang, 25, and Anni Zhao, 23, can do is continue to screen the hundreds or thousands of who recently joined the Eisenberg lab, started with little knowl- different conditions that influence crystallization in hopes that edge of the field. The learning curve was steep, but both were one will work. Even under optimum conditions, a crystal can impressed by the instructors’ creativity and skill in conveying the take years to grow.” needed information. For example, to appreciate the various But the payoff is huge, Chang adds, both in scientific terms kinds of symmetry crystals can adopt, students begin by identi- and as a kind of pure wonder. “Seeing the molecules in the fying symmetrical elements in the mathematically inspired greatest detail possible, it’s beautiful how these intricate atomic- artwork of M.C. Escher. level ‘machines’ evolved by nature operate.” In the sequence of instruction, the first part explains x-ray Atoms are too small to see with visible-light microscopes. crystallography as well as nuclear magnetic resonance (NMR) Instead, scientists infer the positions and orientations of atoms and electron microscopy—techniques that can be applied to indirectly by using x-ray diffraction. They fire x-ray beams into atomic structure. “We teach them how to read a paper, how to the crystal, which are scattered in different directions by the know if a structure is reliable, and what assumptions have been atoms and captured on a detector surface. An experienced made,” Eisenberg says. researcher can then devise a structural model of the protein Next come two five-week segments delving deeper into the from the resulting pattern. Knowing the structure gives insights, actual mechanics of x-ray and NMR crystallography—collecting for example, into how amyloid proteins cause neurological and reducing data and then determining the structure from the disease (see “Chasing Amyloid,” page 10). And structure-based data. Along with the lectures, students practice what they’ve drugs, such as the protease inhibitors created to treat HIV/AIDS, been learning with a set of laboratory problems. “Because it’s are becoming more common. such a complex concept to teach, it really helps that Dr. Eisenberg, whose career has witnessed—and contributed Eisenberg is able to bring in six instructors who specialize in to—many milestones of protein crystallography over the last different areas,” says Zhao.

52 HHMI BULLETIN | February 2009 Finally, it’s time to put it all together: the students are office very frustrated and walk out the door more motivated given a protein from which to grow crystals, freeze them, than ever.” mount them in the x-ray apparatus, gather the data, and inter- In practice, much of the tedious trial-and-error pipetting is pret the structure. “To get a good crystal that gives you a nice now done with automated equipment, Eisenberg says, but going diffraction pattern is a big deal,” says Zhao. “The initial formation through the process manually is part of the learning experience. is difficult: there are many combinations of factors—concen- After completing the course, students are well prepared to join a tration, pH, temperature, salts, buffers—and the possibilities lab group that relies on x-ray crystallography for structure analysis. go up exponentially.” “Some of our students go on to become real experts in the Zhao praises Eisenberg for his supportiveness in helping field—they far surpass me in mastering the software and the students weather the ups and downs. “He does not push you for hardware,” he says. “Others just use it for their research as results, but when you need direction or help, he is always avail- biochemists. What I like about our training system is that it

Drew Beckmeyer able and extremely helpful,” she says. “People can go into his provides a basis for both of those careers.” p – RICHARD SALTUS

February 2009 | HHMI BULLETIN 53 nota bene

SPOTLIGHT

Seven Elected to Institute of Medicine

TOP ROW: HARRY DIETZ III, ARTHUR HORWICH, JOHN KAPPLER, PHILIPPA MARRACK BOTTOM ROW: DAVID PAGE, CHARLES SAWYERS, TERRENCE SEJNOWSKI

A total of seven HHMI investigators were elected to the National Academy of Science’s Institute of Medicine in October 2008. The investigators are Harry C. Dietz III, Johns Hopkins School of Medicine; Arthur L. Horwich, Yale School of Medicine; John W. Kappler, National Jewish Health; Philippa Marrack, National Jewish Health; David C. Page, Massachusetts Institute of Technology; Charles L. Sawyers, Memorial Sloan-Kettering Cancer Center; and Terrence J. Sejnowski, Salk Institute for Biological Studies.

BRUCE ALBERTS, the HHMI undergrad- University of California, Berkeley; DOUGLAS 40” list, which recognizes young innovators uate program director at the University of E. KOSHLAND, Carnegie Institution for breaking ground in their fields. Elowitz California, San Francisco, won the 2008 Science; BARBARA J. MEYER, University of studies how genetically identical cells have

Carl Brändén Award from the Protein California, Berkeley; JEREMY NATHANS, variability in their biological components, Health Society. The award is given annually to an Johns Hopkins University School of Medicine; and Pritchard studies how organisms adapt to outstanding protein scientist who has also NIPAM H. PATEL, University of California, their environments over short periods of time. made exceptional contributions in the areas Berkeley; NORBERT PERRIMON, Harvard of education and/or service to the sciences. Medical School; SUSAN S. TAYLOR, Rutgers University and the Robert Wood University of California, San Diego; and Johnson Medical School awarded HHMI DAVID BAKER, an HHMI investigator at the LI-HUEI TSAI, Massachusetts Institute of investigator STANLEY FIELDS, of the University of Washington, JONATHAN S. Technology. The professors are JO University of Washington School of Medicine, WEISSMAN, an HHMI investigator at the HANDELSMAN, University of Wisconsin- with the 2008 Paul Janssen Prize in Advanced University of California, San Francisco, and Madison; DIANE K. O’DOWD, University of Biotechnology and Medicine. Fields has Martin Gruebele of the University of Illinois California, Irvine; BALDOMERO OLIVERA, developed technologies that use simple genetic at Urbana-Champaign, were awarded the University of Utah; REBECCA RICHARDS- strategies in yeast to analyze protein functions. 2008 Raymond and Beverly Sackler KORTUM, Rice University; and GRAHAM C. International Prize in Biophysics. This annual WALKER, Massachusetts Institute of JO HANDELSMAN, an HHMI professor at award, administered by Tel Aviv University, Technology. Also named were DANIEL J. the University of Wisconsin-Madison, received recognizes the seminal contributions of the KLIONSKY, HHMI undergraduate program the 2009 American Society for Microbiology’s three researchers to studies of protein folding. director at the University of Michigan; and Carski Foundation Distinguished JOAN RUDERMAN of Harvard University, a Undergraduate Teaching Award. This annual A total of ten HHMI investigators and five member of the HHMI medical advisory board. award, which has been supported by the HHMI professors were named fellows of the Carski Foundation since 1968, honors an American Association for the Advancement of Two HHMI investigators—MICHAEL B. educator for outstanding teaching of microbi- Science. The investigators are MICHAEL J. ELOWITZ of the California Institute of ology to undergraduate students. BEVAN, University of Washington School of Technology and JONATHAN K. PRITCHARD Medicine; DAVID E. CLAPHAM, Boston of the University of Chicago—were named to HHMI investigator OLIVER HOBERT of the

Children’s Hospital; JENNIFER DOUDNA, Discover magazine’s “20 Best Brains Under Columbia University College of Physicians UniversityBarry Silverstein/National Kappler: Ray Ng Marrack: Jewish Domian / Yale Jerry Dietz III: Elena Dorfman Horwich: Institute Sawyers:Mantoani Sam Ogden / Whitehead Liz Baylen PR Newswire, ©HHMI Sejnowski:Tim Page:

54 HHMI BULLETIN | February 2oo9 and Surgeons received the 2008 Harland SPOTLIGHT Winfield Mossman Award in Developmental Biology from the American Association of Anatomists. The award is given annually to Tsien Awarded Wilson Medal

an investigator in the early stages of his or The 2008 E.B. Wilson Medal went to HHMI her career for contributions to the field of investigator Roger Y. Tsien of the University of developmental biology. Hobert studies how California, San Diego, and Martin Chalfie of neural diversity and left-right asymmetries Columbia University. The medal is the American Society for Cell Biology’s highest science honor are generated in the nervous system. and is awarded for far-reaching lifetime contri- butions to cell biology. Tsien and Chalfie devel- HHMI-supported undergraduate CAITLIN E. oped green fluorescent protein (GFP) as a tool

MULLARKEY of Swarthmore College and for tagging proteins. The glowing marker allows ROGER TSIEN JARRAD M. AGUIRRE, who worked in the scientists to watch the movements, positions, and interactions of tagged molecules. GFP also allows researchers to follow lab of HHMI investigator Li-Huei Tsai at the the fates of various cells, such as nerves affected by Alzheimer’s disease, or Massachusetts Institute of Technology cells in a growing embryo. through the 2008 HHMI Exceptional Research Opportunities Program, were two of 32 U.S. students to be awarded a Rhodes Latin American Academy of Sciences. The for Excellence in Human Genetics Education Scholarship to study at Oxford University Academy has 222 members across Latin from the American Society of Human next year. A senior at Swarthmore, Mullarkey America and the Caribbean. Genetics. The award recognizes the work of has been studying a gene implicated in glau- Stark, and two colleagues, on the Genetic coma and glioblastoma. She intends to work The 2008 Katz Prize in Cardiovascular Science Learning Center, started with HHMI in an HIV/AIDS lab at Oxford. Aguirre is a Medicine was awarded to HHMI investigator funds in 1994 to educate students, teachers, senior at Yale University majoring in molec- CHRISTINE E. SEIDMAN, of Brigham and and the public about genetics. ular, cellular, and developmental biology. He Women’s Hospital, and Jonathan Seidman, will study medical anthropology at Oxford. of Harvard Medical School. The award, JOAN A. STEITZ, an HHMI investigator at presented by the Columbia University the Yale School of Medicine, received the HHMI international research scholar RAÚL A. Medical Center, recognizes outstanding 2008 New York Academy of Medicine Medal PADRÓN of the Venezuelan Institute for contributions to cardiovascular research. for Distinguished Contributions in Scientific Research won the 2008 Science and The Seidman research team has detected Biomedical Science. She also received a Technology National Prize of Venezuela, the many genetic causes for heart diseases, Connecticut Women’s Hall of Fame Award. top scientific recognition in the country. Padrón including hypertrophic cardiomyopathy—a Steitz is interested in the roles played by small studies how thick filaments of striated muscle condition that thickens the heart muscle and RNA–protein complexes in vertebrate cells. are activated during muscle contraction. often causes arrhythmias and heart failure. HHMI investigator PETER WALTER, of the RAFAEL RADI, an HHMI international LOUISA A. STARK, the HHMI pre-college University of California, San Francisco, research scholar at the Universidad de la program director at the University of Utah received the 2009 Stein and Moore Award República in Uruguay, was elected to the School of Medicine, received the 2008 Award from the Protein Society, which recognizes his contributions to the study of proteins. SPOTLIGHT Walter has discovered how the endoplasmic reticulum of a cell senses when proteins are misfolded and sends them to be degraded. HHMI Graduate Fellow Wins Grand Prize in Inventors Competition Two HHMI-supported Davidson College undergraduates, PALLAVI PENUMETCHA Timothy Lu, an HHMI student fellow in the lab of HHMI investigator James J. Collins at Boston University, won first place in the 2008 Collegiate Inventors and KRISTI MUSCALINO, were on a team Competition. The prize was given for Lu’s engineered bacteriophages— that won a gold medal at the 2008 viruses that infect bacteria—which work in conjunction with existing antibi- International Genetically Engineered otics to enhance their efficacy against bacteria. During one of his clinical Machine competition (iGEM), an under- rotations, Lu, an M.D./Ph.D. student, was struck by the number of infectious graduate synthetic-biology competition with outbreaks he witnessed in patients. So he used his synthetic-biology back- ground to brainstorm solutions. The bacteriophages Lu developed produce 84 teams from 21 countries. The Davidson enzymes that break down the protective coating surrounding communities of team designed, modeled, and constructed a bacteria, enabling increased killing of bacterial cells. bacterial computer. Paul Fetters Paul

February 2oo9 | HHMI BULLETIN 55 CONTINUED FROM PAGE 19 thousands of dollars per patient treated, and they buy you a few extra (LUMINOSITY) months and then you die anyway,” he says. If, for even a few patients These nanoparticles are the molecular equivalents of self-adhe- who need surgery, he can help surgeons cut out all the cancer, he sive name tags that come with a nonstick backing paper. As long as could buy those patients extra years. the “backing paper” is covering the “adhesive,” the molecules don’t stick to cells. Malignant tumor cells secrete specific proteases that What’s Important they use to chew their way through normal tissues to reach the That kind of motivation is what Tsien thinks should drive scien- blood and distant organs. The “backing paper” is carefully designed tific inquiry. At Janelia Farm, fresh from notice of his Nobel, to fall off when chewed by the tumor cells’ proteases, thus exposing Tsien admonished the students that if they wanted a successful the “adhesive” and coating the tumor cells with the nanoparticles. career in science, they shouldn’t be “unduly motivated or impressed” The nanoparticles carry fluorescent and magnetic tags to make by prizes. the tumors visible. Eventually, they may also carry drugs to kill any What they should do, he said, is explore research questions that cancer cells left over after surgery. One obstacle is that other give some form of day-to-day pleasure. They’ll need that interest to enzymes in a normal liver can also cut off the “backing paper” as sustain them through the periods between big discoveries or the currently designed, so that the liver picks up a lot of the nanoparti- times when things just aren’t working, when they find themselves cles. That doesn’t matter for surgery, but it could be a problem for staring at their own valley of death. delivering cell-killing drugs. He acknowledged, however, that are there are some perks to a In transgenic mice with an especially aggressive form of breast Nobel win. “Writing for samples is easier now,” he smiled. “People cancer, surgical removal of the tumor offers only a 10 percent who used to ignore my e-mails are more responsive.” p chance of tumor-free survival. But when Nguyen and Tsien made them glow, tumors were visually distinguishable from healthy tissue; tumor removal was more complete, and tumor-free survival quadru- Subscribe! pled to 40 percent. Knowledge Discovery Research Education “[Tsien] can visualize, almost anthropomorphize, molecules in N OV. ’08 VOL.21  NO.04

a very astute way, so that things work,” explains Nguyen. “He really HHMI BULLETIN has a sense of how these molecules interact.” Their results, while not yet published, appear to bear out Nguyen’s praise. In addition to helping the mice live longer, they’ve tested the technique on biopsied human breast cancer tissue (results

Meiosis Chromosomal movement has long they plan to publish with the mouse studies); the cancer cells take captivated scientists. New research only adds to the fascination. up the marker. But, at least for now, mice are the only animals to benefit on the operating table. (As a side project, Tsien and Nguyen

Breaking News Robert Tjian to Lead Institute are working on a way to make nerves visible during surgery to help Nobel Prize Goes to Roger Tsien surgeons avoid damaging them.) Between the lab and human trials, Tsien says, “there’s something These four key components of HHMI’s work also guide and define the mission of the Institute’s quarterly magazine, called the valley of death, the gap between promising results obtain- the HHMI Bulletin. able with research funding versus the much more expensive studies necessary to convince companies to invest. Right now I’m looking at Subscribing is fast, easy and free. Visit www.hhmi.org/ bulletin and follow the instructions there to subscribe online. that valley of death, which is particularly wide during economic gloom.” He expects that clinical trials to test the safety and effective- While you’re online, read the Web edition of the Bulletin. ness of the technique in humans will cost millions of dollars. But the potential payoff is enough to motivate this leap into new HHMI BULLETIN territory. “Some of the biggest touted therapies cost hundreds of

Correction: In a November 2008 article on funding for the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, the Bulletin incorrectly stated that MBL This paper is certified by SmartWood for FSC standards, which promote has been offering courses since environmentally appropriate, socially beneficial, and economically viable 1982. The correct date is 1892. The management of the world’s forests. Bulletin regrets the error.

56 HHMI BULLETIN | February 2oo9

14 This brightbugmayglowlike organisms. Inthecaseofthis express fluorescent proteins like express fluorescentproteinslike cules localizewithin cellsand winner RogerTsien.Suchfluore- illuminated tick,scientists can been geneticallyengineeredto a firefly, butit’s actuallyadeer how andwheredifferentmole- pathogens likeLyme disease. probe howthecrittercarries those developedbyNobelPrize tick— scence lets researchers visualize scence letsresearchersvisualize Ixodes scapularis —that’s

Utpal Pal, Ruth R. Montgomery, Erol Fikrig

Alfred Russel Wallace: My Life (1905) that fillthehistory ofscience don’tal Tales from theTrenches the fieldofevolution, includinganovel concept ofnatural selection. dramatic setbackslike theonesdescribedhere, Wallace madeseminalcontributions to century scientist whovoyaged to theMalay Archipelago andtheAmazon. Despite some stories. At thestart ofChapter 2,thereader meetsAlfred Russel Wallace, anineteenth- which thehistory ofevolutionary science unfolds through someofitsmost memorable Sean B.Carroll wants to changethat.Sohewrote atextbook, publishedlast summer, in OBSERVATIONS | The| colorful characters, epicadventures, andpersonalstruggles ways ways find theirway into classrooms. HHMIinvestigator permission oftheauthor. ©2009 BenjaminCummings.Reprinted with the Search for Evolution From then the ered itwas leaking. salt water. Once inthelifeboat, hediscov- compounded whenhisinjured handshitthe seared hishandsontherope. Hispainwas to lower himselfinto alifeboat, slipped,and some notes, andadiary. Hegrabbed aline a smalltinbox andthrew insomedrawings, reentered hishot,smoky cabinandsalvaged scene was afeverish dream. Itwasn’t. He bout withyellow fever, looked onasifthe the lifeboats. Wallace, still weak from his smoldering blaze. The captain ordered down out ofthehold. cabin. Andrightfullyso—smoke was pouring was concerned enoughto visitWallace inhis east ofBermuda,thecaptain three weeks outofportandsomewhere see whatyou thinkofit.” Just after breakfast, and setsailfor England. animals, many boxes ofspecimensand notes, boarded thebrig comforts ofhome. OnJuly12,1852, he neat gardens, bread andbutter, andother for sale. he hadnotyet beenableto shipto England both withhimandstored downriver, that had acouple ofyears’ worth ofspecimens, was killinghim.Besidestheanimals,healso all theway to theLondon Zoo. Their upkeep parrots, andatoucan—that hehopedto take erie oflive animals—monkeys, macaws, died before hecould board aboatto England. Herbert was stricken withyellow fever and before turnedback.Unbeknownst to Wallace, panied himupto theRioNegro, hadlong His younger brother, Herbert,whoaccom- yellow fever. Hewas too exhausted to goon. had beenlaidupthelast three monthswith four years exploring andcollecting, but arriving inMay 1848,hehadspentnearly than any European hadever gone. Since dos UaupéstributaryoftheAmazon—further upriver from theAtlantic Ocean, ontheRio It was timeto packupandgohome. Wallace watched hisanimalsperish,and The crew tried,butcould notdousethe “I’m afraid theship’s onfire; come and Wallace beganto dream ofgreen fields, Wallace hadaccumulated alarge menag- Alfred Wallace was two thousandmiles Into theJungle:Great Adventures in Helen , along with all of his specimens. , alongwithallofhisspecimens. Helen with thirty-four live , by Sean B.Carroll. Helen HHMI

BULLETIN F EB. ’09 VOL.22 s NO.01

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Howard Hu HHMI BULLETIN g hes Medical Institute

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www.hhmi.or g Lars Dietrich / Newman lab

A MUTATION IN A GENE FOR ANTIBIOTIC PIGMENTS Where’s My Snorkel? CALLED PHENAZINES MAKES BACTERIAL COLONIES GROW IN THIS SHRIVELED—BUT SURPRISINGLY SYMMETRICAL AND PREDICTABLE—PATTERN. DIANNE NEWMAN’S EXPLANATION: PHENAZINES USUALLY ACT AS SNORKELS, HELPING THE DEEPEST BACTERIA ILLUMINATING IN A THICK COLONY BREATHE WITHOUT OXYGEN. WITHOUT THESE MOLECULES, BACTERIA MUST ARRANGE THEMSELVES IN THIS UNUSUAL WAY SO THAT EACH BIOLOGY CELL HAS DIRECT ACCESS TO OXYGEN IN THE AIR A spectrum of fluorescent proteins (SEE PAGE 26). won Roger Tsien a Nobel Prize. Now he’s shining his light on cancer cells and memory formation.

In This Issue When Cells Grow Old MicroRNA Dianne Newman Introduces Geology to Microbiology

4000 Jones Bridge Road vol. Chevy Chase, Maryland 20815-6789 22 www.hhmi.org / no. 01